From c3ce0b79bd983981048dcfd31ed8a5648b9490b6 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 18 Aug 2021 16:49:26 +0200
Subject: [PATCH] add support for AAindex database (Kawashima et al., 2000)
---
modules/seq/alg/doc/seqalg.rst | 21 +
modules/seq/alg/pymod/CMakeLists.txt | 14 +-
modules/seq/alg/pymod/aaindex.py | 332 +
modules/seq/alg/pymod/aaindex1 | 10575 ++++++++++++++++++++++++
modules/seq/alg/pymod/aaindex2 | 2818 +++++++
modules/seq/alg/pymod/aaindex3 | 1383 ++++
modules/seq/alg/tests/CMakeLists.txt | 1 +
modules/seq/alg/tests/test_aaindex.py | 49 +
8 files changed, 15192 insertions(+), 1 deletion(-)
create mode 100644 modules/seq/alg/pymod/aaindex.py
create mode 100644 modules/seq/alg/pymod/aaindex1
create mode 100644 modules/seq/alg/pymod/aaindex2
create mode 100644 modules/seq/alg/pymod/aaindex3
create mode 100644 modules/seq/alg/tests/test_aaindex.py
diff --git a/modules/seq/alg/doc/seqalg.rst b/modules/seq/alg/doc/seqalg.rst
index caa671577..b4061e23d 100644
--- a/modules/seq/alg/doc/seqalg.rst
+++ b/modules/seq/alg/doc/seqalg.rst
@@ -945,3 +945,24 @@ etc.) to be set, which is the case if you load a file in hhm format.
:type db: :class:`ContextProfileDB`
:raises: Exception if profile doesn't have HMM information assigned
+
+
+AAIndex annotations
+-------------------
+
+.. autoclass:: ost.seq.alg.aaindex.AAIndex
+ :members:
+ :special-members: __getitem__
+
+The annotations/scores can either refer to single amino acids or represent
+pairwise values. The two types are:
+
+.. autoclass:: ost.seq.alg.aaindex.AnnoType
+ :members:
+ :undoc-members:
+
+The actual data of an entry in the aaindex database is stored in a
+:class:`aaindex.AAIndexData` object:
+
+.. autoclass:: ost.seq.alg.aaindex.AAIndexData
+ :members:
diff --git a/modules/seq/alg/pymod/CMakeLists.txt b/modules/seq/alg/pymod/CMakeLists.txt
index 0821b510a..f574f2491 100644
--- a/modules/seq/alg/pymod/CMakeLists.txt
+++ b/modules/seq/alg/pymod/CMakeLists.txt
@@ -4,5 +4,17 @@ set(OST_SEQ_ALG_PYMOD_SOURCES
if (NOT ENABLE_STATIC)
pymod(NAME seq_alg OUTPUT_DIR ost/seq/alg
CPP ${OST_SEQ_ALG_PYMOD_SOURCES}
- PY __init__.py mat.py renumber.py)
+ PY __init__.py mat.py renumber.py aaindex.py)
endif()
+
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure/aaindex"
+ "aaindex1" "AAINDEX1" "ost_seq_alg_pymod")
+install(FILES "aaindex1" DESTINATION "share/openstructure/aaindex/")
+
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure/aaindex"
+ "aaindex2" "AAINDEX2" "ost_seq_alg_pymod")
+install(FILES "aaindex2" DESTINATION "share/openstructure/aaindex/")
+
+copy_if_different("${CMAKE_CURRENT_SOURCE_DIR}" "${STAGE_DIR}/share/openstructure/aaindex"
+ "aaindex3" "AAINDEX3" "ost_seq_alg_pymod")
+install(FILES "aaindex3" DESTINATION "share/openstructure/aaindex/")
diff --git a/modules/seq/alg/pymod/aaindex.py b/modules/seq/alg/pymod/aaindex.py
new file mode 100644
index 000000000..9f0175240
--- /dev/null
+++ b/modules/seq/alg/pymod/aaindex.py
@@ -0,0 +1,332 @@
+import os
+from enum import Enum
+
+from ost import GetSharedDataPath
+
+def _StrToFloat(str_item):
+ """Returns None if *str_item* looks like invalid number, casts to
+ float otherwise"""
+ x = str_item.strip()
+ if x.lower() in ["na", "-", "none"]:
+ return None
+ return float(x)
+
+
+class AnnoType(str, Enum):
+ """Possible types of aaindex entries"""
+ SINGLE = 'SINGLE' #: Single amino acid annotation
+ PAIR = 'PAIR' #: Pairwise amino acid annotation, substitution/pairwise scores
+
+
+class AAIndexData:
+ """Data object representing an annotation in aaindex, preferably
+ constructed from it's static :func:`Parse` method. The following
+ attributes are available:
+
+ * key: aaindex accession number (e.g. ANDN920101)
+ * desc: descriptive title
+ * ref: Reference to article if available
+ * authors: Authors of article if available
+ * title: Title of article if available
+ * journal: Journal of article if available
+ * anno_type: Enum (:class:`AnnoType`) specifying whether we're dealing
+ with a single or pairwise amino acid annotation/score.
+ * anno: :class:`dict` with annotation. If *anno_type* is SINGLE,
+ keys are amino acid one letter codes (single character strings).
+ If *anno_type* is PAIR, keys are two one letter codes added
+ together (two character strings). Even when the thing is
+ symmetric, both keys exist. I.e. 'AB' AND 'BA'.
+ Values are of type :class:`float` (None if not available).
+ """
+ def __init__(self):
+ self.key = None
+ self.desc = None
+ self.ref = None
+ self.authors = None
+ self.title = None
+ self.journal = None
+ self.anno_type = AnnoType.SINGLE
+ self.anno = dict()
+
+ @staticmethod
+ def Parse(data):
+ """Creates :class:`AAIndexData` from data.
+
+ :param data: Iterable with strings in data format described for aaindex.
+ :returns: :class:`AAIndexData`, if iterable contains several entries,
+ parsing stops at separation sequence ('//'). None is returned
+ if nothing could be parsed.
+ :raises: descriptive error in case of corrupt data
+ """
+ key = ""
+ desc = ""
+ ref = ""
+ authors = ""
+ title = ""
+ journal = ""
+ anno = dict()
+ anno_type = None
+
+ # temp variables, used for parsing
+ values = list()
+ pair_rows = None
+ pair_cols = None
+
+ current_data_type = None
+ stuff_read = False
+ for line in data:
+ if line.startswith("//"):
+ break # we're done
+ elif line.strip() == "":
+ continue # nothing to read
+ elif line[0] in ["H", "D", "R", "A", "T", "J", "I", "M"]:
+ stuff_read = True
+ current_data_type = line[0] # something we're interested in
+ elif line.startswith(" "):
+ pass # continuation of previous stuff
+ else:
+ current_data_type = None # unkown data, skip...
+
+ if current_data_type == "H":
+ key = line[2:].strip()
+ elif current_data_type == "D":
+ desc += line[2:]
+ elif current_data_type == "R":
+ ref += line[2:]
+ elif current_data_type == "A":
+ authors += line[2:]
+ elif current_data_type == "T":
+ title += line[2:]
+ elif current_data_type == "J":
+ journal += line[2:]
+ elif current_data_type == "I":
+ if anno_type == AnnoType.PAIR:
+ raise RuntimeError("Observed single AA and pairwise "
+ "features in the same aaindex entry")
+ anno_type = AnnoType.SINGLE
+ if line.startswith("I"):
+ # header, must match expected aa ordering
+ aakeys = [item.strip() for item in line[1:].split()]
+ exp_aa_keys = ["A/L", "R/K", "N/M", "D/F", "C/P", "Q/S",
+ "E/T", "G/W", "H/Y", "I/V"]
+ if aakeys != exp_aa_keys:
+ raise RuntimeError(f"Keys in single AA AAIndex entry "
+ "are expected to be "
+ "I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V "
+ "got {line}")
+ else:
+ # its numbers... will be added to anno dict below
+ values += [_StrToFloat(x) for x in line.split()]
+ elif current_data_type == "M":
+ if anno_type == AnnoType.SINGLE:
+ raise RuntimeError("Observed single AA and pairwise "
+ "features in the same aaindex entry")
+ anno_type = AnnoType.PAIR
+ if line.startswith("M"):
+ # header, don't expect strict one letter code ordering here
+ # also because some pair entries include gaps ('-').
+ # expect something like: "M rows = <x>, cols = <x>"
+ split_line = line[1:].split(',')
+ split_line = sorted([item.strip() for item in split_line])
+ # after sorting we should have exactly two elements, the
+ # first starting with cols and the second with rows
+ if len(split_line) != 2 or \
+ not split_line[0].startswith("cols") or \
+ not split_line[1].startswith("rows"):
+ raise RuntimeError(f"Expect value header in pair "
+ "AAIndex entry to be of form: "
+ "\"M rows = <x>, cols = <x>\" got: "
+ "{line}")
+ pair_cols = split_line[0].split("=")[1].strip()
+ pair_rows = split_line[1].split("=")[1].strip()
+ if len(pair_cols) != len(pair_cols):
+ raise RuntimeError(f"Expect rows and cols to have same "
+ "number of elements when parsing "
+ "pair AAIndex entry got {line}")
+ else:
+ # its numbers... will be added to anno dict below
+ values += [_StrToFloat(x) for x in line.split()]
+
+ if not stuff_read:
+ return None
+
+ if key == "":
+ raise RuntimeError("Cannot parse AAIndex entry without key...")
+
+ if anno_type == AnnoType.SINGLE:
+ olcs = "ARNDCQEGHILKMFPSTWYV"
+ if len(olcs) != len(values):
+ raise RuntimeError(f"Expected {len(olcs)} values in single AA "
+ "AAIndex entry, got {len(values)}")
+ for olc, value in zip(olcs, values):
+ anno[olc] = value
+ elif anno_type == AnnoType.PAIR:
+ # number of values can differ as the provided matrix can either be
+ # diagonal (symmetric A -> B == B -> A) or rectangular (non-symmetric
+ # A -> B != B -> A)
+ # For the former, number of columns and rows must be equal, no such
+ # requirement for non-symmetric case
+ n_values_match = False
+ n_cols = len(pair_cols)
+ n_rows = len(pair_rows)
+ n_nonsym = n_cols * n_rows
+ if len(values) == n_nonsym:
+ n_values_match = True
+ value_idx = 0
+ for a in pair_rows:
+ for b in pair_cols:
+ anno[a+b] = values[value_idx]
+ value_idx += 1
+
+ if n_cols == n_rows:
+ n_values_match = True
+ N = n_cols
+ n_sym = (N*N - N) / 2 # number of elements below diagonal
+ n_sym += N # add diagonal elements again
+ if len(values) == n_sym:
+ value_idx = 0
+ for row_idx, row in enumerate(pair_rows):
+ for col in pair_cols[: row_idx+1]:
+ anno[row+col] = values[value_idx]
+ anno[col+row] = values[value_idx]
+ value_idx += 1
+ if not n_values_match:
+ raise RuntimeError(f"Number of parsed values doesn't match "
+ "parsed rows and cols descriptors")
+ else:
+ raise RuntimeError("Cannot parse AAIndex entry without values...")
+
+ data = AAIndexData()
+ data.key = key
+ data.title = title
+ data.ref = ref
+ data.authors = authors
+ data.title = title
+ data.journal = journal
+ data.anno_type = anno_type
+ data.anno = anno
+ return data
+
+ def GetScore(self, olc):
+ """Score/Annotation getter
+
+ :param olc: One letter code of amino acid
+ :type olc: :class:`string`
+ :returns: Annotation/score for *olc*
+ :raises: :class:`ValueError` if *olc* is not known or
+ :class:`RuntimeError` if anno_type of this
+ :class:`AAIndexData` object is not AnnoType.SINGLE.
+ """
+ if self.anno_type == AnnoType.SINGLE:
+ if olc in self.anno:
+ return self.anno[olc]
+ else:
+ raise ValueError(f"OLC not in AAIndex: {olc}")
+ raise RuntimeError("Cannot return score for single amino acid with "
+ "AAIndex of type PAIR")
+
+ def GetPairScore(self, olc_one, olc_two):
+ """Score/Annotation getter
+
+ :param olc_one: One letter code of first amino acid
+ :type olc_one: :class:`string`
+ :param olc_two: One letter code of second amino acid
+ :type olc_two: :class:`string`
+ :returns: Pairwise annotation/score for *olc_one*/*olc_two*
+ :raises: :class:`ValueError` if key constructed from *olc_one* and
+ *olc_two* is not known or
+ :class:`RuntimeError` if anno_type of this
+ :class:`AAIndexData` object is not AnnoType.PAIR.
+ """
+ if self.anno_type == AnnoType.PAIR:
+ anno_key = olc_one + olc_two
+ if anno_key in self.anno:
+ return self.anno[anno_key]
+ else:
+ raise ValueError(f"Cannot find annotation for following pairs "
+ "of olcs: {olc_one}, {olc_two}")
+ raise RuntimeError("Cannot return score for pair of amino acid "
+ "with AAIndex of type SINGLE")
+
+
+class AAIndex:
+ """Provides access to data from the amino acid index database (aaindex):
+
+ Kawashima, S. and Kanehisa, M.; AAindex: amino acid index database.
+ Nucleic Acids Res. 28, 374 (2000).
+
+ Files are available `here <https://www.genome.jp/aaindex/>`_
+
+ :param aaindex_files: Paths to aaindex files. If not given, the files
+ aaindex1, aaindex2 and aaindex3 from the specified
+ source are used (Release 9.2, Feb 2017).
+ :type aaindex_files: :class:`list` of :class:`str`
+ """
+ def __init__(self, aaindex_files = None):
+ if aaindex_files is None:
+ aaindex_dir = os.path.join(GetSharedDataPath(), 'aaindex')
+ self.files_to_load = [os.path.join(aaindex_dir, "aaindex1"),
+ os.path.join(aaindex_dir, "aaindex2"),
+ os.path.join(aaindex_dir, "aaindex3")]
+ else:
+ self.files_to_load = list(aaindex_files)
+ self.aaindex_entries = dict()
+
+ def keys(self):
+ """Emulate dict like behvaiour and returns all available keys, accession
+ numbers respectively.
+
+ :returns: keys (or accession numbers) of all available aaindex entries
+ """
+ self._LoadAll()
+ return self.aaindex_entries.keys()
+
+ def values(self):
+ """Emulate dict like behvaiour and returns all available entries.
+
+ :returns: iterable of entries (type :class:`AAIndexData`)
+ """
+ self._LoadAll()
+ return self.aaindex_entries.values()
+
+ def __getitem__(self, key):
+ """Getter by aaindex accession number (e.g. ANDN920101)
+
+ :param key: aaindex accession number
+ :type key: :class:`str`
+ :returns: :class:`AAIndexData` object
+ """
+ while True:
+ if key in self.aaindex_entries:
+ return self.aaindex_entries[key]
+ # key is not available let's load the next aaindex file
+ if not self._Load():
+ # all files loaded, there is entry with *key* in any of them
+ break
+ raise KeyError(f"{key} does not exist in provided aa_index files")
+
+ def _LoadAll(self):
+ """Loads all remaining files specified in self.files_to_load
+ """
+ while self._Load():
+ pass
+
+ def _Load(self):
+ """Loads and removes first element in self.files_to_load. Returns False
+ if there is no file to load anymore, True if one is successfully loaded.
+ """
+ if len(self.files_to_load) == 0:
+ return False
+ path = self.files_to_load.pop(0)
+ if not os.path.exists(path):
+ raise RuntimeError(f"Tried to load {path} but file doesnt exist.")
+ with open(path, 'r') as fh:
+ data = fh.readlines()
+ data_it = iter(data)
+ while True: # read as long as it spits out AAIndexData entries
+ entry = AAIndexData.Parse(data_it)
+ if entry is None:
+ break # nothing to read anymore...
+ else:
+ self.aaindex_entries[entry.key] = entry
+ return True
diff --git a/modules/seq/alg/pymod/aaindex1 b/modules/seq/alg/pymod/aaindex1
new file mode 100644
index 000000000..542cf2f96
--- /dev/null
+++ b/modules/seq/alg/pymod/aaindex1
@@ -0,0 +1,10575 @@
+H ANDN920101
+D alpha-CH chemical shifts (Andersen et al., 1992)
+R PMID:1575719
+A Andersen, N.H., Cao, B. and Chen, C.
+T Peptide/protein structure analysis using the chemical shift index method:
+ upfield alpha-CH values reveal dynamic helices and aL sites
+J Biochem. and Biophys. Res. Comm. 184, 1008-1014 (1992)
+C BUNA790102 0.949
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 4.35 4.38 4.75 4.76 4.65 4.37 4.29 3.97 4.63 3.95
+ 4.17 4.36 4.52 4.66 4.44 4.50 4.35 4.70 4.60 3.95
+//
+H ARGP820101
+D Hydrophobicity index (Argos et al., 1982)
+R PMID:7151796
+A Argos, P., Rao, J.K.M. and Hargrave, P.A.
+T Structural prediction of membrane-bound proteins
+J Eur. J. Biochem. 128, 565-575 (1982)
+C JOND750101 1.000 SIMZ760101 0.967 GOLD730101 0.936
+ TAKK010101 0.906 MEEJ810101 0.891 ROSM880104 0.872
+ CIDH920105 0.867 LEVM760106 0.865 CIDH920102 0.862
+ MEEJ800102 0.855 MEEJ810102 0.853 ZHOH040101 0.841
+ CIDH920103 0.827 PLIV810101 0.820 CIDH920104 0.819
+ LEVM760107 0.806 NOZY710101 0.800 GUYH850103 -0.808
+ PARJ860101 -0.835 WOLS870101 -0.838 BULH740101 -0.854
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.61 0.60 0.06 0.46 1.07 0. 0.47 0.07 0.61 2.22
+ 1.53 1.15 1.18 2.02 1.95 0.05 0.05 2.65 1.88 1.32
+//
+H ARGP820102
+D Signal sequence helical potential (Argos et al., 1982)
+R PMID:7151796
+A Argos, P., Rao, J.K.M. and Hargrave, P.A.
+T Structural prediction of membrane-bound proteins
+J Eur. J. Biochem. 128, 565-575 (1982)
+C ARGP820103 0.961 KYTJ820101 0.803 JURD980101 0.802
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.18 0.20 0.23 0.05 1.89 0.72 0.11 0.49 0.31 1.45
+ 3.23 0.06 2.67 1.96 0.76 0.97 0.84 0.77 0.39 1.08
+//
+H ARGP820103
+D Membrane-buried preference parameters (Argos et al., 1982)
+R PMID:7151796
+A Argos, P., Rao, J.K.M. and Hargrave, P.A.
+T Structural prediction of membrane-bound proteins
+J Eur. J. Biochem. 128, 565-575 (1982)
+C ARGP820102 0.961 MIYS850101 0.822 NAKH900106 0.810
+ EISD860103 0.810 KYTJ820101 0.806 JURD980101 0.800
+ PUNT030101 -0.810 MIYS990102 -0.814 MIYS990101 -0.817
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.56 0.45 0.27 0.14 1.23 0.51 0.23 0.62 0.29 1.67
+ 2.93 0.15 2.96 2.03 0.76 0.81 0.91 1.08 0.68 1.14
+//
+H BEGF750101
+D Conformational parameter of inner helix (Beghin-Dirkx, 1975)
+R PMID:50789
+A Beghin, F. and Dirkx, J.
+T Une methode statistique simple de prediction des conformations proteiques
+J Arch. Int. Physiol. Biochim. 83, 167-168 (1975)
+C KANM800103 0.893 AURR980113 0.857 ROBB760103 0.852
+ CHOP780201 0.841 QIAN880105 0.833 AURR980109 0.821
+ QIAN880107 0.815 PALJ810102 0.811 AURR980108 0.810
+ CHOP780101 -0.803 CHOP780210 -0.804 CRAJ730103 -0.812
+ ROBB760108 -0.819 ROBB760113 -0.826 CHAM830101 -0.854
+ PALJ810106 -0.859
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1. 0.52 0.35 0.44 0.06 0.44 0.73 0.35 0.60 0.73
+ 1. 0.60 1. 0.60 0.06 0.35 0.44 0.73 0.44 0.82
+//
+H BEGF750102
+D Conformational parameter of beta-structure (Beghin-Dirkx, 1975)
+R PMID:50789
+A Beghin, F. and Dirkx, J.
+T Une methode statistique simple de prediction des conformations proteiques
+J Arch. Int. Physiol. Biochim. 83, 167-168 (1975)
+C CORJ870105 0.878 CORJ870106 0.853 PRAM900103 0.834
+ LEVM780102 0.834 PALJ810110 0.834 NAGK730102 0.833
+ CORJ870107 0.831 QIAN880120 0.829 QIAN880119 0.811
+ ROBB760106 0.809 PTIO830102 0.807 LIFS790101 0.807
+ MIYS850101 0.806 PONP800107 0.803 PALJ810104 0.801
+ CORJ870108 -0.825 MEIH800101 -0.832 RACS770101 -0.840
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.77 0.72 0.55 0.65 0.65 0.72 0.55 0.65 0.83 0.98
+ 0.83 0.55 0.98 0.98 0.55 0.55 0.83 0.77 0.83 0.98
+//
+H BEGF750103
+D Conformational parameter of beta-turn (Beghin-Dirkx, 1975)
+R PMID:50789
+A Beghin, F. and Dirkx, J.
+T Une methode statistique simple de prediction des conformations proteiques
+J Arch. Int. Physiol. Biochim. 83, 167-168 (1975)
+C ROBB760113 0.924 ROBB760108 0.922 ROBB760110 0.903
+ CHOP780101 0.885 CRAJ730103 0.874 PALJ810106 0.859
+ TANS770110 0.834
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.37 0.84 0.97 0.97 0.84 0.64 0.53 0.97 0.75 0.37
+ 0.53 0.75 0.64 0.53 0.97 0.84 0.75 0.97 0.84 0.37
+//
+H BHAR880101
+D Average flexibility indices (Bhaskaran-Ponnuswamy, 1988)
+R
+A Bhaskaran, R. and Ponnuswamy, P.K.
+T Positional flexibilities of amino acid residues in globular proteins
+J Int. J. Peptide Protein Res. 32, 241-255 (1988)
+C VINM940103 0.869 KARP850102 0.806 WERD780101 -0.803
+ RICJ880111 -0.813
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.357 0.529 0.463 0.511 0.346 0.493 0.497 0.544 0.323 0.462
+ 0.365 0.466 0.295 0.314 0.509 0.507 0.444 0.305 0.420 0.386
+//
+H BIGC670101
+D Residue volume (Bigelow, 1967)
+R PMID:6048539
+A Bigelow, C.C.
+T On the average hydrophobicity of proteins and the relation between it and
+ protein structure
+J J. Theor. Biol. 16, 187-211 (1967) (Asn Gln 5.0)
+C GOLD730102 1.000 KRIW790103 0.993 TSAJ990101 0.993
+ TSAJ990102 0.992 CHOC750101 0.990 GRAR740103 0.984
+ FAUJ880103 0.972 CHAM820101 0.966 HARY940101 0.960
+ CHOC760101 0.960 PONJ960101 0.950 FASG760101 0.919
+ LEVM760105 0.913 ROSG850101 0.910 DAWD720101 0.903
+ LEVM760102 0.896 ZHOH040102 0.884 LEVM760106 0.876
+ CHAM830106 0.870 LEVM760107 0.863 FAUJ880106 0.860
+ RADA880106 0.856 MCMT640101 0.814 RADA880103 -0.865
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 52.6 109.1 75.7 68.4 68.3 89.7 84.7 36.3 91.9 102.0
+ 102.0 105.1 97.7 113.9 73.6 54.9 71.2 135.4 116.2 85.1
+//
+H BIOV880101
+D Information value for accessibility; average fraction 35% (Biou et al., 1988)
+R PMID:3237683
+A Biou, V., Gibrat, J.F., Levin, J.M., Robson, B. and Garnier, J.
+T Secondary structure prediction: combination of three different methods
+J Protein Engineering 2, 185-191 (1988)
+C RADA880108 0.981 ROSG850102 0.981 NISK860101 0.972
+ BIOV880102 0.968 MIYS850101 0.960 WERD780101 0.951
+ FAUJ830101 0.942 ZHOH040103 0.941 NADH010103 0.939
+ NADH010104 0.937 CASG920101 0.935 MEIH800103 0.934
+ CIDH920104 0.933 BASU050103 0.926 PONP800103 0.926
+ PONP800102 0.926 NADH010102 0.921 NISK800101 0.920
+ PONP800101 0.918 CORJ870101 0.917 CIDH920105 0.912
+ PONP930101 0.912 BASU050102 0.909 PONP800108 0.907
+ PLIV810101 0.899 MANP780101 0.899 ROBB790101 0.890
+ CORJ870107 0.889 CIDH920103 0.887 BASU050101 0.883
+ DESM900102 0.878 CORJ870103 0.876 JANJ780102 0.875
+ ROSM880105 0.874 CORJ870106 0.870 CORJ870104 0.867
+ NADH010105 0.867 CIDH920102 0.864 EISD860103 0.864
+ CORJ870105 0.859 MEEJ810101 0.855 BAEK050101 0.853
+ JANJ790102 0.848 CIDH920101 0.847 JURD980101 0.840
+ GUOD860101 0.839 SWER830101 0.839 NADH010101 0.838
+ BLAS910101 0.838 CORJ870102 0.837 KYTJ820101 0.829
+ EISD860101 0.828 JANJ790101 0.827 ZHOH040101 0.825
+ MEEJ810102 0.824 CHOC760103 0.823 PONP800107 0.816
+ EISD840101 0.811 DESM900101 0.807 KRIW710101 -0.813
+ PARS000101 -0.819 FUKS010102 -0.820 KARP850101 -0.825
+ JANJ780103 -0.829 WOEC730101 -0.829 ROSM880101 -0.830
+ LEVM760101 -0.831 KUHL950101 -0.834 FUKS010103 -0.840
+ GUYH850104 -0.844 HOPT810101 -0.848 WOLS870101 -0.854
+ ROSM880102 -0.854 RACS770103 -0.856 OOBM770101 -0.858
+ KRIW790102 -0.869 FUKS010104 -0.873 VINM940102 -0.876
+ PUNT030102 -0.878 KARP850102 -0.880 PUNT030101 -0.883
+ CORJ870108 -0.886 PARJ860101 -0.889 GUYH850103 -0.890
+ KIDA850101 -0.893 RACS770101 -0.893 VINM940103 -0.901
+ GRAR740102 -0.910 KRIW790101 -0.910 OOBM770103 -0.920
+ GUYH850102 -0.922 GUYH850101 -0.929 RACS770102 -0.937
+ VINM940101 -0.941 MIYS990101 -0.947 MIYS990102 -0.948
+ MEIH800101 -0.949 MEIH800102 -0.956 MIYS990103 -0.962
+ MIYS990104 -0.965 MIYS990105 -0.975 FASG890101 -0.982
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 16. -70. -74. -78. 168. -73. -106. -13. 50. 151.
+ 145. -141. 124. 189. -20. -70. -38. 145. 53. 123.
+//
+H BIOV880102
+D Information value for accessibility; average fraction 23% (Biou et al., 1988)
+R PMID:3237683
+A Biou, V., Gibrat, J.F., Levin, J.M., Robson, B. and Garnier, J.
+T Secondary structure prediction: combination of three different methods
+J Protein Engineering 2, 185-191 (1988)
+C BIOV880101 0.968 ROSG850102 0.960 RADA880108 0.942
+ NISK860101 0.939 MIYS850101 0.930 WERD780101 0.929
+ CASG920101 0.919 MEIH800103 0.916 NADH010102 0.914
+ NADH010103 0.913 FAUJ830101 0.911 NADH010104 0.900
+ ZHOH040103 0.891 CIDH920104 0.890 CIDH920105 0.882
+ CORJ870101 0.882 PONP800103 0.879 PONP930101 0.877
+ DESM900102 0.876 NISK800101 0.873 ROSM880105 0.871
+ BASU050103 0.868 PONP800102 0.867 JANJ780102 0.862
+ PONP800101 0.860 CIDH920103 0.860 PLIV810101 0.858
+ JANJ790102 0.856 PONP800108 0.854 WARP780101 0.853
+ CORJ870107 0.850 MANP780101 0.847 EISD860103 0.845
+ CORJ870103 0.840 BASU050102 0.838 CIDH920102 0.837
+ EISD860101 0.832 NAKH900110 0.829 CORJ870105 0.823
+ MEEJ810101 0.822 DESM900101 0.821 ROBB790101 0.821
+ CIDH920101 0.819 CORJ870106 0.818 GUOD860101 0.817
+ CORJ870104 0.815 PONP800107 0.814 EISD840101 0.814
+ BASU050101 0.812 BLAS910101 0.809 JURD980101 0.805
+ NADH010101 0.804 KARP850101 -0.804 KUHL950101 -0.809
+ JANJ780101 -0.809 FUKS010102 -0.810 PARS000101 -0.813
+ GUYH850103 -0.818 WOEC730101 -0.819 ROSM880101 -0.824
+ VINM940102 -0.826 CORJ870108 -0.831 ROSM880102 -0.837
+ WOLS870101 -0.842 LEVM760101 -0.847 GUYH850104 -0.855
+ KARP850102 -0.859 JANJ780103 -0.860 PUNT030102 -0.860
+ HOPT810101 -0.864 PARJ860101 -0.875 RACS770101 -0.875
+ KRIW790101 -0.876 OOBM770101 -0.877 KRIW790102 -0.878
+ GRAR740102 -0.881 GUYH850101 -0.885 FUKS010104 -0.887
+ PUNT030101 -0.888 VINM940103 -0.889 KIDA850101 -0.892
+ MIYS990101 -0.901 MIYS990102 -0.902 GUYH850102 -0.903
+ RACS770103 -0.906 MIYS990103 -0.923 OOBM770103 -0.925
+ FASG890101 -0.928 VINM940101 -0.929 MIYS990104 -0.932
+ RACS770102 -0.932 MEIH800101 -0.937 MIYS990105 -0.947
+ MEIH800102 -0.951
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 44. -68. -72. -91. 90. -117. -139. -8. 47. 100.
+ 108. -188. 121. 148. -36. -60. -54. 163. 22. 117.
+//
+H BROC820101
+D Retention coefficient in TFA (Browne et al., 1982)
+R PMID:7125223
+A Browne, C.A., Bennett, H.P.J. and Solomon, S.
+T The isolation of peptides by high-performance liquid chromatography using
+ predicted elution positions
+J Anal. Biochem. 124, 201-208 (1982)
+C BROC820102 0.925 ZIMJ680105 0.896 MEEJ800102 0.877
+ TAKK010101 0.836 GUOD860101 0.832 NAKH900110 0.830
+ NOZY710101 0.829 MEEJ810102 0.820 RADA880102 0.811
+ BULH740101 -0.815 PARJ860101 -0.849 WOLS870101 -0.871
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 7.3 -3.6 -5.7 -2.9 -9.2 -0.3 -7.1 -1.2 -2.1 6.6
+ 20.0 -3.7 5.6 19.2 5.1 -4.1 0.8 16.3 5.9 3.5
+//
+H BROC820102
+D Retention coefficient in HFBA (Browne et al., 1982)
+R PMID:7125223
+A Browne, C.A., Bennett, H.P.J. and Solomon, S.
+T The isolation of peptides by high-performance liquid chromatography using
+ predicted elution positions
+J Anal. Biochem. 124, 201-208 (1982)
+C BROC820101 0.925 ZIMJ680105 0.865 MEEJ800102 0.857
+ MEEJ800101 0.840 TAKK010101 0.839
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 3.9 3.2 -2.8 -2.8 -14.3 1.8 -7.5 -2.3 2.0 11.0
+ 15.0 -2.5 4.1 14.7 5.6 -3.5 1.1 17.8 3.8 2.1
+//
+H BULH740101
+D Transfer free energy to surface (Bull-Breese, 1974)
+R PMID:4839053
+A Bull, H.B. and Breese, K.
+T Surface tension of amino acid solutions: A hydrophobicity scale of the amino
+ acid residues
+J Arch. Biochem. Biophys. 161, 665-670 (1974)
+C WOLS870101 0.929 PARJ860101 0.909 MIYS990101 0.884
+ MIYS990102 0.880 GRAR740102 0.822 GUYH850103 0.820
+ COWR900101 -0.804 ROBB790101 -0.813 BROC820101 -0.815
+ LEVM760106 -0.818 ZHOH040103 -0.828 CIDH920104 -0.829
+ FAUJ830101 -0.830 BASU050103 -0.833 EISD860101 -0.833
+ MIYS850101 -0.838 WILM950101 -0.845 BASU050102 -0.845
+ CIDH920103 -0.848 CIDH920102 -0.851 JOND750101 -0.853
+ ARGP820101 -0.854 BASU050101 -0.854 RADA880102 -0.856
+ ZHOH040102 -0.860 BLAS910101 -0.860 TAKK010101 -0.865
+ CIDH920105 -0.871 GOLD730101 -0.874 MEEJ800102 -0.875
+ ZHOH040101 -0.876 MEEJ810101 -0.876 ZIMJ680105 -0.879
+ MEEJ810102 -0.880 ROSM880104 -0.884 NOZY710101 -0.892
+ SIMZ760101 -0.894 VENT840101 -0.907 PLIV810101 -0.912
+ GUOD860101 -0.922 SWER830101 -0.923 CORJ870102 -0.923
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.20 -0.12 0.08 -0.20 -0.45 0.16 -0.30 0.00 -0.12 -2.26
+ -2.46 -0.35 -1.47 -2.33 -0.98 -0.39 -0.52 -2.01 -2.24 -1.56
+//
+H BULH740102
+D Apparent partial specific volume (Bull-Breese, 1974)
+R PMID:4839053
+A Bull, H.B. and Breese, K.
+T Surface tension of amino acid solutions: A hydrophobicity scale of the amino
+ acid residues
+J Arch. Biochem. Biophys. 161, 665-670 (1974) (Tyr !)
+C COHE430101 0.923 ZIMJ680102 0.825 GOLD730101 0.825
+ SIMZ760101 0.815
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.691 0.728 0.596 0.558 0.624 0.649 0.632 0.592 0.646 0.809
+ 0.842 0.767 0.709 0.756 0.730 0.594 0.655 0.743 0.743 0.777
+//
+H BUNA790101
+D alpha-NH chemical shifts (Bundi-Wuthrich, 1979)
+R
+A Bundi, A. and Wuthrich, K.
+T 1H-nmr parameters of the common amino acid residues measured in aqueous
+ solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH
+J Biopolymers 18, 285-297 (1979) (Pro !)
+C BLAM930101 0.945 ONEK900101 0.902 ROBB760104 0.823
+ FAUJ880113 0.818 CHOP780213 -0.822 ISOY800104 -0.842
+ MUNV940104 -0.865 TANS770104 -0.867 MUNV940105 -0.874
+ GEOR030109 -0.901 AVBF000104 -0.922 ONEK900102 -0.949
+ FINA910102 -0.992
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 8.249 8.274 8.747 8.410 8.312 8.411 8.368 8.391 8.415 8.195
+ 8.423 8.408 8.418 8.228 0. 8.380 8.236 8.094 8.183 8.436
+//
+H BUNA790102
+D alpha-CH chemical shifts (Bundi-Wuthrich, 1979)
+R
+A Bundi, A. and Wuthrich, K.
+T 1H-nmr parameters of the common amino acid residues measured in aqueous
+ solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH
+J Biopolymers 18, 285-297 (1979)
+C ANDN920101 0.949
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 4.349 4.396 4.755 4.765 4.686 4.373 4.295 3.972 4.630 4.224
+ 4.385 4.358 4.513 4.663 4.471 4.498 4.346 4.702 4.604 4.184
+//
+H BUNA790103
+D Spin-spin coupling constants 3JHalpha-NH (Bundi-Wuthrich, 1979)
+R
+A Bundi, A. and Wuthrich, K.
+T 1H-nmr parameters of the common amino acid residues measured in aqueous
+ solutions of the linear tetrapeptides H-Gly-Gly-X-L-Ala-OH
+J Biopolymers 18, 285-297 (1979) (Met Pro Trp !)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.5 6.9 7.5 7.0 7.7 6.0 7.0 5.6 8.0 7.0
+ 6.5 6.5 0. 9.4 0. 6.5 6.9 0. 6.8 7.0
+//
+H BURA740101
+D Normalized frequency of alpha-helix (Burgess et al., 1974)
+R
+A Burgess, A.W., Ponnuswamy, P.K. and Scheraga, H.A.
+T Analysis of conformations of amino acid residues and prediction of backbone
+ topography in proteins
+J Isr. J. Chem. 12, 239-286 (1974)
+C CHOP780201 0.917 TANS770101 0.917 ROBB760101 0.912
+ CRAJ730101 0.900 PALJ810102 0.900 NAGK730101 0.883
+ GEIM800101 0.858 KANM800101 0.855 MAXF760101 0.852
+ PALJ810101 0.850 ISOY800101 0.839 LEVM780104 0.833
+ GEIM800104 0.819 KANM800103 0.810 RACS820108 0.809
+ AURR980108 0.808 PRAM900102 0.805 LEVM780101 0.805
+ NAGK730103 -0.830
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.486 0.262 0.193 0.288 0.200 0.418 0.538 0.120 0.400 0.370
+ 0.420 0.402 0.417 0.318 0.208 0.200 0.272 0.462 0.161 0.379
+//
+H BURA740102
+D Normalized frequency of extended structure (Burgess et al., 1974)
+R
+A Burgess, A.W., Ponnuswamy, P.K. and Scheraga, H.A.
+T Analysis of conformations of amino acid residues and prediction of backbone
+ topography in proteins
+J Isr. J. Chem. 12, 239-286 (1974)
+C ROBB760105 0.821
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.288 0.362 0.229 0.271 0.533 0.327 0.262 0.312 0.200 0.411
+ 0.400 0.265 0.375 0.318 0.340 0.354 0.388 0.231 0.429 0.495
+//
+H CHAM810101
+D Steric parameter (Charton, 1981)
+R PMID:7300379
+A Charton, M.
+T Protein folding and the genetic code: An alternative quantitative model
+J J. Theor. Biol. 91, 115-123 (1981) (Pro !)
+C FAUJ880102 0.881 LEVM760104 -0.818 KIMC930101 -0.848
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.52 0.68 0.76 0.76 0.62 0.68 0.68 0.00 0.70 1.02
+ 0.98 0.68 0.78 0.70 0.36 0.53 0.50 0.70 0.70 0.76
+//
+H CHAM820101
+D Polarizability parameter (Charton-Charton, 1982)
+R PMID:7183857
+A Charton, M. and Charton, B.I.
+T The structural dependence of amino acid hydrophobicity parameters
+J J. Theor. Biol. 99, 629-644 (1982) (Pro 0.018)
+C FAUJ880103 0.992 CHOC750101 0.982 TSAJ990102 0.978
+ TSAJ990101 0.977 GOLD730102 0.967 CHOC760101 0.966
+ BIGC670101 0.966 KRIW790103 0.963 FASG760101 0.962
+ GRAR740103 0.951 PONJ960101 0.938 HARY940101 0.933
+ ROSG850101 0.917 LEVM760102 0.915 LEVM760105 0.915
+ FAUJ880106 0.902 CHAM830106 0.899 LEVM760107 0.891
+ MCMT640101 0.871 DAWD720101 0.865 RADA880106 0.847
+ ZHOH040102 0.826 LEVM760106 0.818 HUTJ700102 0.815
+ CHAM830105 0.809 SNEP660103 0.808 RADA880103 -0.912
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.046 0.291 0.134 0.105 0.128 0.180 0.151 0.000 0.230 0.186
+ 0.186 0.219 0.221 0.290 0.131 0.062 0.108 0.409 0.298 0.140
+//
+H CHAM820102
+D Free energy of solution in water, kcal/mole (Charton-Charton, 1982)
+R PMID:7183857
+A Charton, M. and Charton, B.I.
+T The structural dependence of amino acid hydrophobicity parameters
+J J. Theor. Biol. 99, 629-644 (1982) (Asn His Lys Thr !)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.368 -1.03 0. 2.06 4.53 0.731 1.77 -0.525 0. 0.791
+ 1.07 0. 0.656 1.06 -2.24 -0.524 0. 1.60 4.91 0.401
+//
+H CHAM830101
+D The Chou-Fasman parameter of the coil conformation (Charton-Charton, 1983)
+R PMID:6876837
+A Charton, M. and Charton, B.
+T The dependence of the Chou-Fasman parameters on amino acid side chain
+ structure
+J J. Theor. Biol. 111, 447-450 (1983)
+C CHOP780101 0.946 CHOP780216 0.942 PALJ810106 0.939
+ GEIM800111 0.938 CHOP780203 0.931 QIAN880132 0.925
+ TANS770110 0.917 GEIM800108 0.916 QIAN880133 0.913
+ LEVM780103 0.909 PRAM900104 0.909 CHOP780210 0.905
+ LEVM780106 0.900 ISOY800103 0.881 QIAN880131 0.860
+ NAGK730103 0.857 ROBB760113 0.841 QIAN880134 0.841
+ PALJ810105 0.826 CRAJ730103 0.821 QIAN880135 0.814
+ ROBB760108 0.812 ROBB760110 0.804 AVBF000102 -0.803
+ QIAN880105 -0.803 PALJ810102 -0.808 FAUJ880102 -0.809
+ ISOY800101 -0.815 RICJ880109 -0.826 CHOP780201 -0.828
+ AURR980113 -0.828 ROBB760101 -0.828 AURR980108 -0.834
+ PTIO830101 -0.841 AURR980114 -0.842 BEGF750101 -0.854
+ QIAN880106 -0.856 QIAN880107 -0.858 ROBB760103 -0.878
+ KANM800103 -0.889 SUEM840101 -0.891 AURR980109 -0.896
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.71 1.06 1.37 1.21 1.19 0.87 0.84 1.52 1.07 0.66
+ 0.69 0.99 0.59 0.71 1.61 1.34 1.08 0.76 1.07 0.63
+//
+H CHAM830102
+D A parameter defined from the residuals obtained from the best correlation of
+ the Chou-Fasman parameter of beta-sheet (Charton-Charton, 1983)
+R PMID:6876837
+A Charton, M. and Charton, B.
+T The dependence of the Chou-Fasman parameters on amino acid side chain
+ structure
+J J. Theor. Biol. 111, 447-450 (1983) (Pro !)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.118 0.124 0.289 0.048 0.083 -0.105 -0.245 0.104 0.138 0.230
+ -0.052 0.032 -0.258 0.015 0. 0.225 0.166 0.158 0.094 0.513
+//
+H CHAM830103
+D The number of atoms in the side chain labelled 1+1 (Charton-Charton, 1983)
+R PMID:6876837
+A Charton, M. and Charton, B.
+T The dependence of the Chou-Fasman parameters on amino acid side chain
+ structure
+J J. Theor. Biol. 111, 447-450 (1983) (Pro !)
+C AVBF000101 0.843
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 1. 1. 1. 1. 1. 1. 0. 1. 2.
+ 1. 1. 1. 1. 0. 1. 2. 1. 1. 2.
+//
+H CHAM830104
+D The number of atoms in the side chain labelled 2+1 (Charton-Charton, 1983)
+R PMID:
+A Charton, M. and Charton, B.
+T The dependence of the Chou-Fasman parameters on amino acid side chain
+ structure
+J J. Theor. Biol. 111, 447-450 (1983) (Pro !)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 1. 1. 1. 0. 1. 1. 0. 1. 1.
+ 2. 1. 1. 1. 0. 0. 0. 1. 1. 0.
+//
+H CHAM830105
+D The number of atoms in the side chain labelled 3+1 (Charton-Charton, 1983)
+R PMID:6876837
+A Charton, M. and Charton, B.
+T The dependence of the Chou-Fasman parameters on amino acid side chain
+ structure
+J J. Theor. Biol. 111, 447-450 (1983) (Pro !)
+C CHAM830106 0.874 LEVM760102 0.843 FASG760101 0.839
+ CHOC760101 0.833 LEVM760105 0.829 FAUJ880103 0.813
+ CHAM820101 0.809 RADA880103 -0.808
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 1. 0. 0. 0. 1. 1. 0. 1. 0.
+ 0. 1. 1. 1. 0. 0. 0. 1.5 1. 0.
+//
+H CHAM830106
+D The number of bonds in the longest chain (Charton-Charton, 1983)
+R PMID:6876837
+A Charton, M. and Charton, B.
+T The dependence of the Chou-Fasman parameters on amino acid side chain
+ structure
+J J. Theor. Biol. 111, 447-450 (1983) (Pro !)
+C LEVM760102 0.962 LEVM760105 0.958 FASG760101 0.943
+ CHOC760101 0.937 FAUJ880103 0.927 RADA880106 0.922
+ PONJ960101 0.917 CHOC750101 0.906 CHAM820101 0.899
+ TSAJ990102 0.896 HARY940101 0.894 GRAR740103 0.890
+ TSAJ990101 0.889 KRIW790103 0.876 CHAM830105 0.874
+ BIGC670101 0.870 GOLD730102 0.869 OOBM770102 0.858
+ FAUJ880106 0.845 FAUJ880104 0.817 RADA880103 -0.901
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 5. 2. 2. 1. 3. 3. 0. 3. 2.
+ 2. 4. 3. 4. 0. 1. 1. 5. 5. 1.
+//
+H CHAM830107
+D A parameter of charge transfer capability (Charton-Charton, 1983)
+R PMID:6876837
+A Charton, M. and Charton, B.
+T The dependence of the Chou-Fasman parameters on amino acid side chain
+ structure
+J J. Theor. Biol. 111, 447-450 (1983) (Pro !)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 0. 1. 1. 0. 0. 1. 1. 0. 0.
+ 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
+//
+H CHAM830108
+D A parameter of charge transfer donor capability (Charton-Charton, 1983)
+R PMID:6876837
+A Charton, M. and Charton, B.
+T The dependence of the Chou-Fasman parameters on amino acid side chain
+ structure
+J J. Theor. Biol. 111, 447-450 (1983) (Pro !)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 1. 1. 0. 1. 1. 0. 0. 1. 0.
+ 0. 1. 1. 1. 0. 0. 0. 1. 1. 0.
+//
+H CHOC750101
+D Average volume of buried residue (Chothia, 1975)
+R PMID:1118010
+A Chothia, C.
+T Structural invariants in protein folding
+J Nature 254, 304-308 (1975) (Arg missing)
+C TSAJ990102 0.996 TSAJ990101 0.995 FAUJ880103 0.990
+ BIGC670101 0.990 GOLD730102 0.989 CHAM820101 0.982
+ KRIW790103 0.982 CHOC760101 0.981 GRAR740103 0.973
+ PONJ960101 0.966 HARY940101 0.961 FASG760101 0.956
+ LEVM760105 0.939 LEVM760102 0.933 ROSG850101 0.908
+ CHAM830106 0.906 DAWD720101 0.901 FAUJ880106 0.888
+ RADA880106 0.867 LEVM760107 0.858 ZHOH040102 0.856
+ LEVM760106 0.841 MCMT640101 0.822 HUTJ700102 0.802
+ RADA880103 -0.892
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 91.5 202.0 135.2 124.5 117.7 161.1 155.1 66.4 167.3 168.8
+ 167.9 171.3 170.8 203.4 129.3 99.1 122.1 237.6 203.6 141.7
+//
+H CHOC760101
+D Residue accessible surface area in tripeptide (Chothia, 1976)
+R PMID:994183
+A Chothia, C.
+T The nature of the accessible and buried surfaces in proteins
+J J. Mol. Biol. 105, 1-14 (1976)
+C FAUJ880103 0.985 CHOC750101 0.981 FASG760101 0.978
+ LEVM760102 0.972 TSAJ990102 0.972 LEVM760105 0.968
+ TSAJ990101 0.968 CHAM820101 0.966 PONJ960101 0.961
+ GOLD730102 0.960 BIGC670101 0.960 KRIW790103 0.948
+ HARY940101 0.946 GRAR740103 0.945 CHAM830106 0.937
+ DAWD720101 0.901 FAUJ880106 0.898 RADA880106 0.875
+ WOLS870102 0.845 ROSG850101 0.842 FAUJ880104 0.835
+ CHAM830105 0.833 OOBM770102 0.824 HUTJ700102 0.819
+ MCMT640101 0.809 LEVM760107 0.807 RADA880103 -0.924
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 115. 225. 160. 150. 135. 180. 190. 75. 195. 175.
+ 170. 200. 185. 210. 145. 115. 140. 255. 230. 155.
+//
+H CHOC760102
+D Residue accessible surface area in folded protein (Chothia, 1976)
+R PMID:994183
+A Chothia, C.
+T The nature of the accessible and buried surfaces in proteins
+J J. Mol. Biol. 105, 1-14 (1976)
+C JANJ780101 0.973 GUYH850104 0.970 JANJ780103 0.959
+ GUYH850105 0.946 OOBM770101 0.925 FAUJ880109 0.872
+ ROSM880102 0.845 MEIH800102 0.839 PRAM900101 0.826
+ ENGD860101 0.826 PUNT030101 0.809 RACS770102 0.809
+ GUYH850101 0.807 KIDA850101 0.804 MEIH800103 -0.802
+ EISD860103 -0.802 JACR890101 -0.803 NADH010104 -0.809
+ JANJ790101 -0.809 RADA880101 -0.814 ROSG850102 -0.819
+ DESM900102 -0.823 RADA880104 -0.830 WOLR790101 -0.834
+ KYTJ820101 -0.838 WOLR810101 -0.840 NADH010103 -0.840
+ CHOC760104 -0.845 WARP780101 -0.849 JURD980101 -0.851
+ OLSK800101 -0.886 EISD840101 -0.892 NADH010102 -0.893
+ CHOC760103 -0.912 RADA880107 -0.925 JANJ780102 -0.935
+ JANJ790102 -0.969
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 25. 90. 63. 50. 19. 71. 49. 23. 43. 18.
+ 23. 97. 31. 24. 50. 44. 47. 32. 60. 18.
+//
+H CHOC760103
+D Proportion of residues 95% buried (Chothia, 1976)
+R PMID:994183
+A Chothia, C.
+T The nature of the accessible and buried surfaces in proteins
+J J. Mol. Biol. 105, 1-14 (1976)
+C OLSK800101 0.981 JURD980101 0.967 KYTJ820101 0.964
+ JANJ780102 0.950 NADH010102 0.910 CHOC760104 0.907
+ JANJ790102 0.905 EISD860103 0.892 JANJ790101 0.887
+ EISD840101 0.885 NADH010101 0.881 DESM900102 0.877
+ NADH010103 0.875 WOLR810101 0.873 RADA880107 0.870
+ MEIH800103 0.865 MANP780101 0.859 WOLR790101 0.857
+ RADA880101 0.853 ROSG850102 0.851 NADH010104 0.848
+ PONP800103 0.837 PONP800102 0.836 PONP800101 0.830
+ RADA880108 0.830 WARP780101 0.824 NAKH920108 0.824
+ BIOV880101 0.823 CORJ870101 0.822 RADA880104 0.821
+ COWR900101 0.820 PONP930101 0.816 PONP800107 0.813
+ MIYS850101 0.810 LIFS790102 0.810 PONP800108 0.809
+ BASU050103 0.805 MIYS990101 -0.803 MIYS990102 -0.805
+ FAUJ880109 -0.806 ENGD860101 -0.813 PRAM900101 -0.814
+ ROSM880101 -0.819 FASG890101 -0.849 GUYH850101 -0.856
+ PUNT030101 -0.859 KUHL950101 -0.865 ROSM880102 -0.869
+ RACS770102 -0.875 JANJ780103 -0.888 JANJ780101 -0.892
+ MEIH800102 -0.894 OOBM770101 -0.902 GUYH850104 -0.907
+ CHOC760102 -0.912 GUYH850105 -0.933
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.38 0.01 0.12 0.15 0.45 0.07 0.18 0.36 0.17 0.60
+ 0.45 0.03 0.40 0.50 0.18 0.22 0.23 0.27 0.15 0.54
+//
+H CHOC760104
+D Proportion of residues 100% buried (Chothia, 1976)
+R PMID:994183
+A Chothia, C.
+T The nature of the accessible and buried surfaces in proteins
+J J. Mol. Biol. 105, 1-14 (1976) (normalized by the total number)
+C CHOC760103 0.907 JANJ780102 0.903 KYTJ820101 0.889
+ JANJ790101 0.886 OLSK800101 0.872 JURD980101 0.870
+ WOLR810101 0.868 WOLR790101 0.851 PONP800104 0.844
+ JANJ790102 0.835 DESM900102 0.824 NADH010102 0.817
+ WARP780101 0.815 NADH010101 0.804 GUYH850105 -0.822
+ CHOC760102 -0.845 GUYH850104 -0.845 JANJ780103 -0.851
+ JANJ780101 -0.854 OOBM770101 -0.857
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.20 0.00 0.03 0.04 0.22 0.01 0.03 0.18 0.02 0.19
+ 0.16 0.00 0.11 0.14 0.04 0.08 0.08 0.04 0.03 0.18
+//
+H CHOP780101
+D Normalized frequency of beta-turn (Chou-Fasman, 1978a)
+R PMID:354496
+A Chou, P.Y. and Fasman, G.D.
+T Empirical predictions of protein conformation
+J Ann. Rev. Biochem. 47, 251-276 (1978)
+C PALJ810106 0.977 TANS770110 0.956 CHAM830101 0.946
+ CHOP780203 0.940 CHOP780216 0.929 CHOP780210 0.921
+ ROBB760113 0.907 GEIM800108 0.899 QIAN880133 0.897
+ QIAN880132 0.896 LEVM780103 0.893 PRAM900104 0.891
+ LEVM780106 0.890 ROBB760108 0.887 BEGF750103 0.885
+ ISOY800103 0.885 CRAJ730103 0.882 GEIM800111 0.878
+ PALJ810105 0.868 ROBB760110 0.863 NAGK730103 0.827
+ QIAN880131 0.824 AURR980114 -0.803 BEGF750101 -0.803
+ QIAN880107 -0.809 KANM800103 -0.824 AURR980109 -0.837
+ SUEM840101 -0.845
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.66 0.95 1.56 1.46 1.19 0.98 0.74 1.56 0.95 0.47
+ 0.59 1.01 0.60 0.60 1.52 1.43 0.96 0.96 1.14 0.50
+//
+H CHOP780201
+D Normalized frequency of alpha-helix (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C PALJ810102 0.981 ROBB760101 0.969 ISOY800101 0.959
+ MAXF760101 0.956 KANM800101 0.956 TANS770101 0.947
+ BURA740101 0.917 GEIM800101 0.912 KANM800103 0.912
+ NAGK730101 0.886 LEVM780104 0.886 PALJ810101 0.881
+ QIAN880106 0.874 PRAM900102 0.873 LEVM780101 0.873
+ GEIM800104 0.868 RACS820108 0.868 AURR980108 0.867
+ AURR980109 0.859 AURR980112 0.856 CRAJ730101 0.851
+ QIAN880107 0.843 BEGF750101 0.841 QIAN880105 0.835
+ AURR980114 0.828 AURR980115 0.816 AURR980110 0.814
+ PALJ810109 0.814 AURR980111 0.813 ROBB760103 0.806
+ MUNV940101 -0.802 CRAJ730103 -0.808 ROBB760113 -0.811
+ MUNV940102 -0.812 CHAM830101 -0.828 NAGK730103 -0.837
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.42 0.98 0.67 1.01 0.70 1.11 1.51 0.57 1.00 1.08
+ 1.21 1.16 1.45 1.13 0.57 0.77 0.83 1.08 0.69 1.06
+//
+H CHOP780202
+D Normalized frequency of beta-sheet (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C PALJ810104 0.970 LIFS790101 0.947 KANM800102 0.945
+ PALJ810103 0.937 ROBB760106 0.931 LEVM780105 0.930
+ GEIM800107 0.929 QIAN880120 0.915 PTIO830102 0.913
+ QIAN880121 0.911 LIFS790103 0.908 GEIM800105 0.890
+ ROBB760105 0.885 BASU050101 0.883 BASU050103 0.874
+ PONP930101 0.867 NAGK730102 0.858 QIAN880119 0.855
+ CHOP780208 0.851 BASU050102 0.841 KANM800104 0.839
+ GEIM800106 0.839 LEVM780102 0.833 PRAM900103 0.833
+ NISK860101 0.832 SWER830101 0.823 CORJ870102 0.822
+ CHOP780209 0.822 CORJ870101 0.815 PALJ810112 0.815
+ PONP800108 0.809 PALJ810110 0.808 MANP780101 0.805
+ VENT840101 0.805 MIYS990102 -0.801 PUNT030102 -0.803
+ VINM940102 -0.810 OOBM770103 -0.820 GEIM800110 -0.824
+ MIYS990103 -0.825 MIYS990104 -0.829 VINM940101 -0.831
+ MUNV940103 -0.892
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.83 0.93 0.89 0.54 1.19 1.10 0.37 0.75 0.87 1.60
+ 1.30 0.74 1.05 1.38 0.55 0.75 1.19 1.37 1.47 1.70
+//
+H CHOP780203
+D Normalized frequency of beta-turn (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C CHOP780216 0.979 CHOP780101 0.940 TANS770110 0.940
+ LEVM780106 0.935 GEIM800111 0.933 ISOY800103 0.933
+ CHAM830101 0.931 PRAM900104 0.928 QIAN880132 0.928
+ LEVM780103 0.927 GEIM800108 0.925 CHOP780210 0.918
+ QIAN880133 0.915 PALJ810106 0.907 PALJ810105 0.878
+ QIAN880131 0.861 QIAN880134 0.838 RACS770101 0.827
+ QIAN880135 0.811 CORJ870106 -0.813 QIAN880119 -0.814
+ CORJ870105 -0.815 PONP800107 -0.818 SUEM840101 -0.892
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.74 1.01 1.46 1.52 0.96 0.96 0.95 1.56 0.95 0.47
+ 0.50 1.19 0.60 0.66 1.56 1.43 0.98 0.60 1.14 0.59
+//
+H CHOP780204
+D Normalized frequency of N-terminal helix (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C ROBB760102 0.911
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.29 0.44 0.81 2.02 0.66 1.22 2.44 0.76 0.73 0.67
+ 0.58 0.66 0.71 0.61 2.01 0.74 1.08 1.47 0.68 0.61
+//
+H CHOP780205
+D Normalized frequency of C-terminal helix (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C ROBB760104 0.841 QIAN880109 0.806
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.20 1.25 0.59 0.61 1.11 1.22 1.24 0.42 1.77 0.98
+ 1.13 1.83 1.57 1.10 0.00 0.96 0.75 0.40 0.73 1.25
+//
+H CHOP780206
+D Normalized frequency of N-terminal non helical region (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.70 0.34 1.42 0.98 0.65 0.75 1.04 1.41 1.22 0.78
+ 0.85 1.01 0.83 0.93 1.10 1.55 1.09 0.62 0.99 0.75
+//
+H CHOP780207
+D Normalized frequency of C-terminal non helical region (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.52 1.24 1.64 1.06 0.94 0.70 0.59 1.64 1.86 0.87
+ 0.84 1.49 0.52 1.04 1.58 0.93 0.86 0.16 0.96 0.32
+//
+H CHOP780208
+D Normalized frequency of N-terminal beta-sheet (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C NAGK730102 0.860 CHOP780202 0.851 ROBB760106 0.846
+ LIFS790101 0.820 QIAN880119 0.807 KANM800102 0.804
+ QIAN880120 0.800
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.86 0.90 0.66 0.38 0.87 1.65 0.35 0.63 0.54 1.94
+ 1.30 1.00 1.43 1.50 0.66 0.63 1.17 1.49 1.07 1.69
+//
+H CHOP780209
+D Normalized frequency of C-terminal beta-sheet (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C PALJ810104 0.849 CHOP780202 0.822 VENT840101 0.817
+ PTIO830102 0.814 QIAN880121 0.809
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.75 0.90 1.21 0.85 1.11 0.65 0.55 0.74 0.90 1.35
+ 1.27 0.74 0.95 1.50 0.40 0.79 0.75 1.19 1.96 1.79
+//
+H CHOP780210
+D Normalized frequency of N-terminal non beta region (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C CHOP780101 0.921 CHOP780203 0.918 PALJ810106 0.905
+ CHAM830101 0.905 CHOP780216 0.896 GEIM800108 0.896
+ GEIM800111 0.867 TANS770110 0.858 QIAN880132 0.852
+ LEVM780103 0.852 PRAM900104 0.850 ISOY800103 0.829
+ QIAN880131 0.826 QIAN880133 0.820 NAGK730103 0.814
+ LEVM780106 0.812 PALJ810105 0.803 RICJ880111 -0.804
+ BEGF750101 -0.804 RICJ880107 -0.818 PONP800107 -0.820
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.67 0.89 1.86 1.39 1.34 1.09 0.92 1.46 0.78 0.59
+ 0.46 1.09 0.52 0.30 1.58 1.41 1.09 0.48 1.23 0.42
+//
+H CHOP780211
+D Normalized frequency of C-terminal non beta region (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C ROBB760112 0.841
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.74 1.05 1.13 1.32 0.53 0.77 0.85 1.68 0.96 0.53
+ 0.59 0.82 0.85 0.44 1.69 1.49 1.16 1.59 1.01 0.59
+//
+H CHOP780212
+D Frequency of the 1st residue in turn (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C PALJ810106 0.801
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.060 0.070 0.161 0.147 0.149 0.074 0.056 0.102 0.140 0.043
+ 0.061 0.055 0.068 0.059 0.102 0.120 0.086 0.077 0.082 0.062
+//
+H CHOP780213
+D Frequency of the 2nd residue in turn (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C TANS770104 0.954 ISOY800104 0.916 QIAN880134 0.870
+ QIAN880135 0.851 MUNV940104 0.836 FINA910102 0.832
+ MUNV940105 0.826 GEOR030109 0.800 BUNA790101 -0.822
+ BLAM930101 -0.824 PTIO830101 -0.835
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.076 0.106 0.083 0.110 0.053 0.098 0.060 0.085 0.047 0.034
+ 0.025 0.115 0.082 0.041 0.301 0.139 0.108 0.013 0.065 0.048
+//
+H CHOP780214
+D Frequency of the 3rd residue in turn (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C ISOY800105 0.923 TANS770105 0.862
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.035 0.099 0.191 0.179 0.117 0.037 0.077 0.190 0.093 0.013
+ 0.036 0.072 0.014 0.065 0.034 0.125 0.065 0.064 0.114 0.028
+//
+H CHOP780215
+D Frequency of the 4th residue in turn (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C ROBB760111 0.825
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.058 0.085 0.091 0.081 0.128 0.098 0.064 0.152 0.054 0.056
+ 0.070 0.095 0.055 0.065 0.068 0.106 0.079 0.167 0.125 0.053
+//
+H CHOP780216
+D Normalized frequency of the 2nd and 3rd residues in turn (Chou-Fasman, 1978b)
+R PMID:364941
+A Chou, P.Y. and Fasman, G.D.
+T Prediction of the secondary structure of proteins from their amino acid
+ sequence
+J Adv. Enzymol. 47, 45-148 (1978)
+C CHOP780203 0.979 GEIM800111 0.955 LEVM780106 0.953
+ LEVM780103 0.952 PRAM900104 0.951 CHAM830101 0.942
+ GEIM800108 0.942 QIAN880133 0.939 QIAN880132 0.931
+ TANS770110 0.930 CHOP780101 0.929 ISOY800103 0.921
+ PALJ810106 0.904 QIAN880134 0.900 CHOP780210 0.896
+ QIAN880135 0.884 PALJ810105 0.881 QIAN880131 0.873
+ NAGK730103 0.819 QIAN880120 -0.800 CORJ870106 -0.803
+ FAUJ880102 -0.807 KANM800103 -0.808 QIAN880107 -0.808
+ ROBB760103 -0.841 PTIO830101 -0.855 SUEM840101 -0.874
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.64 1.05 1.56 1.61 0.92 0.84 0.80 1.63 0.77 0.29
+ 0.36 1.13 0.51 0.62 2.04 1.52 0.98 0.48 1.08 0.43
+//
+H CIDH920101
+D Normalized hydrophobicity scales for alpha-proteins (Cid et al., 1992)
+R PMID:1518784
+A Cid, H., Bunster, M., Canales, M. and Gazitua, F.
+T Hydrophobicity and structural classes in proteins
+J Protein Engineering 5, 373-375 (1992)
+C CIDH920102 0.921 CIDH920105 0.921 NISK860101 0.882
+ WERD780101 0.878 CIDH920103 0.872 RADA880108 0.858
+ BASU050102 0.858 ZHOH040101 0.855 CORJ870102 0.855
+ SWER830101 0.853 BIOV880101 0.847 ROBB790101 0.846
+ ZHOH040103 0.845 CORJ870107 0.843 MIYS850101 0.843
+ PLIV810101 0.843 CORJ870104 0.840 BASU050101 0.839
+ CIDH920104 0.833 CORJ870106 0.832 ROSG850101 0.831
+ CORJ870105 0.828 BASU050103 0.828 LEVM760106 0.826
+ CORJ870103 0.825 BIOV880102 0.819 ZHOH040102 0.811
+ PONP800101 0.805 VINM940103 -0.814 OOBM770103 -0.818
+ KARP850102 -0.828 RACS770101 -0.837 MIYS990103 -0.838
+ GUYH850102 -0.843 CORJ870108 -0.845 MIYS990102 -0.846
+ MIYS990101 -0.847 MIYS990105 -0.849 VINM940101 -0.854
+ FUKS010103 -0.854 GUYH850103 -0.854 MIYS990104 -0.860
+ MEIH800101 -0.863 KARP850101 -0.864 PARJ860101 -0.871
+ PARS000101 -0.877 VINM940102 -0.885
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.45 -0.24 -0.20 -1.52 0.79 -0.99 -0.80 -1.00 1.07 0.76
+ 1.29 -0.36 1.37 1.48 -0.12 -0.98 -0.70 1.38 1.49 1.26
+//
+H CIDH920102
+D Normalized hydrophobicity scales for beta-proteins (Cid et al., 1992)
+R PMID:1518784
+A Cid, H., Bunster, M., Canales, M. and Gazitua, F.
+T Hydrophobicity and structural classes in proteins
+J Protein Engineering 5, 373-375 (1992)
+C CIDH920105 0.969 ZHOH040101 0.939 CIDH920101 0.921
+ BASU050102 0.914 CIDH920103 0.911 ZHOH040103 0.909
+ CIDH920104 0.904 NISK860101 0.897 ROBB790101 0.896
+ NOZY710101 0.889 MEEJ810101 0.887 PLIV810101 0.877
+ LEVM760106 0.873 MIYS850101 0.873 CORJ870102 0.872
+ WERD780101 0.871 SWER830101 0.870 ROSG850101 0.866
+ BIOV880101 0.864 ZHOH040102 0.862 RADA880102 0.862
+ ARGP820101 0.862 JOND750101 0.861 ROSM880104 0.859
+ TAKK010101 0.859 BASU050101 0.858 MEEJ800102 0.856
+ FAUJ830101 0.856 BASU050103 0.856 MEEJ810102 0.843
+ BIOV880102 0.837 WIMW960101 0.837 RADA880108 0.833
+ SIMZ760101 0.832 GUOD860101 0.831 GOLD730101 0.829
+ PONP930101 0.820 EISD860101 0.819 ZASB820101 0.809
+ LIFS790101 0.808 BLAS910101 0.805 CASG920101 0.802
+ RACS770101 -0.825 VINM940103 -0.826 FUKS010103 -0.826
+ GRAR740102 -0.842 MIYS990103 -0.845 BULH740101 -0.851
+ GUYH850102 -0.855 MIYS990105 -0.859 MEIH800101 -0.867
+ WOLS870101 -0.869 MIYS990102 -0.870 PARS000101 -0.871
+ VINM940101 -0.872 MIYS990101 -0.872 KARP850101 -0.873
+ MIYS990104 -0.877 OOBM770103 -0.877 GUYH850103 -0.904
+ VINM940102 -0.925 PARJ860101 -0.930
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.08 -0.09 -0.70 -0.71 0.76 -0.40 -1.31 -0.84 0.43 1.39
+ 1.24 -0.09 1.27 1.53 -0.01 -0.93 -0.59 2.25 1.53 1.09
+//
+H CIDH920103
+D Normalized hydrophobicity scales for alpha+beta-proteins (Cid et al., 1992)
+R PMID:1518784
+A Cid, H., Bunster, M., Canales, M. and Gazitua, F.
+T Hydrophobicity and structural classes in proteins
+J Protein Engineering 5, 373-375 (1992)
+C CIDH920105 0.973 CIDH920104 0.955 CIDH920102 0.911
+ NISK860101 0.909 MIYS850101 0.906 MANP780101 0.905
+ PLIV810101 0.899 PONP930101 0.899 BASU050103 0.894
+ BASU050101 0.894 RADA880108 0.891 BIOV880101 0.887
+ BASU050102 0.887 ROBB790101 0.884 WERD780101 0.881
+ ZHOH040103 0.881 PONP800101 0.876 CIDH920101 0.872
+ FAUJ830101 0.868 CORJ870107 0.866 ROSM880104 0.866
+ SWER830101 0.865 CORJ870102 0.864 BIOV880102 0.860
+ CORJ870104 0.857 CORJ870103 0.856 NISK800101 0.855
+ PONP800102 0.849 ROSG850102 0.846 GUOD860101 0.845
+ PONP800108 0.841 BLAS910101 0.838 MEEJ810101 0.837
+ CORJ870106 0.837 PONP800107 0.833 ROSM880105 0.832
+ CORJ870105 0.832 ZHOH040101 0.829 CASG920101 0.827
+ ARGP820101 0.827 JOND750101 0.826 PONP800103 0.823
+ CORJ870101 0.822 EISD860101 0.821 RADA880102 0.819
+ LIFS790101 0.815 PTIO830102 0.807 MEIH800103 0.802
+ FUKS010103 -0.804 PUNT030102 -0.810 KRIW790101 -0.819
+ PUNT030101 -0.819 PARS000101 -0.821 MEIH800102 -0.825
+ RACS770102 -0.834 VINM940101 -0.837 FASG890101 -0.846
+ BULH740101 -0.848 KARP850102 -0.852 VINM940102 -0.855
+ OOBM770103 -0.863 CORJ870108 -0.864 MIYS990103 -0.870
+ GRAR740102 -0.871 GUYH850102 -0.871 MIYS990105 -0.876
+ WOLS870101 -0.879 RACS770101 -0.881 MIYS990104 -0.883
+ GUYH850103 -0.890 MIYS990102 -0.899 MIYS990101 -0.900
+ MEIH800101 -0.905 PARJ860101 -0.916
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.36 -0.52 -0.90 -1.09 0.70 -1.05 -0.83 -0.82 0.16 2.17
+ 1.18 -0.56 1.21 1.01 -0.06 -0.60 -1.20 1.31 1.05 1.21
+//
+H CIDH920104
+D Normalized hydrophobicity scales for alpha/beta-proteins (Cid et al., 1992)
+R PMID:1518784
+A Cid, H., Bunster, M., Canales, M. and Gazitua, F.
+T Hydrophobicity and structural classes in proteins
+J Protein Engineering 5, 373-375 (1992)
+C CIDH920105 0.970 CIDH920103 0.955 NISK860101 0.944
+ ZHOH040103 0.941 BASU050103 0.941 BASU050102 0.934
+ BIOV880101 0.933 PONP930101 0.930 FAUJ830101 0.922
+ MANP780101 0.918 BASU050101 0.917 MIYS850101 0.915
+ RADA880108 0.914 PONP800108 0.909 CIDH920102 0.904
+ ROBB790101 0.903 CASG920101 0.903 NISK800101 0.900
+ ROSG850102 0.896 CORJ870101 0.896 WERD780101 0.896
+ PLIV810101 0.893 BIOV880102 0.890 PONP800101 0.888
+ NADH010104 0.888 NADH010103 0.885 BLAS910101 0.881
+ PONP800102 0.880 MEEJ810101 0.878 NADH010105 0.869
+ NADH010101 0.865 PONP800103 0.863 SWER830101 0.862
+ ROSM880104 0.860 CORJ870102 0.860 GUOD860101 0.860
+ ZHOH040101 0.858 NADH010102 0.856 ROSM880105 0.855
+ MEIH800103 0.853 PTIO830102 0.842 CORJ870103 0.841
+ MEEJ810102 0.837 CORJ870107 0.835 EISD860103 0.834
+ CIDH920101 0.833 PONP800107 0.832 JURD980101 0.832
+ CORJ870104 0.832 LIFS790101 0.832 KYTJ820101 0.824
+ ARGP820101 0.819 JOND750101 0.818 RADA880102 0.817
+ EISD860101 0.812 BAEK050101 0.809 JANJ780102 0.803
+ COWR900101 0.803 DESM900102 0.802 KARP850101 -0.801
+ GUYH850101 -0.821 KUHL950101 -0.822 WOEC730101 -0.823
+ PUNT030101 -0.827 ROSM880101 -0.828 BULH740101 -0.829
+ CORJ870108 -0.829 ROSM880102 -0.831 KARP850102 -0.833
+ VINM940103 -0.835 KIDA850101 -0.836 RACS770102 -0.854
+ PUNT030102 -0.857 RACS770101 -0.864 KRIW790101 -0.867
+ MEIH800102 -0.868 VINM940101 -0.883 VINM940102 -0.884
+ WOLS870101 -0.891 GUYH850102 -0.894 MIYS990103 -0.902
+ FASG890101 -0.903 GUYH850103 -0.906 OOBM770103 -0.912
+ PARJ860101 -0.913 GRAR740102 -0.915 MIYS990101 -0.915
+ MIYS990102 -0.916 MIYS990104 -0.916 MIYS990105 -0.916
+ MEIH800101 -0.917
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.17 -0.70 -0.90 -1.05 1.24 -1.20 -1.19 -0.57 -0.25 2.06
+ 0.96 -0.62 0.60 1.29 -0.21 -0.83 -0.62 1.51 0.66 1.21
+//
+H CIDH920105
+D Normalized average hydrophobicity scales (Cid et al., 1992)
+R PMID:1518784
+A Cid, H., Bunster, M., Canales, M. and Gazitua, F.
+T Hydrophobicity and structural classes in proteins
+J Protein Engineering 5, 373-375 (1992)
+C CIDH920103 0.973 CIDH920104 0.970 CIDH920102 0.969
+ NISK860101 0.938 BASU050102 0.931 ZHOH040103 0.926
+ ROBB790101 0.921 CIDH920101 0.921 MIYS850101 0.916
+ BASU050103 0.914 PLIV810101 0.914 BIOV880101 0.912
+ BASU050101 0.907 WERD780101 0.905 ZHOH040101 0.904
+ RADA880108 0.898 FAUJ830101 0.893 MEEJ810101 0.892
+ PONP930101 0.891 SWER830101 0.890 CORJ870102 0.890
+ ROSM880104 0.886 BIOV880102 0.882 MANP780101 0.879
+ ARGP820101 0.867 JOND750101 0.866 RADA880102 0.861
+ CASG920101 0.859 GUOD860101 0.858 ROSG850102 0.858
+ NOZY710101 0.857 PONP800101 0.856 NISK800101 0.854
+ BLAS910101 0.852 CORJ870107 0.848 MEEJ810102 0.844
+ PONP800108 0.843 ROSM880105 0.843 MEEJ800102 0.840
+ TAKK010101 0.840 EISD860101 0.839 CORJ870104 0.838
+ CORJ870103 0.838 SIMZ760101 0.837 PONP800102 0.831
+ LIFS790101 0.828 LEVM760106 0.828 CORJ870101 0.827
+ CORJ870106 0.826 CORJ870105 0.822 GOLD730101 0.820
+ ZHOH040102 0.818 PONP800107 0.818 NADH010104 0.817
+ PTIO830102 0.813 VENT840101 0.813 NADH010103 0.810
+ PONP800103 0.807 MEIH800103 0.804 NADH010105 0.800
+ WOEC730101 -0.800 KIDA850101 -0.803 PUNT030101 -0.805
+ KRIW790101 -0.816 FUKS010103 -0.821 PUNT030102 -0.822
+ MEIH800102 -0.826 RACS770102 -0.830 VINM940103 -0.832
+ KARP850102 -0.839 CORJ870108 -0.843 FASG890101 -0.860
+ PARS000101 -0.860 KARP850101 -0.866 BULH740101 -0.871
+ GRAR740102 -0.884 VINM940101 -0.885 MIYS990103 -0.886
+ RACS770101 -0.887 GUYH850102 -0.892 WOLS870101 -0.899
+ MIYS990105 -0.901 OOBM770103 -0.904 MIYS990104 -0.908
+ VINM940102 -0.910 MIYS990102 -0.915 MIYS990101 -0.916
+ MEIH800101 -0.923 GUYH850103 -0.927 PARJ860101 -0.948
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.02 -0.42 -0.77 -1.04 0.77 -1.10 -1.14 -0.80 0.26 1.81
+ 1.14 -0.41 1.00 1.35 -0.09 -0.97 -0.77 1.71 1.11 1.13
+//
+H COHE430101
+D Partial specific volume (Cohn-Edsall, 1943)
+R
+A Cohn, E.J. and Edsall, J.T.
+T
+J "Protein, Amino Acid, and Peptides", Reinhold, New York (1943)
+C BULH740102 0.923
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.75 0.70 0.61 0.60 0.61 0.67 0.66 0.64 0.67 0.90
+ 0.90 0.82 0.75 0.77 0.76 0.68 0.70 0.74 0.71 0.86
+//
+H CRAJ730101
+D Normalized frequency of middle helix (Crawford et al., 1973)
+R PMID:4510294
+A Crawford, J.L., Lipscomb, W.N. and Schellman, C.G.
+T The reverse turn as a polypeptide conformation in globular proteins
+J Proc. Natl. Acad. Sci. USA 70, 538-542 (1973) Reported values normalized by
+ the total percentage
+C NAGK730101 0.925 BURA740101 0.900 PALJ810101 0.891
+ PRAM900102 0.887 LEVM780101 0.887 ROBB760101 0.875
+ PALJ810102 0.872 GEIM800101 0.870 LEVM780104 0.869
+ CHOP780201 0.851 TANS770101 0.843 KANM800101 0.842
+ ISOY800101 0.840 RACS820108 0.839 GEIM800104 0.838
+ MAXF760101 0.826 PALJ810109 0.811 NAGK730103 -0.850
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.33 0.79 0.72 0.97 0.93 1.42 1.66 0.58 1.49 0.99
+ 1.29 1.03 1.40 1.15 0.49 0.83 0.94 1.33 0.49 0.96
+//
+H CRAJ730102
+D Normalized frequency of beta-sheet (Crawford et al., 1973)
+R PMID:4510294
+A Crawford, J.L., Lipscomb, W.N. and Schellman, C.G.
+T The reverse turn as a polypeptide conformation in globular proteins
+J Proc. Natl. Acad. Sci. USA 70, 538-542 (1973) Reported values normalized by
+ the total percentage
+C ROBB760106 0.865 PTIO830102 0.820 PALJ810104 0.817
+ NAGK730102 0.815
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.00 0.74 0.75 0.89 0.99 0.87 0.37 0.56 0.36 1.75
+ 1.53 1.18 1.40 1.26 0.36 0.65 1.15 0.84 1.41 1.61
+//
+H CRAJ730103
+D Normalized frequency of turn (Crawford et al., 1973)
+R PMID:4510294
+A Crawford, J.L., Lipscomb, W.N. and Schellman, C.G.
+T The reverse turn as a polypeptide conformation in globular proteins
+J Proc. Natl. Acad. Sci. USA 70, 538-542 (1973) Reported values normalized by
+ the total percentage
+C ROBB760113 0.916 ROBB760108 0.912 ROBB760110 0.887
+ PALJ810106 0.884 CHOP780101 0.882 BEGF750103 0.874
+ TANS770110 0.859 CHAM830101 0.821 CHOP780201 -0.808
+ PALJ810102 -0.809 BEGF750101 -0.812 QIAN880107 -0.840
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.60 0.79 1.42 1.24 1.29 0.92 0.64 1.38 0.95 0.67
+ 0.70 1.10 0.67 1.05 1.47 1.26 1.05 1.23 1.35 0.48
+//
+H DAWD720101
+D Size (Dawson, 1972)
+R
+A Dawson, D.M.
+T
+J In "The Biochemical Genetics of Man" (Brock, D.J.H. and Mayo, O., eds.),
+ Academic Press, New York, pp.1-38 (1972)
+C TSAJ990102 0.905 GOLD730102 0.904 TSAJ990101 0.903
+ BIGC670101 0.903 CHOC750101 0.901 CHOC760101 0.901
+ HARY940101 0.900 LEVM760105 0.898 KRIW790103 0.893
+ FAUJ880103 0.880 PONJ960101 0.873 LEVM760102 0.873
+ CHAM820101 0.865 FAUJ880106 0.853 GRAR740103 0.853
+ FASG760101 0.833
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.5 7.5 5.0 2.5 3.0 6.0 5.0 0.5 6.0 5.5
+ 5.5 7.0 6.0 6.5 5.5 3.0 5.0 7.0 7.0 5.0
+//
+H DAYM780101
+D Amino acid composition (Dayhoff et al., 1978a)
+R
+A Dayhoff, M.O., Hunt, L.T. and Hurst-Calderone, S.
+T Composition of proteins
+J In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff, M.O.,
+ ed.), National Biomedical Research Foundation, Washington, D.C., p.363 (1978)
+C JUNJ780101 0.986 JUKT750101 0.975 CEDJ970101 0.970
+ JOND920101 0.954 CEDJ970104 0.952 CEDJ970102 0.945
+ NAKH900101 0.940 KUMS000102 0.925 FUKS010110 0.897
+ NAKH900102 0.883 FUKS010111 0.882 NAKH920101 0.882
+ KUMS000101 0.866 NAKH920107 0.861 FUKS010112 0.856
+ NAKH920106 0.856 NAKH920103 0.851 CEDJ970105 0.839
+ NAKH920104 0.819 CEDJ970103 0.807 NAKH920102 0.802
+ FUKS010109 0.801
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 8.6 4.9 4.3 5.5 2.9 3.9 6.0 8.4 2.0 4.5
+ 7.4 6.6 1.7 3.6 5.2 7.0 6.1 1.3 3.4 6.6
+//
+H DAYM780201
+D Relative mutability (Dayhoff et al., 1978b)
+R
+A Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C.
+T A model of evolutionary change in proteins
+J In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff, M.O.,
+ ed.), National Biomedical Research Foundation, Washington, D.C. pp. 345-352
+ (1978)
+C JOND920102 0.889
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 100. 65. 134. 106. 20. 93. 102. 49. 66. 96.
+ 40. 56. 94. 41. 56. 120. 97. 18. 41. 74.
+//
+H DESM900101
+D Membrane preference for cytochrome b: MPH89 (Degli Esposti et al., 1990)
+R PMID:2364947
+A Degli Esposti, M., Crimi, M. and Venturoli, G.
+T A critical evaluation of the hydropathy profile of membrane proteins
+J Eur. J. Biochem. 190, 207-219 (1990)
+C DESM900102 0.955 PONP800103 0.887 NADH010102 0.885
+ PONP800102 0.871 CORJ870101 0.870 NADH010103 0.866
+ ROSG850102 0.866 WARP780101 0.864 JANJ780102 0.853
+ MEIH800103 0.853 PONP800101 0.847 NADH010104 0.843
+ KYTJ820101 0.837 NISK800101 0.837 JURD980101 0.829
+ NADH010101 0.825 BIOV880102 0.821 JANJ790102 0.818
+ CORJ870107 0.815 CORJ870103 0.812 RADA880108 0.812
+ BIOV880101 0.807 PONP930101 0.807 CASG920101 0.806
+ PUNT030102 -0.801 RACS770102 -0.801 VINM940101 -0.806
+ KRIW710101 -0.807 FASG890101 -0.808 CORJ870108 -0.809
+ MEIH800102 -0.822 GUYH850104 -0.824 PUNT030101 -0.828
+ MIYS990104 -0.828 KARP850102 -0.829 GUYH850101 -0.831
+ MIYS990105 -0.832 KRIW790102 -0.835 RACS770103 -0.837
+ JANJ780103 -0.838 KRIW790101 -0.847 MONM990101 -0.848
+ MIYS990103 -0.854 OOBM770101 -0.894
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.56 0.59 0.51 0.23 1.80 0.39 0.19 1.03 1. 1.27
+ 1.38 0.15 1.93 1.42 0.27 0.96 1.11 0.91 1.10 1.58
+//
+H DESM900102
+D Average membrane preference: AMP07 (Degli Esposti et al., 1990)
+R PMID:2364947
+A Degli Esposti, M., Crimi, M. and Venturoli, G.
+T A critical evaluation of the hydropathy profile of membrane proteins
+J Eur. J. Biochem. 190, 207-219 (1990)
+C DESM900101 0.955 JANJ780102 0.935 NADH010102 0.933
+ MEIH800103 0.924 ROSG850102 0.914 NADH010103 0.910
+ NADH010101 0.905 CORJ870101 0.901 JURD980101 0.900
+ KYTJ820101 0.898 JANJ790102 0.897 PONP800103 0.896
+ NADH010104 0.886 WARP780101 0.882 RADA880108 0.881
+ PONP800102 0.880 BIOV880101 0.878 CHOC760103 0.877
+ BIOV880102 0.876 CASG920101 0.869 PONP800101 0.858
+ JANJ790101 0.855 NISK800101 0.852 OLSK800101 0.849
+ EISD860103 0.848 NISK860101 0.843 PONP930101 0.834
+ PONP800108 0.833 MIYS850101 0.831 RADA880101 0.828
+ EISD840101 0.828 ROSM880105 0.825 CHOC760104 0.824
+ CORJ870107 0.819 BASU050103 0.818 MANP780101 0.816
+ NADH010105 0.816 FAUJ830101 0.816 CORJ870103 0.815
+ WERD780101 0.814 CIDH920104 0.802 VINM940104 -0.803
+ MEIH800101 -0.804 MIYS990101 -0.809 CORJ870108 -0.811
+ MIYS990102 -0.811 ROSM880101 -0.812 KARP850102 -0.815
+ ROSM880102 -0.816 GUYH850105 -0.818 CHOC760102 -0.823
+ VINM940103 -0.824 VINM940101 -0.829 WOEC730101 -0.847
+ MONM990101 -0.850 KRIW790102 -0.852 MIYS990104 -0.854
+ KRIW790101 -0.859 GRAR740102 -0.862 KUHL950101 -0.863
+ RACS770102 -0.867 PUNT030102 -0.868 RACS770103 -0.868
+ MIYS990105 -0.875 MIYS990103 -0.876 JANJ780101 -0.878
+ FASG890101 -0.879 PRAM900101 -0.890 ENGD860101 -0.890
+ GUYH850101 -0.895 GUYH850104 -0.896 MEIH800102 -0.898
+ PUNT030101 -0.903 JANJ780103 -0.908 OOBM770101 -0.950
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.26 0.38 0.59 0.27 1.60 0.39 0.23 1.08 1. 1.44
+ 1.36 0.33 1.52 1.46 0.54 0.98 1.01 1.06 0.89 1.33
+//
+H EISD840101
+D Consensus normalized hydrophobicity scale (Eisenberg, 1984)
+R PMID:6383201
+A Eisenberg, D.
+T Three-dimensional structure of membrane and surface proteins
+J Ann. Rev. Biochem. 53, 595-623 (1984) Original references: Eisenberg, D.,
+ Weiss, R.M., Terwilliger, T.C. and Wilcox, W. Faraday Symp. Chem. Soc. 17,
+ 109-120 (1982) Eisenberg, D., Weiss, R.M. and Terwilliger, T.C. The
+ hydrophobic moment detects periodicity in protein hydrophobicity Proc. Natl.
+ Acad. Sci. USA 81, 140-144 (1984)
+C RADA880101 0.968 JACR890101 0.938 RADA880107 0.927
+ ROSM880105 0.923 WOLR810101 0.914 WOLR790101 0.909
+ RADA880104 0.908 JANJ790102 0.900 JURD980101 0.895
+ NADH010102 0.887 CHOC760103 0.885 BLAS910101 0.884
+ EISD860101 0.884 KYTJ820101 0.878 FAUJ830101 0.875
+ JANJ780102 0.874 OLSK800101 0.869 COWR900101 0.863
+ NADH010101 0.861 NADH010103 0.840 NAKH900110 0.838
+ EISD860103 0.837 DESM900102 0.828 RADA880108 0.817
+ BIOV880102 0.814 BIOV880101 0.811 YUTK870101 0.809
+ NADH010104 0.809 ROSG850102 0.806 BASU050103 0.806
+ WOLS870101 -0.820 GRAR740102 -0.823 MEIH800102 -0.829
+ HOPT810101 -0.846 GUYH850101 -0.849 PUNT030102 -0.854
+ LEVM760101 -0.859 OOBM770101 -0.878 JANJ780103 -0.881
+ FAUJ880109 -0.890 GUYH850104 -0.892 CHOC760102 -0.892
+ KIDA850101 -0.900 JANJ780101 -0.907 KUHL950101 -0.907
+ PUNT030101 -0.914 VHEG790101 -0.924 ROSM880102 -0.925
+ ENGD860101 -0.936 PRAM900101 -0.936 ROSM880101 -0.947
+ GUYH850105 -0.951
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.25 -1.76 -0.64 -0.72 0.04 -0.69 -0.62 0.16 -0.40 0.73
+ 0.53 -1.10 0.26 0.61 -0.07 -0.26 -0.18 0.37 0.02 0.54
+//
+H EISD860101
+D Solvation free energy (Eisenberg-McLachlan, 1986)
+R PMID: 3945310
+A Eisenberg, D. and McLachlan, A.D.
+T Solvation energy in protein folding and binding
+J Nature 319, 199-203 (1986)
+C ROSM880105 0.948 FAUJ830101 0.919 RADA880102 0.912
+ BLAS910101 0.911 PLIV810101 0.904 ZIMJ680105 0.900
+ RADA880101 0.891 MEEJ800102 0.890 EISD840101 0.884
+ RADA880108 0.844 MIYS850101 0.842 GUOD860101 0.839
+ CIDH920105 0.839 BIOV880102 0.832 BIOV880101 0.828
+ JACR890101 0.827 SWER830101 0.824 CORJ870102 0.822
+ NOZY710101 0.822 CIDH920103 0.821 NAKH900110 0.820
+ CIDH920102 0.819 CIDH920104 0.812 NAKH900104 0.812
+ NAKH900106 0.812 BASU050103 0.809 MEEJ810102 0.808
+ MEEJ810101 0.805 GUYH850101 -0.823 MIYS990102 -0.824
+ MIYS990101 -0.827 BULH740101 -0.833 KUHL950101 -0.835
+ WOEC730101 -0.838 PRAM900101 -0.862 ENGD860101 -0.862
+ VHEG790101 -0.862 ROSM880102 -0.868 PUNT030102 -0.869
+ GRAR740102 -0.871 PARJ860101 -0.876 KIDA850101 -0.890
+ PUNT030101 -0.890 HOPT810101 -0.905 ROSM880101 -0.917
+ WOLS870101 -0.918 LEVM760101 -0.921
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.67 -2.1 -0.6 -1.2 0.38 -0.22 -0.76 0. 0.64 1.9
+ 1.9 -0.57 2.4 2.3 1.2 0.01 0.52 2.6 1.6 1.5
+//
+H EISD860102
+D Atom-based hydrophobic moment (Eisenberg-McLachlan, 1986)
+R PMID: 3945310
+A Eisenberg, D. and McLachlan, A.D.
+T Solvation energy in protein folding and binding
+J Nature 319, 199-203 (1986)
+C FAUJ880109 0.841 HUTJ700103 0.841 RADA880107 -0.837
+ YUTK870103 -0.839 YUTK870104 -0.840 JACR890101 -0.871
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 10. 1.3 1.9 0.17 1.9 3. 0. 0.99 1.2
+ 1.0 5.7 1.9 1.1 0.18 0.73 1.5 1.6 1.8 0.48
+//
+H EISD860103
+D Direction of hydrophobic moment (Eisenberg-McLachlan, 1986)
+R PMID: 3945310
+A Eisenberg, D. and McLachlan, A.D.
+T Solvation energy in protein folding and binding
+J Nature 319, 199-203 (1986) (Gly Ala missing)
+C JURD980101 0.901 KYTJ820101 0.897 CHOC760103 0.892
+ JANJ780102 0.883 OLSK800101 0.881 FAUJ830101 0.876
+ RADA880108 0.873 NADH010102 0.872 MEIH800103 0.870
+ NADH010101 0.868 COWR900101 0.868 BIOV880101 0.864
+ MIYS850101 0.858 NADH010103 0.855 PLIV810101 0.852
+ RADA880101 0.850 DESM900102 0.848 ROSG850102 0.846
+ BIOV880102 0.845 PONP800103 0.842 NADH010104 0.840
+ JANJ790102 0.838 EISD840101 0.837 CIDH920104 0.834
+ BLAS910101 0.830 JANJ790101 0.829 MANP780101 0.826
+ WARP780101 0.820 PONP800102 0.814 RADA880107 0.812
+ NISK860101 0.811 ARGP820103 0.810 PONP800108 0.809
+ CORJ870101 0.809 BASU050103 0.806 ROSM880105 0.801
+ CHOC760102 -0.802 WOEC730101 -0.803 JANJ780101 -0.808
+ MEIH800101 -0.810 GUYH850105 -0.812 MIYS990105 -0.815
+ FAUJ880110 -0.815 JANJ780103 -0.819 PUNT030101 -0.829
+ MIYS990101 -0.829 ENGD860101 -0.831 PRAM900101 -0.831
+ MIYS990102 -0.831 GUYH850101 -0.832 KIDA850101 -0.832
+ GUYH850104 -0.835 WOLS870101 -0.841 PUNT030102 -0.853
+ RACS770102 -0.858 FASG890101 -0.863 ROSM880101 -0.871
+ GRAR740102 -0.871 OOBM770101 -0.880 MEIH800102 -0.882
+ KUHL950101 -0.894 ROSM880102 -0.943
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. -0.96 -0.86 -0.98 0.76 -1.0 -0.89 0. -0.75 0.99
+ 0.89 -0.99 0.94 0.92 0.22 -0.67 0.09 0.67 -0.93 0.84
+//
+H FASG760101
+D Molecular weight (Fasman, 1976)
+R
+A Fasman, G.D., ed.
+T
+J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume
+ 1, CRC Press, Cleveland (1976)
+C FAUJ880103 0.979 CHOC760101 0.978 LEVM760102 0.966
+ CHAM820101 0.962 CHOC750101 0.956 LEVM760105 0.951
+ PONJ960101 0.945 CHAM830106 0.943 TSAJ990102 0.940
+ TSAJ990101 0.935 BIGC670101 0.919 GOLD730102 0.918
+ KRIW790103 0.910 HARY940101 0.910 GRAR740103 0.908
+ FAUJ880106 0.899 RADA880106 0.870 WOLS870102 0.866
+ MCMT640101 0.845 CHAM830105 0.839 ROSG850101 0.838
+ DAWD720101 0.833 FAUJ880104 0.825 OOBM770102 0.821
+ LEVM760107 0.815 RADA880103 -0.954
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 89.09 174.20 132.12 133.10 121.15 146.15 147.13 75.07 155.16 131.17
+ 131.17 146.19 149.21 165.19 115.13 105.09 119.12 204.24 181.19 117.15
+//
+H FASG760102
+D Melting point (Fasman, 1976)
+R
+A Fasman, G.D., ed.
+T
+J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume
+ 1, CRC Press, Cleveland (1976)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 297. 238. 236. 270. 178. 185. 249. 290. 277. 284.
+ 337. 224. 283. 284. 222. 228. 253. 282. 344. 293.
+//
+H FASG760103
+D Optical rotation (Fasman, 1976)
+R
+A Fasman, G.D., ed.
+T
+J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume
+ 1, CRC Press, Cleveland (1976)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.80 12.50 -5.60 5.05 -16.50 6.30 12.00 0.00 -38.50 12.40
+ -11.00 14.60 -10.00 -34.50 -86.20 -7.50 -28.00 -33.70 -10.00 5.63
+//
+H FASG760104
+D pK-N (Fasman, 1976)
+R
+A Fasman, G.D., ed.
+T
+J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume
+ 1, CRC Press, Cleveland (1976)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 9.69 8.99 8.80 9.60 8.35 9.13 9.67 9.78 9.17 9.68
+ 9.60 9.18 9.21 9.18 10.64 9.21 9.10 9.44 9.11 9.62
+//
+H FASG760105
+D pK-C (Fasman, 1976)
+R
+A Fasman, G.D., ed.
+T
+J "Handbook of Biochemistry and Molecular Biology", 3rd ed., Proteins - Volume
+ 1, CRC Press, Cleveland (1976)
+C JOND750102 0.833
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.34 1.82 2.02 1.88 1.92 2.17 2.10 2.35 1.82 2.36
+ 2.36 2.16 2.28 2.16 1.95 2.19 2.09 2.43 2.20 2.32
+//
+H FAUJ830101
+D Hydrophobic parameter pi (Fauchere-Pliska, 1983)
+R
+A Fauchere, J.L. and Pliska, V.
+T Hydrophobic parameters pi of amino-acid side chains from the partitioning of
+ N-acetyl-amino-acid amides
+J Eur. J. Med. Chem. 18, 369-375 (1983)
+C BIOV880101 0.942 ROSM880105 0.937 ZHOH040103 0.933
+ RADA880108 0.932 PLIV810101 0.931 BLAS910101 0.923
+ CIDH920104 0.922 EISD860101 0.919 MIYS850101 0.914
+ BIOV880102 0.911 NISK860101 0.906 ROSG850102 0.904
+ BASU050103 0.903 MEEJ810101 0.902 GUOD860101 0.900
+ NADH010103 0.899 NADH010104 0.894 CIDH920105 0.893
+ NADH010102 0.891 MEEJ810102 0.890 BASU050102 0.885
+ COWR900101 0.876 EISD860103 0.876 CASG920101 0.875
+ EISD840101 0.875 PONP800108 0.875 RADA880101 0.873
+ ROBB790101 0.868 CIDH920103 0.868 PONP800103 0.863
+ WERD780101 0.862 MEEJ800102 0.858 CIDH920102 0.856
+ BASU050101 0.852 NISK800101 0.849 MEIH800103 0.849
+ RADA880102 0.846 CORJ870101 0.845 MANP780101 0.843
+ PONP930101 0.843 PONP800102 0.841 ZHOH040101 0.841
+ NADH010101 0.837 SWER830101 0.833 JURD980101 0.833
+ CORJ870102 0.831 JANJ790102 0.826 JANJ780102 0.825
+ NADH010105 0.822 PONP800101 0.822 ZIMJ680105 0.816
+ DESM900102 0.816 KYTJ820101 0.811 NOZY710101 0.803
+ VINM940103 -0.804 FUKS010102 -0.805 GUYH850104 -0.816
+ BULH740101 -0.830 OOBM770101 -0.832 FUKS010104 -0.832
+ RACS770102 -0.843 VINM940102 -0.844 PRAM900101 -0.853
+ ENGD860101 -0.853 GUYH850102 -0.857 GUYH850101 -0.863
+ MEIH800101 -0.863 KUHL950101 -0.863 KRIW790101 -0.865
+ GUYH850103 -0.870 VINM940101 -0.871 MEIH800102 -0.875
+ PUNT030101 -0.876 WOEC730101 -0.880 MIYS990103 -0.893
+ OOBM770103 -0.899 MIYS990104 -0.906 PARJ860101 -0.907
+ ROSM880101 -0.907 MIYS990101 -0.907 PUNT030102 -0.908
+ MIYS990102 -0.908 HOPT810101 -0.909 FASG890101 -0.911
+ LEVM760101 -0.919 MIYS990105 -0.920 ROSM880102 -0.927
+ WOLS870101 -0.928 KIDA850101 -0.946 GRAR740102 -0.948
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.31 -1.01 -0.60 -0.77 1.54 -0.22 -0.64 0.00 0.13 1.80
+ 1.70 -0.99 1.23 1.79 0.72 -0.04 0.26 2.25 0.96 1.22
+//
+H FAUJ880101
+D Graph shape index (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988) Original reference: Kier,
+ L.B. Quant. Struct. Act. Relat. 6, 117-122 (1987)
+C ZIMJ680102 0.888
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.28 2.34 1.60 1.60 1.77 1.56 1.56 0.00 2.99 4.19
+ 2.59 1.89 2.35 2.94 2.67 1.31 3.03 3.21 2.94 3.67
+//
+H FAUJ880102
+D Smoothed upsilon steric parameter (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988) (Pro missing) Original
+ reference of these two data: Fauchere, L.J. In "QSAR in Design of Bioactive
+ Compounds", (Kuchar, M., ed.), Prous, Barcelona pp.135-144 (1984)
+C AVBF000102 0.881 CHAM810101 0.881 PTIO830101 0.832
+ CHOP780216 -0.807 CHAM830101 -0.809 GEIM800108 -0.819
+ MUNV940104 -0.824 PRAM900104 -0.844 LEVM780103 -0.846
+ QIAN880132 -0.849 QIAN880133 -0.851 QIAN880134 -0.852
+ LEVM780106 -0.865 GEIM800111 -0.873 KIMC930101 -0.886
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.53 0.69 0.58 0.59 0.66 0.71 0.72 0.00 0.64 0.96
+ 0.92 0.78 0.77 0.71 0. 0.55 0.63 0.84 0.71 0.89
+//
+H FAUJ880103
+D Normalized van der Waals volume (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988) (Pro !) Original reference of
+ these two data: Fauchere, L.J. In "QSAR in Design of Bioactive Compounds",
+ (Kuchar, M., ed.), Prous, Barcelona pp.135-144 (1984)
+C CHAM820101 0.992 CHOC750101 0.990 CHOC760101 0.985
+ TSAJ990102 0.985 TSAJ990101 0.983 FASG760101 0.979
+ BIGC670101 0.972 GOLD730102 0.972 KRIW790103 0.965
+ PONJ960101 0.963 GRAR740103 0.959 HARY940101 0.951
+ LEVM760102 0.947 LEVM760105 0.945 CHAM830106 0.927
+ FAUJ880106 0.908 ROSG850101 0.892 DAWD720101 0.880
+ LEVM760107 0.875 RADA880106 0.869 MCMT640101 0.847
+ ZHOH040102 0.816 WOLS870102 0.814 CHAM830105 0.813
+ HUTJ700102 0.807 FAUJ880104 0.804 OOBM770102 0.801
+ RADA880103 -0.923
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.00 6.13 2.95 2.78 2.43 3.95 3.78 0.00 4.66 4.00
+ 4.00 4.77 4.43 5.89 2.72 1.60 2.60 8.08 6.47 3.00
+//
+H FAUJ880104
+D STERIMOL length of the side chain (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988) (Pro !) Original reference of
+ these three data: Verloop, A. In "IUPAC, Pesticide Chemistry", Vol.1
+ (Miyamoto, J. and Kearney, P.C., eds.),Pergamon, Oxford pp.339-334 (1983)
+C LEVM760105 0.896 LEVM760102 0.867 HUTJ700103 0.839
+ CHOC760101 0.835 HUTJ700102 0.835 FASG760101 0.825
+ CHAM830106 0.817 FAUJ880103 0.804 RADA880103 -0.806
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.87 7.82 4.58 4.74 4.47 6.11 5.97 2.06 5.23 4.92
+ 4.92 6.89 6.36 4.62 4.11 3.97 4.11 7.68 4.73 4.11
+//
+H FAUJ880105
+D STERIMOL minimum width of the side chain (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988) (Pro !) Original reference of
+ these three data: Verloop, A. In "IUPAC, Pesticide Chemistry", Vol.1
+ (Miyamoto, J. and Kearney, P.C., eds.),Pergamon, Oxford pp.339-334 (1983)
+C AVBF000102 0.802
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.52 1.52 1.52 1.52 1.52 1.52 1.52 1.00 1.52 1.90
+ 1.52 1.52 1.52 1.52 1.52 1.52 1.73 1.52 1.52 1.90
+//
+H FAUJ880106
+D STERIMOL maximum width of the side chain (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988) Original reference of these
+ three data: Verloop, A. In "IUPAC, Pesticide Chemistry", Vol.1 (Miyamoto, J.
+ and Kearney, P.C., eds.),Pergamon, Oxford pp.339-334 (1983)
+C PONJ960101 0.913 HARY940101 0.909 FAUJ880103 0.908
+ CHAM820101 0.902 LEVM760102 0.900 FASG760101 0.899
+ CHOC760101 0.898 LEVM760105 0.889 CHOC750101 0.888
+ TSAJ990102 0.882 TSAJ990101 0.879 WOLS870102 0.866
+ BIGC670101 0.860 GOLD730102 0.857 DAWD720101 0.853
+ KRIW790103 0.845 CHAM830106 0.845 GRAR740103 0.819
+ HUTJ700102 0.806 RADA880103 -0.823
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.04 6.24 4.37 3.78 3.41 3.53 3.31 1.00 5.66 3.49
+ 4.45 4.87 4.80 6.02 4.31 2.70 3.17 5.90 6.72 3.17
+//
+H FAUJ880107
+D N.m.r. chemical shift of alpha-carbon (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988) Original reference: Fauchere,
+ J.L. and Lauterwein, J. Quant. Struct. Act. Rel. 4, 11-13 (1985)
+C AVBF000105 0.931 AVBF000107 0.884 AVBF000103 0.873
+ AVBF000106 0.853 AVBF000108 0.802
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 7.3 11.1 8.0 9.2 14.4 10.6 11.4 0.0 10.2 16.1
+ 10.1 10.9 10.4 13.9 17.8 13.1 16.7 13.2 13.9 17.2
+//
+H FAUJ880108
+D Localized electrical effect (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988) (Pro missing) Original
+ reference: Charton, M. and Charton, B.I. J. Theor. Biol. 102, 121-134 (1983)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.01 0.04 0.06 0.15 0.12 0.05 0.07 0.00 0.08 -0.01
+ -0.01 0.00 0.04 0.03 0. 0.11 0.04 0.00 0.03 0.01
+//
+H FAUJ880109
+D Number of hydrogen bond donors (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988) Original reference of these
+ two data: IUPAC-IUB Joint Commission on Biochemical Nomenclature Eur. J.
+ Biochem. 138, 9-37 (1984)
+C GUYH850105 0.927 CHOC760102 0.872 JANJ780101 0.850
+ ROSM880101 0.846 EISD860102 0.841 KUHL950101 0.827
+ ROSM880102 0.824 PRAM900101 0.815 ENGD860101 0.814
+ GUYH850104 0.812 CHOC760103 -0.806 OLSK800101 -0.821
+ JANJ790102 -0.822 RADA880101 -0.873 JACR890101 -0.889
+ RADA880105 -0.889 EISD840101 -0.890 WOLR810101 -0.904
+ WOLR790101 -0.920 RADA880104 -0.926 RADA880107 -0.957
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 4. 2. 1. 0. 2. 1. 0. 1. 0.
+ 0. 2. 0. 0. 0. 1. 1. 1. 1. 0.
+//
+H FAUJ880110
+D Number of full nonbonding orbitals (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988) Original reference of these
+ two data: IUPAC-IUB Joint Commission on Biochemical Nomenclature Eur. J.
+ Biochem. 138, 9-37 (1984)
+C KUHL950101 0.922 ROSM880101 0.888 WOEC730101 0.812
+ ROSM880105 -0.803 SNEP660102 -0.804 NADH010101 -0.813
+ EISD860103 -0.815 RADA880101 -0.838
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 3. 3. 4. 0. 3. 4. 0. 1. 0.
+ 0. 1. 0. 0. 0. 2. 2. 0. 2. 0.
+//
+H FAUJ880111
+D Positive charge (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988)
+C ZIMJ680104 0.813
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 1. 0. 0. 0. 0. 0. 0. 1. 0.
+ 0. 1. 0. 0. 0. 0. 0. 0. 0. 0.
+//
+H FAUJ880112
+D Negative charge (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988)
+C RICJ880106 0.849
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 0. 0. 1. 0. 0. 1. 0. 0. 0.
+ 0. 0. 0. 0. 0. 0. 0. 0. 0. 0.
+//
+H FAUJ880113
+D pK-a(RCOOH) (Fauchere et al., 1988)
+R PMID:3209351
+A Fauchere, J.L., Charton, M., Kier, L.B., Verloop, A. and Pliska, V.
+T Amino acid side chain parameters for correlation studies in biology and
+ pharmacology
+J Int. J. Peptide Protein Res. 32, 269-278 (1988) (Pro missing)
+C BLAM930101 0.839 ONEK900101 0.820 BUNA790101 0.818
+ ROBB760103 0.802 MUNV940102 -0.826 MUNV940101 -0.836
+ ONEK900102 -0.839 GEOR030109 -0.848
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 4.76 4.30 3.64 5.69 3.67 4.54 5.48 3.77 2.84 4.81
+ 4.79 4.27 4.25 4.31 0. 3.83 3.87 4.75 4.30 4.86
+//
+H FINA770101
+D Helix-coil equilibrium constant (Finkelstein-Ptitsyn, 1977)
+R PMID:843599
+A Finkelstein, A.V. and Ptitsyn, O.B.
+T Theory of protein molecule self-organization. II. A comparison of calculated
+ thermodynamic parameters of local secondary structures with experiments
+J Biopolymers 16, 497-524 (1977) (Pro 0.096)
+C SUEM840101 0.883 AURR980114 0.875 AURR980113 0.849
+ PTIO830101 0.826 KANM800103 0.823 QIAN880107 0.814
+ QIAN880106 0.810 MAXF760101 0.810 AURR980109 0.802
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.08 1.05 0.85 0.85 0.95 0.95 1.15 0.55 1.00 1.05
+ 1.25 1.15 1.15 1.10 0.71 0.75 0.75 1.10 1.10 0.95
+//
+H FINA910101
+D Helix initiation parameter at posision i-1 (Finkelstein et al., 1991)
+R PMID:1946339
+A Finkelstein, A.V., Badretdinov, A.Y. and Ptitsyn, O.B.
+T Physical reasons for secondary structure stability: alpha-helices in short
+ peptides
+J Proteins 10, 287-299 (1991) In these four data, each of Arg, Asp, Glu, His
+ and Lys has two value. See comment lines. Arg pH < 12 ( 1 when pH > 12 ) Asp
+ pH > 4 ( 1.7 when pH < 4 ) Glu pH > 4.3 ( 1 when pH < 4.3 ) His pH > 6.3 (
+ 0.7 when pH < 6.3 ) Lys pH < 10.5 ( 1 when pH > 10.5 )
+C MONM990201 0.812 AURR980104 0.804
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1. 0.70 1.70 3.20 1. 1. 1.70 1. 1. 0.60
+ 1. 0.70 1. 1. 1. 1.70 1.70 1. 1. 0.60
+//
+H FINA910102
+D Helix initiation parameter at posision i,i+1,i+2 (Finkelstein et al., 1991)
+R PMID:1946339
+A Finkelstein, A.V., Badretdinov, A.Y. and Ptitsyn, O.B.
+T Physical reasons for secondary structure stability: alpha-helices in short
+ peptides
+J Proteins 10, 287-299 (1991) In these four data, each of Arg, Asp, Glu, His
+ and Lys has two value. See comment lines. Arg pH < 12 ( 1 when pH > 12 ) Asp
+ pH > 4 ( 1 when pH < 4 ) Glu pH > 4.3 ( 1 when pH < 4.3 ) His pH > 6.3 ( 0.7
+ when pH < 6.3 ) Lys pH < 10.5 ( 1 when pH > 10.5 ) (Pro !)
+C ONEK900102 0.964 MUNV940105 0.911 AVBF000104 0.901
+ MUNV940104 0.896 GEOR030109 0.890 TANS770104 0.876
+ ISOY800104 0.844 CHOP780213 0.832 ROBB760104 -0.844
+ ONEK900101 -0.920 BLAM930101 -0.961 BUNA790101 -0.992
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1. 0.70 1. 1.70 1. 1. 1.70 1.30 1. 1.
+ 1. 0.70 1. 1. 13. 1. 1. 1. 1. 1.
+//
+H FINA910103
+D Helix termination parameter at posision j-2,j-1,j (Finkelstein et al., 1991)
+R PMID:1946339
+A Finkelstein, A.V., Badretdinov, A.Y. and Ptitsyn, O.B.
+T Physical reasons for secondary structure stability: alpha-helices in short
+ peptides
+J Proteins 10, 287-299 (1991) In these four data, each of Arg, Asp, Glu, His
+ and Lys has two value. See comment lines. Arg pH < 12 ( 1 when pH > 12 ) Asp
+ pH > 4 ( 1 when pH < 4 ) Glu pH > 4.3 ( 1 when pH < 4.3 ) His pH > 6.3 ( 1.7
+ when pH < 6.3 ) Lys pH < 10.5 ( 1 when pH > 10.5 )
+C ZIMJ680104 0.805
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.20 1.70 1.20 0.70 1. 1. 0.70 0.80 1.20 0.80
+ 1. 1.70 1. 1. 1. 1.50 1. 1. 1. 0.80
+//
+H FINA910104
+D Helix termination parameter at posision j+1 (Finkelstein et al., 1991)
+R PMID:1946339
+A Finkelstein, A.V., Badretdinov, A.Y. and Ptitsyn, O.B.
+T Physical reasons for secondary structure stability: alpha-helices in short
+ peptides
+J Proteins 10, 287-299 (1991) In these four data, each of Arg, Asp, Glu, His
+ and Lys has two value. See comment lines. Arg pH < 12 ( 1 when pH > 12 ) Asp
+ pH > 4 ( 1 when pH < 4 ) Glu pH > 4.3 ( 1 when pH < 4.3 ) His pH > 6.3 ( 1.7
+ when pH < 6.3 ) Lys pH < 10.5 ( 1 when pH > 10.5 )
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1. 1.70 1. 0.70 1. 1. 0.70 1.50 1. 1.
+ 1. 1.70 1. 1. 0.10 1. 1. 1. 1. 1.
+//
+H GARJ730101
+D Partition coefficient (Garel et al., 1973)
+R PMID:4700470
+A Garel, J.P., Filliol, D. and Mandel, P.
+T Coefficients de partage d'aminoacides, nucleobases, nucleosides et
+ nucleotides dans un systeme solvant salin
+J J. Chromatogr. 78, 381-391 (1973)
+C LEVM760107 0.860 NOZY710101 0.821 OOBM850102 -0.877
+ WEBA780101 -0.924
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.28 0.10 0.25 0.21 0.28 0.35 0.33 0.17 0.21 0.82
+ 1.00 0.09 0.74 2.18 0.39 0.12 0.21 5.70 1.26 0.60
+//
+H GEIM800101
+D Alpha-helix indices (Geisow-Roberts, 1980)
+R
+A Geisow, M.J. and Roberts, R.D.B.
+T Amino acid preferences for secondary structure vary with protein class
+J Int. J. Biol. Macromol. 2, 387-389 (1980)
+C PALJ810101 0.951 LEVM780104 0.950 KANM800101 0.942
+ TANS770101 0.918 CHOP780201 0.912 NAGK730101 0.912
+ PRAM900102 0.912 LEVM780101 0.912 PALJ810102 0.910
+ GEIM800104 0.903 ISOY800101 0.903 ROBB760101 0.897
+ MAXF760101 0.895 KANM800103 0.881 RACS820108 0.880
+ CRAJ730101 0.870 BURA740101 0.858 PALJ810109 0.816
+ AURR980115 0.804 AURR980112 0.802
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.29 1. 0.81 1.10 0.79 1.07 1.49 0.63 1.33 1.05
+ 1.31 1.33 1.54 1.13 0.63 0.78 0.77 1.18 0.71 0.81
+//
+H GEIM800102
+D Alpha-helix indices for alpha-proteins (Geisow-Roberts, 1980)
+R
+A Geisow, M.J. and Roberts, R.D.B.
+T Amino acid preferences for secondary structure vary with protein class
+J Int. J. Biol. Macromol. 2, 387-389 (1980)
+C PALJ810107 0.919 GEIM800109 -0.993
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.13 1.09 1.06 0.94 1.32 0.93 1.20 0.83 1.09 1.05
+ 1.13 1.08 1.23 1.01 0.82 1.01 1.17 1.32 0.88 1.13
+//
+H GEIM800103
+D Alpha-helix indices for beta-proteins (Geisow-Roberts, 1980)
+R
+A Geisow, M.J. and Roberts, R.D.B.
+T Amino acid preferences for secondary structure vary with protein class
+J Int. J. Biol. Macromol. 2, 387-389 (1980)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.55 0.20 1.20 1.55 1.44 1.13 1.67 0.59 1.21 1.27
+ 1.25 1.20 1.37 0.40 0.21 1.01 0.55 1.86 1.08 0.64
+//
+H GEIM800104
+D Alpha-helix indices for alpha/beta-proteins (Geisow-Roberts, 1980)
+R
+A Geisow, M.J. and Roberts, R.D.B.
+T Amino acid preferences for secondary structure vary with protein class
+J Int. J. Biol. Macromol. 2, 387-389 (1980)
+C PALJ810109 0.937 KANM800101 0.916 LEVM780101 0.907
+ PRAM900102 0.907 GEIM800101 0.903 MAXF760101 0.897
+ ISOY800101 0.891 PALJ810102 0.886 LEVM780104 0.872
+ CHOP780201 0.868 ROBB760101 0.855 RACS820108 0.851
+ PALJ810101 0.841 TANS770101 0.841 CRAJ730101 0.838
+ NAGK730101 0.828 BURA740101 0.819 AURR980112 0.815
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.19 1. 0.94 1.07 0.95 1.32 1.64 0.60 1.03 1.12
+ 1.18 1.27 1.49 1.02 0.68 0.81 0.85 1.18 0.77 0.74
+//
+H GEIM800105
+D Beta-strand indices (Geisow-Roberts, 1980)
+R
+A Geisow, M.J. and Roberts, R.D.B.
+T Amino acid preferences for secondary structure vary with protein class
+J Int. J. Biol. Macromol. 2, 387-389 (1980)
+C PALJ810103 0.945 LEVM780105 0.926 KANM800102 0.916
+ GEIM800107 0.901 CHOP780202 0.890 ROBB760105 0.877
+ KANM800104 0.861 PALJ810104 0.856 ROBB760106 0.856
+ LIFS790101 0.855 TANS770103 0.850 ISOY800102 0.843
+ LIFS790103 0.832 PALJ810112 0.830 QIAN880119 0.829
+ QIAN880120 0.822 MAXF760102 0.819 QIAN880121 0.811
+ PTIO830102 0.810 QIAN880118 0.810 MUNV940103 -0.841
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.84 1.04 0.66 0.59 1.27 1.02 0.57 0.94 0.81 1.29
+ 1.10 0.86 0.88 1.15 0.80 1.05 1.20 1.15 1.39 1.56
+//
+H GEIM800106
+D Beta-strand indices for beta-proteins (Geisow-Roberts, 1980)
+R
+A Geisow, M.J. and Roberts, R.D.B.
+T Amino acid preferences for secondary structure vary with protein class
+J Int. J. Biol. Macromol. 2, 387-389 (1980)
+C GEIM800107 0.878 PALJ810110 0.851 CHOP780202 0.839
+ ROBB760106 0.838 QIAN880120 0.825 KANM800102 0.821
+ LIFS790103 0.814 MUNV940103 -0.800 GEIM800110 -0.929
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.86 1.15 0.60 0.66 0.91 1.11 0.37 0.86 1.07 1.17
+ 1.28 1.01 1.15 1.34 0.61 0.91 1.14 1.13 1.37 1.31
+//
+H GEIM800107
+D Beta-strand indices for alpha/beta-proteins (Geisow-Roberts, 1980)
+R
+A Geisow, M.J. and Roberts, R.D.B.
+T Amino acid preferences for secondary structure vary with protein class
+J Int. J. Biol. Macromol. 2, 387-389 (1980)
+C KANM800102 0.955 CHOP780202 0.929 PALJ810104 0.928
+ PALJ810112 0.905 GEIM800105 0.901 ROBB760106 0.899
+ PALJ810103 0.890 LIFS790101 0.888 LEVM780105 0.884
+ GEIM800106 0.878 KANM800104 0.876 QIAN880121 0.875
+ PTIO830102 0.850 BASU050103 0.847 BASU050101 0.847
+ QIAN880120 0.843 LEVM780102 0.842 PRAM900103 0.842
+ PONP930101 0.838 ROBB760105 0.836 NAGK730102 0.830
+ PALJ810110 0.826 LIFS790103 0.823 CORJ870101 0.821
+ PONP800108 0.817 NISK860101 0.813 QIAN880119 0.807
+ MIYS990103 -0.803 GEIM800110 -0.815 VINM940101 -0.819
+ MUNV940103 -0.869
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.91 0.99 0.72 0.74 1.12 0.90 0.41 0.91 1.01 1.29
+ 1.23 0.86 0.96 1.26 0.65 0.93 1.05 1.15 1.21 1.58
+//
+H GEIM800108
+D Aperiodic indices (Geisow-Roberts, 1980)
+R
+A Geisow, M.J. and Roberts, R.D.B.
+T Amino acid preferences for secondary structure vary with protein class
+J Int. J. Biol. Macromol. 2, 387-389 (1980)
+C GEIM800111 0.967 CHOP780216 0.942 LEVM780106 0.932
+ PRAM900104 0.931 LEVM780103 0.931 QIAN880133 0.930
+ ISOY800103 0.930 CHOP780203 0.925 CHAM830101 0.916
+ QIAN880132 0.906 CHOP780101 0.899 CHOP780210 0.896
+ TANS770110 0.886 QIAN880134 0.884 QIAN880135 0.877
+ PALJ810105 0.873 GEIM800110 0.870 PALJ810106 0.862
+ QIAN880131 0.860 MUNV940103 0.806 ROBB760103 -0.802
+ QIAN880120 -0.804 QIAN880119 -0.810 FAUJ880102 -0.819
+ PTIO830101 -0.840 SUEM840101 -0.875
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.91 1. 1.64 1.40 0.93 0.94 0.97 1.51 0.90 0.65
+ 0.59 0.82 0.58 0.72 1.66 1.23 1.04 0.67 0.92 0.60
+//
+H GEIM800109
+D Aperiodic indices for alpha-proteins (Geisow-Roberts, 1980)
+R
+A Geisow, M.J. and Roberts, R.D.B.
+T Amino acid preferences for secondary structure vary with protein class
+J Int. J. Biol. Macromol. 2, 387-389 (1980)
+C PALJ810107 -0.909 GEIM800102 -0.993
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.80 0.96 1.10 1.60 0. 1.60 0.40 2. 0.96 0.85
+ 0.80 0.94 0.39 1.20 2.10 1.30 0.60 0. 1.80 0.80
+//
+H GEIM800110
+D Aperiodic indices for beta-proteins (Geisow-Roberts, 1980)
+R
+A Geisow, M.J. and Roberts, R.D.B.
+T Amino acid preferences for secondary structure vary with protein class
+J Int. J. Biol. Macromol. 2, 387-389 (1980)
+C MUNV940103 0.880 GEIM800108 0.870 GEIM800111 0.857
+ QIAN880134 0.853 QIAN880135 0.842 PARS000101 0.831
+ QIAN880133 0.822 LEVM780106 0.809 QIAN880121 -0.806
+ CORJ870105 -0.807 CORJ870106 -0.812 KANM800102 -0.814
+ GEIM800107 -0.815 ROBB760106 -0.819 CHOP780202 -0.824
+ AVBF000101 -0.825 PALJ810110 -0.840 QIAN880119 -0.853
+ LIFS790101 -0.862 LIFS790103 -0.889 QIAN880120 -0.898
+ GEIM800106 -0.929
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.10 0.93 1.57 1.41 1.05 0.81 1.40 1.30 0.85 0.67
+ 0.52 0.94 0.69 0.60 1.77 1.13 0.88 0.62 0.41 0.58
+//
+H GEIM800111
+D Aperiodic indices for alpha/beta-proteins (Geisow-Roberts, 1980)
+R
+A Geisow, M.J. and Roberts, R.D.B.
+T Amino acid preferences for secondary structure vary with protein class
+J Int. J. Biol. Macromol. 2, 387-389 (1980)
+C GEIM800108 0.967 CHOP780216 0.955 PRAM900104 0.954
+ LEVM780103 0.952 LEVM780106 0.951 QIAN880133 0.943
+ CHAM830101 0.938 CHOP780203 0.933 ISOY800103 0.929
+ QIAN880132 0.929 QIAN880134 0.919 QIAN880135 0.895
+ TANS770110 0.883 CHOP780101 0.878 CHOP780210 0.867
+ QIAN880131 0.857 GEIM800110 0.857 PALJ810105 0.855
+ PALJ810106 0.844 LIFS790101 -0.801 AVBF000101 -0.806
+ KANM800103 -0.812 AURR980109 -0.814 QIAN880120 -0.816
+ ROBB760103 -0.843 FAUJ880102 -0.873 PTIO830101 -0.876
+ SUEM840101 -0.885
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.93 1.01 1.36 1.22 0.92 0.83 1.05 1.45 0.96 0.58
+ 0.59 0.91 0.60 0.71 1.67 1.25 1.08 0.68 0.98 0.62
+//
+H GOLD730101
+D Hydrophobicity factor (Goldsack-Chalifoux, 1973)
+R PMID:4354159
+A Goldsack, D.E. and Chalifoux, R.C.
+T Contribution of the free energy of mixing of hydrophobic side chains to the
+ stability of the tertiary structure
+J J. Theor. Biol. 39, 645-651 (1973) (Asn Gln !)
+C SIMZ760101 0.939 ARGP820101 0.936 JOND750101 0.935
+ TAKK010101 0.872 MEEJ800102 0.866 LAWE840101 0.829
+ CIDH920102 0.829 LEVM760106 0.827 BULH740102 0.825
+ MEEJ810101 0.824 BLAS910101 0.821 ZIMJ680105 0.820
+ CIDH920105 0.820 ZIMJ680102 0.818 ZHOH040101 0.817
+ ROSM880104 0.808 MEEJ800101 0.808 MEEJ810102 0.806
+ VENT840101 0.802 PARJ860101 -0.827 WOLS870101 -0.854
+ BULH740101 -0.874
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.75 0.75 0.69 0.00 1.00 0.59 0.00 0.00 0.00 2.95
+ 2.40 1.50 1.30 2.65 2.60 0.00 0.45 3.00 2.85 1.70
+//
+H GOLD730102
+D Residue volume (Goldsack-Chalifoux, 1973)
+R PMID:4354159
+A Goldsack, D.E. and Chalifoux, R.C.
+T Contribution of the free energy of mixing of hydrophobic side chains to the
+ stability of the tertiary structure
+J J. Theor. Biol. 39, 645-651 (1973) (Asn Gln 8.8)
+C BIGC670101 1.000 KRIW790103 0.994 TSAJ990101 0.993
+ TSAJ990102 0.991 CHOC750101 0.989 GRAR740103 0.984
+ FAUJ880103 0.972 CHAM820101 0.967 CHOC760101 0.960
+ HARY940101 0.959 PONJ960101 0.947 FASG760101 0.918
+ LEVM760105 0.911 ROSG850101 0.909 DAWD720101 0.904
+ LEVM760102 0.893 ZHOH040102 0.882 LEVM760106 0.875
+ CHAM830106 0.869 LEVM760107 0.865 FAUJ880106 0.857
+ RADA880106 0.854 MCMT640101 0.814 RADA880103 -0.864
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 88.3 181.2 125.1 110.8 112.4 148.7 140.5 60.0 152.6 168.5
+ 168.5 175.6 162.2 189.0 122.2 88.7 118.2 227.0 193.0 141.4
+//
+H GRAR740101
+D Composition (Grantham, 1974)
+R PMID:4843792
+A Grantham, R.
+T Amino acid difference formula to help explain protein evolution
+J Science 185, 862-864 (1974) (Atomic weight ratio of noncarbons to carbons in
+ the side chain)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.00 0.65 1.33 1.38 2.75 0.89 0.92 0.74 0.58 0.00
+ 0.00 0.33 0.00 0.00 0.39 1.42 0.71 0.13 0.20 0.00
+//
+H GRAR740102
+D Polarity (Grantham, 1974)
+R PMID:4843792
+A Grantham, R.
+T Amino acid difference formula to help explain protein evolution
+J Science 185, 862-864 (1974)
+C WOEC730101 0.960 MIYS990105 0.928 PUNT030102 0.915
+ MIYS990104 0.910 WOLS870101 0.910 MIYS990103 0.904
+ MIYS990101 0.903 MIYS990102 0.903 OOBM770103 0.896
+ PARJ860101 0.891 ROSM880101 0.887 KIDA850101 0.881
+ HOPT810101 0.874 PUNT030101 0.873 FASG890101 0.872
+ ROSM880102 0.870 VINM940101 0.869 LEVM760101 0.865
+ KUHL950101 0.865 PRAM900101 0.855 ENGD860101 0.855
+ KRIW790101 0.847 OOBM770101 0.841 CORJ870108 0.838
+ VINM940102 0.837 MEIH800102 0.836 GUYH850103 0.831
+ MONM990101 0.831 MEIH800101 0.824 BULH740101 0.822
+ GUYH850101 0.818 GUYH850102 0.806 WIMW960101 -0.804
+ JANJ780102 -0.809 MEEJ810102 -0.811 NADH010105 -0.812
+ EISD840101 -0.823 WERD780101 -0.826 ROBB790101 -0.832
+ CORJ870103 -0.836 MEEJ810101 -0.839 CORJ870107 -0.840
+ CIDH920102 -0.842 PONP800101 -0.849 CORJ870104 -0.850
+ CASG920101 -0.850 COWR900101 -0.854 GUOD860101 -0.855
+ KYTJ820101 -0.859 NADH010101 -0.859 RADA880101 -0.861
+ DESM900102 -0.862 JURD980101 -0.864 BASU050102 -0.864
+ MEIH800103 -0.866 NADH010104 -0.868 MANP780101 -0.868
+ PONP800102 -0.871 EISD860101 -0.871 EISD860103 -0.871
+ CIDH920103 -0.871 PONP930101 -0.872 NISK800101 -0.879
+ ROSG850102 -0.880 BIOV880102 -0.881 NADH010103 -0.881
+ NADH010102 -0.881 CIDH920105 -0.884 PLIV810101 -0.888
+ BASU050101 -0.889 CORJ870101 -0.890 CORJ870102 -0.893
+ ZHOH040103 -0.895 MIYS850101 -0.895 SWER830101 -0.896
+ PONP800103 -0.897 RADA880108 -0.899 NISK860101 -0.900
+ BASU050103 -0.906 PONP800108 -0.907 BIOV880101 -0.910
+ CIDH920104 -0.915 ROSM880105 -0.924 FAUJ830101 -0.948
+ BLAS910101 -0.950
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 8.1 10.5 11.6 13.0 5.5 10.5 12.3 9.0 10.4 5.2
+ 4.9 11.3 5.7 5.2 8.0 9.2 8.6 5.4 6.2 5.9
+//
+H GRAR740103
+D Volume (Grantham, 1974)
+R PMID:4843792
+A Grantham, R.
+T Amino acid difference formula to help explain protein evolution
+J Science 185, 862-864 (1974)
+C KRIW790103 0.989 BIGC670101 0.984 GOLD730102 0.984
+ TSAJ990101 0.979 TSAJ990102 0.978 CHOC750101 0.973
+ FAUJ880103 0.959 CHAM820101 0.951 HARY940101 0.946
+ CHOC760101 0.945 PONJ960101 0.937 ROSG850101 0.922
+ RADA880106 0.920 FASG760101 0.908 LEVM760105 0.900
+ CHAM830106 0.890 LEVM760102 0.885 ZHOH040102 0.872
+ DAWD720101 0.853 LEVM760106 0.846 LEVM760107 0.841
+ FAUJ880106 0.819 MCMT640101 0.817 RADA880103 -0.881
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 31. 124. 56. 54. 55. 85. 83. 3. 96. 111.
+ 111. 119. 105. 132. 32.5 32. 61. 170. 136. 84.
+//
+H GUYH850101
+D Partition energy (Guy, 1985)
+R PMID:3978191
+A Guy, H.R.
+T Amino acid side-chain partition energies and distribution of residues in
+ soluble proteins
+J Biophys. J. 47, 61-70 (1985)
+C MEIH800102 0.934 RACS770102 0.934 FASG890101 0.934
+ PUNT030101 0.910 MIYS990103 0.907 MIYS990105 0.895
+ MEIH800101 0.893 MIYS990102 0.892 MIYS990101 0.891
+ MIYS990104 0.889 KRIW790101 0.885 VINM940103 0.865
+ KRIW790102 0.864 GUYH850104 0.857 RACS770101 0.853
+ CORJ870108 0.851 OOBM770101 0.848 GUYH850105 0.843
+ KARP850102 0.840 ROSM880102 0.837 PUNT030102 0.836
+ KIDA850101 0.834 KRIW710101 0.831 VINM940101 0.829
+ JANJ780103 0.829 KUHL950101 0.827 JANJ780101 0.821
+ PRAM900101 0.820 ENGD860101 0.820 GRAR740102 0.818
+ RACS770103 0.816 CHOC760102 0.807 GUYH850102 0.805
+ ROSM880101 0.803 HOPT810101 0.802 BASU050102 -0.801
+ BASU050101 -0.807 CORJ870105 -0.810 NISK800101 -0.811
+ YUTK870101 -0.813 CORJ870103 -0.813 RADA880101 -0.815
+ CORJ870104 -0.815 PONP930101 -0.817 CORJ870101 -0.820
+ CIDH920104 -0.821 OLSK800101 -0.823 EISD860101 -0.823
+ PONP800106 -0.826 DESM900101 -0.831 EISD860103 -0.832
+ ROSM880105 -0.832 CORJ870106 -0.833 CASG920101 -0.836
+ PLIV810101 -0.836 MANP780101 -0.838 ZHOH040103 -0.839
+ CORJ870107 -0.841 KYTJ820101 -0.843 EISD840101 -0.849
+ NADH010105 -0.855 CHOC760103 -0.856 NADH010101 -0.862
+ FAUJ830101 -0.863 JURD980101 -0.864 JANJ790102 -0.865
+ BASU050103 -0.871 WERD780101 -0.871 JANJ780102 -0.872
+ PONP800101 -0.877 NISK860101 -0.877 MEIH800103 -0.880
+ PONP800102 -0.883 BIOV880102 -0.885 PONP800103 -0.887
+ DESM900102 -0.895 MIYS850101 -0.909 NADH010104 -0.910
+ NADH010102 -0.910 NADH010103 -0.916 BIOV880101 -0.929
+ ROSG850102 -0.929 RADA880108 -0.948
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.10 1.91 0.48 0.78 -1.42 0.95 0.83 0.33 -0.50 -1.13
+ -1.18 1.40 -1.59 -2.12 0.73 0.52 0.07 -0.51 -0.21 -1.27
+//
+H HOPA770101
+D Hydration number (Hopfinger, 1971), Cited by Charton-Charton (1982)
+R
+A Hopfinger, A.J.
+T
+J "Intermolecular Interactions and Biomolecular Organizations", Wiley, New York
+ (1977) Cited by Charton-Charton (1982) (Cys !)
+C WOEC730101 0.876 ZIMJ680103 0.815
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.0 2.3 2.2 6.5 0.1 2.1 6.2 1.1 2.8 0.8
+ 0.8 5.3 0.7 1.4 0.9 1.7 1.5 1.9 2.1 0.9
+//
+H HOPT810101
+D Hydrophilicity value (Hopp-Woods, 1981)
+R PMID:6167991
+A Hopp, T.P. and Woods, K.R.
+T Prediction of protein antigenic determinants from amino acid sequecces
+J Proc. Natl. Acad. Sci. USA 78, 3824-3828 (1981)
+C LEVM760101 0.985 WOEC730101 0.886 PUNT030102 0.886
+ FUKS010104 0.884 ENGD860101 0.882 PRAM900101 0.881
+ KIDA850101 0.881 GRAR740102 0.874 MIYS990105 0.862
+ VINM940101 0.859 PUNT030101 0.858 FUKS010102 0.854
+ VHEG790101 0.849 ROSM880101 0.848 MIYS990104 0.843
+ OOBM770103 0.833 WOLS870101 0.830 MIYS990103 0.825
+ PARJ860101 0.819 MIYS990102 0.804 MIYS990101 0.803
+ GUYH850101 0.802 MIYS850101 -0.800 NADH010103 -0.805
+ NAKH900110 -0.812 ZIMJ680105 -0.816 JACR890101 -0.816
+ NADH010102 -0.820 NISK860101 -0.822 ROSG850102 -0.825
+ MEEJ800102 -0.826 RADA880101 -0.829 ZHOH040103 -0.829
+ BASU050103 -0.830 RADA880108 -0.831 CASG920101 -0.839
+ EISD840101 -0.846 BIOV880101 -0.848 WIMW960101 -0.855
+ RADA880102 -0.859 BIOV880102 -0.864 BLAS910101 -0.877
+ EISD860101 -0.905 FAUJ830101 -0.909 ROSM880105 -0.955
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.5 3.0 0.2 3.0 -1.0 0.2 3.0 0.0 -0.5 -1.8
+ -1.8 3.0 -1.3 -2.5 0.0 0.3 -0.4 -3.4 -2.3 -1.5
+//
+H HUTJ700101
+D Heat capacity (Hutchens, 1970)
+R
+A Hutchens, J.O.
+T Heat capacities, absolute entropies, and entropies of formation of amino
+ acids and related compounds
+J In "Handbook of Biochemistry", 2nd ed. (Sober, H.A., ed.), Chemical Rubber
+ Co., Cleveland, Ohio, pp. B60-B61 (1970)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 29.22 26.37 38.30 37.09 50.70 44.02 41.84 23.71 59.64 45.00
+ 48.03 57.10 69.32 48.52 36.13 32.40 35.20 56.92 51.73 40.35
+//
+H HUTJ700102
+D Absolute entropy (Hutchens, 1970)
+R
+A Hutchens, J.O.
+T Heat capacities, absolute entropies, and entropies of formation of amino
+ acids and related compounds
+J In "Handbook of Biochemistry", 2nd ed. (Sober, H.A., ed.), Chemical Rubber
+ Co., Cleveland, Ohio, pp. B60-B61 (1970)
+C HUTJ700103 0.867 LEVM760105 0.864 LEVM760102 0.835
+ FAUJ880104 0.835 CHOC760101 0.819 CHAM820101 0.815
+ FAUJ880103 0.807 FAUJ880106 0.806 CHOC750101 0.802
+ RADA880103 -0.812
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 30.88 68.43 41.70 40.66 53.83 46.62 44.98 24.74 65.99 49.71
+ 50.62 63.21 55.32 51.06 39.21 35.65 36.50 60.00 51.15 42.75
+//
+H HUTJ700103
+D Entropy of formation (Hutchens, 1970)
+R
+A Hutchens, J.O.
+T Heat capacities, absolute entropies, and entropies of formation of amino
+ acids and related compounds
+J In "Handbook of Biochemistry", 2nd ed. (Sober, H.A., ed.), Chemical Rubber
+ Co., Cleveland, Ohio, pp. B60-B61 (1970)
+C HUTJ700102 0.867 EISD860102 0.841 FAUJ880104 0.839
+ LEVM760105 0.834
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 154.33 341.01 207.90 194.91 219.79 235.51 223.16 127.90 242.54 233.21
+ 232.30 300.46 202.65 204.74 179.93 174.06 205.80 237.01 229.15 207.60
+//
+H ISOY800101
+D Normalized relative frequency of alpha-helix (Isogai et al., 1980)
+R PMID:7378550
+A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A
+T Characterization of multiple bends in proteins
+J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set
+ of proteins
+C MAXF760101 0.982 PALJ810102 0.965 KANM800101 0.963
+ CHOP780201 0.959 ROBB760101 0.957 KANM800103 0.931
+ LEVM780101 0.929 PRAM900102 0.929 TANS770101 0.906
+ LEVM780104 0.904 RACS820108 0.904 QIAN880106 0.903
+ GEIM800101 0.903 AURR980109 0.894 GEIM800104 0.891
+ QIAN880107 0.887 PALJ810101 0.882 PALJ810109 0.874
+ AURR980112 0.870 NAGK730101 0.862 AURR980114 0.857
+ AURR980108 0.856 AURR980110 0.855 AURR980115 0.844
+ ROBB760103 0.841 CRAJ730101 0.840 BURA740101 0.839
+ QIAN880105 0.828 AURR980113 0.815 AURR980111 0.801
+ CHAM830101 -0.815 NAGK730103 -0.821 MUNV940101 -0.875
+ MUNV940102 -0.877
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.53 1.17 0.60 1.00 0.89 1.27 1.63 0.44 1.03 1.07
+ 1.32 1.26 1.66 1.22 0.25 0.65 0.86 1.05 0.70 0.93
+//
+H ISOY800102
+D Normalized relative frequency of extended structure (Isogai et al., 1980)
+R PMID:7378550
+A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A
+T Characterization of multiple bends in proteins
+J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set
+ of proteins
+C MAXF760102 0.931 TANS770103 0.929 ROBB760105 0.847
+ GEIM800105 0.843 PALJ810103 0.807 WOEC730101 -0.803
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.86 0.98 0.74 0.69 1.39 0.89 0.66 0.70 1.06 1.31
+ 1.01 0.77 1.06 1.16 1.16 1.09 1.24 1.17 1.28 1.40
+//
+H ISOY800103
+D Normalized relative frequency of bend (Isogai et al., 1980)
+R PMID:7378550
+A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A
+T Characterization of multiple bends in proteins
+J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set
+ of proteins
+C LEVM780106 0.941 PRAM900104 0.934 CHOP780203 0.933
+ LEVM780103 0.932 GEIM800108 0.930 GEIM800111 0.929
+ PALJ810105 0.928 CHOP780216 0.921 QIAN880133 0.908
+ TANS770110 0.897 QIAN880132 0.892 CHOP780101 0.885
+ CHAM830101 0.881 CHOP780210 0.829 QIAN880134 0.828
+ PALJ810116 0.814 PALJ810114 0.809 PALJ810106 0.807
+ ROBB760112 0.807 AVBF000102 -0.821 SUEM840101 -0.850
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.78 1.06 1.56 1.50 0.60 0.78 0.97 1.73 0.83 0.40
+ 0.57 1.01 0.30 0.67 1.55 1.19 1.09 0.74 1.14 0.44
+//
+H ISOY800104
+D Normalized relative frequency of bend R (Isogai et al., 1980)
+R PMID:7378550
+A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A
+T Characterization of multiple bends in proteins
+J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set
+ of proteins
+C TANS770104 0.918 CHOP780213 0.916 QIAN880134 0.893
+ MUNV940104 0.866 FINA910102 0.844 MUNV940105 0.844
+ QIAN880135 0.837 ONEK900102 0.828 GEOR030109 0.812
+ ROBB760104 -0.817 ROBB760103 -0.830 PTIO830101 -0.832
+ BUNA790101 -0.842 QIAN880108 -0.847 BLAM930101 -0.860
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.09 0.97 1.14 0.77 0.50 0.83 0.92 1.25 0.67 0.66
+ 0.44 1.25 0.45 0.50 2.96 1.21 1.33 0.62 0.94 0.56
+//
+H ISOY800105
+D Normalized relative frequency of bend S (Isogai et al., 1980)
+R PMID:7378550
+A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A
+T Characterization of multiple bends in proteins
+J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set
+ of proteins
+C CHOP780214 0.923 TANS770105 0.836 ISOY800108 0.812
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.35 0.75 2.12 2.16 0.50 0.73 0.65 2.40 1.19 0.12
+ 0.58 0.83 0.22 0.89 0.43 1.24 0.85 0.62 1.44 0.43
+//
+H ISOY800106
+D Normalized relative frequency of helix end (Isogai et al., 1980)
+R PMID:7378550
+A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A
+T Characterization of multiple bends in proteins
+J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set
+ of proteins
+C MAXF760106 0.849
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.09 1.07 0.88 1.24 1.04 1.09 1.14 0.27 1.07 0.97
+ 1.30 1.20 0.55 0.80 1.78 1.20 0.99 1.03 0.69 0.77
+//
+H ISOY800107
+D Normalized relative frequency of double bend (Isogai et al., 1980)
+R PMID:7378550
+A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A
+T Characterization of multiple bends in proteins
+J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set
+ of proteins
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.34 2.78 0.92 1.77 1.44 0.79 2.54 0.95 0.00 0.52
+ 1.05 0.79 0.00 0.43 0.37 0.87 1.14 1.79 0.73 0.00
+//
+H ISOY800108
+D Normalized relative frequency of coil (Isogai et al., 1980)
+R PMID:7378550
+A Isogai, Y., Nemethy, G., Rackovsky, S., Leach, S.J. and Scheraga,H.A
+T Characterization of multiple bends in proteins
+J Biopolymers 19, 1183-1210 (1980) Recalculated by Kidera using a different set
+ of proteins
+C MAXF760104 0.945 RICJ880115 0.889 RACS820109 0.848
+ RACS820106 0.831 TANS770107 0.827 AURR980117 0.822
+ TANS770109 0.816 ISOY800105 0.812 MAXF760105 0.810
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.47 0.52 2.16 1.15 0.41 0.95 0.64 3.03 0.89 0.62
+ 0.53 0.98 0.68 0.61 0.63 1.03 0.39 0.63 0.83 0.76
+//
+H JANJ780101
+D Average accessible surface area (Janin et al., 1978)
+R PMID:731698
+A Janin, J., Wodak, S., Levitt, M. and Maigret, B.
+T Conformation of amino acid side-chains in proteins
+J J. Mol. Biol. 125, 357-386 (1978)
+C GUYH850104 0.989 JANJ780103 0.985 CHOC760102 0.973
+ OOBM770101 0.953 GUYH850105 0.923 PRAM900101 0.901
+ ENGD860101 0.901 ROSM880102 0.853 FAUJ880109 0.850
+ KIDA850101 0.843 MEIH800102 0.843 KUHL950101 0.839
+ PUNT030101 0.824 ROSM880101 0.822 GUYH850101 0.821
+ FASG890101 0.813 EISD860103 -0.808 BIOV880102 -0.809
+ MEIH800103 -0.811 JANJ790101 -0.824 RADA880104 -0.825
+ NADH010104 -0.832 ROSG850102 -0.836 RADA880101 -0.844
+ KYTJ820101 -0.852 CHOC760104 -0.854 WOLR790101 -0.856
+ OLSK800101 -0.858 JURD980101 -0.862 WOLR810101 -0.864
+ JACR890101 -0.865 NADH010103 -0.868 WARP780101 -0.869
+ DESM900102 -0.878 CHOC760103 -0.892 EISD840101 -0.907
+ RADA880107 -0.917 NADH010102 -0.924 JANJ780102 -0.949
+ JANJ790102 -0.989
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 27.8 94.7 60.1 60.6 15.5 68.7 68.2 24.5 50.7 22.8
+ 27.6 103.0 33.5 25.5 51.5 42.0 45.0 34.7 55.2 23.7
+//
+H JANJ780102
+D Percentage of buried residues (Janin et al., 1978)
+R PMID:731698
+A Janin, J., Wodak, S., Levitt, M. and Maigret, B.
+T Conformation of amino acid side-chains in proteins
+J J. Mol. Biol. 125, 357-386 (1978)
+C JANJ790102 0.966 CHOC760103 0.950 NADH010102 0.949
+ JANJ790101 0.941 DESM900102 0.935 JURD980101 0.928
+ NADH010103 0.923 KYTJ820101 0.922 ROSG850102 0.909
+ OLSK800101 0.905 CHOC760104 0.903 NADH010104 0.898
+ MEIH800103 0.897 NADH010101 0.892 CORJ870101 0.885
+ EISD860103 0.883 PONP800103 0.882 WARP780101 0.878
+ PONP800102 0.875 BIOV880101 0.875 EISD840101 0.874
+ RADA880108 0.869 PONP800108 0.863 BIOV880102 0.862
+ RADA880107 0.856 RADA880101 0.855 CASG920101 0.853
+ DESM900101 0.853 NISK800101 0.853 PONP800101 0.851
+ WOLR810101 0.851 MANP780101 0.842 WOLR790101 0.833
+ PONP930101 0.825 FAUJ830101 0.825 NADH010105 0.814
+ NISK860101 0.813 MIYS850101 0.806 BASU050103 0.803
+ CIDH920104 0.803 GRAR740102 -0.809 MIYS990104 -0.811
+ KRIW790102 -0.818 RACS770103 -0.828 KIDA850101 -0.828
+ PUNT030102 -0.830 MIYS990103 -0.834 ROSM880101 -0.835
+ KRIW790101 -0.837 MIYS990105 -0.846 PUNT030101 -0.848
+ ENGD860101 -0.860 PRAM900101 -0.860 RACS770102 -0.869
+ ROSM880102 -0.870 GUYH850101 -0.872 KUHL950101 -0.890
+ GUYH850105 -0.898 FASG890101 -0.903 MEIH800102 -0.907
+ CHOC760102 -0.935 JANJ780101 -0.949 JANJ780103 -0.957
+ OOBM770101 -0.968 GUYH850104 -0.968
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 51. 5. 22. 19. 74. 16. 16. 52. 34. 66.
+ 60. 3. 52. 58. 25. 35. 30. 49. 24. 64.
+//
+H JANJ780103
+D Percentage of exposed residues (Janin et al., 1978)
+R PMID:731698
+A Janin, J., Wodak, S., Levitt, M. and Maigret, B.
+T Conformation of amino acid side-chains in proteins
+J J. Mol. Biol. 125, 357-386 (1978)
+C JANJ780101 0.985 GUYH850104 0.983 OOBM770101 0.965
+ CHOC760102 0.959 GUYH850105 0.885 ENGD860101 0.884
+ PRAM900101 0.884 MEIH800102 0.873 KRIW790102 0.848
+ PUNT030101 0.848 RACS770103 0.847 KIDA850101 0.842
+ FASG890101 0.838 ROSM880102 0.838 GUYH850101 0.829
+ KUHL950101 0.826 RACS770102 0.823 MIYS990105 0.816
+ VINM940104 0.811 ROSM880101 0.810 KRIW790101 0.805
+ NADH010101 -0.804 RADA880108 -0.805 WOLR790101 -0.806
+ JACR890101 -0.809 PONP800103 -0.812 RADA880101 -0.817
+ EISD860103 -0.819 WOLR810101 -0.822 CASG920101 -0.825
+ CORJ870101 -0.826 BIOV880101 -0.829 JANJ790101 -0.832
+ DESM900101 -0.838 OLSK800101 -0.845 KYTJ820101 -0.845
+ CHOC760104 -0.851 JURD980101 -0.853 RADA880107 -0.856
+ BIOV880102 -0.860 NADH010104 -0.860 MEIH800103 -0.866
+ ROSG850102 -0.879 EISD840101 -0.881 CHOC760103 -0.888
+ WARP780101 -0.890 NADH010103 -0.892 DESM900102 -0.908
+ NADH010102 -0.938 JANJ780102 -0.957 JANJ790102 -0.980
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 15. 67. 49. 50. 5. 56. 55. 10. 34. 13.
+ 16. 85. 20. 10. 45. 32. 32. 17. 41. 14.
+//
+H JANJ790101
+D Ratio of buried and accessible molar fractions (Janin, 1979)
+R PMID:763335
+A Janin, J.
+T Surface and inside volumes in globular proteins
+J Nature 277, 491-492 (1979)
+C JANJ780102 0.941 PONP800102 0.897 CORJ870101 0.891
+ CHOC760103 0.887 CHOC760104 0.886 PONP800103 0.886
+ PONP800108 0.881 NADH010103 0.879 NISK800101 0.875
+ NADH010102 0.872 NADH010104 0.871 JURD980101 0.868
+ KYTJ820101 0.867 PONP800101 0.866 JANJ790102 0.860
+ ROSG850102 0.857 DESM900102 0.855 NADH010101 0.847
+ NADH010105 0.843 MANP780101 0.842 MEIH800103 0.838
+ EISD860103 0.829 OLSK800101 0.828 CASG920101 0.828
+ BIOV880101 0.827 RADA880108 0.824 PONP930101 0.816
+ CHOC760102 -0.809 KRIW790101 -0.810 KUHL950101 -0.811
+ KRIW710101 -0.815 MEIH800102 -0.821 JANJ780101 -0.824
+ JANJ780103 -0.832 GUYH850104 -0.862 OOBM770101 -0.871
+ FASG890101 -0.885
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.7 0.1 0.4 0.4 4.6 0.3 0.3 1.8 0.8 3.1
+ 2.4 0.05 1.9 2.2 0.6 0.8 0.7 1.6 0.5 2.9
+//
+H JANJ790102
+D Transfer free energy (Janin, 1979)
+R PMID:763335
+A Janin, J.
+T Surface and inside volumes in globular proteins
+J Nature 277, 491-492 (1979)
+C JANJ780102 0.966 NADH010102 0.945 RADA880107 0.906
+ CHOC760103 0.905 EISD840101 0.900 NADH010103 0.899
+ DESM900102 0.897 ROSG850102 0.892 JURD980101 0.879
+ WARP780101 0.877 OLSK800101 0.870 NADH010104 0.868
+ KYTJ820101 0.866 JANJ790101 0.860 BIOV880102 0.856
+ RADA880108 0.853 MEIH800103 0.853 BIOV880101 0.848
+ PONP800103 0.844 JACR890101 0.840 RADA880101 0.839
+ EISD860103 0.838 CHOC760104 0.835 WOLR810101 0.828
+ FAUJ830101 0.826 CORJ870101 0.825 CASG920101 0.822
+ PONP800102 0.822 DESM900101 0.818 WOLR790101 0.818
+ NADH010101 0.808 ROSM880105 0.805 PONP800108 0.802
+ MIYS990103 -0.804 MIYS990105 -0.820 FAUJ880109 -0.822
+ ROSM880101 -0.824 KRIW790101 -0.825 RACS770103 -0.834
+ KUHL950101 -0.844 PUNT030101 -0.846 KRIW790102 -0.847
+ RACS770102 -0.851 KIDA850101 -0.858 GUYH850101 -0.865
+ ROSM880102 -0.866 FASG890101 -0.875 ENGD860101 -0.890
+ PRAM900101 -0.890 MEIH800102 -0.894 GUYH850105 -0.913
+ OOBM770101 -0.963 CHOC760102 -0.969 JANJ780103 -0.980
+ JANJ780101 -0.989 GUYH850104 -0.999
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.3 -1.4 -0.5 -0.6 0.9 -0.7 -0.7 0.3 -0.1 0.7
+ 0.5 -1.8 0.4 0.5 -0.3 -0.1 -0.2 0.3 -0.4 0.6
+//
+H JOND750101
+D Hydrophobicity (Jones, 1975)
+R PMID:1127956
+A Jones, D.D.
+T Amino acid properties and side-chain orientation in proteins: A cross
+ correlation approach
+J J. Theor. Biol. 50, 167-183 (1975)
+C ARGP820101 1.000 SIMZ760101 0.966 GOLD730101 0.935
+ TAKK010101 0.906 MEEJ810101 0.891 ROSM880104 0.872
+ CIDH920105 0.866 LEVM760106 0.864 CIDH920102 0.861
+ MEEJ800102 0.855 MEEJ810102 0.852 ZHOH040101 0.841
+ CIDH920103 0.826 PLIV810101 0.819 CIDH920104 0.818
+ LEVM760107 0.806 GUYH850103 -0.807 PARJ860101 -0.834
+ WOLS870101 -0.837 BULH740101 -0.853
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.87 0.85 0.09 0.66 1.52 0.00 0.67 0.10 0.87 3.15
+ 2.17 1.64 1.67 2.87 2.77 0.07 0.07 3.77 2.67 1.87
+//
+H JOND750102
+D pK (-COOH) (Jones, 1975)
+R PMID:1127956
+A Jones, D.D.
+T Amino acid properties and side-chain orientation in proteins: A cross
+ correlation approach
+J J. Theor. Biol. 50, 167-183 (1975) Original reference of this data: McMeekin,
+ T.L., Groves, M.L. and Hipp, N.J. In "Amino Acids and Serum Proteins"
+ (Stekol, J.A., ed.), American Chemical Society, Washington, D.C., p. 54
+ (1964)
+C FASG760105 0.833
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.34 1.18 2.02 2.01 1.65 2.17 2.19 2.34 1.82 2.36
+ 2.36 2.18 2.28 1.83 1.99 2.21 2.10 2.38 2.20 2.32
+//
+H JOND920101
+D Relative frequency of occurrence (Jones et al., 1992)
+R PMID:1633570
+A Jones, D.T., Taylor, W.R. and Thornton, J.M.
+T The rapid generation of mutation data matrices from protein sequences
+J CABIOS 8, 275-282 (1992)
+C CEDJ970102 0.995 NAKH900101 0.993 CEDJ970104 0.983
+ CEDJ970101 0.968 DAYM780101 0.954 JUKT750101 0.953
+ FUKS010110 0.944 FUKS010112 0.943 JUNJ780101 0.932
+ CEDJ970103 0.911 KUMS000102 0.909 NAKH920101 0.900
+ NAKH920107 0.893 NAKH920106 0.889 NAKH920104 0.887
+ NAKH920103 0.881 NAKH900109 0.878 KUMS000101 0.863
+ FUKS010109 0.861 NAKH900102 0.846 CEDJ970105 0.834
+ FUKS010111 0.832
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.077 0.051 0.043 0.052 0.020 0.041 0.062 0.074 0.023 0.053
+ 0.091 0.059 0.024 0.040 0.051 0.069 0.059 0.014 0.032 0.066
+//
+H JOND920102
+D Relative mutability (Jones et al., 1992)
+R PMID:1633570
+A Jones, D.T., Taylor, W.R. and Thornton, J.M.
+T The rapid generation of mutation data matrices from protein sequences
+J CABIOS 8, 275-282 (1992)
+C DAYM780201 0.889
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 100. 83. 104. 86. 44. 84. 77. 50. 91. 103.
+ 54. 72. 93. 51. 58. 117. 107. 25. 50. 98.
+//
+H JUKT750101
+D Amino acid distribution (Jukes et al., 1975)
+R PMID:237322
+A Jukes, T.H., Holmquist, R. and Moise, H.
+T Amino acid composition of proteins: Selection against the genetic code
+J Science 189, 50-51 (1975)
+C JUNJ780101 0.980 DAYM780101 0.975 CEDJ970101 0.973
+ JOND920101 0.953 KUMS000102 0.948 CEDJ970104 0.942
+ CEDJ970102 0.942 NAKH900101 0.941 FUKS010111 0.927
+ FUKS010110 0.908 KUMS000101 0.879 FUKS010112 0.875
+ NAKH920107 0.862 NAKH920101 0.849 NAKH920103 0.837
+ CEDJ970103 0.835 NAKH920106 0.831 NAKH920104 0.827
+ NAKH900109 0.815
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 5.3 2.6 3.0 3.6 1.3 2.4 3.3 4.8 1.4 3.1
+ 4.7 4.1 1.1 2.3 2.5 4.5 3.7 0.8 2.3 4.2
+//
+H JUNJ780101
+D Sequence frequency (Jungck, 1978)
+R PMID:691072
+A Jungck, J.R.
+T The genetic code as a periodic table
+J J. Mol. Evol. 11, 211-224 (1978)
+C DAYM780101 0.986 JUKT750101 0.980 CEDJ970101 0.968
+ JOND920101 0.932 KUMS000102 0.927 CEDJ970104 0.921
+ CEDJ970102 0.920 NAKH900101 0.918 FUKS010111 0.906
+ FUKS010110 0.868 NAKH920107 0.856 KUMS000101 0.854
+ NAKH900102 0.853 FUKS010112 0.836 NAKH920106 0.829
+ NAKH920101 0.826 NAKH920103 0.820 NAKH920104 0.807
+ CEDJ970103 0.806 CEDJ970105 0.803
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 685. 382. 397. 400. 241. 313. 427. 707. 155. 394.
+ 581. 575. 132. 303. 366. 593. 490. 99. 292. 553.
+//
+H KANM800101
+D Average relative probability of helix (Kanehisa-Tsong, 1980)
+R PMID:7426680
+A Kanehisa, M.I. and Tsong, T.Y.
+T Local hydrophobicity stabilizes secondary structures in proteins
+J Biopolymers 19, 1617-1628 (1980)
+C ISOY800101 0.963 PALJ810102 0.962 LEVM780104 0.958
+ CHOP780201 0.956 MAXF760101 0.950 ROBB760101 0.945
+ GEIM800101 0.942 LEVM780101 0.942 PRAM900102 0.942
+ PALJ810101 0.928 TANS770101 0.927 GEIM800104 0.916
+ RACS820108 0.914 KANM800103 0.912 NAGK730101 0.883
+ AURR980115 0.858 BURA740101 0.855 QIAN880106 0.854
+ QIAN880107 0.854 AURR980109 0.852 AURR980114 0.852
+ PALJ810109 0.849 AURR980112 0.847 CRAJ730101 0.842
+ AURR980110 0.830 QIAN880105 0.827 MUNV940102 -0.843
+ MUNV940101 -0.846
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.36 1.00 0.89 1.04 0.82 1.14 1.48 0.63 1.11 1.08
+ 1.21 1.22 1.45 1.05 0.52 0.74 0.81 0.97 0.79 0.94
+//
+H KANM800102
+D Average relative probability of beta-sheet (Kanehisa-Tsong, 1980)
+R PMID:7426680
+A Kanehisa, M.I. and Tsong, T.Y.
+T Local hydrophobicity stabilizes secondary structures in proteins
+J Biopolymers 19, 1617-1628 (1980)
+C GEIM800107 0.955 PALJ810104 0.948 CHOP780202 0.945
+ LIFS790101 0.940 LEVM780105 0.938 ROBB760106 0.938
+ PALJ810103 0.932 KANM800104 0.928 PTIO830102 0.917
+ GEIM800105 0.916 QIAN880121 0.900 ROBB760105 0.898
+ QIAN880120 0.896 QIAN880119 0.888 NAGK730102 0.878
+ PALJ810112 0.869 BASU050103 0.869 PONP930101 0.866
+ LIFS790103 0.863 AVBF000101 0.859 BASU050101 0.856
+ LEVM780102 0.856 PRAM900103 0.856 PONP800108 0.849
+ CORJ870101 0.839 PALJ810110 0.836 MANP780101 0.833
+ PONP800101 0.829 GEIM800106 0.821 NISK860101 0.819
+ PONP800102 0.815 NISK800101 0.809 CHOP780208 0.804
+ PONP800103 0.803 LIFS790102 0.801 QIAN880118 0.801
+ PUNT030102 -0.803 MIYS990104 -0.808 OOBM770103 -0.812
+ GEIM800110 -0.814 MIYS990103 -0.823 MUNV940103 -0.916
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.81 0.85 0.62 0.71 1.17 0.98 0.53 0.88 0.92 1.48
+ 1.24 0.77 1.05 1.20 0.61 0.92 1.18 1.18 1.23 1.66
+//
+H KANM800103
+D Average relative probability of inner helix (Kanehisa-Tsong, 1980)
+R PMID:7426680
+A Kanehisa, M.I. and Tsong, T.Y.
+T Local hydrophobicity stabilizes secondary structures in proteins
+J Biopolymers 19, 1617-1628 (1980)
+C AURR980109 0.944 ISOY800101 0.931 PALJ810102 0.916
+ AURR980114 0.916 KANM800101 0.912 CHOP780201 0.912
+ QIAN880107 0.908 AURR980113 0.905 MAXF760101 0.901
+ BEGF750101 0.893 QIAN880106 0.889 ROBB760103 0.887
+ ROBB760101 0.886 GEIM800101 0.881 AURR980112 0.871
+ LEVM780104 0.859 RACS820108 0.858 AURR980108 0.857
+ PRAM900102 0.850 LEVM780101 0.850 TANS770101 0.843
+ PALJ810101 0.836 RICJ880109 0.829 QIAN880108 0.829
+ QIAN880109 0.824 FINA770101 0.823 QIAN880110 0.820
+ SUEM840101 0.820 QIAN880105 0.820 BURA740101 0.810
+ CHOP780216 -0.808 GEIM800111 -0.812 PRAM900104 -0.814
+ LEVM780103 -0.816 MUNV940102 -0.823 CHOP780101 -0.824
+ MUNV940101 -0.826 PALJ810106 -0.840 NAGK730103 -0.847
+ CHAM830101 -0.889
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.45 1.15 0.64 0.91 0.70 1.14 1.29 0.53 1.13 1.23
+ 1.56 1.27 1.83 1.20 0.21 0.48 0.77 1.17 0.74 1.10
+//
+H KANM800104
+D Average relative probability of inner beta-sheet (Kanehisa-Tsong, 1980)
+R PMID:7426680
+A Kanehisa, M.I. and Tsong, T.Y.
+T Local hydrophobicity stabilizes secondary structures in proteins
+J Biopolymers 19, 1617-1628 (1980)
+C KANM800102 0.928 ROBB760105 0.885 ROBB760106 0.877
+ GEIM800107 0.876 GEIM800105 0.861 PTIO830102 0.858
+ PALJ810104 0.851 BASU050101 0.850 PONP800108 0.849
+ BASU050103 0.848 LEVM780105 0.841 QIAN880119 0.841
+ CHOP780202 0.839 LIFS790101 0.834 PONP930101 0.833
+ CORJ870101 0.833 QIAN880121 0.829 MANP780101 0.827
+ JURD980101 0.826 KYTJ820101 0.824 PALJ810103 0.823
+ PONP800101 0.823 PALJ810112 0.813 PONP800102 0.813
+ LIFS790102 0.809 QIAN880120 0.803 MUNV940103 -0.857
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.75 0.79 0.33 0.31 1.46 0.75 0.46 0.83 0.83 1.87
+ 1.56 0.66 0.86 1.37 0.52 0.82 1.36 0.79 1.08 2.00
+//
+H KARP850101
+D Flexibility parameter for no rigid neighbors (Karplus-Schulz, 1985)
+R
+A Karplus, P.A. and Schulz, G.E.
+T Prediction of chain flexibility in proteins
+J Naturwiss. 72, 212-213 (1985)
+C VINM940102 0.874 VINM940103 0.837 RACS770101 0.837
+ FUKS010103 0.834 MEIH800101 0.832 MIYS990104 0.822
+ VINM940101 0.821 PARS000101 0.816 GUYH850102 0.811
+ CIDH920104 -0.801 BIOV880102 -0.804 RADA880108 -0.804
+ ROSG850101 -0.807 MIYS850101 -0.811 MEEJ810101 -0.818
+ BASU050102 -0.819 BIOV880101 -0.825 NISK860101 -0.828
+ ZHOH040101 -0.833 WERD780101 -0.842 ZHOH040103 -0.846
+ CIDH920101 -0.864 CIDH920105 -0.866 CIDH920102 -0.873
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.041 1.038 1.117 1.033 0.960 1.165 1.094 1.142 0.982 1.002
+ 0.967 1.093 0.947 0.930 1.055 1.169 1.073 0.925 0.961 0.982
+//
+H KARP850102
+D Flexibility parameter for one rigid neighbor (Karplus-Schulz, 1985)
+R
+A Karplus, P.A. and Schulz, G.E.
+T Prediction of chain flexibility in proteins
+J Naturwiss. 72, 212-213 (1985)
+C KRIW790101 0.917 MIYS990104 0.909 MIYS990103 0.901
+ MIYS990105 0.888 VINM940101 0.885 MEIH800101 0.884
+ GUYH850102 0.882 FASG890101 0.871 RACS770101 0.869
+ CORJ870108 0.868 VINM940103 0.863 KRIW710101 0.855
+ PARS000101 0.852 RACS770102 0.852 KRIW790102 0.843
+ GUYH850101 0.840 MEIH800102 0.837 FUKS010103 0.835
+ VINM940102 0.834 MIYS990102 0.828 MIYS990101 0.825
+ FUKS010104 0.822 OOBM770103 0.820 BHAR880101 0.806
+ PUNT030101 0.805 BASU050103 -0.806 NADH010102 -0.807
+ DESM900102 -0.815 PONP800106 -0.820 BASU050102 -0.825
+ CIDH920101 -0.828 DESM900101 -0.829 CORJ870104 -0.830
+ CIDH920104 -0.833 NADH010103 -0.834 CORJ870105 -0.834
+ NADH010104 -0.835 ZHOH040103 -0.836 CIDH920105 -0.839
+ BAEK050101 -0.839 CORJ870103 -0.850 CIDH920103 -0.852
+ BIOV880102 -0.859 MANP780101 -0.863 CORJ870101 -0.865
+ CORJ870107 -0.866 PONP800103 -0.870 CORJ870106 -0.870
+ MIYS850101 -0.878 RADA880108 -0.879 BIOV880101 -0.880
+ NISK800101 -0.885 PONP800102 -0.887 PONP800101 -0.889
+ PONP930101 -0.893 ROSG850102 -0.897 CASG920101 -0.901
+ NISK860101 -0.901 WERD780101 -0.909
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.946 1.028 1.006 1.089 0.878 1.025 1.036 1.042 0.952 0.892
+ 0.961 1.082 0.862 0.912 1.085 1.048 1.051 0.917 0.930 0.927
+//
+H KARP850103
+D Flexibility parameter for two rigid neighbors (Karplus-Schulz, 1985)
+R
+A Karplus, P.A. and Schulz, G.E.
+T Prediction of chain flexibility in proteins
+J Naturwiss. 72, 212-213 (1985)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.892 0.901 0.930 0.932 0.925 0.885 0.933 0.923 0.894 0.872
+ 0.921 1.057 0.804 0.914 0.932 0.923 0.934 0.803 0.837 0.913
+//
+H KHAG800101
+D The Kerr-constant increments (Khanarian-Moore, 1980)
+R
+A Khanarian, G. and Moore, W.J.
+T The Kerr effect of amino acids in water
+J Aust. J. Chem. 33, 1727-1741 (1980) (Cys Lys Tyr !)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 49.1 133. -3.6 0. 0. 20. 0. 64.6 75.7 18.9
+ 15.6 0. 6.8 54.7 43.8 44.4 31.0 70.5 0. 29.5
+//
+H KLEP840101
+D Net charge (Klein et al., 1984)
+R PMID:6547351
+A Klein, P., Kanehisa, M. and DeLisi, C.
+T Prediction of protein function from sequence properties: Discriminant
+ analysis of a data base
+J Biochim. Biophys. Acta 787, 221-226 (1984)
+C ZIMJ680104 0.941
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 1. 0. -1. 0. 0. -1. 0. 0. 0.
+ 0. 1. 0. 0. 0. 0. 0. 0. 0. 0.
+//
+H KRIW710101
+D Side chain interaction parameter (Krigbaum-Rubin, 1971)
+R PMID:5553983
+A Krigbaum, W.R. and Rubin, B.H.
+T Local interactions as structure determinant for globular proteins
+J Biochim. Biophys. Acta 229, 368-383 (1971)
+C KRIW790101 0.908 FASG890101 0.865 MIYS990103 0.856
+ KARP850102 0.855 KRIW790102 0.839 MIYS990104 0.837
+ GUYH850101 0.831 GUYH850102 0.811 MIYS990105 0.801
+ DESM900101 -0.807 CASG920101 -0.808 CORJ870101 -0.812
+ BIOV880101 -0.813 JANJ790101 -0.815 WERD780101 -0.819
+ NADH010102 -0.825 NISK800101 -0.831 PONP800106 -0.841
+ NADH010105 -0.842 NADH010106 -0.846 RADA880108 -0.847
+ PONP800101 -0.850 ROSG850102 -0.852 NADH010103 -0.860
+ NADH010104 -0.874 PONP800102 -0.887 PONP800103 -0.890
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 4.60 6.50 5.90 5.70 -1.00 6.10 5.60 7.60 4.50 2.60
+ 3.25 7.90 1.40 3.20 7.00 5.25 4.80 4.00 4.35 3.40
+//
+H KRIW790101
+D Side chain interaction parameter (Krigbaum-Komoriya, 1979)
+R PMID:760806
+A Krigbaum, W.R. and Komoriya, A.
+T Local interactions as a structure determinant for protein molecules: II
+J Biochim. Biophys. Acta 576, 204-228 (1979)
+C MIYS990104 0.945 MIYS990103 0.944 MIYS990105 0.925
+ KARP850102 0.917 FASG890101 0.914 KRIW790102 0.914
+ KRIW710101 0.908 VINM940101 0.890 GUYH850101 0.885
+ GUYH850102 0.878 MEIH800102 0.876 VINM940103 0.875
+ MIYS990102 0.873 RACS770102 0.871 MIYS990101 0.870
+ MEIH800101 0.869 OOBM770103 0.865 GRAR740102 0.847
+ VINM940102 0.834 PUNT030101 0.833 CORJ870108 0.833
+ MONM990101 0.830 RACS770101 0.828 FUKS010104 0.828
+ PUNT030102 0.826 GUYH850104 0.822 OOBM770101 0.816
+ JANJ780103 0.805 PARS000101 0.804 CORJ870104 -0.801
+ PTIO830102 -0.801 QIAN880121 -0.803 KYTJ820101 -0.805
+ JANJ790101 -0.810 CIDH920105 -0.816 CIDH920103 -0.819
+ BASU050101 -0.821 JURD980101 -0.824 JANJ790102 -0.825
+ CORJ870106 -0.825 NADH010101 -0.827 CORJ870103 -0.830
+ CORJ870107 -0.832 JANJ780102 -0.837 DESM900101 -0.847
+ MEIH800103 -0.850 DESM900102 -0.859 PONP800108 -0.860
+ BAEK050101 -0.860 BASU050103 -0.860 NADH010106 -0.861
+ FAUJ830101 -0.865 BASU050102 -0.867 CIDH920104 -0.867
+ MANP780101 -0.870 BIOV880102 -0.876 PONP800101 -0.888
+ NISK800101 -0.896 RADA880108 -0.897 NADH010105 -0.898
+ WERD780101 -0.899 CORJ870101 -0.902 ZHOH040103 -0.905
+ NISK860101 -0.907 PONP930101 -0.909 MIYS850101 -0.910
+ BIOV880101 -0.910 CASG920101 -0.911 PONP800102 -0.915
+ NADH010102 -0.929 PONP800103 -0.930 ROSG850102 -0.935
+ NADH010103 -0.954 NADH010104 -0.958
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 4.32 6.55 6.24 6.04 1.73 6.13 6.17 6.09 5.66 2.31
+ 3.93 7.92 2.44 2.59 7.19 5.37 5.16 2.78 3.58 3.31
+//
+H KRIW790102
+D Fraction of site occupied by water (Krigbaum-Komoriya, 1979)
+R PMID:760806
+A Krigbaum, W.R. and Komoriya, A.
+T Local interactions as a structure determinant for protein molecules: II
+J Biochim. Biophys. Acta 576, 204-228 (1979)
+C KRIW790101 0.914 MIYS990103 0.899 MEIH800102 0.898
+ RACS770102 0.895 RACS770103 0.889 MIYS990104 0.889
+ MIYS990105 0.887 FASG890101 0.882 GUYH850101 0.864
+ FUKS010104 0.853 VINM940101 0.853 GUYH850104 0.849
+ JANJ780103 0.848 KARP850102 0.843 GUYH850102 0.841
+ KRIW710101 0.839 VINM940103 0.836 MEIH800101 0.835
+ MIYS990102 0.826 OOBM770103 0.824 OOBM770101 0.822
+ MIYS990101 0.821 RACS770101 0.814 PUNT030101 0.811
+ PONP800101 -0.804 CORJ870103 -0.812 CORJ870107 -0.816
+ JANJ780102 -0.818 PONP930101 -0.821 PONP800102 -0.830
+ DESM900101 -0.835 CORJ870101 -0.838 JANJ790102 -0.847
+ DESM900102 -0.852 PONP800103 -0.853 NISK860101 -0.855
+ RADA880108 -0.856 CASG920101 -0.865 BIOV880101 -0.869
+ MIYS850101 -0.869 WERD780101 -0.875 BIOV880102 -0.878
+ NADH010104 -0.882 MEIH800103 -0.885 NADH010103 -0.887
+ NADH010102 -0.890 ROSG850102 -0.922
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.28 0.34 0.31 0.33 0.11 0.39 0.37 0.28 0.23 0.12
+ 0.16 0.59 0.08 0.10 0.46 0.27 0.26 0.15 0.25 0.22
+//
+H KRIW790103
+D Side chain volume (Krigbaum-Komoriya, 1979)
+R PMID:760806
+A Krigbaum, W.R. and Komoriya, A.
+T Local interactions as a structure determinant for protein molecules: II
+J Biochim. Biophys. Acta 576, 204-228 (1979) (Gly Pro 7.8)
+C GOLD730102 0.994 BIGC670101 0.993 GRAR740103 0.989
+ TSAJ990101 0.988 TSAJ990102 0.987 CHOC750101 0.982
+ FAUJ880103 0.965 CHAM820101 0.963 HARY940101 0.956
+ CHOC760101 0.948 PONJ960101 0.943 ROSG850101 0.920
+ FASG760101 0.910 LEVM760105 0.900 DAWD720101 0.893
+ ZHOH040102 0.884 LEVM760102 0.884 RADA880106 0.883
+ CHAM830106 0.876 LEVM760106 0.862 LEVM760107 0.860
+ FAUJ880106 0.845 MCMT640101 0.810 RADA880103 -0.871
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 27.5 105.0 58.7 40.0 44.6 80.7 62.0 0.0 79.0 93.5
+ 93.5 100.0 94.1 115.5 41.9 29.3 51.3 145.5 117.3 71.5
+//
+H KYTJ820101
+D Hydropathy index (Kyte-Doolittle, 1982)
+R PMID:7108955
+A Kyte, J. and Doolittle, R.F.
+T A simple method for displaying the hydropathic character of a protein
+J J. Mol. Biol. 157, 105-132 (1982)
+C JURD980101 0.996 CHOC760103 0.964 OLSK800101 0.942
+ JANJ780102 0.922 NADH010102 0.920 NADH010101 0.918
+ DESM900102 0.898 EISD860103 0.897 CHOC760104 0.889
+ NADH010103 0.885 WOLR810101 0.885 RADA880101 0.884
+ MANP780101 0.881 EISD840101 0.878 PONP800103 0.870
+ WOLR790101 0.869 NAKH920108 0.868 JANJ790101 0.867
+ JANJ790102 0.866 BASU050103 0.863 PONP800102 0.861
+ MEIH800103 0.856 NADH010104 0.856 PONP800101 0.851
+ PONP800108 0.850 CORJ870101 0.848 WARP780101 0.845
+ COWR900101 0.845 PONP930101 0.844 RADA880108 0.842
+ ROSG850102 0.841 DESM900101 0.837 BLAS910101 0.836
+ BIOV880101 0.829 RADA880107 0.828 BASU050101 0.826
+ KANM800104 0.824 LIFS790102 0.824 CIDH920104 0.824
+ MIYS850101 0.821 RADA880104 0.819 NAKH900111 0.817
+ CORJ870104 0.812 NISK800101 0.812 FAUJ830101 0.811
+ ROSM880105 0.806 ARGP820103 0.806 CORJ870103 0.806
+ NADH010105 0.804 NAKH920105 0.803 ARGP820102 0.803
+ CORJ870107 0.801 MIYS990104 -0.800 CORJ870108 -0.802
+ KRIW790101 -0.805 MIYS990105 -0.818 MIYS990103 -0.833
+ CHOC760102 -0.838 MIYS990101 -0.840 MIYS990102 -0.840
+ MONM990101 -0.842 GUYH850101 -0.843 FASG890101 -0.844
+ RACS770102 -0.844 ROSM880101 -0.845 JANJ780103 -0.845
+ ENGD860101 -0.850 PRAM900101 -0.850 JANJ780101 -0.852
+ GRAR740102 -0.859 PUNT030102 -0.862 GUYH850104 -0.869
+ MEIH800102 -0.871 PUNT030101 -0.872 ROSM880102 -0.878
+ KUHL950101 -0.883 GUYH850105 -0.883 OOBM770101 -0.899
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.8 -4.5 -3.5 -3.5 2.5 -3.5 -3.5 -0.4 -3.2 4.5
+ 3.8 -3.9 1.9 2.8 -1.6 -0.8 -0.7 -0.9 -1.3 4.2
+//
+H LAWE840101
+D Transfer free energy, CHP/water (Lawson et al., 1984)
+R PMID:6699000
+A Lawson, E.Q., Sadler, A.J., Harmatz, D., Brandau, D.T., Micanovic, R.
+ MacElroy, R.D. and Middaught, C.R.
+T A simple experimental model for hydrophobic interactions in proteins
+J J. Biol. Chem. 259, 2910-2912 (1984)
+C GOLD730101 0.829 SIMZ760101 0.815 ZIMJ680105 0.809
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.48 -0.06 -0.87 -0.75 -0.32 -0.32 -0.71 0.00 -0.51 0.81
+ 1.02 -0.09 0.81 1.03 2.03 0.05 -0.35 0.66 1.24 0.56
+//
+H LEVM760101
+D Hydrophobic parameter (Levitt, 1976)
+R PMID:957439
+A Levitt, M.
+T A simplified representation of protein conformations for rapid simulation of
+ protein folfing
+J J. Mol. Biol. 104, 59-107 (1976)
+C HOPT810101 0.985 KIDA850101 0.915 ENGD860101 0.881
+ PRAM900101 0.881 ROSM880101 0.876 WOEC730101 0.872
+ FUKS010104 0.869 GRAR740102 0.865 PUNT030102 0.848
+ WOLS870101 0.845 FUKS010102 0.837 PUNT030101 0.835
+ MIYS990105 0.828 VHEG790101 0.825 ROSM880102 0.823
+ VINM940101 0.815 KUHL950101 0.807 PARJ860101 0.806
+ OOBM770103 0.805 MIYS990104 0.801 PLIV810101 -0.801
+ BASU050103 -0.808 ZHOH040103 -0.811 WIMW960101 -0.812
+ RADA880108 -0.824 BIOV880101 -0.831 JACR890101 -0.832
+ RADA880101 -0.838 RADA880102 -0.838 ZIMJ680105 -0.844
+ BIOV880102 -0.847 MEEJ800102 -0.855 EISD840101 -0.859
+ BLAS910101 -0.889 FAUJ830101 -0.919 EISD860101 -0.921
+ ROSM880105 -0.954
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.5 3.0 0.2 2.5 -1.0 0.2 2.5 0.0 -0.5 -1.8
+ -1.8 3.0 -1.3 -2.5 -1.4 0.3 -0.4 -3.4 -2.3 -1.5
+//
+H LEVM760102
+D Distance between C-alpha and centroid of side chain (Levitt, 1976)
+R PMID:957439
+A Levitt, M.
+T A simplified representation of protein conformations for rapid simulation of
+ protein folfing
+J J. Mol. Biol. 104, 59-107 (1976)
+C LEVM760105 0.987 CHOC760101 0.972 FASG760101 0.966
+ CHAM830106 0.962 FAUJ880103 0.947 CHOC750101 0.933
+ PONJ960101 0.930 TSAJ990102 0.918 CHAM820101 0.915
+ TSAJ990101 0.910 HARY940101 0.905 FAUJ880106 0.900
+ BIGC670101 0.896 GOLD730102 0.893 GRAR740103 0.885
+ KRIW790103 0.884 WOLS870102 0.881 DAWD720101 0.873
+ RADA880106 0.871 OOBM770102 0.869 FAUJ880104 0.867
+ CHAM830105 0.843 HUTJ700102 0.835 RADA880103 -0.913
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.77 3.72 1.98 1.99 1.38 2.58 2.63 0.00 2.76 1.83
+ 2.08 2.94 2.34 2.97 1.42 1.28 1.43 3.58 3.36 1.49
+//
+H LEVM760103
+D Side chain angle theta(AAR) (Levitt, 1976)
+R PMID:957439
+A Levitt, M.
+T A simplified representation of protein conformations for rapid simulation of
+ protein folfing
+J J. Mol. Biol. 104, 59-107 (1976) (Gly missing)
+C AVBF000102 0.816 RICJ880115 -0.829 LEVM760104 -0.840
+ KIMC930101 -0.861
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 121.9 121.4 117.5 121.2 113.7 118.0 118.2 0. 118.2 118.9
+ 118.1 122.0 113.1 118.2 81.9 117.9 117.1 118.4 110.0 121.7
+//
+H LEVM760104
+D Side chain torsion angle phi(AAAR) (Levitt, 1976)
+R PMID:957439
+A Levitt, M.
+T A simplified representation of protein conformations for rapid simulation of
+ protein folfing
+J J. Mol. Biol. 104, 59-107 (1976)
+C KIMC930101 0.842 PRAM820102 0.812 CHAM810101 -0.818
+ LEVM760103 -0.840
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 243.2 206.6 207.1 215.0 209.4 205.4 213.6 300.0 219.9 217.9
+ 205.6 210.9 204.0 203.7 237.4 232.0 226.7 203.7 195.6 220.3
+//
+H LEVM760105
+D Radius of gyration of side chain (Levitt, 1976)
+R PMID:957439
+A Levitt, M.
+T A simplified representation of protein conformations for rapid simulation of
+ protein folfing
+J J. Mol. Biol. 104, 59-107 (1976) (Gly 0.089)
+C LEVM760102 0.987 CHOC760101 0.968 CHAM830106 0.958
+ FASG760101 0.951 FAUJ880103 0.945 CHOC750101 0.939
+ PONJ960101 0.928 TSAJ990102 0.928 TSAJ990101 0.922
+ HARY940101 0.919 CHAM820101 0.915 BIGC670101 0.913
+ GOLD730102 0.911 GRAR740103 0.900 KRIW790103 0.900
+ DAWD720101 0.898 FAUJ880104 0.896 FAUJ880106 0.889
+ RADA880106 0.871 OOBM770102 0.868 HUTJ700102 0.864
+ WOLS870102 0.836 HUTJ700103 0.834 CHAM830105 0.829
+ RADA880103 -0.893
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.77 2.38 1.45 1.43 1.22 1.75 1.77 0.58 1.78 1.56
+ 1.54 2.08 1.80 1.90 1.25 1.08 1.24 2.21 2.13 1.29
+//
+H LEVM760106
+D van der Waals parameter R0 (Levitt, 1976)
+R PMID:957439
+A Levitt, M.
+T A simplified representation of protein conformations for rapid simulation of
+ protein folfing
+J J. Mol. Biol. 104, 59-107 (1976)
+C ZHOH040102 0.905 ROSG850101 0.896 ZHOH040101 0.883
+ BIGC670101 0.876 GOLD730102 0.875 ZIMJ680102 0.873
+ CIDH920102 0.873 ARGP820101 0.865 JOND750101 0.864
+ KRIW790103 0.862 TSAJ990101 0.849 SIMZ760101 0.848
+ GRAR740103 0.846 CHOC750101 0.841 TSAJ990102 0.841
+ TAKK010101 0.841 PLIV810101 0.830 HARY940101 0.829
+ CIDH920105 0.828 GOLD730101 0.827 MEEJ810101 0.827
+ CIDH920101 0.826 CHAM820101 0.818 BASU050102 0.805
+ ROBB790101 0.804 LEVM760107 0.804 BULH740101 -0.818
+ GUYH850103 -0.822 FUKS010103 -0.829 PARJ860101 -0.832
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 5.2 6.0 5.0 5.0 6.1 6.0 6.0 4.2 6.0 7.0
+ 7.0 6.0 6.8 7.1 6.2 4.9 5.0 7.6 7.1 6.4
+//
+H LEVM760107
+D van der Waals parameter epsilon (Levitt, 1976)
+R PMID:957439
+A Levitt, M.
+T A simplified representation of protein conformations for rapid simulation of
+ protein folfing
+J J. Mol. Biol. 104, 59-107 (1976)
+C CHAM820101 0.891 FAUJ880103 0.875 TSAJ990101 0.866
+ GOLD730102 0.865 BIGC670101 0.863 TSAJ990102 0.861
+ GARJ730101 0.860 KRIW790103 0.860 CHOC750101 0.858
+ ZHOH040101 0.855 ROSG850101 0.852 NOZY710101 0.845
+ ZHOH040102 0.843 GRAR740103 0.841 PONJ960101 0.827
+ TAKK010101 0.819 SNEP660103 0.818 HARY940101 0.815
+ FASG760101 0.815 CHOC760101 0.807 JOND750101 0.806
+ ARGP820101 0.806 LEVM760106 0.804 WEBA780101 -0.923
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.025 0.20 0.10 0.10 0.10 0.10 0.10 0.025 0.10 0.19
+ 0.19 0.20 0.19 0.39 0.17 0.025 0.10 0.56 0.39 0.15
+//
+H LEVM780101
+D Normalized frequency of alpha-helix, with weights (Levitt, 1978)
+R PMID:708713
+A Levitt, M.
+T Conformational preferences of amino acids in globular proteins
+J Biochemistry 17, 4277-4285 (1978)
+C PRAM900102 1.000 LEVM780104 0.964 PALJ810101 0.943
+ KANM800101 0.942 ISOY800101 0.929 MAXF760101 0.924
+ ROBB760101 0.916 GEIM800101 0.912 GEIM800104 0.907
+ RACS820108 0.904 PALJ810102 0.902 PALJ810109 0.898
+ NAGK730101 0.894 CRAJ730101 0.887 CHOP780201 0.873
+ TANS770101 0.854 KANM800103 0.850 QIAN880107 0.829
+ QIAN880106 0.827 BURA740101 0.805 NAGK730103 -0.809
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.29 0.96 0.90 1.04 1.11 1.27 1.44 0.56 1.22 0.97
+ 1.30 1.23 1.47 1.07 0.52 0.82 0.82 0.99 0.72 0.91
+//
+H LEVM780102
+D Normalized frequency of beta-sheet, with weights (Levitt, 1978)
+R PMID:708713
+A Levitt, M.
+T Conformational preferences of amino acids in globular proteins
+J Biochemistry 17, 4277-4285 (1978)
+C PRAM900103 1.000 PALJ810112 0.913 LEVM780105 0.899
+ PALJ810104 0.868 PTIO830102 0.865 LIFS790101 0.864
+ QIAN880120 0.858 KANM800102 0.856 PALJ810103 0.846
+ GEIM800107 0.842 BEGF750102 0.834 QIAN880119 0.834
+ CHOP780202 0.833 AVBF000101 0.815 QIAN880121 0.805
+ MUNV940103 -0.848
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.90 0.99 0.76 0.72 0.74 0.80 0.75 0.92 1.08 1.45
+ 1.02 0.77 0.97 1.32 0.64 0.95 1.21 1.14 1.25 1.49
+//
+H LEVM780103
+D Normalized frequency of reverse turn, with weights (Levitt, 1978)
+R PMID:708713
+A Levitt, M.
+T Conformational preferences of amino acids in globular proteins
+J Biochemistry 17, 4277-4285 (1978)
+C PRAM900104 1.000 LEVM780106 0.984 GEIM800111 0.952
+ CHOP780216 0.952 QIAN880133 0.948 QIAN880134 0.935
+ ISOY800103 0.932 QIAN880132 0.931 GEIM800108 0.931
+ CHOP780203 0.927 CHAM830101 0.909 PALJ810105 0.909
+ QIAN880135 0.906 CHOP780101 0.893 TANS770110 0.875
+ CHOP780210 0.852 PALJ810106 0.848 RACS770101 0.808
+ AURR980109 -0.814 KANM800103 -0.816 QIAN880108 -0.820
+ QIAN880107 -0.834 AVBF000102 -0.834 ROBB760103 -0.843
+ FAUJ880102 -0.846 QIAN880109 -0.848 PTIO830101 -0.860
+ SUEM840101 -0.864
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.77 0.88 1.28 1.41 0.81 0.98 0.99 1.64 0.68 0.51
+ 0.58 0.96 0.41 0.59 1.91 1.32 1.04 0.76 1.05 0.47
+//
+H LEVM780104
+D Normalized frequency of alpha-helix, unweighted (Levitt, 1978)
+R PMID:708713
+A Levitt, M.
+T Conformational preferences of amino acids in globular proteins
+J Biochemistry 17, 4277-4285 (1978)
+C PALJ810101 0.988 PRAM900102 0.964 LEVM780101 0.964
+ KANM800101 0.958 GEIM800101 0.950 NAGK730101 0.918
+ ROBB760101 0.911 TANS770101 0.908 PALJ810102 0.906
+ MAXF760101 0.904 ISOY800101 0.904 RACS820108 0.889
+ CHOP780201 0.886 GEIM800104 0.872 CRAJ730101 0.869
+ KANM800103 0.859 BURA740101 0.833 QIAN880107 0.822
+ PALJ810109 0.819 AURR980115 0.818 QIAN880106 0.804
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.32 0.98 0.95 1.03 0.92 1.10 1.44 0.61 1.31 0.93
+ 1.31 1.25 1.39 1.02 0.58 0.76 0.79 0.97 0.73 0.93
+//
+H LEVM780105
+D Normalized frequency of beta-sheet, unweighted (Levitt, 1978)
+R PMID:708713
+A Levitt, M.
+T Conformational preferences of amino acids in globular proteins
+J Biochemistry 17, 4277-4285 (1978)
+C PALJ810103 0.980 KANM800102 0.938 CHOP780202 0.930
+ LIFS790101 0.928 GEIM800105 0.926 PALJ810104 0.921
+ QIAN880120 0.913 QIAN880119 0.903 PRAM900103 0.899
+ LEVM780102 0.899 LIFS790103 0.897 PTIO830102 0.894
+ GEIM800107 0.884 QIAN880121 0.876 PALJ810112 0.870
+ ROBB760106 0.869 ROBB760105 0.842 KANM800104 0.841
+ AVBF000101 0.824 QIAN880118 0.819 MUNV940103 -0.891
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.86 0.97 0.73 0.69 1.04 1.00 0.66 0.89 0.85 1.47
+ 1.04 0.77 0.93 1.21 0.68 1.02 1.27 1.26 1.31 1.43
+//
+H LEVM780106
+D Normalized frequency of reverse turn, unweighted (Levitt, 1978)
+R PMID:708713
+A Levitt, M.
+T Conformational preferences of amino acids in globular proteins
+J Biochemistry 17, 4277-4285 (1978)
+C LEVM780103 0.984 PRAM900104 0.983 QIAN880133 0.971
+ CHOP780216 0.953 GEIM800111 0.951 QIAN880132 0.943
+ ISOY800103 0.941 CHOP780203 0.935 QIAN880134 0.932
+ GEIM800108 0.932 QIAN880135 0.902 PALJ810105 0.902
+ CHAM830101 0.900 TANS770110 0.892 CHOP780101 0.890
+ PALJ810106 0.850 MUNV940103 0.815 CHOP780210 0.812
+ GEIM800110 0.809 AVBF000101 -0.805 LIFS790101 -0.806
+ QIAN880119 -0.810 QIAN880107 -0.813 QIAN880109 -0.815
+ QIAN880120 -0.831 PTIO830101 -0.854 AVBF000102 -0.860
+ FAUJ880102 -0.865 SUEM840101 -0.878
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.79 0.90 1.25 1.47 0.79 0.92 1.02 1.67 0.81 0.50
+ 0.57 0.99 0.51 0.77 1.78 1.30 0.97 0.79 0.93 0.46
+//
+H LEWP710101
+D Frequency of occurrence in beta-bends (Lewis et al., 1971)
+R PMID:5289387
+A Lewis, P. N., Momany, F.A. and Scheraga, H.A.
+T Folding of polypeptide chains in proteins: A proposed mechanism for folding
+J Proc. Natl. Acad. Sci. USA 68, 2293-2297 (1971)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.22 0.28 0.42 0.73 0.20 0.26 0.08 0.58 0.14 0.22
+ 0.19 0.27 0.38 0.08 0.46 0.55 0.49 0.43 0.46 0.08
+//
+H LIFS790101
+D Conformational preference for all beta-strands (Lifson-Sander, 1979)
+R PMID:503185
+A Lifson, S. and Sander, C.
+T Antiparallel and parallel beta-strands differ in amino acid residue
+ preference
+J Nature 282, 109-111 (1979)
+C QIAN880120 0.969 CHOP780202 0.947 LIFS790103 0.944
+ PTIO830102 0.941 KANM800102 0.940 QIAN880121 0.930
+ PALJ810104 0.929 QIAN880119 0.929 LEVM780105 0.928
+ PALJ810103 0.912 PONP930101 0.908 ROBB760106 0.906
+ GEIM800107 0.888 BASU050101 0.886 ROBB760105 0.867
+ BASU050103 0.865 PRAM900103 0.864 LEVM780102 0.864
+ BASU050102 0.861 MANP780101 0.859 NISK860101 0.859
+ AVBF000101 0.857 GEIM800105 0.855 PALJ810112 0.845
+ CORJ870106 0.836 KANM800104 0.834 CIDH920104 0.832
+ CORJ870105 0.830 CIDH920105 0.828 PONP800108 0.828
+ NISK800101 0.827 CORJ870101 0.826 PONP800101 0.823
+ CHOP780208 0.820 CORJ870107 0.820 PALJ810110 0.817
+ SWER830101 0.815 CIDH920103 0.815 CORJ870102 0.815
+ ZHOH040103 0.815 VENT840101 0.814 CIDH920102 0.808
+ BEGF750102 0.807 LIFS790102 0.803 PONP800107 0.801
+ GEIM800111 -0.801 QIAN880134 -0.804 LEVM780106 -0.806
+ QIAN880132 -0.806 MEIH800101 -0.809 PUNT030102 -0.809
+ MIYS990101 -0.811 CORJ870108 -0.811 MIYS990102 -0.813
+ VINM940101 -0.834 MIYS990103 -0.838 VINM940102 -0.843
+ MIYS990104 -0.843 PARS000101 -0.844 QIAN880133 -0.848
+ OOBM770103 -0.855 GEIM800110 -0.862 MUNV940103 -0.941
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.92 0.93 0.60 0.48 1.16 0.95 0.61 0.61 0.93 1.81
+ 1.30 0.70 1.19 1.25 0.40 0.82 1.12 1.54 1.53 1.81
+//
+H LIFS790102
+D Conformational preference for parallel beta-strands (Lifson-Sander, 1979)
+R PMID:503185
+A Lifson, S. and Sander, C.
+T Antiparallel and parallel beta-strands differ in amino acid residue
+ preference
+J Nature 282, 109-111 (1979)
+C PTIO830102 0.874 MANP780101 0.870 PONP800107 0.849
+ PONP930101 0.833 JURD980101 0.824 KYTJ820101 0.824
+ OLSK800101 0.818 CHOC760103 0.810 KANM800104 0.809
+ PONP800101 0.804 LIFS790101 0.803 KANM800102 0.801
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.00 0.68 0.54 0.50 0.91 0.28 0.59 0.79 0.38 2.60
+ 1.42 0.59 1.49 1.30 0.35 0.70 0.59 0.89 1.08 2.63
+//
+H LIFS790103
+D Conformational preference for antiparallel beta-strands (Lifson-Sander, 1979)
+R PMID:503185
+A Lifson, S. and Sander, C.
+T Antiparallel and parallel beta-strands differ in amino acid residue
+ preference
+J Nature 282, 109-111 (1979)
+C LIFS790101 0.944 QIAN880120 0.939 CHOP780202 0.908
+ LEVM780105 0.897 QIAN880121 0.882 PALJ810103 0.877
+ QIAN880119 0.877 KANM800102 0.863 PALJ810104 0.860
+ GEIM800105 0.832 ROBB760106 0.827 BASU050102 0.826
+ GEIM800107 0.823 PTIO830102 0.822 GEIM800106 0.814
+ AVBF000101 0.814 ZHOH040101 0.801 OOBM770103 -0.807
+ VINM940101 -0.829 PARS000101 -0.861 VINM940102 -0.862
+ GEIM800110 -0.889 MUNV940103 -0.902
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.90 1.02 0.62 0.47 1.24 1.18 0.62 0.56 1.12 1.54
+ 1.26 0.74 1.09 1.23 0.42 0.87 1.30 1.75 1.68 1.53
+//
+H MANP780101
+D Average surrounding hydrophobicity (Manavalan-Ponnuswamy, 1978)
+R PMID:703834
+A Manavalan, P. and Ponnuswamy, P.K.
+T Hydrophobic character of amino acid residues in globular proteins
+J Nature 275, 673-674 (1978)
+C PONP930101 0.967 PONP800101 0.963 PONP800102 0.945
+ NISK800101 0.940 PONP800108 0.935 NISK860101 0.930
+ BASU050101 0.925 BASU050103 0.923 CIDH920104 0.918
+ CORJ870101 0.918 PONP800103 0.913 MIYS850101 0.909
+ CORJ870107 0.908 CORJ870104 0.908 CORJ870103 0.906
+ CIDH920103 0.905 ROSG850102 0.903 RADA880108 0.900
+ BIOV880101 0.899 JURD980101 0.887 KYTJ820101 0.881
+ BASU050102 0.879 CIDH920105 0.879 NADH010103 0.878
+ NADH010104 0.873 PONP800107 0.871 LIFS790102 0.870
+ CORJ870106 0.867 ZHOH040103 0.864 NADH010102 0.863
+ PTIO830102 0.861 LIFS790101 0.859 CHOC760103 0.859
+ PLIV810101 0.856 WERD780101 0.853 CORJ870105 0.853
+ CASG920101 0.848 BIOV880102 0.847 NADH010101 0.847
+ FAUJ830101 0.843 JANJ790101 0.842 NADH010105 0.842
+ JANJ780102 0.842 MEIH800103 0.839 ROBB790101 0.834
+ KANM800102 0.833 KANM800104 0.827 EISD860103 0.826
+ ROBB760106 0.824 SWER830101 0.821 CORJ870102 0.818
+ OLSK800101 0.817 DESM900102 0.816 GUOD860101 0.815
+ PONP800106 0.813 QIAN880120 0.806 PALJ810104 0.805
+ CHOP780202 0.805 ROBB760105 0.805 ROSM880105 0.803
+ BLAS910101 0.802 QIAN880121 0.802 OOBM770101 -0.806
+ WOLS870101 -0.809 MUNV940103 -0.815 VINM940102 -0.821
+ PUNT030101 -0.824 GUYH850103 -0.833 VINM940101 -0.836
+ GUYH850101 -0.838 PARJ860101 -0.841 GUYH850102 -0.850
+ OOBM770103 -0.859 KARP850102 -0.863 RACS770102 -0.865
+ MEIH800102 -0.865 GRAR740102 -0.868 KRIW790101 -0.870
+ PUNT030102 -0.873 RACS770101 -0.878 MEIH800101 -0.897
+ FASG890101 -0.904 MIYS990105 -0.906 MIYS990104 -0.909
+ CORJ870108 -0.911 MIYS990101 -0.913 MIYS990102 -0.915
+ MIYS990103 -0.918
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 12.97 11.72 11.42 10.85 14.63 11.76 11.89 12.43 12.16 15.67
+ 14.90 11.36 14.39 14.00 11.37 11.23 11.69 13.93 13.42 15.71
+//
+H MAXF760101
+D Normalized frequency of alpha-helix (Maxfield-Scheraga, 1976)
+R PMID:990270
+A Maxfield, F.R. and Scheraga, H.A.
+T Status of empirical methods for the prediction of protein backbone topography
+J Biochemistry 15, 5138-5153 (1976) Recalculated by Kidera using a different
+ set of proteins Reported values normalized by the total number
+C ISOY800101 0.982 PALJ810102 0.959 CHOP780201 0.956
+ ROBB760101 0.956 KANM800101 0.950 TANS770101 0.930
+ PRAM900102 0.924 LEVM780101 0.924 LEVM780104 0.904
+ KANM800103 0.901 GEIM800104 0.897 GEIM800101 0.895
+ PALJ810101 0.889 QIAN880107 0.885 QIAN880106 0.881
+ NAGK730101 0.877 PALJ810109 0.876 AURR980109 0.865
+ AURR980110 0.860 RACS820108 0.860 AURR980114 0.853
+ BURA740101 0.852 AURR980115 0.852 AURR980108 0.841
+ AURR980112 0.838 CRAJ730101 0.826 QIAN880105 0.811
+ AURR980111 0.811 FINA770101 0.810 NAGK730103 -0.801
+ MUNV940102 -0.829 MUNV940101 -0.833
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.43 1.18 0.64 0.92 0.94 1.22 1.67 0.46 0.98 1.04
+ 1.36 1.27 1.53 1.19 0.49 0.70 0.78 1.01 0.69 0.98
+//
+H MAXF760102
+D Normalized frequency of extended structure (Maxfield-Scheraga, 1976)
+R PMID:990270
+A Maxfield, F.R. and Scheraga, H.A.
+T Status of empirical methods for the prediction of protein backbone topography
+J Biochemistry 15, 5138-5153 (1976) Recalculated by Kidera using a different
+ set of proteins Reported values normalized by the total number
+C ISOY800102 0.931 TANS770103 0.891 GEIM800105 0.819
+ RACS820111 0.815 WOEC730101 -0.842
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.86 0.94 0.74 0.72 1.17 0.89 0.62 0.97 1.06 1.24
+ 0.98 0.79 1.08 1.16 1.22 1.04 1.18 1.07 1.25 1.33
+//
+H MAXF760103
+D Normalized frequency of zeta R (Maxfield-Scheraga, 1976)
+R PMID:990270
+A Maxfield, F.R. and Scheraga, H.A.
+T Status of empirical methods for the prediction of protein backbone topography
+J Biochemistry 15, 5138-5153 (1976) Recalculated by Kidera using a different
+ set of proteins Reported values normalized by the total number
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.64 0.62 3.14 1.92 0.32 0.80 1.01 0.63 2.05 0.92
+ 0.37 0.89 1.07 0.86 0.50 1.01 0.92 1.00 1.31 0.87
+//
+H MAXF760104
+D Normalized frequency of left-handed alpha-helix (Maxfield-Scheraga, 1976)
+R PMID:990270
+A Maxfield, F.R. and Scheraga, H.A.
+T Status of empirical methods for the prediction of protein backbone topography
+J Biochemistry 15, 5138-5153 (1976) Recalculated by Kidera using a different
+ set of proteins Reported values normalized by the total number
+C ISOY800108 0.945 RICJ880115 0.919 TANS770107 0.913
+ MAXF760105 0.850 AURR980117 0.849 RACS820109 0.844
+ TANS770109 0.821
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.17 0.76 2.62 1.08 0.95 0.91 0.28 5.02 0.57 0.26
+ 0.21 1.17 0.00 0.28 0.12 0.57 0.23 0.00 0.97 0.24
+//
+H MAXF760105
+D Normalized frequency of zeta L (Maxfield-Scheraga, 1976)
+R PMID:990270
+A Maxfield, F.R. and Scheraga, H.A.
+T Status of empirical methods for the prediction of protein backbone topography
+J Biochemistry 15, 5138-5153 (1976) Recalculated by Kidera using a different
+ set of proteins Reported values normalized by the total number
+C TANS770109 0.878 MAXF760104 0.850 ISOY800108 0.810
+ RICJ880115 0.802
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.13 0.48 1.11 1.18 0.38 0.41 1.02 3.84 0.30 0.40
+ 0.65 1.13 0.00 0.45 0.00 0.81 0.71 0.93 0.38 0.48
+//
+H MAXF760106
+D Normalized frequency of alpha region (Maxfield-Scheraga, 1976)
+R PMID:990270
+A Maxfield, F.R. and Scheraga, H.A.
+T Status of empirical methods for the prediction of protein backbone topography
+J Biochemistry 15, 5138-5153 (1976) Recalculated by Kidera using a different
+ set of proteins Reported values normalized by the total number
+C ISOY800106 0.849
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.00 1.18 0.87 1.39 1.09 1.13 1.04 0.46 0.71 0.68
+ 1.01 1.05 0.36 0.65 1.95 1.56 1.23 1.10 0.87 0.58
+//
+H MCMT640101
+D Refractivity (McMeekin et al., 1964), Cited by Jones (1975)
+R
+A McMeekin, T.L., Groves, M.L. and Hipp, N.J.
+T
+J In "Amino Acids and Serum Proteins" (Stekol, J.A., ed.), American Chemical
+ Society, Washington, D.C., p. 54 (1964)
+C CHAM820101 0.871 ROSG850101 0.857 FAUJ880103 0.847
+ FASG760101 0.845 CHOC750101 0.822 GRAR740103 0.817
+ BIGC670101 0.814 GOLD730102 0.814 KRIW790103 0.810
+ CHOC760101 0.809 FUKS010111 -0.806 RADA880103 -0.833
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 4.34 26.66 13.28 12.00 35.77 17.56 17.26 0.00 21.81 19.06
+ 18.78 21.29 21.64 29.40 10.93 6.35 11.01 42.53 31.53 13.92
+//
+H MEEJ800101
+D Retention coefficient in HPLC, pH7.4 (Meek, 1980)
+R PMID:6929513
+A Meek, J.L.
+T Prediction of peptide retention times in high-pressure liquid chromatography
+ on the basis of amino acid composition
+J Proc. Natl. Acad. Sci. USA 77, 1632-1636 (1980)
+C MEEJ800102 0.886 ZIMJ680105 0.842 BROC820102 0.840
+ WIMW960101 0.838 GOLD730101 0.808 PARJ860101 -0.806
+ WOLS870101 -0.823
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.5 0.8 0.8 -8.2 -6.8 -4.8 -16.9 0.0 -3.5 13.9
+ 8.8 0.1 4.8 13.2 6.1 1.2 2.7 14.9 6.1 2.7
+//
+H MEEJ800102
+D Retention coefficient in HPLC, pH2.1 (Meek, 1980)
+R PMID:6929513
+A Meek, J.L.
+T Prediction of peptide retention times in high-pressure liquid chromatography
+ on the basis of amino acid composition
+J Proc. Natl. Acad. Sci. USA 77, 1632-1636 (1980)
+C ZIMJ680105 0.921 RADA880102 0.900 NOZY710101 0.895
+ TAKK010101 0.891 EISD860101 0.890 MEEJ800101 0.886
+ MEEJ810102 0.881 BROC820101 0.877 MEEJ810101 0.871
+ PLIV810101 0.867 GOLD730101 0.866 GUOD860101 0.866
+ SIMZ760101 0.861 FAUJ830101 0.858 BROC820102 0.857
+ CIDH920102 0.856 ARGP820101 0.855 JOND750101 0.855
+ BLAS910101 0.849 ROSM880105 0.841 CIDH920105 0.840
+ ZHOH040101 0.838 WIMW960101 0.821 ZHOH040102 0.808
+ ROBB790101 0.807 WEBA780101 -0.808 GUYH850103 -0.809
+ KIDA850101 -0.823 HOPT810101 -0.826 LEVM760101 -0.855
+ BULH740101 -0.875 PARJ860101 -0.902 WOLS870101 -0.925
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.1 -4.5 -1.6 -2.8 -2.2 -2.5 -7.5 -0.5 0.8 11.8
+ 10.0 -3.2 7.1 13.9 8.0 -3.7 1.5 18.1 8.2 3.3
+//
+H MEEJ810101
+D Retention coefficient in NaClO4 (Meek-Rossetti, 1981)
+R
+A Meek, J.L. and Rossetti, Z.L.
+T Factors affecting retention and resolution of peptides in high-performance
+ liquid chromatography
+J J. Chromatogr. 211, 15-28 (1981)
+C MEEJ810102 0.987 ZHOH040101 0.935 GUOD860101 0.931
+ ZHOH040103 0.921 PLIV810101 0.914 ROSM880104 0.911
+ FAUJ830101 0.902 BASU050102 0.898 CIDH920105 0.892
+ ARGP820101 0.891 JOND750101 0.891 CIDH920102 0.887
+ NOZY710101 0.882 CIDH920104 0.878 MEEJ800102 0.871
+ MIYS850101 0.863 ROBB790101 0.861 BIOV880101 0.855
+ NISK860101 0.848 CIDH920103 0.837 SIMZ760101 0.836
+ TAKK010101 0.836 BLAS910101 0.831 LEVM760106 0.827
+ WERD780101 0.825 GOLD730101 0.824 COWR900101 0.823
+ BIOV880102 0.822 VENT840101 0.813 BASU050101 0.810
+ CORJ870102 0.807 SWER830101 0.806 EISD860101 0.805
+ ZHOH040102 0.804 RADA880108 0.804 ROSM880105 0.802
+ MEIH800101 -0.809 GUYH850102 -0.813 KARP850101 -0.818
+ MIYS990104 -0.831 WEBA780101 -0.831 GRAR740102 -0.839
+ VINM940102 -0.839 MIYS990105 -0.839 KIDA850101 -0.850
+ OOBM770103 -0.861 GUYH850103 -0.864 MIYS990102 -0.866
+ MIYS990101 -0.867 BULH740101 -0.876 WOLS870101 -0.906
+ PARJ860101 -0.920
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.1 -0.4 -4.2 -1.6 7.1 -2.9 0.7 -0.2 -0.7 8.5
+ 11.0 -1.9 5.4 13.4 4.4 -3.2 -1.7 17.1 7.4 5.9
+//
+H MEEJ810102
+D Retention coefficient in NaH2PO4 (Meek-Rossetti, 1981)
+R
+A Meek, J.L. and Rossetti, Z.L.
+T Factors affecting retention and resolution of peptides in high-performance
+ liquid chromatography
+J J. Chromatogr. 211, 15-28 (1981)
+C MEEJ810101 0.987 GUOD860101 0.949 ZHOH040101 0.922
+ ZHOH040103 0.902 NOZY710101 0.899 PLIV810101 0.898
+ FAUJ830101 0.890 ROSM880104 0.885 MEEJ800102 0.881
+ BASU050102 0.871 ARGP820101 0.853 JOND750101 0.852
+ WILM950101 0.849 COWR900101 0.849 MIYS850101 0.844
+ CIDH920105 0.844 CIDH920102 0.843 CIDH920104 0.837
+ VENT840101 0.831 BLAS910101 0.830 BIOV880101 0.824
+ ROBB790101 0.821 BROC820101 0.820 TAKK010101 0.819
+ RADA880102 0.813 NISK860101 0.810 WILM950102 0.809
+ EISD860101 0.808 SIMZ760101 0.808 GOLD730101 0.806
+ ROSM880105 0.804 MIYS990104 -0.807 GRAR740102 -0.811
+ MIYS990105 -0.817 GUYH850103 -0.823 OOBM770103 -0.831
+ KIDA850101 -0.851 MIYS990102 -0.853 WEBA780101 -0.854
+ MIYS990101 -0.854 BULH740101 -0.880 PARJ860101 -0.897
+ WOLS870101 -0.905
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.0 -2.0 -3.0 -0.5 4.6 -2.0 1.1 0.2 -2.2 7.0
+ 9.6 -3.0 4.0 12.6 3.1 -2.9 -0.6 15.1 6.7 4.6
+//
+H MEIH800101
+D Average reduced distance for C-alpha (Meirovitch et al., 1980)
+R
+A Meirovitch, H., Rackovsky, S. and Scheraga, H.A.
+T Empirical studies of hydrophobicity. 1. Effect of protein size on the
+ hydrophobic behavior of amino acids
+J Macromolecules 13, 1398-1405 (1980) Database taken from group C
+C RACS770101 0.973 RACS770102 0.963 MEIH800102 0.952
+ MIYS990102 0.941 MIYS990101 0.940 MIYS990104 0.925
+ MIYS990103 0.923 FASG890101 0.919 MIYS990105 0.912
+ PARJ860101 0.905 VINM940101 0.900 GUYH850102 0.899
+ OOBM770103 0.897 GUYH850101 0.893 CORJ870108 0.889
+ KARP850102 0.884 VINM940103 0.875 GUYH850103 0.873
+ KRIW790101 0.869 PUNT030101 0.860 WOLS870101 0.852
+ PUNT030102 0.837 RACS770103 0.837 KRIW790102 0.835
+ VINM940102 0.833 KARP850101 0.832 FUKS010103 0.832
+ GRAR740102 0.824 PARS000101 0.813 RICJ880111 -0.802
+ ROSM880105 -0.802 DESM900102 -0.804 NADH010105 -0.806
+ LIFS790101 -0.809 MEEJ810101 -0.809 EISD860103 -0.810
+ RADA880102 -0.816 PONP800108 -0.825 ZHOH040101 -0.827
+ PTIO830102 -0.828 CORJ870102 -0.829 SWER830101 -0.830
+ BEGF750102 -0.832 GUOD860101 -0.833 NADH010102 -0.847
+ NISK800101 -0.852 CORJ870101 -0.855 PONP800103 -0.856
+ CORJ870104 -0.862 CIDH920101 -0.863 FAUJ830101 -0.863
+ NADH010104 -0.867 CIDH920102 -0.867 NADH010103 -0.868
+ ROBB790101 -0.868 PONP800102 -0.870 CORJ870103 -0.871
+ CASG920101 -0.875 MEIH800103 -0.875 CORJ870106 -0.882
+ CORJ870105 -0.883 BASU050101 -0.887 PONP800101 -0.888
+ BASU050102 -0.892 PLIV810101 -0.896 MANP780101 -0.897
+ CORJ870107 -0.897 ZHOH040103 -0.898 CIDH920103 -0.905
+ BASU050103 -0.906 PONP800107 -0.909 PONP930101 -0.916
+ CIDH920104 -0.917 CIDH920105 -0.923 ROSG850102 -0.930
+ BIOV880102 -0.937 RADA880108 -0.940 WERD780101 -0.943
+ BIOV880101 -0.949 MIYS850101 -0.957 NISK860101 -0.960
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.93 0.98 0.98 1.01 0.88 1.02 1.02 1.01 0.89 0.79
+ 0.85 1.05 0.84 0.78 1.00 1.02 0.99 0.83 0.93 0.81
+//
+H MEIH800102
+D Average reduced distance for side chain (Meirovitch et al., 1980)
+R
+A Meirovitch, H., Rackovsky, S. and Scheraga, H.A.
+T Empirical studies of hydrophobicity. 1. Effect of protein size on the
+ hydrophobic behavior of amino acids
+J Macromolecules 13, 1398-1405 (1980) Database taken from group C (Gly 0.067)
+C RACS770102 0.987 MEIH800101 0.952 FASG890101 0.951
+ GUYH850101 0.934 MIYS990103 0.917 MIYS990102 0.916
+ MIYS990105 0.914 MIYS990101 0.913 RACS770101 0.905
+ MIYS990104 0.903 RACS770103 0.903 PUNT030101 0.901
+ KRIW790102 0.898 GUYH850104 0.892 OOBM770101 0.881
+ KRIW790101 0.876 JANJ780103 0.873 VINM940101 0.872
+ CORJ870108 0.860 ROSM880102 0.859 OOBM770103 0.859
+ GUYH850102 0.856 PUNT030102 0.849 JANJ780101 0.843
+ VINM940103 0.841 CHOC760102 0.839 KARP850102 0.837
+ GRAR740102 0.836 KIDA850101 0.834 PARJ860101 0.831
+ KUHL950101 0.822 FUKS010104 0.822 WOLS870101 0.813
+ GUYH850105 0.811 VINM940104 0.808 NAKH900110 -0.802
+ BASU050102 -0.812 NADH010101 -0.818 JANJ790101 -0.821
+ ROSM880105 -0.821 DESM900101 -0.822 BASU050101 -0.825
+ CIDH920103 -0.825 WARP780101 -0.826 CIDH920105 -0.826
+ EISD840101 -0.829 CORJ870106 -0.835 PONP800108 -0.836
+ CORJ870105 -0.839 CORJ870104 -0.840 NISK800101 -0.844
+ ZHOH040103 -0.848 PLIV810101 -0.849 CORJ870103 -0.855
+ OLSK800101 -0.858 PONP800107 -0.858 MANP780101 -0.865
+ CIDH920104 -0.868 CORJ870107 -0.871 KYTJ820101 -0.871
+ FAUJ830101 -0.875 PONP800101 -0.877 CORJ870101 -0.878
+ CASG920101 -0.879 JURD980101 -0.879 BASU050103 -0.880
+ PONP930101 -0.881 EISD860103 -0.882 PONP800102 -0.883
+ PONP800103 -0.891 CHOC760103 -0.894 JANJ790102 -0.894
+ DESM900102 -0.898 NADH010104 -0.900 WERD780101 -0.903
+ JANJ780102 -0.907 NADH010103 -0.916 NISK860101 -0.920
+ NADH010102 -0.928 MIYS850101 -0.934 MEIH800103 -0.941
+ BIOV880102 -0.951 RADA880108 -0.953 BIOV880101 -0.956
+ ROSG850102 -0.959
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.94 1.09 1.04 1.08 0.84 1.11 1.12 1.01 0.92 0.76
+ 0.82 1.23 0.83 0.73 1.04 1.04 1.02 0.87 1.03 0.81
+//
+H MEIH800103
+D Average side chain orientation angle (Meirovitch et al., 1980)
+R
+A Meirovitch, H., Rackovsky, S. and Scheraga, H.A.
+T Empirical studies of hydrophobicity. 1. Effect of protein size on the
+ hydrophobic behavior of amino acids
+J Macromolecules 13, 1398-1405 (1980) Database taken from group C (Gly 7.4)
+C ROSG850102 0.948 BIOV880101 0.934 DESM900102 0.924
+ RADA880108 0.916 BIOV880102 0.916 NISK860101 0.909
+ MIYS850101 0.908 NADH010102 0.907 CORJ870101 0.902
+ NADH010103 0.901 JANJ780102 0.897 WERD780101 0.895
+ PONP800103 0.895 NADH010104 0.890 PONP800102 0.885
+ CORJ870107 0.883 CASG920101 0.881 CORJ870103 0.880
+ NISK800101 0.871 EISD860103 0.870 PONP800101 0.869
+ CHOC760103 0.865 PONP930101 0.863 PONP800108 0.862
+ JURD980101 0.861 KYTJ820101 0.856 CORJ870104 0.856
+ CIDH920104 0.853 DESM900101 0.853 JANJ790102 0.853
+ FAUJ830101 0.849 MANP780101 0.839 JANJ790101 0.838
+ WARP780101 0.835 BASU050103 0.832 CORJ870105 0.827
+ OLSK800101 0.826 NADH010101 0.824 CORJ870106 0.822
+ ZHOH040103 0.820 NADH010105 0.816 PLIV810101 0.811
+ CIDH920105 0.804 CIDH920103 0.802 ROBB790101 0.801
+ BASU050102 0.801 WOEC730101 -0.802 CHOC760102 -0.802
+ PARJ860101 -0.808 KUHL950101 -0.809 JANJ780101 -0.811
+ KIDA850101 -0.813 PUNT030102 -0.815 ROSM880102 -0.829
+ VINM940103 -0.830 RACS770101 -0.845 KRIW790101 -0.850
+ GUYH850102 -0.854 GUYH850104 -0.854 VINM940101 -0.861
+ GRAR740102 -0.866 OOBM770103 -0.866 JANJ780103 -0.866
+ CORJ870108 -0.870 MEIH800101 -0.875 GUYH850101 -0.880
+ PUNT030101 -0.882 KRIW790102 -0.885 MIYS990101 -0.891
+ MIYS990102 -0.893 MIYS990104 -0.894 OOBM770101 -0.896
+ MIYS990103 -0.906 RACS770102 -0.918 MIYS990105 -0.919
+ RACS770103 -0.919 FASG890101 -0.924 MEIH800102 -0.941
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 87. 81. 70. 71. 104. 66. 72. 90. 90. 105.
+ 104. 65. 100. 108. 78. 83. 83. 94. 83. 94.
+//
+H MIYS850101
+D Effective partition energy (Miyazawa-Jernigan, 1985)
+R
+A Miyazawa, S. and Jernigan, R.L.
+T Estimation of effective interresidue contact energies from protein crystal
+ structures: Quasi-chemical approximation
+J Macromolecules 18, 534-552 (1985)
+C BIOV880101 0.960 NISK860101 0.960 RADA880108 0.950
+ PLIV810101 0.944 ROSG850102 0.937 WERD780101 0.934
+ BIOV880102 0.930 CIDH920105 0.916 CIDH920104 0.915
+ FAUJ830101 0.914 ZHOH040103 0.914 CORJ870107 0.911
+ PONP930101 0.910 MANP780101 0.909 MEIH800103 0.908
+ GUOD860101 0.908 CIDH920103 0.906 BASU050102 0.904
+ BASU050103 0.899 PONP800103 0.898 NADH010104 0.897
+ NADH010103 0.896 ROBB790101 0.895 CORJ870104 0.892
+ PONP800101 0.892 CORJ870103 0.892 PONP800102 0.891
+ SWER830101 0.889 BASU050101 0.888 CORJ870102 0.887
+ CORJ870106 0.884 PONP800107 0.884 CORJ870105 0.879
+ NADH010102 0.878 CIDH920102 0.873 NISK800101 0.864
+ MEEJ810101 0.863 CASG920101 0.863 CORJ870101 0.861
+ EISD860103 0.858 ZHOH040101 0.855 PONP800108 0.847
+ MEEJ810102 0.844 NADH010105 0.844 ROSM880105 0.844
+ CIDH920101 0.843 EISD860101 0.842 JURD980101 0.837
+ DESM900102 0.831 BLAS910101 0.829 RADA880102 0.824
+ COWR900101 0.824 ROSM880104 0.824 ARGP820103 0.822
+ KYTJ820101 0.821 NADH010101 0.815 PONP800106 0.812
+ CHOC760103 0.810 NOZY710101 0.810 PTIO830102 0.807
+ BEGF750102 0.806 JANJ780102 0.806 NAKH900110 0.804
+ HOPT810101 -0.800 KARP850101 -0.811 RACS770103 -0.818
+ PARS000101 -0.821 ROSM880102 -0.825 FUKS010103 -0.828
+ KIDA850101 -0.831 VINM940102 -0.832 BULH740101 -0.838
+ VINM940103 -0.849 PUNT030102 -0.868 KRIW790102 -0.869
+ KARP850102 -0.878 VINM940101 -0.883 GUYH850102 -0.884
+ PUNT030101 -0.892 GRAR740102 -0.895 GUYH850103 -0.897
+ WOLS870101 -0.899 GUYH850101 -0.909 OOBM770103 -0.910
+ KRIW790101 -0.910 CORJ870108 -0.910 PARJ860101 -0.929
+ MEIH800102 -0.934 FASG890101 -0.938 RACS770101 -0.940
+ RACS770102 -0.943 MIYS990105 -0.951 MIYS990103 -0.952
+ MIYS990104 -0.953 MEIH800101 -0.957 MIYS990101 -0.977
+ MIYS990102 -0.978
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.36 1.92 1.70 1.67 3.36 1.75 1.74 2.06 2.41 4.17
+ 3.93 1.23 4.22 4.37 1.89 1.81 2.04 3.82 2.91 3.49
+//
+H NAGK730101
+D Normalized frequency of alpha-helix (Nagano, 1973)
+R PMID:4728695
+A Nagano, K.
+T Local analysis of the mechanism of protein folding. I. Prediction of helices,
+ loops, and beta-structures from primary structure
+J J. Mol. Biol. 75, 401-420 (1973)
+C PALJ810101 0.953 CRAJ730101 0.925 TANS770101 0.925
+ LEVM780104 0.918 GEIM800101 0.912 ROBB760101 0.910
+ PRAM900102 0.894 LEVM780101 0.894 CHOP780201 0.886
+ KANM800101 0.883 BURA740101 0.883 MAXF760101 0.877
+ PALJ810102 0.876 ISOY800101 0.862 GEIM800104 0.828
+ RACS820108 0.820 NAGK730103 -0.870
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.29 0.83 0.77 1.00 0.94 1.10 1.54 0.72 1.29 0.94
+ 1.23 1.23 1.23 1.23 0.70 0.78 0.87 1.06 0.63 0.97
+//
+H NAGK730102
+D Normalized frequency of bata-structure (Nagano, 1973)
+R PMID:4728695
+A Nagano, K.
+T Local analysis of the mechanism of protein folding. I. Prediction of helices,
+ loops, and beta-structures from primary structure
+J J. Mol. Biol. 75, 401-420 (1973)
+C ROBB760106 0.887 KANM800102 0.878 PALJ810104 0.867
+ CHOP780208 0.860 CHOP780202 0.858 BASU050103 0.837
+ BEGF750102 0.833 GEIM800107 0.830 ROBB760105 0.815
+ CRAJ730102 0.815 PTIO830102 0.811 PUNT030102 -0.836
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.96 0.67 0.72 0.90 1.13 1.18 0.33 0.90 0.87 1.54
+ 1.26 0.81 1.29 1.37 0.75 0.77 1.23 1.13 1.07 1.41
+//
+H NAGK730103
+D Normalized frequency of coil (Nagano, 1973)
+R PMID:4728695
+A Nagano, K.
+T Local analysis of the mechanism of protein folding. I. Prediction of helices,
+ loops, and beta-structures from primary structure
+J J. Mol. Biol. 75, 401-420 (1973)
+C CHAM830101 0.857 CHOP780101 0.827 CHOP780216 0.819
+ CHOP780210 0.814 ROBB760113 0.811 PALJ810105 0.804
+ TANS770101 -0.800 MAXF760101 -0.801 PALJ810101 -0.808
+ LEVM780101 -0.809 PRAM900102 -0.809 PALJ810102 -0.818
+ ISOY800101 -0.821 BURA740101 -0.830 CHOP780201 -0.837
+ KANM800103 -0.847 CRAJ730101 -0.850 ROBB760101 -0.861
+ NAGK730101 -0.870
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.72 1.33 1.38 1.04 1.01 0.81 0.75 1.35 0.76 0.80
+ 0.63 0.84 0.62 0.58 1.43 1.34 1.03 0.87 1.35 0.83
+//
+H NAKH900101
+D AA composition of total proteins (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C JOND920101 0.993 CEDJ970102 0.988 CEDJ970104 0.978
+ CEDJ970101 0.954 FUKS010112 0.948 FUKS010110 0.946
+ JUKT750101 0.941 DAYM780101 0.940 JUNJ780101 0.918
+ CEDJ970103 0.908 NAKH920101 0.907 NAKH920106 0.900
+ KUMS000102 0.894 FUKS010109 0.868 NAKH900109 0.866
+ NAKH920107 0.863 CEDJ970105 0.860 NAKH900102 0.858
+ NAKH920104 0.857 KUMS000101 0.856 NAKH920103 0.854
+ FUKS010111 0.812
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 7.99 5.86 4.33 5.14 1.81 3.98 6.10 6.91 2.17 5.48
+ 9.16 6.01 2.50 3.83 4.95 6.84 5.77 1.34 3.15 6.65
+//
+H NAKH900102
+D SD of AA composition of total proteins (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C CEDJ970105 0.903 DAYM780101 0.883 NAKH920106 0.872
+ CEDJ970104 0.860 NAKH900101 0.858 NAKH920101 0.854
+ JUNJ780101 0.853 JOND920101 0.846 CEDJ970102 0.841
+ CEDJ970101 0.832 RACS820105 -0.839
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 3.73 3.34 2.33 2.23 2.30 2.36 3. 3.36 1.55 2.52
+ 3.40 3.36 1.37 1.94 3.18 2.83 2.63 1.15 1.76 2.53
+//
+H NAKH900103
+D AA composition of mt-proteins (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C NAKH900105 0.992 NAKH900112 0.966 NAKH900107 0.927
+ FUKS010108 0.864 NAKH900111 0.832 NAKH920105 0.829
+ NAKH920108 0.826 CEDJ970103 0.815
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 5.74 1.92 5.25 2.11 1.03 2.30 2.63 5.66 2.30 9.12
+ 15.36 3.20 5.30 6.51 4.79 7.55 7.51 2.51 4.08 5.12
+//
+H NAKH900104
+D Normalized composition of mt-proteins (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C NAKH900106 0.986 NAKH900108 0.849 EISD860101 0.812
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.60 -1.18 0.39 -1.36 -0.34 -0.71 -1.16 -0.37 0.08 1.44
+ 1.82 -0.84 2.04 1.38 -0.05 0.25 0.66 1.02 0.53 -0.60
+//
+H NAKH900105
+D AA composition of mt-proteins from animal (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C NAKH900103 0.992 NAKH900112 0.974 NAKH900107 0.870
+ FUKS010108 0.846 NAKH900111 0.815 NAKH920105 0.806
+ NAKH920108 0.801
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 5.88 1.54 4.38 1.70 1.11 2.30 2.60 5.29 2.33 8.78
+ 16.52 2.58 6.00 6.58 5.29 7.68 8.38 2.89 3.51 4.66
+//
+H NAKH900106
+D Normalized composition from animal (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C NAKH900104 0.986 EISD860101 0.812 ARGP820103 0.810
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.57 -1.29 0.02 -1.54 -0.30 -0.71 -1.17 -0.48 0.10 1.31
+ 2.16 -1.02 2.55 1.42 0.11 0.30 0.99 1.35 0.20 -0.79
+//
+H NAKH900107
+D AA composition of mt-proteins from fungi and plant (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C NAKH900103 0.927 NAKH900105 0.870 NAKH900112 0.850
+ FUKS010108 0.830 CEDJ970103 0.820 NAKH920108 0.816
+ NAKH920105 0.814
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 5.39 2.81 7.31 3.07 0.86 2.31 2.70 6.52 2.23 9.94
+ 12.64 4.67 3.68 6.34 3.62 7.24 5.44 1.64 5.42 6.18
+//
+H NAKH900108
+D Normalized composition from fungi and plant (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C NAKH900104 0.849
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.70 -0.91 1.28 -0.93 -0.41 -0.71 -1.13 -0.12 0.04 1.77
+ 1.02 -0.40 0.86 1.29 -0.42 0.14 -0.13 0.26 1.29 -0.19
+//
+H NAKH900109
+D AA composition of membrane proteins (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C CEDJ970103 0.970 FUKS010106 0.927 FUKS010107 0.903
+ FUKS010105 0.892 NAKH900111 0.890 JOND920101 0.878
+ FUKS010108 0.872 NAKH900101 0.866 CEDJ970102 0.865
+ CEDJ970101 0.861 FUKS010110 0.853 KUMS000102 0.837
+ NAKH920105 0.823 CEDJ970104 0.821 JUKT750101 0.815
+ NAKH920108 0.811
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 9.25 3.96 3.71 3.89 1.07 3.17 4.80 8.51 1.88 6.47
+ 10.94 3.50 3.14 6.36 4.36 6.26 5.66 2.22 3.28 7.55
+//
+H NAKH900110
+D Normalized composition of membrane proteins (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C ROSM880105 0.859 EISD840101 0.838 BROC820101 0.830
+ BIOV880102 0.829 EISD860101 0.820 GUOD860101 0.805
+ MIYS850101 0.804 BLAS910101 0.801 MEIH800102 -0.802
+ KIDA850101 -0.808 PARJ860101 -0.808 ROSM880101 -0.812
+ HOPT810101 -0.812 WOLS870101 -0.832 VHEG790101 -0.848
+ PUNT030101 -0.886
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.34 -0.57 -0.27 -0.56 -0.32 -0.34 -0.43 0.48 -0.19 0.39
+ 0.52 -0.75 0.47 1.30 -0.19 -0.20 -0.04 0.77 0.07 0.36
+//
+H NAKH900111
+D Transmembrane regions of non-mt-proteins (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C NAKH920108 0.975 NAKH920105 0.958 FUKS010108 0.954
+ FUKS010106 0.933 FUKS010105 0.911 NAKH900109 0.890
+ NAKH900112 0.878 FUKS010107 0.867 CEDJ970103 0.865
+ NAKH900103 0.832 KYTJ820101 0.817 NAKH900105 0.815
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 10.17 1.21 1.36 1.18 1.48 1.57 1.15 8.87 1.07 10.91
+ 16.22 1.04 4.12 9.60 2.24 5.38 5.61 2.67 2.68 11.44
+//
+H NAKH900112
+D Transmembrane regions of mt-proteins (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C NAKH900105 0.974 NAKH900103 0.966 FUKS010108 0.896
+ NAKH920105 0.881 NAKH920108 0.879 NAKH900111 0.878
+ NAKH900107 0.850
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.61 0.41 1.84 0.59 0.83 1.20 1.63 4.88 1.14 12.91
+ 21.66 1.15 7.17 7.76 3.51 6.84 8.89 2.11 2.57 6.30
+//
+H NAKH900113
+D Ratio of average and computed composition (Nakashima et al., 1990)
+R PMID:2235995
+A Nakashima, H., Nishikawa, K. and Ooi, T.
+T Distinct character in hydrophobicity of amino acid composition of
+ mitochondrial proteins
+J Proteins 8, 173-178 (1990)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.61 0.40 0.73 0.75 0.37 0.61 1.50 3.12 0.46 1.61
+ 1.37 0.62 1.59 1.24 0.67 0.68 0.92 1.63 0.67 1.30
+//
+H NAKH920101
+D AA composition of CYT of single-spanning proteins (Nakashima-Nishikawa, 1992)
+R PMID:1607012
+A Nakashima, H. and Nishikawa, K.
+T The amino acid composition is different between the cytoplasmic and
+ extracellular sides in membrane proteins
+J FEBS Lett. 303, 141-146 (1992)
+C CEDJ970105 0.942 NAKH920106 0.929 NAKH920102 0.929
+ CEDJ970104 0.920 NAKH900101 0.907 JOND920101 0.900
+ CEDJ970102 0.898 DAYM780101 0.882 FUKS010112 0.856
+ NAKH900102 0.854 CEDJ970101 0.850 JUKT750101 0.849
+ FUKS010110 0.833 JUNJ780101 0.826 NAKH920104 0.822
+ NAKH920103 0.811
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 8.63 6.75 4.18 6.24 1.03 4.76 7.82 6.80 2.70 3.48
+ 8.44 6.25 2.14 2.73 6.28 8.53 4.43 0.80 2.54 5.44
+//
+H NAKH920102
+D AA composition of CYT2 of single-spanning proteins (Nakashima-Nishikawa,
+ 1992)
+R PMID:1607012
+A Nakashima, H. and Nishikawa, K.
+T The amino acid composition is different between the cytoplasmic and
+ extracellular sides in membrane proteins
+J FEBS Lett. 303, 141-146 (1992)
+C NAKH920101 0.929 CEDJ970105 0.843 CEDJ970104 0.834
+ NAKH920106 0.832 DAYM780101 0.802
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 10.88 6.01 5.75 6.13 0.69 4.68 9.34 7.72 2.15 1.80
+ 8.03 6.11 3.79 2.93 7.21 7.25 3.51 0.47 1.01 4.57
+//
+H NAKH920103
+D AA composition of EXT of single-spanning proteins (Nakashima-Nishikawa, 1992)
+R PMID:1607012
+A Nakashima, H. and Nishikawa, K.
+T The amino acid composition is different between the cytoplasmic and
+ extracellular sides in membrane proteins
+J FEBS Lett. 303, 141-146 (1992)
+C CEDJ970102 0.906 NAKH920104 0.904 NAKH920107 0.882
+ JOND920101 0.881 CEDJ970104 0.863 NAKH900101 0.854
+ DAYM780101 0.851 CEDJ970101 0.843 FUKS010112 0.842
+ JUKT750101 0.837 JUNJ780101 0.820 NAKH920101 0.811
+ NAKH920106 0.809
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 5.15 4.38 4.81 5.75 3.24 4.45 7.05 6.38 2.69 4.40
+ 8.11 5.25 1.60 3.52 5.65 8.04 7.41 1.68 3.42 7.00
+//
+H NAKH920104
+D AA composition of EXT2 of single-spanning proteins (Nakashima-Nishikawa,
+ 1992)
+R PMID:1607012
+A Nakashima, H. and Nishikawa, K.
+T The amino acid composition is different between the cytoplasmic and
+ extracellular sides in membrane proteins
+J FEBS Lett. 303, 141-146 (1992)
+C CEDJ970102 0.905 NAKH920103 0.904 NAKH920107 0.889
+ JOND920101 0.887 FUKS010112 0.882 CEDJ970104 0.865
+ CEDJ970101 0.859 NAKH900101 0.857 NAKH920106 0.829
+ JUKT750101 0.827 NAKH920101 0.822 DAYM780101 0.819
+ JUNJ780101 0.807
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 5.04 3.73 5.94 5.26 2.20 4.50 6.07 7.09 2.99 4.32
+ 9.88 6.31 1.85 3.72 6.22 8.05 5.20 2.10 3.32 6.19
+//
+H NAKH920105
+D AA composition of MEM of single-spanning proteins (Nakashima-Nishikawa, 1992)
+R PMID:1607012
+A Nakashima, H. and Nishikawa, K.
+T The amino acid composition is different between the cytoplasmic and
+ extracellular sides in membrane proteins
+J FEBS Lett. 303, 141-146 (1992)
+C FUKS010108 0.968 NAKH920108 0.959 NAKH900111 0.958
+ FUKS010106 0.931 FUKS010105 0.929 NAKH900112 0.881
+ CEDJ970103 0.836 FUKS010107 0.833 NAKH900103 0.829
+ NAKH900109 0.823 NAKH900107 0.814 NAKH900105 0.806
+ KYTJ820101 0.803
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 9.90 0.09 0.94 0.35 2.55 0.87 0.08 8.14 0.20 15.25
+ 22.28 0.16 1.85 6.47 2.38 4.17 4.33 2.21 3.42 14.34
+//
+H NAKH920106
+D AA composition of CYT of multi-spanning proteins (Nakashima-Nishikawa, 1992)
+R PMID:1607012
+A Nakashima, H. and Nishikawa, K.
+T The amino acid composition is different between the cytoplasmic and
+ extracellular sides in membrane proteins
+J FEBS Lett. 303, 141-146 (1992)
+C CEDJ970105 0.930 NAKH920101 0.929 CEDJ970104 0.923
+ FUKS010112 0.921 NAKH900101 0.900 JOND920101 0.889
+ CEDJ970102 0.886 NAKH900102 0.872 DAYM780101 0.856
+ NAKH920102 0.832 JUKT750101 0.831 NAKH920104 0.829
+ JUNJ780101 0.829 CEDJ970101 0.826 FUKS010110 0.824
+ FUKS010104 0.818 FUKS010109 0.814 NAKH920103 0.809
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.69 6.65 4.49 4.97 1.70 5.39 7.76 6.32 2.11 4.51
+ 8.23 8.36 2.46 3.59 5.20 7.40 5.18 1.06 2.75 5.27
+//
+H NAKH920107
+D AA composition of EXT of multi-spanning proteins (Nakashima-Nishikawa, 1992)
+R PMID:1607012
+A Nakashima, H. and Nishikawa, K.
+T The amino acid composition is different between the cytoplasmic and
+ extracellular sides in membrane proteins
+J FEBS Lett. 303, 141-146 (1992)
+C JOND920101 0.893 CEDJ970102 0.891 NAKH920104 0.889
+ NAKH920103 0.882 NAKH900101 0.863 JUKT750101 0.862
+ DAYM780101 0.861 CEDJ970101 0.860 CEDJ970104 0.857
+ JUNJ780101 0.856 FUKS010111 0.841 KUMS000102 0.839
+ FUKS010112 0.824 FUKS010110 0.810 KUMS000101 0.800
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 5.08 4.75 5.75 5.96 2.95 4.24 6.04 8.20 2.10 4.95
+ 8.03 4.93 2.61 4.36 4.84 6.41 5.87 2.31 4.55 6.07
+//
+H NAKH920108
+D AA composition of MEM of multi-spanning proteins (Nakashima-Nishikawa, 1992)
+R PMID:1607012
+A Nakashima, H. and Nishikawa, K.
+T The amino acid composition is different between the cytoplasmic and
+ extracellular sides in membrane proteins
+J FEBS Lett. 303, 141-146 (1992)
+C NAKH900111 0.975 NAKH920105 0.959 FUKS010108 0.948
+ FUKS010106 0.898 FUKS010105 0.890 NAKH900112 0.879
+ KYTJ820101 0.868 JURD980101 0.858 NAKH900103 0.826
+ CHOC760103 0.824 FUKS010107 0.817 NAKH900107 0.816
+ NAKH900109 0.811 CEDJ970103 0.811 NAKH900105 0.801
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 9.36 0.27 2.31 0.94 2.56 1.14 0.94 6.17 0.47 13.73
+ 16.64 0.58 3.93 10.99 1.96 5.58 4.68 2.20 3.13 12.43
+//
+H NISK800101
+D 8 A contact number (Nishikawa-Ooi, 1980)
+R PMID:7440060
+A Nishikawa, K. and Ooi, T.
+T Prediction of the surface-interior diagram of globular proteins by an
+ empirical method
+J Int. J. Peptide Protein Res. 16, 19-32 (1980)
+C PONP800108 0.976 CORJ870101 0.976 PONP800102 0.965
+ PONP800101 0.960 PONP930101 0.956 NISK860101 0.943
+ ROSG850102 0.942 PONP800103 0.941 MANP780101 0.940
+ CASG920101 0.935 BIOV880101 0.920 NADH010104 0.909
+ NADH010103 0.908 RADA880108 0.902 CIDH920104 0.900
+ BASU050103 0.896 WERD780101 0.891 ZHOH040103 0.888
+ CORJ870103 0.886 CORJ870107 0.884 BASU050102 0.884
+ NADH010102 0.881 BAEK050101 0.881 BASU050101 0.876
+ JANJ790101 0.875 BIOV880102 0.873 MEIH800103 0.871
+ CORJ870104 0.868 MIYS850101 0.864 NADH010105 0.860
+ CORJ870106 0.857 CIDH920103 0.855 CIDH920105 0.854
+ JANJ780102 0.853 DESM900102 0.852 FAUJ830101 0.849
+ DESM900101 0.837 CORJ870105 0.834 ROBB790101 0.830
+ LIFS790101 0.827 QIAN880121 0.818 JURD980101 0.816
+ NADH010101 0.813 KYTJ820101 0.812 KANM800102 0.809
+ QIAN880122 0.808 RACS770101 -0.805 GUYH850101 -0.811
+ MUNV940103 -0.813 PARS000102 -0.814 RACS770102 -0.818
+ GUYH850103 -0.828 KRIW710101 -0.831 PARS000101 -0.832
+ VINM940103 -0.836 MEIH800102 -0.844 OOBM770101 -0.845
+ MEIH800101 -0.852 PUNT030102 -0.855 MIYS990101 -0.860
+ MIYS990102 -0.863 GRAR740102 -0.879 CORJ870108 -0.880
+ KARP850102 -0.885 OOBM770103 -0.894 KRIW790101 -0.896
+ VINM940102 -0.900 GUYH850102 -0.914 VINM940101 -0.922
+ FASG890101 -0.923 MIYS990105 -0.935 MIYS990103 -0.938
+ MIYS990104 -0.938
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.23 -0.26 -0.94 -1.13 1.78 -0.57 -0.75 -0.07 0.11 1.19
+ 1.03 -1.05 0.66 0.48 -0.76 -0.67 -0.36 0.90 0.59 1.24
+//
+H NISK860101
+D 14 A contact number (Nishikawa-Ooi, 1986)
+R PMID:3818558
+A Nishikawa, K. and Ooi, T.
+T Radial locations of amino acid residues in a globular protein: Correlation
+ with the sequence
+J J. Biochem. 100, 1043-1047 (1986) Values supplied by the author
+C BIOV880101 0.972 WERD780101 0.966 ROSG850102 0.962
+ PONP930101 0.961 MIYS850101 0.960 BASU050102 0.951
+ RADA880108 0.950 ZHOH040103 0.946 CIDH920104 0.944
+ NISK800101 0.943 BIOV880102 0.939 CIDH920105 0.938
+ CASG920101 0.938 BASU050103 0.937 CORJ870101 0.935
+ MANP780101 0.930 PONP800101 0.930 CORJ870107 0.928
+ BASU050101 0.926 PONP800102 0.924 PONP800108 0.921
+ NADH010104 0.915 CORJ870103 0.914 ROBB790101 0.912
+ PONP800103 0.910 NADH010103 0.910 MEIH800103 0.909
+ CIDH920103 0.909 CORJ870106 0.908 FAUJ830101 0.906
+ CORJ870104 0.901 CORJ870105 0.901 CIDH920102 0.897
+ PLIV810101 0.892 BAEK050101 0.886 CIDH920101 0.882
+ NADH010102 0.878 ZHOH040101 0.871 SWER830101 0.865
+ CORJ870102 0.864 NADH010105 0.863 LIFS790101 0.859
+ MEEJ810101 0.848 PONP800107 0.847 DESM900102 0.843
+ GUOD860101 0.840 QIAN880120 0.837 ROSM880105 0.836
+ CHOP780202 0.832 QIAN880121 0.829 PTIO830102 0.825
+ KANM800102 0.819 JANJ780102 0.813 GEIM800107 0.813
+ EISD860103 0.811 NADH010101 0.810 ROBB760106 0.810
+ MEEJ810102 0.810 PALJ810104 0.809 JURD980101 0.808
+ BLAS910101 0.803 ROSM880104 0.801 HOPT810101 -0.822
+ WOEC730101 -0.822 KARP850101 -0.828 FUKS010104 -0.832
+ RACS770103 -0.837 MUNV940103 -0.840 WOLS870101 -0.848
+ FUKS010103 -0.850 PUNT030101 -0.854 KRIW790102 -0.855
+ GUYH850101 -0.877 PARS000101 -0.884 PUNT030102 -0.885
+ GRAR740102 -0.900 KARP850102 -0.901 VINM940103 -0.903
+ KRIW790101 -0.907 RACS770102 -0.913 GUYH850103 -0.914
+ PARJ860101 -0.916 VINM940102 -0.919 CORJ870108 -0.920
+ MEIH800102 -0.920 RACS770101 -0.923 FASG890101 -0.949
+ OOBM770103 -0.949 GUYH850102 -0.950 MIYS990101 -0.957
+ VINM940101 -0.959 MEIH800101 -0.960 MIYS990102 -0.960
+ MIYS990105 -0.972 MIYS990103 -0.974 MIYS990104 -0.980
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.22 -0.93 -2.65 -4.12 4.66 -2.76 -3.64 -1.62 1.28 5.58
+ 5.01 -4.18 3.51 5.27 -3.03 -2.84 -1.20 5.20 2.15 4.45
+//
+H NOZY710101
+D Transfer energy, organic solvent/water (Nozaki-Tanford, 1971)
+R PMID:5555568
+A Nozaki, Y. and Tanford, C.
+T The solubility of amino acids and two glycine peptides in aqueous ethanol and
+ dioxane solutions
+J J. Biol. Chem. 246, 2211-2217 (1971) Missing values filled with zeros
+C ZHOH040101 0.932 RADA880102 0.917 MEEJ810102 0.899
+ VENT840101 0.897 ZHOH040102 0.897 MEEJ800102 0.895
+ CIDH920102 0.889 TAKK010101 0.884 GUOD860101 0.884
+ MEEJ810101 0.882 CIDH920105 0.857 ROSM880104 0.847
+ BASU050102 0.847 LEVM760107 0.845 ZHOH040103 0.842
+ PLIV810101 0.839 CORJ870102 0.838 ZIMJ680105 0.837
+ SWER830101 0.836 ROSG850101 0.834 BROC820101 0.829
+ EISD860101 0.822 GARJ730101 0.821 WIMW960101 0.818
+ MIYS850101 0.810 SIMZ760101 0.807 FAUJ830101 0.803
+ ARGP820101 0.800 MIYS990102 -0.819 MIYS990101 -0.821
+ OOBM770103 -0.828 PARS000101 -0.829 WOLS870101 -0.874
+ WEBA780101 -0.890 BULH740101 -0.892 PARJ860101 -0.900
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.5 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.5 1.8
+ 1.8 0.0 1.3 2.5 0.0 0.0 0.4 3.4 2.3 1.5
+//
+H OOBM770101
+D Average non-bonded energy per atom (Oobatake-Ooi, 1977)
+R PMID:904331
+A Oobatake, M. and Ooi, T.
+T An analysis of non-bonded energy of proteins
+J J. Theor. Biol. 67, 567-584 (1977) Last two calcualted by Kidera; multiplied
+ by the number of heavy atoms
+C GUYH850104 0.966 JANJ780103 0.965 JANJ780101 0.953
+ CHOC760102 0.925 ENGD860101 0.907 PRAM900101 0.907
+ MEIH800102 0.881 KUHL950101 0.876 GUYH850105 0.874
+ RACS770103 0.871 FASG890101 0.868 ROSM880102 0.867
+ PUNT030101 0.865 ROSM880101 0.854 GUYH850101 0.848
+ PUNT030102 0.845 MIYS990105 0.844 KIDA850101 0.843
+ GRAR740102 0.841 RACS770102 0.838 MIYS990103 0.827
+ KRIW790102 0.822 KRIW790101 0.816 MIYS990104 0.806
+ WOEC730101 0.804 MANP780101 -0.806 JACR890101 -0.812
+ ROSM880105 -0.824 WOLR790101 -0.831 FAUJ830101 -0.832
+ PONP800101 -0.835 CASG920101 -0.838 NISK800101 -0.845
+ WOLR810101 -0.847 PONP800108 -0.851 RADA880107 -0.854
+ CHOC760104 -0.857 BIOV880101 -0.858 NADH010101 -0.861
+ PONP800102 -0.862 RADA880101 -0.863 RADA880108 -0.864
+ NADH010104 -0.871 JANJ790101 -0.871 CORJ870101 -0.875
+ BIOV880102 -0.877 OLSK800101 -0.878 EISD840101 -0.878
+ EISD860103 -0.880 PONP800103 -0.880 DESM900101 -0.894
+ MEIH800103 -0.896 KYTJ820101 -0.899 CHOC760103 -0.902
+ NADH010103 -0.902 JURD980101 -0.903 ROSG850102 -0.903
+ WARP780101 -0.937 NADH010102 -0.944 DESM900102 -0.950
+ JANJ790102 -0.963 JANJ780102 -0.968
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -1.895 -1.475 -1.560 -1.518 -2.035 -1.521 -1.535 -1.898 -1.755 -1.951
+ -1.966 -1.374 -1.963 -1.864 -1.699 -1.753 -1.767 -1.869 -1.686 -1.981
+//
+H OOBM770102
+D Short and medium range non-bonded energy per atom (Oobatake-Ooi, 1977)
+R PMID:904331
+A Oobatake, M. and Ooi, T.
+T An analysis of non-bonded energy of proteins
+J J. Theor. Biol. 67, 567-584 (1977) Last two calcualted by Kidera; multiplied
+ by the number of heavy atoms
+C LEVM760102 0.869 LEVM760105 0.868 CHAM830106 0.858
+ CHOC760101 0.824 FASG760101 0.821 FAUJ880103 0.801
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -1.404 -0.921 -1.178 -1.162 -1.365 -1.116 -1.163 -1.364 -1.215 -1.189
+ -1.315 -1.074 -1.303 -1.135 -1.236 -1.297 -1.252 -1.030 -1.030 -1.254
+//
+H OOBM770103
+D Long range non-bonded energy per atom (Oobatake-Ooi, 1977)
+R PMID:904331
+A Oobatake, M. and Ooi, T.
+T An analysis of non-bonded energy of proteins
+J J. Theor. Biol. 67, 567-584 (1977) Last two calcualted by Kidera; multiplied
+ by the number of heavy atoms
+C MIYS990105 0.936 VINM940101 0.936 MIYS990104 0.931
+ MIYS990103 0.908 GUYH850103 0.906 GUYH850102 0.904
+ MEIH800101 0.897 GRAR740102 0.896 PARJ860101 0.891
+ VINM940102 0.891 MIYS990102 0.891 MIYS990101 0.887
+ FASG890101 0.869 KRIW790101 0.865 PARS000101 0.864
+ MEIH800102 0.859 WOLS870101 0.852 FUKS010104 0.849
+ VINM940103 0.845 WOEC730101 0.835 RACS770101 0.835
+ HOPT810101 0.833 CORJ870108 0.829 RACS770102 0.828
+ PUNT030102 0.828 KRIW790102 0.824 RACS770103 0.823
+ KARP850102 0.820 MUNV940103 0.805 LEVM760101 0.805
+ PTIO830102 -0.801 LIFS790103 -0.807 BAEK050101 -0.810
+ KANM800102 -0.812 WIMW960101 -0.814 CORJ870104 -0.814
+ CIDH920101 -0.818 PONP800107 -0.819 CHOP780202 -0.820
+ QIAN880120 -0.824 CORJ870106 -0.826 ROSM880105 -0.828
+ NOZY710101 -0.828 MEEJ810102 -0.831 CORJ870102 -0.832
+ CORJ870105 -0.833 SWER830101 -0.833 NADH010102 -0.838
+ GUOD860101 -0.838 CORJ870103 -0.839 PONP800101 -0.848
+ BASU050101 -0.850 CORJ870107 -0.851 PLIV810101 -0.852
+ PONP800102 -0.854 LIFS790101 -0.855 MANP780101 -0.859
+ MEEJ810101 -0.861 NADH010103 -0.861 ZHOH040101 -0.862
+ NADH010104 -0.863 CIDH920103 -0.863 PONP800103 -0.865
+ MEIH800103 -0.866 BASU050103 -0.866 CIDH920102 -0.877
+ RADA880108 -0.878 BASU050102 -0.893 NISK800101 -0.894
+ PONP800108 -0.896 FAUJ830101 -0.899 CIDH920105 -0.904
+ WERD780101 -0.906 CORJ870101 -0.907 ZHOH040103 -0.907
+ ROBB790101 -0.909 MIYS850101 -0.910 CIDH920104 -0.912
+ PONP930101 -0.914 CASG920101 -0.914 ROSG850102 -0.916
+ BIOV880101 -0.920 BIOV880102 -0.925 NISK860101 -0.949
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.491 -0.554 -0.382 -0.356 -0.670 -0.405 -0.371 -0.534 -0.540 -0.762
+ -0.650 -0.300 -0.659 -0.729 -0.463 -0.455 -0.515 -0.839 -0.656 -0.728
+//
+H OOBM770104
+D Average non-bonded energy per residue (Oobatake-Ooi, 1977)
+R PMID:904331
+A Oobatake, M. and Ooi, T.
+T An analysis of non-bonded energy of proteins
+J J. Theor. Biol. 67, 567-584 (1977) Last two calcualted by Kidera; multiplied
+ by the number of heavy atoms
+C OOBM770105 0.980
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -9.475 -16.225 -12.480 -12.144 -12.210 -13.689 -13.815 -7.592 -17.550 -15.608
+ -15.728 -12.366 -15.704 -20.504 -11.893 -10.518 -12.369 -26.166 -20.232 -13.867
+//
+H OOBM770105
+D Short and medium range non-bonded energy per residue (Oobatake-Ooi, 1977)
+R PMID:904331
+A Oobatake, M. and Ooi, T.
+T An analysis of non-bonded energy of proteins
+J J. Theor. Biol. 67, 567-584 (1977) Last two calcualted by Kidera; multiplied
+ by the number of heavy atoms
+C OOBM770104 0.980
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -7.020 -10.131 -9.424 -9.296 -8.190 -10.044 -10.467 -5.456 -12.150 -9.512
+ -10.520 -9.666 -10.424 -12.485 -8.652 -7.782 -8.764 -14.420 -12.360 -8.778
+//
+H OOBM850101
+D Optimized beta-structure-coil equilibrium constant (Oobatake et al., 1985)
+R
+A Oobatake, M., Kubota, Y. and Ooi, T.
+T Optimization of amino acid parameters for correspondence of sequence to
+ tertiary structures of proteuins
+J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985)
+C QIAN880119 0.825
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.01 0.84 0.03 -2.05 1.98 1.02 0.93 0.12 -0.14 3.70
+ 2.73 2.55 1.75 2.68 0.41 1.47 2.39 2.49 2.23 3.50
+//
+H OOBM850102
+D Optimized propensity to form reverse turn (Oobatake et al., 1985)
+R
+A Oobatake, M., Kubota, Y. and Ooi, T.
+T Optimization of amino acid parameters for correspondence of sequence to
+ tertiary structures of proteuins
+J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985)
+C ZASB820101 -0.853 GARJ730101 -0.877
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.34 0.95 2.49 3.32 1.07 1.49 2.20 2.07 1.27 0.66
+ 0.54 0.61 0.70 0.80 2.12 0.94 1.09 -4.65 -0.17 1.32
+//
+H OOBM850103
+D Optimized transfer energy parameter (Oobatake et al., 1985)
+R
+A Oobatake, M., Kubota, Y. and Ooi, T.
+T Optimization of amino acid parameters for correspondence of sequence to
+ tertiary structures of proteuins
+J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.46 -1.54 1.31 -0.33 0.20 -1.12 0.48 0.64 -1.31 3.28
+ 0.43 -1.71 0.15 0.52 -0.58 -0.83 -1.52 1.25 -2.21 0.54
+//
+H OOBM850104
+D Optimized average non-bonded energy per atom (Oobatake et al., 1985)
+R
+A Oobatake, M., Kubota, Y. and Ooi, T.
+T Optimization of amino acid parameters for correspondence of sequence to
+ tertiary structures of proteuins
+J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -2.49 2.55 2.27 8.86 -3.13 1.79 4.04 -0.56 4.22 -10.87
+ -7.16 -9.97 -4.96 -6.64 5.19 -1.60 -4.75 -17.84 9.25 -3.97
+//
+H OOBM850105
+D Optimized side chain interaction parameter (Oobatake et al., 1985)
+R
+A Oobatake, M., Kubota, Y. and Ooi, T.
+T Optimization of amino acid parameters for correspondence of sequence to
+ tertiary structures of proteuins
+J Bull. Inst. Chem. Res., Kyoto Univ. 63, 82-94 (1985)
+C QIAN880127 -0.813
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 4.55 5.97 5.56 2.85 -0.78 4.15 5.16 9.14 4.48 2.10
+ 3.24 10.68 2.18 4.37 5.14 6.78 8.60 1.97 2.40 3.81
+//
+H PALJ810101
+D Normalized frequency of alpha-helix from LG (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C LEVM780104 0.988 NAGK730101 0.953 GEIM800101 0.951
+ LEVM780101 0.943 PRAM900102 0.943 KANM800101 0.928
+ TANS770101 0.918 ROBB760101 0.914 CRAJ730101 0.891
+ PALJ810102 0.889 MAXF760101 0.889 ISOY800101 0.882
+ CHOP780201 0.881 RACS820108 0.872 BURA740101 0.850
+ GEIM800104 0.841 KANM800103 0.836 NAGK730103 -0.808
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.30 0.93 0.90 1.02 0.92 1.04 1.43 0.63 1.33 0.87
+ 1.30 1.23 1.32 1.09 0.63 0.78 0.80 1.03 0.71 0.95
+//
+H PALJ810102
+D Normalized frequency of alpha-helix from CF (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C CHOP780201 0.981 ISOY800101 0.965 KANM800101 0.962
+ MAXF760101 0.959 ROBB760101 0.946 TANS770101 0.923
+ KANM800103 0.916 GEIM800101 0.910 LEVM780104 0.906
+ PRAM900102 0.902 LEVM780101 0.902 BURA740101 0.900
+ PALJ810101 0.889 AURR980112 0.888 GEIM800104 0.886
+ RACS820108 0.881 AURR980109 0.877 NAGK730101 0.876
+ CRAJ730101 0.872 AURR980108 0.871 QIAN880106 0.871
+ PALJ810109 0.864 QIAN880107 0.856 AURR980114 0.848
+ AURR980111 0.830 AURR980115 0.827 AURR980110 0.812
+ BEGF750101 0.811 CHAM830101 -0.808 CRAJ730103 -0.809
+ MUNV940101 -0.815 NAGK730103 -0.818 MUNV940102 -0.824
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.32 1.04 0.74 0.97 0.70 1.25 1.48 0.59 1.06 1.01
+ 1.22 1.13 1.47 1.10 0.57 0.77 0.86 1.02 0.72 1.05
+//
+H PALJ810103
+D Normalized frequency of beta-sheet from LG (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C LEVM780105 0.980 GEIM800105 0.945 CHOP780202 0.937
+ KANM800102 0.932 LIFS790101 0.912 PALJ810104 0.907
+ GEIM800107 0.890 ROBB760106 0.886 QIAN880120 0.886
+ LIFS790103 0.877 QIAN880121 0.875 ROBB760105 0.869
+ PTIO830102 0.867 QIAN880119 0.861 PRAM900103 0.846
+ LEVM780102 0.846 QIAN880118 0.845 PALJ810112 0.841
+ TANS770103 0.824 KANM800104 0.823 ISOY800102 0.807
+ MUNV940103 -0.857
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.81 1.03 0.81 0.71 1.12 1.03 0.59 0.94 0.85 1.47
+ 1.03 0.77 0.96 1.13 0.75 1.02 1.19 1.24 1.35 1.44
+//
+H PALJ810104
+D Normalized frequency of beta-sheet from CF (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C CHOP780202 0.970 KANM800102 0.948 PTIO830102 0.937
+ LIFS790101 0.929 GEIM800107 0.928 LEVM780105 0.921
+ QIAN880121 0.910 PALJ810103 0.907 ROBB760106 0.894
+ QIAN880120 0.886 BASU050103 0.882 BASU050101 0.873
+ LEVM780102 0.868 PRAM900103 0.868 NAGK730102 0.867
+ LIFS790103 0.860 PONP930101 0.857 GEIM800105 0.856
+ KANM800104 0.851 CHOP780209 0.849 PALJ810112 0.849
+ ROBB760105 0.835 VENT840101 0.831 BASU050102 0.826
+ QIAN880119 0.822 AVBF000101 0.818 CRAJ730102 0.817
+ SWER830101 0.809 CORJ870102 0.809 NISK860101 0.809
+ MANP780101 0.805 BEGF750102 0.801 VINM940101 -0.801
+ MIYS990104 -0.810 MIYS990103 -0.811 MUNV940103 -0.888
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.90 0.75 0.82 0.75 1.12 0.95 0.44 0.83 0.86 1.59
+ 1.24 0.75 0.94 1.41 0.46 0.70 1.20 1.28 1.45 1.73
+//
+H PALJ810105
+D Normalized frequency of turn from LG (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C ISOY800103 0.928 LEVM780103 0.909 PRAM900104 0.906
+ LEVM780106 0.902 PALJ810116 0.891 CHOP780216 0.881
+ CHOP780203 0.878 GEIM800108 0.873 CHOP780101 0.868
+ TANS770110 0.860 GEIM800111 0.855 QIAN880133 0.843
+ QIAN880132 0.830 CHAM830101 0.826 PALJ810106 0.809
+ NAGK730103 0.804 CHOP780210 0.803 AVBF000102 -0.815
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.84 0.91 1.48 1.28 0.69 1. 0.78 1.76 0.53 0.55
+ 0.49 0.95 0.52 0.88 1.47 1.29 1.05 0.88 1.28 0.51
+//
+H PALJ810106
+D Normalized frequency of turn from CF (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C CHOP780101 0.977 CHAM830101 0.939 TANS770110 0.925
+ CHOP780203 0.907 CHOP780210 0.905 CHOP780216 0.904
+ ROBB760113 0.895 CRAJ730103 0.884 ROBB760108 0.882
+ ROBB760110 0.864 GEIM800108 0.862 QIAN880133 0.860
+ BEGF750103 0.859 QIAN880132 0.859 LEVM780106 0.850
+ LEVM780103 0.848 GEIM800111 0.844 PRAM900104 0.844
+ QIAN880131 0.809 PALJ810105 0.809 ISOY800103 0.807
+ CHOP780212 0.801 QIAN880107 -0.821 SUEM840101 -0.832
+ KANM800103 -0.840 AURR980114 -0.842 AURR980109 -0.845
+ BEGF750101 -0.859
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.65 0.93 1.45 1.47 1.43 0.94 0.75 1.53 0.96 0.57
+ 0.56 0.95 0.71 0.72 1.51 1.46 0.96 0.90 1.12 0.55
+//
+H PALJ810107
+D Normalized frequency of alpha-helix in all-alpha class (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C GEIM800102 0.919 GEIM800109 -0.909
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.08 0.93 1.05 0.86 1.22 0.95 1.09 0.85 1.02 0.98
+ 1.04 1.01 1.11 0.96 0.91 0.95 1.15 1.17 0.80 1.03
+//
+H PALJ810108
+D Normalized frequency of alpha-helix in alpha+beta class (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.34 0.91 0.83 1.06 1.27 1.13 1.69 0.47 1.11 0.84
+ 1.39 1.08 0.90 1.02 0.48 1.05 0.74 0.64 0.73 1.18
+//
+H PALJ810109
+D Normalized frequency of alpha-helix in alpha/beta class (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C GEIM800104 0.937 PRAM900102 0.898 LEVM780101 0.898
+ MAXF760101 0.876 ISOY800101 0.874 PALJ810102 0.864
+ KANM800101 0.849 LEVM780104 0.819 AURR980112 0.817
+ GEIM800101 0.816 CHOP780201 0.814 CRAJ730101 0.811
+ ROBB760101 0.805
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.15 1.06 0.87 1. 1.03 1.43 1.37 0.64 0.95 0.99
+ 1.22 1.20 1.45 0.92 0.72 0.84 0.97 1.11 0.72 0.82
+//
+H PALJ810110
+D Normalized frequency of beta-sheet in all-beta class (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C GEIM800106 0.851 ROBB760106 0.836 KANM800102 0.836
+ BEGF750102 0.834 GEIM800107 0.826 QIAN880120 0.824
+ QIAN880119 0.824 LIFS790101 0.817 AVBF000101 0.816
+ CHOP780202 0.808 ROBB760105 0.804 GEIM800110 -0.840
+ MUNV940103 -0.845
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.89 1.06 0.67 0.71 1.04 1.06 0.72 0.87 1.04 1.14
+ 1.02 1. 1.41 1.32 0.69 0.86 1.15 1.06 1.35 1.66
+//
+H PALJ810111
+D Normalized frequency of beta-sheet in alpha+beta class (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.82 0.99 1.27 0.98 0.71 1.01 0.54 0.94 1.26 1.67
+ 0.94 0.73 1.30 1.56 0.69 0.65 0.98 1.25 1.26 1.22
+//
+H PALJ810112
+D Normalized frequency of beta-sheet in alpha/beta class (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C PRAM900103 0.913 LEVM780102 0.913 GEIM800107 0.905
+ LEVM780105 0.870 KANM800102 0.869 PALJ810104 0.849
+ LIFS790101 0.845 PALJ810103 0.841 GEIM800105 0.830
+ CHOP780202 0.815 KANM800104 0.813 QIAN880121 0.812
+ PTIO830102 0.811 MUNV940103 -0.830
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.98 1.03 0.66 0.74 1.01 0.63 0.59 0.90 1.17 1.38
+ 1.05 0.83 0.82 1.23 0.73 0.98 1.20 1.26 1.23 1.62
+//
+H PALJ810113
+D Normalized frequency of turn in all-alpha class (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+ (Arg Cys Leu Trp missing)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.69 0. 1.52 2.42 0. 1.44 0.63 2.64 0.22 0.43
+ 0. 1.18 0.88 2.20 1.34 1.43 0.28 0. 1.53 0.14
+//
+H PALJ810114
+D Normalized frequency of turn in all-beta class (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+ (Met missing)
+C ISOY800103 0.809
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.87 1.30 1.36 1.24 0.83 1.06 0.91 1.69 0.91 0.27
+ 0.67 0.66 0. 0.47 1.54 1.08 1.12 1.24 0.54 0.69
+//
+H PALJ810115
+D Normalized frequency of turn in alpha+beta class (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C ROBB760112 0.885 QIAN880132 0.804
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.91 0.77 1.32 0.90 0.50 1.06 0.53 1.61 1.08 0.36
+ 0.77 1.27 0.76 0.37 1.62 1.34 0.87 1.10 1.24 0.52
+//
+H PALJ810116
+D Normalized frequency of turn in alpha/beta class (Palau et al., 1981)
+R PMID:7118409
+A Palau, J., Argos, P. and Puigdomenech, P.
+T Protein secondary structure
+J Int. J. Peptide Protein Res. 19, 394-401 (1981) LG :a set of protein samples
+ formed by 44 proteins. CF :a set of protein samples formed by 33 proteins.
+C PALJ810105 0.891 ISOY800103 0.814
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.92 0.90 1.57 1.22 0.62 0.66 0.92 1.61 0.39 0.79
+ 0.50 0.86 0.50 0.96 1.30 1.40 1.11 0.57 1.78 0.50
+//
+H PARJ860101
+D HPLC parameter (Parker et al., 1986)
+R PMID:2430611
+A Parker, J.M.R., Guo, D. and Hodges, R.S.
+T New hydrophilicity scale derived from high-performance liquid chromatography
+ peptide retention data: Correlation of predicted surface residues with
+ antigencity and x-ray-derived accessible sites
+J Biochemistry 25, 5425-5432 (1986)
+C WOLS870101 0.964 MIYS990101 0.944 MIYS990102 0.942
+ BULH740101 0.909 MEIH800101 0.905 GUYH850103 0.897
+ GRAR740102 0.891 OOBM770103 0.891 MIYS990105 0.878
+ MIYS990104 0.877 RACS770101 0.871 PUNT030102 0.867
+ MIYS990103 0.859 PUNT030101 0.845 VINM940101 0.837
+ GUYH850102 0.836 RACS770102 0.834 VINM940102 0.833
+ MEIH800102 0.831 CORJ870108 0.831 FASG890101 0.825
+ WOEC730101 0.821 HOPT810101 0.819 PARS000101 0.812
+ KIDA850101 0.809 LEVM760101 0.806 ROSM880101 0.803
+ ROSM880102 0.801 WIMW960101 -0.804 MEEJ800101 -0.806
+ CORJ870103 -0.807 MEIH800103 -0.808 NAKH900110 -0.808
+ CORJ870106 -0.820 CORJ870104 -0.823 ROSG850102 -0.823
+ SIMZ760101 -0.825 GOLD730101 -0.827 LEVM760106 -0.832
+ JOND750101 -0.834 ARGP820101 -0.835 CORJ870105 -0.837
+ CORJ870107 -0.838 MANP780101 -0.841 PONP930101 -0.846
+ VENT840101 -0.846 BROC820101 -0.849 ZHOH040102 -0.854
+ RADA880108 -0.865 PONP800107 -0.868 WERD780101 -0.869
+ TAKK010101 -0.870 BLAS910101 -0.870 CIDH920101 -0.871
+ ROSM880105 -0.871 BASU050103 -0.874 BIOV880102 -0.875
+ EISD860101 -0.876 RADA880102 -0.883 ZIMJ680105 -0.886
+ BIOV880101 -0.889 CORJ870102 -0.892 SWER830101 -0.893
+ ROBB790101 -0.893 ROSM880104 -0.896 ZHOH040103 -0.897
+ MEEJ810102 -0.897 BASU050101 -0.897 NOZY710101 -0.900
+ MEEJ800102 -0.902 FAUJ830101 -0.907 BASU050102 -0.908
+ ZHOH040101 -0.912 CIDH920104 -0.913 NISK860101 -0.916
+ CIDH920103 -0.916 MEEJ810101 -0.920 GUOD860101 -0.925
+ MIYS850101 -0.929 CIDH920102 -0.930 CIDH920105 -0.948
+ PLIV810101 -0.958
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.1 4.2 7.0 10.0 1.4 6.0 7.8 5.7 2.1 -8.0
+ -9.2 5.7 -4.2 -9.2 2.1 6.5 5.2 -10.0 -1.9 -3.7
+//
+H PLIV810101
+D Partition coefficient (Pliska et al., 1981)
+R
+A Pliska, V., Schmidt, M. and Fauchere, J.L.
+T Partition coefficients of amino acids and hydrophobic parameters pi of their
+ side-chains as measured by thin-layer chromatography
+J J. Chromatogr. 216, 79-92 (1981) (Arg 0.25)
+C MIYS850101 0.944 GUOD860101 0.943 FAUJ830101 0.931
+ MEEJ810101 0.914 CIDH920105 0.914 RADA880108 0.906
+ EISD860101 0.904 CIDH920103 0.899 BIOV880101 0.899
+ MEEJ810102 0.898 CIDH920104 0.893 NISK860101 0.892
+ ZHOH040103 0.889 BASU050103 0.880 BASU050101 0.879
+ CIDH920102 0.877 BASU050102 0.876 SWER830101 0.875
+ ZIMJ680105 0.875 ROBB790101 0.875 CORJ870102 0.873
+ BLAS910101 0.871 MEEJ800102 0.867 ROSM880104 0.866
+ PONP800107 0.866 ZHOH040101 0.864 ROSM880105 0.862
+ BIOV880102 0.858 COWR900101 0.857 MANP780101 0.856
+ EISD860103 0.852 RADA880102 0.845 CIDH920101 0.843
+ WERD780101 0.841 ROSG850102 0.841 NOZY710101 0.839
+ LEVM760106 0.830 CORJ870107 0.829 CORJ870105 0.827
+ TAKK010101 0.822 CORJ870104 0.821 CORJ870106 0.820
+ ARGP820101 0.820 PONP930101 0.819 JOND750101 0.819
+ MEIH800103 0.811 ZHOH040102 0.809 PONP800101 0.806
+ NADH010104 0.806 SIMZ760101 0.805 NADH010103 0.804
+ PONP800103 0.802 LEVM760101 -0.801 GUYH850102 -0.802
+ FUKS010103 -0.805 VINM940102 -0.808 ROSM880101 -0.834
+ GUYH850101 -0.836 CORJ870108 -0.838 KIDA850101 -0.841
+ MEIH800102 -0.849 OOBM770103 -0.852 FASG890101 -0.858
+ PUNT030102 -0.858 RACS770102 -0.859 PUNT030101 -0.860
+ MIYS990103 -0.861 ROSM880102 -0.864 RACS770101 -0.868
+ MIYS990104 -0.869 MIYS990105 -0.869 GUYH850103 -0.881
+ GRAR740102 -0.888 MEIH800101 -0.896 BULH740101 -0.912
+ MIYS990102 -0.942 MIYS990101 -0.944 PARJ860101 -0.958
+ WOLS870101 -0.963
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -2.89 -3.30 -3.41 -3.38 -2.49 -3.15 -2.94 -3.25 -2.84 -1.72
+ -1.61 -3.31 -1.84 -1.63 -2.50 -3.30 -2.91 -1.75 -2.42 -2.08
+//
+H PONP800101
+D Surrounding hydrophobicity in folded form (Ponnuswamy et al., 1980)
+R PMID:7397216
+A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P.
+T Hydrophobic packing and spatial arrangement of amino acid residues in
+ globular proteins
+J Biochim. Biophys. Acta 623, 301-316 (1980)
+C PONP800102 0.990 MANP780101 0.963 NISK800101 0.960
+ PONP800103 0.957 PONP930101 0.945 CORJ870101 0.939
+ PONP800108 0.938 ROSG850102 0.938 RADA880108 0.934
+ NISK860101 0.930 CORJ870107 0.923 BIOV880101 0.918
+ CORJ870103 0.917 BASU050103 0.915 CORJ870104 0.913
+ NADH010103 0.894 MIYS850101 0.892 NADH010104 0.892
+ CIDH920104 0.888 CORJ870106 0.887 BASU050101 0.882
+ WERD780101 0.880 CIDH920103 0.876 NADH010102 0.875
+ CASG920101 0.874 PONP800106 0.871 MEIH800103 0.869
+ CORJ870105 0.867 JANJ790101 0.866 BIOV880102 0.860
+ DESM900102 0.858 JURD980101 0.858 CIDH920105 0.856
+ NADH010105 0.853 KYTJ820101 0.851 JANJ780102 0.851
+ BASU050102 0.848 DESM900101 0.847 ZHOH040103 0.847
+ CHOC760103 0.830 ROBB760106 0.829 KANM800102 0.829
+ NADH010101 0.826 ROBB760105 0.823 KANM800104 0.823
+ LIFS790101 0.823 FAUJ830101 0.822 ROBB790101 0.822
+ PTIO830102 0.819 QIAN880121 0.815 BAEK050101 0.812
+ PLIV810101 0.806 CIDH920101 0.805 LIFS790102 0.804
+ QIAN880122 0.801 PUNT030101 -0.800 FUKS010103 -0.801
+ KRIW790102 -0.804 VINM940103 -0.813 MUNV940103 -0.819
+ GUYH850103 -0.822 PUNT030102 -0.827 OOBM770101 -0.835
+ VINM940102 -0.845 OOBM770103 -0.848 GRAR740102 -0.849
+ KRIW710101 -0.850 RACS770101 -0.863 RACS770102 -0.870
+ GUYH850102 -0.873 MEIH800102 -0.877 GUYH850101 -0.877
+ VINM940101 -0.878 MIYS990101 -0.883 MIYS990102 -0.886
+ KRIW790101 -0.888 MEIH800101 -0.888 KARP850102 -0.889
+ MIYS990105 -0.918 MIYS990104 -0.924 CORJ870108 -0.928
+ FASG890101 -0.932 MIYS990103 -0.940
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 12.28 11.49 11.00 10.97 14.93 11.28 11.19 12.01 12.84 14.77
+ 14.10 10.80 14.33 13.43 11.19 11.26 11.65 12.95 13.29 15.07
+//
+H PONP800102
+D Average gain in surrounding hydrophobicity (Ponnuswamy et al., 1980)
+R PMID:7397216
+A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P.
+T Hydrophobic packing and spatial arrangement of amino acid residues in
+ globular proteins
+J Biochim. Biophys. Acta 623, 301-316 (1980)
+C PONP800101 0.990 PONP800103 0.986 NISK800101 0.965
+ CORJ870101 0.954 ROSG850102 0.949 PONP800108 0.948
+ MANP780101 0.945 RADA880108 0.938 PONP930101 0.934
+ BIOV880101 0.926 NISK860101 0.924 NADH010103 0.919
+ NADH010104 0.917 CORJ870103 0.907 CORJ870107 0.905
+ BASU050103 0.902 NADH010102 0.901 CORJ870104 0.901
+ JANJ790101 0.897 MIYS850101 0.891 CASG920101 0.889
+ MEIH800103 0.885 PONP800106 0.883 WERD780101 0.883
+ DESM900102 0.880 CIDH920104 0.880 JANJ780102 0.875
+ DESM900101 0.871 NADH010105 0.869 JURD980101 0.869
+ BIOV880102 0.867 CORJ870106 0.864 BASU050101 0.864
+ KYTJ820101 0.861 ZHOH040103 0.858 CIDH920103 0.849
+ BASU050102 0.843 CORJ870105 0.841 FAUJ830101 0.841
+ CHOC760103 0.836 NADH010101 0.832 CIDH920105 0.831
+ ROBB760105 0.828 JANJ790102 0.822 ROBB760106 0.822
+ BAEK050101 0.818 KANM800102 0.815 EISD860103 0.814
+ KANM800104 0.813 ROBB790101 0.807 MUNV940103 -0.802
+ GUYH850103 -0.808 RACS770103 -0.809 VINM940103 -0.820
+ GUYH850104 -0.824 PUNT030102 -0.827 RACS770101 -0.827
+ KRIW790102 -0.830 VINM940102 -0.842 OOBM770103 -0.854
+ OOBM770101 -0.862 RACS770102 -0.864 MEIH800101 -0.870
+ GRAR740102 -0.871 MIYS990101 -0.874 GUYH850102 -0.874
+ MIYS990102 -0.877 GUYH850101 -0.883 MEIH800102 -0.883
+ VINM940101 -0.883 KARP850102 -0.887 KRIW710101 -0.887
+ CORJ870108 -0.911 KRIW790101 -0.915 MIYS990105 -0.927
+ MIYS990104 -0.930 FASG890101 -0.944 MIYS990103 -0.946
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 7.62 6.81 6.17 6.18 10.93 6.67 6.38 7.31 7.85 9.99
+ 9.37 5.72 9.83 8.99 6.64 6.93 7.08 8.41 8.53 10.38
+//
+H PONP800103
+D Average gain ratio in surrounding hydrophobicity (Ponnuswamy et al., 1980)
+R PMID:7397216
+A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P.
+T Hydrophobic packing and spatial arrangement of amino acid residues in
+ globular proteins
+J Biochim. Biophys. Acta 623, 301-316 (1980)
+C PONP800102 0.986 PONP800101 0.957 ROSG850102 0.947
+ CORJ870101 0.944 NISK800101 0.941 RADA880108 0.934
+ NADH010103 0.932 PONP800108 0.931 BIOV880101 0.926
+ NADH010104 0.926 NADH010102 0.921 MANP780101 0.913
+ NISK860101 0.910 PONP930101 0.909 MIYS850101 0.898
+ DESM900102 0.896 MEIH800103 0.895 CORJ870103 0.889
+ DESM900101 0.887 JANJ790101 0.886 CORJ870107 0.884
+ CORJ870104 0.884 PONP800106 0.883 JANJ780102 0.882
+ JURD980101 0.879 BIOV880102 0.879 BASU050103 0.879
+ CASG920101 0.879 WERD780101 0.876 KYTJ820101 0.870
+ NADH010105 0.866 FAUJ830101 0.863 CIDH920104 0.863
+ ZHOH040103 0.861 JANJ790102 0.844 BASU050101 0.842
+ EISD860103 0.842 CORJ870106 0.840 CHOC760103 0.837
+ NADH010101 0.833 BASU050102 0.828 ROBB760105 0.823
+ CIDH920103 0.823 CORJ870105 0.821 ROBB760106 0.812
+ CIDH920105 0.807 NADH010106 0.803 KANM800102 0.803
+ PLIV810101 0.802 OLSK800101 0.801 PUNT030101 -0.812
+ JANJ780103 -0.812 VINM940103 -0.817 RACS770103 -0.819
+ VINM940102 -0.820 WOEC730101 -0.823 PUNT030102 -0.834
+ GUYH850104 -0.845 KRIW790102 -0.853 GUYH850102 -0.856
+ MEIH800101 -0.856 RACS770102 -0.860 OOBM770103 -0.865
+ KARP850102 -0.870 MIYS990101 -0.871 MIYS990102 -0.875
+ VINM940101 -0.878 OOBM770101 -0.880 GUYH850101 -0.887
+ CORJ870108 -0.889 KRIW710101 -0.890 MEIH800102 -0.891
+ GRAR740102 -0.897 MIYS990105 -0.928 MIYS990104 -0.929
+ KRIW790101 -0.930 FASG890101 -0.936 MIYS990103 -0.943
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.63 2.45 2.27 2.29 3.36 2.45 2.31 2.55 2.57 3.08
+ 2.98 2.12 3.18 3.02 2.46 2.60 2.55 2.85 2.79 3.21
+//
+H PONP800104
+D Surrounding hydrophobicity in alpha-helix (Ponnuswamy et al., 1980)
+R PMID:7397216
+A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P.
+T Hydrophobic packing and spatial arrangement of amino acid residues in
+ globular proteins
+J Biochim. Biophys. Acta 623, 301-316 (1980)
+C CHOC760104 0.844
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 13.65 11.28 12.24 10.98 14.49 11.30 12.55 15.36 11.59 14.63
+ 14.01 11.96 13.40 14.08 11.51 11.26 13.00 12.06 12.64 12.88
+//
+H PONP800105
+D Surrounding hydrophobicity in beta-sheet (Ponnuswamy et al., 1980)
+R PMID:7397216
+A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P.
+T Hydrophobic packing and spatial arrangement of amino acid residues in
+ globular proteins
+J Biochim. Biophys. Acta 623, 301-316 (1980)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 14.60 13.24 11.79 13.78 15.90 12.02 13.59 14.18 15.35 14.10
+ 16.49 13.28 16.23 14.18 14.10 13.36 14.50 13.90 14.76 16.30
+//
+H PONP800106
+D Surrounding hydrophobicity in turn (Ponnuswamy et al., 1980)
+R PMID:7397216
+A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P.
+T Hydrophobic packing and spatial arrangement of amino acid residues in
+ globular proteins
+J Biochim. Biophys. Acta 623, 301-316 (1980)
+C PONP800102 0.883 PONP800103 0.883 PONP800101 0.871
+ CORJ870104 0.842 RADA880108 0.835 CORJ870107 0.834
+ CORJ870103 0.821 MANP780101 0.813 MIYS850101 0.812
+ CORJ870106 0.807 ROSG850102 0.807 MIYS990103 -0.807
+ KARP850102 -0.820 FASG890101 -0.823 GUYH850101 -0.826
+ KRIW710101 -0.841 CORJ870108 -0.859
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 10.67 11.05 10.85 10.21 14.15 11.71 11.71 10.95 12.07 12.95
+ 13.07 9.93 15.00 13.27 10.62 11.18 10.53 11.41 11.52 13.86
+//
+H PONP800107
+D Accessibility reduction ratio (Ponnuswamy et al., 1980)
+R PMID:7397216
+A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P.
+T Hydrophobic packing and spatial arrangement of amino acid residues in
+ globular proteins
+J Biochim. Biophys. Acta 623, 301-316 (1980)
+C MIYS850101 0.884 MANP780101 0.871 PLIV810101 0.866
+ GUOD860101 0.854 PONP930101 0.851 LIFS790102 0.849
+ NISK860101 0.847 PTIO830102 0.837 CIDH920103 0.833
+ CIDH920104 0.832 BASU050101 0.825 CIDH920105 0.818
+ BIOV880101 0.816 BIOV880102 0.814 CHOC760103 0.813
+ CORJ870105 0.812 BASU050103 0.812 VENT840101 0.805
+ CORJ870107 0.805 BEGF750102 0.803 ROSG850102 0.803
+ LIFS790101 0.801 RADA880108 0.800 CORJ870106 0.800
+ PUNT030101 -0.804 CHOP780203 -0.818 OOBM770103 -0.819
+ CHOP780210 -0.820 WOLS870101 -0.852 MEIH800102 -0.858
+ PARJ860101 -0.868 MIYS990101 -0.877 RACS770102 -0.878
+ MIYS990102 -0.879 RACS770101 -0.905 MEIH800101 -0.909
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 3.70 2.53 2.12 2.60 3.03 2.70 3.30 3.13 3.57 7.69
+ 5.88 1.79 5.21 6.60 2.12 2.43 2.60 6.25 3.03 7.14
+//
+H PONP800108
+D Average number of surrounding residues (Ponnuswamy et al., 1980)
+R PMID:7397216
+A Ponnuswamy, P.K., Prabhakaran, M. and Manavalan, P.
+T Hydrophobic packing and spatial arrangement of amino acid residues in
+ globular proteins
+J Biochim. Biophys. Acta 623, 301-316 (1980)
+C NISK800101 0.976 CORJ870101 0.969 PONP800102 0.948
+ PONP930101 0.944 PONP800101 0.938 MANP780101 0.935
+ PONP800103 0.931 BASU050103 0.921 NISK860101 0.921
+ ROSG850102 0.919 CIDH920104 0.909 BIOV880101 0.907
+ NADH010103 0.907 NADH010104 0.902 CASG920101 0.901
+ BASU050101 0.894 NADH010102 0.890 RADA880108 0.889
+ ZHOH040103 0.887 JANJ790101 0.881 BASU050102 0.880
+ FAUJ830101 0.875 CORJ870103 0.873 JANJ780102 0.863
+ MEIH800103 0.862 CORJ870104 0.861 CORJ870107 0.859
+ JURD980101 0.856 BIOV880102 0.854 KYTJ820101 0.850
+ KANM800102 0.849 KANM800104 0.849 MIYS850101 0.847
+ NADH010105 0.845 WERD780101 0.843 CIDH920105 0.843
+ CIDH920103 0.841 DESM900102 0.833 BAEK050101 0.833
+ ROBB790101 0.831 LIFS790101 0.828 NADH010101 0.820
+ ROBB760105 0.820 GEIM800107 0.817 CORJ870106 0.813
+ QIAN880122 0.811 BLAS910101 0.810 EISD860103 0.809
+ CHOC760103 0.809 CHOP780202 0.809 ROSM880105 0.808
+ ROBB760106 0.808 QIAN880121 0.802 JANJ790102 0.802
+ CORJ870105 0.801 GUYH850104 -0.807 MEIH800101 -0.825
+ GUYH850103 -0.828 WOEC730101 -0.831 MEIH800102 -0.836
+ OOBM770101 -0.851 CORJ870108 -0.853 PUNT030102 -0.855
+ KRIW790101 -0.860 MIYS990101 -0.866 MIYS990102 -0.869
+ VINM940102 -0.871 GUYH850102 -0.873 VINM940101 -0.891
+ OOBM770103 -0.896 GRAR740102 -0.907 FASG890101 -0.913
+ MIYS990104 -0.918 MIYS990103 -0.920 MIYS990105 -0.927
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.05 5.70 5.04 4.95 7.86 5.45 5.10 6.16 5.80 7.51
+ 7.37 4.88 6.39 6.62 5.65 5.53 5.81 6.98 6.73 7.62
+//
+H PRAM820101
+D Intercept in regression analysis (Prabhakaran-Ponnuswamy, 1982)
+R
+A Prabhakaran, M. and Ponnuswamy, P.K.
+T Shape and surface features of globular proteins
+J Macromolecules 15, 314-320 (1982) Regression analysis of solvent contact area
+ and spatial position
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.305 0.227 0.322 0.335 0.339 0.306 0.282 0.352 0.215 0.278
+ 0.262 0.391 0.280 0.195 0.346 0.326 0.251 0.291 0.293 0.291
+//
+H PRAM820102
+D Slope in regression analysis x 1.0E1 (Prabhakaran-Ponnuswamy, 1982)
+R
+A Prabhakaran, M. and Ponnuswamy, P.K.
+T Shape and surface features of globular proteins
+J Macromolecules 15, 314-320 (1982) Regression analysis of solvent contact area
+ and spatial position
+C LEVM760104 0.812 PRAM820103 0.802
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.175 0.083 0.090 0.140 0.074 0.093 0.135 0.201 0.125 0.100
+ 0.104 0.058 0.054 0.104 0.136 0.155 0.152 0.092 0.081 0.096
+//
+H PRAM820103
+D Correlation coefficient in regression analysis (Prabhakaran-Ponnuswamy, 1982)
+R
+A Prabhakaran, M. and Ponnuswamy, P.K.
+T Shape and surface features of globular proteins
+J Macromolecules 15, 314-320 (1982) Regression analysis of solvent contact area
+ and spatial position
+C PRAM820102 0.802
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.687 0.590 0.489 0.632 0.263 0.527 0.669 0.670 0.594 0.564
+ 0.541 0.407 0.328 0.577 0.600 0.692 0.713 0.632 0.495 0.529
+//
+H PRAM900101
+D Hydrophobicity (Prabhakaran, 1990)
+R PMID:2390062
+A Prabhakaran, M.
+T The distribution of physical, chemical and conformational properties in
+ signal and nascent peptides
+J Biochem. J. 269, 691-696 (1990) Original references: Engelman, D.M., Steitz,
+ T.A. and Terwilliger, T.C. Annu. Rev. Biophys. Chem. 15, 321-353 (1986)
+C ENGD860101 1.000 ROSM880101 0.917 VHEG790101 0.909
+ KUHL950101 0.908 OOBM770101 0.907 JANJ780101 0.901
+ ROSM880102 0.892 PUNT030101 0.889 JANJ780103 0.884
+ HOPT810101 0.881 GUYH850104 0.881 LEVM760101 0.881
+ WOEC730101 0.871 PUNT030102 0.869 GUYH850105 0.867
+ KIDA850101 0.866 GRAR740102 0.855 ZIMJ680103 0.854
+ CHOC760102 0.826 MONM990101 0.820 GUYH850101 0.820
+ FAUJ880109 0.815 RADA880104 -0.803 OLSK800101 -0.806
+ CHOC760103 -0.814 NADH010103 -0.815 WARP780101 -0.827
+ EISD860103 -0.831 NADH010101 -0.843 KYTJ820101 -0.850
+ FAUJ830101 -0.853 JANJ780102 -0.860 EISD860101 -0.862
+ JURD980101 -0.862 BLAS910101 -0.864 RADA880107 -0.865
+ NADH010102 -0.870 WOLR790101 -0.877 WOLR810101 -0.887
+ JANJ790102 -0.890 DESM900102 -0.890 ROSM880105 -0.912
+ RADA880101 -0.932 EISD840101 -0.936 JACR890101 -0.948
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -6.70 51.50 20.10 38.50 -8.40 17.20 34.30 -4.20 12.60 -13.
+ -11.70 36.80 -14.20 -15.50 0.80 -2.50 -5. -7.90 2.90 -10.90
+//
+H PRAM900102
+D Relative frequency in alpha-helix (Prabhakaran, 1990)
+R PMID:2390062
+A Prabhakaran, M.
+T The distribution of physical, chemical and conformational properties in
+ signal and nascent peptides
+J Biochem. J. 269, 691-696 (1990) Original reference of these three data:
+ Creighton, T.E. In "Protein Structure and Melecular Properties", (Freeman,
+ W.H., ed.), San Francisco P.235 (1983)
+C LEVM780101 1.000 LEVM780104 0.964 PALJ810101 0.943
+ KANM800101 0.942 ISOY800101 0.929 MAXF760101 0.924
+ ROBB760101 0.916 GEIM800101 0.912 GEIM800104 0.907
+ RACS820108 0.904 PALJ810102 0.902 PALJ810109 0.898
+ NAGK730101 0.894 CRAJ730101 0.887 CHOP780201 0.873
+ TANS770101 0.854 KANM800103 0.850 QIAN880107 0.829
+ QIAN880106 0.827 BURA740101 0.805 NAGK730103 -0.809
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.29 0.96 0.90 1.04 1.11 1.27 1.44 0.56 1.22 0.97
+ 1.30 1.23 1.47 1.07 0.52 0.82 0.82 0.99 0.72 0.91
+//
+H PRAM900103
+D Relative frequency in beta-sheet (Prabhakaran, 1990)
+R PMID:2390062
+A Prabhakaran, M.
+T The distribution of physical, chemical and conformational properties in
+ signal and nascent peptides
+J Biochem. J. 269, 691-696 (1990) Original reference of these three data:
+ Creighton, T.E. In "Protein Structure and Melecular Properties", (Freeman,
+ W.H., ed.), San Francisco P.235 (1983)
+C LEVM780102 1.000 PALJ810112 0.913 LEVM780105 0.899
+ PALJ810104 0.868 PTIO830102 0.865 LIFS790101 0.864
+ QIAN880120 0.858 KANM800102 0.856 PALJ810103 0.846
+ GEIM800107 0.842 BEGF750102 0.834 QIAN880119 0.834
+ CHOP780202 0.833 AVBF000101 0.815 QIAN880121 0.805
+ MUNV940103 -0.848
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.90 0.99 0.76 0.72 0.74 0.80 0.75 0.92 1.08 1.45
+ 1.02 0.77 0.97 1.32 0.64 0.95 1.21 1.14 1.25 1.49
+//
+H PRAM900104
+D Relative frequency in reverse-turn (Prabhakaran, 1990)
+R PMID:2390062
+A Prabhakaran, M.
+T The distribution of physical, chemical and conformational properties in
+ signal and nascent peptides
+J Biochem. J. 269, 691-696 (1990) Original reference of these three data:
+ Creighton, T.E. In "Protein Structure and Melecular Properties", (Freeman,
+ W.H., ed.), San Francisco P.235 (1983)
+C LEVM780103 1.000 LEVM780106 0.983 GEIM800111 0.954
+ CHOP780216 0.951 QIAN880133 0.947 QIAN880134 0.934
+ ISOY800103 0.934 QIAN880132 0.932 GEIM800108 0.931
+ CHOP780203 0.928 CHAM830101 0.909 PALJ810105 0.906
+ QIAN880135 0.903 CHOP780101 0.891 TANS770110 0.873
+ CHOP780210 0.850 PALJ810106 0.844 RACS770101 0.809
+ KANM800103 -0.814 AURR980109 -0.815 QIAN880108 -0.819
+ QIAN880107 -0.829 AVBF000102 -0.834 ROBB760103 -0.840
+ FAUJ880102 -0.844 QIAN880109 -0.846 PTIO830101 -0.858
+ SUEM840101 -0.865
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.78 0.88 1.28 1.41 0.80 0.97 1. 1.64 0.69 0.51
+ 0.59 0.96 0.39 0.58 1.91 1.33 1.03 0.75 1.05 0.47
+//
+H PTIO830101
+D Helix-coil equilibrium constant (Ptitsyn-Finkelstein, 1983)
+R PMID:6673754
+A Ptitsyn, O.B. and Finkelstein, A.V.
+T Theory of protein secondary structure and algorithm of its prediction
+J Biopolymers 22, 15-25 (1983) Charged state for Arg, His, Lys, Asp, and Glu
+C ROBB760103 0.903 QIAN880109 0.886 QIAN880108 0.884
+ SUEM840101 0.877 BLAM930101 0.868 QIAN880111 0.857
+ ONEK900101 0.847 QIAN880107 0.846 QIAN880110 0.835
+ AURR980113 0.833 FAUJ880102 0.832 FINA770101 0.826
+ AURR980109 0.820 ROBB760104 0.817 AURR980114 0.809
+ MUNV940104 -0.807 QIAN880131 -0.826 ONEK900102 -0.830
+ ISOY800104 -0.832 MUNV940105 -0.833 QIAN880132 -0.833
+ CHOP780213 -0.835 GEIM800108 -0.840 CHAM830101 -0.841
+ MUNV940102 -0.844 LEVM780106 -0.854 CHOP780216 -0.855
+ PRAM900104 -0.858 LEVM780103 -0.860 QIAN880133 -0.864
+ GEIM800111 -0.876 MUNV940101 -0.880 QIAN880135 -0.899
+ QIAN880134 -0.920
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.10 0.95 0.80 0.65 0.95 1.00 1.00 0.60 0.85 1.10
+ 1.25 1.00 1.15 1.10 0.10 0.75 0.75 1.10 1.10 0.95
+//
+H PTIO830102
+D Beta-coil equilibrium constant (Ptitsyn-Finkelstein, 1983)
+R PMID:6673754
+A Ptitsyn, O.B. and Finkelstein, A.V.
+T Theory of protein secondary structure and algorithm of its prediction
+J Biopolymers 22, 15-25 (1983) Charged state for Arg, His, Lys, Asp, and Glu
+C LIFS790101 0.941 PALJ810104 0.937 KANM800102 0.917
+ CHOP780202 0.913 QIAN880120 0.908 BASU050101 0.903
+ LEVM780105 0.894 BASU050103 0.888 ROBB760106 0.882
+ QIAN880121 0.880 PONP930101 0.879 ROBB760105 0.878
+ LIFS790102 0.874 PALJ810103 0.867 QIAN880119 0.865
+ LEVM780102 0.865 PRAM900103 0.865 AVBF000101 0.861
+ MANP780101 0.861 KANM800104 0.858 SWER830101 0.856
+ CORJ870102 0.854 GEIM800107 0.850 BASU050102 0.848
+ VENT840101 0.842 CIDH920104 0.842 PONP800107 0.837
+ NISK860101 0.825 LIFS790103 0.822 CRAJ730102 0.820
+ PONP800101 0.819 CHOP780209 0.814 ZHOH040103 0.813
+ CIDH920105 0.813 NAGK730102 0.811 PALJ810112 0.811
+ GEIM800105 0.810 CORJ870107 0.810 CORJ870106 0.809
+ CIDH920103 0.807 BEGF750102 0.807 MIYS850101 0.807
+ OOBM770103 -0.801 KRIW790101 -0.801 CORJ870108 -0.812
+ MIYS990104 -0.818 MIYS990103 -0.820 MEIH800101 -0.828
+ MIYS990101 -0.833 MIYS990102 -0.834 MUNV940103 -0.903
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.00 0.70 0.60 0.50 1.90 1.00 0.70 0.30 0.80 4.00
+ 2.00 0.70 1.90 3.10 0.20 0.90 1.70 2.20 2.80 4.00
+//
+H QIAN880101
+D Weights for alpha-helix at the window position of -6 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.12 0.04 -0.10 0.01 -0.25 -0.03 -0.02 -0.02 -0.06 -0.07
+ 0.05 0.26 0.00 0.05 -0.19 -0.19 -0.04 -0.06 -0.14 -0.03
+//
+H QIAN880102
+D Weights for alpha-helix at the window position of -5 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.26 -0.14 -0.03 0.15 -0.15 -0.13 0.21 -0.37 0.10 -0.03
+ -0.02 0.12 0.00 0.12 -0.08 0.01 -0.34 -0.01 -0.29 0.02
+//
+H QIAN880103
+D Weights for alpha-helix at the window position of -4 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.64 -0.10 0.09 0.33 0.03 -0.23 0.51 -0.09 -0.23 -0.22
+ 0.41 -0.17 0.13 -0.03 -0.43 -0.10 -0.07 -0.02 -0.38 -0.01
+//
+H QIAN880104
+D Weights for alpha-helix at the window position of -3 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880106 0.851 QIAN880105 0.824 AURR980108 0.815
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.29 -0.03 -0.04 0.11 -0.05 0.26 0.28 -0.67 -0.26 0.00
+ 0.47 -0.19 0.27 0.24 -0.34 -0.17 -0.20 0.25 -0.30 -0.01
+//
+H QIAN880105
+D Weights for alpha-helix at the window position of -2 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C ROBB760101 0.874 QIAN880106 0.846 CHOP780201 0.835
+ AURR980113 0.833 BEGF750101 0.833 QIAN880107 0.829
+ ISOY800101 0.828 KANM800101 0.827 QIAN880104 0.824
+ RACS820108 0.820 KANM800103 0.820 ROBB760103 0.811
+ MAXF760101 0.811 CHAM830101 -0.803 MUNV940102 -0.816
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.68 -0.22 -0.09 -0.02 -0.15 -0.15 0.44 -0.73 -0.14 -0.08
+ 0.61 0.03 0.39 0.06 -0.76 -0.26 -0.10 0.20 -0.04 0.12
+//
+H QIAN880106
+D Weights for alpha-helix at the window position of -1 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C ROBB760101 0.904 ISOY800101 0.903 QIAN880107 0.896
+ KANM800103 0.889 MAXF760101 0.881 CHOP780201 0.874
+ PALJ810102 0.871 RACS820108 0.866 AURR980109 0.862
+ ROBB760103 0.854 KANM800101 0.854 QIAN880104 0.851
+ QIAN880105 0.846 AURR980112 0.839 AURR980108 0.838
+ AURR980113 0.835 RICJ880109 0.834 PRAM900102 0.827
+ LEVM780101 0.827 TANS770101 0.819 FINA770101 0.810
+ LEVM780104 0.804 AURR980110 0.804 AURR980114 0.803
+ QIAN880132 -0.813 MUNV940101 -0.835 CHAM830101 -0.856
+ MUNV940102 -0.867
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.34 0.22 -0.33 0.06 -0.18 0.01 0.20 -0.88 -0.09 -0.03
+ 0.20 -0.11 0.43 0.15 -0.81 -0.35 -0.37 0.07 -0.31 0.13
+//
+H QIAN880107
+D Weights for alpha-helix at the window position of 0 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C KANM800103 0.908 QIAN880106 0.896 AURR980109 0.893
+ ROBB760103 0.889 ISOY800101 0.887 MAXF760101 0.885
+ AURR980114 0.876 QIAN880108 0.872 ROBB760101 0.867
+ QIAN880109 0.865 PALJ810102 0.856 KANM800101 0.854
+ QIAN880110 0.853 PTIO830101 0.846 CHOP780201 0.843
+ AURR980113 0.832 RACS820108 0.831 LEVM780101 0.829
+ PRAM900102 0.829 QIAN880105 0.829 LEVM780104 0.822
+ BEGF750101 0.815 AURR980110 0.815 FINA770101 0.814
+ TANS770101 0.804 AURR980108 0.803 SUEM840101 0.803
+ AURR980112 0.802 CHOP780216 -0.808 QIAN880133 -0.809
+ CHOP780101 -0.809 LEVM780106 -0.813 PALJ810106 -0.821
+ PRAM900104 -0.829 LEVM780103 -0.834 CRAJ730103 -0.840
+ CHAM830101 -0.858 MUNV940101 -0.880 MUNV940102 -0.882
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.57 0.23 -0.36 -0.46 -0.15 0.15 0.26 -0.71 -0.05 0.00
+ 0.48 0.16 0.41 0.03 -1.12 -0.47 -0.54 -0.10 -0.35 0.31
+//
+H QIAN880108
+D Weights for alpha-helix at the window position of 1 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880109 0.951 ROBB760103 0.914 QIAN880110 0.901
+ PTIO830101 0.884 ROBB760104 0.879 QIAN880107 0.872
+ ONEK900101 0.866 BLAM930101 0.860 KANM800103 0.829
+ RACS820108 0.820 QIAN880111 0.819 PRAM900104 -0.819
+ LEVM780103 -0.820 QIAN880135 -0.836 MUNV940102 -0.839
+ QIAN880136 -0.843 QIAN880134 -0.845 ISOY800104 -0.847
+ ONEK900102 -0.860 MUNV940101 -0.864
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.33 0.10 -0.19 -0.44 -0.03 0.19 0.21 -0.46 0.27 -0.33
+ 0.57 0.23 0.79 0.48 -1.86 -0.23 -0.33 0.15 -0.19 0.24
+//
+H QIAN880109
+D Weights for alpha-helix at the window position of 2 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880110 0.953 QIAN880108 0.951 QIAN880111 0.912
+ PTIO830101 0.886 ROBB760104 0.871 ROBB760103 0.868
+ QIAN880107 0.865 BLAM930101 0.828 KANM800103 0.824
+ QIAN880112 0.824 ONEK900101 0.824 AURR980114 0.810
+ AURR980109 0.807 CHOP780205 0.806 ONEK900102 -0.800
+ LEVM780106 -0.815 MUNV940101 -0.841 QIAN880134 -0.841
+ PRAM900104 -0.846 LEVM780103 -0.848 QIAN880135 -0.884
+ QIAN880136 -0.927
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.13 0.08 -0.07 -0.71 -0.09 0.12 0.13 -0.39 0.32 0.00
+ 0.50 0.37 0.63 0.15 -1.40 -0.28 -0.21 0.02 -0.10 0.17
+//
+H QIAN880110
+D Weights for alpha-helix at the window position of 3 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880109 0.953 QIAN880111 0.922 QIAN880108 0.901
+ QIAN880107 0.853 PTIO830101 0.835 QIAN880112 0.828
+ KANM800103 0.820 AURR980114 0.819 ROBB760103 0.807
+ ROBB760104 0.806 AURR980109 0.802 QIAN880136 -0.890
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.31 0.18 -0.10 -0.81 -0.26 0.41 -0.06 -0.42 0.51 -0.15
+ 0.56 0.47 0.58 0.10 -1.33 -0.49 -0.44 0.14 -0.08 -0.01
+//
+H QIAN880111
+D Weights for alpha-helix at the window position of 4 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880110 0.922 QIAN880109 0.912 QIAN880112 0.861
+ PTIO830101 0.857 QIAN880108 0.819 QIAN880135 -0.878
+ QIAN880136 -0.900
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.21 0.07 -0.04 -0.58 -0.12 0.13 -0.23 -0.15 0.37 0.31
+ 0.70 0.28 0.61 -0.06 -1.03 -0.28 -0.25 0.21 0.16 0.00
+//
+H QIAN880112
+D Weights for alpha-helix at the window position of 5 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880111 0.861 QIAN880113 0.859 QIAN880110 0.828
+ QIAN880109 0.824 QIAN880136 -0.812
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.18 0.21 -0.03 -0.32 -0.29 -0.27 -0.25 -0.40 0.28 -0.03
+ 0.62 0.41 0.21 0.05 -0.84 -0.05 -0.16 0.32 0.11 0.06
+//
+H QIAN880113
+D Weights for alpha-helix at the window position of 6 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880112 0.859
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.08 0.05 -0.08 -0.24 -0.25 -0.28 -0.19 -0.10 0.29 -0.01
+ 0.28 0.45 0.11 0.00 -0.42 0.07 -0.33 0.36 0.00 -0.13
+//
+H QIAN880114
+D Weights for beta-sheet at the window position of -6 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880115 0.832
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.18 -0.13 0.28 0.05 -0.26 0.21 -0.06 0.23 0.24 -0.42
+ -0.23 0.03 -0.42 -0.18 -0.13 0.41 0.33 -0.10 -0.10 -0.07
+//
+H QIAN880115
+D Weights for beta-sheet at the window position of -5 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880114 0.832
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.01 0.02 0.41 -0.09 -0.27 0.01 0.09 0.13 0.22 -0.27
+ -0.25 0.08 -0.57 -0.12 0.26 0.44 0.35 -0.15 0.15 -0.09
+//
+H QIAN880116
+D Weights for beta-sheet at the window position of -4 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880126 0.823
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.19 0.03 0.02 -0.06 -0.29 0.02 -0.10 0.19 -0.16 -0.08
+ -0.42 -0.09 -0.38 -0.32 0.05 0.25 0.22 -0.19 0.05 -0.15
+//
+H QIAN880117
+D Weights for beta-sheet at the window position of -3 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.14 0.14 -0.27 -0.10 -0.64 -0.11 -0.39 0.46 -0.04 0.16
+ -0.57 0.04 0.24 0.08 0.02 -0.12 0.00 -0.10 0.18 0.29
+//
+H QIAN880118
+D Weights for beta-sheet at the window position of -2 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C PALJ810103 0.845 LEVM780105 0.819 QIAN880119 0.812
+ GEIM800105 0.810 KANM800102 0.801
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.31 0.25 -0.53 -0.54 -0.06 0.07 -0.52 0.37 -0.32 0.57
+ 0.09 -0.29 0.29 0.24 -0.31 0.11 0.03 0.15 0.29 0.48
+//
+H QIAN880119
+D Weights for beta-sheet at the window position of -1 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880120 0.959 LIFS790101 0.929 LEVM780105 0.903
+ ROBB760106 0.897 KANM800102 0.888 LIFS790103 0.877
+ PTIO830102 0.865 QIAN880121 0.862 PALJ810103 0.861
+ ROBB760105 0.859 AVBF000101 0.859 CHOP780202 0.855
+ KANM800104 0.841 PONP930101 0.836 PRAM900103 0.834
+ LEVM780102 0.834 GEIM800105 0.829 OOBM850101 0.825
+ PALJ810110 0.824 PALJ810104 0.822 QIAN880118 0.812
+ BEGF750102 0.811 CORJ870105 0.810 GEIM800107 0.807
+ CHOP780208 0.807 BASU050101 0.805 CORJ870106 0.803
+ LEVM780106 -0.810 GEIM800108 -0.810 CHOP780203 -0.814
+ QIAN880131 -0.830 QIAN880133 -0.849 GEIM800110 -0.853
+ QIAN880132 -0.858 MUNV940103 -0.927
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.10 0.19 -0.89 -0.89 0.13 -0.04 -0.34 -0.45 -0.34 0.95
+ 0.32 -0.46 0.43 0.36 -0.91 -0.12 0.49 0.34 0.42 0.76
+//
+H QIAN880120
+D Weights for beta-sheet at the window position of 0 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C LIFS790101 0.969 QIAN880119 0.959 LIFS790103 0.939
+ QIAN880121 0.935 CHOP780202 0.915 LEVM780105 0.913
+ PTIO830102 0.908 ROBB760106 0.908 KANM800102 0.896
+ PALJ810103 0.886 PALJ810104 0.886 PONP930101 0.879
+ AVBF000101 0.876 CORJ870106 0.866 ROBB760105 0.860
+ PRAM900103 0.858 LEVM780102 0.858 CORJ870105 0.858
+ BASU050101 0.856 GEIM800107 0.843 CORJ870107 0.840
+ BASU050102 0.837 NISK860101 0.837 BEGF750102 0.829
+ CORJ870102 0.825 SWER830101 0.825 GEIM800106 0.825
+ PALJ810110 0.824 GEIM800105 0.822 BASU050103 0.811
+ MANP780101 0.806 KANM800104 0.803 CORJ870101 0.802
+ CHOP780208 0.800 CHOP780216 -0.800 QIAN880131 -0.801
+ GEIM800108 -0.804 VINM940102 -0.813 GEIM800111 -0.816
+ VINM940101 -0.823 OOBM770103 -0.824 MIYS990103 -0.829
+ LEVM780106 -0.831 MIYS990104 -0.833 CORJ870108 -0.834
+ QIAN880132 -0.839 QIAN880134 -0.842 PARS000101 -0.863
+ QIAN880133 -0.863 GEIM800110 -0.898 MUNV940103 -0.959
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.25 -0.02 -0.77 -1.01 0.13 -0.12 -0.62 -0.72 -0.16 1.10
+ 0.23 -0.59 0.32 0.48 -1.24 -0.31 0.17 0.45 0.77 0.69
+//
+H QIAN880121
+D Weights for beta-sheet at the window position of 1 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880120 0.935 LIFS790101 0.930 CHOP780202 0.911
+ PALJ810104 0.910 ROBB760106 0.907 KANM800102 0.900
+ PONP930101 0.893 LIFS790103 0.882 PTIO830102 0.880
+ LEVM780105 0.876 PALJ810103 0.875 GEIM800107 0.875
+ QIAN880119 0.862 AVBF000101 0.855 CORJ870101 0.842
+ QIAN880122 0.838 BAEK050101 0.836 ROBB760105 0.834
+ NISK860101 0.829 KANM800104 0.829 BASU050103 0.828
+ BASU050101 0.828 BASU050102 0.825 NISK800101 0.818
+ PONP800101 0.815 PALJ810112 0.812 GEIM800105 0.811
+ CHOP780209 0.809 CORJ870107 0.806 CORJ870106 0.806
+ PRAM900103 0.805 LEVM780102 0.805 PONP800108 0.802
+ MANP780101 0.802 QIAN880133 -0.802 KRIW790101 -0.803
+ GEIM800110 -0.806 PARS000101 -0.809 VINM940101 -0.828
+ MIYS990104 -0.832 QIAN880134 -0.838 MIYS990103 -0.838
+ MUNV940103 -0.938
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.26 -0.09 -0.34 -0.55 0.47 -0.33 -0.75 -0.56 -0.04 0.94
+ 0.25 -0.55 -0.05 0.20 -1.28 -0.28 0.08 0.22 0.53 0.67
+//
+H QIAN880122
+D Weights for beta-sheet at the window position of 2 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880121 0.838 PONP930101 0.837 CORJ870101 0.826
+ PONP800108 0.811 NADH010103 0.809 CORJ870103 0.808
+ NISK800101 0.808 NADH010104 0.804 PONP800101 0.801
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.05 -0.11 -0.40 -0.11 0.36 -0.67 -0.35 0.14 0.02 0.47
+ 0.32 -0.51 -0.10 0.20 -0.79 0.03 -0.15 0.09 0.34 0.58
+//
+H QIAN880123
+D Weights for beta-sheet at the window position of 3 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.44 -0.13 0.05 -0.20 0.13 -0.58 -0.28 0.08 0.09 -0.04
+ -0.12 -0.33 -0.21 -0.13 -0.48 0.27 0.47 -0.22 -0.11 0.06
+//
+H QIAN880124
+D Weights for beta-sheet at the window position of 4 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.31 -0.10 0.06 0.13 -0.11 -0.47 -0.05 0.45 -0.06 -0.25
+ -0.44 -0.44 -0.28 -0.04 -0.29 0.34 0.27 -0.08 0.06 0.11
+//
+H QIAN880125
+D Weights for beta-sheet at the window position of 5 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.02 0.04 0.03 0.11 -0.02 -0.17 0.10 0.38 -0.09 -0.48
+ -0.26 -0.39 -0.14 -0.03 -0.04 0.41 0.36 -0.01 -0.08 -0.18
+//
+H QIAN880126
+D Weights for beta-sheet at the window position of 6 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880116 0.823
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.06 0.02 0.10 0.24 -0.19 -0.04 -0.04 0.17 0.19 -0.20
+ -0.46 -0.43 -0.52 -0.33 0.37 0.43 0.50 -0.32 0.35 0.00
+//
+H QIAN880127
+D Weights for coil at the window position of -6 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C OOBM850105 -0.813
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.05 0.06 0.00 0.15 0.30 -0.08 -0.02 -0.14 -0.07 0.26
+ 0.04 -0.42 0.25 0.09 0.31 -0.11 -0.06 0.19 0.33 0.04
+//
+H QIAN880128
+D Weights for coil at the window position of -5 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.19 0.17 -0.38 0.09 0.41 0.04 -0.20 0.28 -0.19 -0.06
+ 0.34 -0.20 0.45 0.07 0.04 -0.23 -0.02 0.16 0.22 0.05
+//
+H QIAN880129
+D Weights for coil at the window position of -4 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.43 0.06 0.00 -0.31 0.19 0.14 -0.41 -0.21 0.21 0.29
+ -0.10 0.33 -0.01 0.25 0.28 -0.23 -0.26 0.15 0.09 -0.10
+//
+H QIAN880130
+D Weights for coil at the window position of -3 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.19 -0.07 0.17 -0.27 0.42 -0.29 -0.22 0.17 0.17 -0.34
+ -0.22 0.00 -0.53 -0.31 0.14 0.22 0.10 -0.15 -0.02 -0.33
+//
+H QIAN880131
+D Weights for coil at the window position of -2 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C CHOP780216 0.873 TANS770110 0.873 QIAN880133 0.871
+ CHOP780203 0.861 CHAM830101 0.860 GEIM800108 0.860
+ GEIM800111 0.857 QIAN880132 0.847 QIAN880135 0.844
+ QIAN880134 0.832 CHOP780210 0.826 CHOP780101 0.824
+ PALJ810106 0.809 QIAN880120 -0.801 SUEM840101 -0.823
+ PTIO830101 -0.826 QIAN880119 -0.830
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.25 0.12 0.61 0.60 0.18 0.09 -0.12 0.09 0.42 -0.54
+ -0.55 0.14 -0.47 -0.29 0.89 0.24 0.16 -0.44 -0.19 -0.45
+//
+H QIAN880132
+D Weights for coil at the window position of -1 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880133 0.957 LEVM780106 0.943 PRAM900104 0.932
+ LEVM780103 0.931 CHOP780216 0.931 GEIM800111 0.929
+ CHOP780203 0.928 CHAM830101 0.925 QIAN880134 0.909
+ GEIM800108 0.906 TANS770110 0.903 CHOP780101 0.896
+ ISOY800103 0.892 PALJ810106 0.859 CHOP780210 0.852
+ QIAN880131 0.847 PALJ810105 0.830 QIAN880135 0.824
+ PALJ810115 0.804 ROBB760112 0.800 AURR980109 -0.806
+ LIFS790101 -0.806 AVBF000101 -0.809 QIAN880106 -0.813
+ ROBB760103 -0.827 PTIO830101 -0.833 QIAN880120 -0.839
+ AVBF000102 -0.849 FAUJ880102 -0.849 QIAN880119 -0.858
+ SUEM840101 -0.880
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.27 -0.40 0.71 0.54 0.00 -0.08 -0.12 1.14 0.18 -0.74
+ -0.54 0.45 -0.76 -0.47 1.40 0.40 -0.10 -0.46 -0.05 -0.86
+//
+H QIAN880133
+D Weights for coil at the window position of 0 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C LEVM780106 0.971 QIAN880132 0.957 LEVM780103 0.948
+ PRAM900104 0.947 GEIM800111 0.943 CHOP780216 0.939
+ QIAN880134 0.938 GEIM800108 0.930 TANS770110 0.920
+ CHOP780203 0.915 CHAM830101 0.913 ISOY800103 0.908
+ QIAN880135 0.907 CHOP780101 0.897 QIAN880131 0.871
+ PALJ810106 0.860 PALJ810105 0.843 MUNV940103 0.836
+ GEIM800110 0.822 CHOP780210 0.820 ROBB760112 0.814
+ QIAN880121 -0.802 ROBB760103 -0.807 AVBF000101 -0.807
+ QIAN880107 -0.809 AVBF000102 -0.823 LIFS790101 -0.848
+ QIAN880119 -0.849 FAUJ880102 -0.851 QIAN880120 -0.863
+ PTIO830101 -0.864 SUEM840101 -0.879
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.42 -0.23 0.81 0.95 -0.18 -0.01 -0.09 1.24 0.05 -1.17
+ -0.69 0.09 -0.86 -0.39 1.77 0.63 0.29 -0.37 -0.41 -1.32
+//
+H QIAN880134
+D Weights for coil at the window position of 1 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880135 0.961 QIAN880133 0.938 LEVM780103 0.935
+ PRAM900104 0.934 LEVM780106 0.932 GEIM800111 0.919
+ QIAN880132 0.909 CHOP780216 0.900 MUNV940105 0.899
+ MUNV940104 0.897 ISOY800104 0.893 GEIM800108 0.884
+ CHOP780213 0.870 MUNV940103 0.858 GEIM800110 0.853
+ CHAM830101 0.841 CHOP780203 0.838 TANS770104 0.837
+ QIAN880131 0.832 ISOY800103 0.828 ROBB760104 -0.802
+ LIFS790101 -0.804 AVBF000101 -0.822 BLAM930101 -0.836
+ QIAN880121 -0.838 QIAN880109 -0.841 QIAN880120 -0.842
+ QIAN880108 -0.845 FAUJ880102 -0.852 ROBB760103 -0.855
+ PTIO830101 -0.920
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.24 -0.04 0.45 0.65 -0.38 0.01 0.07 0.85 -0.21 -0.65
+ -0.80 0.17 -0.71 -0.61 2.27 0.33 0.13 -0.44 -0.49 -0.99
+//
+H QIAN880135
+D Weights for coil at the window position of 2 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988) (Gin !)
+C QIAN880134 0.961 QIAN880133 0.907 LEVM780103 0.906
+ PRAM900104 0.903 LEVM780106 0.902 GEIM800111 0.895
+ CHOP780216 0.884 GEIM800108 0.877 CHOP780213 0.851
+ QIAN880131 0.844 GEIM800110 0.842 QIAN880136 0.838
+ ISOY800104 0.837 MUNV940105 0.829 QIAN880132 0.824
+ MUNV940103 0.820 MUNV940104 0.819 CHAM830101 0.814
+ CHOP780203 0.811 ROBB760103 -0.834 QIAN880108 -0.836
+ QIAN880111 -0.878 QIAN880109 -0.884 PTIO830101 -0.899
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.14 0.21 0.35 0.66 -0.09 0.11 0.06 0.36 -0.31 -0.51
+ -0.80 -0.14 -0.56 -0.25 1.59 0.32 0.21 -0.17 -0.35 -0.70
+//
+H QIAN880136
+D Weights for coil at the window position of 3 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C QIAN880135 0.838 QIAN880112 -0.812 QIAN880108 -0.843
+ QIAN880110 -0.890 QIAN880111 -0.900 QIAN880109 -0.927
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.01 -0.13 -0.11 0.78 -0.31 -0.13 0.09 0.14 -0.56 -0.09
+ -0.81 -0.43 -0.49 -0.20 1.14 0.13 -0.02 -0.20 0.10 -0.11
+//
+H QIAN880137
+D Weights for coil at the window position of 4 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.30 -0.09 -0.12 0.44 0.03 0.24 0.18 -0.12 -0.20 -0.07
+ -0.18 0.06 -0.44 0.11 0.77 -0.09 -0.27 -0.09 -0.25 -0.06
+//
+H QIAN880138
+D Weights for coil at the window position of 5 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.23 -0.20 0.06 0.34 0.19 0.47 0.28 0.14 -0.22 0.42
+ -0.36 -0.15 -0.19 -0.02 0.78 -0.29 -0.30 -0.18 0.07 0.29
+//
+H QIAN880139
+D Weights for coil at the window position of 6 (Qian-Sejnowski, 1988)
+R PMID:3172241
+A Qian, N. and Sejnowski, T.J.
+T Predicting the secondary structure of globular proteins using neural network
+ models
+J J. Mol. Biol. 202, 865-884 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.08 -0.01 -0.06 0.04 0.37 0.48 0.36 -0.02 -0.45 0.09
+ 0.24 -0.27 0.16 0.34 0.16 -0.35 -0.04 -0.06 -0.20 0.18
+//
+H RACS770101
+D Average reduced distance for C-alpha (Rackovsky-Scheraga, 1977)
+R PMID:271950
+A Rackovsky, S. and Scheraga, H.A.
+T Hydrophobicity, hydrophilicity, and the radial and orientational
+ distributions of residues in native proteins
+J Proc. Natl. Acad. Sci. USA 74, 5248-5251 (1977)
+C MEIH800101 0.973 RACS770102 0.946 MIYS990102 0.921
+ MIYS990101 0.920 MEIH800102 0.905 CORJ870108 0.891
+ MIYS990103 0.887 MIYS990104 0.884 FASG890101 0.872
+ PARJ860101 0.871 KARP850102 0.869 MIYS990105 0.866
+ GUYH850102 0.859 GUYH850101 0.853 GUYH850103 0.844
+ KARP850101 0.837 VINM940101 0.835 OOBM770103 0.835
+ VINM940103 0.829 KRIW790101 0.828 CHOP780203 0.827
+ PUNT030101 0.821 FUKS010103 0.819 KRIW790102 0.814
+ PRAM900104 0.809 LEVM780103 0.808 PARS000101 0.804
+ RACS770103 0.801 CORJ870102 -0.802 SWER830101 -0.803
+ GUOD860101 -0.805 NISK800101 -0.805 NADH010103 -0.807
+ CASG920101 -0.807 NADH010104 -0.813 CIDH920102 -0.825
+ PONP800102 -0.827 ZHOH040103 -0.835 CIDH920101 -0.837
+ ROBB790101 -0.839 BEGF750102 -0.840 MEIH800103 -0.845
+ RICJ880111 -0.846 BASU050103 -0.848 BASU050101 -0.850
+ BASU050102 -0.854 CORJ870104 -0.860 PONP800101 -0.863
+ CIDH920104 -0.864 PLIV810101 -0.868 CORJ870103 -0.870
+ BIOV880102 -0.875 CORJ870105 -0.876 MANP780101 -0.878
+ CORJ870106 -0.879 ROSG850102 -0.880 CIDH920103 -0.881
+ PONP930101 -0.886 RADA880108 -0.887 CIDH920105 -0.887
+ BIOV880101 -0.893 CORJ870107 -0.898 PONP800107 -0.905
+ WERD780101 -0.912 NISK860101 -0.923 MIYS850101 -0.940
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.934 0.962 0.986 0.994 0.900 1.047 0.986 1.015 0.882 0.766
+ 0.825 1.040 0.804 0.773 1.047 1.056 1.008 0.848 0.931 0.825
+//
+H RACS770102
+D Average reduced distance for side chain (Rackovsky-Scheraga, 1977)
+R PMID:271950
+A Rackovsky, S. and Scheraga, H.A.
+T Hydrophobicity, hydrophilicity, and the radial and orientational
+ distributions of residues in native proteins
+J Proc. Natl. Acad. Sci. USA 74, 5248-5251 (1977) (Gly 0.080)
+C MEIH800102 0.987 MEIH800101 0.963 RACS770101 0.946
+ FASG890101 0.935 GUYH850101 0.934 MIYS990102 0.919
+ MIYS990101 0.917 MIYS990103 0.908 KRIW790102 0.895
+ PUNT030101 0.894 MIYS990105 0.893 MIYS990104 0.892
+ RACS770103 0.889 KRIW790101 0.871 CORJ870108 0.863
+ GUYH850102 0.853 KARP850102 0.852 GUYH850104 0.849
+ VINM940101 0.844 VINM940103 0.839 OOBM770101 0.838
+ PARJ860101 0.834 PUNT030102 0.828 OOBM770103 0.828
+ ROSM880102 0.824 JANJ780103 0.823 CHOC760102 0.809
+ WOLS870101 0.802 NADH010105 -0.800 DESM900101 -0.801
+ BASU050102 -0.807 NADH010101 -0.808 BASU050101 -0.813
+ NISK800101 -0.818 CIDH920105 -0.830 ZHOH040103 -0.832
+ CIDH920103 -0.834 CORJ870101 -0.837 CORJ870104 -0.838
+ CORJ870106 -0.839 CORJ870105 -0.839 FAUJ830101 -0.843
+ KYTJ820101 -0.844 OLSK800101 -0.845 CASG920101 -0.849
+ JANJ790102 -0.851 CORJ870103 -0.852 CIDH920104 -0.854
+ JURD980101 -0.855 EISD860103 -0.858 PLIV810101 -0.859
+ PONP800103 -0.860 BASU050103 -0.861 PONP800102 -0.864
+ MANP780101 -0.865 DESM900102 -0.867 JANJ780102 -0.869
+ PONP800101 -0.870 PONP930101 -0.871 CORJ870107 -0.871
+ CHOC760103 -0.875 PONP800107 -0.878 NADH010104 -0.883
+ NADH010103 -0.893 NADH010102 -0.899 WERD780101 -0.906
+ NISK860101 -0.913 MEIH800103 -0.918 BIOV880102 -0.932
+ BIOV880101 -0.937 ROSG850102 -0.940 RADA880108 -0.942
+ MIYS850101 -0.943
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.941 1.112 1.038 1.071 0.866 1.150 1.100 1.055 0.911 0.742
+ 0.798 1.232 0.781 0.723 1.093 1.082 1.043 0.867 1.050 0.817
+//
+H RACS770103
+D Side chain orientational preference (Rackovsky-Scheraga, 1977)
+R PMID:271950
+A Rackovsky, S. and Scheraga, H.A.
+T Hydrophobicity, hydrophilicity, and the radial and orientational
+ distributions of residues in native proteins
+J Proc. Natl. Acad. Sci. USA 74, 5248-5251 (1977) (Gly !) (Ratio of the numbers
+ of occurrences in two orientations)
+C MEIH800102 0.903 RACS770102 0.889 KRIW790102 0.889
+ OOBM770101 0.871 MIYS990105 0.852 JANJ780103 0.847
+ FASG890101 0.842 MIYS990103 0.840 GUYH850104 0.839
+ MEIH800101 0.837 MIYS990104 0.833 VINM940101 0.830
+ PUNT030101 0.830 OOBM770103 0.823 GUYH850102 0.821
+ GUYH850101 0.816 VINM940104 0.804 RACS770101 0.801
+ CORJ870107 -0.808 PONP800102 -0.809 MIYS850101 -0.818
+ PONP800103 -0.819 CORJ870103 -0.827 JANJ780102 -0.828
+ NADH010104 -0.832 CORJ870101 -0.832 JANJ790102 -0.834
+ DESM900101 -0.837 NISK860101 -0.837 WERD780101 -0.846
+ CASG920101 -0.846 WARP780101 -0.848 NADH010103 -0.851
+ BIOV880101 -0.856 RADA880108 -0.863 DESM900102 -0.868
+ NADH010102 -0.876 ROSG850102 -0.901 BIOV880102 -0.906
+ MEIH800103 -0.919
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.16 1.72 1.97 2.66 0.50 3.87 2.40 1.63 0.86 0.57
+ 0.51 3.90 0.40 0.43 2.04 1.61 1.48 0.75 1.72 0.59
+//
+H RACS820101
+D Average relative fractional occurrence in A0(i) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.85 2.02 0.88 1.50 0.90 1.71 1.79 1.54 1.59 0.67
+ 1.03 0.88 1.17 0.85 1.47 1.50 1.96 0.83 1.34 0.89
+//
+H RACS820102
+D Average relative fractional occurrence in AR(i) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.58 1.14 0.77 0.98 1.04 1.24 1.49 0.66 0.99 1.09
+ 1.21 1.27 1.41 1.00 1.46 1.05 0.87 1.23 0.68 0.88
+//
+H RACS820103
+D Average relative fractional occurrence in AL(i) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.82 2.60 2.07 2.64 0.00 0.00 2.62 1.63 0.00 2.32
+ 0.00 2.86 0.00 0.00 0.00 1.23 2.48 0.00 1.90 1.62
+//
+H RACS820104
+D Average relative fractional occurrence in EL(i) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.78 1.75 1.32 1.25 3.14 0.93 0.94 1.13 1.03 1.26
+ 0.91 0.85 0.41 1.07 1.73 1.31 1.57 0.98 1.31 1.11
+//
+H RACS820105
+D Average relative fractional occurrence in E0(i) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C NAKH900102 -0.839
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.88 0.99 1.02 1.16 1.14 0.93 1.01 0.70 1.87 1.61
+ 1.09 0.83 1.71 1.52 0.87 1.14 0.96 1.96 1.68 1.56
+//
+H RACS820106
+D Average relative fractional occurrence in ER(i) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C ISOY800108 0.831
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.30 0.90 2.73 1.26 0.72 0.97 1.33 3.09 1.33 0.45
+ 0.96 0.71 1.89 1.20 0.83 1.16 0.97 1.58 0.86 0.64
+//
+H RACS820107
+D Average relative fractional occurrence in A0(i-1) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.40 1.20 1.24 1.59 2.98 0.50 1.26 1.89 2.71 1.31
+ 0.57 0.87 0.00 1.27 0.38 0.92 1.38 1.53 1.79 0.95
+//
+H RACS820108
+D Average relative fractional occurrence in AR(i-1) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C KANM800101 0.914 LEVM780101 0.904 PRAM900102 0.904
+ ISOY800101 0.904 ROBB760101 0.889 LEVM780104 0.889
+ PALJ810102 0.881 GEIM800101 0.880 PALJ810101 0.872
+ CHOP780201 0.868 QIAN880106 0.866 MAXF760101 0.860
+ KANM800103 0.858 ROBB760103 0.851 GEIM800104 0.851
+ TANS770101 0.845 AURR980112 0.840 CRAJ730101 0.839
+ QIAN880107 0.831 QIAN880108 0.820 NAGK730101 0.820
+ QIAN880105 0.820 AURR980114 0.818 BURA740101 0.809
+ AURR980109 0.804 AURR980115 0.802 MUNV940101 -0.859
+ MUNV940102 -0.894
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.48 1.02 0.99 1.19 0.86 1.42 1.43 0.46 1.27 1.12
+ 1.33 1.36 1.41 1.30 0.25 0.89 0.81 1.27 0.91 0.93
+//
+H RACS820109
+D Average relative fractional occurrence in AL(i-1) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C ISOY800108 0.848 MAXF760104 0.844
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.00 0.00 4.14 2.15 0.00 0.00 0.00 6.49 0.00 0.00
+ 0.00 0.00 0.00 2.11 1.99 0.00 1.24 0.00 1.90 0.00
+//
+H RACS820110
+D Average relative fractional occurrence in EL(i-1) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C MUNV940105 0.833 MUNV940104 0.831 AVBF000102 -0.801
+ ROBB760104 -0.818
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.02 1.00 1.31 1.76 1.05 1.05 0.83 2.39 0.40 0.83
+ 1.06 0.94 1.33 0.41 2.73 1.18 0.77 1.22 1.09 0.88
+//
+H RACS820111
+D Average relative fractional occurrence in E0(i-1) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C TANS770103 0.841 MAXF760102 0.815 ROBB760105 0.803
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.93 1.52 0.92 0.60 1.08 0.94 0.73 0.78 1.08 1.74
+ 1.03 1.00 1.31 1.51 1.37 0.97 1.38 1.12 1.65 1.70
+//
+H RACS820112
+D Average relative fractional occurrence in ER(i-1) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.99 1.19 1.15 1.18 2.32 1.52 1.36 1.40 1.06 0.81
+ 1.26 0.91 1.00 1.25 0.00 1.50 1.18 1.33 1.09 1.01
+//
+H RACS820113
+D Value of theta(i) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 17.05 21.25 34.81 19.27 28.84 15.42 20.12 38.14 23.07 16.66
+ 10.89 16.46 20.61 16.26 23.94 19.95 18.92 23.36 26.49 17.06
+//
+H RACS820114
+D Value of theta(i-1) (Rackovsky-Scheraga, 1982)
+R
+A Rackovsky, S. and Scheraga, H.A.
+T Differential geometry and polymer conformation. 4. Conformational and
+ nucleation properties of individual amino acids
+J Macromolecules 15, 1340-1346 (1982)
+C MUNV940102 0.877 ONEK900102 0.855 MUNV940101 0.828
+ ROBB760103 -0.806 BLAM930101 -0.862 ONEK900101 -0.880
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 14.53 17.82 13.59 19.78 30.57 22.18 18.19 37.16 22.63 20.28
+ 14.30 14.07 20.61 19.61 52.63 18.56 21.09 19.78 26.36 21.87
+//
+H RADA880101
+D Transfer free energy from chx to wat (Radzicka-Wolfenden, 1988)
+R
+A Radzicka, A. and Wolfenden, R.
+T Comparing the polarities of the amino acids: Side-chain distribution
+ coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral
+ aqueous solution
+J Biochemistry 27, 1664-1670 (1988) (Pro missing)
+C EISD840101 0.968 WOLR810101 0.939 JACR890101 0.936
+ ROSM880105 0.933 WOLR790101 0.933 BLAS910101 0.922
+ NADH010101 0.902 RADA880104 0.901 JURD980101 0.893
+ EISD860101 0.891 KYTJ820101 0.884 RADA880107 0.881
+ FAUJ830101 0.873 JANJ780102 0.855 CHOC760103 0.853
+ EISD860103 0.850 NADH010102 0.845 COWR900101 0.840
+ OLSK800101 0.840 JANJ790102 0.839 DESM900102 0.828
+ BASU050103 0.809 NADH010103 0.809 RADA880108 0.807
+ YUTK870101 0.803 WOEC730101 -0.812 CHOC760102 -0.814
+ GUYH850101 -0.815 JANJ780103 -0.817 WOLS870101 -0.823
+ HOPT810101 -0.829 GUYH850104 -0.831 FAUJ880110 -0.838
+ LEVM760101 -0.838 JANJ780101 -0.844 GRAR740102 -0.861
+ OOBM770101 -0.863 FAUJ880109 -0.873 PUNT030102 -0.881
+ KIDA850101 -0.883 PUNT030101 -0.886 GUYH850105 -0.899
+ ROSM880102 -0.917 VHEG790101 -0.925 ENGD860101 -0.932
+ PRAM900101 -0.932 KUHL950101 -0.950 ROSM880101 -0.978
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.81 -14.92 -6.64 -8.72 1.28 -5.54 -6.81 0.94 -4.66 4.92
+ 4.92 -5.55 2.35 2.98 0. -3.40 -2.57 2.33 -0.14 4.04
+//
+H RADA880102
+D Transfer free energy from oct to wat (Radzicka-Wolfenden, 1988)
+R
+A Radzicka, A. and Wolfenden, R.
+T Comparing the polarities of the amino acids: Side-chain distribution
+ coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral
+ aqueous solution
+J Biochemistry 27, 1664-1670 (1988) (Pro Cys Asp missing)
+C NOZY710101 0.917 EISD860101 0.912 MEEJ800102 0.900
+ ROSM880105 0.870 CIDH920102 0.862 CIDH920105 0.861
+ ZIMJ680105 0.851 FAUJ830101 0.846 PLIV810101 0.845
+ TAKK010101 0.830 GUOD860101 0.829 ZHOH040101 0.828
+ VENT840101 0.826 BLAS910101 0.826 MIYS850101 0.824
+ CORJ870102 0.821 SWER830101 0.820 CIDH920103 0.819
+ CIDH920104 0.817 BASU050103 0.815 MEEJ810102 0.813
+ ZHOH040103 0.813 BROC820101 0.811 BASU050102 0.809
+ PUNT030102 -0.811 MEIH800101 -0.816 VHEG790101 -0.818
+ PUNT030101 -0.821 MIYS990102 -0.834 MIYS990101 -0.837
+ LEVM760101 -0.838 BULH740101 -0.856 HOPT810101 -0.859
+ WOLS870101 -0.873 PARJ860101 -0.883
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.52 -1.32 -0.01 0. 0. -0.07 -0.79 0. 0.95 2.04
+ 1.76 0.08 1.32 2.09 0. 0.04 0.27 2.51 1.63 1.18
+//
+H RADA880103
+D Transfer free energy from vap to chx (Radzicka-Wolfenden, 1988)
+R
+A Radzicka, A. and Wolfenden, R.
+T Comparing the polarities of the amino acids: Side-chain distribution
+ coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral
+ aqueous solution
+J Biochemistry 27, 1664-1670 (1988) (Pro missing)
+C FAUJ880104 -0.806 CHAM830105 -0.808 HUTJ700102 -0.812
+ ROSG850101 -0.814 FAUJ880106 -0.823 MCMT640101 -0.833
+ HARY940101 -0.840 GOLD730102 -0.864 BIGC670101 -0.865
+ KRIW790103 -0.871 PONJ960101 -0.873 TSAJ990101 -0.875
+ TSAJ990102 -0.879 GRAR740103 -0.881 CHOC750101 -0.892
+ LEVM760105 -0.893 RADA880106 -0.895 CHAM830106 -0.901
+ CHAM820101 -0.912 LEVM760102 -0.913 FAUJ880103 -0.923
+ CHOC760101 -0.924 FASG760101 -0.954
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.13 -5. -3.04 -2.23 -2.52 -3.84 -3.43 1.45 -5.61 -2.77
+ -2.64 -3.97 -3.83 -3.74 0. -1.66 -2.31 -8.21 -5.97 -2.05
+//
+H RADA880104
+D Transfer free energy from chx to oct (Radzicka-Wolfenden, 1988)
+R
+A Radzicka, A. and Wolfenden, R.
+T Comparing the polarities of the amino acids: Side-chain distribution
+ coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral
+ aqueous solution
+J Biochemistry 27, 1664-1670 (1988) (Pro Cys Asp missing)
+C WOLR790101 0.926 RADA880105 0.918 WOLR810101 0.910
+ EISD840101 0.908 RADA880101 0.901 RADA880107 0.897
+ JACR890101 0.868 JURD980101 0.824 CHOC760103 0.821
+ KYTJ820101 0.819 NADH010101 0.819 COWR900101 0.818
+ OLSK800101 0.814 ENGD860101 -0.803 PRAM900101 -0.803
+ KIDA850101 -0.805 JANJ780101 -0.825 CHOC760102 -0.830
+ KUHL950101 -0.847 ROSM880102 -0.855 ROSM880101 -0.863
+ GUYH850105 -0.899 FAUJ880109 -0.926
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.29 -13.60 -6.63 0. 0. -5.47 -6.02 0.94 -5.61 2.88
+ 3.16 -5.63 1.03 0.89 0. -3.44 -2.84 -0.18 -1.77 2.86
+//
+H RADA880105
+D Transfer free energy from vap to oct (Radzicka-Wolfenden, 1988)
+R
+A Radzicka, A. and Wolfenden, R.
+T Comparing the polarities of the amino acids: Side-chain distribution
+ coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral
+ aqueous solution
+J Biochemistry 27, 1664-1670 (1988) (Pro Cys Asp missing)
+C RADA880104 0.918 WOLR790101 0.903 WOLR810101 0.875
+ RADA880107 0.846 GUYH850105 -0.809 FAUJ880109 -0.889
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.42 -18.60 -9.67 0. 0. -9.31 -9.45 2.39 -11.22 0.11
+ 0.52 -9.60 -2.80 -2.85 0. -5.10 -5.15 -8.39 -7.74 0.81
+//
+H RADA880106
+D Accessible surface area (Radzicka-Wolfenden, 1988)
+R
+A Radzicka, A. and Wolfenden, R.
+T Comparing the polarities of the amino acids: Side-chain distribution
+ coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral
+ aqueous solution
+J Biochemistry 27, 1664-1670 (1988) (Pro missing)
+C CHAM830106 0.922 GRAR740103 0.920 KRIW790103 0.883
+ CHOC760101 0.875 LEVM760102 0.871 LEVM760105 0.871
+ FASG760101 0.870 FAUJ880103 0.869 CHOC750101 0.867
+ TSAJ990102 0.864 TSAJ990101 0.861 PONJ960101 0.860
+ BIGC670101 0.856 GOLD730102 0.854 CHAM820101 0.847
+ HARY940101 0.846 ROSG850101 0.814 RADA880103 -0.895
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 93.7 250.4 146.3 142.6 135.2 177.7 182.9 52.6 188.1 182.2
+ 173.7 215.2 197.6 228.6 0. 109.5 142.1 271.6 239.9 157.2
+//
+H RADA880107
+D Energy transfer from out to in(95%buried) (Radzicka-Wolfenden, 1988)
+R
+A Radzicka, A. and Wolfenden, R.
+T Comparing the polarities of the amino acids: Side-chain distribution
+ coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral
+ aqueous solution
+J Biochemistry 27, 1664-1670 (1988) (Pro missing)
+C EISD840101 0.927 JANJ790102 0.906 WOLR790101 0.905
+ RADA880104 0.897 JACR890101 0.895 WOLR810101 0.890
+ RADA880101 0.881 OLSK800101 0.874 CHOC760103 0.870
+ JANJ780102 0.856 RADA880105 0.846 JURD980101 0.842
+ KYTJ820101 0.828 NADH010102 0.823 EISD860103 0.812
+ COWR900101 0.810 EISD860102 -0.837 KIDA850101 -0.837
+ OOBM770101 -0.854 JANJ780103 -0.856 KUHL950101 -0.857
+ ENGD860101 -0.865 PRAM900101 -0.865 ROSM880101 -0.867
+ ROSM880102 -0.894 GUYH850104 -0.896 JANJ780101 -0.917
+ CHOC760102 -0.925 GUYH850105 -0.953 FAUJ880109 -0.957
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.29 -2.71 -1.18 -1.02 0. -1.53 -0.90 -0.34 -0.94 0.24
+ -0.12 -2.05 -0.24 0. 0. -0.75 -0.71 -0.59 -1.02 0.09
+//
+H RADA880108
+D Mean polarity (Radzicka-Wolfenden, 1988)
+R
+A Radzicka, A. and Wolfenden, R.
+T Comparing the polarities of the amino acids: Side-chain distribution
+ coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral
+ aqueous solution
+J Biochemistry 27, 1664-1670 (1988) (Pro missing)
+C BIOV880101 0.981 ROSG850102 0.967 MIYS850101 0.950
+ NISK860101 0.950 BIOV880102 0.942 PONP800102 0.938
+ PONP800103 0.934 PONP800101 0.934 FAUJ830101 0.932
+ WERD780101 0.930 BASU050103 0.926 NADH010103 0.919
+ MEIH800103 0.916 NADH010104 0.915 CIDH920104 0.914
+ NADH010102 0.911 PLIV810101 0.906 ZHOH040103 0.904
+ CASG920101 0.903 NISK800101 0.902 MANP780101 0.900
+ CIDH920105 0.898 CORJ870101 0.895 PONP930101 0.891
+ CIDH920103 0.891 CORJ870107 0.889 PONP800108 0.889
+ DESM900102 0.881 CORJ870104 0.880 CORJ870103 0.876
+ EISD860103 0.873 BASU050102 0.870 JANJ780102 0.869
+ BASU050101 0.867 ROBB790101 0.867 CORJ870106 0.863
+ ROSM880105 0.861 CIDH920101 0.858 JURD980101 0.857
+ CORJ870105 0.854 JANJ790102 0.853 NADH010105 0.845
+ EISD860101 0.844 KYTJ820101 0.842 NADH010101 0.838
+ PONP800106 0.835 CIDH920102 0.833 CHOC760103 0.830
+ BLAS910101 0.826 SWER830101 0.826 JANJ790101 0.824
+ CORJ870102 0.823 EISD840101 0.817 GUOD860101 0.812
+ DESM900101 0.812 RADA880101 0.807 MEEJ810101 0.804
+ PONP800107 0.800 KARP850101 -0.804 JANJ780103 -0.805
+ FUKS010102 -0.815 LEVM760101 -0.824 WOEC730101 -0.825
+ ROSM880101 -0.831 HOPT810101 -0.831 KUHL950101 -0.839
+ FUKS010103 -0.840 WOLS870101 -0.840 VINM940102 -0.846
+ GUYH850104 -0.847 KRIW710101 -0.847 FUKS010104 -0.851
+ KRIW790102 -0.856 ROSM880102 -0.861 VINM940103 -0.862
+ RACS770103 -0.863 OOBM770101 -0.864 PARJ860101 -0.865
+ PUNT030102 -0.869 GUYH850103 -0.870 KIDA850101 -0.875
+ OOBM770103 -0.878 KARP850102 -0.879 PUNT030101 -0.884
+ RACS770101 -0.887 CORJ870108 -0.893 KRIW790101 -0.897
+ GRAR740102 -0.899 GUYH850102 -0.902 VINM940101 -0.906
+ MIYS990101 -0.932 MIYS990102 -0.934 MEIH800101 -0.940
+ RACS770102 -0.942 MIYS990104 -0.943 GUYH850101 -0.948
+ MIYS990105 -0.950 MIYS990103 -0.950 MEIH800102 -0.953
+ FASG890101 -0.977
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.06 -0.84 -0.48 -0.80 1.36 -0.73 -0.77 -0.41 0.49 1.31
+ 1.21 -1.18 1.27 1.27 0. -0.50 -0.27 0.88 0.33 1.09
+//
+H RICJ880101
+D Relative preference value at N" (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C RICJ880102 1.000
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.7 0.4 1.2 1.4 0.6 1. 1. 1.6 1.2 0.9
+ 0.9 1. 0.3 1.2 0.7 1.6 0.3 1.1 1.9 0.7
+//
+H RICJ880102
+D Relative preference value at N' (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C RICJ880101 1.000
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.7 0.4 1.2 1.4 0.6 1. 1. 1.6 1.2 0.9
+ 0.9 1. 0.3 1.2 0.7 1.6 0.3 1.1 1.9 0.7
+//
+H RICJ880103
+D Relative preference value at N-cap (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.5 0.4 3.5 2.1 0.6 0.4 0.4 1.8 1.1 0.2
+ 0.2 0.7 0.8 0.2 0.8 2.3 1.6 0.3 0.8 0.1
+//
+H RICJ880104
+D Relative preference value at N1 (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.2 0.7 0.7 0.8 0.8 0.7 2.2 0.3 0.7 0.9
+ 0.9 0.6 0.3 0.5 2.6 0.7 0.8 2.1 1.8 1.1
+//
+H RICJ880105
+D Relative preference value at N2 (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.6 0.9 0.7 2.6 1.2 0.8 2. 0.9 0.7 0.7
+ 0.3 1. 1. 0.9 0.5 0.8 0.7 1.7 0.4 0.6
+//
+H RICJ880106
+D Relative preference value at N3 (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C FAUJ880112 0.849 AURR980107 0.800
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1. 0.4 0.7 2.2 0.6 1.5 3.3 0.6 0.7 0.4
+ 0.6 0.8 1. 0.6 0.4 0.4 1. 1.4 1.2 1.1
+//
+H RICJ880107
+D Relative preference value at N4 (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C CHOP780210 -0.818
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.1 1.5 0. 0.3 1.1 1.3 0.5 0.4 1.5 1.1
+ 2.6 0.8 1.7 1.9 0.1 0.4 0.5 3.1 0.6 1.5
+//
+H RICJ880108
+D Relative preference value at N5 (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.4 1.2 1.2 0.6 1.6 1.4 0.9 0.6 0.9 0.9
+ 1.1 1.9 1.7 1. 0.3 1.1 0.6 1.4 0.2 0.8
+//
+H RICJ880109
+D Relative preference value at Mid (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C QIAN880106 0.834 ROBB760103 0.831 KANM800103 0.829
+ AURR980109 0.828 AURR980113 0.808 CHAM830101 -0.826
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.8 1.3 0.9 1. 0.7 1.3 0.8 0.5 1. 1.2
+ 1.2 1.1 1.5 1.3 0.3 0.6 1. 1.5 0.8 1.2
+//
+H RICJ880110
+D Relative preference value at C5 (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.8 1. 0.6 0.7 0. 1. 1.1 0.5 2.4 1.3
+ 1.2 1.4 2.7 1.9 0.3 0.5 0.5 1.1 1.3 0.4
+//
+H RICJ880111
+D Relative preference value at C4 (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C MEIH800101 -0.802 CHOP780210 -0.804 BHAR880101 -0.813
+ RACS770101 -0.846
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.3 0.8 0.6 0.5 0.7 0.2 0.7 0.5 1.9 1.6
+ 1.4 1. 2.8 2.9 0. 0.5 0.6 2.1 0.8 1.4
+//
+H RICJ880112
+D Relative preference value at C3 (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.7 0.8 0.8 0.6 0.2 1.3 1.6 0.1 1.1 1.4
+ 1.9 2.2 1. 1.8 0. 0.6 0.7 0.4 1.1 1.3
+//
+H RICJ880113
+D Relative preference value at C2 (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.4 2.1 0.9 0.7 1.2 1.6 1.7 0.2 1.8 0.4
+ 0.8 1.9 1.3 0.3 0.2 1.6 0.9 0.4 0.3 0.7
+//
+H RICJ880114
+D Relative preference value at C1 (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.1 1. 1.2 0.4 1.6 2.1 0.8 0.2 3.4 0.7
+ 0.7 2. 1. 0.7 0. 1.7 1. 0. 1.2 0.7
+//
+H RICJ880115
+D Relative preference value at C-cap (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C AURR980117 0.921 MAXF760104 0.919 ISOY800108 0.889
+ TANS770107 0.807 MAXF760105 0.802 LEVM760103 -0.829
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.8 0.9 1.6 0.7 0.4 0.9 0.3 3.9 1.3 0.7
+ 0.7 1.3 0.8 0.5 0.7 0.8 0.3 0. 0.8 0.2
+//
+H RICJ880116
+D Relative preference value at C' (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1. 1.4 0.9 1.4 0.8 1.4 0.8 1.2 1.2 1.1
+ 0.9 1.2 0.8 0.1 1.9 0.7 0.8 0.4 0.9 0.6
+//
+H RICJ880117
+D Relative preference value at C" (Richardson-Richardson, 1988)
+R PMID:3381086
+A Richardson, J.S. and Richardson, D.C.
+T Amino acid preferences for specific locations at the ends of alpha helices
+J Science 240, 1648-1652 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.7 1.1 1.5 1.4 0.4 1.1 0.7 0.6 1. 0.7
+ 0.5 1.3 0. 1.2 1.5 0.9 2.1 2.7 0.5 1.
+//
+H ROBB760101
+D Information measure for alpha-helix (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C CHOP780201 0.969 ISOY800101 0.957 MAXF760101 0.956
+ TANS770101 0.948 PALJ810102 0.946 KANM800101 0.945
+ PRAM900102 0.916 LEVM780101 0.916 PALJ810101 0.914
+ BURA740101 0.912 LEVM780104 0.911 NAGK730101 0.910
+ QIAN880106 0.904 GEIM800101 0.897 RACS820108 0.889
+ KANM800103 0.886 CRAJ730101 0.875 QIAN880105 0.874
+ QIAN880107 0.867 GEIM800104 0.855 AURR980108 0.814
+ AURR980109 0.810 ROBB760103 0.807 AURR980112 0.806
+ PALJ810109 0.805 MUNV940101 -0.822 MUNV940102 -0.827
+ CHAM830101 -0.828 NAGK730103 -0.861
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.5 -0.9 -5.1 0.5 -1.3 1.0 7.8 -8.6 1.2 0.6
+ 3.2 2.3 5.3 1.6 -7.7 -3.9 -2.6 1.2 -4.5 1.4
+//
+H ROBB760102
+D Information measure for N-terminal helix (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C CHOP780204 0.911
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.3 -5.2 0.3 7.4 0.8 -0.7 10.3 -5.2 -2.8 -4.0
+ -2.1 -4.1 -3.5 -1.1 8.1 -3.5 2.3 -0.9 -3.7 -4.4
+//
+H ROBB760103
+D Information measure for middle helix (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C QIAN880108 0.914 PTIO830101 0.903 QIAN880107 0.889
+ KANM800103 0.887 BLAM930101 0.883 ONEK900101 0.878
+ QIAN880109 0.868 AURR980109 0.857 QIAN880106 0.854
+ BEGF750101 0.852 RACS820108 0.851 ISOY800101 0.841
+ AURR980113 0.838 AURR980108 0.835 RICJ880109 0.831
+ QIAN880105 0.811 ROBB760101 0.807 QIAN880110 0.807
+ CHOP780201 0.806 FAUJ880113 0.802 AURR980114 0.801
+ GEIM800108 -0.802 RACS820114 -0.806 QIAN880133 -0.807
+ QIAN880132 -0.827 ISOY800104 -0.830 QIAN880135 -0.834
+ PRAM900104 -0.840 CHOP780216 -0.841 LEVM780103 -0.843
+ GEIM800111 -0.843 QIAN880134 -0.855 ONEK900102 -0.867
+ CHAM830101 -0.878 MUNV940102 -0.913 MUNV940101 -0.918
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.7 0.3 -6.1 -3.1 -4.9 0.6 2.2 -6.8 -1.0 3.2
+ 5.5 0.5 7.2 2.8 -22.8 -3.0 -4.0 4.0 -4.6 2.5
+//
+H ROBB760104
+D Information measure for C-terminal helix (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C QIAN880108 0.879 BLAM930101 0.878 QIAN880109 0.871
+ ONEK900101 0.844 CHOP780205 0.841 BUNA790101 0.823
+ PTIO830101 0.817 QIAN880110 0.806 QIAN880134 -0.802
+ MUNV940102 -0.803 ISOY800104 -0.817 RACS820110 -0.818
+ MUNV940101 -0.831 MUNV940104 -0.840 FINA910102 -0.844
+ MUNV940105 -0.859 ONEK900102 -0.861
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.3 1.4 -3.3 -4.4 6.1 2.7 2.5 -8.3 5.9 -0.5
+ 0.1 7.3 3.5 1.6 -24.4 -1.9 -3.7 -0.9 -0.6 2.3
+//
+H ROBB760105
+D Information measure for extended (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C ROBB760106 0.949 KANM800102 0.898 KANM800104 0.885
+ CHOP780202 0.885 PTIO830102 0.878 GEIM800105 0.877
+ TANS770103 0.871 PALJ810103 0.869 LIFS790101 0.867
+ QIAN880120 0.860 QIAN880119 0.859 BASU050101 0.853
+ ISOY800102 0.847 LEVM780105 0.842 BASU050103 0.839
+ GEIM800107 0.836 PALJ810104 0.835 QIAN880121 0.834
+ PONP930101 0.829 PONP800102 0.828 PONP800101 0.823
+ PONP800103 0.823 BURA740102 0.821 PONP800108 0.820
+ NAGK730102 0.815 CORJ870101 0.809 MANP780101 0.805
+ PALJ810110 0.804 CORJ870104 0.803 RACS820111 0.803
+ CORJ870107 0.800 CORJ870108 -0.811 MUNV940103 -0.832
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -2.3 0.4 -4.1 -4.4 4.4 1.2 -5.0 -4.2 -2.5 6.7
+ 2.3 -3.3 2.3 2.6 -1.8 -1.7 1.3 -1.0 4.0 6.8
+//
+H ROBB760106
+D Information measure for pleated-sheet (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C ROBB760105 0.949 KANM800102 0.938 CHOP780202 0.931
+ QIAN880120 0.908 QIAN880121 0.907 LIFS790101 0.906
+ GEIM800107 0.899 QIAN880119 0.897 PALJ810104 0.894
+ NAGK730102 0.887 PALJ810103 0.886 PTIO830102 0.882
+ KANM800104 0.877 LEVM780105 0.869 PONP930101 0.866
+ CRAJ730102 0.865 GEIM800105 0.856 BASU050101 0.851
+ CHOP780208 0.846 BASU050103 0.840 GEIM800106 0.838
+ PALJ810110 0.836 AVBF000101 0.834 CORJ870101 0.829
+ PONP800101 0.829 LIFS790103 0.827 MANP780101 0.824
+ PONP800102 0.822 CORJ870107 0.819 PONP800103 0.812
+ NISK860101 0.810 BEGF750102 0.809 PONP800108 0.808
+ CORJ870104 0.808 MIYS990104 -0.815 GEIM800110 -0.819
+ CORJ870108 -0.820 MIYS990103 -0.836 MUNV940103 -0.888
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -2.7 0.4 -4.2 -4.4 3.7 0.8 -8.1 -3.9 -3.0 7.7
+ 3.7 -2.9 3.7 3.0 -6.6 -2.4 1.7 0.3 3.3 7.1
+//
+H ROBB760107
+D Information measure for extended without H-bond (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.0 1.1 -2.0 -2.6 5.4 2.4 3.1 -3.4 0.8 -0.1
+ -3.7 -3.1 -2.1 0.7 7.4 1.3 0.0 -3.4 4.8 2.7
+//
+H ROBB760108
+D Information measure for turn (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C ROBB760113 0.994 ROBB760110 0.960 BEGF750103 0.922
+ CRAJ730103 0.912 CHOP780101 0.887 PALJ810106 0.882
+ TANS770110 0.839 CHAM830101 0.812 BEGF750101 -0.819
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -5.0 2.1 4.2 3.1 4.4 0.4 -4.7 5.7 -0.3 -4.6
+ -5.6 1.0 -4.8 -1.8 2.6 2.6 0.3 3.4 2.9 -6.0
+//
+H ROBB760109
+D Information measure for N-terminal turn (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -3.3 0.0 5.4 3.9 -0.3 -0.4 -1.8 -1.2 3.0 -0.5
+ -2.3 -1.2 -4.3 0.8 6.5 1.8 -0.7 -0.8 3.1 -3.5
+//
+H ROBB760110
+D Information measure for middle turn (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C ROBB760108 0.960 ROBB760113 0.957 BEGF750103 0.903
+ CRAJ730103 0.887 PALJ810106 0.864 CHOP780101 0.863
+ TANS770110 0.805 CHAM830101 0.804
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -4.7 2.0 3.9 1.9 6.2 -2.0 -4.2 5.7 -2.6 -7.0
+ -6.2 2.8 -4.8 -3.7 3.6 2.1 0.6 3.3 3.8 -6.2
+//
+H ROBB760111
+D Information measure for C-terminal turn (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C CHOP780215 0.825
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -3.7 1.0 -0.6 -0.6 4.0 3.4 -4.3 5.9 -0.8 -0.5
+ -2.8 1.3 -1.6 1.6 -6.0 1.5 1.2 6.5 1.3 -4.6
+//
+H ROBB760112
+D Information measure for coil (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C PALJ810115 0.885 CHOP780211 0.841 QIAN880133 0.814
+ ISOY800103 0.807 QIAN880132 0.800
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -2.5 -1.2 4.6 0.0 -4.7 -0.5 -4.4 4.9 1.6 -3.3
+ -2.0 -0.8 -4.1 -4.1 5.8 2.5 1.7 1.2 -0.6 -3.5
+//
+H ROBB760113
+D Information measure for loop (Robson-Suzuki, 1976)
+R PMID:1003471
+A Robson, B. and Suzuki, E.
+T Conformational properties of amino acid residues in globular proteins
+J J. Mol. Biol. 107, 327-356 (1976)
+C ROBB760108 0.994 ROBB760110 0.957 BEGF750103 0.924
+ CRAJ730103 0.916 CHOP780101 0.907 PALJ810106 0.895
+ TANS770110 0.853 CHAM830101 0.841 NAGK730103 0.811
+ CHOP780201 -0.811 BEGF750101 -0.826
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -5.1 2.6 4.7 3.1 3.8 0.2 -5.2 5.6 -0.9 -4.5
+ -5.4 1.0 -5.3 -2.4 3.5 3.2 0.0 2.9 3.2 -6.3
+//
+H ROBB790101
+D Hydration free energy (Robson-Osguthorpe, 1979)
+R PMID:513136
+A Robson, B. and Osguthorpe, D.J.
+T Refined models for computer simulation of protein folding: Applications to
+ the study of conserved secondary structure and flexible hinge points during
+ the folding of pancreatic trypsin inhibitor
+J J. Mol. Biol. 132, 19-51 (1979) (Gly 0.67)
+C CIDH920105 0.921 NISK860101 0.912 CIDH920104 0.903
+ BASU050102 0.897 CIDH920102 0.896 MIYS850101 0.895
+ BIOV880101 0.890 CIDH920103 0.884 PLIV810101 0.875
+ ZHOH040101 0.872 WERD780101 0.872 ZHOH040103 0.872
+ FAUJ830101 0.868 RADA880108 0.867 MEEJ810101 0.861
+ PONP930101 0.858 CASG920101 0.850 BASU050103 0.849
+ ROSG850102 0.846 CIDH920101 0.846 BASU050101 0.845
+ CORJ870102 0.835 SWER830101 0.835 MANP780101 0.834
+ CORJ870106 0.834 CORJ870107 0.832 PONP800108 0.831
+ NISK800101 0.830 CORJ870105 0.827 PONP800101 0.822
+ MEEJ810102 0.821 BIOV880102 0.821 CORJ870101 0.819
+ GUOD860101 0.815 ROSM880104 0.807 MEEJ800102 0.807
+ PONP800102 0.807 CORJ870104 0.807 CORJ870103 0.804
+ LEVM760106 0.804 MEIH800103 0.801 BULH740101 -0.813
+ PARS000101 -0.819 CORJ870108 -0.829 WOLS870101 -0.831
+ GRAR740102 -0.832 RACS770101 -0.839 MIYS990103 -0.854
+ VINM940101 -0.858 FASG890101 -0.860 GUYH850102 -0.862
+ FUKS010103 -0.865 VINM940102 -0.866 MEIH800101 -0.868
+ MIYS990104 -0.877 MIYS990101 -0.883 MIYS990102 -0.885
+ MIYS990105 -0.885 PARJ860101 -0.893 OOBM770103 -0.909
+ GUYH850103 -0.999
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -1.0 0.3 -0.7 -1.2 2.1 -0.1 -0.7 0.3 1.1 4.0
+ 2.0 -0.9 1.8 2.8 0.4 -1.2 -0.5 3.0 2.1 1.4
+//
+H ROSG850101
+D Mean area buried on transfer (Rose et al., 1985)
+R PMID:4023714
+A Rose, G.D., Geselowitz, A.R., Lesser, G.J., Lee, R.H. and Zehfus, M.H.
+T Hydrophobicity of amino acid residues in globular proteins
+J Science 229, 834-838 (1985)
+C ZHOH040102 0.930 GRAR740103 0.922 KRIW790103 0.920
+ CHAM820101 0.917 TSAJ990101 0.914 BIGC670101 0.910
+ GOLD730102 0.909 TSAJ990102 0.909 CHOC750101 0.908
+ ZHOH040101 0.904 LEVM760106 0.896 FAUJ880103 0.892
+ HARY940101 0.869 CIDH920102 0.866 PONJ960101 0.862
+ MCMT640101 0.857 LEVM760107 0.852 CHOC760101 0.842
+ FASG760101 0.838 NOZY710101 0.834 CIDH920101 0.831
+ RADA880106 0.814 PARS000101 -0.805 KARP850101 -0.807
+ VINM940102 -0.810 RADA880103 -0.814 WEBA780101 -0.817
+ FUKS010103 -0.819
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 86.6 162.2 103.3 97.8 132.3 119.2 113.9 62.9 155.8 158.0
+ 164.1 115.5 172.9 194.1 92.9 85.6 106.5 224.6 177.7 141.0
+//
+H ROSG850102
+D Mean fractional area loss (Rose et al., 1985)
+R PMID:4023714
+A Rose, G.D., Geselowitz, A.R., Lesser, G.J., Lee, R.H. and Zehfus, M.H.
+T Hydrophobicity of amino acid residues in globular proteins
+J Science 229, 834-838 (1985)
+C BIOV880101 0.981 RADA880108 0.967 NISK860101 0.962
+ BIOV880102 0.960 NADH010103 0.958 NADH010104 0.953
+ CASG920101 0.952 PONP800102 0.949 MEIH800103 0.948
+ NADH010102 0.948 CORJ870101 0.948 PONP800103 0.947
+ WERD780101 0.943 NISK800101 0.942 PONP800101 0.938
+ MIYS850101 0.937 PONP930101 0.928 PONP800108 0.919
+ DESM900102 0.914 JANJ780102 0.909 FAUJ830101 0.904
+ MANP780101 0.903 BASU050103 0.903 ZHOH040103 0.903
+ CORJ870107 0.898 CIDH920104 0.896 JANJ790102 0.892
+ CORJ870103 0.883 CORJ870106 0.878 BASU050102 0.870
+ BAEK050101 0.868 DESM900101 0.866 NADH010105 0.865
+ CORJ870105 0.864 CORJ870104 0.860 CIDH920105 0.858
+ JANJ790101 0.857 JURD980101 0.854 CHOC760103 0.851
+ BASU050101 0.849 CIDH920103 0.846 EISD860103 0.846
+ ROBB790101 0.846 PLIV810101 0.841 KYTJ820101 0.841
+ ROSM880105 0.838 NADH010101 0.833 WARP780101 0.823
+ PONP800106 0.807 EISD840101 0.806 PONP800107 0.803
+ WOEC730101 -0.804 FUKS010103 -0.808 VINM940104 -0.809
+ CHOC760102 -0.819 PARS000101 -0.820 ROSM880102 -0.822
+ PARJ860101 -0.823 HOPT810101 -0.825 JANJ780101 -0.836
+ GUYH850103 -0.844 KIDA850101 -0.849 VINM940102 -0.849
+ KRIW710101 -0.852 PUNT030102 -0.869 FUKS010104 -0.877
+ JANJ780103 -0.879 GRAR740102 -0.880 RACS770101 -0.880
+ PUNT030101 -0.883 CORJ870108 -0.890 GUYH850104 -0.891
+ KARP850102 -0.897 VINM940103 -0.901 RACS770103 -0.901
+ OOBM770101 -0.903 MIYS990101 -0.913 MIYS990102 -0.916
+ OOBM770103 -0.916 KRIW790102 -0.922 GUYH850102 -0.925
+ GUYH850101 -0.929 MEIH800101 -0.930 KRIW790101 -0.935
+ RACS770102 -0.940 VINM940101 -0.943 MEIH800102 -0.959
+ MIYS990104 -0.962 MIYS990103 -0.966 MIYS990105 -0.968
+ FASG890101 -0.976
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.74 0.64 0.63 0.62 0.91 0.62 0.62 0.72 0.78 0.88
+ 0.85 0.52 0.85 0.88 0.64 0.66 0.70 0.85 0.76 0.86
+//
+H ROSM880101
+D Side chain hydropathy, uncorrected for solvation (Roseman, 1988)
+R PMID:3398047
+A Roseman, M.A.
+T Hydrophilicity of polar amino acid side-chains is markedly reduced by
+ flanking peptide bonds
+J J. Mol. Biol. 200, 513-522 (1988)
+C KUHL950101 0.962 ROSM880102 0.938 KIDA850101 0.933
+ PRAM900101 0.917 ENGD860101 0.917 FAUJ880110 0.888
+ GRAR740102 0.887 PUNT030101 0.884 VHEG790101 0.883
+ LEVM760101 0.876 WOLS870101 0.866 PUNT030102 0.864
+ OOBM770101 0.854 GUYH850105 0.849 HOPT810101 0.848
+ FAUJ880109 0.846 WOEC730101 0.844 JANJ780101 0.822
+ GUYH850104 0.814 JANJ780103 0.810 GUYH850101 0.803
+ PARJ860101 0.803 BASU050103 -0.804 OLSK800101 -0.806
+ NAKH900110 -0.812 DESM900102 -0.812 WARP780101 -0.816
+ CHOC760103 -0.819 BIOV880102 -0.824 JANJ790102 -0.824
+ CIDH920104 -0.828 BIOV880101 -0.830 NADH010102 -0.830
+ RADA880108 -0.831 PLIV810101 -0.834 JANJ780102 -0.835
+ KYTJ820101 -0.845 COWR900101 -0.849 JURD980101 -0.851
+ RADA880104 -0.863 NADH010101 -0.866 RADA880107 -0.867
+ EISD860103 -0.871 WOLR810101 -0.884 WOLR790101 -0.887
+ JACR890101 -0.892 FAUJ830101 -0.907 EISD860101 -0.917
+ BLAS910101 -0.940 EISD840101 -0.947 ROSM880105 -0.951
+ RADA880101 -0.978
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.67 12.1 7.23 8.72 -0.34 6.39 7.35 0.00 3.82 -3.02
+ -3.02 6.13 -1.30 -3.24 -1.75 4.35 3.86 -2.86 0.98 -2.18
+//
+H ROSM880102
+D Side chain hydropathy, corrected for solvation (Roseman, 1988)
+R PMID:3398047
+A Roseman, M.A.
+T Hydrophilicity of polar amino acid side-chains is markedly reduced by
+ flanking peptide bonds
+J J. Mol. Biol. 200, 513-522 (1988)
+C ROSM880101 0.938 KUHL950101 0.922 KIDA850101 0.920
+ PRAM900101 0.892 ENGD860101 0.891 WOLS870101 0.877
+ GUYH850105 0.874 GRAR740102 0.870 OOBM770101 0.867
+ PUNT030101 0.861 MEIH800102 0.859 GUYH850104 0.856
+ JANJ780101 0.853 PUNT030102 0.851 CHOC760102 0.845
+ FASG890101 0.839 JANJ780103 0.838 GUYH850101 0.837
+ VHEG790101 0.828 FAUJ880109 0.824 RACS770102 0.824
+ LEVM760101 0.823 MIYS990101 0.819 MIYS990102 0.818
+ WOEC730101 0.801 PARJ860101 0.801 WARP780101 -0.801
+ BASU050103 -0.814 DESM900102 -0.816 ROSG850102 -0.822
+ MIYS850101 -0.825 GUOD860101 -0.829 WOLR810101 -0.829
+ MEIH800103 -0.829 CIDH920104 -0.831 WOLR790101 -0.836
+ JACR890101 -0.837 BIOV880102 -0.837 NADH010104 -0.839
+ OLSK800101 -0.847 BIOV880101 -0.854 RADA880104 -0.855
+ NADH010103 -0.857 RADA880108 -0.861 PLIV810101 -0.864
+ JANJ790102 -0.866 EISD860101 -0.868 CHOC760103 -0.869
+ NADH010101 -0.870 JANJ780102 -0.870 ROSM880105 -0.871
+ KYTJ820101 -0.878 NADH010102 -0.881 BLAS910101 -0.884
+ JURD980101 -0.894 RADA880107 -0.894 COWR900101 -0.897
+ RADA880101 -0.917 EISD840101 -0.925 FAUJ830101 -0.927
+ EISD860103 -0.943
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.67 3.89 2.27 1.57 -2.00 2.12 1.78 0.00 1.09 -3.02
+ -3.02 2.46 -1.67 -3.24 -1.75 0.10 -0.42 -2.86 0.98 -2.18
+//
+H ROSM880103
+D Loss of Side chain hydropathy by helix formation (Roseman, 1988)
+R PMID:3398047
+A Roseman, M.A.
+T Hydrophilicity of polar amino acid side-chains is markedly reduced by
+ flanking peptide bonds
+J J. Mol. Biol. 200, 513-522 (1988)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.4 0.3 0.9 0.8 0.5 0.7 1.3 0.0 1.0 0.4
+ 0.6 0.4 0.3 0.7 0.9 0.4 0.4 0.6 1.2 0.4
+//
+H SIMZ760101
+D Transfer free energy (Simon, 1976), Cited by Charton-Charton (1982)
+R
+A Simon, Z.
+T
+J Quantum Biochemistry and Specific Interactions, Abacus Press, Tunbridge
+ Wells, Kent, England (1976) Cited by Charton-Charton (1982)
+C ARGP820101 0.967 JOND750101 0.966 GOLD730101 0.939
+ TAKK010101 0.936 MEEJ800102 0.861 ROSM880104 0.855
+ LEVM760106 0.848 CIDH920105 0.837 MEEJ810101 0.836
+ CIDH920102 0.832 ZIMJ680101 0.821 BULH740102 0.815
+ LAWE840101 0.815 ZHOH040102 0.814 ZIMJ680102 0.810
+ ZHOH040101 0.808 MEEJ810102 0.808 NOZY710101 0.807
+ VENT840101 0.806 ZIMJ680105 0.805 PLIV810101 0.805
+ PARJ860101 -0.825 WOLS870101 -0.830 BULH740101 -0.894
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.73 0.73 -0.01 0.54 0.70 -0.10 0.55 0.00 1.10 2.97
+ 2.49 1.50 1.30 2.65 2.60 0.04 0.44 3.00 2.97 1.69
+//
+H SNEP660101
+D Principal component I (Sneath, 1966)
+R PMID:4291386
+A Sneath, P.H.A.
+T Relations between chemical structure and biological activity in peptides
+J J. Theor. Biol. 12, 157-195 (1966)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.239 0.211 0.249 0.171 0.220 0.260 0.187 0.160 0.205 0.273
+ 0.281 0.228 0.253 0.234 0.165 0.236 0.213 0.183 0.193 0.255
+//
+H SNEP660102
+D Principal component II (Sneath, 1966)
+R PMID:4291386
+A Sneath, P.H.A.
+T Relations between chemical structure and biological activity in peptides
+J J. Theor. Biol. 12, 157-195 (1966)
+C FAUJ880110 -0.804
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.330 -0.176 -0.233 -0.371 0.074 -0.254 -0.409 0.370 -0.078 0.149
+ 0.129 -0.075 -0.092 -0.011 0.370 0.022 0.136 -0.011 -0.138 0.245
+//
+H SNEP660103
+D Principal component III (Sneath, 1966)
+R PMID:4291386
+A Sneath, P.H.A.
+T Relations between chemical structure and biological activity in peptides
+J J. Theor. Biol. 12, 157-195 (1966)
+C LEVM760107 0.818 CHAM820101 0.808 ZASB820101 0.804
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.110 0.079 -0.136 -0.285 -0.184 -0.067 -0.246 -0.073 0.320 0.001
+ -0.008 0.049 -0.041 0.438 -0.016 -0.153 -0.208 0.493 0.381 -0.155
+//
+H SNEP660104
+D Principal component IV (Sneath, 1966)
+R PMID:4291386
+A Sneath, P.H.A.
+T Relations between chemical structure and biological activity in peptides
+J J. Theor. Biol. 12, 157-195 (1966)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.062 -0.167 0.166 -0.079 0.380 -0.025 -0.184 -0.017 0.056 -0.309
+ -0.264 -0.371 0.077 0.074 -0.036 0.470 0.348 0.050 0.220 -0.212
+//
+H SUEM840101
+D Zimm-Bragg parameter s at 20 C (Sueki et al., 1984)
+R
+A Sueki, M., Lee, S., Powers, S.P., Denton, J.B., Konishi, Y. and Scheraga,
+ H.A.
+T Helix-coil stability constants for the naturally occurring amino acids in
+ water. 22. Histidine parameters from random
+ poly{(hydroxybutyl)glutamine-co-L-histidine}
+J Macromolecules 17, 148-155 (1984) Charged state for Arg, His, Asp, and Glu
+ (Cys Pro 0.100)
+C AURR980113 0.887 FINA770101 0.883 AURR980109 0.882
+ PTIO830101 0.877 AURR980114 0.845 KANM800103 0.820
+ QIAN880107 0.803 QIAN880131 -0.823 PALJ810106 -0.832
+ CHOP780101 -0.845 ISOY800103 -0.850 LEVM780103 -0.864
+ TANS770110 -0.864 PRAM900104 -0.865 CHOP780216 -0.874
+ GEIM800108 -0.875 LEVM780106 -0.878 QIAN880133 -0.879
+ QIAN880132 -0.880 GEIM800111 -0.885 CHAM830101 -0.891
+ CHOP780203 -0.892
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.071 1.033 0.784 0.680 0.922 0.977 0.970 0.591 0.850 1.140
+ 1.140 0.939 1.200 1.086 0.659 0.760 0.817 1.107 1.020 0.950
+//
+H SUEM840102
+D Zimm-Bragg parameter sigma x 1.0E4 (Sueki et al., 1984)
+R
+A Sueki, M., Lee, S., Powers, S.P., Denton, J.B., Konishi, Y. and Scheraga,
+ H.A.
+T Helix-coil stability constants for the naturally occurring amino acids in
+ water. 22. Histidine parameters from random
+ poly{(hydroxybutyl)glutamine-co-L-histidine}
+J Macromolecules 17, 148-155 (1984) Charged state for Arg, His, Asp, and Glu
+ (Cys Pro !)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 8.0 0.1 0.1 70.0 26.0 33.0 6.0 0.1 0.1 55.0
+ 33.0 1.0 54.0 18.0 42.0 0.1 0.1 77.0 66.0 0.1
+//
+H SWER830101
+D Optimal matching hydrophobicity (Sweet-Eisenberg, 1983)
+R PMID:6663622
+A Sweet, R.M. and Eisenberg, D.
+T Correlation of sequence hydrophobicities measures similarity in
+ three-dimensional protein structure
+J J. Mol. Biol. 171, 479-488 (1983)
+C CORJ870102 1.000 BASU050101 0.922 BASU050103 0.892
+ CIDH920105 0.890 MIYS850101 0.889 BLAS910101 0.887
+ CORJ870104 0.883 CORJ870107 0.883 BASU050102 0.880
+ PLIV810101 0.875 CIDH920102 0.870 CIDH920103 0.865
+ NISK860101 0.865 ZHOH040103 0.863 CIDH920104 0.862
+ CORJ870103 0.862 ZHOH040101 0.860 PTIO830102 0.856
+ GUOD860101 0.853 CIDH920101 0.853 CORJ870105 0.848
+ CORJ870106 0.845 ROSM880104 0.844 ROSM880105 0.843
+ BIOV880101 0.839 VENT840101 0.836 NOZY710101 0.836
+ ROBB790101 0.835 PONP930101 0.835 FAUJ830101 0.833
+ ZIMJ680105 0.829 RADA880108 0.826 QIAN880120 0.825
+ EISD860101 0.824 CHOP780202 0.823 MANP780101 0.821
+ RADA880102 0.820 LIFS790101 0.815 PALJ810104 0.809
+ MEEJ810101 0.806 WERD780101 0.804 MUNV940103 -0.802
+ RACS770101 -0.803 VINM940102 -0.811 VINM940101 -0.817
+ MEIH800101 -0.830 WOEC730101 -0.832 OOBM770103 -0.833
+ PUNT030101 -0.838 GUYH850103 -0.839 PARS000101 -0.846
+ MIYS990103 -0.878 MIYS990105 -0.883 CORJ870108 -0.884
+ MIYS990104 -0.887 WOLS870101 -0.887 PARJ860101 -0.893
+ GRAR740102 -0.896 MIYS990102 -0.921 BULH740101 -0.923
+ MIYS990101 -0.923
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.40 -0.59 -0.92 -1.31 0.17 -0.91 -1.22 -0.67 -0.64 1.25
+ 1.22 -0.67 1.02 1.92 -0.49 -0.55 -0.28 0.50 1.67 0.91
+//
+H TANS770101
+D Normalized frequency of alpha-helix (Tanaka-Scheraga, 1977)
+R PMID:557155
+A Tanaka, S. and Scheraga, H.A.
+T Statistical mechanical treatment of protein conformation. 5. A multiphasic
+ model for specific-sequence copolymers of amino acids
+J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized
+ frequencies
+C ROBB760101 0.948 CHOP780201 0.947 MAXF760101 0.930
+ KANM800101 0.927 NAGK730101 0.925 PALJ810102 0.923
+ GEIM800101 0.918 PALJ810101 0.918 BURA740101 0.917
+ LEVM780104 0.908 ISOY800101 0.906 PRAM900102 0.854
+ LEVM780101 0.854 RACS820108 0.845 KANM800103 0.843
+ CRAJ730101 0.843 GEIM800104 0.841 AURR980115 0.834
+ QIAN880106 0.819 AURR980111 0.817 QIAN880107 0.804
+ AURR980114 0.800 NAGK730103 -0.800
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.42 1.06 0.71 1.01 0.73 1.02 1.63 0.50 1.20 1.12
+ 1.29 1.24 1.21 1.16 0.65 0.71 0.78 1.05 0.67 0.99
+//
+H TANS770102
+D Normalized frequency of isolated helix (Tanaka-Scheraga, 1977)
+R PMID:557155
+A Tanaka, S. and Scheraga, H.A.
+T Statistical mechanical treatment of protein conformation. 5. A multiphasic
+ model for specific-sequence copolymers of amino acids
+J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized
+ frequencies
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.946 1.128 0.432 1.311 0.481 1.615 0.698 0.360 2.168 1.283
+ 1.192 1.203 0.000 0.963 2.093 0.523 1.961 1.925 0.802 0.409
+//
+H TANS770103
+D Normalized frequency of extended structure (Tanaka-Scheraga, 1977)
+R PMID:557155
+A Tanaka, S. and Scheraga, H.A.
+T Statistical mechanical treatment of protein conformation. 5. A multiphasic
+ model for specific-sequence copolymers of amino acids
+J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized
+ frequencies
+C ISOY800102 0.929 MAXF760102 0.891 ROBB760105 0.871
+ GEIM800105 0.850 RACS820111 0.841 PALJ810103 0.824
+ WOEC730101 -0.806
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.790 1.087 0.832 0.530 1.268 1.038 0.643 0.725 0.864 1.361
+ 1.111 0.735 1.092 1.052 1.249 1.093 1.214 1.114 1.340 1.428
+//
+H TANS770104
+D Normalized frequency of chain reversal R (Tanaka-Scheraga, 1977)
+R PMID:557155
+A Tanaka, S. and Scheraga, H.A.
+T Statistical mechanical treatment of protein conformation. 5. A multiphasic
+ model for specific-sequence copolymers of amino acids
+J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized
+ frequencies
+C CHOP780213 0.954 ISOY800104 0.918 FINA910102 0.876
+ MUNV940104 0.870 MUNV940105 0.846 QIAN880134 0.837
+ ONEK900102 0.826 FODM020101 -0.802 BLAM930101 -0.837
+ BUNA790101 -0.867
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.194 0.795 0.659 1.056 0.678 1.290 0.928 1.015 0.611 0.603
+ 0.595 1.060 0.831 0.377 3.159 1.444 1.172 0.452 0.816 0.640
+//
+H TANS770105
+D Normalized frequency of chain reversal S (Tanaka-Scheraga, 1977)
+R PMID:557155
+A Tanaka, S. and Scheraga, H.A.
+T Statistical mechanical treatment of protein conformation. 5. A multiphasic
+ model for specific-sequence copolymers of amino acids
+J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized
+ frequencies
+C CHOP780214 0.862 ISOY800105 0.836
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.497 0.677 2.072 1.498 1.348 0.711 0.651 1.848 1.474 0.471
+ 0.656 0.932 0.425 1.348 0.179 1.151 0.749 1.283 1.283 0.654
+//
+H TANS770106
+D Normalized frequency of chain reversal D (Tanaka-Scheraga, 1977)
+R PMID:557155
+A Tanaka, S. and Scheraga, H.A.
+T Statistical mechanical treatment of protein conformation. 5. A multiphasic
+ model for specific-sequence copolymers of amino acids
+J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized
+ frequencies
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.937 1.725 1.080 1.640 1.004 1.078 0.679 0.901 1.085 0.178
+ 0.808 1.254 0.886 0.803 0.748 1.145 1.487 0.803 1.227 0.625
+//
+H TANS770107
+D Normalized frequency of left-handed helix (Tanaka-Scheraga, 1977)
+R PMID:557155
+A Tanaka, S. and Scheraga, H.A.
+T Statistical mechanical treatment of protein conformation. 5. A multiphasic
+ model for specific-sequence copolymers of amino acids
+J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized
+ frequencies
+C MAXF760104 0.913 ISOY800108 0.827 RICJ880115 0.807
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.289 1.380 3.169 0.917 1.767 2.372 0.285 4.259 1.061 0.262
+ 0.000 1.288 0.000 0.393 0.000 0.160 0.218 0.000 0.654 0.167
+//
+H TANS770108
+D Normalized frequency of zeta R (Tanaka-Scheraga, 1977)
+R PMID:557155
+A Tanaka, S. and Scheraga, H.A.
+T Statistical mechanical treatment of protein conformation. 5. A multiphasic
+ model for specific-sequence copolymers of amino acids
+J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized
+ frequencies
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.328 2.088 1.498 3.379 0.000 0.000 0.000 0.500 1.204 2.078
+ 0.414 0.835 0.982 1.336 0.415 1.089 1.732 1.781 0.000 0.946
+//
+H TANS770109
+D Normalized frequency of coil (Tanaka-Scheraga, 1977)
+R PMID:557155
+A Tanaka, S. and Scheraga, H.A.
+T Statistical mechanical treatment of protein conformation. 5. A multiphasic
+ model for specific-sequence copolymers of amino acids
+J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized
+ frequencies
+C MAXF760105 0.878 MAXF760104 0.821 ISOY800108 0.816
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.945 0.364 1.202 1.315 0.932 0.704 1.014 2.355 0.525 0.673
+ 0.758 0.947 1.028 0.622 0.579 1.140 0.863 0.777 0.907 0.561
+//
+H TANS770110
+D Normalized frequency of chain reversal (Tanaka-Scheraga, 1977)
+R PMID:557155
+A Tanaka, S. and Scheraga, H.A.
+T Statistical mechanical treatment of protein conformation. 5. A multiphasic
+ model for specific-sequence copolymers of amino acids
+J Macromolecules 10, 9-20 (1977) Recalculated by Kidera as normalized
+ frequencies
+C CHOP780101 0.956 CHOP780203 0.940 CHOP780216 0.930
+ PALJ810106 0.925 QIAN880133 0.920 CHAM830101 0.917
+ QIAN880132 0.903 ISOY800103 0.897 LEVM780106 0.892
+ GEIM800108 0.886 GEIM800111 0.883 LEVM780103 0.875
+ PRAM900104 0.873 QIAN880131 0.873 PALJ810105 0.860
+ CRAJ730103 0.859 CHOP780210 0.858 ROBB760113 0.853
+ ROBB760108 0.839 BEGF750103 0.834 ROBB760110 0.805
+ AURR980109 -0.816 SUEM840101 -0.864
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.842 0.936 1.352 1.366 1.032 0.998 0.758 1.349 1.079 0.459
+ 0.665 1.045 0.668 0.881 1.385 1.257 1.055 0.881 1.101 0.643
+//
+H VASM830101
+D Relative population of conformational state A (Vasquez et al., 1983)
+R
+A Vasquez, M., Nemethy, G. and Scheraga, H.A.
+T Computed conformational states of the 20 naturally occurring amino acid
+ residues and of the prototype residue alpha-aminobutyric acid
+J Macromolecules 16, 1043-1049 (1983)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.135 0.296 0.196 0.289 0.159 0.236 0.184 0.051 0.223 0.173
+ 0.215 0.170 0.239 0.087 0.151 0.010 0.100 0.166 0.066 0.285
+//
+H VASM830102
+D Relative population of conformational state C (Vasquez et al., 1983)
+R
+A Vasquez, M., Nemethy, G. and Scheraga, H.A.
+T Computed conformational states of the 20 naturally occurring amino acid
+ residues and of the prototype residue alpha-aminobutyric acid
+J Macromolecules 16, 1043-1049 (1983)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.507 0.459 0.287 0.223 0.592 0.383 0.445 0.390 0.310 0.111
+ 0.619 0.559 0.431 0.077 0.739 0.689 0.785 0.160 0.060 0.356
+//
+H VASM830103
+D Relative population of conformational state E (Vasquez et al., 1983)
+R
+A Vasquez, M., Nemethy, G. and Scheraga, H.A.
+T Computed conformational states of the 20 naturally occurring amino acid
+ residues and of the prototype residue alpha-aminobutyric acid
+J Macromolecules 16, 1043-1049 (1983) (Pro !)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.159 0.194 0.385 0.283 0.187 0.236 0.206 0.049 0.233 0.581
+ 0.083 0.159 0.198 0.682 0.366 0.150 0.074 0.463 0.737 0.301
+//
+H VELV850101
+D Electron-ion interaction potential (Veljkovic et al., 1985)
+R
+A Veljkovic, V., Cosic, I., Dimitrijevic, B. and Lalovic, D.
+T Is it possible to analyze DNA and protein sequences by the method of digital
+ signal processing?
+J IEEE Trans. Biomed. Eng. 32, 337-341 (1985)
+C COSI940101 1.000
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ .03731 .09593 .00359 .12630 .08292 .07606 .00580 .00499 .02415 .00000
+ .00000 .03710 .08226 .09460 .01979 .08292 .09408 .05481 .05159 .00569
+//
+H VENT840101
+D Bitterness (Venanzi, 1984)
+R PMID:6521488
+A Venanzi, T.J.
+T Hydrophobicity parameters and the bitter taste of L-amino acids
+J J. Theor. Biol. 111, 447-450 (1984)
+C NOZY710101 0.897 BASU050101 0.858 ZHOH040101 0.858
+ BASU050102 0.851 GUOD860101 0.848 PTIO830102 0.842
+ WILM950101 0.840 CORJ870102 0.837 SWER830101 0.836
+ ZHOH040102 0.831 MEEJ810102 0.831 PALJ810104 0.831
+ ROSM880104 0.829 RADA880102 0.826 CHOP780209 0.817
+ BASU050103 0.814 LIFS790101 0.814 MEEJ810101 0.813
+ CIDH920105 0.813 TAKK010101 0.812 ZHOH040103 0.807
+ SIMZ760101 0.806 PONP800107 0.805 CHOP780202 0.805
+ GOLD730101 0.802 MIYS990102 -0.820 MIYS990101 -0.821
+ WOLS870101 -0.835 PARJ860101 -0.846 BULH740101 -0.907
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0. 0. 0. 0. 0. 0. 0. 0. 0. 1.
+ 1. 0. 0. 1. 0. 0. 0. 1. 1. 1.
+//
+H VHEG790101
+D Transfer free energy to lipophilic phase (von Heijne-Blomberg, 1979)
+R PMID:477664
+A von Heijne, G. and Blomberg, C.
+T Trans-membrane translocation of proteins: The direct transfer model
+J Eur. J. Biochem. 97, 175-181 (1979)
+C ENGD860101 0.909 PRAM900101 0.909 ROSM880101 0.883
+ PUNT030101 0.876 PUNT030102 0.873 KUHL950101 0.858
+ HOPT810101 0.849 GUYH850105 0.845 ROSM880102 0.828
+ LEVM760101 0.825 JURD980101 -0.814 RADA880102 -0.818
+ NADH010101 -0.827 WOLR790101 -0.844 BLAS910101 -0.847
+ NAKH900110 -0.848 EISD860101 -0.862 WOLR810101 -0.867
+ ROSM880105 -0.901 JACR890101 -0.903 EISD840101 -0.924
+ RADA880101 -0.925
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -12.04 39.23 4.25 23.22 3.95 2.16 16.81 -7.85 6.28 -18.32
+ -17.79 9.71 -8.86 -21.98 5.82 -1.54 -4.15 -16.19 -1.51 -16.22
+//
+H WARP780101
+D Average interactions per side chain atom (Warme-Morgan, 1978)
+R PMID:633361
+A Warme, P.K. and Morgan, R.S.
+T A survey of amino acid side-chain interactions in 21 proteins
+J J. Mol. Biol. 118, 289-304 (1978) (Gly 0.81)
+C DESM900102 0.882 JANJ780102 0.878 JANJ790102 0.877
+ NADH010102 0.870 DESM900101 0.864 BIOV880102 0.853
+ KYTJ820101 0.845 MEIH800103 0.835 JURD980101 0.827
+ CHOC760103 0.824 ROSG850102 0.823 EISD860103 0.820
+ OLSK800101 0.818 CHOC760104 0.815 NADH010103 0.811
+ CORJ870101 0.800 ROSM880102 -0.801 KUHL950101 -0.811
+ PUNT030101 -0.814 ROSM880101 -0.816 MEIH800102 -0.826
+ PRAM900101 -0.827 ENGD860101 -0.827 RACS770103 -0.848
+ CHOC760102 -0.849 JANJ780101 -0.869 GUYH850104 -0.882
+ JANJ780103 -0.890 OOBM770101 -0.937
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 10.04 6.18 5.63 5.76 8.89 5.41 5.37 7.99 7.49 8.72
+ 8.79 4.40 9.15 7.98 7.79 7.08 7.00 8.07 6.90 8.88
+//
+H WEBA780101
+D RF value in high salt chromatography (Weber-Lacey, 1978)
+R PMID:691071
+A Weber, A.L. and Lacey, J.C.,Jr.
+T Genetic code correlations: Amino acids and their anticodon nucleotides
+J J. Mol. Evol. 11, 199-210 (1978)
+C ZHOH040102 -0.807 MEEJ800102 -0.808 ROSG850101 -0.817
+ MEEJ810101 -0.831 MEEJ810102 -0.854 ZHOH040101 -0.865
+ NOZY710101 -0.890 LEVM760107 -0.923 GARJ730101 -0.924
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.89 0.88 0.89 0.87 0.85 0.82 0.84 0.92 0.83 0.76
+ 0.73 0.97 0.74 0.52 0.82 0.96 0.92 0.20 0.49 0.85
+//
+H WERD780101
+D Propensity to be buried inside (Wertz-Scheraga, 1978)
+R PMID:621952
+A Wertz, D.H. and Scheraga, H.A.
+T Influence of water on protein structure. An analysis of the preferences of
+ amino acid residues for the inside or outside and for specific conformations
+ in a protein molecule
+J Macromolecules 11, 9-15 (1978) Adjusted values
+C NISK860101 0.966 BIOV880101 0.951 ROSG850102 0.943
+ MIYS850101 0.934 RADA880108 0.930 BIOV880102 0.929
+ CASG920101 0.927 ZHOH040103 0.923 BASU050102 0.920
+ CIDH920105 0.905 CIDH920104 0.896 PONP930101 0.895
+ MEIH800103 0.895 BAEK050101 0.895 NISK800101 0.891
+ NADH010104 0.890 CORJ870107 0.887 PONP800102 0.883
+ CORJ870103 0.882 CIDH920103 0.881 NADH010103 0.880
+ PONP800101 0.880 CIDH920101 0.878 CORJ870106 0.878
+ PONP800103 0.876 CORJ870101 0.873 ROBB790101 0.872
+ CIDH920102 0.871 FAUJ830101 0.862 ZHOH040101 0.859
+ CORJ870105 0.858 BASU050103 0.857 MANP780101 0.853
+ CORJ870104 0.850 PONP800108 0.843 BASU050101 0.843
+ PLIV810101 0.841 NADH010102 0.841 NADH010105 0.837
+ MEEJ810101 0.825 DESM900102 0.814 CORJ870102 0.804
+ SWER830101 0.804 FUKS010102 -0.801 BHAR880101 -0.803
+ KRIW710101 -0.819 PUNT030101 -0.821 GRAR740102 -0.826
+ FUKS010104 -0.832 KARP850101 -0.842 RACS770103 -0.846
+ PARS000101 -0.853 PARJ860101 -0.869 FUKS010103 -0.869
+ GUYH850101 -0.871 KRIW790102 -0.875 GUYH850103 -0.876
+ CORJ870108 -0.878 VINM940102 -0.886 KRIW790101 -0.899
+ MEIH800102 -0.903 RACS770102 -0.906 OOBM770103 -0.906
+ KARP850102 -0.909 MIYS990101 -0.912 RACS770101 -0.912
+ MIYS990102 -0.914 FASG890101 -0.926 VINM940103 -0.926
+ VINM940101 -0.931 MIYS990105 -0.936 MIYS990103 -0.938
+ MEIH800101 -0.943 MIYS990104 -0.949 GUYH850102 -0.976
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.52 0.49 0.42 0.37 0.83 0.35 0.38 0.41 0.70 0.79
+ 0.77 0.31 0.76 0.87 0.35 0.49 0.38 0.86 0.64 0.72
+//
+H WERD780102
+D Free energy change of epsilon(i) to epsilon(ex) (Wertz-Scheraga, 1978)
+R PMID:621952
+A Wertz, D.H. and Scheraga, H.A.
+T Influence of water on protein structure. An analysis of the preferences of
+ amino acid residues for the inside or outside and for specific conformations
+ in a protein molecule
+J Macromolecules 11, 9-15 (1978) Adjusted values
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.16 -0.20 1.03 -0.24 -0.12 -0.55 -0.45 -0.16 -0.18 -0.19
+ -0.44 -0.12 -0.79 -0.25 -0.59 -0.01 0.05 -0.33 -0.42 -0.46
+//
+H WERD780103
+D Free energy change of alpha(Ri) to alpha(Rh) (Wertz-Scheraga, 1978)
+R PMID:621952
+A Wertz, D.H. and Scheraga, H.A.
+T Influence of water on protein structure. An analysis of the preferences of
+ amino acid residues for the inside or outside and for specific conformations
+ in a protein molecule
+J Macromolecules 11, 9-15 (1978) Adjusted values (Met !)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.15 -0.37 0.69 -0.22 -0.19 -0.06 0.14 0.36 -0.25 0.02
+ 0.06 -0.16 0.11 1.18 0.11 0.13 0.28 -0.12 0.19 -0.08
+//
+H WERD780104
+D Free energy change of epsilon(i) to alpha(Rh) (Wertz-Scheraga, 1978)
+R PMID:621952
+A Wertz, D.H. and Scheraga, H.A.
+T Influence of water on protein structure. An analysis of the preferences of
+ amino acid residues for the inside or outside and for specific conformations
+ in a protein molecule
+J Macromolecules 11, 9-15 (1978) Adjusted values
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.07 -0.40 -0.57 -0.80 0.17 -0.26 -0.63 0.27 -0.49 0.06
+ -0.17 -0.45 0.03 0.40 -0.47 -0.11 0.09 -0.61 -0.61 -0.11
+//
+H WOEC730101
+D Polar requirement (Woese, 1973)
+R PMID:4588588
+A Woese, C.R.
+T Evolution of genetic code
+J Naturwiss. 60, 447-459 (1973)
+C GRAR740102 0.960 PUNT030102 0.894 HOPT810101 0.886
+ HOPA770101 0.876 LEVM760101 0.872 ENGD860101 0.871
+ PRAM900101 0.871 MIYS990105 0.849 ROSM880101 0.844
+ WOLS870101 0.841 KUHL950101 0.837 OOBM770103 0.835
+ VINM940101 0.834 MIYS990104 0.827 PUNT030101 0.825
+ MIYS990103 0.824 PARJ860101 0.821 FUKS010102 0.820
+ FAUJ880110 0.812 KIDA850101 0.807 MIYS990102 0.805
+ MIYS990101 0.805 OOBM770101 0.804 ROSM880102 0.801
+ NADH010102 -0.800 CIDH920105 -0.800 MEIH800103 -0.802
+ ISOY800102 -0.803 EISD860103 -0.803 ROSG850102 -0.804
+ TANS770103 -0.806 BASU050101 -0.811 RADA880101 -0.812
+ BIOV880102 -0.819 WIMW960101 -0.821 NISK860101 -0.822
+ PONP800103 -0.823 CIDH920104 -0.823 RADA880108 -0.825
+ CORJ870102 -0.828 BIOV880101 -0.829 PONP800108 -0.831
+ SWER830101 -0.832 BASU050103 -0.836 EISD860101 -0.838
+ CORJ870101 -0.841 MAXF760102 -0.842 DESM900102 -0.847
+ FAUJ830101 -0.880 ROSM880105 -0.902 BLAS910101 -0.902
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 7.0 9.1 10.0 13.0 5.5 8.6 12.5 7.9 8.4 4.9
+ 4.9 10.1 5.3 5.0 6.6 7.5 6.6 5.3 5.7 5.6
+//
+H WOLR810101
+D Hydration potential (Wolfenden et al., 1981)
+R PMID:7213619
+A Wolfenden, R. andersson, L., Cullis, P.M. and Southgate, C.C.B.
+T Affinties of amino acid side chains for solvent water
+J Biochemistry 20, 849-855 (1981) (Pro 2.9)
+C WOLR790101 0.996 RADA880101 0.939 EISD840101 0.914
+ RADA880104 0.910 JACR890101 0.908 RADA880107 0.890
+ KYTJ820101 0.885 JURD980101 0.881 RADA880105 0.875
+ CHOC760103 0.873 OLSK800101 0.869 CHOC760104 0.868
+ JANJ780102 0.851 NADH010101 0.848 JANJ790102 0.828
+ JANJ780103 -0.822 GUYH850104 -0.826 ROSM880102 -0.829
+ CHOC760102 -0.840 OOBM770101 -0.847 JANJ780101 -0.864
+ VHEG790101 -0.867 ROSM880101 -0.884 ENGD860101 -0.887
+ PRAM900101 -0.887 KUHL950101 -0.898 FAUJ880109 -0.904
+ GUYH850105 -0.916
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.94 -19.92 -9.68 -10.95 -1.24 -9.38 -10.20 2.39 -10.27 2.15
+ 2.28 -9.52 -1.48 -0.76 -3.68 -5.06 -4.88 -5.88 -6.11 1.99
+//
+H WOLS870101
+D Principal property value z1 (Wold et al., 1987)
+R
+A Wold, S., Eriksson, L., Hellberg, S., Jonsson, J., Sjostrom, M., Skagerberg,
+ B. and Wikstrom, C.
+T Principal property values for six non-natural amino acids and their
+ application to a structure-activity relationship for oxytocin peptide
+ analogues
+J Can. J. Chem. 65, 1814-1820 (1987)
+C PARJ860101 0.964 BULH740101 0.929 MIYS990101 0.912
+ MIYS990102 0.910 GRAR740102 0.910 ROSM880102 0.877
+ PUNT030102 0.868 ROSM880101 0.866 PUNT030101 0.853
+ MEIH800101 0.852 OOBM770103 0.852 KIDA850101 0.852
+ LEVM760101 0.845 WOEC730101 0.841 MIYS990105 0.838
+ GUYH850103 0.836 HOPT810101 0.830 MIYS990104 0.830
+ MIYS990103 0.815 MEIH800102 0.813 RACS770102 0.802
+ MANP780101 -0.809 EISD840101 -0.820 RADA880101 -0.823
+ MEEJ800101 -0.823 SIMZ760101 -0.830 ROBB790101 -0.831
+ NAKH900110 -0.832 VENT840101 -0.835 JOND750101 -0.837
+ ARGP820101 -0.838 RADA880108 -0.840 EISD860103 -0.841
+ BIOV880102 -0.842 NISK860101 -0.848 BASU050102 -0.849
+ WILM950101 -0.851 PONP800107 -0.852 BIOV880101 -0.854
+ GOLD730101 -0.854 ZHOH040101 -0.858 TAKK010101 -0.858
+ BASU050103 -0.866 BASU050101 -0.869 CIDH920102 -0.869
+ ZHOH040103 -0.870 ROSM880104 -0.870 BROC820101 -0.871
+ RADA880102 -0.873 NOZY710101 -0.874 CIDH920103 -0.879
+ COWR900101 -0.883 CORJ870102 -0.885 SWER830101 -0.887
+ CIDH920104 -0.891 CIDH920105 -0.899 ROSM880105 -0.899
+ MIYS850101 -0.899 MEEJ810102 -0.905 MEEJ810101 -0.906
+ EISD860101 -0.918 MEEJ800102 -0.925 FAUJ830101 -0.928
+ BLAS910101 -0.930 ZIMJ680105 -0.937 GUOD860101 -0.955
+ PLIV810101 -0.963
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.07 2.88 3.22 3.64 0.71 2.18 3.08 2.23 2.41 -4.44
+ -4.19 2.84 -2.49 -4.92 -1.22 1.96 0.92 -4.75 -1.39 -2.69
+//
+H WOLS870102
+D Principal property value z2 (Wold et al., 1987)
+R
+A Wold, S., Eriksson, L., Hellberg, S., Jonsson, J., Sjostrom, M., Skagerberg,
+ B. and Wikstrom, C.
+T Principal property values for six non-natural amino acids and their
+ application to a structure-activity relationship for oxytocin peptide
+ analogues
+J Can. J. Chem. 65, 1814-1820 (1987)
+C LEVM760102 0.881 FASG760101 0.866 FAUJ880106 0.866
+ CHOC760101 0.845 LEVM760105 0.836 FAUJ880103 0.814
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -1.73 2.52 1.45 1.13 -0.97 0.53 0.39 -5.36 1.74 -1.68
+ -1.03 1.41 -0.27 1.30 0.88 -1.63 -2.09 3.65 2.32 -2.53
+//
+H WOLS870103
+D Principal property value z3 (Wold et al., 1987)
+R
+A Wold, S., Eriksson, L., Hellberg, S., Jonsson, J., Sjostrom, M., Skagerberg,
+ B. and Wikstrom, C.
+T Principal property values for six non-natural amino acids and their
+ application to a structure-activity relationship for oxytocin peptide
+ analogues
+J Can. J. Chem. 65, 1814-1820 (1987)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.09 -3.44 0.84 2.36 4.13 -1.14 -0.07 0.30 1.11 -1.03
+ -0.98 -3.14 -0.41 0.45 2.23 0.57 -1.40 0.85 0.01 -1.29
+//
+H YUTK870101
+D Unfolding Gibbs energy in water, pH7.0 (Yutani et al., 1987)
+R PMID:3299367
+A Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y.
+T Dependence of conformational stability on hydrophobicity of the amino acid
+ residue in a series of variant proteins substituted at a unique position of
+ tryptophan synthase alpha subunit
+J Proc. Natl. Acad. Sci. USA 84, 4441-4444 (1987) (Arg missing)
+C YUTK870102 0.827 EISD840101 0.809 RADA880101 0.803
+ GUYH850101 -0.813 GUYH850105 -0.841
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 8.5 0. 8.2 8.5 11.0 6.3 8.8 7.1 10.1 16.8
+ 15.0 7.9 13.3 11.2 8.2 7.4 8.8 9.9 8.8 12.0
+//
+H YUTK870102
+D Unfolding Gibbs energy in water, pH9.0 (Yutani et al., 1987)
+R PMID:3299367
+A Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y.
+T Dependence of conformational stability on hydrophobicity of the amino acid
+ residue in a series of variant proteins substituted at a unique position of
+ tryptophan synthase alpha subunit
+J Proc. Natl. Acad. Sci. USA 84, 4441-4444 (1987) (Arg missing)
+C YUTK870101 0.827
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.8 0. 6.2 7.0 8.3 8.5 4.9 6.4 9.2 10.0
+ 12.2 7.5 8.4 8.3 6.9 8.0 7.0 5.7 6.8 9.4
+//
+H YUTK870103
+D Activation Gibbs energy of unfolding, pH7.0 (Yutani et al., 1987)
+R PMID:3299367
+A Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y.
+T Dependence of conformational stability on hydrophobicity of the amino acid
+ residue in a series of variant proteins substituted at a unique position of
+ tryptophan synthase alpha subunit
+J Proc. Natl. Acad. Sci. USA 84, 4441-4444 (1987) (Arg missing)
+C YUTK870104 0.997 EISD860102 -0.839
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 18.08 0. 17.47 17.36 18.17 17.93 18.16 18.24 18.49 18.62
+ 18.60 17.96 18.11 17.30 18.16 17.57 17.54 17.19 17.99 18.30
+//
+H YUTK870104
+D Activation Gibbs energy of unfolding, pH9.0 (Yutani et al., 1987)
+R PMID:3299367
+A Yutani, K., Ogasahara, K., Tsujita, T. and Sugino, Y.
+T Dependence of conformational stability on hydrophobicity of the amino acid
+ residue in a series of variant proteins substituted at a unique position of
+ tryptophan synthase alpha subunit
+J Proc. Natl. Acad. Sci. USA 84, 4441-4444 (1987) (Arg missing)
+C YUTK870103 0.997 EISD860102 -0.840
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 18.56 0. 18.24 17.94 17.84 18.51 17.97 18.57 18.64 19.21
+ 19.01 18.36 18.49 17.95 18.77 18.06 17.71 16.87 18.23 18.98
+//
+H ZASB820101
+D Dependence of partition coefficient on ionic strength (Zaslavsky et al.,
+ 1982)
+R
+A Zaslavsky, B.Yu, Mestechkina, N.M., Miheeva, L.M. and Rogozhin, S.V.
+T Measurement of relative hydrophobicity of amino acid side-chains by partition
+ in an aqueous two-phase polymeric system: Hydrophobicity scale for non-polar
+ and ionogenic side-chains
+J J. Chromatogr. 240, 21-28 (1982) (C H Y missing?)
+C WIMW960101 0.885 CIDH920102 0.809 SNEP660103 0.804
+ OOBM850102 -0.853
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.152 -0.089 -0.203 -0.355 0. -0.181 -0.411 -0.190 0. -0.086
+ -0.102 -0.062 -0.107 0.001 -0.181 -0.203 -0.170 0.275 0. -0.125
+//
+H ZIMJ680101
+D Hydrophobicity (Zimmerman et al., 1968)
+R PMID:5700434
+A Zimmerman, J.M., Eliezer, N. and Simha, R.
+T The characterization of amino acid sequences in proteins by statistical
+ methods
+J J. Theor. Biol. 21, 170-201 (1968)
+C SIMZ760101 0.821
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.83 0.83 0.09 0.64 1.48 0.00 0.65 0.10 1.10 3.07
+ 2.52 1.60 1.40 2.75 2.70 0.14 0.54 0.31 2.97 1.79
+//
+H ZIMJ680102
+D Bulkiness (Zimmerman et al., 1968)
+R PMID:5700434
+A Zimmerman, J.M., Eliezer, N. and Simha, R.
+T The characterization of amino acid sequences in proteins by statistical
+ methods
+J J. Theor. Biol. 21, 170-201 (1968)
+C FAUJ880101 0.888 ZHOH040102 0.878 LEVM760106 0.873
+ TAKK010101 0.840 BULH740102 0.825 GOLD730101 0.818
+ SIMZ760101 0.810
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 11.50 14.28 12.82 11.68 13.46 14.45 13.57 3.40 13.69 21.40
+ 21.40 15.71 16.25 19.80 17.43 9.47 15.77 21.67 18.03 21.57
+//
+H ZIMJ680103
+D Polarity (Zimmerman et al., 1968)
+R PMID:5700434
+A Zimmerman, J.M., Eliezer, N. and Simha, R.
+T The characterization of amino acid sequences in proteins by statistical
+ methods
+J J. Theor. Biol. 21, 170-201 (1968)
+C PRAM900101 0.854 ENGD860101 0.854 HOPA770101 0.815
+ JACR890101 -0.835
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.00 52.00 3.38 49.70 1.48 3.53 49.90 0.00 51.60 0.13
+ 0.13 49.50 1.43 0.35 1.58 1.67 1.66 2.10 1.61 0.13
+//
+H ZIMJ680104
+D Isoelectric point (Zimmerman et al., 1968)
+R PMID:5700434
+A Zimmerman, J.M., Eliezer, N. and Simha, R.
+T The characterization of amino acid sequences in proteins by statistical
+ methods
+J J. Theor. Biol. 21, 170-201 (1968)
+C KLEP840101 0.941 FAUJ880111 0.813 FINA910103 0.805
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.00 10.76 5.41 2.77 5.05 5.65 3.22 5.97 7.59 6.02
+ 5.98 9.74 5.74 5.48 6.30 5.68 5.66 5.89 5.66 5.96
+//
+H ZIMJ680105
+D RF rank (Zimmerman et al., 1968)
+R PMID:5700434
+A Zimmerman, J.M., Eliezer, N. and Simha, R.
+T The characterization of amino acid sequences in proteins by statistical
+ methods
+J J. Theor. Biol. 21, 170-201 (1968)
+C MEEJ800102 0.921 EISD860101 0.900 BROC820101 0.896
+ PLIV810101 0.875 BROC820102 0.865 ROSM880105 0.857
+ TAKK010101 0.856 BLAS910101 0.855 RADA880102 0.851
+ GUOD860101 0.850 MEEJ800101 0.842 NOZY710101 0.837
+ SWER830101 0.829 CORJ870102 0.828 GOLD730101 0.820
+ FAUJ830101 0.816 LAWE840101 0.809 SIMZ760101 0.805
+ MIYS990101 -0.801 HOPT810101 -0.816 LEVM760101 -0.844
+ BULH740101 -0.879 PARJ860101 -0.886 WOLS870101 -0.937
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 9.9 4.6 5.4 2.8 2.8 9.0 3.2 5.6 8.2 17.1
+ 17.6 3.5 14.9 18.8 14.8 6.9 9.5 17.1 15.0 14.3
+//
+H AURR980101
+D Normalized positional residue frequency at helix termini N4'(Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.94 1.15 0.79 1.19 0.60 0.94 1.41 1.18 1.15 1.07
+ 0.95 1.03 0.88 1.06 1.18 0.69 0.87 0.91 1.04 0.90
+//
+H AURR980102
+D Normalized positional residue frequency at helix termini N"' (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.98 1.14 1.05 1.05 0.41 0.90 1.04 1.25 1.01 0.88
+ 0.80 1.06 1.12 1.12 1.31 1.02 0.80 0.90 1.12 0.87
+//
+H AURR980103
+D Normalized positional residue frequency at helix termini N" (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.05 0.81 0.91 1.39 0.60 0.87 1.11 1.26 1.43 0.95
+ 0.96 0.97 0.99 0.95 1.05 0.96 1.03 1.06 0.94 0.62
+//
+H AURR980104
+D Normalized positional residue frequency at helix termini N'(Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C AURR980105 0.839 FINA910101 0.804
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.75 0.90 1.24 1.72 0.66 1.08 1.10 1.14 0.96 0.80
+ 1.01 0.66 1.02 0.88 1.33 1.20 1.13 0.68 0.80 0.58
+//
+H AURR980105
+D Normalized positional residue frequency at helix termini Nc (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C AURR980104 0.839
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.67 0.76 1.28 1.58 0.37 1.05 0.94 0.98 0.83 0.78
+ 0.79 0.84 0.98 0.96 1.12 1.25 1.41 0.94 0.82 0.67
+//
+H AURR980106
+D Normalized positional residue frequency at helix termini N1 (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.10 1.05 0.72 1.14 0.26 1.31 2.30 0.55 0.83 1.06
+ 0.84 1.08 0.90 0.90 1.67 0.81 0.77 1.26 0.99 0.76
+//
+H AURR980107
+D Normalized positional residue frequency at helix termini N2 (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C RICJ880106 0.800
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.39 0.95 0.67 1.64 0.52 1.60 2.07 0.65 1.36 0.64
+ 0.91 0.80 1.10 1.00 0.94 0.69 0.92 1.10 0.73 0.70
+//
+H AURR980108
+D Normalized positional residue frequency at helix termini N3 (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C AURR980112 0.910 PALJ810102 0.871 CHOP780201 0.867
+ KANM800103 0.857 ISOY800101 0.856 AURR980109 0.848
+ MAXF760101 0.841 QIAN880106 0.838 ROBB760103 0.835
+ AURR980113 0.821 QIAN880104 0.815 ROBB760101 0.814
+ BEGF750101 0.810 BURA740101 0.808 QIAN880107 0.803
+ MUNV940102 -0.803 MUNV940101 -0.814 CHAM830101 -0.834
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.43 1.33 0.55 0.90 0.52 1.43 1.70 0.56 0.66 1.18
+ 1.52 0.82 1.68 1.10 0.15 0.61 0.75 1.68 0.65 1.14
+//
+H AURR980109
+D Normalized positional residue frequency at helix termini N4 (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C KANM800103 0.944 AURR980114 0.939 ISOY800101 0.894
+ QIAN880107 0.893 AURR980113 0.892 SUEM840101 0.882
+ PALJ810102 0.877 AURR980112 0.875 MAXF760101 0.865
+ QIAN880106 0.862 CHOP780201 0.859 ROBB760103 0.857
+ KANM800101 0.852 AURR980108 0.848 RICJ880109 0.828
+ BEGF750101 0.821 PTIO830101 0.820 AURR980110 0.817
+ ROBB760101 0.810 QIAN880109 0.807 RACS820108 0.804
+ QIAN880110 0.802 FINA770101 0.802 QIAN880132 -0.806
+ LEVM780103 -0.814 GEIM800111 -0.814 PRAM900104 -0.815
+ TANS770110 -0.816 MUNV940102 -0.818 MUNV940101 -0.828
+ CHOP780101 -0.837 PALJ810106 -0.845 CHAM830101 -0.896
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.55 1.39 0.60 0.61 0.59 1.43 1.34 0.37 0.89 1.47
+ 1.36 1.27 2.13 1.39 0.03 0.44 0.65 1.10 0.93 1.18
+//
+H AURR980110
+D Normalized positional residue frequency at helix termini N5 (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C AURR980115 0.907 AURR980111 0.867 MAXF760101 0.860
+ ISOY800101 0.855 KANM800101 0.830 AURR980109 0.817
+ AURR980112 0.816 QIAN880107 0.815 CHOP780201 0.814
+ PALJ810102 0.812 AURR980114 0.811 GEOR030108 0.804
+ QIAN880106 0.804 MUNV940101 -0.822 MUNV940102 -0.846
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.80 1.73 0.73 0.90 0.55 0.97 1.73 0.32 0.46 1.09
+ 1.47 1.24 1.64 0.96 0.15 0.67 0.70 0.68 0.91 0.81
+//
+H AURR980111
+D Normalized positional residue frequency at helix termini C5 (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C AURR980110 0.867 GEOR030108 0.846 AURR980115 0.835
+ PALJ810102 0.830 TANS770101 0.817 CHOP780201 0.813
+ AURR980114 0.811 MAXF760101 0.811 ISOY800101 0.801
+ AURR980112 0.800
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.52 1.49 0.58 1.04 0.26 1.41 1.76 0.30 0.83 1.25
+ 1.26 1.10 1.14 1.14 0.44 0.66 0.73 0.68 1.04 1.03
+//
+H AURR980112
+D Normalized positional residue frequency at helix termini C4 (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C AURR980108 0.910 PALJ810102 0.888 AURR980109 0.875
+ KANM800103 0.871 ISOY800101 0.870 CHOP780201 0.856
+ AURR980114 0.853 AURR980115 0.850 AURR980113 0.848
+ KANM800101 0.847 GEOR030108 0.846 RACS820108 0.840
+ QIAN880106 0.839 MAXF760101 0.838 PALJ810109 0.817
+ AURR980110 0.816 GEIM800104 0.815 ROBB760101 0.806
+ QIAN880107 0.802 GEIM800101 0.802 AURR980111 0.800
+ MUNV940101 -0.819 MUNV940102 -0.853
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.49 1.41 0.67 0.94 0.37 1.52 1.55 0.29 0.96 1.04
+ 1.40 1.17 1.84 0.86 0.20 0.68 0.79 1.52 1.06 0.94
+//
+H AURR980113
+D Normalized positional residue frequency at helix termini C3 (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C KANM800103 0.905 AURR980109 0.892 SUEM840101 0.887
+ BEGF750101 0.857 FINA770101 0.849 AURR980112 0.848
+ ROBB760103 0.838 AURR980114 0.836 QIAN880106 0.835
+ QIAN880105 0.833 PTIO830101 0.833 QIAN880107 0.832
+ AURR980108 0.821 ISOY800101 0.815 RICJ880109 0.808
+ CHAM830101 -0.828
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.73 1.24 0.70 0.68 0.63 0.88 1.16 0.32 0.76 1.15
+ 1.80 1.22 2.21 1.35 0.07 0.65 0.46 1.57 1.10 0.94
+//
+H AURR980114
+D Normalized positional residue frequency at helix termini C2 (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C AURR980109 0.939 KANM800103 0.916 QIAN880107 0.876
+ FINA770101 0.875 ISOY800101 0.857 MAXF760101 0.853
+ AURR980112 0.853 KANM800101 0.852 PALJ810102 0.848
+ SUEM840101 0.845 AURR980113 0.836 CHOP780201 0.828
+ QIAN880110 0.819 RACS820108 0.818 AURR980111 0.811
+ AURR980110 0.811 QIAN880109 0.810 PTIO830101 0.809
+ AURR980115 0.804 GEOR030108 0.804 QIAN880106 0.803
+ ROBB760103 0.801 TANS770101 0.800 CHOP780101 -0.803
+ MUNV940102 -0.820 MUNV940101 -0.821 CHAM830101 -0.842
+ PALJ810106 -0.842
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.33 1.39 0.64 0.60 0.44 1.37 1.43 0.20 1.02 1.58
+ 1.63 1.71 1.76 1.22 0.07 0.42 0.57 1.00 1.02 1.08
+//
+H AURR980115
+D Normalized positional residue frequency at helix termini C1 (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C AURR980110 0.907 KANM800101 0.858 MAXF760101 0.852
+ AURR980112 0.850 ISOY800101 0.844 AURR980111 0.835
+ TANS770101 0.834 PALJ810102 0.827 GEOR030108 0.821
+ LEVM780104 0.818 CHOP780201 0.816 GEIM800101 0.804
+ AURR980114 0.804 RACS820108 0.802 MUNV940101 -0.807
+ MUNV940102 -0.852
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.87 1.66 0.70 0.91 0.33 1.24 1.88 0.33 0.89 0.90
+ 1.65 1.63 1.35 0.67 0.03 0.71 0.50 1.00 0.73 0.51
+//
+H AURR980116
+D Normalized positional residue frequency at helix termini Cc (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.19 1.45 1.33 0.72 0.44 1.43 1.27 0.74 1.55 0.61
+ 1.36 1.45 1.35 1.20 0.10 1.02 0.82 0.58 1.06 0.46
+//
+H AURR980117
+D Normalized positional residue frequency at helix termini C' (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C RICJ880115 0.921 MAXF760104 0.849 ISOY800108 0.822
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.77 1.11 1.39 0.79 0.44 0.95 0.92 2.74 1.65 0.64
+ 0.66 1.19 0.74 1.04 0.66 0.64 0.82 0.58 0.93 0.53
+//
+H AURR980118
+D Normalized positional residue frequency at helix termini C" (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.93 0.96 0.82 1.15 0.67 1.02 1.07 1.08 1.40 1.14
+ 1.16 1.27 1.11 1.05 1.01 0.71 0.84 1.06 1.15 0.74
+//
+H AURR980119
+D Normalized positional residue frequency at helix termini C"' (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C MUNV940104 0.804
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.09 1.29 1.03 1.17 0.26 1.08 1.31 0.97 0.88 0.97
+ 0.87 1.13 0.96 0.84 2.01 0.76 0.79 0.91 0.64 0.77
+//
+H AURR980120
+D Normalized positional residue frequency at helix termini C4' (Aurora-Rose,
+ 1998)
+R PMID:9514257
+A Aurora, R. and Rose, G.
+T Helix capping
+J Protein Science 7, 21-38 (1998)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.71 1.09 0.95 1.43 0.65 0.87 1.19 1.07 1.13 1.05
+ 0.84 1.10 0.80 0.95 1.70 0.65 .086 1.25 0.85 1.12
+//
+H ONEK900101
+D Delta G values for the peptides extrapolated to 0 M urea (O'Neil-DeGrado,
+ 1990)
+R PMID:2237415
+A O'Neil, K.T. and DeGrado, W.F.
+T A thermodynamic scale for the helix-forming tendencies of the commonly
+ occurring amino acids
+J Science 250, 646-651 (1990)
+C BLAM930101 0.965 BUNA790101 0.902 ROBB760103 0.878
+ QIAN880108 0.866 PTIO830101 0.847 ROBB760104 0.844
+ QIAN880109 0.824 FAUJ880113 0.820 MUNV940105 -0.839
+ RACS820114 -0.880 GEOR030109 -0.884 MUNV940101 -0.890
+ AVBF000104 -0.899 MUNV940102 -0.910 FINA910102 -0.920
+ ONEK900102 -0.982
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 13.4 13.3 12.0 11.7 11.6 12.8 12.2 11.3 11.6 12.0
+ 13.0 13.0 12.8 12.1 6.5 12.2 11.7 12.4 12.1 11.9
+//
+H ONEK900102
+D Helix formation parameters (delta delta G) (O'Neil-DeGrado, 1990)
+R PMID:2237415
+A O'Neil, K.T. and DeGrado, W.F.
+T A thermodynamic scale for the helix-forming tendencies of the commonly
+ occurring amino acids
+J Science 250, 646-651 (1990)
+C FINA910102 0.964 AVBF000104 0.919 GEOR030109 0.908
+ MUNV940105 0.876 MUNV940101 0.861 MUNV940102 0.860
+ RACS820114 0.855 MUNV940104 0.845 ISOY800104 0.828
+ TANS770104 0.826 QIAN880109 -0.800 PTIO830101 -0.830
+ FAUJ880113 -0.839 QIAN880108 -0.860 ROBB760104 -0.861
+ ROBB760103 -0.867 BUNA790101 -0.949 BLAM930101 -0.974
+ ONEK900101 -0.982
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.77 -0.68 -0.07 -0.15 -0.23 -0.33 -0.27 0.00 -0.06 -0.23
+ -0.62 -0.65 -0.50 -0.41 3 -0.35 -0.11 -0.45 -0.17 -0.14
+//
+H VINM940101
+D Normalized flexibility parameters (B-values), average (Vihinen et al., 1994)
+R PMID:8090708
+A Vihinen, M., Torkkila, E. and Riikonen, P.
+T Accuracy of protein flexibility predictions
+J Proteins 19, 141-149 (1994)
+C MIYS990104 0.965 MIYS990105 0.952 MIYS990103 0.951
+ VINM940102 0.940 OOBM770103 0.936 GUYH850102 0.924
+ VINM940103 0.921 FUKS010104 0.919 PARS000101 0.919
+ FASG890101 0.904 MEIH800101 0.900 KRIW790101 0.890
+ KARP850102 0.885 MIYS990102 0.883 MIYS990101 0.880
+ PARS000102 0.877 FUKS010102 0.876 MEIH800102 0.872
+ GRAR740102 0.869 CORJ870108 0.862 GUYH850103 0.860
+ HOPT810101 0.859 KRIW790102 0.853 PUNT030102 0.850
+ RACS770102 0.844 PARJ860101 0.837 RACS770101 0.835
+ WOEC730101 0.834 RACS770103 0.830 GUYH850101 0.829
+ FUKS010103 0.827 KARP850101 0.821 VINM940104 0.815
+ LEVM760101 0.815 MUNV940103 0.811 PUNT030101 0.805
+ PALJ810104 -0.801 WIMW960101 -0.804 DESM900101 -0.806
+ NADH010105 -0.808 CORJ870102 -0.817 SWER830101 -0.817
+ ROSM880105 -0.818 GEIM800107 -0.819 QIAN880120 -0.823
+ CORJ870104 -0.826 QIAN880121 -0.828 LIFS790103 -0.829
+ DESM900102 -0.829 CHOP780202 -0.831 ZHOH040101 -0.833
+ LIFS790101 -0.834 MANP780101 -0.836 CIDH920103 -0.837
+ CORJ870103 -0.848 CIDH920101 -0.854 ROBB790101 -0.858
+ NADH010102 -0.859 MEIH800103 -0.861 BASU050101 -0.867
+ FAUJ830101 -0.871 CIDH920102 -0.872 CORJ870105 -0.873
+ CORJ870107 -0.877 PONP800103 -0.878 PONP800101 -0.878
+ CORJ870106 -0.881 CIDH920104 -0.883 MIYS850101 -0.883
+ PONP800102 -0.883 CIDH920105 -0.885 NADH010103 -0.889
+ PONP800108 -0.891 NADH010104 -0.891 BAEK050101 -0.896
+ BASU050103 -0.902 BASU050102 -0.904 RADA880108 -0.906
+ PONP930101 -0.913 NISK800101 -0.922 ZHOH040103 -0.922
+ CORJ870101 -0.924 BIOV880102 -0.929 WERD780101 -0.931
+ BIOV880101 -0.941 ROSG850102 -0.943 CASG920101 -0.947
+ NISK860101 -0.959
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.984 1.008 1.048 1.068 0.906 1.037 1.094 1.031 0.950 0.927
+ 0.935 1.102 0.952 0.915 1.049 1.046 0.997 0.904 0.929 0.931
+//
+H VINM940102
+D Normalized flexibility parameters (B-values) for each residue surrounded by
+ none rigid neighbours (Vihinen et al., 1994)
+R PMID:8090708
+A Vihinen, M., Torkkila, E. and Riikonen, P.
+T Accuracy of protein flexibility predictions
+J Proteins 19, 141-149 (1994)
+C VINM940101 0.940 MIYS990104 0.922 PARS000101 0.917
+ GUYH850102 0.905 MIYS990103 0.895 MIYS990105 0.891
+ OOBM770103 0.891 GUYH850103 0.875 KARP850101 0.874
+ FUKS010103 0.864 VINM940103 0.855 MIYS990102 0.842
+ MIYS990101 0.841 GRAR740102 0.837 FASG890101 0.836
+ KARP850102 0.834 KRIW790101 0.834 PARJ860101 0.833
+ MEIH800101 0.833 CORJ870108 0.810 FUKS010102 0.808
+ FUKS010104 0.807 MUNV940103 0.803 PARS000102 0.803
+ CORJ870105 -0.807 PLIV810101 -0.808 NADH010105 -0.809
+ ROSG850101 -0.810 CHOP780202 -0.810 SWER830101 -0.811
+ CORJ870107 -0.811 NADH010103 -0.812 CORJ870102 -0.812
+ QIAN880120 -0.813 PONP800103 -0.820 MANP780101 -0.821
+ BIOV880102 -0.826 CORJ870106 -0.830 MIYS850101 -0.832
+ NADH010104 -0.834 MEEJ810101 -0.839 PONP800102 -0.842
+ LIFS790101 -0.843 FAUJ830101 -0.844 PONP800101 -0.845
+ RADA880108 -0.846 CORJ870101 -0.847 ROSG850102 -0.849
+ CIDH920103 -0.855 LIFS790103 -0.862 ROBB790101 -0.866
+ PONP930101 -0.869 PONP800108 -0.871 BAEK050101 -0.873
+ CASG920101 -0.874 BASU050101 -0.874 BIOV880101 -0.876
+ BASU050103 -0.880 CIDH920104 -0.884 CIDH920101 -0.885
+ WERD780101 -0.886 ZHOH040101 -0.899 NISK800101 -0.900
+ CIDH920105 -0.910 NISK860101 -0.919 CIDH920102 -0.925
+ BASU050102 -0.937 ZHOH040103 -0.939
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.315 1.310 1.380 1.372 1.196 1.342 1.376 1.382 1.279 1.241
+ 1.234 1.367 1.269 1.247 1.342 1.381 1.324 1.186 1.199 1.235
+//
+H VINM940103
+D Normalized flexibility parameters (B-values) for each residue surrounded by
+ one rigid neighbours (Vihinen et al., 1994)
+R PMID:8090708
+A Vihinen, M., Torkkila, E. and Riikonen, P.
+T Accuracy of protein flexibility predictions
+J Proteins 19, 141-149 (1994)
+C VINM940101 0.921 MIYS990104 0.898 GUYH850102 0.895
+ MIYS990103 0.886 MIYS990105 0.880 MEIH800101 0.875
+ KRIW790101 0.875 BHAR880101 0.869 FASG890101 0.868
+ GUYH850101 0.865 KARP850102 0.863 VINM940102 0.855
+ OOBM770103 0.845 MEIH800102 0.841 RACS770102 0.839
+ FUKS010104 0.838 KARP850101 0.837 KRIW790102 0.836
+ RACS770101 0.829 PARS000101 0.823 MIYS990102 0.818
+ MIYS990101 0.817 FUKS010102 0.809 PARS000102 0.808
+ FAUJ830101 -0.804 NADH010106 -0.813 PONP800101 -0.813
+ CIDH920101 -0.814 BASU050103 -0.814 PONP800103 -0.817
+ PONP930101 -0.818 PONP800102 -0.820 NADH010102 -0.824
+ DESM900102 -0.824 CIDH920102 -0.826 MEIH800103 -0.830
+ CIDH920105 -0.832 CIDH920104 -0.835 NISK800101 -0.836
+ CORJ870101 -0.837 MIYS850101 -0.849 BASU050102 -0.856
+ RADA880108 -0.862 ZHOH040103 -0.882 NADH010103 -0.882
+ NADH010105 -0.884 BIOV880102 -0.889 NADH010104 -0.899
+ ROSG850102 -0.901 BIOV880101 -0.901 NISK860101 -0.903
+ BAEK050101 -0.906 CASG920101 -0.915 WERD780101 -0.926
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.994 1.026 1.022 1.022 0.939 1.041 1.052 1.018 0.967 0.977
+ 0.982 1.029 0.963 0.934 1.050 1.025 0.998 0.938 0.981 0.968
+//
+H VINM940104
+D Normalized flexibility parameters (B-values) for each residue surrounded by
+ two rigid neighbours (Vihinen et al., 1994)
+R PMID:8090708
+A Vihinen, M., Torkkila, E. and Riikonen, P.
+T Accuracy of protein flexibility predictions
+J Proteins 19, 141-149 (1994)
+C VINM940101 0.815 JANJ780103 0.811 MEIH800102 0.808
+ RACS770103 0.804 DESM900102 -0.803 CORJ870101 -0.805
+ ROSG850102 -0.809 CASG920101 -0.810
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.783 0.807 0.799 0.822 0.785 0.817 0.826 0.784 0.777 0.776
+ 0.783 0.834 0.806 0.774 0.809 0.811 0.795 0.796 0.788 0.781
+//
+H MUNV940101
+D Free energy in alpha-helical conformation (Munoz-Serrano, 1994)
+R PMID:7731949
+A Munoz, V. and Serrano, L.
+T Intrinsic secondary structure propensities of the amino acids, using
+ statistical phi-psi matrices: comparison with experimental scales
+J Proteins 20, 301-311 (1994)
+C MUNV940102 0.964 ONEK900102 0.861 RACS820114 0.828
+ GEOR030109 0.801 CHOP780201 -0.802 AURR980115 -0.807
+ AURR980108 -0.814 PALJ810102 -0.815 AURR980112 -0.819
+ AURR980114 -0.821 ROBB760101 -0.822 AURR980110 -0.822
+ KANM800103 -0.826 AURR980109 -0.828 ROBB760104 -0.831
+ MAXF760101 -0.833 QIAN880106 -0.835 FAUJ880113 -0.836
+ QIAN880109 -0.841 KANM800101 -0.846 RACS820108 -0.859
+ QIAN880108 -0.864 ISOY800101 -0.875 QIAN880107 -0.880
+ PTIO830101 -0.880 BLAM930101 -0.882 ONEK900101 -0.890
+ ROBB760103 -0.918
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.423 0.503 0.906 0.870 0.877 0.594 0.167 1.162 0.802 0.566
+ 0.494 0.615 0.444 0.706 1.945 0.928 0.884 0.690 0.778 0.706
+//
+H MUNV940102
+D Free energy in alpha-helical region (Munoz-Serrano, 1994)
+R PMID:7731949
+A Munoz, V. and Serrano, L.
+T Intrinsic secondary structure propensities of the amino acids, using
+ statistical phi-psi matrices: comparison with experimental scales
+J Proteins 20, 301-311 (1994)
+C MUNV940101 0.964 RACS820114 0.877 ONEK900102 0.860
+ AURR980108 -0.803 ROBB760104 -0.803 CHOP780201 -0.812
+ QIAN880105 -0.816 AURR980109 -0.818 AURR980114 -0.820
+ KANM800103 -0.823 PALJ810102 -0.824 FAUJ880113 -0.826
+ ROBB760101 -0.827 MAXF760101 -0.829 QIAN880108 -0.839
+ KANM800101 -0.843 PTIO830101 -0.844 AURR980110 -0.846
+ AURR980115 -0.852 AURR980112 -0.853 QIAN880106 -0.867
+ BLAM930101 -0.876 ISOY800101 -0.877 QIAN880107 -0.882
+ RACS820108 -0.894 ONEK900101 -0.910 ROBB760103 -0.913
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.619 0.753 1.089 0.932 1.107 0.770 0.675 1.361 1.034 0.876
+ 0.740 0.784 0.736 0.968 1.780 0.969 1.053 0.910 1.009 0.939
+//
+H MUNV940103
+D Free energy in beta-strand conformation (Munoz-Serrano, 1994)
+R PMID:7731949
+A Munoz, V. and Serrano, L.
+T Intrinsic secondary structure propensities of the amino acids, using
+ statistical phi-psi matrices: comparison with experimental scales
+J Proteins 20, 301-311 (1994)
+C GEIM800110 0.880 QIAN880134 0.858 QIAN880133 0.836
+ MIYS990103 0.831 CORJ870108 0.830 MIYS990104 0.827
+ PARS000101 0.826 QIAN880135 0.820 LEVM780106 0.815
+ VINM940101 0.811 GEIM800108 0.806 OOBM770103 0.805
+ VINM940102 0.803 GEIM800106 -0.800 PONP800102 -0.802
+ CORJ870102 -0.802 SWER830101 -0.802 NISK800101 -0.813
+ BASU050103 -0.814 MANP780101 -0.815 CORJ870101 -0.817
+ PONP800101 -0.819 CORJ870105 -0.829 PALJ810112 -0.830
+ ROBB760105 -0.832 CORJ870107 -0.832 BASU050102 -0.839
+ NISK860101 -0.840 GEIM800105 -0.841 PALJ810110 -0.845
+ BASU050101 -0.846 CORJ870106 -0.848 LEVM780102 -0.848
+ PRAM900103 -0.848 PALJ810103 -0.857 KANM800104 -0.857
+ PONP930101 -0.864 GEIM800107 -0.869 PALJ810104 -0.888
+ ROBB760106 -0.888 LEVM780105 -0.891 CHOP780202 -0.892
+ LIFS790103 -0.902 PTIO830102 -0.903 KANM800102 -0.916
+ AVBF000101 -0.917 QIAN880119 -0.927 QIAN880121 -0.938
+ LIFS790101 -0.941 QIAN880120 -0.959
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.080 0.976 1.197 1.266 0.733 1.050 1.085 1.104 0.906 0.583
+ 0.789 1.026 0.812 0.685 1.412 0.987 0.784 0.755 0.665 0.546
+//
+H MUNV940104
+D Free energy in beta-strand region (Munoz-Serrano, 1994)
+R PMID:7731949
+A Munoz, V. and Serrano, L.
+T Intrinsic secondary structure propensities of the amino acids, using
+ statistical phi-psi matrices: comparison with experimental scales
+J Proteins 20, 301-311 (1994)
+C MUNV940105 0.987 QIAN880134 0.897 FINA910102 0.896
+ TANS770104 0.870 ISOY800104 0.866 ONEK900102 0.845
+ CHOP780213 0.836 RACS820110 0.831 QIAN880135 0.819
+ AURR980119 0.804 PTIO830101 -0.807 AVBF000101 -0.821
+ FAUJ880102 -0.824 ROBB760104 -0.840 BUNA790101 -0.865
+ BLAM930101 -0.904
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.978 0.784 0.915 1.038 0.573 0.863 0.962 1.405 0.724 0.502
+ 0.766 0.841 0.729 0.585 2.613 0.784 0.569 0.671 0.560 0.444
+//
+H MUNV940105
+D Free energy in beta-strand region (Munoz-Serrano, 1994)
+R PMID:7731949
+A Munoz, V. and Serrano, L.
+T Intrinsic secondary structure propensities of the amino acids, using
+ statistical phi-psi matrices: comparison with experimental scales
+J Proteins 20, 301-311 (1994)
+C MUNV940104 0.987 FINA910102 0.911 QIAN880134 0.899
+ ONEK900102 0.876 TANS770104 0.846 ISOY800104 0.844
+ RACS820110 0.833 QIAN880135 0.829 CHOP780213 0.826
+ PTIO830101 -0.833 ONEK900101 -0.839 ROBB760104 -0.859
+ BUNA790101 -0.874 BLAM930101 -0.925
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.40 1.23 1.61 1.89 1.14 1.33 1.42 2.06 1.25 1.02
+ 1.33 1.34 1.12 1.07 3.90 1.20 0.99 1.10 0.98 0.87
+//
+H WIMW960101
+D Free energies of transfer of AcWl-X-LL peptides from bilayer interface to
+ water (Wimley-White, 1996)
+R PMID:8836100
+A Wimley, W.C. and White, S.
+T Experimentally determined hydrophobicity scale for proteins at membrane
+ interfaces
+J Nature Structual biol. 3, 842-848 (1996)
+C ZASB820101 0.885 MEEJ800101 0.838 CIDH920102 0.837
+ MEEJ800102 0.821 ZHOH040101 0.821 NOZY710101 0.818
+ PARJ860101 -0.804 VINM940101 -0.804 GRAR740102 -0.804
+ FUKS010102 -0.808 LEVM760101 -0.812 OOBM770103 -0.814
+ WOEC730101 -0.821 HOPT810101 -0.855
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 4.08 3.91 3.83 3.02 4.49 3.67 2.23 4.24 4.08 4.52
+ 4.81 3.77 4.48 5.38 3.80 4.12 4.11 6.10 5.19 4.18
+//
+H KIMC930101
+D Thermodynamic beta sheet propensity (Kim-Berg, 1993)
+R PMID:8459852
+A Kim, C.A. and Berg, J.M.
+T Thermodynamic beta-sheet propensities measured using a zinc-finger host
+ peptide
+J Nature 362, 267-270 (1993)
+C LEVM760104 0.842 AVBF000101 -0.814 CHAM810101 -0.848
+ LEVM760103 -0.861 FAUJ880102 -0.886 AVBF000102 -0.900
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.35 -0.44 -0.38 -0.41 -0.47 -0.40 -0.41 0.0 -0.46 -0.56
+ -0.48 -0.41 -0.46 -0.55 -0.23 -0.39 -0.48 -0.48 -0.50 -0.53
+//
+H MONM990101
+D Turn propensity scale for transmembrane helices (Monne et al., 1999)
+R PMID:10329132
+A Monne, M., Hermansson, M. and von Heijne, G.
+T A turn propensity scale for transmembrane helices
+J J. Mol. Biol. 288, 141-145 (1999)
+C PUNT030102 0.839 PUNT030101 0.839 GRAR740102 0.831
+ KRIW790101 0.830 ENGD860101 0.820 PRAM900101 0.820
+ MIYS990103 0.809 NADH010105 -0.815 KYTJ820101 -0.842
+ DESM900101 -0.848 NADH010104 -0.848 DESM900102 -0.850
+ JURD980101 -0.853 NADH010101 -0.860 NADH010103 -0.862
+ NADH010102 -0.871
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.5 1.7 1.7 1.6 0.6 1.6 1.6 1.3 1.6 0.6
+ 0.4 1.6 0.5 0.4 1.7 0.7 0.4 0.7 0.6 0.5
+//
+H BLAM930101
+D Alpha helix propensity of position 44 in T4 lysozyme (Blaber et al., 1993)
+R PMID:8503008
+A Blaber, M., Zhang, X.J. and Matthews, B.W.
+T Structural basis of amino acid alpha helix propensity
+J Science 260, 1637-1640 (1993)
+C ONEK900101 0.965 BUNA790101 0.945 ROBB760103 0.883
+ ROBB760104 0.878 PTIO830101 0.868 QIAN880108 0.860
+ FAUJ880113 0.839 QIAN880109 0.828 CHOP780213 -0.824
+ QIAN880134 -0.836 TANS770104 -0.837 ISOY800104 -0.860
+ RACS820114 -0.862 AVBF000104 -0.872 MUNV940102 -0.876
+ MUNV940101 -0.882 GEOR030109 -0.889 MUNV940104 -0.904
+ MUNV940105 -0.925 FINA910102 -0.961 ONEK900102 -0.974
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.96 0.77 0.39 0.42 0.42 0.80 0.53 0.00 0.57 0.84
+ 0.92 0.73 0.86 0.59 -2.50 0.53 0.54 0.58 0.72 0.63
+//
+H PARS000101
+D p-Values of mesophilic proteins based on the distributions of B values
+ (Parthasarathy-Murthy, 2000)
+R PMID:10679524
+A Parthasarathy, S. and Murthy, M.R.
+T Protein thermal stability: insights from atomic displacement parameters (B
+ values)
+J Protein Eng. 13, 9-13 (2000)
+C VINM940101 0.919 VINM940102 0.917 MIYS990104 0.903
+ MIYS990103 0.879 MIYS990105 0.877 OOBM770103 0.864
+ CORJ870108 0.854 KARP850102 0.852 GUYH850102 0.839
+ GEIM800110 0.831 MIYS990102 0.830 MIYS990101 0.830
+ MUNV940103 0.826 VINM940103 0.823 GUYH850103 0.822
+ KARP850101 0.816 MEIH800101 0.813 PARJ860101 0.812
+ RACS770101 0.804 KRIW790101 0.804 CORJ870104 -0.800
+ ROSG850101 -0.805 QIAN880121 -0.809 BIOV880102 -0.813
+ CORJ870103 -0.815 BIOV880101 -0.819 ROBB790101 -0.819
+ ROSG850102 -0.820 BASU050103 -0.820 BAEK050101 -0.821
+ CIDH920103 -0.821 MIYS850101 -0.821 CASG920101 -0.826
+ NOZY710101 -0.829 NISK800101 -0.832 BASU050101 -0.835
+ LIFS790101 -0.844 ZHOH040101 -0.845 SWER830101 -0.846
+ ZHOH040103 -0.846 CORJ870102 -0.848 PONP930101 -0.849
+ WERD780101 -0.853 CIDH920105 -0.860 LIFS790103 -0.861
+ QIAN880120 -0.863 BASU050102 -0.864 CORJ870107 -0.865
+ CIDH920102 -0.871 CIDH920101 -0.877 CORJ870105 -0.878
+ NISK860101 -0.884 CORJ870106 -0.891
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.343 0.353 0.409 0.429 0.319 0.395 0.405 0.389 0.307 0.296
+ 0.287 0.429 0.293 0.292 0.432 0.416 0.362 0.268 0.22 0.307
+//
+H PARS000102
+D p-Values of thermophilic proteins based on the distributions of B values
+ (Parthasarathy-Murthy, 2000)
+R PMID:10679524
+A Parthasarathy, S. and Murthy, M.R.
+T Protein thermal stability: insights from atomic displacement parameters (B
+ values)
+J Protein Eng. 13, 9-13 (2000)
+C VINM940101 0.877 FUKS010102 0.868 FUKS010104 0.850
+ VINM940103 0.808 VINM940102 0.803 NISK800101 -0.814
+ CORJ870101 -0.850 CASG920101 -0.859
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.320 0.327 0.384 0.424 0.198 0.436 0.514 0.374 0.299 0.306
+ 0.340 0.446 0.313 0.314 0.354 0.376 0.339 0.291 0.287 0.294
+//
+H KUMS000101
+D Distribution of amino acid residues in the 18 non-redundant families of
+ thermophilic proteins (Kumar et al., 2000)
+R PMID:10775659
+A Kumar, S., Tsai, C.J. and Nussinov, R.
+T Factors enhancing protein thermostability
+J Protein Eng. 13, 179-191 (2000)
+C KUMS000102 0.971 FUKS010110 0.947 FUKS010109 0.894
+ JUKT750101 0.879 CEDJ970104 0.871 DAYM780101 0.866
+ JOND920101 0.863 NAKH900101 0.856 JUNJ780101 0.854
+ CEDJ970101 0.830 CEDJ970102 0.826 FUKS010111 0.826
+ NAKH920107 0.800
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 8.9 4.6 4.4 6.3 0.6 2.8 6.9 9.4 2.2 7.0
+ 7.4 6.1 2.3 3.3 4.2 4.0 5.7 1.3 4.5 8.2
+//
+H KUMS000102
+D Distribution of amino acid residues in the 18 non-redundant families of
+ mesophilic proteins (Kumar et al., 2000)
+R PMID:10775659
+A Kumar, S., Tsai, C.J. and Nussinov, R.
+T Factors enhancing protein thermostability
+J Protein Eng. 13, 179-191 (2000)
+C KUMS000101 0.971 JUKT750101 0.948 FUKS010110 0.943
+ JUNJ780101 0.927 DAYM780101 0.925 CEDJ970101 0.914
+ JOND920101 0.909 CEDJ970104 0.908 FUKS010111 0.898
+ NAKH900101 0.894 CEDJ970102 0.881 FUKS010109 0.850
+ NAKH920107 0.839 NAKH900109 0.837 FUKS010112 0.819
+ CEDJ970103 0.812
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 9.2 3.6 5.1 6.0 1.0 2.9 6.0 9.4 2.1 6.0
+ 7.7 6.5 2.4 3.4 4.2 5.5 5.7 1.2 3.7 8.2
+//
+H KUMS000103
+D Distribution of amino acid residues in the alpha-helices in thermophilic
+ proteins (Kumar et al., 2000)
+R PMID:10775659
+A Kumar, S., Tsai, C.J. and Nussinov, R.
+T Factors enhancing protein thermostability
+J Protein Eng. 13, 179-191 (2000)
+C KUMS000104 0.961 FUKS010110 0.827
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 14.1 5.5 3.2 5.7 0.1 3.7 8.8 4.1 2.0 7.1
+ 9.1 7.7 3.3 5.0 0.7 3.9 4.4 1.2 4.5 5.9
+//
+H KUMS000104
+D Distribution of amino acid residues in the alpha-helices in mesophilic
+ proteins (Kumar et al., 2000)
+R PMID:10775659
+A Kumar, S., Tsai, C.J. and Nussinov, R.
+T Factors enhancing protein thermostability
+J Protein Eng. 13, 179-191 (2000)
+C KUMS000103 0.961 FUKS010110 0.861
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 13.4 3.9 3.7 4.6 0.8 4.8 7.8 4.6 3.3 6.5
+ 10.6 7.5 3.0 4.5 1.3 3.8 4.6 1.0 3.3 7.1
+//
+H TAKK010101
+D Side-chain contribution to protein stability (kJ/mol) (Takano-Yutani, 2001)
+R PMID:11579219
+A Takano, K., Yutani, K.
+T A new scale for side-chain contribution to protein stability based on the
+ empirical stability analysis of mutant proteins
+J Protein Eng. 14, 525-528 (2001)
+C SIMZ760101 0.936 ARGP820101 0.906 JOND750101 0.906
+ MEEJ800102 0.891 NOZY710101 0.884 ZHOH040102 0.874
+ GOLD730101 0.872 CIDH920102 0.859 ZIMJ680105 0.856
+ ZHOH040101 0.846 LEVM760106 0.841 ZIMJ680102 0.840
+ CIDH920105 0.840 ROSM880104 0.840 BROC820102 0.839
+ BROC820101 0.836 MEEJ810101 0.836 RADA880102 0.830
+ PLIV810101 0.822 MEEJ810102 0.819 LEVM760107 0.819
+ VENT840101 0.812 WOLS870101 -0.858 BULH740101 -0.865
+ PARJ860101 -0.870
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 9.8 7.3 3.6 4.9 3.0 2.4 4.4 0 11.9 17.2
+ 17.0 10.5 11.9 23.0 15.0 2.6 6.9 24.2 17.2 15.3
+//
+H FODM020101
+D Propensity of amino acids within pi-helices (Fodje-Al-Karadaghi, 2002)
+R PMID:12034854
+A Fodje, M.N. and Al-Karadaghi, S.
+T Occurrence, conformational features and amino acid propensities for the
+ pi-helix
+J Protein Eng. 15, 353-358 (2002)
+C TANS770104 -0.802
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.70 0.95 1.47 0.87 1.17 0.73 0.96 0.64 1.39 1.29
+ 1.44 0.91 0.91 1.34 0.12 0.84 0.74 1.80 1.68 1.20
+//
+H NADH010101
+D Hydropathy scale based on self-information values in the two-state model (5%
+ accessibility) (Naderi-Manesh et al., 2001)
+R PMID:11170200
+A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A.
+T Prediction of protein surface accessibility with information theory
+J Proteins 42, 452-459 (2001)
+C JURD980101 0.925 KYTJ820101 0.918 NADH010105 0.912
+ DESM900102 0.905 NADH010103 0.904 RADA880101 0.902
+ NADH010102 0.898 NADH010104 0.895 JANJ780102 0.892
+ CHOC760103 0.881 EISD860103 0.868 CIDH920104 0.865
+ EISD840101 0.861 BLAS910101 0.855 BASU050103 0.852
+ WOLR810101 0.848 JANJ790101 0.847 MANP780101 0.847
+ OLSK800101 0.843 RADA880108 0.838 BIOV880101 0.838
+ FAUJ830101 0.837 PONP800103 0.833 ROSG850102 0.833
+ PONP800102 0.832 CORJ870101 0.827 PONP800101 0.826
+ WOLR790101 0.826 ROSM880105 0.825 DESM900101 0.825
+ MEIH800103 0.824 PONP800108 0.820 RADA880104 0.819
+ MIYS850101 0.815 PONP930101 0.813 NISK800101 0.813
+ NISK860101 0.810 JANJ790102 0.808 CHOC760104 0.804
+ BIOV880102 0.804 ZHOH040103 0.803 KIDA850101 -0.803
+ GUYH850104 -0.804 JANJ780103 -0.804 RACS770102 -0.808
+ MIYS990104 -0.810 FAUJ880110 -0.813 MIYS990102 -0.815
+ MIYS990101 -0.816 MEIH800102 -0.818 MIYS990105 -0.821
+ MIYS990103 -0.825 KRIW790101 -0.827 VHEG790101 -0.827
+ FASG890101 -0.838 ENGD860101 -0.843 PRAM900101 -0.843
+ GUYH850105 -0.847 GRAR740102 -0.859 MONM990101 -0.860
+ OOBM770101 -0.861 PUNT030101 -0.862 GUYH850101 -0.862
+ ROSM880101 -0.866 ROSM880102 -0.870 PUNT030102 -0.872
+ KUHL950101 -0.898
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 58 -184 -93 -97 116 -139 -131 -11 -73 107
+ 95 -24 78 92 -79 -34 -7 59 -11 100
+//
+H NADH010102
+D Hydropathy scale based on self-information values in the two-state model (9%
+ accessibility) (Naderi-Manesh et al., 2001)
+R PMID:11170200
+A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A.
+T Prediction of protein surface accessibility with information theory
+J Proteins 42, 452-459 (2001)
+C NADH010103 0.986 NADH010104 0.968 JANJ780102 0.949
+ ROSG850102 0.948 JANJ790102 0.945 DESM900102 0.933
+ JURD980101 0.931 BIOV880101 0.921 PONP800103 0.921
+ KYTJ820101 0.920 BIOV880102 0.914 RADA880108 0.911
+ CHOC760103 0.910 CORJ870101 0.909 MEIH800103 0.907
+ PONP800102 0.901 NADH010101 0.898 FAUJ830101 0.891
+ PONP800108 0.890 CASG920101 0.889 EISD840101 0.887
+ BASU050103 0.886 DESM900101 0.885 NISK800101 0.881
+ PONP930101 0.880 MIYS850101 0.878 NISK860101 0.878
+ NADH010105 0.876 PONP800101 0.875 JANJ790101 0.872
+ EISD860103 0.872 WARP780101 0.870 ZHOH040103 0.864
+ MANP780101 0.863 OLSK800101 0.856 CIDH920104 0.856
+ COWR900101 0.848 RADA880101 0.845 ROSM880105 0.845
+ WERD780101 0.841 BLAS910101 0.824 RADA880107 0.823
+ CORJ870103 0.823 CHOC760104 0.817 CORJ870107 0.812
+ BASU050101 0.812 NADH010106 0.808 BASU050102 0.802
+ WOEC730101 -0.800 FUKS010104 -0.801 CORJ870108 -0.803
+ KARP850102 -0.807 HOPT810101 -0.820 VINM940103 -0.824
+ GUYH850102 -0.824 KRIW710101 -0.825 ROSM880101 -0.830
+ KUHL950101 -0.836 OOBM770103 -0.838 MEIH800101 -0.847
+ VINM940101 -0.859 GUYH850105 -0.867 MIYS990101 -0.870
+ ENGD860101 -0.870 PRAM900101 -0.870 MONM990101 -0.871
+ MIYS990102 -0.872 PUNT030102 -0.872 KIDA850101 -0.874
+ RACS770103 -0.876 ROSM880102 -0.881 GRAR740102 -0.881
+ KRIW790102 -0.890 CHOC760102 -0.893 PUNT030101 -0.897
+ RACS770102 -0.899 GUYH850101 -0.910 MIYS990104 -0.910
+ MIYS990105 -0.923 MIYS990103 -0.923 JANJ780101 -0.924
+ MEIH800102 -0.928 KRIW790101 -0.929 FASG890101 -0.929
+ JANJ780103 -0.938 OOBM770101 -0.944 GUYH850104 -0.946
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 51 -144 -84 -78 137 -128 -115 -13 -55 106
+ 103 -205 73 108 -79 -26 -3 69 11 108
+//
+H NADH010103
+D Hydropathy scale based on self-information values in the two-state model (16%
+ accessibility) (Naderi-Manesh et al., 2001)
+R PMID:11170200
+A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A.
+T Prediction of protein surface accessibility with information theory
+J Proteins 42, 452-459 (2001)
+C NADH010104 0.996 NADH010102 0.986 ROSG850102 0.958
+ BIOV880101 0.939 NADH010105 0.936 PONP800103 0.932
+ JANJ780102 0.923 CORJ870101 0.921 RADA880108 0.919
+ PONP800102 0.919 CASG920101 0.914 ZHOH040103 0.913
+ BIOV880102 0.913 NISK860101 0.910 DESM900102 0.910
+ NISK800101 0.908 PONP800108 0.907 NADH010101 0.904
+ BASU050103 0.903 MEIH800103 0.901 JURD980101 0.900
+ JANJ790102 0.899 FAUJ830101 0.899 PONP930101 0.898
+ MIYS850101 0.896 PONP800101 0.894 KYTJ820101 0.885
+ CIDH920104 0.885 NADH010106 0.881 WERD780101 0.880
+ JANJ790101 0.879 MANP780101 0.878 CHOC760103 0.875
+ DESM900101 0.866 BASU050102 0.862 EISD860103 0.855
+ BAEK050101 0.853 EISD840101 0.840 BASU050101 0.839
+ CORJ870103 0.830 COWR900101 0.825 ROSM880105 0.822
+ CORJ870107 0.817 BLAS910101 0.812 WARP780101 0.811
+ CIDH920105 0.810 QIAN880122 0.809 RADA880101 0.809
+ OLSK800101 0.807 PLIV810101 0.804 GUOD860101 0.803
+ CORJ870104 0.802 FUKS010104 -0.805 HOPT810101 -0.805
+ RACS770101 -0.807 KUHL950101 -0.807 VINM940102 -0.812
+ CORJ870108 -0.812 GUYH850105 -0.815 ENGD860101 -0.815
+ PRAM900101 -0.815 KARP850102 -0.834 CHOC760102 -0.840
+ RACS770103 -0.851 ROSM880102 -0.857 KIDA850101 -0.859
+ KRIW710101 -0.860 OOBM770103 -0.861 MONM990101 -0.862
+ PUNT030102 -0.865 GUYH850102 -0.866 MEIH800101 -0.868
+ PUNT030101 -0.868 JANJ780101 -0.868 GRAR740102 -0.881
+ VINM940103 -0.882 MIYS990101 -0.887 KRIW790102 -0.887
+ MIYS990102 -0.889 VINM940101 -0.889 JANJ780103 -0.892
+ RACS770102 -0.893 GUYH850104 -0.899 OOBM770101 -0.902
+ MEIH800102 -0.916 GUYH850101 -0.916 MIYS990104 -0.938
+ MIYS990105 -0.939 MIYS990103 -0.944 FASG890101 -0.945
+ KRIW790101 -0.954
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 41 -109 -74 -47 169 -104 -90 -18 -35 104
+ 103 -148 77 128 -81 -31 10 102 36 116
+//
+H NADH010104
+D Hydropathy scale based on self-information values in the two-state model (20%
+ accessibility) (Naderi-Manesh et al., 2001)
+R PMID:11170200
+A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A.
+T Prediction of protein surface accessibility with information theory
+J Proteins 42, 452-459 (2001)
+C NADH010103 0.996 NADH010102 0.968 NADH010105 0.957
+ ROSG850102 0.953 BIOV880101 0.937 PONP800103 0.926
+ ZHOH040103 0.925 PONP800102 0.917 CASG920101 0.915
+ NISK860101 0.915 RADA880108 0.915 NADH010106 0.914
+ CORJ870101 0.914 NISK800101 0.909 PONP800108 0.902
+ BIOV880102 0.900 BASU050103 0.899 JANJ780102 0.898
+ MIYS850101 0.897 NADH010101 0.895 PONP930101 0.895
+ FAUJ830101 0.894 PONP800101 0.892 MEIH800103 0.890
+ WERD780101 0.890 CIDH920104 0.888 DESM900102 0.886
+ BASU050102 0.879 BAEK050101 0.875 MANP780101 0.873
+ JURD980101 0.873 JANJ790101 0.871 JANJ790102 0.868
+ KYTJ820101 0.856 CHOC760103 0.848 DESM900101 0.843
+ EISD860103 0.840 BASU050101 0.837 CORJ870103 0.820
+ CIDH920105 0.817 EISD840101 0.809 CORJ870107 0.808
+ COWR900101 0.807 PLIV810101 0.806 QIAN880122 0.804
+ GUOD860101 0.803 CORJ870108 -0.805 CHOC760102 -0.809
+ RACS770101 -0.813 RACS770103 -0.832 JANJ780101 -0.832
+ VINM940102 -0.834 KARP850102 -0.835 ROSM880102 -0.839
+ KIDA850101 -0.842 PUNT030101 -0.843 MONM990101 -0.848
+ PUNT030102 -0.851 JANJ780103 -0.860 OOBM770103 -0.863
+ MEIH800101 -0.867 GUYH850104 -0.867 GRAR740102 -0.868
+ OOBM770101 -0.871 KRIW710101 -0.874 GUYH850102 -0.879
+ KRIW790102 -0.882 RACS770102 -0.883 MIYS990101 -0.885
+ MIYS990102 -0.888 VINM940101 -0.891 VINM940103 -0.899
+ MEIH800102 -0.900 GUYH850101 -0.910 MIYS990105 -0.934
+ MIYS990104 -0.940 MIYS990103 -0.944 FASG890101 -0.944
+ KRIW790101 -0.958
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 32 -95 -73 -29 182 -95 -74 -22 -25 106
+ 104 -124 82 132 -82 -34 20 118 44 113
+//
+H NADH010105
+D Hydropathy scale based on self-information values in the two-state model (25%
+ accessibility) (Naderi-Manesh et al., 2001)
+R PMID:11170200
+A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A.
+T Prediction of protein surface accessibility with information theory
+J Proteins 42, 452-459 (2001)
+C NADH010106 0.958 NADH010104 0.957 NADH010103 0.936
+ NADH010101 0.912 ZHOH040103 0.890 NADH010102 0.876
+ PONP800102 0.869 CIDH920104 0.869 BASU050102 0.869
+ BIOV880101 0.867 PONP800103 0.866 ROSG850102 0.865
+ NISK860101 0.863 NISK800101 0.860 BASU050103 0.857
+ PONP800101 0.853 BAEK050101 0.850 CORJ870101 0.846
+ PONP800108 0.845 RADA880108 0.845 MIYS850101 0.844
+ JANJ790101 0.843 MANP780101 0.842 PONP930101 0.839
+ CASG920101 0.838 WERD780101 0.837 FAUJ830101 0.822
+ JURD980101 0.821 DESM900102 0.816 MEIH800103 0.816
+ JANJ780102 0.814 BASU050101 0.811 KYTJ820101 0.804
+ CIDH920105 0.800 RACS770102 -0.800 MEIH800101 -0.806
+ VINM940101 -0.808 VINM940102 -0.809 GRAR740102 -0.812
+ MONM990101 -0.815 GUYH850102 -0.826 MIYS990101 -0.837
+ MIYS990102 -0.838 KRIW710101 -0.842 GUYH850101 -0.855
+ MIYS990105 -0.856 MIYS990104 -0.874 FASG890101 -0.877
+ MIYS990103 -0.879 VINM940103 -0.884 KRIW790101 -0.898
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 24 -79 -76 0 194 -87 -57 -28 -31 102
+ 103 -9 90 131 -85 -36 34 116 43 111
+//
+H NADH010106
+D Hydropathy scale based on self-information values in the two-state model (36%
+ accessibility) (Naderi-Manesh et al., 2001)
+R PMID:11170200
+A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A.
+T Prediction of protein surface accessibility with information theory
+J Proteins 42, 452-459 (2001)
+C NADH010105 0.958 NADH010104 0.914 NADH010103 0.881
+ ZHOH040103 0.819 NADH010107 0.811 BAEK050101 0.809
+ NADH010102 0.808 PONP800103 0.803 VINM940103 -0.813
+ KRIW710101 -0.846 KRIW790101 -0.861
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 5 -57 -77 45 224 -67 -8 -47 -50 83
+ 82 -38 83 117 -103 -41 79 130 27 117
+//
+H NADH010107
+D Hydropathy scale based on self-information values in the two-state model (50%
+ accessibility) (Naderi-Manesh et al., 2001)
+R PMID:11170200
+A Naderi-Manesh, H., Sadeghi, M., Arab, S. and Moosavi Movahedi, A.A.
+T Prediction of protein surface accessibility with information theory
+J Proteins 42, 452-459 (2001)
+C NADH010106 0.811
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -2 -41 -97 248 329 -37 117 -66 -70 28
+ 36 115 62 120 -132 -52 174 179 -7 114
+//
+H MONM990201
+D Averaged turn propensities in a transmembrane helix (Monne et al., 1999)
+R PMID:10543969
+A Monne, M., Nilsson, I., Elofsson, A. and von Heijne, G.
+T Turns in transmembrane helices: determination of the minimal length of a
+ "helical hairpin" and derivation of a fine-grained turn propensity scale
+J J. Mol. Biol. 293, 807-814 (1999)
+C FINA910101 0.812
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.4 1.5 1.6 1.5 0.7 1.4 1.3 1.1 1.4 0.5
+ 0.3 1.4 0.5 0.3 1.6 0.9 0.7 0.9 0.9 0.4
+//
+H KOEP990101
+D Alpha-helix propensity derived from designed sequences (Koehl-Levitt, 1999)
+R PMID:10535955
+A Koehl, P. and Levitt, M.
+T Structure-based conformational preferences of amino acids
+J Proc Natl Acad Sci U S A. 96, 12524-12529 (1999) (Pro missing)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.04 -0.30 0.25 0.27 0.57 -0.02 -0.33 1.24 -0.11 -0.26
+ -0.38 -0.18 -0.09 -0.01 0. 0.15 0.39 0.21 0.05 -0.06
+//
+H KOEP990102
+D Beta-sheet propensity derived from designed sequences (Koehl-Levitt, 1999)
+R PMID:10535955
+A Koehl, P. and Levitt, M.
+T Structure-based conformational preferences of amino acids
+J Proc Natl Acad Sci U S A. 96, 12524-12529 (1999) (Pro!)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.12 0.34 1.05 1.12 -0.63 1.67 0.91 0.76 1.34 -0.77
+ 0.15 0.29 -0.71 -0.67 0. 1.45 -0.70 -0.14 -0.49 -0.70
+//
+H CEDJ970101
+D Composition of amino acids in extracellular proteins (percent) (Cedano et
+ al., 1997)
+R PMID:9067612
+A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E.
+T Relation between amino acid composition and cellular location of proteins
+J J. Mol. Biol. 266, 594-600 (1997)
+C JUKT750101 0.973 DAYM780101 0.970 JOND920101 0.968
+ JUNJ780101 0.968 CEDJ970102 0.965 NAKH900101 0.954
+ CEDJ970104 0.944 KUMS000102 0.914 FUKS010110 0.889
+ CEDJ970103 0.889 FUKS010112 0.882 FUKS010111 0.878
+ NAKH900109 0.861 NAKH920107 0.860 NAKH920104 0.859
+ NAKH920101 0.850 NAKH920103 0.843 NAKH900102 0.832
+ KUMS000101 0.830 NAKH920106 0.826
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 8.6 4.2 4.6 4.9 2.9 4.0 5.1 7.8 2.1 4.6
+ 8.8 6.3 2.5 3.7 4.9 7.3 6.0 1.4 3.6 6.7
+//
+H CEDJ970102
+D Composition of amino acids in anchored proteins (percent) (Cedano et al.,
+ 1997)
+R PMID:9067612
+A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E.
+T Relation between amino acid composition and cellular location of proteins
+J J. Mol. Biol. 266, 594-600 (1997)
+C JOND920101 0.995 NAKH900101 0.988 CEDJ970104 0.976
+ CEDJ970101 0.965 FUKS010112 0.946 DAYM780101 0.945
+ JUKT750101 0.942 FUKS010110 0.921 JUNJ780101 0.920
+ CEDJ970103 0.912 NAKH920103 0.906 NAKH920104 0.905
+ NAKH920101 0.898 NAKH920107 0.891 NAKH920106 0.886
+ KUMS000102 0.881 NAKH900109 0.865 NAKH900102 0.841
+ FUKS010109 0.839 CEDJ970105 0.835 KUMS000101 0.826
+ FUKS010111 0.819
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 7.6 5.0 4.4 5.2 2.2 4.1 6.2 6.9 2.1 5.1
+ 9.4 5.8 2.1 4.0 5.4 7.2 6.1 1.4 3.2 6.7
+//
+H CEDJ970103
+D Composition of amino acids in membrane proteins (percent) (Cedano et al.,
+ 1997)
+R PMID:9067612
+A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E.
+T Relation between amino acid composition and cellular location of proteins
+J J. Mol. Biol. 266, 594-600 (1997)
+C NAKH900109 0.970 FUKS010106 0.919 CEDJ970102 0.912
+ JOND920101 0.911 NAKH900101 0.908 FUKS010105 0.901
+ FUKS010108 0.897 CEDJ970101 0.889 NAKH900111 0.865
+ FUKS010107 0.860 CEDJ970104 0.854 FUKS010112 0.850
+ FUKS010110 0.848 NAKH920105 0.836 JUKT750101 0.835
+ NAKH900107 0.820 NAKH900103 0.815 KUMS000102 0.812
+ NAKH920108 0.811 DAYM780101 0.807 JUNJ780101 0.806
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 8.1 4.6 3.7 3.8 2.0 3.1 4.6 7.0 2.0 6.7
+ 11.0 4.4 2.8 5.6 4.7 7.3 5.6 1.8 3.3 7.7
+//
+H CEDJ970104
+D Composition of amino acids in intracellular proteins (percent) (Cedano et
+ al., 1997)
+R PMID:9067612
+A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E.
+T Relation between amino acid composition and cellular location of proteins
+J J. Mol. Biol. 266, 594-600 (1997)
+C JOND920101 0.983 NAKH900101 0.978 CEDJ970102 0.976
+ FUKS010112 0.956 FUKS010110 0.956 DAYM780101 0.952
+ CEDJ970101 0.944 JUKT750101 0.942 NAKH920106 0.923
+ JUNJ780101 0.921 NAKH920101 0.920 KUMS000102 0.908
+ FUKS010109 0.901 KUMS000101 0.871 NAKH920104 0.865
+ NAKH920103 0.863 NAKH900102 0.860 NAKH920107 0.857
+ CEDJ970103 0.854 CEDJ970105 0.852 NAKH920102 0.834
+ NAKH900109 0.821
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 7.9 4.9 4.0 5.5 1.9 4.4 7.1 7.1 2.1 5.2
+ 8.6 6.7 2.4 3.9 5.3 6.6 5.3 1.2 3.1 6.8
+//
+H CEDJ970105
+D Composition of amino acids in nuclear proteins (percent) (Cedano et al.,
+ 1997)
+R PMID:9067612
+A Cedano, J., Aloy, P., Perez-Pons, J.A. and Querol, E.
+T Relation between amino acid composition and cellular location of proteins
+J J. Mol. Biol. 266, 594-600 (1997)
+C NAKH920101 0.942 NAKH920106 0.930 NAKH900102 0.903
+ NAKH900101 0.860 CEDJ970104 0.852 NAKH920102 0.843
+ DAYM780101 0.839 CEDJ970102 0.835 JOND920101 0.834
+ JUNJ780101 0.803
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 8.3 8.7 3.7 4.7 1.6 4.7 6.5 6.3 2.1 3.7
+ 7.4 7.9 2.3 2.7 6.9 8.8 5.1 0.7 2.4 5.3
+//
+H FUKS010101
+D Surface composition of amino acids in intracellular proteins of thermophiles
+ (percent) (Fukuchi-Nishikawa, 2001)
+R PMID:11399062
+A Fukuchi, S. and Nishikawa, K.
+T Protein surface amino acid compositions distinctively differ between
+ thermophilic and mesophilic bacteria
+J J. Mol. Biol. 309, 835-843 (2001)
+C FUKS010102 0.932 FUKS010104 0.885
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 4.47 8.48 3.89 7.05 0.29 2.87 16.56 8.29 1.74 3.30
+ 5.06 12.98 1.71 2.32 5.41 4.27 3.83 0.67 2.75 4.05
+//
+H FUKS010102
+D Surface composition of amino acids in intracellular proteins of mesophiles
+ (percent) (Fukuchi-Nishikawa, 2001)
+R PMID:11399062
+A Fukuchi, S. and Nishikawa, K.
+T Protein surface amino acid compositions distinctively differ between
+ thermophilic and mesophilic bacteria
+J J. Mol. Biol. 309, 835-843 (2001)
+C FUKS010104 0.938 FUKS010101 0.932 VINM940101 0.876
+ PARS000102 0.868 HOPT810101 0.854 LEVM760101 0.837
+ WOEC730101 0.820 MIYS990104 0.818 MIYS990105 0.813
+ VINM940103 0.809 VINM940102 0.808 MIYS990103 0.803
+ WERD780101 -0.801 FAUJ830101 -0.805 WIMW960101 -0.808
+ BIOV880102 -0.810 RADA880108 -0.815 BIOV880101 -0.820
+ CASG920101 -0.831
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.77 6.87 5.50 8.57 0.31 5.24 12.93 7.95 2.80 2.72
+ 4.43 10.20 1.87 1.92 4.79 5.41 5.36 0.54 2.26 3.57
+//
+H FUKS010103
+D Surface composition of amino acids in extracellular proteins of mesophiles
+ (percent) (Fukuchi-Nishikawa, 2001)
+R PMID:11399062
+A Fukuchi, S. and Nishikawa, K.
+T Protein surface amino acid compositions distinctively differ between
+ thermophilic and mesophilic bacteria
+J J. Mol. Biol. 309, 835-843 (2001)
+C GUYH850103 0.874 VINM940102 0.864 GUYH850102 0.848
+ KARP850102 0.835 KARP850101 0.834 MEIH800101 0.832
+ VINM940101 0.827 MIYS990104 0.822 RACS770101 0.819
+ CORJ870108 0.818 FASG890101 0.812 MIYS990103 0.805
+ PONP800101 -0.801 CIDH920103 -0.804 PLIV810101 -0.805
+ CORJ870107 -0.805 ZHOH040103 -0.808 ROSG850102 -0.808
+ BASU050102 -0.809 ROSG850101 -0.819 CIDH920105 -0.821
+ CIDH920102 -0.826 MIYS850101 -0.828 CORJ870105 -0.829
+ LEVM760106 -0.829 BIOV880101 -0.840 RADA880108 -0.840
+ CORJ870106 -0.846 NISK860101 -0.850 CIDH920101 -0.854
+ ROBB790101 -0.865 WERD780101 -0.869
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 7.43 4.51 9.12 8.71 0.42 5.42 5.86 9.40 1.49 1.76
+ 2.74 9.67 0.60 1.18 5.60 9.60 8.95 1.18 3.26 3.10
+//
+H FUKS010104
+D Surface composition of amino acids in nuclear proteins (percent)
+ (Fukuchi-Nishikawa, 2001)
+R PMID:11399062
+A Fukuchi, S. and Nishikawa, K.
+T Protein surface amino acid compositions distinctively differ between
+ thermophilic and mesophilic bacteria
+J J. Mol. Biol. 309, 835-843 (2001)
+C FUKS010102 0.938 VINM940101 0.919 FUKS010101 0.885
+ HOPT810101 0.884 MIYS990105 0.870 LEVM760101 0.869
+ MIYS990104 0.862 KRIW790102 0.853 PARS000102 0.850
+ OOBM770103 0.849 MIYS990103 0.845 FASG890101 0.844
+ VINM940103 0.838 KRIW790101 0.828 MEIH800102 0.822
+ KARP850102 0.822 GUYH850102 0.819 NAKH920106 0.818
+ KIDA850101 0.814 VINM940102 0.807 NADH010102 -0.801
+ ZHOH040103 -0.803 NADH010103 -0.805 CORJ870101 -0.814
+ WERD780101 -0.832 NISK860101 -0.832 FAUJ830101 -0.832
+ RADA880108 -0.851 BIOV880101 -0.873 ROSG850102 -0.877
+ BIOV880102 -0.887 CASG920101 -0.892
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 5.22 7.30 6.06 7.91 1.01 6.00 10.66 5.81 2.27 2.36
+ 4.52 12.68 1.85 1.68 5.70 6.99 5.16 0.56 2.16 4.10
+//
+H FUKS010105
+D Interior composition of amino acids in intracellular proteins of thermophiles
+ (percent) (Fukuchi-Nishikawa, 2001)
+R PMID:11399062
+A Fukuchi, S. and Nishikawa, K.
+T Protein surface amino acid compositions distinctively differ between
+ thermophilic and mesophilic bacteria
+J J. Mol. Biol. 309, 835-843 (2001)
+C FUKS010106 0.982 NAKH920105 0.929 FUKS010108 0.923
+ NAKH900111 0.911 CEDJ970103 0.901 NAKH900109 0.892
+ FUKS010107 0.891 NAKH920108 0.890
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 9.88 3.71 2.35 3.50 1.12 1.66 4.02 6.88 1.88 10.08
+ 13.21 3.39 2.44 5.27 3.80 4.10 4.98 1.11 4.07 12.53
+//
+H FUKS010106
+D Interior composition of amino acids in intracellular proteins of mesophiles
+ (percent) (Fukuchi-Nishikawa, 2001)
+R PMID:11399062
+A Fukuchi, S. and Nishikawa, K.
+T Protein surface amino acid compositions distinctively differ between
+ thermophilic and mesophilic bacteria
+J J. Mol. Biol. 309, 835-843 (2001)
+C FUKS010105 0.982 NAKH900111 0.933 NAKH920105 0.931
+ NAKH900109 0.927 FUKS010108 0.927 FUKS010107 0.924
+ CEDJ970103 0.919 NAKH920108 0.898
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 10.98 3.26 2.85 3.37 1.47 2.30 3.51 7.48 2.20 9.74
+ 12.79 2.54 3.10 4.97 3.42 4.93 5.55 1.28 3.55 10.69
+//
+H FUKS010107
+D Interior composition of amino acids in extracellular proteins of mesophiles
+ (percent) (Fukuchi-Nishikawa, 2001)
+R PMID:11399062
+A Fukuchi, S. and Nishikawa, K.
+T Protein surface amino acid compositions distinctively differ between
+ thermophilic and mesophilic bacteria
+J J. Mol. Biol. 309, 835-843 (2001)
+C FUKS010106 0.924 NAKH900109 0.903 FUKS010105 0.891
+ NAKH900111 0.867 CEDJ970103 0.860 NAKH920105 0.833
+ FUKS010108 0.832 NAKH920108 0.817
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 9.95 3.05 4.84 4.46 1.30 2.64 2.58 8.87 1.99 7.73
+ 9.66 2.00 2.45 5.41 3.20 6.03 5.62 2.60 6.15 9.46
+//
+H FUKS010108
+D Interior composition of amino acids in nuclear proteins (percent)
+ (Fukuchi-Nishikawa, 2001)
+R PMID:11399062
+A Fukuchi, S. and Nishikawa, K.
+T Protein surface amino acid compositions distinctively differ between
+ thermophilic and mesophilic bacteria
+J J. Mol. Biol. 309, 835-843 (2001)
+C NAKH920105 0.968 NAKH900111 0.954 NAKH920108 0.948
+ FUKS010106 0.927 FUKS010105 0.923 CEDJ970103 0.897
+ NAKH900112 0.896 NAKH900109 0.872 NAKH900103 0.864
+ NAKH900105 0.846 FUKS010107 0.832 NAKH900107 0.830
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 8.26 2.80 2.54 2.80 2.67 2.86 2.67 5.62 1.98 8.95
+ 16.46 1.89 2.67 7.32 3.30 6.00 5.00 2.01 3.96 10.24
+//
+H FUKS010109
+D Entire chain composition of amino acids in intracellular proteins of
+ thermophiles (percent) (Fukuchi-Nishikawa, 2001)
+R PMID:11399062
+A Fukuchi, S. and Nishikawa, K.
+T Protein surface amino acid compositions distinctively differ between
+ thermophilic and mesophilic bacteria
+J J. Mol. Biol. 309, 835-843 (2001)
+C FUKS010110 0.936 CEDJ970104 0.901 KUMS000101 0.894
+ FUKS010112 0.890 NAKH900101 0.868 JOND920101 0.861
+ KUMS000102 0.850 CEDJ970102 0.839 NAKH920106 0.814
+ DAYM780101 0.801
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 7.39 5.91 3.06 5.14 0.74 2.22 9.80 7.53 1.82 6.96
+ 9.45 7.81 2.10 3.91 4.54 4.18 4.45 0.90 3.46 8.62
+//
+H FUKS010110
+D Entire chain composition of amino acids in intracellular proteins of
+ mesophiles (percent) (Fukuchi-Nishikawa, 2001)
+R PMID:11399062
+A Fukuchi, S. and Nishikawa, K.
+T Protein surface amino acid compositions distinctively differ between
+ thermophilic and mesophilic bacteria
+J J. Mol. Biol. 309, 835-843 (2001)
+C CEDJ970104 0.956 KUMS000101 0.947 NAKH900101 0.946
+ JOND920101 0.944 KUMS000102 0.943 FUKS010109 0.936
+ CEDJ970102 0.921 JUKT750101 0.908 FUKS010112 0.904
+ DAYM780101 0.897 CEDJ970101 0.889 JUNJ780101 0.868
+ KUMS000104 0.861 NAKH900109 0.853 CEDJ970103 0.848
+ NAKH920101 0.833 KUMS000103 0.827 NAKH920106 0.824
+ NAKH920107 0.810
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 9.07 4.90 4.05 5.73 0.95 3.63 7.77 7.69 2.47 6.56
+ 9.00 6.01 2.54 3.59 4.04 5.15 5.46 0.95 2.96 7.47
+//
+H FUKS010111
+D Entire chain composition of amino acids in extracellular proteins of
+ mesophiles (percent) (Fukuchi-Nishikawa, 2001)
+R PMID:11399062
+A Fukuchi, S. and Nishikawa, K.
+T Protein surface amino acid compositions distinctively differ between
+ thermophilic and mesophilic bacteria
+J J. Mol. Biol. 309, 835-843 (2001)
+C JUKT750101 0.927 JUNJ780101 0.906 KUMS000102 0.898
+ DAYM780101 0.882 CEDJ970101 0.878 NAKH920107 0.841
+ JOND920101 0.832 KUMS000101 0.826 CEDJ970102 0.819
+ NAKH900101 0.812 MCMT640101 -0.806
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 8.82 3.71 6.77 6.38 0.90 3.89 4.05 9.11 1.77 5.05
+ 6.54 5.45 1.62 3.51 4.28 7.64 7.12 1.96 4.85 6.60
+//
+H FUKS010112
+D Entire chain compositino of amino acids in nuclear proteins (percent)
+ (Fukuchi-Nishikawa, 2001)
+R PMID:11399062
+A Fukuchi, S. and Nishikawa, K.
+T Protein surface amino acid compositions distinctively differ between
+ thermophilic and mesophilic bacteria
+J J. Mol. Biol. 309, 835-843 (2001)
+C CEDJ970104 0.956 NAKH900101 0.948 CEDJ970102 0.946
+ JOND920101 0.943 NAKH920106 0.921 FUKS010110 0.904
+ FUKS010109 0.890 NAKH920104 0.882 CEDJ970101 0.882
+ JUKT750101 0.875 NAKH920101 0.856 DAYM780101 0.856
+ CEDJ970103 0.850 NAKH920103 0.842 JUNJ780101 0.836
+ NAKH920107 0.824 KUMS000102 0.819
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.65 5.17 4.40 5.50 1.79 4.52 6.89 5.72 2.13 5.47
+ 10.15 7.59 2.24 4.34 4.56 6.52 5.08 1.24 3.01 7.00
+//
+H AVBF000101
+D Screening coefficients gamma, local (Avbelj, 2000)
+R PMID:10903873
+A Avbelj, F.
+T Amino acid conformational preferences and solvation of polar backbone atoms
+ in peptides and proteins
+J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing)
+C QIAN880120 0.876 PTIO830102 0.861 KANM800102 0.859
+ QIAN880119 0.859 LIFS790101 0.857 QIAN880121 0.855
+ CHAM830103 0.843 ROBB760106 0.834 LEVM780105 0.824
+ PALJ810104 0.818 PALJ810110 0.816 PRAM900103 0.815
+ LEVM780102 0.815 LIFS790103 0.814 AVBF000102 0.805
+ LEVM780106 -0.805 GEIM800111 -0.806 QIAN880133 -0.807
+ QIAN880132 -0.809 KIMC930101 -0.814 MUNV940104 -0.821
+ QIAN880134 -0.822 GEIM800110 -0.825 MUNV940103 -0.917
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.163 0.220 0.124 0.212 0.316 0.274 0.212 0.080 0.315 0.474
+ 0.315 0.255 0.356 0.410 NA 0.290 0.412 0.325 0.354 0.515
+//
+H AVBF000102
+D Screening coefficients gamma, non-local (Avbelj, 2000)
+R PMID:10903873
+A Avbelj, F.
+T Amino acid conformational preferences and solvation of polar backbone atoms
+ in peptides and proteins
+J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing)
+C FAUJ880102 0.881 LEVM760103 0.816 AVBF000101 0.805
+ FAUJ880105 0.802 RACS820110 -0.801 CHAM830101 -0.803
+ PALJ810105 -0.815 ISOY800103 -0.821 QIAN880133 -0.823
+ LEVM780103 -0.834 PRAM900104 -0.834 QIAN880132 -0.849
+ LEVM780106 -0.860 KIMC930101 -0.900
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.236 0.233 0.189 0.168 0.259 0.314 0.306 -0.170 0.256 0.391
+ 0.293 0.231 0.367 0.328 NA 0.202 0.308 0.197 0.223 0.436
+//
+H AVBF000103
+D Slopes tripeptide, FDPB VFF neutral (Avbelj, 2000)
+R PMID:10903873
+A Avbelj, F.
+T Amino acid conformational preferences and solvation of polar backbone atoms
+ in peptides and proteins
+J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing)
+C AVBF000105 0.965 AVBF000106 0.897 AVBF000107 0.875
+ FAUJ880107 0.873 AVBF000108 0.868 AVBF000104 0.865
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.490 -0.429 -0.387 -0.375 -0.352 -0.422 -0.382 -0.647 -0.357 -0.268
+ -0.450 -0.409 -0.375 -0.309 NA -0.426 -0.240 -0.325 -0.288 -0.220
+//
+H AVBF000104
+D Slopes tripeptides, LD VFF neutral (Avbelj, 2000)
+R PMID:10903873
+A Avbelj, F.
+T Amino acid conformational preferences and solvation of polar backbone atoms
+ in peptides and proteins
+J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing)
+C ONEK900102 0.919 GEOR030109 0.907 FINA910102 0.901
+ AVBF000103 0.865 AVBF000107 0.839 AVBF000108 0.819
+ BLAM930101 -0.872 ONEK900101 -0.899 BUNA790101 -0.922
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.871 -0.727 -0.741 -0.737 -0.666 -0.728 -0.773 -0.822 -0.685 -0.617
+ -0.798 -0.715 -0.717 -0.649 NA -0.679 -0.629 -0.669 -0.655 -0.599
+//
+H AVBF000105
+D Slopes tripeptide, FDPB VFF noside (Avbelj, 2000)
+R PMID:10903873
+A Avbelj, F.
+T Amino acid conformational preferences and solvation of polar backbone atoms
+ in peptides and proteins
+J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing)
+C AVBF000103 0.965 AVBF000106 0.939 FAUJ880107 0.931
+ AVBF000107 0.879 AVBF000108 0.816 YANJ020101 0.807
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.393 -0.317 -0.268 -0.247 -0.222 -0.291 -0.260 -0.570 -0.244 -0.144
+ -0.281 -0.294 -0.274 -0.189 NA -0.280 -0.152 -0.206 -0.155 -0.080
+//
+H AVBF000106
+D Slopes tripeptide FDPB VFF all (Avbelj, 2000)
+R PMID:10903873
+A Avbelj, F.
+T Amino acid conformational preferences and solvation of polar backbone atoms
+ in peptides and proteins
+J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing)
+C AVBF000105 0.939 AVBF000103 0.897 FAUJ880107 0.853
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.378 -0.369 -0.245 -0.113 -0.206 -0.290 -0.165 -0.560 -0.295 -0.134
+ -0.266 -0.335 -0.260 -0.187 NA -0.251 -0.093 -0.188 -0.147 -0.084
+//
+H AVBF000107
+D Slopes tripeptide FDPB PARSE neutral (Avbelj, 2000)
+R PMID:10903873
+A Avbelj, F.
+T Amino acid conformational preferences and solvation of polar backbone atoms
+ in peptides and proteins
+J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing)
+C FAUJ880107 0.884 AVBF000105 0.879 AVBF000103 0.875
+ AVBF000104 0.839 AVBF000108 0.832
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.729 -0.535 -0.597 -0.545 -0.408 -0.492 -0.532 -0.860 -0.519 -0.361
+ -0.462 -0.508 -0.518 -0.454 NA -0.278 -0.367 -0.455 -0.439 -0.323
+//
+H AVBF000108
+D Slopes dekapeptide, FDPB VFF neutral (Avbelj, 2000)
+R PMID:10903873
+A Avbelj, F.
+T Amino acid conformational preferences and solvation of polar backbone atoms
+ in peptides and proteins
+J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing)
+C AVBF000103 0.868 AVBF000107 0.832 AVBF000104 0.819
+ AVBF000105 0.816 FAUJ880107 0.802
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.623 -0.567 -0.619 -0.626 -0.571 -0.559 -0.572 -0.679 -0.508 -0.199
+ -0.527 -0.581 -0.571 -0.461 NA -0.458 -0.233 -0.327 -0.451 -0.263
+//
+H AVBF000109
+D Slopes proteins, FDPB VFF neutral (Avbelj, 2000)
+R PMID:10903873
+A Avbelj, F.
+T Amino acid conformational preferences and solvation of polar backbone atoms
+ in peptides and proteins
+J J. Mol. Biol. 300, 1335-1359 (2000) (Pro missing)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.376 -0.280 -0.403 -0.405 -0.441 -0.362 -0.362 -0.392 -0.345 -0.194
+ -0.317 -0.412 -0.312 -0.237 NA -0.374 -0.243 -0.111 -0.171 -0.355
+//
+H YANJ020101
+D Side-chain conformation by gaussian evolutionary method (Yang et al., 2002)
+R PMID:12142444
+A Yang, J.M., Tsai, C.H., Hwang, M.J., Tsai, H.K., Hwang, J.K. and Kao, C.Y.
+T GEM: a Gaussian Evolutionary Method for predicting protein side-chain
+ conformations
+J Protein Sci. 11, 1897-1907 (2002) (Gly Ala missing)
+C AVBF000105 0.807
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ NA 0.62 0.76 0.66 0.83 0.59 0.73 NA 0.92 0.88
+ 0.89 0.77 0.77 0.92 0.94 0.58 0.73 0.86 0.93 0.88
+//
+H MITS020101
+D Amphiphilicity index (Mitaku et al., 2002)
+R PMID:12016058
+A Mitaku, S., Hirokawa, T. and Tsuji, T.
+T Amphiphilicity index of polar amino acids as an aid in the characterization
+ of amino acid preference at membrane-water interfaces
+J Bioinformatics. 18, 608-616 (2002)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0 2.45 0 0 0 1.25 1.27 0 1.45 0
+ 0 3.67 0 0 0 0 0 6.93 5.06 0
+//
+H TSAJ990101
+D Volumes including the crystallographic waters using the ProtOr (Tsai et al.,
+ 1999)
+R PMID:10388571
+A Tsai, J., Taylor, R., Chothia, C. and Gerstein, M.
+T The packing density in proteins: standard radii and volumes
+J J. Mol. Biol. 290, 253-266 (1999) (Cyh 112.8)
+C TSAJ990102 1.000 CHOC750101 0.995 BIGC670101 0.993
+ GOLD730102 0.993 KRIW790103 0.988 FAUJ880103 0.983
+ GRAR740103 0.979 CHAM820101 0.977 CHOC760101 0.968
+ HARY940101 0.964 PONJ960101 0.960 FASG760101 0.935
+ LEVM760105 0.922 ROSG850101 0.914 LEVM760102 0.910
+ DAWD720101 0.903 CHAM830106 0.889 FAUJ880106 0.879
+ ZHOH040102 0.874 LEVM760107 0.866 RADA880106 0.861
+ LEVM760106 0.849 RADA880103 -0.875
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 89.3 190.3 122.4 114.4 102.5 146.9 138.8 63.8 157.5 163.0
+ 163.1 165.1 165.8 190.8 121.6 94.2 119.6 226.4 194.6 138.2
+//
+H TSAJ990102
+D Volumes not including the crystallographic waters using the ProtOr (Tsai et
+ al., 1999)
+R PMID:10388571
+A Tsai, J., Taylor, R., Chothia, C. and Gerstein, M.
+T The packing density in proteins: standard radii and volumes
+J J. Mol. Biol. 290, 253-266 (1999) (Cyh 113.7)
+C TSAJ990101 1.000 CHOC750101 0.996 BIGC670101 0.992
+ GOLD730102 0.991 KRIW790103 0.987 FAUJ880103 0.985
+ GRAR740103 0.978 CHAM820101 0.978 CHOC760101 0.972
+ HARY940101 0.965 PONJ960101 0.962 FASG760101 0.940
+ LEVM760105 0.928 LEVM760102 0.918 ROSG850101 0.909
+ DAWD720101 0.905 CHAM830106 0.896 FAUJ880106 0.882
+ ZHOH040102 0.867 RADA880106 0.864 LEVM760107 0.861
+ LEVM760106 0.841 RADA880103 -0.879
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 90.0 194.0 124.7 117.3 103.3 149.4 142.2 64.9 160.0 163.9
+ 164.0 167.3 167.0 191.9 122.9 95.4 121.5 228.2 197.0 139.0
+//
+H COSI940101
+D Electron-ion interaction potential values (Cosic, 1994)
+R PMID:7851912
+A Cosic, I.
+T Macromolecular bioactivity: is it resonant interaction between
+ macromolecules?--Theory and applications
+J IEEE Trans Biomed Eng. 41, 1101-1114 (1994) (values are cited from Protein
+ Eng. 15:193-203)
+C VELV850101 1.000
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.0373 0.0959 0.0036 0.1263 0.0829 0.0761 0.0058 0.0050 0.0242 0.0000
+ 0.0000 0.0371 0.0823 0.0946 0.0198 0.0829 0.0941 0.0548 0.0516 0.0057
+//
+H PONP930101
+D Hydrophobicity scales (Ponnuswamy, 1993)
+R PMID:8419986
+A Ponnuswamy, P.K.
+T Hydrophobic characteristics of folded proteins
+J Prog Biophys Mol Biol. 59, 57-103 (1993)
+C MANP780101 0.967 NISK860101 0.961 CORJ870101 0.960
+ NISK800101 0.956 PONP800101 0.945 PONP800108 0.944
+ PONP800102 0.934 BASU050103 0.933 BASU050101 0.932
+ CIDH920104 0.930 ROSG850102 0.928 CORJ870107 0.923
+ CORJ870103 0.920 BASU050102 0.913 BIOV880101 0.912
+ CASG920101 0.911 MIYS850101 0.910 PONP800103 0.909
+ LIFS790101 0.908 CORJ870104 0.901 CIDH920103 0.899
+ NADH010103 0.898 ZHOH040103 0.896 WERD780101 0.895
+ NADH010104 0.895 QIAN880121 0.893 RADA880108 0.891
+ CIDH920105 0.891 CORJ870106 0.889 NADH010102 0.880
+ QIAN880120 0.879 PTIO830102 0.879 CORJ870105 0.878
+ BIOV880102 0.877 CHOP780202 0.867 ROBB760106 0.866
+ KANM800102 0.866 MEIH800103 0.863 ROBB790101 0.858
+ PALJ810104 0.857 BAEK050101 0.856 PONP800107 0.851
+ JURD980101 0.849 KYTJ820101 0.844 FAUJ830101 0.843
+ NADH010105 0.839 GEIM800107 0.838 QIAN880122 0.837
+ QIAN880119 0.836 SWER830101 0.835 DESM900102 0.834
+ LIFS790102 0.833 KANM800104 0.833 CORJ870102 0.832
+ ROBB760105 0.829 JANJ780102 0.825 CIDH920102 0.820
+ PLIV810101 0.819 JANJ790101 0.816 CHOC760103 0.816
+ NADH010101 0.813 DESM900101 0.807 GUOD860101 0.802
+ GUYH850101 -0.817 VINM940103 -0.818 PUNT030101 -0.820
+ KRIW790102 -0.821 PARJ860101 -0.846 PARS000101 -0.849
+ GUYH850103 -0.858 MUNV940103 -0.864 VINM940102 -0.869
+ RACS770102 -0.871 GRAR740102 -0.872 PUNT030102 -0.872
+ MEIH800102 -0.881 RACS770101 -0.886 KARP850102 -0.893
+ GUYH850102 -0.897 FASG890101 -0.907 KRIW790101 -0.909
+ CORJ870108 -0.912 VINM940101 -0.913 OOBM770103 -0.914
+ MIYS990101 -0.916 MEIH800101 -0.916 MIYS990102 -0.919
+ MIYS990105 -0.936 MIYS990104 -0.949 MIYS990103 -0.951
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.85 0.20 -0.48 -1.10 2.10 -0.42 -0.79 0 0.22 3.14
+ 1.99 -1.19 1.42 1.69 -1.14 -0.52 -0.08 1.76 1.37 2.53
+//
+H WILM950101
+D Hydrophobicity coefficient in RP-HPLC, C18 with 0.1%TFA/MeCN/H2O (Wilce et
+ al. 1995)
+R
+A Wilce, M.C., Aguilar, M.I. and Hearn, M.T.
+T Physicochemical basis of amino acid hydrophobicity scales: evaluation of four
+ new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of
+ peptides
+J Anal Chem. 67, 1210-1219 (1995)
+C GUOD860101 0.893 COWR900101 0.860 MEEJ810102 0.849
+ VENT840101 0.840 WILM950102 0.838 BLAS910101 0.810
+ MIYS990102 -0.822 MIYS990101 -0.822 BULH740101 -0.845
+ WOLS870101 -0.851
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.06 -0.85 0.25 -0.20 0.49 0.31 -0.10 0.21 -2.24 3.48
+ 3.50 -1.62 0.21 4.80 0.71 -0.62 0.65 2.29 1.89 1.59
+//
+H WILM950102
+D Hydrophobicity coefficient in RP-HPLC, C8 with 0.1%TFA/MeCN/H2O (Wilce et al.
+ 1995)
+R
+A Wilce, M.C., Aguilar, M.I. and Hearn, M.T.
+T Physicochemical basis of amino acid hydrophobicity scales: evaluation of four
+ new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of
+ peptides
+J Anal Chem. 67, 1210-1219 (1995)
+C WILM950101 0.838 MEEJ810102 0.809
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.62 1.26 -1.27 -2.84 0.73 -1.69 -0.45 -1.15 -0.74 4.38
+ 6.57 -2.78 -3.12 9.14 -0.12 -1.39 1.81 5.91 1.39 2.30
+//
+H WILM950103
+D Hydrophobicity coefficient in RP-HPLC, C4 with 0.1%TFA/MeCN/H2O (Wilce et al.
+ 1995)
+R
+A Wilce, M.C., Aguilar, M.I. and Hearn, M.T.
+T Physicochemical basis of amino acid hydrophobicity scales: evaluation of four
+ new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of
+ peptides
+J Anal Chem. 67, 1210-1219 (1995)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -1.64 -3.28 0.83 0.70 9.30 -0.04 1.18 -1.85 7.17 3.02
+ 0.83 -2.36 4.26 -1.36 3.12 1.59 2.31 2.61 2.37 0.52
+//
+H WILM950104
+D Hydrophobicity coefficient in RP-HPLC, C18 with 0.1%TFA/2-PrOH/MeCN/H2O
+ (Wilce et al. 1995)
+R
+A Wilce, M.C., Aguilar, M.I. and Hearn, M.T.
+T Physicochemical basis of amino acid hydrophobicity scales: evaluation of four
+ new scales of amino acid hydrophobicity coefficients derived from RP-HPLC of
+ peptides
+J Anal Chem. 67, 1210-1219 (1995)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -2.34 1.60 2.81 -0.48 5.03 0.16 1.30 -1.06 -3.00 7.26
+ 1.09 1.56 0.62 2.57 -0.15 1.93 0.19 3.59 -2.58 2.06
+//
+H KUHL950101
+D Hydrophilicity scale (Kuhn et al., 1995)
+R PMID:8749849
+A Kuhn, L.A., Swanson, C.A., Pique, M.E., Tainer, J.A. and Getzoff, E.D.
+T Atomic and residue hydrophilicity in the context of folded protein structures
+J Proteins 23, 536-547 (1995)
+C ROSM880101 0.962 ROSM880102 0.922 FAUJ880110 0.922
+ PRAM900101 0.908 ENGD860101 0.908 KIDA850101 0.882
+ OOBM770101 0.876 GRAR740102 0.865 VHEG790101 0.858
+ GUYH850105 0.850 PUNT030101 0.844 PUNT030102 0.841
+ JANJ780101 0.839 WOEC730101 0.837 GUYH850104 0.835
+ GUYH850101 0.827 FAUJ880109 0.827 JANJ780103 0.826
+ MEIH800102 0.822 FASG890101 0.821 LEVM760101 0.807
+ BASU050103 -0.804 NADH010103 -0.807 BIOV880102 -0.809
+ MEIH800103 -0.809 WARP780101 -0.811 JANJ790101 -0.811
+ CIDH920104 -0.822 BIOV880101 -0.834 EISD860101 -0.835
+ NADH010102 -0.836 RADA880108 -0.839 JANJ790102 -0.844
+ RADA880104 -0.847 OLSK800101 -0.849 RADA880107 -0.857
+ FAUJ830101 -0.863 DESM900102 -0.863 JACR890101 -0.864
+ CHOC760103 -0.865 KYTJ820101 -0.883 JURD980101 -0.884
+ JANJ780102 -0.890 EISD860103 -0.894 BLAS910101 -0.894
+ ROSM880105 -0.896 WOLR790101 -0.898 WOLR810101 -0.898
+ NADH010101 -0.898 EISD840101 -0.907 RADA880101 -0.950
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.78 1.58 1.20 1.35 0.55 1.19 1.45 0.68 0.99 0.47
+ 0.56 1.10 0.66 0.47 0.69 1.00 1.05 0.70 1.00 0.51
+//
+H GUOD860101
+D Retention coefficient at pH 2 (Guo et al., 1986)
+R
+A Guo, D., Mant, C.T., Taneja, A.K., Parker, J.M. and Hodges, R.S.
+T Prediction of peptide retention times in reversed-phase high-performance
+ liquid chromatography; I. determination of retention coefficients of amino
+ acid residues of model synthetic peptides
+J J Chromatogr. 359, 499-517 (1986)
+C MEEJ810102 0.949 PLIV810101 0.943 MEEJ810101 0.931
+ COWR900101 0.920 MIYS850101 0.908 FAUJ830101 0.900
+ WILM950101 0.893 ZHOH040103 0.889 ZHOH040101 0.884
+ NOZY710101 0.884 BASU050102 0.868 ROSM880104 0.868
+ BLAS910101 0.866 MEEJ800102 0.866 CIDH920104 0.860
+ CIDH920105 0.858 PONP800107 0.854 SWER830101 0.853
+ CORJ870102 0.852 ZIMJ680105 0.850 VENT840101 0.848
+ BASU050101 0.847 CIDH920103 0.845 NISK860101 0.840
+ EISD860101 0.839 BIOV880101 0.839 BASU050103 0.833
+ BROC820101 0.832 CIDH920102 0.831 RADA880102 0.829
+ ROSM880105 0.826 BIOV880102 0.817 MANP780101 0.815
+ ROBB790101 0.815 RADA880108 0.812 ZHOH040102 0.812
+ NAKH900110 0.805 NADH010104 0.803 NADH010103 0.803
+ PONP930101 0.802 FASG890101 -0.801 RACS770101 -0.805
+ PUNT030101 -0.810 PUNT030102 -0.813 GUYH850103 -0.819
+ MIYS990103 -0.828 KIDA850101 -0.828 ROSM880102 -0.829
+ MEIH800101 -0.833 OOBM770103 -0.838 MIYS990105 -0.846
+ MIYS990104 -0.846 GRAR740102 -0.855 MIYS990102 -0.916
+ MIYS990101 -0.917 BULH740101 -0.922 PARJ860101 -0.925
+ WOLS870101 -0.955
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 25 -7 -7 2 32 0 14 -2 -26 91
+ 100 -26 68 100 25 -2 7 109 56 62
+//
+H JURD980101
+D Modified Kyte-Doolittle hydrophobicity scale (Juretic et al., 1998)
+R
+A Juretic, D., Lucic, B., Zucic, D. and Trinajstic, N.
+T Protein transmembrane structure: recognition and prediction by using
+ hydrophobicity scales through preference functions
+J Theoretical and Computational Chemistry, 5, 405-445 (1998)
+C KYTJ820101 0.996 CHOC760103 0.967 OLSK800101 0.943
+ NADH010102 0.931 JANJ780102 0.928 NADH010101 0.925
+ EISD860103 0.901 DESM900102 0.900 NADH010103 0.900
+ EISD840101 0.895 RADA880101 0.893 MANP780101 0.887
+ WOLR810101 0.881 PONP800103 0.879 JANJ790102 0.879
+ NADH010104 0.873 BASU050103 0.871 CHOC760104 0.870
+ PONP800102 0.869 JANJ790101 0.868 WOLR790101 0.864
+ MEIH800103 0.861 PONP800101 0.858 NAKH920108 0.858
+ RADA880108 0.857 PONP800108 0.856 COWR900101 0.855
+ ROSG850102 0.854 CORJ870101 0.849 PONP930101 0.849
+ RADA880107 0.842 BLAS910101 0.841 BIOV880101 0.840
+ MIYS850101 0.837 FAUJ830101 0.833 CIDH920104 0.832
+ BASU050101 0.830 DESM900101 0.829 WARP780101 0.827
+ KANM800104 0.826 LIFS790102 0.824 RADA880104 0.824
+ NADH010105 0.821 ROSM880105 0.818 NISK800101 0.816
+ CORJ870104 0.812 NISK860101 0.808 CORJ870103 0.808
+ BIOV880102 0.805 CORJ870107 0.804 ARGP820102 0.802
+ ARGP820103 0.800 CORJ870108 -0.806 MIYS990104 -0.813
+ VHEG790101 -0.814 KRIW790101 -0.824 MIYS990105 -0.829
+ MIYS990103 -0.845 CHOC760102 -0.851 ROSM880101 -0.851
+ MIYS990101 -0.852 MONM990101 -0.853 JANJ780103 -0.853
+ MIYS990102 -0.853 RACS770102 -0.855 FASG890101 -0.857
+ ENGD860101 -0.861 PRAM900101 -0.862 JANJ780101 -0.862
+ GUYH850101 -0.864 GRAR740102 -0.864 PUNT030102 -0.869
+ MEIH800102 -0.879 GUYH850104 -0.880 KUHL950101 -0.884
+ PUNT030101 -0.884 ROSM880102 -0.894 GUYH850105 -0.900
+ OOBM770101 -0.903
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.10 -5.10 -3.50 -3.60 2.50 -3.68 -3.20 -0.64 -3.20 4.50
+ 3.80 -4.11 1.90 2.80 -1.90 -0.50 -0.70 -0.46 -1.3 4.2
+//
+H BASU050101
+D Interactivity scale obtained from the contact matrix (Bastolla et al., 2005)
+R PMID:15523667
+A Bastolla, U., Porto M., Roman H.E. and Vendruscolo M.
+T Principal eigenvector of contact matrices and hydrophobicity profiles in
+ prote
+J Proteins 58, 22-30 (2005)
+C BASU050103 0.965 BASU050102 0.946 PONP930101 0.932
+ NISK860101 0.926 MANP780101 0.925 SWER830101 0.922
+ CORJ870102 0.921 CIDH920104 0.917 ZHOH040103 0.917
+ CORJ870107 0.913 CORJ870104 0.910 CIDH920105 0.907
+ PTIO830102 0.903 CIDH920103 0.894 PONP800108 0.894
+ CORJ870106 0.891 CORJ870103 0.890 CORJ870105 0.888
+ MIYS850101 0.888 LIFS790101 0.886 CHOP780202 0.883
+ BIOV880101 0.883 PONP800101 0.882 PLIV810101 0.879
+ NISK800101 0.876 PALJ810104 0.873 RADA880108 0.867
+ PONP800102 0.864 CORJ870101 0.863 CIDH920102 0.858
+ VENT840101 0.858 QIAN880120 0.856 KANM800102 0.856
+ BLAS910101 0.853 ROBB760105 0.853 FAUJ830101 0.852
+ ROBB760106 0.851 ZHOH040101 0.851 KANM800104 0.850
+ ROSG850102 0.849 GUOD860101 0.847 GEIM800107 0.847
+ ROBB790101 0.845 WERD780101 0.843 PONP800103 0.842
+ NADH010103 0.839 CIDH920101 0.839 NADH010104 0.837
+ ROSM880104 0.830 JURD980101 0.830 QIAN880121 0.828
+ ROSM880105 0.828 KYTJ820101 0.826 PONP800107 0.825
+ BIOV880102 0.812 NADH010102 0.812 NADH010105 0.811
+ MEEJ810101 0.810 CASG920101 0.806 QIAN880119 0.805
+ GUYH850101 -0.807 WOEC730101 -0.811 RACS770102 -0.813
+ GUYH850102 -0.815 KRIW790101 -0.821 PUNT030101 -0.822
+ MEIH800102 -0.825 PARS000101 -0.835 MUNV940103 -0.846
+ OOBM770103 -0.850 RACS770101 -0.850 GUYH850103 -0.852
+ BULH740101 -0.854 FASG890101 -0.856 VINM940101 -0.867
+ WOLS870101 -0.869 PUNT030102 -0.873 VINM940102 -0.874
+ MEIH800101 -0.887 GRAR740102 -0.889 PARJ860101 -0.897
+ MIYS990105 -0.900 CORJ870108 -0.916 MIYS990103 -0.918
+ MIYS990104 -0.918 MIYS990102 -0.945 MIYS990101 -0.945
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.1366 0.0363 -0.0345 -0.1233 0.2745 0.0325 -0.0484 -0.0464 0.0549 0.4172
+ 0.4251 -0.0101 0.1747 0.4076 0.0019 -0.0433 0.0589 0.2362 0.3167 0.4084
+//
+H BASU050102
+D Interactivity scale obtained by maximizing the mean of correlation
+ coefficient over single-domain globular proteins (Bastolla et al., 2005)
+R PMID:15523667
+A Bastolla, U., Porto M., Roman H.E. and Vendruscolo M.
+T Principal eigenvector of contact matrices and hydrophobicity profiles in
+ prote
+J Proteins 58, 22-30 (2005)
+C ZHOH040103 0.978 NISK860101 0.951 ZHOH040101 0.948
+ BASU050101 0.946 CIDH920104 0.934 CIDH920105 0.931
+ BASU050103 0.925 WERD780101 0.920 CIDH920102 0.914
+ PONP930101 0.913 BIOV880101 0.909 MIYS850101 0.904
+ BAEK050101 0.898 MEEJ810101 0.898 ROBB790101 0.897
+ CIDH920103 0.887 FAUJ830101 0.885 NISK800101 0.884
+ CORJ870102 0.881 SWER830101 0.880 PONP800108 0.880
+ MANP780101 0.879 NADH010104 0.879 PLIV810101 0.876
+ CASG920101 0.873 MEEJ810102 0.871 ROSG850102 0.870
+ RADA880108 0.870 NADH010105 0.869 GUOD860101 0.868
+ NADH010103 0.862 LIFS790101 0.861 CORJ870106 0.859
+ CIDH920101 0.858 CORJ870101 0.855 CORJ870107 0.855
+ VENT840101 0.851 PONP800101 0.848 PTIO830102 0.848
+ NOZY710101 0.847 ROSM880104 0.846 CORJ870103 0.845
+ PONP800102 0.843 CHOP780202 0.841 BIOV880102 0.838
+ CORJ870104 0.838 QIAN880120 0.837 CORJ870105 0.834
+ PONP800103 0.828 PALJ810104 0.826 LIFS790103 0.826
+ QIAN880121 0.825 RADA880102 0.809 ZHOH040102 0.808
+ BLAS910101 0.807 LEVM760106 0.805 NADH010102 0.802
+ MEIH800103 0.801 GUYH850101 -0.801 RACS770102 -0.807
+ FUKS010103 -0.809 MEIH800102 -0.812 KARP850101 -0.819
+ KARP850102 -0.825 PUNT030102 -0.832 MUNV940103 -0.839
+ BULH740101 -0.845 WOLS870101 -0.849 RACS770101 -0.854
+ CORJ870108 -0.855 VINM940103 -0.856 PARS000101 -0.864
+ GRAR740102 -0.864 KRIW790101 -0.867 FASG890101 -0.881
+ MEIH800101 -0.892 OOBM770103 -0.893 VINM940101 -0.904
+ GUYH850103 -0.904 PARJ860101 -0.908 GUYH850102 -0.911
+ MIYS990105 -0.919 MIYS990103 -0.924 MIYS990101 -0.935
+ MIYS990102 -0.936 VINM940102 -0.937 MIYS990104 -0.942
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.0728 0.0394 -0.0390 -0.0552 0.3557 0.0126 -0.0295 -0.0589 0.0874 0.3805
+ 0.3819 -0.0053 0.1613 0.4201 -0.0492 -0.0282 0.0239 0.4114 0.3113 0.2947
+//
+H BASU050103
+D Interactivity scale obtained by maximizing the mean of correlation
+ coefficient over pairs of sequences sharing the TIM barrel fold (Bastolla et
+ al., 2005)
+R PMID:15523667
+A Bastolla, U., Porto M., Roman H.E. and Vendruscolo M.
+T Principal eigenvector of contact matrices and hydrophobicity profiles in
+ prote
+J Proteins 58, 22-30 (2005)
+C BASU050101 0.965 CIDH920104 0.941 NISK860101 0.937
+ PONP930101 0.933 ZHOH040103 0.927 BIOV880101 0.926
+ RADA880108 0.926 BASU050102 0.925 MANP780101 0.923
+ PONP800108 0.921 PONP800101 0.915 CIDH920105 0.914
+ NADH010103 0.903 FAUJ830101 0.903 ROSG850102 0.903
+ PONP800102 0.902 NADH010104 0.899 MIYS850101 0.899
+ CORJ870101 0.897 NISK800101 0.896 CIDH920103 0.894
+ SWER830101 0.892 CORJ870102 0.889 PTIO830102 0.888
+ NADH010102 0.886 CORJ870107 0.883 PALJ810104 0.882
+ PLIV810101 0.880 PONP800103 0.879 BLAS910101 0.878
+ CORJ870104 0.877 CHOP780202 0.874 JURD980101 0.871
+ KANM800102 0.869 BIOV880102 0.868 CORJ870103 0.867
+ LIFS790101 0.865 ROSM880105 0.864 KYTJ820101 0.863
+ CASG920101 0.860 CORJ870106 0.858 NADH010105 0.857
+ WERD780101 0.857 CIDH920102 0.856 NADH010101 0.852
+ CORJ870105 0.852 ROBB790101 0.849 KANM800104 0.848
+ GEIM800107 0.847 ROBB760106 0.840 ROBB760105 0.839
+ NAGK730102 0.837 GUOD860101 0.833 MEIH800103 0.832
+ CIDH920101 0.828 QIAN880121 0.828 DESM900102 0.818
+ RADA880102 0.815 VENT840101 0.814 ZHOH040101 0.813
+ PONP800107 0.812 QIAN880120 0.811 EISD860101 0.809
+ RADA880101 0.809 BAEK050101 0.806 EISD840101 0.806
+ EISD860103 0.806 CHOC760103 0.805 JANJ780102 0.803
+ ROSM880101 -0.804 KUHL950101 -0.804 KARP850102 -0.806
+ KIDA850101 -0.806 LEVM760101 -0.808 ROSM880102 -0.814
+ VINM940103 -0.814 MUNV940103 -0.814 PARS000101 -0.820
+ HOPT810101 -0.830 BULH740101 -0.833 WOEC730101 -0.836
+ PUNT030101 -0.844 GUYH850102 -0.845 RACS770101 -0.848
+ GUYH850103 -0.854 KRIW790101 -0.860 RACS770102 -0.861
+ WOLS870101 -0.866 OOBM770103 -0.866 GUYH850101 -0.871
+ PARJ860101 -0.874 MEIH800102 -0.880 VINM940102 -0.880
+ CORJ870108 -0.883 PUNT030102 -0.895 VINM940101 -0.902
+ MEIH800101 -0.906 GRAR740102 -0.906 FASG890101 -0.915
+ MIYS990105 -0.928 MIYS990104 -0.938 MIYS990101 -0.940
+ MIYS990102 -0.940 MIYS990103 -0.943
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.1510 -0.0103 0.0381 0.0047 0.3222 0.0246 -0.0639 0.0248 0.1335 0.4238
+ 0.3926 -0.0158 0.2160 0.3455 0.0844 0.0040 0.1462 0.2657 0.2998 0.3997
+//
+H SUYM030101
+D Linker propensity index (Suyama-Ohara, 2003)
+R PMID:12651735
+A Suyama, M. and Ohara, O.
+T DomCut: Prediction of inter-domain linker regions in amino acid sequences
+J Bioinformatics 19, 673-674 (2003)
+C BAEK050101 0.805
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.058 0.000 0.027 0.016 0.447 -0.073 -0.128 0.331 0.195 0.060
+ 0.138 -0.112 0.275 0.240 -0.478 -0.177 -0.163 0.564 0.322 -0.052
+//
+H PUNT030101
+D Knowledge-based membrane-propensity scale from 1D_Helix in MPtopo databases
+ (Punta-Maritan, 2003)
+R PMID:12471604
+A Punta, M. and Maritan, A.
+T A knowledge-based scale for amino acid membrane propensity
+J Proteins 50, 114-121 (2003)
+C GUYH850101 0.910 MEIH800102 0.901 PUNT030102 0.899
+ RACS770102 0.894 ENGD860101 0.889 PRAM900101 0.889
+ MIYS990101 0.888 MIYS990102 0.887 ROSM880101 0.884
+ MIYS990105 0.876 VHEG790101 0.876 GRAR740102 0.873
+ OOBM770101 0.865 MIYS990103 0.864 ROSM880102 0.861
+ MEIH800101 0.860 HOPT810101 0.858 GUYH850105 0.858
+ MIYS990104 0.857 KIDA850101 0.856 WOLS870101 0.853
+ JANJ780103 0.848 CORJ870108 0.845 FASG890101 0.845
+ PARJ860101 0.845 KUHL950101 0.844 GUYH850104 0.840
+ MONM990101 0.839 LEVM760101 0.835 KRIW790101 0.833
+ RACS770103 0.830 WOEC730101 0.825 JANJ780101 0.824
+ RACS770101 0.821 KRIW790102 0.811 CHOC760102 0.809
+ VINM940101 0.805 KARP850102 0.805 PONP800101 -0.800
+ CORJ870103 -0.802 CORJ870104 -0.804 PONP800107 -0.804
+ CIDH920105 -0.805 ZHOH040103 -0.809 GUOD860101 -0.810
+ ARGP820103 -0.810 CASG920101 -0.811 JACR890101 -0.812
+ PONP800103 -0.812 WARP780101 -0.814 CIDH920103 -0.819
+ PONP930101 -0.820 WERD780101 -0.821 RADA880102 -0.821
+ BASU050101 -0.822 MANP780101 -0.824 CIDH920104 -0.827
+ DESM900101 -0.828 EISD860103 -0.829 CORJ870106 -0.833
+ CORJ870105 -0.834 CORJ870102 -0.835 OLSK800101 -0.838
+ SWER830101 -0.838 NADH010104 -0.843 BASU050103 -0.844
+ JANJ790102 -0.846 CORJ870107 -0.848 JANJ780102 -0.848
+ NISK860101 -0.854 CHOC760103 -0.859 PLIV810101 -0.860
+ NADH010101 -0.862 BLAS910101 -0.865 NADH010103 -0.868
+ KYTJ820101 -0.872 FAUJ830101 -0.876 MEIH800103 -0.882
+ BIOV880101 -0.883 ROSG850102 -0.883 JURD980101 -0.884
+ RADA880108 -0.884 NAKH900110 -0.886 RADA880101 -0.886
+ BIOV880102 -0.888 EISD860101 -0.890 MIYS850101 -0.892
+ NADH010102 -0.897 DESM900102 -0.903 EISD840101 -0.914
+ ROSM880105 -0.922
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.17 0.37 0.18 0.37 -0.06 0.26 0.15 0.01 -0.02 -0.28
+ -0.28 0.32 -0.26 -0.41 0.13 0.05 0.02 -0.15 -0.09 -0.17
+//
+H PUNT030102
+D Knowledge-based membrane-propensity scale from 3D_Helix in MPtopo databases
+ (Punta-Maritan, 2003)
+R PMID:12471604
+A Punta, M. and Maritan, A.
+T A knowledge-based scale for amino acid membrane propensity
+J Proteins 50, 114-121 (2003)
+C GRAR740102 0.915 PUNT030101 0.899 WOEC730101 0.894
+ HOPT810101 0.886 MIYS990102 0.882 MIYS990101 0.881
+ MIYS990103 0.881 MIYS990104 0.874 MIYS990105 0.874
+ VHEG790101 0.873 ENGD860101 0.870 PRAM900101 0.869
+ WOLS870101 0.868 PARJ860101 0.867 ROSM880101 0.864
+ FASG890101 0.853 ROSM880102 0.851 VINM940101 0.850
+ MEIH800102 0.849 LEVM760101 0.848 OOBM770101 0.845
+ KUHL950101 0.841 MONM990101 0.839 MEIH800101 0.837
+ GUYH850101 0.836 RACS770102 0.828 OOBM770103 0.828
+ KRIW790101 0.826 CORJ870108 0.810 KIDA850101 0.807
+ DESM900101 -0.801 CHOP780202 -0.803 KANM800102 -0.803
+ LIFS790101 -0.809 CIDH920103 -0.810 CORJ870107 -0.810
+ RADA880102 -0.811 GUOD860101 -0.813 CORJ870106 -0.814
+ MEIH800103 -0.815 CORJ870105 -0.817 CIDH920105 -0.822
+ PONP800101 -0.827 PONP800102 -0.827 JANJ780102 -0.830
+ CASG920101 -0.831 BASU050102 -0.832 PONP800103 -0.834
+ NAGK730102 -0.836 ZHOH040103 -0.847 NADH010104 -0.851
+ EISD860103 -0.853 EISD840101 -0.854 NISK800101 -0.855
+ PONP800108 -0.855 CIDH920104 -0.857 PLIV810101 -0.858
+ CORJ870101 -0.860 BIOV880102 -0.860 KYTJ820101 -0.862
+ NADH010103 -0.865 MIYS850101 -0.868 DESM900102 -0.868
+ EISD860101 -0.869 ROSG850102 -0.869 RADA880108 -0.869
+ JURD980101 -0.869 PONP930101 -0.872 NADH010101 -0.872
+ NADH010102 -0.872 MANP780101 -0.873 BASU050101 -0.873
+ BLAS910101 -0.877 BIOV880101 -0.878 RADA880101 -0.881
+ NISK860101 -0.885 BASU050103 -0.895 FAUJ830101 -0.908
+ ROSM880105 -0.917
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.15 0.32 0.22 0.41 -0.15 0.03 0.30 0.08 0.06 -0.29
+ -0.36 0.24 -0.19 -0.22 0.15 0.16 -0.08 -0.28 -0.03 -0.24
+//
+H GEOR030101
+D Linker propensity from all dataset (George-Heringa, 2003)
+R PMID:12538906
+A George, R.A. and Heringa, J.
+T An analysis of protein domain linkers: their classification and role in
+ protein folding
+J Protein Eng. 15, 871-879 (2003)
+C GEOR030106 0.938 GEOR030102 0.859 GEOR030103 0.839
+ GEOR030104 0.834
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.964 1.143 0.944 0.916 0.778 1.047 1.051 0.835 1.014 0.922
+ 1.085 0.944 1.032 1.119 1.299 0.947 1.017 0.895 1 0.955
+//
+H GEOR030102
+D Linker propensity from 1-linker dataset (George-Heringa, 2003)
+R PMID:12538906
+A George, R.A. and Heringa, J.
+T An analysis of protein domain linkers: their classification and role in
+ protein folding
+J Protein Eng. 15, 871-879 (2003)
+C GEOR030101 0.859 GEOR030107 0.815
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.974 1.129 0.988 0.892 0.972 1.092 1.054 0.845 0.949 0.928
+ 1.11 0.946 0.923 1.122 1.362 0.932 1.023 0.879 0.902 0.923
+//
+H GEOR030103
+D Linker propensity from 2-linker dataset (George-Heringa, 2003)
+R PMID:12538906
+A George, R.A. and Heringa, J.
+T An analysis of protein domain linkers: their classification and role in
+ protein folding
+J Protein Eng. 15, 871-879 (2003)
+C GEOR030106 0.913 GEOR030101 0.839
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.938 1.137 0.902 0.857 0.6856 0.916 1.139 0.892 1.109 0.986
+ 1 0.952 1.077 1.11 1.266 0.956 1.018 0.971 1.157 0.959
+//
+H GEOR030104
+D Linker propensity from 3-linker dataset (George-Heringa, 2003)
+R PMID:12538906
+A George, R.A. and Heringa, J.
+T An analysis of protein domain linkers: their classification and role in
+ protein folding
+J Protein Eng. 15, 871-879 (2003)
+C GEOR030106 0.904 GEOR030101 0.834
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.042 1.069 0.828 0.97 0.5 1.111 0.992 0.743 1.034 0.852
+ 1.193 0.979 0.998 0.981 1.332 0.984 0.992 0.96 1.12 1.001
+//
+H GEOR030105
+D Linker propensity from small dataset (linker length is less than six
+ residues) (George-Heringa, 2003)
+R PMID:12538906
+A George, R.A. and Heringa, J.
+T An analysis of protein domain linkers: their classification and role in
+ protein folding
+J Protein Eng. 15, 871-879 (2003)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.065 1.131 0.762 0.836 1.015 0.861 0.736 1.022 0.973 1.189
+ 1.192 0.478 1.369 1.368 1.241 1.097 0.822 1.017 0.836 1.14
+//
+H GEOR030106
+D Linker propensity from medium dataset (linker length is between six and 14
+ residues) (George-Heringa, 2003)
+R PMID:12538906
+A George, R.A. and Heringa, J.
+T An analysis of protein domain linkers: their classification and role in
+ protein folding
+J Protein Eng. 15, 871-879 (2003)
+C GEOR030101 0.938 GEOR030103 0.913 GEOR030104 0.904
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.99 1.132 0.873 0.915 0.644 0.999 1.053 0.785 1.054 0.95
+ 1.106 1.003 1.093 1.121 1.314 0.911 0.988 0.939 1.09 0.957
+//
+H GEOR030107
+D Linker propensity from long dataset (linker length is greater than 14
+ residues) (George-Heringa, 2003)
+R PMID:12538906
+A George, R.A. and Heringa, J.
+T An analysis of protein domain linkers: their classification and role in
+ protein folding
+J Protein Eng. 15, 871-879 (2003)
+C GEOR030102 0.815
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.892 1.154 1.144 0.925 1.035 1.2 1.115 0.917 0.992 0.817
+ 0.994 0.944 0.782 1.058 1.309 0.986 1.11 0.841 0.866 0.9
+//
+H GEOR030108
+D Linker propensity from helical (annotated by DSSP) dataset (George-Heringa,
+ 2003)
+R PMID:12538906
+A George, R.A. and Heringa, J.
+T An analysis of protein domain linkers: their classification and role in
+ protein folding
+J Protein Eng. 15, 871-879 (2003)
+C AURR980111 0.846 AURR980112 0.846 AURR980115 0.821
+ AURR980110 0.804 AURR980114 0.804
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.092 1.239 0.927 0.919 0.662 1.124 1.199 0.698 1.012 0.912
+ 1.276 1.008 1.171 1.09 0.8 0.886 0.832 0.981 1.075 0.908
+//
+H GEOR030109
+D Linker propensity from non-helical (annotated by DSSP) dataset
+ (George-Heringa, 2003)
+R PMID:12538906
+A George, R.A. and Heringa, J.
+T An analysis of protein domain linkers: their classification and role in
+ protein folding
+J Protein Eng. 15, 871-879 (2003)
+C ONEK900102 0.908 AVBF000104 0.907 FINA910102 0.890
+ ISOY800104 0.812 MUNV940101 0.801 CHOP780213 0.800
+ FAUJ880113 -0.848 ONEK900101 -0.884 BLAM930101 -0.889
+ BUNA790101 -0.901
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.843 1.038 0.956 0.906 0.896 0.968 0.9 0.978 1.05 0.946
+ 0.885 0.893 0.878 1.151 1.816 1.003 1.189 0.852 0.945 0.999
+//
+H ZHOH040101
+D The stability scale from the knowledge-based atom-atom potential (Zhou-Zhou,
+ 2004)
+R PMID:14696193
+A Zhou, H. and Zhou, Y.
+T Quantifying the effect of burial of amino acid residues on protein stability
+J Proteins 54, 315-322 (2004)
+C BASU050102 0.948 CIDH920102 0.939 MEEJ810101 0.935
+ ZHOH040103 0.935 NOZY710101 0.932 MEEJ810102 0.922
+ ZHOH040102 0.910 CIDH920105 0.904 ROSG850101 0.904
+ GUOD860101 0.884 LEVM760106 0.883 ROBB790101 0.872
+ NISK860101 0.871 PLIV810101 0.864 CORJ870102 0.862
+ SWER830101 0.860 WERD780101 0.859 CIDH920104 0.858
+ ROSM880104 0.858 VENT840101 0.858 CIDH920101 0.855
+ MIYS850101 0.855 LEVM760107 0.855 BASU050101 0.851
+ TAKK010101 0.846 ARGP820101 0.841 FAUJ830101 0.841
+ JOND750101 0.841 MEEJ800102 0.838 CIDH920103 0.829
+ RADA880102 0.828 BIOV880101 0.825 WIMW960101 0.821
+ GOLD730101 0.817 BASU050103 0.813 SIMZ760101 0.808
+ LIFS790103 0.801 MIYS990103 -0.824 MEIH800101 -0.827
+ KARP850101 -0.833 VINM940101 -0.833 GUYH850102 -0.836
+ MIYS990105 -0.838 PARS000101 -0.845 WOLS870101 -0.858
+ OOBM770103 -0.862 MIYS990104 -0.864 WEBA780101 -0.865
+ MIYS990102 -0.870 MIYS990101 -0.871 BULH740101 -0.876
+ GUYH850103 -0.882 VINM940102 -0.899 PARJ860101 -0.912
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.18 2.71 1.85 1.75 3.89 2.16 1.89 1.17 2.51 4.50
+ 4.71 2.12 3.63 5.88 2.09 1.66 2.18 6.46 5.01 3.77
+//
+H ZHOH040102
+D The relative stability scale extracted from mutation experiments (Zhou-Zhou,
+ 2004)
+R PMID:14696193
+A Zhou, H. and Zhou, Y.
+T Quantifying the effect of burial of amino acid residues on protein stability
+J Proteins 54, 315-322 (2004)
+C ROSG850101 0.930 ZHOH040101 0.910 LEVM760106 0.905
+ NOZY710101 0.897 BIGC670101 0.884 KRIW790103 0.884
+ GOLD730102 0.882 ZIMJ680102 0.878 TSAJ990101 0.874
+ TAKK010101 0.874 GRAR740103 0.872 TSAJ990102 0.867
+ CIDH920102 0.862 CHOC750101 0.856 LEVM760107 0.843
+ VENT840101 0.831 HARY940101 0.830 CHAM820101 0.826
+ PONJ960101 0.823 CIDH920105 0.818 FAUJ880103 0.816
+ SIMZ760101 0.814 GUOD860101 0.812 CIDH920101 0.811
+ PLIV810101 0.809 MEEJ800102 0.808 BASU050102 0.808
+ MEEJ810101 0.804 WEBA780101 -0.807 PARJ860101 -0.854
+ BULH740101 -0.860
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.79 3.20 2.83 2.33 2.22 2.37 2.52 0.70 3.06 4.59
+ 4.72 2.50 3.91 4.84 2.45 1.82 2.45 5.64 4.46 3.67
+//
+H ZHOH040103
+D Buriability (Zhou-Zhou, 2004)
+R PMID:14696193
+A Zhou, H. and Zhou, Y.
+T Quantifying the effect of burial of amino acid residues on protein stability
+J Proteins 54, 315-322 (2004)
+C BASU050102 0.978 NISK860101 0.946 BIOV880101 0.941
+ CIDH920104 0.941 ZHOH040101 0.935 FAUJ830101 0.933
+ BASU050103 0.927 CIDH920105 0.926 NADH010104 0.925
+ WERD780101 0.923 MEEJ810101 0.921 BASU050101 0.917
+ MIYS850101 0.914 NADH010103 0.913 CIDH920102 0.909
+ RADA880108 0.904 ROSG850102 0.903 MEEJ810102 0.902
+ CASG920101 0.900 PONP930101 0.896 BIOV880102 0.891
+ NADH010105 0.890 GUOD860101 0.889 PLIV810101 0.889
+ NISK800101 0.888 PONP800108 0.887 BAEK050101 0.884
+ CIDH920103 0.881 ROBB790101 0.872 NADH010102 0.864
+ MANP780101 0.864 CORJ870101 0.864 SWER830101 0.863
+ CORJ870102 0.863 PONP800103 0.861 PONP800102 0.858
+ PONP800101 0.847 BLAS910101 0.846 CIDH920101 0.845
+ NOZY710101 0.842 ROSM880105 0.839 ROSM880104 0.826
+ CORJ870106 0.822 CORJ870107 0.822 MEIH800103 0.820
+ NADH010106 0.819 CORJ870103 0.819 LIFS790101 0.815
+ PTIO830102 0.813 RADA880102 0.813 CORJ870104 0.809
+ VENT840101 0.807 NADH010101 0.803 FUKS010104 -0.803
+ FUKS010103 -0.808 PUNT030101 -0.809 LEVM760101 -0.811
+ CORJ870108 -0.821 BULH740101 -0.828 HOPT810101 -0.829
+ RACS770102 -0.832 RACS770101 -0.835 KARP850102 -0.836
+ GUYH850101 -0.839 KARP850101 -0.846 PARS000101 -0.846
+ PUNT030102 -0.847 MEIH800102 -0.848 KIDA850101 -0.851
+ WOLS870101 -0.870 GUYH850103 -0.879 VINM940103 -0.882
+ GRAR740102 -0.895 PARJ860101 -0.897 MEIH800101 -0.898
+ KRIW790101 -0.905 OOBM770103 -0.907 FASG890101 -0.910
+ GUYH850102 -0.912 VINM940101 -0.922 MIYS990101 -0.926
+ MIYS990102 -0.927 MIYS990103 -0.933 MIYS990105 -0.939
+ VINM940102 -0.939 MIYS990104 -0.954
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 13.4 8.5 7.6 8.2 22.6 8.5 7.3 7.0 11.3 20.3
+ 20.8 6.1 15.7 23.9 9.9 8.2 10.3 24.5 19.5 19.5
+//
+H BAEK050101
+D Linker index (Bae et al., 2005)
+R PMID:15746283
+A Bae, K., Mallick, B.K. and Elsik, C.G.
+T Prediction of protein inter-domain linker regions by a hidden Markov model
+J Bioinformatics 21, ??-?? (2005)
+C CASG920101 0.919 BASU050102 0.898 WERD780101 0.895
+ NISK860101 0.886 ZHOH040103 0.884 NISK800101 0.881
+ NADH010104 0.875 ROSG850102 0.868 CORJ870101 0.862
+ PONP930101 0.856 BIOV880101 0.853 NADH010103 0.853
+ NADH010105 0.850 QIAN880121 0.836 PONP800108 0.833
+ PONP800102 0.818 PONP800101 0.812 CIDH920104 0.809
+ NADH010106 0.809 BASU050103 0.806 SUYM030101 0.805
+ OOBM770103 -0.810 PARS000101 -0.821 KARP850102 -0.839
+ FASG890101 -0.859 KRIW790101 -0.860 MIYS990105 -0.871
+ VINM940102 -0.873 MIYS990103 -0.877 MIYS990104 -0.892
+ VINM940101 -0.896 VINM940103 -0.906 GUYH850102 -0.907
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.0166 -0.0762 -0.0786 -0.1278 0.5724 -0.1051 -0.1794 -0.0442 0.1643 0.2758
+ 0.2523 -0.2134 0.0197 0.3561 -0.4188 -0.1629 -0.0701 0.3836 0.2500 0.1782
+//
+H HARY940101
+D Mean volumes of residues buried in protein interiors (Harpaz et al., 1994)
+R PMID: 7922041
+A Harpaz, Y., Gerstein, M. and Chothia, C.
+T Volume changes on protein folding
+J Structure 2, 641-649 (1994) (Disulfide bonded cysteine, 103.5)
+C PONJ960101 0.989 TSAJ990102 0.965 TSAJ990101 0.964
+ CHOC750101 0.961 BIGC670101 0.960 GOLD730102 0.959
+ KRIW790103 0.956 FAUJ880103 0.951 CHOC760101 0.946
+ GRAR740103 0.946 CHAM820101 0.933 LEVM760105 0.919
+ FASG760101 0.910 FAUJ880106 0.909 LEVM760102 0.905
+ DAWD720101 0.900 CHAM830106 0.894 ROSG850101 0.869
+ RADA880106 0.846 ZHOH040102 0.830 LEVM760106 0.829
+ LEVM760107 0.815 RADA880103 -0.840
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 90.1 192.8 127.5 117.1 113.2 149.4 140.8 63.8 159.3 164.9
+ 164.6 170.0 167.7 193.5 123.1 94.2 120.0 197.1 231.7 139.1
+//
+H PONJ960101
+D Average volumes of residues (Pontius et al., 1996)
+R PMID: 8950272
+A Pontius, J., Richelle, J. and Wodak, S.J.
+T Deviations from standard atomic volumes as a quality measure for protein
+ crystal structures
+J J. Mol. Biol 264, 121-136 (1996) (Disulfide bonded cysteine, 102.4)
+C HARY940101 0.989 CHOC750101 0.966 FAUJ880103 0.963
+ TSAJ990102 0.962 CHOC760101 0.961 TSAJ990101 0.960
+ BIGC670101 0.950 GOLD730102 0.947 FASG760101 0.945
+ KRIW790103 0.943 CHAM820101 0.938 GRAR740103 0.937
+ LEVM760102 0.930 LEVM760105 0.928 CHAM830106 0.917
+ FAUJ880106 0.913 DAWD720101 0.873 ROSG850101 0.862
+ RADA880106 0.860 LEVM760107 0.827 ZHOH040102 0.823
+ RADA880103 -0.873
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 91.5 196.1 138.3 135.2 114.4 156.4 154.6 67.5 163.2 162.6
+ 163.4 162.5 165.9 198.8 123.4 102.0 126.0 209.8 237.2 138.4
+//
+H DIGM050101
+D Hydrostatic pressure asymmetry index, PAI (Di Giulio, 2005)
+R PMID: 15716096
+A Di Giulio M.
+T A comparison of proteins from Pyrococcus furiosus and Pyrococcus abyssi:
+ barophily in the physicochemical properties of amino acids and in the genetic
+ code
+J Gene 346, 1-6 (2005)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.076 1.361 1.056 1.290 0.753 0.729 1.118 1.346 0.985 0.926
+ 1.054 1.105 0.974 0.869 0.820 1.342 0.871 0.666 0.531 1.131
+//
+H WOLR790101
+D Hydrophobicity index (Wolfenden et al., 1979)
+R PMID:493962
+A Wolfenden, R.V., Cullis, P.M. and Southgate, C.C.F.
+T Water, protein folding, and the genetic code
+J Science 206, 575-577 (1979)
+C WOLR810101 0.996 RADA880101 0.933 RADA880104 0.926
+ EISD840101 0.909 JACR890101 0.906 RADA880107 0.905
+ RADA880105 0.903 KYTJ820101 0.869 JURD980101 0.864
+ OLSK800101 0.859 CHOC760103 0.857 CHOC760104 0.851
+ JANJ780102 0.833 NADH010101 0.826 JANJ790102 0.818
+ JANJ780103 -0.806 GUYH850104 -0.815 OOBM770101 -0.831
+ CHOC760102 -0.834 ROSM880102 -0.836 VHEG790101 -0.844
+ JANJ780101 -0.856 ENGD860101 -0.877 PRAM900101 -0.877
+ ROSM880101 -0.887 KUHL950101 -0.898 GUYH850105 -0.908
+ FAUJ880109 -0.920
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.12 -2.55 -0.83 -0.83 0.59 -0.78 -0.92 1.20 -0.93 1.16
+ 1.18 -0.80 0.55 0.67 0.54 -0.05 -0.02 -0.19 -0.23 1.13
+//
+H OLSK800101
+D Average internal preferences (Olsen, 1980)
+R PMID:7378453
+A Olsen, K.W.
+T Internal residue criteria for predicting three-dimensional protein structures
+J Biochim. Biophys. Acta 622, 259-267 (1980)
+C CHOC760103 0.981 JURD980101 0.943 KYTJ820101 0.942
+ JANJ780102 0.905 EISD860103 0.881 RADA880107 0.874
+ CHOC760104 0.872 JANJ790102 0.870 WOLR810101 0.869
+ EISD840101 0.869 WOLR790101 0.859 NADH010102 0.856
+ DESM900102 0.849 NADH010101 0.843 RADA880101 0.840
+ JANJ790101 0.828 MEIH800103 0.826 WARP780101 0.818
+ LIFS790102 0.818 MANP780101 0.817 RADA880104 0.814
+ NADH010103 0.807 PONP800103 0.801 ENGD860101 -0.805
+ PRAM900101 -0.806 ROSM880101 -0.806 FAUJ880109 -0.821
+ GUYH850101 -0.823 PUNT030101 -0.838 JANJ780103 -0.845
+ RACS770102 -0.845 ROSM880102 -0.847 KUHL950101 -0.849
+ MEIH800102 -0.858 JANJ780101 -0.858 GUYH850104 -0.871
+ OOBM770101 -0.878 CHOC760102 -0.886 GUYH850105 -0.927
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.38 0.00 0.37 0.52 1.43 0.22 0.71 1.34 0.66 2.32
+ 1.47 0.15 1.78 1.72 0.85 0.86 0.89 0.82 0.47 1.99
+//
+H KIDA850101
+D Hydrophobicity-related index (Kidera et al., 1985)
+R
+A Kidera, A., Konishi, Y., Oka, M., Ooi, T. and Scheraga, A.
+T Statistical Analysis of the Physical Properties of the 20 Naturally Occuring
+ Amino Acids
+J J. Prot. Chem. 4, 23-55 (1985)
+C ROSM880101 0.933 ROSM880102 0.920 LEVM760101 0.915
+ KUHL950101 0.882 HOPT810101 0.881 GRAR740102 0.881
+ PRAM900101 0.866 ENGD860101 0.866 MIYS990105 0.865
+ FASG890101 0.861 PUNT030101 0.856 WOLS870101 0.852
+ GUYH850104 0.848 JANJ780101 0.843 OOBM770101 0.843
+ JANJ780103 0.842 MEIH800102 0.834 GUYH850101 0.834
+ MIYS990104 0.822 MIYS990101 0.817 MIYS990102 0.817
+ FUKS010104 0.814 PARJ860101 0.809 WOEC730101 0.807
+ PUNT030102 0.807 MIYS990103 0.805 CHOC760102 0.804
+ NADH010101 -0.803 CIDH920105 -0.803 RADA880104 -0.805
+ BASU050103 -0.806 NAKH900110 -0.808 MEIH800103 -0.813
+ CASG920101 -0.817 MEEJ800102 -0.823 GUOD860101 -0.828
+ JANJ780102 -0.828 MIYS850101 -0.831 EISD860103 -0.832
+ JACR890101 -0.836 CIDH920104 -0.836 RADA880107 -0.837
+ PLIV810101 -0.841 NADH010104 -0.842 ROSG850102 -0.849
+ MEEJ810101 -0.850 MEEJ810102 -0.851 ZHOH040103 -0.851
+ JANJ790102 -0.858 NADH010103 -0.859 COWR900101 -0.868
+ NADH010102 -0.874 RADA880108 -0.875 RADA880101 -0.883
+ EISD860101 -0.890 BIOV880102 -0.892 BIOV880101 -0.893
+ EISD840101 -0.900 BLAS910101 -0.901 ROSM880105 -0.922
+ FAUJ830101 -0.946
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.27 1.87 0.81 0.81 -1.05 1.10 1.17 -0.16 0.28 -0.77
+ -1.10 1.70 -0.73 -1.43 -0.75 0.42 0.63 -1.57 -0.56 -0.40
+//
+H GUYH850102
+D Apparent partition energies calculated from Wertz-Scheraga index (Guy, 1985)
+R PMID:3978191
+A Guy, H.R.
+T Amino acid side-chain partition energies and distribution of residues in
+ soluble proteins
+J Biophys. J. 47, 61-70 (1985)
+C MIYS990104 0.928 VINM940101 0.924 MIYS990103 0.914
+ MIYS990105 0.912 FASG890101 0.909 VINM940102 0.905
+ OOBM770103 0.904 MEIH800101 0.899 VINM940103 0.895
+ KARP850102 0.882 KRIW790101 0.878 MIYS990102 0.868
+ GUYH850103 0.866 MIYS990101 0.865 RACS770101 0.859
+ MEIH800102 0.856 RACS770102 0.853 FUKS010103 0.848
+ KRIW790102 0.841 PARS000101 0.839 PARJ860101 0.836
+ CORJ870108 0.821 RACS770103 0.821 FUKS010104 0.819
+ KARP850101 0.811 KRIW710101 0.811 GRAR740102 0.806
+ GUYH850101 0.805 PLIV810101 -0.802 CORJ870105 -0.804
+ MEEJ810101 -0.813 BASU050101 -0.815 NADH010102 -0.824
+ NADH010105 -0.826 CORJ870106 -0.830 CORJ870107 -0.834
+ ZHOH040101 -0.836 CORJ870103 -0.841 CIDH920101 -0.843
+ BASU050103 -0.845 MANP780101 -0.850 MEIH800103 -0.854
+ CIDH920102 -0.855 PONP800103 -0.856 FAUJ830101 -0.857
+ ROBB790101 -0.862 NADH010103 -0.866 CIDH920103 -0.871
+ PONP800108 -0.873 PONP800101 -0.873 PONP800102 -0.874
+ NADH010104 -0.879 CORJ870101 -0.883 MIYS850101 -0.884
+ CIDH920105 -0.892 CIDH920104 -0.894 PONP930101 -0.897
+ RADA880108 -0.902 BIOV880102 -0.903 BAEK050101 -0.907
+ BASU050102 -0.911 ZHOH040103 -0.912 NISK800101 -0.914
+ BIOV880101 -0.922 ROSG850102 -0.925 CASG920101 -0.941
+ NISK860101 -0.950 WERD780101 -0.976
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.05 0.12 0.29 0.41 -0.84 0.46 0.38 0.31 -0.41 -0.69
+ -0.62 0.57 -0.38 -0.45 0.46 0.12 0.38 -0.98 -0.25 -0.46
+//
+H GUYH850103
+D Apparent partition energies calculated from Robson-Osguthorpe index (Guy,
+ 1985)
+R PMID:3978191
+A Guy, H.R.
+T Amino acid side-chain partition energies and distribution of residues in
+ soluble proteins
+J Biophys. J. 47, 61-70 (1985) (Gly missing)
+C OOBM770103 0.906 PARJ860101 0.897 MIYS990102 0.888
+ MIYS990101 0.886 MIYS990105 0.883 MIYS990104 0.879
+ VINM940102 0.875 FUKS010103 0.874 MEIH800101 0.873
+ GUYH850102 0.866 VINM940101 0.860 FASG890101 0.860
+ MIYS990103 0.857 RACS770101 0.844 WOLS870101 0.836
+ CORJ870108 0.831 GRAR740102 0.831 PARS000101 0.822
+ BULH740101 0.820 CORJ870103 -0.804 JOND750101 -0.807
+ ROSM880104 -0.807 PONP800102 -0.808 ARGP820101 -0.808
+ CORJ870104 -0.809 MEEJ800102 -0.809 CORJ870101 -0.815
+ BIOV880102 -0.818 GUOD860101 -0.819 LEVM760106 -0.822
+ PONP800101 -0.822 MEEJ810102 -0.823 PONP800108 -0.828
+ NISK800101 -0.828 CORJ870105 -0.830 MANP780101 -0.833
+ CORJ870107 -0.833 CORJ870106 -0.837 SWER830101 -0.839
+ CORJ870102 -0.839 ROSG850102 -0.844 CASG920101 -0.846
+ BASU050101 -0.852 CIDH920101 -0.854 BASU050103 -0.854
+ PONP930101 -0.858 MEEJ810101 -0.864 FAUJ830101 -0.870
+ RADA880108 -0.870 WERD780101 -0.876 ZHOH040103 -0.879
+ PLIV810101 -0.881 ZHOH040101 -0.882 BIOV880101 -0.890
+ CIDH920103 -0.890 MIYS850101 -0.897 CIDH920102 -0.904
+ BASU050102 -0.904 CIDH920104 -0.906 NISK860101 -0.914
+ CIDH920105 -0.927 ROBB790101 -0.999
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.54 -0.16 0.38 0.65 -1.13 0.05 0.38 NA -0.59 -2.15
+ -1.08 0.48 -0.97 -1.51 -0.22 0.65 0.27 -1.61 -1.13 -0.75
+//
+H GUYH850104
+D Apparent partition energies calculated from Janin index (Guy, 1985)
+R PMID:3978191
+A Guy, H.R.
+T Amino acid side-chain partition energies and distribution of residues in
+ soluble proteins
+J Biophys. J. 47, 61-70 (1985)
+C JANJ780101 0.989 JANJ780103 0.983 CHOC760102 0.970
+ OOBM770101 0.966 GUYH850105 0.908 MEIH800102 0.892
+ ENGD860101 0.881 PRAM900101 0.881 FASG890101 0.872
+ GUYH850101 0.857 ROSM880102 0.856 KRIW790102 0.849
+ RACS770102 0.849 KIDA850101 0.848 PUNT030101 0.840
+ RACS770103 0.839 KUHL950101 0.835 KRIW790101 0.822
+ MIYS990105 0.821 ROSM880101 0.814 FAUJ880109 0.812
+ MIYS990103 0.805 NADH010101 -0.804 PONP800108 -0.807
+ WOLR790101 -0.815 FAUJ830101 -0.816 CASG920101 -0.819
+ DESM900101 -0.824 PONP800102 -0.824 WOLR810101 -0.826
+ JACR890101 -0.827 CORJ870101 -0.830 RADA880101 -0.831
+ EISD860103 -0.835 BIOV880101 -0.844 CHOC760104 -0.845
+ PONP800103 -0.845 RADA880108 -0.847 MEIH800103 -0.854
+ BIOV880102 -0.855 JANJ790101 -0.862 NADH010104 -0.867
+ KYTJ820101 -0.869 OLSK800101 -0.871 JURD980101 -0.880
+ WARP780101 -0.882 ROSG850102 -0.891 EISD840101 -0.892
+ DESM900102 -0.896 RADA880107 -0.896 NADH010103 -0.899
+ CHOC760103 -0.907 NADH010102 -0.946 JANJ780102 -0.968
+ JANJ790102 -0.999
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.31 1.30 0.49 0.58 -0.87 0.70 0.68 -0.33 0.13 -0.66
+ -0.53 1.79 -0.38 -0.45 0.34 0.10 0.21 -0.27 0.40 -0.62
+//
+H GUYH850105
+D Apparent partition energies calculated from Chothia index (Guy, 1985)
+R PMID:3978191
+A Guy, H.R.
+T Amino acid side-chain partition energies and distribution of residues in
+ soluble proteins
+J Biophys. J. 47, 61-70 (1985)
+C CHOC760102 0.946 FAUJ880109 0.927 JANJ780101 0.923
+ GUYH850104 0.908 JANJ780103 0.885 OOBM770101 0.874
+ ROSM880102 0.874 PRAM900101 0.867 ENGD860101 0.867
+ PUNT030101 0.858 KUHL950101 0.850 ROSM880101 0.849
+ VHEG790101 0.845 GUYH850101 0.843 MEIH800102 0.811
+ RADA880105 -0.809 EISD860103 -0.812 NADH010103 -0.815
+ DESM900102 -0.818 CHOC760104 -0.822 YUTK870101 -0.841
+ NADH010101 -0.847 NADH010102 -0.867 KYTJ820101 -0.883
+ JACR890101 -0.887 JANJ780102 -0.898 RADA880104 -0.899
+ RADA880101 -0.899 JURD980101 -0.900 WOLR790101 -0.908
+ JANJ790102 -0.913 WOLR810101 -0.916 OLSK800101 -0.927
+ CHOC760103 -0.933 EISD840101 -0.951 RADA880107 -0.953
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.27 2.00 0.61 0.50 -0.23 1.00 0.33 -0.22 0.37 -0.80
+ -0.44 1.17 -0.31 -0.55 0.36 0.17 0.18 0.05 0.48 -0.65
+//
+H ROSM880104
+D Hydropathies of amino acid side chains, neutral form (Roseman, 1988)
+R PMID:3398047
+A Roseman, M.A.
+T Hydrophilicity of Polar Amino Acid Side-chains is Markedly Reduced by
+ Flanking Peptide Bonds
+J J. Mol. Biol. 200, 513-522 (1988) (Arg Pro missing)
+C MEEJ810101 0.911 CIDH920105 0.886 MEEJ810102 0.885
+ ARGP820101 0.872 JOND750101 0.872 GUOD860101 0.868
+ PLIV810101 0.866 CIDH920103 0.866 CIDH920104 0.860
+ CIDH920102 0.859 ZHOH040101 0.858 SIMZ760101 0.855
+ NOZY710101 0.847 BASU050102 0.846 SWER830101 0.844
+ CORJ870102 0.844 TAKK010101 0.840 BASU050101 0.830
+ VENT840101 0.829 ZHOH040103 0.826 MIYS850101 0.824
+ GOLD730101 0.808 ROBB790101 0.807 BLAS910101 0.802
+ NISK860101 0.801 GUYH850103 -0.807 MIYS990102 -0.839
+ MIYS990101 -0.843 WOLS870101 -0.870 BULH740101 -0.884
+ PARJ860101 -0.896
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.39 NA -1.91 -0.71 0.25 -1.30 -0.18 0.00 -0.60 1.82
+ 1.82 0.32 0.96 2.27 NA -1.24 -1.00 2.13 1.47 1.30
+//
+H ROSM880105
+D Hydropathies of amino acid side chains, pi-values in pH 7.0 (Roseman, 1988)
+R PMID:3398047
+A Roseman, M.A.
+T Hydrophilicity of Polar Amino Acid Side-chains is Markedly Reduced by
+ Flanking Peptide Bonds
+J J. Mol. Biol. 200, 513-522 (1988) (Pro missing)
+C BLAS910101 0.954 EISD860101 0.948 FAUJ830101 0.937
+ RADA880101 0.933 EISD840101 0.923 BIOV880101 0.874
+ BIOV880102 0.871 RADA880102 0.870 BASU050103 0.864
+ JACR890101 0.863 PLIV810101 0.862 RADA880108 0.861
+ NAKH900110 0.859 ZIMJ680105 0.857 CIDH920104 0.855
+ NADH010102 0.845 MIYS850101 0.844 SWER830101 0.843
+ CIDH920105 0.843 CORJ870102 0.841 MEEJ800102 0.841
+ ZHOH040103 0.839 ROSG850102 0.838 NISK860101 0.836
+ CIDH920103 0.832 BASU050101 0.828 GUOD860101 0.826
+ NADH010101 0.825 DESM900102 0.825 NADH010103 0.822
+ JURD980101 0.818 COWR900101 0.817 CASG920101 0.814
+ PONP800108 0.808 KYTJ820101 0.806 JANJ790102 0.805
+ MEEJ810102 0.804 MANP780101 0.803 MEEJ810101 0.802
+ EISD860103 0.801 MEIH800101 -0.802 FAUJ880110 -0.803
+ VINM940101 -0.818 MEIH800102 -0.821 FASG890101 -0.822
+ OOBM770101 -0.824 OOBM770103 -0.828 MIYS990103 -0.829
+ GUYH850101 -0.832 MIYS990104 -0.841 MIYS990102 -0.854
+ MIYS990101 -0.854 ROSM880102 -0.871 PARJ860101 -0.871
+ MIYS990105 -0.873 KUHL950101 -0.896 WOLS870101 -0.899
+ VHEG790101 -0.901 WOEC730101 -0.902 ENGD860101 -0.912
+ PRAM900101 -0.912 PUNT030102 -0.917 KIDA850101 -0.922
+ PUNT030101 -0.922 GRAR740102 -0.924 ROSM880101 -0.951
+ LEVM760101 -0.954 HOPT810101 -0.955
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.39 -3.95 -1.91 -3.81 0.25 -1.30 -2.91 0.00 -0.64 1.82
+ 1.82 -2.77 0.96 2.27 NA -1.24 -1.00 2.13 1.47 1.30
+//
+H JACR890101
+D Weights from the IFH scale (Jacobs-White, 1989)
+R PMID:2742845
+A Jacobs, R. and White, S.H.
+T The nature of the hydrophobic bonding of small peptides at the bilayer
+ interface: implications for the insertion of transbilayer helices
+J Biochemistry 28, 3421-3437 (1989)
+C EISD840101 0.938 RADA880101 0.936 WOLR810101 0.908
+ WOLR790101 0.906 RADA880107 0.895 RADA880104 0.868
+ ROSM880105 0.863 JANJ790102 0.840 EISD860101 0.827
+ BLAS910101 0.819 CHOC760102 -0.803 JANJ780103 -0.809
+ PUNT030101 -0.812 OOBM770101 -0.812 HOPT810101 -0.816
+ GUYH850104 -0.827 LEVM760101 -0.832 ZIMJ680103 -0.835
+ KIDA850101 -0.836 ROSM880102 -0.837 KUHL950101 -0.864
+ JANJ780101 -0.865 EISD860102 -0.871 GUYH850105 -0.887
+ FAUJ880109 -0.889 ROSM880101 -0.892 VHEG790101 -0.903
+ ENGD860101 -0.948 PRAM900101 -0.948
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.18 -5.40 -1.30 -2.36 0.27 -1.22 -2.10 0.09 -1.48 0.37
+ 0.41 -2.53 0.44 0.50 -0.20 -0.40 -0.34 -0.01 -0.08 0.32
+//
+H COWR900101
+D Hydrophobicity index, 3.0 pH (Cowan-Whittaker, 1990)
+R PMID:2134053
+A Cowan, R. and Whittaker, R.G.
+T Hydrophobicity indices for amino acid residues as determined by
+ high-performance liquid chromatography
+J Peptide Res. 3, 75-80 (1990)
+C GUOD860101 0.920 BLAS910101 0.885 FAUJ830101 0.876
+ EISD860103 0.868 EISD840101 0.863 WILM950101 0.860
+ PLIV810101 0.857 JURD980101 0.855 MEEJ810102 0.849
+ NADH010102 0.848 KYTJ820101 0.845 RADA880101 0.840
+ NADH010103 0.825 MIYS850101 0.824 MEEJ810101 0.823
+ CHOC760103 0.820 RADA880104 0.818 ROSM880105 0.817
+ RADA880107 0.810 NADH010104 0.807 CIDH920104 0.803
+ BULH740101 -0.804 MIYS990102 -0.825 MIYS990101 -0.826
+ ROSM880101 -0.849 GRAR740102 -0.854 KIDA850101 -0.868
+ WOLS870101 -0.883 ROSM880102 -0.897
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.42 -1.56 -1.03 -0.51 0.84 -0.96 -0.37 0.00 -2.28 1.81
+ 1.80 -2.03 1.18 1.74 0.86 -0.64 -0.26 1.46 0.51 1.34
+//
+H BLAS910101
+D Scaled side chain hydrophobicity values (Black-Mould, 1991)
+R PMID:2042744
+A Black, S.D. and Mould D.R.
+T Development of Hydrophobicity Parameters to Analyze Proteins Which Bear Post-
+ or Cotranslational Modifications
+J Analytical Biochemistry 193, 72-82 (1991)
+C ROSM880105 0.954 FAUJ830101 0.923 RADA880101 0.922
+ EISD860101 0.911 SWER830101 0.887 COWR900101 0.885
+ CORJ870102 0.884 EISD840101 0.884 CIDH920104 0.881
+ BASU050103 0.878 PLIV810101 0.871 GUOD860101 0.866
+ ZIMJ680105 0.855 NADH010101 0.855 BASU050101 0.853
+ CIDH920105 0.852 MEEJ800102 0.849 ZHOH040103 0.846
+ JURD980101 0.841 CIDH920103 0.838 BIOV880101 0.838
+ KYTJ820101 0.836 MEEJ810101 0.831 MEEJ810102 0.830
+ EISD860103 0.830 MIYS850101 0.829 RADA880108 0.826
+ RADA880102 0.826 NADH010102 0.824 GOLD730101 0.821
+ JACR890101 0.819 NADH010103 0.812 PONP800108 0.810
+ WILM950101 0.810 BIOV880102 0.809 BASU050102 0.807
+ CIDH920102 0.805 NISK860101 0.803 ROSM880104 0.802
+ MANP780101 0.802 NAKH900110 0.801 MIYS990103 -0.806
+ MIYS990104 -0.818 VHEG790101 -0.847 MIYS990105 -0.848
+ MIYS990102 -0.854 MIYS990101 -0.857 BULH740101 -0.860
+ ENGD860101 -0.864 PRAM900101 -0.864 PUNT030101 -0.865
+ PARJ860101 -0.870 HOPT810101 -0.877 PUNT030102 -0.877
+ ROSM880102 -0.884 LEVM760101 -0.889 KUHL950101 -0.894
+ KIDA850101 -0.901 WOEC730101 -0.902 WOLS870101 -0.930
+ ROSM880101 -0.940 GRAR740102 -0.950
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.616 0.000 0.236 0.028 0.680 0.251 0.043 0.501 0.165 0.943
+ 0.943 0.283 0.738 1.000 0.711 0.359 0.450 0.878 0.880 0.825
+//
+H CASG920101
+D Hydrophobicity scale from native protein structures (Casari-Sippl, 1992)
+R PMID:1569551
+A Casari, G. and Sippl, M.
+T Structure-derived Hydrophobic Potential. Hydrophobic Potential Derived from
+ X-ray Structures of Globular Proteins is able to Identify Native Folds
+J J. Mol. Biol. 224, 725-732 (1992)
+C ROSG850102 0.952 CORJ870101 0.947 NISK860101 0.938
+ BIOV880101 0.935 NISK800101 0.935 WERD780101 0.927
+ BAEK050101 0.919 BIOV880102 0.919 NADH010104 0.915
+ NADH010103 0.914 PONP930101 0.911 RADA880108 0.903
+ CIDH920104 0.903 PONP800108 0.901 ZHOH040103 0.900
+ PONP800102 0.889 NADH010102 0.889 MEIH800103 0.881
+ PONP800103 0.879 FAUJ830101 0.875 PONP800101 0.874
+ BASU050102 0.873 DESM900102 0.869 MIYS850101 0.863
+ BASU050103 0.860 CIDH920105 0.859 JANJ780102 0.853
+ ROBB790101 0.850 MANP780101 0.848 NADH010105 0.838
+ JANJ790101 0.828 CIDH920103 0.827 JANJ790102 0.822
+ CORJ870103 0.821 ROSM880105 0.814 CORJ870107 0.813
+ DESM900101 0.806 BASU050101 0.806 CIDH920102 0.802
+ RACS770101 -0.807 KRIW710101 -0.808 VINM940104 -0.810
+ PUNT030101 -0.811 KIDA850101 -0.817 GUYH850104 -0.819
+ JANJ780103 -0.825 PARS000101 -0.826 FUKS010102 -0.831
+ PUNT030102 -0.831 MIYS990101 -0.834 GUYH850101 -0.836
+ OOBM770101 -0.838 MIYS990102 -0.838 HOPT810101 -0.839
+ RACS770103 -0.846 GUYH850103 -0.846 RACS770102 -0.849
+ GRAR740102 -0.850 PARS000102 -0.859 KRIW790102 -0.865
+ VINM940102 -0.874 MEIH800101 -0.875 MEIH800102 -0.879
+ FUKS010104 -0.892 KARP850102 -0.901 KRIW790101 -0.911
+ OOBM770103 -0.914 VINM940103 -0.915 MIYS990103 -0.915
+ FASG890101 -0.924 MIYS990104 -0.931 MIYS990105 -0.937
+ GUYH850102 -0.941 VINM940101 -0.947
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.2 -0.7 -0.5 -1.4 1.9 -1.1 -1.3 -0.1 0.4 1.4
+ 0.5 -1.6 0.5 1.0 -1.0 -0.7 -0.4 1.6 0.5 0.7
+//
+H CORJ870101
+D NNEIG index (Cornette et al., 1987)
+R PMID:3656427
+A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and
+ DeLisi, C.
+T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic
+ Structures in Proteins
+J J. Mol. Biol. 196, 659-685, (1987)
+C NISK800101 0.976 PONP800108 0.969 PONP930101 0.960
+ PONP800102 0.954 ROSG850102 0.948 CASG920101 0.947
+ PONP800103 0.944 PONP800101 0.939 NISK860101 0.935
+ NADH010103 0.921 MANP780101 0.918 BIOV880101 0.917
+ NADH010104 0.914 NADH010102 0.909 MEIH800103 0.902
+ DESM900102 0.901 BASU050103 0.897 CIDH920104 0.896
+ RADA880108 0.895 JANJ790101 0.891 CORJ870103 0.889
+ JANJ780102 0.885 BIOV880102 0.882 CORJ870107 0.878
+ WERD780101 0.873 DESM900101 0.870 ZHOH040103 0.864
+ BASU050101 0.863 CORJ870104 0.863 BAEK050101 0.862
+ MIYS850101 0.861 BASU050102 0.855 JURD980101 0.849
+ KYTJ820101 0.848 NADH010105 0.846 FAUJ830101 0.845
+ QIAN880121 0.842 KANM800102 0.839 KANM800104 0.833
+ CORJ870106 0.829 ROBB760106 0.829 NADH010101 0.827
+ CIDH920105 0.827 QIAN880122 0.826 LIFS790101 0.826
+ JANJ790102 0.825 CIDH920103 0.822 CHOC760103 0.822
+ GEIM800107 0.821 ROBB790101 0.819 CORJ870105 0.818
+ CHOP780202 0.815 ROBB760105 0.809 EISD860103 0.809
+ QIAN880120 0.802 WARP780101 0.800 VINM940104 -0.805
+ KRIW710101 -0.812 FUKS010104 -0.814 GUYH850103 -0.815
+ MUNV940103 -0.817 GUYH850101 -0.820 JANJ780103 -0.826
+ GUYH850104 -0.830 RACS770103 -0.832 VINM940103 -0.837
+ RACS770102 -0.837 KRIW790102 -0.838 WOEC730101 -0.841
+ VINM940102 -0.847 PARS000102 -0.850 MIYS990101 -0.854
+ MEIH800101 -0.855 MIYS990102 -0.859 PUNT030102 -0.860
+ KARP850102 -0.865 CORJ870108 -0.866 OOBM770101 -0.875
+ MEIH800102 -0.878 GUYH850102 -0.883 GRAR740102 -0.890
+ KRIW790101 -0.902 OOBM770103 -0.907 FASG890101 -0.921
+ VINM940101 -0.924 MIYS990104 -0.932 MIYS990103 -0.936
+ MIYS990105 -0.937
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 50.76 48.66 45.80 43.17 58.74 46.09 43.48 50.27 49.33 57.30
+ 53.89 42.92 52.75 53.45 45.39 47.24 49.26 53.59 51.79 56.12
+//
+H CORJ870102
+D SWEIG index (Cornette et al., 1987)
+R PMID:3656427
+A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and
+ DeLisi, C.
+T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic
+ Structures in Proteins
+J J. Mol. Biol. 196, 659-685, (1987)
+C SWER830101 1.000 BASU050101 0.921 CIDH920105 0.890
+ BASU050103 0.889 MIYS850101 0.887 BLAS910101 0.884
+ CORJ870104 0.881 CORJ870107 0.881 BASU050102 0.881
+ PLIV810101 0.873 CIDH920102 0.872 NISK860101 0.864
+ CIDH920103 0.864 ZHOH040103 0.863 ZHOH040101 0.862
+ CORJ870103 0.860 CIDH920104 0.860 CIDH920101 0.855
+ PTIO830102 0.854 GUOD860101 0.852 CORJ870105 0.848
+ CORJ870106 0.845 ROSM880104 0.844 ROSM880105 0.841
+ NOZY710101 0.838 VENT840101 0.837 BIOV880101 0.837
+ ROBB790101 0.835 PONP930101 0.832 FAUJ830101 0.831
+ ZIMJ680105 0.828 QIAN880120 0.825 RADA880108 0.823
+ EISD860101 0.822 CHOP780202 0.822 RADA880102 0.821
+ MANP780101 0.818 LIFS790101 0.815 PALJ810104 0.809
+ MEEJ810101 0.807 WERD780101 0.804 MUNV940103 -0.802
+ RACS770101 -0.802 VINM940102 -0.812 VINM940101 -0.817
+ WOEC730101 -0.828 MEIH800101 -0.829 OOBM770103 -0.832
+ PUNT030101 -0.835 GUYH850103 -0.839 PARS000101 -0.848
+ MIYS990103 -0.877 MIYS990105 -0.882 CORJ870108 -0.883
+ WOLS870101 -0.885 MIYS990104 -0.886 PARJ860101 -0.892
+ GRAR740102 -0.893 MIYS990102 -0.920 MIYS990101 -0.922
+ BULH740101 -0.923
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.414 -0.584 -0.916 -1.310 0.162 -0.905 -1.218 -0.684 -0.630 1.237
+ 1.215 -0.670 1.020 1.938 -0.503 -0.563 -0.289 0.514 1.699 0.899
+//
+H CORJ870103
+D PRIFT index (Cornette et al., 1987)
+R PMID:3656427
+A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and
+ DeLisi, C.
+T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic
+ Structures in Proteins
+J J. Mol. Biol. 196, 659-685, (1987)
+C CORJ870104 0.988 CORJ870107 0.969 PONP930101 0.920
+ PONP800101 0.917 NISK860101 0.914 PONP800102 0.907
+ MANP780101 0.906 MIYS850101 0.892 BASU050101 0.890
+ PONP800103 0.889 CORJ870101 0.889 NISK800101 0.886
+ ROSG850102 0.883 WERD780101 0.882 MEIH800103 0.880
+ CORJ870106 0.880 CORJ870105 0.880 RADA880108 0.876
+ BIOV880101 0.876 PONP800108 0.873 BASU050103 0.867
+ SWER830101 0.862 CORJ870102 0.860 CIDH920103 0.856
+ BASU050102 0.845 CIDH920104 0.841 BIOV880102 0.840
+ CIDH920105 0.838 NADH010103 0.830 CIDH920101 0.825
+ NADH010102 0.823 CASG920101 0.821 PONP800106 0.821
+ NADH010104 0.820 ZHOH040103 0.819 DESM900102 0.815
+ DESM900101 0.812 QIAN880122 0.808 JURD980101 0.808
+ KYTJ820101 0.806 ROBB790101 0.804 PUNT030101 -0.802
+ GUYH850103 -0.804 PARJ860101 -0.807 KRIW790102 -0.812
+ GUYH850101 -0.813 PARS000101 -0.815 RACS770103 -0.827
+ KRIW790101 -0.830 GRAR740102 -0.836 OOBM770103 -0.839
+ GUYH850102 -0.841 VINM940101 -0.848 KARP850102 -0.850
+ RACS770102 -0.852 MEIH800102 -0.855 RACS770101 -0.870
+ MEIH800101 -0.871 FASG890101 -0.876 MIYS990101 -0.911
+ MIYS990102 -0.913 MIYS990104 -0.920 MIYS990105 -0.923
+ MIYS990103 -0.930 CORJ870108 -0.959
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.96 0.75 -1.94 -5.68 4.54 -5.30 -3.86 -1.28 -0.62 5.54
+ 6.81 -5.62 4.76 5.06 -4.47 -1.92 -3.99 0.21 3.34 5.39
+//
+H CORJ870104
+D PRILS index (Cornette et al., 1987)
+R PMID:3656427
+A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and
+ DeLisi, C.
+T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic
+ Structures in Proteins
+J J. Mol. Biol. 196, 659-685, (1987)
+C CORJ870103 0.988 CORJ870107 0.973 PONP800101 0.913
+ BASU050101 0.910 MANP780101 0.908 PONP800102 0.901
+ NISK860101 0.901 PONP930101 0.901 CORJ870105 0.895
+ MIYS850101 0.892 CORJ870106 0.889 PONP800103 0.884
+ SWER830101 0.883 CORJ870102 0.881 RADA880108 0.880
+ BASU050103 0.877 NISK800101 0.868 BIOV880101 0.867
+ CORJ870101 0.863 PONP800108 0.861 ROSG850102 0.860
+ CIDH920103 0.857 MEIH800103 0.856 WERD780101 0.850
+ PONP800106 0.842 CIDH920101 0.840 BASU050102 0.838
+ CIDH920105 0.838 CIDH920104 0.832 PLIV810101 0.821
+ BIOV880102 0.815 KYTJ820101 0.812 JURD980101 0.812
+ ZHOH040103 0.809 ROBB760106 0.808 ROBB790101 0.807
+ ROBB760105 0.803 NADH010103 0.802 PARS000101 -0.800
+ KRIW790101 -0.801 PUNT030101 -0.804 GUYH850103 -0.809
+ OOBM770103 -0.814 GUYH850101 -0.815 PARJ860101 -0.823
+ VINM940101 -0.826 KARP850102 -0.830 RACS770102 -0.838
+ MEIH800102 -0.840 GRAR740102 -0.850 RACS770101 -0.860
+ MEIH800101 -0.862 FASG890101 -0.865 MIYS990104 -0.905
+ MIYS990105 -0.908 MIYS990103 -0.919 MIYS990101 -0.919
+ MIYS990102 -0.920 CORJ870108 -0.972
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.26 0.08 -0.46 -1.30 0.83 -0.83 -0.73 -0.40 -0.18 1.10
+ 1.52 -1.01 1.09 1.09 -0.62 -0.55 -0.71 -0.13 0.69 1.15
+//
+H CORJ870105
+D ALTFT index (Cornette et al., 1987)
+R PMID:3656427
+A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and
+ DeLisi, C.
+T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic
+ Structures in Proteins
+J J. Mol. Biol. 196, 659-685, (1987)
+C CORJ870106 0.991 CORJ870107 0.968 NISK860101 0.901
+ CORJ870104 0.895 BASU050101 0.888 CORJ870103 0.880
+ MIYS850101 0.879 PONP930101 0.878 BEGF750102 0.878
+ PONP800101 0.867 ROSG850102 0.864 BIOV880101 0.859
+ WERD780101 0.858 QIAN880120 0.858 RADA880108 0.854
+ MANP780101 0.853 BASU050103 0.852 SWER830101 0.848
+ CORJ870102 0.848 PONP800102 0.841 BASU050102 0.834
+ NISK800101 0.834 CIDH920103 0.832 LIFS790101 0.830
+ CIDH920101 0.828 MEIH800103 0.827 PLIV810101 0.827
+ ROBB790101 0.827 BIOV880102 0.823 CIDH920105 0.822
+ PONP800103 0.821 CORJ870101 0.818 PONP800107 0.812
+ QIAN880119 0.810 PONP800108 0.801 GUYH850102 -0.804
+ VINM940102 -0.807 GEIM800110 -0.807 GUYH850101 -0.810
+ CHOP780203 -0.815 PUNT030102 -0.817 FASG890101 -0.821
+ MUNV940103 -0.829 FUKS010103 -0.829 GUYH850103 -0.830
+ OOBM770103 -0.833 KARP850102 -0.834 PUNT030101 -0.834
+ PARJ860101 -0.837 RACS770102 -0.839 MEIH800102 -0.839
+ MIYS990105 -0.867 VINM940101 -0.873 RACS770101 -0.876
+ PARS000101 -0.878 MEIH800101 -0.883 MIYS990104 -0.885
+ MIYS990103 -0.894 MIYS990101 -0.897 MIYS990102 -0.898
+ CORJ870108 -0.967
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.73 -1.03 -5.29 -6.13 0.64 -0.96 -2.90 -2.67 3.03 5.04
+ 4.91 -5.99 3.34 5.20 -4.32 -3.00 -1.91 0.51 2.87 3.98
+//
+H CORJ870106
+D ALTLS index (Cornette et al., 1987)
+R PMID:3656427
+A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and
+ DeLisi, C.
+T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic
+ Structures in Proteins
+J J. Mol. Biol. 196, 659-685, (1987)
+C CORJ870105 0.991 CORJ870107 0.963 NISK860101 0.908
+ BASU050101 0.891 CORJ870104 0.889 PONP930101 0.889
+ PONP800101 0.887 MIYS850101 0.884 CORJ870103 0.880
+ WERD780101 0.878 ROSG850102 0.878 BIOV880101 0.870
+ MANP780101 0.867 QIAN880120 0.866 PONP800102 0.864
+ RADA880108 0.863 BASU050102 0.859 BASU050103 0.858
+ NISK800101 0.857 BEGF750102 0.853 CORJ870102 0.845
+ SWER830101 0.845 PONP800103 0.840 CIDH920103 0.837
+ LIFS790101 0.836 ROBB790101 0.834 CIDH920101 0.832
+ CORJ870101 0.829 CIDH920105 0.826 ZHOH040103 0.822
+ MEIH800103 0.822 PLIV810101 0.820 BIOV880102 0.818
+ PONP800108 0.813 PTIO830102 0.809 PONP800106 0.807
+ QIAN880121 0.806 QIAN880119 0.803 PONP800107 0.800
+ CHOP780216 -0.803 GEIM800110 -0.812 CHOP780203 -0.813
+ PUNT030102 -0.814 PARJ860101 -0.820 KRIW790101 -0.825
+ OOBM770103 -0.826 GUYH850102 -0.830 VINM940102 -0.830
+ PUNT030101 -0.833 GUYH850101 -0.833 MEIH800102 -0.835
+ GUYH850103 -0.837 RACS770102 -0.839 FASG890101 -0.841
+ FUKS010103 -0.846 MUNV940103 -0.848 KARP850102 -0.870
+ RACS770101 -0.879 MIYS990105 -0.879 VINM940101 -0.881
+ MEIH800101 -0.882 PARS000101 -0.891 MIYS990101 -0.898
+ MIYS990102 -0.899 MIYS990104 -0.902 MIYS990103 -0.909
+ CORJ870108 -0.968
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -1.35 -3.89 -10.96 -11.88 4.37 -1.34 -4.56 -5.82 6.54 10.93
+ 9.88 -11.92 7.47 11.35 -10.86 -6.21 -4.83 1.80 7.61 8.20
+//
+H CORJ870107
+D TOTFT index (Cornette et al., 1987)
+R PMID:3656427
+A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and
+ DeLisi, C.
+T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic
+ Structures in Proteins
+J J. Mol. Biol. 196, 659-685, (1987)
+C CORJ870104 0.973 CORJ870103 0.969 CORJ870105 0.968
+ CORJ870106 0.963 NISK860101 0.928 PONP930101 0.923
+ PONP800101 0.923 BASU050101 0.913 MIYS850101 0.911
+ MANP780101 0.908 PONP800102 0.905 ROSG850102 0.898
+ RADA880108 0.889 BIOV880101 0.889 WERD780101 0.887
+ PONP800103 0.884 NISK800101 0.884 MEIH800103 0.883
+ BASU050103 0.883 SWER830101 0.883 CORJ870102 0.881
+ CORJ870101 0.878 CIDH920103 0.866 PONP800108 0.859
+ BASU050102 0.855 BIOV880102 0.850 CIDH920105 0.848
+ CIDH920101 0.843 QIAN880120 0.840 CIDH920104 0.835
+ PONP800106 0.834 ROBB790101 0.832 BEGF750102 0.831
+ PLIV810101 0.829 ZHOH040103 0.822 LIFS790101 0.820
+ ROBB760106 0.819 DESM900102 0.819 NADH010103 0.817
+ DESM900101 0.815 CASG920101 0.813 NADH010102 0.812
+ PTIO830102 0.810 NADH010104 0.808 QIAN880121 0.806
+ PONP800107 0.805 JURD980101 0.804 KYTJ820101 0.801
+ ROBB760105 0.800 FUKS010103 -0.805 RACS770103 -0.808
+ PUNT030102 -0.810 VINM940102 -0.811 KRIW790102 -0.816
+ MUNV940103 -0.832 KRIW790101 -0.832 GUYH850103 -0.833
+ GUYH850102 -0.834 PARJ860101 -0.838 GRAR740102 -0.840
+ GUYH850101 -0.841 PUNT030101 -0.848 OOBM770103 -0.851
+ PARS000101 -0.865 KARP850102 -0.866 MEIH800102 -0.871
+ RACS770102 -0.871 FASG890101 -0.871 VINM940101 -0.877
+ MEIH800101 -0.897 RACS770101 -0.898 MIYS990105 -0.918
+ MIYS990104 -0.924 MIYS990101 -0.929 MIYS990102 -0.930
+ MIYS990103 -0.937 CORJ870108 -0.996
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.56 -0.26 -2.87 -4.31 1.78 -2.31 -2.35 -1.35 0.81 3.83
+ 4.09 -4.08 3.11 3.67 -3.22 -1.85 -1.97 -0.11 2.17 3.31
+//
+H CORJ870108
+D TOTLS index (Cornette et al., 1987)
+R PMID:3656427
+A Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and
+ DeLisi, C.
+T Hydrophobicity Scales and Computational Techniques for Detecting Amphipathic
+ Structures in Proteins
+J J. Mol. Biol. 196, 659-685, (1987)
+C MIYS990103 0.933 MIYS990102 0.929 MIYS990101 0.928
+ MIYS990104 0.918 MIYS990105 0.909 RACS770101 0.891
+ MEIH800101 0.889 FASG890101 0.872 KARP850102 0.868
+ RACS770102 0.863 VINM940101 0.862 MEIH800102 0.860
+ PARS000101 0.854 GUYH850101 0.851 PUNT030101 0.845
+ GRAR740102 0.838 KRIW790101 0.833 GUYH850103 0.831
+ PARJ860101 0.831 MUNV940103 0.830 OOBM770103 0.829
+ GUYH850102 0.821 FUKS010103 0.818 PUNT030102 0.810
+ VINM940102 0.810 KYTJ820101 -0.802 NADH010102 -0.803
+ NADH010104 -0.805 JURD980101 -0.806 DESM900101 -0.809
+ DESM900102 -0.811 ROBB760105 -0.811 LIFS790101 -0.811
+ PTIO830102 -0.812 NADH010103 -0.812 ROBB760106 -0.820
+ ZHOH040103 -0.821 BEGF750102 -0.825 ROBB790101 -0.829
+ CIDH920104 -0.829 BIOV880102 -0.831 QIAN880120 -0.834
+ PLIV810101 -0.838 CIDH920105 -0.843 CIDH920101 -0.845
+ PONP800108 -0.853 BASU050102 -0.855 PONP800106 -0.859
+ CIDH920103 -0.864 CORJ870101 -0.866 MEIH800103 -0.870
+ WERD780101 -0.878 NISK800101 -0.880 BASU050103 -0.883
+ CORJ870102 -0.883 SWER830101 -0.884 BIOV880101 -0.886
+ PONP800103 -0.889 ROSG850102 -0.890 RADA880108 -0.893
+ MIYS850101 -0.910 PONP800102 -0.911 MANP780101 -0.911
+ PONP930101 -0.912 BASU050101 -0.916 NISK860101 -0.920
+ PONP800101 -0.928 CORJ870103 -0.959 CORJ870105 -0.967
+ CORJ870106 -0.968 CORJ870104 -0.972 CORJ870107 -0.996
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.37 1.33 6.29 8.93 -4.47 3.88 4.04 3.39 -1.65 -7.92
+ -8.68 7.70 -7.13 -7.96 6.25 4.08 4.02 0.79 -4.73 -6.94
+//
+H MIYS990101
+D Relative partition energies derived by the Bethe approximation
+ (Miyazawa-Jernigan, 1999)
+R PMID:10336383
+A Miyazawa, S. and Jernigan, R. L.
+T Self-consistent estimation of inter-residue protein contact energies based on
+ an equilibrium mixture approximation of residues
+J Proteins 34, 49-68 (1999)
+C MIYS990102 1.000 MIYS990103 0.957 MIYS990104 0.954
+ MIYS990105 0.951 PARJ860101 0.944 MEIH800101 0.940
+ CORJ870108 0.928 FASG890101 0.926 RACS770101 0.920
+ RACS770102 0.917 MEIH800102 0.913 WOLS870101 0.912
+ GRAR740102 0.903 GUYH850101 0.891 PUNT030101 0.888
+ OOBM770103 0.887 GUYH850103 0.886 BULH740101 0.884
+ PUNT030102 0.881 VINM940101 0.880 KRIW790101 0.870
+ GUYH850102 0.865 VINM940102 0.841 PARS000101 0.830
+ KARP850102 0.825 KRIW790102 0.821 ROSM880102 0.819
+ KIDA850101 0.817 VINM940103 0.817 WOEC730101 0.805
+ HOPT810101 0.803 ZIMJ680105 -0.801 CHOC760103 -0.803
+ DESM900102 -0.809 LIFS790101 -0.811 NADH010101 -0.816
+ ARGP820103 -0.817 VENT840101 -0.821 NOZY710101 -0.821
+ WILM950101 -0.822 COWR900101 -0.826 EISD860101 -0.827
+ EISD860103 -0.829 PTIO830102 -0.833 CASG920101 -0.834
+ RADA880102 -0.837 NADH010105 -0.837 KYTJ820101 -0.840
+ ROSM880104 -0.843 CIDH920101 -0.847 JURD980101 -0.852
+ MEEJ810102 -0.854 CORJ870101 -0.854 ROSM880105 -0.854
+ BLAS910101 -0.857 NISK800101 -0.860 PONP800108 -0.866
+ MEEJ810101 -0.867 NADH010102 -0.870 ZHOH040101 -0.871
+ PONP800103 -0.871 CIDH920102 -0.872 PONP800102 -0.874
+ PONP800107 -0.877 ROBB790101 -0.883 PONP800101 -0.883
+ NADH010104 -0.885 NADH010103 -0.887 MEIH800103 -0.891
+ CORJ870105 -0.897 CORJ870106 -0.898 CIDH920103 -0.900
+ BIOV880102 -0.901 FAUJ830101 -0.907 CORJ870103 -0.911
+ WERD780101 -0.912 ROSG850102 -0.913 MANP780101 -0.913
+ CIDH920104 -0.915 PONP930101 -0.916 CIDH920105 -0.916
+ GUOD860101 -0.917 CORJ870104 -0.919 CORJ870102 -0.922
+ SWER830101 -0.923 ZHOH040103 -0.926 CORJ870107 -0.929
+ RADA880108 -0.932 BASU050102 -0.935 BASU050103 -0.940
+ PLIV810101 -0.944 BASU050101 -0.945 BIOV880101 -0.947
+ NISK860101 -0.957 MIYS850101 -0.977
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.02 0.44 0.63 0.72 -0.96 0.56 0.74 0.38 0.00 -1.89
+ -2.29 1.01 -1.36 -2.22 0.47 0.55 0.25 -1.28 -0.88 -1.34
+//
+H MIYS990102
+D Optimized relative partition energies - method A (Miyazawa-Jernigan, 1999)
+R PMID:10336383
+A Miyazawa, S. and Jernigan, R. L.
+T Self-consistent estimation of inter-residue protein contact energies based on
+ an equilibrium mixture approximation of residues
+J Proteins 34, 49-68 (1999)
+C MIYS990101 1.000 MIYS990103 0.958 MIYS990104 0.956
+ MIYS990105 0.953 PARJ860101 0.942 MEIH800101 0.941
+ FASG890101 0.929 CORJ870108 0.929 RACS770101 0.921
+ RACS770102 0.919 MEIH800102 0.916 WOLS870101 0.910
+ GRAR740102 0.903 GUYH850101 0.892 OOBM770103 0.891
+ GUYH850103 0.888 PUNT030101 0.887 VINM940101 0.883
+ PUNT030102 0.882 BULH740101 0.880 KRIW790101 0.873
+ GUYH850102 0.868 VINM940102 0.842 PARS000101 0.830
+ KARP850102 0.828 KRIW790102 0.826 VINM940103 0.818
+ ROSM880102 0.818 KIDA850101 0.817 WOEC730101 0.805
+ HOPT810101 0.804 CHOP780202 -0.801 CHOC760103 -0.805
+ DESM900102 -0.811 LIFS790101 -0.813 ARGP820103 -0.814
+ NADH010101 -0.815 NOZY710101 -0.819 VENT840101 -0.820
+ WILM950101 -0.822 EISD860101 -0.824 COWR900101 -0.825
+ EISD860103 -0.831 RADA880102 -0.834 PTIO830102 -0.834
+ NADH010105 -0.838 CASG920101 -0.838 ROSM880104 -0.839
+ KYTJ820101 -0.840 CIDH920101 -0.846 MEEJ810102 -0.853
+ JURD980101 -0.853 ROSM880105 -0.854 BLAS910101 -0.854
+ CORJ870101 -0.859 NISK800101 -0.863 MEEJ810101 -0.866
+ PONP800108 -0.869 ZHOH040101 -0.870 CIDH920102 -0.870
+ NADH010102 -0.872 PONP800103 -0.875 PONP800102 -0.877
+ PONP800107 -0.879 ROBB790101 -0.885 PONP800101 -0.886
+ NADH010104 -0.888 NADH010103 -0.889 MEIH800103 -0.893
+ CORJ870105 -0.898 CORJ870106 -0.899 CIDH920103 -0.899
+ BIOV880102 -0.902 FAUJ830101 -0.908 CORJ870103 -0.913
+ WERD780101 -0.914 CIDH920105 -0.915 MANP780101 -0.915
+ GUOD860101 -0.916 CIDH920104 -0.916 ROSG850102 -0.916
+ PONP930101 -0.919 CORJ870102 -0.920 CORJ870104 -0.920
+ SWER830101 -0.921 ZHOH040103 -0.927 CORJ870107 -0.930
+ RADA880108 -0.934 BASU050102 -0.936 BASU050103 -0.940
+ PLIV810101 -0.942 BASU050101 -0.945 BIOV880101 -0.948
+ NISK860101 -0.960 MIYS850101 -0.978
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.00 0.07 0.10 0.12 -0.16 0.09 0.12 0.06 0.00 -0.31
+ -0.37 0.17 -0.22 -0.36 0.08 0.09 0.04 -0.21 -0.14 -0.22
+//
+H MIYS990103
+D Optimized relative partition energies - method B (Miyazawa-Jernigan, 1999)
+R PMID:10336383
+A Miyazawa, S. and Jernigan, R. L.
+T Self-consistent estimation of inter-residue protein contact energies based on
+ an equilibrium mixture approximation of residues
+J Proteins 34, 49-68 (1999)
+C MIYS990104 0.995 MIYS990105 0.984 MIYS990102 0.958
+ FASG890101 0.957 MIYS990101 0.957 VINM940101 0.951
+ KRIW790101 0.944 CORJ870108 0.933 MEIH800101 0.923
+ MEIH800102 0.917 GUYH850102 0.914 OOBM770103 0.908
+ RACS770102 0.908 GUYH850101 0.907 GRAR740102 0.904
+ KARP850102 0.901 KRIW790102 0.899 VINM940102 0.895
+ RACS770101 0.887 VINM940103 0.886 PUNT030102 0.881
+ PARS000101 0.879 PUNT030101 0.864 PARJ860101 0.859
+ GUYH850103 0.857 KRIW710101 0.856 FUKS010104 0.845
+ RACS770103 0.840 MUNV940103 0.831 OOBM770101 0.827
+ HOPT810101 0.825 WOEC730101 0.824 WOLS870101 0.815
+ MONM990101 0.809 KIDA850101 0.805 GUYH850104 0.805
+ FUKS010103 0.805 FUKS010102 0.803 GEIM800107 -0.803
+ JANJ790102 -0.804 BLAS910101 -0.806 PONP800106 -0.807
+ PALJ810104 -0.811 PTIO830102 -0.820 KANM800102 -0.823
+ ZHOH040101 -0.824 CHOP780202 -0.825 NADH010101 -0.825
+ GUOD860101 -0.828 QIAN880120 -0.829 ROSM880105 -0.829
+ KYTJ820101 -0.833 JANJ780102 -0.834 ROBB760106 -0.836
+ LIFS790101 -0.838 QIAN880121 -0.838 CIDH920101 -0.838
+ JURD980101 -0.845 CIDH920102 -0.845 ROBB790101 -0.854
+ DESM900101 -0.854 PLIV810101 -0.861 CIDH920103 -0.870
+ DESM900102 -0.876 BAEK050101 -0.877 CORJ870102 -0.877
+ SWER830101 -0.878 NADH010105 -0.879 CIDH920105 -0.886
+ FAUJ830101 -0.893 CORJ870105 -0.894 CIDH920104 -0.902
+ MEIH800103 -0.906 CORJ870106 -0.909 CASG920101 -0.915
+ BASU050101 -0.918 MANP780101 -0.918 CORJ870104 -0.919
+ PONP800108 -0.920 NADH010102 -0.923 BIOV880102 -0.923
+ BASU050102 -0.924 CORJ870103 -0.930 ZHOH040103 -0.933
+ CORJ870101 -0.936 CORJ870107 -0.937 NISK800101 -0.938
+ WERD780101 -0.938 PONP800101 -0.940 PONP800103 -0.943
+ BASU050103 -0.943 NADH010104 -0.944 NADH010103 -0.944
+ PONP800102 -0.946 RADA880108 -0.950 PONP930101 -0.951
+ MIYS850101 -0.952 BIOV880101 -0.962 ROSG850102 -0.966
+ NISK860101 -0.974
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.03 0.09 0.13 0.17 -0.36 0.13 0.23 0.09 -0.04 -0.33
+ -0.38 0.32 -0.30 -0.34 0.20 0.10 0.01 -0.24 -0.23 -0.29
+//
+H MIYS990104
+D Optimized relative partition energies - method C (Miyazawa-Jernigan, 1999)
+R PMID:10336383
+A Miyazawa, S. and Jernigan, R. L.
+T Self-consistent estimation of inter-residue protein contact energies based on
+ an equilibrium mixture approximation of residues
+J Proteins 34, 49-68 (1999)
+C MIYS990103 0.995 MIYS990105 0.990 VINM940101 0.965
+ MIYS990102 0.956 MIYS990101 0.954 FASG890101 0.949
+ KRIW790101 0.945 OOBM770103 0.931 GUYH850102 0.928
+ MEIH800101 0.925 VINM940102 0.922 CORJ870108 0.918
+ GRAR740102 0.910 KARP850102 0.909 MEIH800102 0.903
+ PARS000101 0.903 VINM940103 0.898 RACS770102 0.892
+ GUYH850101 0.889 KRIW790102 0.889 RACS770101 0.884
+ GUYH850103 0.879 PARJ860101 0.877 PUNT030102 0.874
+ FUKS010104 0.862 PUNT030101 0.857 HOPT810101 0.843
+ KRIW710101 0.837 RACS770103 0.833 WOLS870101 0.830
+ MUNV940103 0.827 WOEC730101 0.827 FUKS010103 0.822
+ KARP850101 0.822 KIDA850101 0.822 FUKS010102 0.818
+ OOBM770101 0.806 LEVM760101 0.801 KYTJ820101 -0.800
+ MEEJ810102 -0.807 KANM800102 -0.808 NADH010101 -0.810
+ PALJ810104 -0.810 JANJ780102 -0.811 JURD980101 -0.813
+ ROBB760106 -0.815 PTIO830102 -0.818 BLAS910101 -0.818
+ DESM900101 -0.828 CHOP780202 -0.829 MEEJ810101 -0.831
+ QIAN880121 -0.832 QIAN880120 -0.833 ROSM880105 -0.841
+ LIFS790101 -0.843 GUOD860101 -0.846 DESM900102 -0.854
+ CIDH920101 -0.860 ZHOH040101 -0.864 PLIV810101 -0.869
+ NADH010105 -0.874 CIDH920102 -0.877 ROBB790101 -0.877
+ CIDH920103 -0.883 CORJ870105 -0.885 CORJ870102 -0.886
+ SWER830101 -0.887 BAEK050101 -0.892 MEIH800103 -0.894
+ CORJ870106 -0.902 CORJ870104 -0.905 FAUJ830101 -0.906
+ CIDH920105 -0.908 MANP780101 -0.909 NADH010102 -0.910
+ CIDH920104 -0.916 BASU050101 -0.918 PONP800108 -0.918
+ CORJ870103 -0.920 PONP800101 -0.924 CORJ870107 -0.924
+ PONP800103 -0.929 PONP800102 -0.930 CASG920101 -0.931
+ BIOV880102 -0.932 CORJ870101 -0.932 BASU050103 -0.938
+ NISK800101 -0.938 NADH010103 -0.938 NADH010104 -0.940
+ BASU050102 -0.942 RADA880108 -0.943 WERD780101 -0.949
+ PONP930101 -0.949 MIYS850101 -0.953 ZHOH040103 -0.954
+ ROSG850102 -0.962 BIOV880101 -0.965 NISK860101 -0.980
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.04 0.07 0.13 0.19 -0.38 0.14 0.23 0.09 -0.04 -0.34
+ -0.37 0.33 -0.30 -0.38 0.19 0.12 0.03 -0.33 -0.29 -0.29
+//
+H MIYS990105
+D Optimized relative partition energies - method D (Miyazawa-Jernigan, 1999)
+R PMID:10336383
+A Miyazawa, S. and Jernigan, R. L.
+T Self-consistent estimation of inter-residue protein contact energies based on
+ an equilibrium mixture approximation of residues
+J Proteins 34, 49-68 (1999)
+C MIYS990104 0.990 MIYS990103 0.984 FASG890101 0.959
+ MIYS990102 0.953 VINM940101 0.952 MIYS990101 0.951
+ OOBM770103 0.936 GRAR740102 0.928 KRIW790101 0.925
+ MEIH800102 0.914 GUYH850102 0.912 MEIH800101 0.912
+ CORJ870108 0.909 GUYH850101 0.895 RACS770102 0.893
+ VINM940102 0.891 KARP850102 0.888 KRIW790102 0.887
+ GUYH850103 0.883 VINM940103 0.880 PARJ860101 0.878
+ PARS000101 0.877 PUNT030101 0.876 PUNT030102 0.874
+ FUKS010104 0.870 RACS770101 0.866 KIDA850101 0.865
+ HOPT810101 0.862 RACS770103 0.852 WOEC730101 0.849
+ OOBM770101 0.844 WOLS870101 0.838 LEVM760101 0.828
+ GUYH850104 0.821 JANJ780103 0.816 FUKS010102 0.813
+ KRIW710101 0.801 EISD860103 -0.815 MEEJ810102 -0.817
+ KYTJ820101 -0.818 JANJ790102 -0.820 NADH010101 -0.821
+ JURD980101 -0.829 DESM900101 -0.832 ZHOH040101 -0.838
+ MEEJ810101 -0.839 JANJ780102 -0.846 GUOD860101 -0.846
+ BLAS910101 -0.848 CIDH920101 -0.849 NADH010105 -0.856
+ CIDH920102 -0.859 CORJ870105 -0.867 PLIV810101 -0.869
+ BAEK050101 -0.871 ROSM880105 -0.873 DESM900102 -0.875
+ CIDH920103 -0.876 CORJ870106 -0.879 CORJ870102 -0.882
+ SWER830101 -0.883 ROBB790101 -0.885 BASU050101 -0.900
+ CIDH920105 -0.901 MANP780101 -0.906 CORJ870104 -0.908
+ CIDH920104 -0.916 CORJ870107 -0.918 PONP800101 -0.918
+ BASU050102 -0.919 MEIH800103 -0.919 FAUJ830101 -0.920
+ NADH010102 -0.923 CORJ870103 -0.923 PONP800102 -0.927
+ PONP800108 -0.927 BASU050103 -0.928 PONP800103 -0.928
+ NADH010104 -0.934 NISK800101 -0.935 WERD780101 -0.936
+ PONP930101 -0.936 CASG920101 -0.937 CORJ870101 -0.937
+ ZHOH040103 -0.939 NADH010103 -0.939 BIOV880102 -0.947
+ RADA880108 -0.950 MIYS850101 -0.951 ROSG850102 -0.968
+ NISK860101 -0.972 BIOV880101 -0.975
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.02 0.08 0.10 0.19 -0.32 0.15 0.21 -0.02 -0.02 -0.28
+ -0.32 0.30 -0.25 -0.33 0.11 0.11 0.05 -0.27 -0.23 -0.23
+//
+H ENGD860101
+D Hydrophobicity index (Engelman et al., 1986)
+R PMID:3521657
+A Engelman, D.M., Steitz, T.A. and Goldman, A.
+T Identifying Nonpolar Transbilayer Helices in Amino Acid Sequences of Membrane
+ Proteins
+J Ann.Rev.Biophys.Biophys.Chem. 15, 321-353 (1986)
+C PRAM900101 1.000 ROSM880101 0.917 VHEG790101 0.909
+ KUHL950101 0.908 OOBM770101 0.907 JANJ780101 0.901
+ ROSM880102 0.891 PUNT030101 0.889 JANJ780103 0.884
+ HOPT810101 0.882 GUYH850104 0.881 LEVM760101 0.881
+ WOEC730101 0.871 PUNT030102 0.870 GUYH850105 0.867
+ KIDA850101 0.866 GRAR740102 0.855 ZIMJ680103 0.854
+ CHOC760102 0.826 MONM990101 0.820 GUYH850101 0.820
+ FAUJ880109 0.814 RADA880104 -0.803 OLSK800101 -0.805
+ CHOC760103 -0.813 NADH010103 -0.815 WARP780101 -0.827
+ EISD860103 -0.831 NADH010101 -0.843 KYTJ820101 -0.850
+ FAUJ830101 -0.853 JANJ780102 -0.860 JURD980101 -0.861
+ EISD860101 -0.862 BLAS910101 -0.864 RADA880107 -0.865
+ NADH010102 -0.870 WOLR790101 -0.877 WOLR810101 -0.887
+ JANJ790102 -0.890 DESM900102 -0.890 ROSM880105 -0.912
+ RADA880101 -0.932 EISD840101 -0.936 JACR890101 -0.948
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -1.6 12.3 4.8 9.2 -2.0 4.1 8.2 -1.0 3.0 -3.1
+ -2.8 8.8 -3.4 -3.7 0.2 -0.6 -1.2 -1.9 0.7 -2.6
+//
+H FASG890101
+D Hydrophobicity index (Fasman, 1989)
+R
+A Fasman, G.D.
+T Prediction of Protein Structure and the Principles of Protein Conformation
+J Plenum, New York 1989, page 457, Table XVII
+C MIYS990105 0.959 MIYS990103 0.957 MEIH800102 0.951
+ MIYS990104 0.949 RACS770102 0.935 GUYH850101 0.934
+ MIYS990102 0.929 MIYS990101 0.926 MEIH800101 0.919
+ KRIW790101 0.914 GUYH850102 0.909 VINM940101 0.904
+ KRIW790102 0.882 GUYH850104 0.872 RACS770101 0.872
+ GRAR740102 0.872 CORJ870108 0.872 KARP850102 0.871
+ OOBM770103 0.869 VINM940103 0.868 OOBM770101 0.868
+ KRIW710101 0.865 KIDA850101 0.861 GUYH850103 0.860
+ PUNT030102 0.853 PUNT030101 0.845 FUKS010104 0.844
+ RACS770103 0.842 ROSM880102 0.839 JANJ780103 0.838
+ VINM940102 0.836 PARJ860101 0.825 KUHL950101 0.821
+ JANJ780101 0.813 FUKS010103 0.812 GUOD860101 -0.801
+ DESM900101 -0.808 CORJ870105 -0.821 ROSM880105 -0.822
+ PONP800106 -0.823 NADH010101 -0.838 CORJ870106 -0.841
+ KYTJ820101 -0.844 CIDH920103 -0.846 CHOC760103 -0.849
+ BASU050101 -0.856 JURD980101 -0.857 PLIV810101 -0.858
+ BAEK050101 -0.859 CIDH920105 -0.860 ROBB790101 -0.860
+ EISD860103 -0.863 CORJ870104 -0.865 CORJ870107 -0.871
+ JANJ790102 -0.875 CORJ870103 -0.876 NADH010105 -0.877
+ DESM900102 -0.879 BASU050102 -0.881 JANJ790101 -0.885
+ CIDH920104 -0.903 JANJ780102 -0.903 MANP780101 -0.904
+ PONP930101 -0.907 ZHOH040103 -0.910 FAUJ830101 -0.911
+ PONP800108 -0.913 BASU050103 -0.915 CORJ870101 -0.921
+ NISK800101 -0.923 MEIH800103 -0.924 CASG920101 -0.924
+ WERD780101 -0.926 BIOV880102 -0.928 NADH010102 -0.929
+ PONP800101 -0.932 PONP800103 -0.936 MIYS850101 -0.938
+ PONP800102 -0.944 NADH010104 -0.944 NADH010103 -0.945
+ NISK860101 -0.949 ROSG850102 -0.976 RADA880108 -0.977
+ BIOV880101 -0.982
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ -0.21 2.11 0.96 1.36 -6.04 1.52 2.30 0.00 -1.23 -4.81
+ -4.68 3.88 -3.66 -4.65 0.75 1.74 0.78 -3.32 -1.01 -3.50
+//
+H KARS160101
+D Number of vertices (order of the graph) (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.00 8.00 5.00 5.00 3.00 6.00 6.00 1.00 7.00 5.00
+ 5.00 6.00 5.00 8.00 4.00 3.00 4.00 11.00 9.00 4.00
+//
+H KARS160102
+D Number of edges (size of the graph) (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.00 7.00 4.00 4.00 2.00 5.00 5.00 0.00 6.00 4.00
+ 4.00 5.00 4.00 8.00 4.00 2.00 3.00 12.00 9.00 3.00
+//
+H KARS160103
+D Total weighted degree of the graph (obtained by adding all the weights of
+ all the vertices) (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.00 12.00 8.00 8.00 4.00 10.00 10.00 0.00 14.00 8.00
+ 8.00 10.00 8.00 14.00 8.00 4.00 6.00 24.00 18.00 6.00
+//
+H KARS160104
+D Weighted domination number (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.00 6.00 4.00 4.00 2.00 4.00 5.00 1.00 6.000 4.00
+ 4.00 4.00 4.00 6.00 4.00 2.00 3.00 8.00 7.00 3.00
+//
+H KARS160105
+D Average eccentricity (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.00 8.120 5.00 5.17 2.33 5.860 6.00 0.00 6.71 3.25
+ 5.00 7.00 5.40 7.00 4.00 1.670 3.250 11.10 8.88 3.25
+//
+H KARS160106
+D Radius (minimum eccentricity) (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.00 6.00 3.00 3.00 1.00 4.00 4.00 0.00 6.000 3.00
+ 3.00 5.00 3.00 6.000 4.00 2.00 1.00 9.000 6.000 1.00
+//
+H KARS160107
+D Diameter (maximum eccentricity) (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.00 12.00 6.00 6.00 3.00 8.00 8.00 0.00 9.00 6.00
+ 6.00 9.00 7.00 11.000 4.000 3.00 4.00 14.000 13.000 4.00
+//
+H KARS160108
+D Average weighted degree (total degree, divided by the number of vertices)
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.00 1.50 1.60 1.60 1.333 1.667 1.667 0.00 2.00 1.600
+ 1.60 1.667 1.60 1.750 2.00 1.333 1.50 2.182 2.000 1.50
+//
+H KARS160109
+D Maximum eigenvalue of the weighted Laplacian matrix of the graph
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.00 12.499 11.539 11.539 6.243 12.207 11.530 0.00 12.876 10.851
+ 11.029 10.363 9.49 14.851 12.00 5.00 9.928 13.511 12.868 9.928
+//
+H KARS160110
+D Minimum eigenvalue of the weighted Laplacian matrix of the graph
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.00 -4.307 -4.178 -4.178 -2.243 -4.255 -3.425 0.00 -3.721 -6.085
+ -4.729 -3.151 -2.812 -4.801 -4.00 1.00 -3.928 -6.324 -4.793 -3.928
+//
+H KARS160111
+D Average eigenvalue of the Laplacian matrix of the the graph
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 1.00 3.500 3.20 3.20 2.00 3.333 3.333 0.00 4.286 1.80
+ 3.20 3.00 2.80 4.25 4.00 2.00 3.00 4.00 4.333 3.00
+//
+H KARS160112
+D Second smallest eigenvalue of the Laplacian matrix of the graph
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 2.00 -2.590 0.528 0.528 2.00 -1.043 -0.538 0.00 -1.185 -1.517
+ 1.052 -0.536 0.678 -1.672 4.00 2.00 3.00 -2.576 -2.054 3.00
+//
+H KARS160113
+D Weighted domination number using the atomic number (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.00 19.00 12.00 12.00 6.00 12.00 12.00 1.00 15.00 12.00
+ 12.00 12.00 18.00 18.00 12.00 6.00 6.00 24.00 18.00 6.00
+//
+H KARS160114
+D Average weighted eccentricity based on the the atomic number
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.00 31.444 16.50 16.40 16.670 21.167 21.00 3.50 23.10 15.60
+ 15.60 24.50 27.20 23.25 12.00 13.33 12.40 27.50 27.78 10.50
+//
+H KARS160115
+D Weighted radius based on the atomic number (minimum eccentricity)
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.00 20.00 14.00 12.00 12.00 15.00 14.00 1.00 18.00 12.00
+ 12.00 18.00 18.00 18.00 12.00 8.00 8.00 18.00 20.00 6.00
+//
+H KARS160116
+D Weighted diameter based on the atomic number (maximum eccentricity)
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.00 38.00 20.00 20.00 22.00 24.00 26.00 6.00 31.00 18.00
+ 18.00 31.00 34.00 24.00 12.00 20.00 14.00 36.00 38.00 12.00
+//
+H KARS160117
+D Total weighted atomic number of the graph (obtained by summing all the atomic
+ number of each of the vertices in the graph) (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 12.00 45.00 33.007 34.00 28.00 39.00 40.00 7.00 47.00 30.00
+ 30.00 37.00 40.00 48.00 24.00 22.00 27.00 68.00 56.00 24.007
+//
+H KARS160118
+D Average weighted atomic number or degree based on atomic number in the graph
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.00 5.00 6.60 6.80 9.33 6.50 6.67 3.50 4.70 6.00
+ 6.00 6.17 8.00 6.00 6.00 7.33 5.40 5.667 6.22 6.00
+//
+H KARS160119
+D Weighted maximum eigenvalue based on the atomic numbers
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 12.00 23.343 27.708 28.634 28.00 27.831 28.731 7.00 24.243 24.841
+ 25.021 22.739 31.344 26.993 24.00 20.00 23.819 29.778 28.252 24.00
+//
+H KARS160120
+D Weighted minimum eigenvalue based on the atomic numbers
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -1.734 -1.641
+ 0.00 -0.179 0.00 0.00 0.00 0.00 -4.227 0.211 -0.96 0.00
+//
+H KARS160121
+D Weighted average eigenvalue based on the atomic numbers
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 6.00 10.667 10.00 10.40 11.333 10.50 10.667 3.50 10.400 9.60
+ 9.60 10.167 13.60 12.00 12.00 8.667 9.00 12.75 12.222 9.00
+//
+H KARS160122
+D Weighted second smallest eigenvalue of the weighted Laplacian matrix
+ (Karkbara-Knisley, 2016)
+R
+A Karkbara, S. and Knisley, D.
+T A graph-theoretic model of single point mutations in the cystic fibrosis
+ transmembrane conductance regulator
+J J. Adv. Biotechnol. Vol.6, No.1, 780-786 (2016)
+C
+I A/L R/K N/M D/F C/P Q/S E/T G/W H/Y I/V
+ 0.00 4.20 3.00 2.969 6.00 1.849 1.822 0.00 1.605 3.373
+ 3.113 1.372 2.656 2.026 12.00 6.00 6.00 2.044 1.599 6.00
+//
diff --git a/modules/seq/alg/pymod/aaindex2 b/modules/seq/alg/pymod/aaindex2
new file mode 100644
index 000000000..51d038c21
--- /dev/null
+++ b/modules/seq/alg/pymod/aaindex2
@@ -0,0 +1,2818 @@
+H ALTS910101
+D The PAM-120 matrix (Altschul, 1991)
+R PMID:2051488
+A Altschul, S.F.
+T Amino acid substitution matrices from an information theoretic perspective
+J J. Mol. Biol. 219, 555-565 (1991)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 3.
+ -3. 6.
+ 0. -1. 4.
+ 0. -3. 2. 5.
+ -3. -4. -5. -7. 9.
+ -1. 1. 0. 1. -7. 6.
+ 0. -3. 1. 3. -7. 2. 5.
+ 1. -4. 0. 0. -5. -3. -1. 5.
+ -3. 1. 2. 0. -4. 3. -1. -4. 7.
+ -1. -2. -2. -3. -3. -3. -3. -4. -4. 6.
+ -3. -4. -4. -5. -7. -2. -4. -5. -3. 1. 5.
+ -2. 2. 1. -1. -7. 0. -1. -3. -2. -2. -4. 5.
+ -2. -1. -3. -4. -6. -1. -4. -4. -4. 1. 3. 0. 8.
+ -4. -4. -4. -7. -6. -6. -6. -5. -2. 0. 0. -6. -1. 8.
+ 1. -1. -2. -2. -3. 0. -1. -2. -1. -3. -3. -2. -3. -5. 6.
+ 1. -1. 1. 0. -1. -2. -1. 1. -2. -2. -4. -1. -2. -3. 1. 3.
+ 1. -2. 0. -1. -3. -2. -2. -1. -3. 0. -3. -1. -1. -4. -1. 2. 4.
+ -7. 1. -5. -8. -8. -6. -8. -8. -5. -7. -5. -5. -7. -1. -7. -2. -6. 12.
+ -4. -6. -2. -5. -1. -5. -4. -6. -1. -2. -3. -6. -4. 4. -6. -3. -3. -1. 8.
+ 0. -3. -3. -3. -2. -3. -3. -2. -3. 3. 1. -4. 1. -3. -2. -2. 0. -8. -3. 5.
+//
+H BENS940101
+D Log-odds scoring matrix collected in 6.4-8.7 PAM (Benner et al., 1994)
+R PMID:7700864
+A Benner, S.A., Cohen, M.A. and Gonnet, G.H.
+T Amino acid substitution during functionally constrained divergent
+ evolution of protein sequences
+J Protein Engineering 7, 1323-1332 (1994)
+* extrapolated to 250 PAM
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 2.5
+ -1.7 5.1
+ 0.0 -0.1 3.6
+ -0.6 -1.5 2.5 5.2
+ -1.7 -0.4 -1.6 -3.7 12.1
+ -1.7 2.5 0.1 0.6 -3.2 5.3
+ -0.7 -0.4 1.1 4.4 -4.7 2.1 5.2
+ 0.8 -0.1 -0.1 0.8 -1.3 -1.6 0.5 5.8
+ -2.1 1.8 1.4 0.1 -1.2 3.2 -0.2 -2.1 6.1
+ 0.1 -3.8 -2.5 -4.2 -3.6 -3.8 -4.1 -3.4 -3.7 4.4
+ -1.3 -3.2 -3.4 -5.3 -3.8 -2.4 -5.0 -4.6 -2.2 2.4 4.8
+ -1.9 4.3 1.0 -0.2 -2.8 2.5 0.9 -1.4 0.9 -3.8 -4.1 5.6
+ -0.2 -3.0 -2.5 -4.3 -3.7 -3.1 -4.1 -3.7 -3.4 4.0 2.9 -2.9 4.8
+ -3.2 -4.9 -3.5 -5.7 -0.1 -4.4 -6.7 -5.7 0.1 0.0 2.4 -6.3 -0.1 8.3
+ 1.1 -1.3 -1.1 -2.8 -2.7 0.1 -2.6 -1.7 -0.4 -2.0 -0.2 -2.3 -1.8 -3.2 6.5
+ 1.4 -0.9 1.2 -0.4 0.9 -1.4 -1.2 0.8 -0.9 -1.2 -1.5 -1.2 -1.3 -1.8 1.4 2.1
+ 1.7 -1.3 0.5 -1.2 -1.5 -1.7 -1.6 -0.5 -1.7 0.7 -0.4 -1.1 0.6 -2.4 0.6 1.5 2.4
+ -4.3 2.0 -4.4 -6.3 1.6 -2.6 -5.6 -1.7 -2.8 -5.0 -3.0 -1.4 -4.4 -1.6 -4.8 -2.9 -2.6 14.7
+ -4.0 -2.6 -0.9 -2.3 2.6 -1.4 -4.1 -4.9 4.4 -3.3 -1.6 -4.0 -3.6 5.6 -3.8 -1.8 -3.4 -0.3 9.5
+ 0.7 -3.7 -2.4 -3.3 -3.1 -3.5 -3.0 -2.3 -3.8 3.9 1.9 -3.8 3.3 -0.5 -1.6 -0.9 0.6 -4.8 -3.8 4.0
+//
+H BENS940102
+D Log-odds scoring matrix collected in 22-29 PAM (Benner et al., 1994)
+R PMID:7700864
+A Benner, S.A., Cohen, M.A. and Gonnet, G.H.
+T Amino acid substitution during functionally constrained divergent
+ evolution of protein sequences
+J Protein Engineering 7, 1323-1332 (1994)
+* extrapolated to 250 PAM
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 2.5
+ -1.2 5.0
+ 0.0 0.4 3.3
+ -0.2 -1.0 2.4 4.8
+ -1.2 -1.6 -1.9 -3.7 12.6
+ -0.9 2.2 0.5 0.6 -3.3 4.2
+ -0.3 -0.1 1.2 3.9 -4.3 1.7 4.6
+ 0.8 -0.7 0.4 0.7 -1.7 -1.4 0.5 6.2
+ -1.6 1.5 1.4 0.3 -1.5 2.4 -0.2 -2.0 6.1
+ -0.4 -3.2 -2.7 -4.0 -2.4 -2.7 -3.6 -3.8 -3.2 4.2
+ -1.7 -2.9 -3.5 -4.9 -2.6 -2.0 -4.4 -4.9 -2.1 2.7 4.6
+ -1.0 3.9 1.0 0.2 -3.3 2.2 1.0 -1.0 0.8 -3.0 -3.3 4.4
+ -0.8 -2.1 -2.6 -3.9 -2.5 -1.7 -3.4 -3.8 -2.4 3.1 3.2 -2.0 4.9
+ -3.1 -4.3 -3.5 -5.4 -0.1 -3.6 -5.7 -5.8 0.3 0.5 2.2 -5.1 0.7 7.7
+ 0.8 -1.2 -1.1 -1.8 -3.1 -0.1 -1.7 -1.8 -0.4 -2.3 -1.3 -1.6 -2.0 -3.4 7.0
+ 1.3 -0.5 1.1 0.1 0.3 -0.6 -0.5 0.6 -0.5 -1.4 -2.1 -0.4 -1.5 -2.2 1.1 2.0
+ 1.4 -0.7 0.5 -0.7 -1.1 -0.7 -0.9 -0.7 -1.1 0.3 -1.0 -0.4 0.1 -2.6 0.4 1.5 2.5
+ -5.5 -1.1 -5.2 -6.4 0.5 -3.3 -6.3 -4.5 -2.7 -4.4 -1.8 -3.7 -2.8 0.5 -5.8 -3.9 -4.5 15.7
+ -3.5 -2.7 -1.2 -3.0 0.6 -1.9 -4.0 -4.8 3.7 -2.2 -0.7 -3.6 -1.8 5.9 -3.5 -1.9 -3.0 1.5 9.0
+ 0.4 -2.9 -2.3 -3.0 -1.7 -2.4 -2.7 -2.5 -3.0 3.6 2.0 -2.7 2.5 -0.1 -1.7 -0.9 0.4 -4.5 -2.6 3.7
+//
+H BENS940103
+D Log-odds scoring matrix collected in 74-100 PAM (Benner et al., 1994)
+R PMID:7700864
+A Benner, S.A., Cohen, M.A. and Gonnet, G.H.
+T Amino acid substitution during functionally constrained divergent
+ evolution of protein sequences
+J Protein Engineering 7, 1323-1332 (1994)
+* extrapolated to 250 PAM
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 2.4
+ -0.8 4.8
+ -0.2 0.3 3.6
+ -0.3 -0.5 2.2 4.8
+ 0.3 -2.2 -1.8 -3.2 11.8
+ -0.3 1.6 0.7 0.8 -2.6 3.0
+ -0.1 0.3 1.0 2.9 -3.2 1.7 3.7
+ 0.6 -1.0 0.4 0.2 -2.0 -1.1 -0.5 6.6
+ -1.0 1.0 1.2 0.4 -1.3 1.4 0.2 -1.6 6.1
+ -0.8 -2.6 -2.8 -3.9 -1.2 -2.0 -2.9 -4.3 -2.3 4.0
+ -1.4 -2.4 -3.1 -4.2 -1.6 -1.7 -3.1 -4.6 -1.9 2.8 4.2
+ -0.4 2.9 0.9 0.4 -2.9 1.7 1.2 -1.1 0.6 -2.3 -2.4 3.4
+ -0.8 -1.8 -2.2 -3.2 -1.2 -1.0 -2.2 -3.5 -1.5 2.6 2.9 -1.5 4.5
+ -2.6 -3.5 -3.2 -4.7 -0.7 -2.8 -4.3 -5.4 0.0 0.9 2.1 -3.6 1.3 7.2
+ 0.4 -1.0 -1.0 -1.0 -3.1 -0.2 -0.7 -1.7 -1.0 -2.6 -2.2 -0.8 -2.4 -3.8 7.5
+ 1.1 -0.2 0.9 0.4 0.1 0.1 0.1 0.4 -0.3 -1.8 -2.2 0.0 -1.4 -2.6 0.5 2.1
+ 0.7 -0.3 0.4 -0.2 -0.6 -0.1 -0.2 -1.0 -0.5 -0.3 -1.1 0.1 -0.4 -2.2 0.1 1.4 2.5
+ -4.1 -1.6 -4.0 -5.5 -0.9 -2.8 -4.7 -4.1 -1.0 -2.3 -0.9 -3.6 -1.3 3.0 -5.2 -3.4 -3.7 14.7
+ -2.6 -2.0 -1.4 -2.8 -0.4 -1.8 -3.0 -4.3 2.5 -1.0 -0.1 -2.4 -0.5 5.3 -3.4 -1.9 -2.1 3.6 8.1
+ 0.1 -2.2 -2.2 -2.9 -0.2 -1.7 -2.1 -3.1 -2.1 3.2 1.9 -1.9 1.8 0.1 -1.9 -1.0 0.2 -2.9 -1.4 3.4
+//
+H BENS940104
+D Genetic code matrix (Benner et al., 1994)
+R PMID:7700864
+A Benner, S.A., Cohen, M.A. and Gonnet, G.H.
+T Amino acid substitution during functionally constrained divergent
+ evolution of protein sequences
+J Protein Engineering 7, 1323-1332 (1994)
+* extrapolated to 250 PAM
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 4.0
+ -1.6 2.9
+ -1.7 -1.5 4.7
+ 1.0 -2.3 1.7 4.8
+ -1.9 0.7 -1.5 -1.6 5.5
+ -2.1 0.3 0.4 0.3 -3.1 5.5
+ 1.3 -2.0 0.3 3.8 -3.0 2.0 5.7
+ 1.2 0.8 -2.6 1.1 1.0 -2.1 1.4 4.2
+ -2.1 3.6 1.8 1.7 -1.6 3.6 0.3 -2.2 4.7
+ -1.8 -1.2 0.9 -2.1 -1.9 -1.9 -2.3 -2.5 -1.8 4.1
+ -2.3 -0.4 -2.2 -2.4 -1.3 0.1 -2.5 -2.2 -0.1 1.2 3.4
+ -1.9 -0.2 3.5 0.3 -3.2 2.2 2.0 -2.2 0.6 0.7 -2.0 5.6
+ -2.0 -0.4 0.1 -2.5 -2.7 -1.2 -1.8 -2.3 -1.8 3.3 1.5 1.6 5.4
+ -2.4 -1.5 -1.3 -1.7 1.8 -2.1 -2.9 -1.9 -1.1 1.3 2.2 -2.8 0.5 4.5
+ 0.8 0.3 -1.6 -2.2 -1.9 1.0 -2.1 -1.8 0.7 -1.6 0.0 -1.5 -1.4 -1.8 3.8
+ 0.1 0.3 -0.3 -2.1 1.5 -2.3 -2.8 -0.6 -1.6 -0.5 -1.2 -1.5 -1.3 0.0 0.4 2.6
+ 0.9 -0.6 0.9 -2.1 -1.9 -1.7 -2.1 -2.1 -1.8 0.8 -1.9 1.0 0.7 -2.1 1.1 1.0 4.0
+ -2.2 1.8 -3.0 -2.9 4.1 -2.3 -3.2 1.4 -2.1 -2.2 -0.3 -3.0 -2.0 0.0 -1.6 0.8 -2.2 7.5
+ -2.4 -1.9 2.5 2.3 2.6 -0.8 -0.9 -1.8 2.3 -1.6 -1.6 -0.8 -2.9 2.0 -2.3 0.3 -2.1 -0.5 6.5
+ 1.0 -2.1 -2.2 1.0 -2.2 -2.0 1.3 1.1 -2.1 1.0 1.1 -2.1 1.0 1.0 -2.1 -2.2 -2.2 -2.1 -2.2 4.1
+//
+H CSEM940101
+D Residue replace ability matrix (Cserzo et al., 1994)
+R PMID:7966267
+A Cserzo, M., Bernassau, J.-M., Simon, I. and Maigret, B.
+T New alignment strategy for transmembrane proteins
+J J. Mol. Biol. 243, 388-396 (1994)
+* Diagonal elements are missing.
+* We use 1 as diagonal elements.
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 1.
+ -0.07 1.
+ -0.14 0.12 1.
+ -0.08 -0.01 0.56 1.
+ 0.04 -0.20 -0.14 -0.24 1.
+ -0.01 0.57 0.20 0.19 -0.29 1.
+ 0.08 0.34 0.13 0.37 -0.51 0.51 1.
+ 0.11 -0.11 0.22 0.11 0.25 -0.13 -0.23 1.
+ -0.11 0.13 0.32 0.22 0.18 0.05 -0.19 0.18 1.
+ -0.10 -0.29 -0.37 -0.54 0.26 -0.43 -0.51 -0.22 -0.14 1.
+ 0.20 -0.20 -0.39 -0.55 0.23 -0.30 -0.45 -0.14 -0.12 0.60 1.
+ -0.07 0.47 0.22 0.18 -0.43 0.52 0.54 -0.23 -0.09 -0.40 -0.34 1.
+ 0.15 -0.17 -0.11 -0.25 0.10 -0.18 -0.14 -0.01 -0.19 0.36 0.38 -0.16 1.
+ -0.25 -0.31 -0.33 -0.40 0.30 -0.44 -0.50 -0.09 -0.06 0.60 0.44 -0.41 0.22 1.
+ -0.07 -0.17 0.05 0.09 0.02 -0.03 -0.11 0.25 0.05 -0.19 -0.20 -0.17 -0.17 -0.12 1.
+ 0.14 -0.16 0.14 0.22 0.10 -0.06 -0.17 0.29 0.14 -0.27 -0.19 -0.24 -0.17 -0.01 0.27 1.
+ 0.11 -0.32 0.13 0.23 0.14 -0.15 -0.27 -0.02 0.08 0.00 -0.04 -0.24 -0.02 0.02 0.20 0.45 1.
+ -0.25 -0.03 -0.39 -0.41 0.18 -0.17 -0.22 -0.08 -0.11 0.36 0.22 -0.22 0.16 0.41 -0.13 -0.17 -0.12 1.
+ -0.36 -0.03 -0.27 -0.34 0.21 -0.28 -0.32 -0.24 0.08 0.43 0.17 -0.20 0.07 0.54 -0.23 -0.21 -0.14 0.43 1.
+ 0.06 -0.29 -0.46 -0.48 0.33 -0.38 -0.44 -0.12 -0.18 0.70 0.49 -0.36 0.23 0.47 -0.17 -0.18 0.07 0.29 0.31 1.
+//
+H DAYM780301
+D Log odds matrix for 250 PAMs (Dayhoff et al., 1978)
+R
+A Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C.
+T A model of evolutionary change in proteins
+J In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff,
+ M.O., ed.), National Biomedical Research Foundation, Washington, D.C.,
+ p.352 (1978)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 2.
+ -2. 6.
+ 0. 0. 2.
+ 0. -1. 2. 4.
+ -2. -4. -4. -5. 12.
+ 0. 1. 1. 2. -5. 4.
+ 0. -1. 1. 3. -5. 2. 4.
+ 1. -3. 0. 1. -3. -1. 0. 5.
+ -1. 2. 2. 1. -3. 3. 1. -2. 6.
+ -1. -2. -2. -2. -2. -2. -2. -3. -2. 5.
+ -2. -3. -3. -4. -6. -2. -3. -4. -2. 2. 6.
+ -1. 3. 1. 0. -5. 1. 0. -2. 0. -2. -3. 5.
+ -1. 0. -2. -3. -5. -1. -2. -3. -2. 2. 4. 0. 6.
+ -4. -4. -4. -6. -4. -5. -5. -5. -2. 1. 2. -5. 0. 9.
+ 1. 0. -1. -1. -3. 0. -1. -1. 0. -2. -3. -1. -2. -5. 6.
+ 1. 0. 1. 0. 0. -1. 0. 1. -1. -1. -3. 0. -2. -3. 1. 2.
+ 1. -1. 0. 0. -2. -1. 0. 0. -1. 0. -2. 0. -1. -3. 0. 1. 3.
+ -6. 2. -4. -7. -8. -5. -7. -7. -3. -5. -2. -3. -4. 0. -6. -2. -5. 17.
+ -3. -4. -2. -4. 0. -4. -4. -5. 0. -1. -1. -4. -2. 7. -5. -3. -3. 0. 10.
+ 0. -2. -2. -2. -2. -2. -2. -1. -2. 4. 2. -2. 2. -1. -1. -1. 0. -6. -2. 4.
+//
+H FEND850101
+D Structure-Genetic matrix (Feng et al., 1985)
+R PMID:6100188
+A Feng, D.F., Johnson, M.S. and Doolittle, R.F.
+T Aligning amino acid sequences: comparison of commonly used methods
+J J. Mol. Evol. 21, 112-125 (1985)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 6.
+ 2. 6.
+ 3. 2. 6.
+ 4. 2. 5. 6.
+ 2. 2. 2. 1. 6.
+ 3. 3. 3. 4. 1. 6.
+ 4. 2. 3. 5. 0. 4. 6.
+ 5. 3. 3. 4. 3. 2. 4. 6.
+ 2. 4. 4. 3. 2. 4. 2. 1. 6.
+ 2. 2. 2. 1. 2. 1. 1. 2. 1. 6.
+ 2. 2. 1. 1. 2. 2. 1. 2. 3. 5. 6.
+ 3. 5. 4. 3. 0. 4. 4. 2. 3. 2. 2. 6.
+ 2. 2. 1. 0. 2. 2. 1. 1. 1. 4. 5. 2. 6.
+ 2. 1. 1. 1. 3. 1. 0. 1. 2. 4. 4. 0. 2. 6.
+ 5. 3. 2. 2. 2. 3. 3. 3. 3. 2. 3. 2. 2. 2. 6.
+ 5. 3. 5. 3. 4. 3. 3. 5. 3. 2. 2. 3. 1. 3. 4. 6.
+ 5. 3. 4. 2. 2. 3. 3. 2. 2. 3. 2. 4. 3. 1. 4. 5. 6.
+ 2. 2. 0. 0. 3. 1. 1. 3. 1. 2. 4. 1. 3. 3. 2. 2. 1. 6.
+ 2. 1. 3. 2. 3. 2. 1. 2. 3. 3. 3. 1. 2. 5. 2. 3. 2. 3. 6.
+ 5. 2. 2. 3. 2. 2. 4. 4. 1. 5. 5. 3. 4. 4. 3. 2. 3. 3. 3. 6.
+//
+H FITW660101
+D Mutation values for the interconversion of amino acid pairs (Fitch, 1966)
+R PMID:5917736
+A Fitch, W.M.
+T An improved method of testing for evolutionary homology
+J J. Mol. Biol. 16, 9-16 (1966)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 0.
+ 2. 0.
+ 2. 2. 0.
+ 1. 2. 1. 0.
+ 2. 1. 2. 2. 0.
+ 2. 1. 2. 2. 2. 0.
+ 1. 2. 2. 1. 3. 1. 0.
+ 1. 1. 2. 1. 1. 2. 1. 0.
+ 2. 1. 1. 1. 2. 1. 2. 2. 0.
+ 2. 2. 1. 2. 2. 3. 3. 2. 2. 0.
+ 2. 1. 2. 2. 2. 1. 2. 1. 1. 1. 0.
+ 2. 1. 1. 2. 3. 1. 1. 2. 2. 2. 2. 0.
+ 2. 1. 2. 3. 3. 2. 2. 2. 3. 1. 1. 1. 0.
+ 2. 2. 2. 2. 1. 2. 3. 2. 2. 1. 1. 3. 2. 0.
+ 1. 1. 2. 2. 2. 1. 2. 2. 1. 2. 1. 2. 2. 2. 0.
+ 1. 1. 1. 2. 1. 1. 2. 1. 2. 1. 1. 2. 2. 1. 1. 0.
+ 1. 1. 1. 2. 2. 2. 2. 2. 2. 1. 2. 1. 1. 2. 1. 1. 0.
+ 2. 1. 3. 3. 1. 1. 2. 1. 3. 3. 1. 2. 2. 2. 2. 1. 2. 0.
+ 2. 2. 1. 1. 1. 1. 2. 2. 1. 2. 2. 2. 3. 1. 2. 1. 2. 2. 0.
+ 1. 2. 2. 1. 1. 2. 1. 1. 2. 1. 1. 2. 1. 1. 2. 2. 2. 2. 2. 0.
+//
+H GEOD900101
+D Hydrophobicity scoring matrix (George et al., 1990)
+R PMID:2314281
+A George, D.G., Barker, W.C. and Hunt, L.T.
+T Mutation data matrix and its uses
+J Methods Enzymol. 183, 333-351 (1990)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 10.
+ 5. 10.
+ 9. 6. 10.
+ 5. 9. 6. 10.
+ 9. 4. 8. 5. 10.
+ 9. 6. 10. 6. 8. 10.
+ 5. 9. 6. 10. 5. 6. 10.
+ 9. 5. 10. 6. 8. 10. 6. 10.
+ 10. 5. 9. 5. 9. 9. 5. 9. 10.
+ 8. 3. 7. 3. 9. 7. 3. 7. 8. 10.
+ 8. 3. 7. 3. 9. 7. 3. 7. 8. 10. 10.
+ 5. 10. 6. 9. 4. 6. 9. 5. 5. 3. 3. 10.
+ 9. 3. 8. 4. 10. 8. 4. 8. 9. 9. 9. 3. 10.
+ 7. 1. 6. 2. 8. 6. 2. 6. 7. 9. 9. 1. 8. 10.
+ 9. 3. 8. 4. 9. 8. 4. 8. 9. 9. 9. 3. 10. 8. 10.
+ 9. 6. 10. 7. 8. 10. 7. 10. 9. 7. 7. 6. 8. 6. 7. 10.
+ 10. 5. 9. 5. 9. 9. 5. 9. 10. 8. 8. 5. 9. 7. 8. 9. 10.
+ 5. 0. 4. 1. 6. 4. 1. 5. 5. 8. 8. 0. 7. 9. 7. 4. 5. 10.
+ 7. 2. 6. 3. 8. 6. 3. 6. 7. 9. 9. 2. 8. 10. 9. 6. 7. 8. 10.
+ 8. 3. 7. 4. 9. 7. 4. 8. 8. 10. 10. 3. 10. 8. 10. 7. 8. 7. 9. 10.
+//
+H GONG920101
+D The mutation matrix for initially aligning (Gonnet et al., 1992)
+R PMID:1604319
+A Gonnet, G.H., Cohen, M.A. and Benner, S.A.
+T Exhaustive matching of the entire protein sequence database
+J Science 256, 1443-1445 (1992)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 2.4
+ -0.6 4.7
+ -0.3 0.3 3.8
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+//
+H GRAR740104
+D Chemical distance (Grantham, 1974)
+R PMID:4843792
+A Grantham, R.
+T Amino acid difference formula to help explain protein evolution
+J Science 185, 862-864 (1974)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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+H HENS920101
+D BLOSUM45 substitution matrix (Henikoff-Henikoff, 1992)
+R PMID:1438297
+A Henikoff, S. and Henikoff, J.G.
+T Amino acid substitution matrices from protein blocks
+J Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
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+H HENS920102
+D BLOSUM62 substitution matrix (Henikoff-Henikoff, 1992)
+R PMID:1438297
+A Henikoff, S. and Henikoff, J.G.
+T Amino acid substitution matrices from protein blocks
+J Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
+* matrix in 1/3 Bit Units
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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+//
+H HENS920103
+D BLOSUM80 substitution matrix (Henikoff-Henikoff, 1992)
+R PMID:1438297
+A Henikoff, S. and Henikoff, J.G.
+T Amino acid substitution matrices from protein blocks
+J Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
+* matrix in 1/3 Bit Units
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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+//
+H JOHM930101
+D Structure-based amino acid scoring table (Johnson-Overington, 1993)
+R PMID:8411177
+A Johnson, M.S. and Overington, J.P.
+T A structural basis for sequence comparisons
+ An evaluation of scoring methodologies
+J J. Mol. Biol. 233, 716-738 (1993)
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+H JOND920103
+D The 250 PAM PET91 matrix (Jones et al., 1992)
+R PMID:1633570
+A Jones, D.T., Taylor, W.R. and Thornton, J.M.
+T The rapid generation of mutation data matrices from protein sequences
+J CABIOS 8, 275-282 (1992)
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+H JOND940101
+D The 250 PAM transmembrane protein exchange matrix (Jones et al., 1994)
+R PMID:8112466
+A Jones, D.T., Taylor, W.R. and Thornton, J.M.
+T A mutation data matrix for transmembrane proteins
+J FEBS Lett. 339, 269-275 (1994)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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+//
+H KOLA920101
+D Conformational similarity weight matrix (Kolaskar-Kulkarni-Kale, 1992)
+R PMID:1538389
+A Kolaskar, A.S. and Kulkarni-Kale, U.
+T Sequence alignment approach to pick up conformationally similar
+ protein fragments
+J J. Mol. Biol. 223, 1053-1061 (1992)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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+//
+H LEVJ860101
+D The secondary structure similarity matrix (Levin et al., 1986)
+R PMID:3743779
+A Levin, J.M., Robson, B. and Garnier, J.
+T An algorithm for secondary structure determination in proteins based on
+ sequence similarity
+J FEBS Lett. 205, 303-308 (1986)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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+H LUTR910101
+D Structure-based comparison table for outside other class (Luthy et al., 1991)
+R PMID:1881879
+A Luthy, R., McLachlan, A.D. and Eisenberg, D.
+T Secondary structure-based profiles: Use of structure-conserving scoring
+ tables in searching protein sequence databases for structural similarities
+J Proteins 10, 229-239 (1991)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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+ 3. -1. 2. -2. -7. 1. 1. -12. -5. 0. -4. -3. -2. -13. -6. 4. 30.
+ -6. 3. -6. -10. -3. -13. -14. -12. -3. 1. 1. -19. 9. 10. -11. -7. -14. 124.
+ -6. -3. -4. -10. 3. -9. -10. -16. 2. -3. 2. -16. 4. 22. -17. -6. -9. 29. 64.
+ 3. -3. -3. -7. -7. -2. -2. -12. -9. 24. 13. -9. 14. 0. -8. -4. -1. -1. -2. 39.
+//
+H LUTR910102
+D Structure-based comparison table for inside other class (Luthy et al., 1991)
+R PMID:1881879
+A Luthy, R., McLachlan, A.D. and Eisenberg, D.
+T Secondary structure-based profiles: Use of structure-conserving scoring
+ tables in searching protein sequence databases for structural similarities
+J Proteins 10, 229-239 (1991)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 12.
+ 5. 9.
+ 5. 5. 6.
+ 6. 8. 8. 17.
+ 1. -10. -11. -14. 93.
+ 6. 6. 6. 8. -5. 7.
+ 7. 8. 8. 12. -16. 9. 15.
+ 5. -2. 5. 6. -36. 3. 8. 52.
+ -2. 5. 6. 5. -20. 4. -3. -14. 65.
+ -1. -4. -3. -6. -17. -4. -5. -20. -10. 31.
+ -10. -10. -10. -16. -35. -12. -14. -32. -18. 9. 37.
+ 6. 10. 10. 13. -22. 10. 13. 2. 6. -5. -15. 31.
+ -6. -6. -8. -13. -17. -5. -12. -32. -5. 18. 13. -11. 61.
+ -24. -11. -19. -25. -36. -20. -30. -52. -10. -4. 2. -30. 2. 67.
+ -5. -12. -11. -7. -30. -7. -7. -11. -23. -28. -36. -5. -25. -28. 83.
+ 9. 6. 8. 8. -11. 8. 9. 7. -1. -11. -25. 8. -18. -37. -9. 36.
+ 8. 6. 6. 8. 1. 8. 10. 0. -5. -1. -18. 6. -9. -37. -14. 10. 35.
+ -20. 2. -6. -16. 0. -2. -18. -23. -21. -19. -18. -21. -20. 11. -47. -29. -29. 129.
+ -4. 3. 0. 0. -7. 0. -3. -16. 5. 0. -2. -1. 1. 21. -20. -6. -8. 44. 26.
+ 0. -3. -3. -4. -12. -3. -4. -20. -6. 17. 8. -4. 12. -9. -20. -10. -2. -8. -2. 26.
+//
+H LUTR910103
+D Structure-based comparison table for outside alpha class (Luthy et al., 1991)
+R PMID:1881879
+A Luthy, R., McLachlan, A.D. and Eisenberg, D.
+T Secondary structure-based profiles: Use of structure-conserving scoring
+ tables in searching protein sequence databases for structural similarities
+J Proteins 10, 229-239 (1991)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 24.
+ -2. 18.
+ -1. 2. 16.
+ -2. 0. 4. 23.
+ 2. 2. 1. -1. 9.
+ -1. 2. 2. 3. 2. 13.
+ -2. -1. 1. 6. -3. 3. 24.
+ 1. 2. 4. 2. 4. 2. 1. 29.
+ -5. 0. 3. 1. 0. 2. -1. 0. 43.
+ -5. -3. -6. -9. 4. -4. -10. -5. -4. 41.
+ -18. -7. -12. -18. -3. -13. -16. -15. -12. 13. 54.
+ -10. 5. -2. -4. -4. -1. -4. -4. -6. -11. -21. 32.
+ -3. 0. -5. -7. 4. 0. -5. -5. -5. 17. 13. -7. 44.
+ -20. -18. -18. -18. 4. -13. -24. -21. -9. 10. 12. -30. 13. 99.
+ -2. -2. -2. 1. -1. 1. -1. 0. -7. -8. -24. -8. -10. -32. 67.
+ 1. 2. 4. 3. 5. 2. 1. 5. 0. -4. -12. -3. -3. -18. 1. 17.
+ 1. 2. 3. 1. 4. 2. 0. 3. 1. 3. -6. -3. 2. -16. -3. 4. 16.
+ -20. -8. -18. -12. 16. -3. -16. -21. 7. -14. -3. -31. -14. 36. -29. -19. -2. 170.
+ -21. -10. -10. -14. -7. -12. -21. -14. -1. -14. -13. -25. -19. 40. -17. -16. -15. 47. 105.
+ -5. -3. -6. -4. 5. -5. -6. -5. -8. 18. -1. -11. 7. -11. -6. -2. 3. -9. -18. 44.
+//
+H LUTR910104
+D Structure-based comparison table for inside alpha class (Luthy et al., 1991)
+R PMID:1881879
+A Luthy, R., McLachlan, A.D. and Eisenberg, D.
+T Secondary structure-based profiles: Use of structure-conserving scoring
+ tables in searching protein sequence databases for structural similarities
+J Proteins 10, 229-239 (1991)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 22.
+ -2. 38.
+ 4. 5. 4.
+ -1. 5. 11. 71.
+ 8. -1. 4. -13. 50.
+ 2. 9. 4. 10. 0. 6.
+ 4. 12. 5. 20. -2. 7. 12.
+ 5. 0. 7. 0. 3. 5. 8. 53.
+ -30. 4. -3. 7. -30. 13. -3. -32. 95.
+ -2. -1. 0. -13. 3. 0. -2. -6. -17. 17.
+ -14. -3. -6. -20. -11. -7. -10. -21. -10. 0. 25.
+ 1. 22. 6. 9. -2. 9. 14. 2. -9. -1. -8. 33.
+ -2. 2. 0. -11. 0. -1. -3. -6. -8. 3. 2. -3. 17.
+ -18. -14. -15. -26. -12. -14. -21. -25. -7. -4. -4. -23. 1. 58.
+ 5. 2. 2. 5. 2. 2. 4. 6. -14. 1. -7. 3. -1. -8. 4.
+ 9. 4. 4. 3. 10. 4. 5. 7. -19. 1. -10. 5. 0. -14. 9. 23.
+ 6. 3. 3. 1. 8. 3. 4. 4. -16. 2. -6. 5. 1. -13. 4. 9. 10.
+ -50. -35. -34. -55. -45. -15. -40. -57. -41. -27. -30. -23. -12. 4. -33. -45. -39. 130.
+ -15. -3. -4. -8. -8. 0. -8. -17. 23. -4. -5. -13. -2. 25. -3. -10. -9. 31. 68.
+ -1. -3. -1. -15. 1. -2. -3. -10. -27. 5. -6. -4. 3. -9. 0. -1. 2. -23. -14. 21.
+//
+H LUTR910105
+D Structure-based comparison table for outside beta class (Luthy et al., 1991)
+R PMID:1881879
+A Luthy, R., McLachlan, A.D. and Eisenberg, D.
+T Secondary structure-based profiles: Use of structure-conserving scoring
+ tables in searching protein sequence databases for structural similarities
+J Proteins 10, 229-239 (1991)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 27.
+ -3. 32.
+ -2. 0. 18.
+ -4. 0. 9. 38.
+ -22. -28. 6. -26. 156.
+ -3. 2. 1. 3. -29. 30.
+ -3. -1. 0. 10. -30. 6. 25.
+ 9. 6. -4. 3. -33. 3. 4. 59.
+ -11. -7. 14. 12. -33. 4. -5. -4. 84.
+ -2. -2. -8. -10. -26. -7. -7. -8. -13. 29.
+ -7. -8. -11. -21. -34. -13. -13. -21. -9. 16. 42.
+ -6. 9. -1. -2. -32. 4. 2. -1. -19. -9. -14. 30.
+ 2. 2. -3. -7. -17. -5. -5. -2. -11. 10. 12. -5. 7.
+ -4. -9. -8. -17. 12. -9. -12. -10. -3. 7. 6. -11. 2. 47.
+ 6. -1. 5. -2. -22. 1. -10. -10. -9. 8. 3. -12. 6. 2. 56.
+ 5. -4. 0. 0. 6. -6. -3. 0. -11. -10. -15. -4. -2. -9. -4. 25.
+ 3. 2. -4. -1. -7. 2. 0. -1. -19. -3. -12. -1. 2. -8. -2. 4. 20.
+ -2. -31. -30. -40. -34. -34. -35. -33. -36. -25. -29. -14. -21. 32. -25. -13. -31. 150.
+ -10. -13. -2. -13. -25. -14. -13. -14. 18. -10. -1. -14. -4. 24. 3. -7. -16. 11. 56.
+ -2. -4. -9. -13. -11. -8. -8. -14. -19. 11. 8. -8. 7. -3. 1. -7. -1. -15. -13. 24.
+//
+H LUTR910106
+D Structure-based comparison table for inside beta class (Luthy et al., 1991)
+R PMID:1881879
+A Luthy, R., McLachlan, A.D. and Eisenberg, D.
+T Secondary structure-based profiles: Use of structure-conserving scoring
+ tables in searching protein sequence databases for structural similarities
+J Proteins 10, 229-239 (1991)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 18.
+ 1. 60.
+ 6. 10. 18.
+ 4. -1. 18. 80.
+ 0. -7. 5. 0. 66.
+ 6. 24. 18. 18. 7. 42.
+ 8. -1. 22. 29. -1. 15. 59.
+ 14. -8. 6. -4. -10. 4. 13. 48.
+ 2. 11. 13. 24. -2. 13. 16. -3. 18.
+ -8. -14. -14. -22. -29. -14. -18. -9. -15. 20.
+ -6. -12. -15. -27. -29. -9. -21. -9. -15. 11. 25.
+ 4. 22. 16. 30. 2. 22. 10. -2. 14. -13. -11. 35.
+ 1. 3. 3. 5. -23. 4. 5. 4. 3. 3. 2. 6. 35.
+ -12. -10. -6. -24. -40. -16. -7. -17. 6. -10. -4. -14. -2. 58.
+ 4. -20. -13. -26. -8. -17. -19. -14. -15. -9. -3. -16. -16. -9. 95.
+ 12. 3. 13. 17. -1. 10. 13. 16. 10. -12. -15. 11. -2. -16. -4. 28.
+ 6. 10. 8. 2. -11. 4. 9. 8. 5. -7. -11. 7. 3. -17. -1. 12. 24.
+ -23. 16. -11. -24. -43. -14. -19. -32. 18. -8. -8. -11. -15. 3. -32. -21. -7. 115.
+ 0. 7. 13. 7. -9. 9. 14. -9. 20. -16. -12. 11. 2. 16. -7. 3. 1. 15. 37.
+ -7. -11. -17. -30. -28. -15. -24. -9. -19. 11. 9. -12. -5. -13. -9. -14. -7. -15. -18. 21.
+//
+H LUTR910107
+D Structure-based comparison table for other class (Luthy et al., 1991)
+R PMID:1881879
+A Luthy, R., McLachlan, A.D. and Eisenberg, D.
+T Secondary structure-based profiles: Use of structure-conserving scoring
+ tables in searching protein sequence databases for structural similarities
+J Proteins 10, 229-239 (1991)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 11.
+ 1. 28.
+ 2. 3. 10.
+ 2. 1. 5. 27.
+ -5. -9. -9. -15. 108.
+ 3. 7. 4. 4. -11. 14.
+ 3. 3. 3. 8. -15. 6. 15.
+ -4. -6. -2. -5. -21. -6. -4. 41.
+ -3. 0. 2. -3. -23. 2. -2. -12. 55.
+ -1. -6. -4. -9. -13. -4. -5. -18. -12. 49.
+ -3. -7. -7. -14. -10. -6. -8. -22. -10. 19. 48.
+ 1. 7. 2. 1. -19. 6. 5. -12. -6. -11. -15. 38.
+ -1. -2. -3. -9. -7. -2. -7. -15. -4. 22. 24. -10. 52.
+ -16. -15. -14. -20. -19. -18. -22. -30. -9. 5. 10. -29. 11. 83.
+ 0. -8. -7. -8. -30. -6. -3. -17. -12. -15. -16. -8. -15. -26. 58.
+ 4. 2. 4. 3. -11. 3. 3. -4. -3. -8. -10. 1. -7. -19. -3. 19.
+ 3. 0. 3. -1. -6. 2. 2. -10. -5. -1. -9. -2. -4. -19. -7. 5. 31.
+ -9. 2. -7. -13. -1. -13. -17. -15. -7. -5. -5. -21. 4. 10. -16. -11. -18. 129.
+ -5. -1. -2. -7. 0. -6. -9. -16. 3. -2. 0. -12. 3. 22. -16. -5. -9. 35. 59.
+ 2. -4. -4. -7. -8. -3. -3. -14. -9. 24. 14. -9. 15. -2. -11. -6. -2. -3. -3. 37.
+//
+H LUTR910108
+D Structure-based comparison table for alpha helix class (Luthy et al., 1991)
+R PMID:1881879
+A Luthy, R., McLachlan, A.D. and Eisenberg, D.
+T Secondary structure-based profiles: Use of structure-conserving scoring
+ tables in searching protein sequence databases for structural similarities
+J Proteins 10, 229-239 (1991)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 23.
+ -1. 19.
+ 1. 5. 13.
+ 0. 3. 7. 28.
+ 4. 1. 1. -4. 51.
+ 1. 5. 5. 6. 1. 11.
+ 0. 4. 5. 10. -5. 7. 23.
+ 2. 3. 6. 4. 4. 3. 3. 37.
+ -6. 2. 5. 3. -5. 4. 1. -1. 52.
+ -6. -6. -7. -12. 5. -6. -10. -8. -9. 38.
+ -19. -10. -14. -21. -8. -14. -18. -19. -14. 7. 45.
+ -6. 9. 3. 2. -6. 4. 3. -1. -2. -12. -21. 34.
+ -4. -2. -5. -9. 3. -2. -7. -6. -7. 12. 8. -8. 40.
+ -23. -22. -22. -24. -4. -19. -28. -26. -13. 3. 4. -34. 8. 88.
+ 1. 2. 3. 5. -2. 5. 6. 3. -4. -7. -21. -1. -8. -28. 59.
+ 3. 4. 5. 5. 7. 4. 4. 6. 0. -5. -15. 1. -4. -21. 6. 17.
+ 2. 2. 4. 2. 6. 3. 2. 4. 0. 1. -9. 0. 0. -19. 1. 5. 14.
+ -43. -29. -38. -35. -13. -19. -38. -46. -17. -25. -22. -43. -11. 19. -46. -41. -25. 162.
+ -19. -8. -7. -12. -8. -8. -16. -14. 4. -11. -12. -20. -12. 33. -10. -14. -13. 36. 97.
+ -6. -6. -8. -9. 3. -7. -8. -9. -14. 13. -4. -13. 6. -9. -7. -4. 1. -18. -19. 40.
+//
+H LUTR910109
+D Structure-based comparison table for beta strand class (Luthy et al., 1991)
+R PMID:1881879
+A Luthy, R., McLachlan, A.D. and Eisenberg, D.
+T Secondary structure-based profiles: Use of structure-conserving scoring
+ tables in searching protein sequence databases for structural similarities
+J Proteins 10, 229-239 (1991)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 23.
+ -2. 40.
+ 1. 4. 15.
+ -1. 2. 13. 49.
+ -5. -19. -5. -16. 97.
+ 0. 9. 7. 9. -11. 31.
+ 0. 2. 8. 17. -21. 11. 31.
+ 12. 2. 0. 1. -18. 4. 6. 54.
+ -4. 2. 13. 17. -12. 8. 5. -5. 55.
+ -7. -9. -12. -17. -30. -13. -13. -11. -15. 28.
+ -7. -10. -13. -22. -34. -12. -14. -15. -13. 13. 34.
+ -3. 14. 7. 8. -23. 12. 10. 0. -1. -14. -13. 34.
+ 1. 2. -2. -5. -28. -3. -3. 2. -3. 8. 8. -4. 25.
+ -9. -11. -9. -21. -31. -12. -13. -15. 3. -3. 1. -14. -1. 57.
+ 5. -6. 2. -7. -12. -2. -13. -13. -10. -1. -1. -14. 0. -4. 78.
+ 7. 1. 6. 8. -10. 2. 5. 8. 3. -13. -15. 4. -3. -14. -4. 26.
+ 4. 6. 2. 2. -18. 4. 4. 3. -4. -7. -12. 4. 2. -13. -3. 8. 21.
+ -17. -5. -22. -32. -53. -26. -29. -33. 7. -12. -15. -15. -20. 16. -28. -19. -20. 133.
+ -5. -5. 4. -5. -19. -4. -3. -13. 21. -15. -7. -5. -3. 20. -1. -3. -8. 13. 47.
+ -5. -7. -12. -18. -27. -11. -12. -12. -18. 11. 8. -10. 2. -9. -4. -10. -4. -17. -15. 23.
+//
+H MCLA710101
+D The similarity of pairs of amino acids (McLachlan, 1971)
+R PMID:5167087
+A McLachlan, A.D.
+T Tests for comparing related amino-acid sequences
+ cytochrome c and cytochrome c551
+J J. Mol. Biol. 61, 409-424 (1971)
+* (RR 9.)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 8.
+ 2. 8.
+ 3. 3. 8.
+ 3. 1. 5. 8.
+ 1. 1. 1. 1. 9.
+ 3. 5. 4. 4. 0. 8.
+ 4. 3. 4. 5. 0. 5. 8.
+ 3. 3. 3. 3. 1. 2. 3. 8.
+ 3. 5. 4. 4. 3. 4. 2. 2. 8.
+ 2. 1. 1. 0. 1. 0. 1. 1. 2. 8.
+ 2. 2. 1. 1. 0. 3. 1. 1. 2. 5. 8.
+ 3. 5. 4. 3. 0. 4. 4. 3. 4. 1. 2. 8.
+ 3. 1. 2. 2. 3. 3. 1. 1. 3. 5. 6. 1. 8.
+ 1. 1. 0. 1. 0. 0. 0. 0. 4. 3. 5. 0. 5. 9.
+ 4. 3. 1. 3. 0. 3. 4. 3. 3. 1. 1. 3. 1. 1. 8.
+ 4. 4. 5. 3. 2. 4. 4. 3. 3. 2. 2. 3. 2. 2. 3. 8.
+ 3. 3. 3. 3. 2. 3. 4. 2. 4. 3. 3. 3. 3. 1. 3. 5. 8.
+ 1. 3. 0. 0. 2. 2. 1. 1. 3. 3. 3. 1. 1. 6. 0. 3. 2. 9.
+ 1. 2. 2. 1. 1. 1. 2. 0. 4. 3. 3. 1. 2. 6. 0. 3. 1. 6. 9.
+ 3. 2. 1. 1. 1. 2. 2. 2. 2. 5. 5. 2. 4. 3. 2. 2. 3. 2. 3. 8.
+//
+H MCLA720101
+D Chemical similarity scores (McLachlan, 1972)
+R PMID:5023183
+A McLachlan, A.D.
+T Repeating sequences and gene duplication in proteins
+J J. Mol. Biol. 64, 417-437 (1972)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 5.
+ 0. 6.
+ 0. 0. 5.
+ 0. 0. 3. 5.
+ 0. 0. 0. 0. 6.
+ 0. 0. 2. 1. 0. 5.
+ 0. 0. 1. 2. 0. 3. 5.
+ 3. 0. 0. 0. 0. 0. 0. 6.
+ 0. 0. 1. 0. 0. 2. 0. 0. 6.
+ 0. 0. 0. 0. 0. 0. 0. 0. 0. 5.
+ 0. 0. 0. 0. 0. 0. 0. 0. 0. 3. 5.
+ 0. 3. 0. 0. 0. 1. 0. 0. 0. 0. 0. 5.
+ 0. 0. 0. 0. 0. 0. 0. 0. 0. 3. 3. 0. 6.
+ 0. 0. 0. 0. 0. 0. 0. 0. 2. 1. 2. 0. 2. 6.
+ 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 5.
+ 1. 0. 1. 0. 2. 1. 0. 0. 0. 0. 0. 0. 0. 0. 0. 5.
+ 1. 0. 1. 0. 0. 0. 0. 0. 0. 1. 0. 0. 0. 0. 1. 3. 5.
+ 0. 0. 0. 0. 0. 0. 0. 0. 1. 1. 1. 0. 1. 3. 0. 0. 0. 6.
+ 0. 0. 0. 0. 0. 0. 0. 0. 2. 1. 1. 0. 1. 3. 0. 0. 0. 2. 6.
+ 0. 0. 0. 0. 0. 0. 0. 0. 0. 2. 1. 0. 1. 1. 1. 0. 0. 0. 0. 5.
+//
+H MIYS930101
+D Base-substitution-protein-stability matrix (Miyazawa-Jernigan, 1993)
+R PMID:8506261
+A Miyazawa, S. and Jernigan, R.L.
+T A new substitution matrix for protein sequence searches based on
+ contact frequencies in protein structures
+J Protein Engineering 6, 267-278 (1993)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 0.34
+ -0.08 0.65
+ -0.16 0.01 0.38
+ 0.04 -0.06 0.20 0.36
+ -0.51 -0.35 -0.46 -0.41 1.02
+ -0.16 0.15 0.20 0.16 -0.74 0.48
+ 0.03 -0.02 0.19 0.32 -0.64 0.25 0.36
+ 0.19 0.20 -0.11 0.15 -0.18 -0.14 0.13 0.43
+ -0.21 0.11 0.21 0.18 -0.29 0.37 0.13 -0.19 0.54
+ -0.45 -0.82 -0.83 -0.78 -0.13 -0.95 -0.86 -0.58 -0.69 0.75
+ -0.45 -0.74 -0.90 -0.75 -0.02 -0.74 -0.80 -0.56 -0.50 0.48 0.61
+ -0.20 0.04 0.38 0.16 -0.81 0.30 0.25 -0.16 0.14 -1.01 -1.06 0.49
+ -0.47 -0.83 -0.97 -0.90 -0.29 -0.97 -0.87 -0.61 -0.86 0.67 0.50 -1.03 0.97
+ -0.47 -0.79 -0.71 -0.62 0.39 -0.85 -0.81 -0.52 -0.43 0.45 0.48 -1.03 0.35 0.61
+ 0.17 0.14 -0.12 -0.15 -0.65 0.15 -0.13 -0.14 0.14 -0.78 -0.67 -0.14 -0.82 -0.76 0.56
+ 0.16 0.05 -0.02 -0.14 -0.20 -0.20 -0.19 0.00 -0.15 -0.68 -0.70 -0.14 -0.75 -0.53 0.24 0.48
+ 0.18 0.00 0.11 -0.10 -0.62 -0.07 -0.09 -0.09 -0.13 -0.59 -0.77 0.09 -0.61 -0.75 0.25 0.28 0.45
+ -0.51 -0.26 -0.79 -0.64 0.82 -0.83 -0.66 -0.15 -0.70 -0.23 0.13 -0.92 0.04 0.25 -0.71 -0.29 -0.70 1.42
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+D Amino acid pair distance (Miyata et al., 1979)
+R PMID:439147
+A Miyata, T., Miyazawa, S. and Yasunaga, T.
+T Two types of amino acid substitutions in protein evolution
+J J. Mol. Evol. 12, 219-236 (1979)
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+A Mohana Rao, J.K.
+T New scoring matrix for amino acid residue exchanges based on residue
+ characteristic physical parameters
+J Int. J. Peptide Protein Res. 29, 276-281 (1987)
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+T Amino acid similarity coefficients for protein modeling and sequence
+ alignment derived from main-chain folding angles
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+A Niefind, K. and Schomburg, D.
+T Amino acid similarity coefficients for protein modeling and sequence
+ alignment derived from main-chain folding angles
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+H OVEJ920101
+D STR matrix from structure-based alignments (Overington et al., 1992)
+R PMID:1304904
+A Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L.
+T Environment-specific amino acid substitution tables: tertiary templates
+ and prediction of protein folds
+J Protein Science 1, 216-226 (1992)
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+H QU_C930101
+D Cross-correlation coefficients of preference factors
+ main chain (Qu et al., 1993)
+R PMID:8381879
+A Qu, C., Lai, L., Xu, X. and Tang, Y.
+T Phyletic relationships of protein structures based on spatial prefernce
+ of residues
+J J. Mol. Evol. 36, 67-78 (1993)
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+//
+H QU_C930102
+D Cross-correlation coefficients of preference factors
+ side chain (Qu et al., 1993)
+R PMID:8381879
+A Qu, C., Lai, L., Xu, X. and Tang, Y.
+T Phyletic relationships of protein structures based on spatial prefernce
+ of residues
+J J. Mol. Evol. 36, 67-78 (1993)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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+//
+H QU_C930103
+D The mutant distance based on spatial preference factor (Qu et al., 1993)
+R PMID:8381879
+A Qu, C., Lai, L., Xu, X. and Tang, Y.
+T Phyletic relationships of protein structures based on spatial prefernce
+ of residues
+J J. Mol. Evol. 36, 67-78 (1993)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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+//
+H RISJ880101
+D Scoring matrix (Risler et al., 1988)
+R PMID:3221397
+A Risler, J.L., Delorme, M.O., Delacroix, H. and Henaut, A.
+T Amino acid substitutions in structurally related proteins
+ A pattern recognition approach
+ Determination of a new and efficient scoring matrix
+J J. Mol. Biol. 204, 1019-1029 (1988)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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+//
+H TUDE900101
+D isomorphicity of replacements (Tudos et al., 1990)
+R PMID:2279846
+A Tudos, E., Cserzo, M. and Simon, I.
+T Predicting isomorphic residue replacements for protein design
+J Int. J. Peptide Protein Res. 36, 236-239 (1990)
+* Diagonal elements are missing.
+* We use 100 as diagonal elements.
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+ -2. -4. 8. 1. -3. 0. -7. 4. -2. -18. -16. -2. -10. -2. 100.
+ 10. -10. 1. 7. -6. -7. -10. 9. -3. -17. -11. -10. -10. 0. 15. 100.
+ -3. -5. 12. 11. -4. -10. -12. -13. -7. -5. -11. -8. -8. 4. 2. 24. 100.
+ -12. -7. -6. -20. 8. -3. -10. -13. -6. 12. 8. -10. 12. 8. -9. -18. -8. 100.
+ -18. 0. -13. -22. 5. -23. -28. -18. 12. 29. 16. -21. 8. 24. -9. -16. -2. 6. 100.
+ -12. -18. -30. -32. 8. -12. -20. -14. -10. 46. 26. -14. 10. 16. -18. -16. -4. 14. 17. 100.
+//
+H AZAE970101
+D The single residue substitution matrix from interchanges of
+ spatially neighbouring residues (Azarya-Sprinzak et al., 1997)
+R PMID:9488136
+A Azarya-Sprinzak, E., Naor, D., Wolfson, H.J. and Nussinov, R.
+T Interchanges of spatially neighbouring residues in structurally conserved
+ environments.
+J Protein Engineering 10, 1109-1122 (1997)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 14
+ 1 16
+ 1 10 15
+ 0 13 16 26
+ 5 -9 -4 -8 18
+ 0 16 13 16 -10 21
+ 2 13 10 15 -8 17 11
+ 5 0 8 7 1 0 1 24
+ -2 4 5 8 -2 6 4 6 7
+ -6 -11 -11 -14 2 -12 -11 -10 -4 10
+ -2 -8 -9 -11 1 -9 -8 -9 -5 8 9
+ 1 21 12 16 -11 22 17 -1 3 -13 -10 28
+ 2 -1 -3 -7 0 -2 1 -3 -1 2 5 -4 2
+ -4 -8 -9 -10 2 -10 -7 -4 -1 6 5 -11 2 8
+ 2 2 11 11 0 1 5 13 4 -14 -12 5 -10 -6 51
+ 1 6 7 8 -1 6 6 8 3 -8 -7 6 -5 -5 6 9
+ -2 5 4 4 -5 6 3 1 4 -4 -6 7 -4 -4 5 5 10
+ -2 -3 -5 -5 -1 -3 -6 -1 3 4 2 -8 2 5 -5 -4 -2 8
+ -2 -1 -3 -4 -1 -3 -1 -2 0 2 0 -3 1 3 -5 -1 0 2 4
+ -5 -11 -11 -13 3 -12 -12 -8 -4 9 5 -14 0 5 -7 -6 -3 4 2 11
+//
+H AZAE970102
+D The substitution matrix derived from spatially conserved motifs
+ (Azarya-Sprinzak et al., 1997)
+R PMID:9488136
+A Azarya-Sprinzak, E., Naor, D., Wolfson, H.J. and Nussinov, R.
+T Interchanges of spatially neighbouring residues in structurally conserved
+ environments.
+J Protein Engineering 10, 1109-1122 (1997)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 8
+ 1 11
+ 0 7 11
+ 0 9 12 16
+ 2 -7 -5 -8 14
+ 1 12 10 13 -9 17
+ 1 10 8 10 -6 13 8
+ 1 0 7 8 0 0 0 18
+ -2 2 2 4 -1 2 1 5 5
+ -3 -10 -11 -12 4 -12 -10 -8 -3 11
+ 0 -7 -9 -10 2 -9 -7 -8 -4 8 10
+ 1 14 10 11 -10 16 13 0 2 -12 -9 20
+ 1 -2 -4 -6 1 -3 0 -5 -2 3 6 -5 4
+ -2 -8 -9 -9 3 -10 -7 -3 -1 7 6 -10 3 8
+ -1 1 8 7 -2 0 0 10 3 -9 -9 1 -9 -5 33
+ 0 4 6 6 -2 4 3 6 2 -7 -6 4 -5 -5 5 7
+ -2 2 2 3 -3 2 1 1 3 -2 -4 2 -3 -3 3 4 6
+ -1 -4 -4 -4 0 -5 -5 -1 -1 4 3 -7 2 4 -4 -3 -1 6
+ -1 -3 -4 -5 0 -4 -1 -1 0 3 2 -4 2 3 -4 -1 0 2 3
+ -4 -10 -11 -12 5 -12 -11 -7 -3 11 6 -13 1 7 -5 -5 -1 4 2 12
+//
+H RIER950101
+D Hydrophobicity scoring matrix (Riek et al., 1995)
+R PMID:7715195
+A Riek, R.P., Handschumacher, M.D., Sung, S.S., Tan, M., Glynias, M.J.,
+ Schluchter, M.D., Novotny, J. and Graham, R.M.
+T Evolutionary conservation of both the hydrophilic and hydrophobic nature of
+ transmembrane residues.
+J J. Theor. Biol. 172, 245-258 (1995)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 100
+ 13 100
+ 60 53 100
+ 33 81 73 100
+ 98 11 58 30 100
+ 64 49 96 68 62 100
+ 39 74 79 94 36 74 100
+ 96 17 64 36 94 68 43 100
+ 71 42 89 61 69 93 68 75 100
+ 91 4 51 23 93 55 29 87 62 100
+ 93 6 52 25 95 57 31 89 64 98 100
+ 35 78 75 98 33 71 96 39 64 26 27 100
+ 89 2 49 21 91 53 27 85 60 98 96 24 100
+ 87 0 47 19 89 51 26 83 58 96 94 22 98 100
+ 89 24 71 44 86 76 50 93 83 79 81 46 78 76 100
+ 94 19 66 39 91 71 45 98 78 84 86 41 83 81 95 100
+ 98 16 63 35 95 67 41 99 74 88 90 38 86 84 91 96 100
+ 98 11 58 31 99 63 37 94 69 93 94 33 91 89 87 92 96 100
+ 94 19 66 38 92 70 44 98 77 85 87 41 83 81 94 99 97 93 100
+ 94 7 54 26 96 58 33 90 65 97 99 29 95 93 83 88 91 96 88 100
+//
+H WEIL970101
+D WAC matrix constructed from amino acid comparative profiles (Wei et al., 1997)
+R PMID:9390315
+A Wei, L., Altman, R.B. and Chang, J.T.
+T Using the radial distributions of physical features to compare amino
+ acid environments and align amino acid sequences.
+J Pac. Symp. Biocomput. 1997 5, 465-476 (1997)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 4
+ -1 4
+ 0 0 4
+ -2 -1 0 4
+ 0 -1 0 -2 4
+ 0 0 1 -1 0 4
+ -3 -1 0 0 -2 0 4
+ -1 -1 0 -2 0 0 -2 4
+ 0 0 0 -1 0 0 -1 -1 4
+ 0 -2 -1 -4 0 0 -4 -2 -1 4
+ 0 -1 -1 -3 0 0 -3 -1 -1 1 4
+ -1 2 0 -1 -2 0 -1 -1 0 -2 -2 4
+ 1 0 0 -1 1 1 -1 0 0 2 2 0 4
+ 0 -2 -1 -4 0 0 -4 -2 0 0 1 -2 2 4
+ 0 0 0 -1 -1 0 -1 0 0 0 0 0 1 0 4
+ 0 -1 1 -1 0 0 -2 0 -1 -1 -1 0 0 -2 0 4
+ 0 0 1 -1 0 1 -1 0 -1 0 0 0 0 -2 0 1 4
+ 0 0 -1 -3 0 0 -2 -2 0 0 1 -2 2 2 0 -1 -1 4
+ 0 -1 0 -3 0 1 -4 -2 0 0 0 -2 0 1 -1 -1 -1 1 4
+ 1 -2 -1 -3 0 -1 -4 -2 -1 2 1 -3 1 0 0 -1 0 0 0 4
+//
+H WEIL970102
+D Difference matrix obtained by subtracting the BLOSUM62 from the WAC
+ matrix (Wei et al., 1997)
+R PMID:9390315
+A Wei, L., Altman, R.B. and Chang, J.T.
+T Using the radial distributions of physical features to compare amino
+ acid environments and align amino acid sequences.
+J Pac. Symp. Biocomput. 1997 5, 465-476 (1997)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 0
+ 0 -1
+ 2 0 -2
+ 0 1 -1 -2
+ 0 2 3 1 -5
+ 1 -1 1 -1 3 -1
+ -2 -1 0 -2 2 -2 -1
+ -1 1 0 -1 3 2 0 -2
+ 2 0 -1 0 3 0 -1 1 -4
+ 1 1 2 -1 1 3 -1 2 2 0
+ 1 1 2 1 1 2 0 3 2 -1 0
+ 0 0 0 0 1 -1 -2 1 1 1 0 -1
+ 2 1 2 2 2 1 1 3 2 1 0 1 -1
+ 2 1 2 -1 2 3 -1 1 1 0 1 1 2 -2
+ 1 2 2 0 2 1 0 2 2 3 3 1 3 4 -3
+ -1 0 0 -1 1 0 -2 0 0 1 1 0 1 0 1 0
+ 0 1 1 0 1 2 0 2 1 1 1 1 1 0 1 0 -1
+ 3 3 3 1 2 2 1 0 2 3 3 1 3 -1 4 2 1 -7
+ 2 1 2 0 2 2 -2 1 -2 1 1 0 1 0 2 1 1 -1 -3
+ 1 1 2 0 1 1 -2 1 2 -1 0 -1 0 1 2 1 0 3 1 0
+//
+H MEHP950101
+D (Mehta et al., 1995)
+R PMID:8580842
+A Mehta, P.K., Heringa, J. and Argos, P.
+T A simple and fast approach to prediction of protein secondary structure from
+ multiply aligned sequences with accuracy above 70%
+J Protein Science 4, 2517-2525 (1995)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 1.23
+ 1.17 1.06
+ 1.28 1.03 1.02
+ 1.31 1.18 1.08 1.11
+ 1.41 1.21 1.36 1.44 1.04
+ 1.31 1.10 1.20 1.25 1.49 1.16
+ 1.34 1.15 1.21 1.31 1.43 1.26 1.19
+ 1.11 0.99 0.96 1.02 1.36 1.11 1.06 0.86
+ 1.17 1.06 1.13 1.05 1.50 1.22 1.23 1.10 0.99
+ 1.08 0.91 0.89 0.93 1.24 1.02 0.96 0.79 0.86 0.90
+ 1.19 1.02 0.98 1.00 1.41 1.01 1.01 0.88 1.08 0.99 1.04
+ 1.29 1.11 1.14 1.18 1.31 1.21 1.22 1.05 1.10 0.94 1.07 1.13
+ 1.20 0.97 1.01 0.94 1.36 1.10 1.02 0.81 1.08 1.01 1.08 0.99 1.04
+ 0.94 0.74 0.83 0.79 1.16 0.88 0.91 0.68 0.94 0.74 0.90 0.78 0.91 0.82
+ 0.94 0.69 0.74 0.84 1.30 0.91 0.96 0.92 0.80 0.67 0.75 0.67 0.59 0.69 0.75
+ 1.17 0.90 1.01 0.97 1.33 1.09 1.02 0.94 1.03 0.89 1.01 0.98 0.59 0.78 0.79 0.93
+ 1.06 0.88 0.93 1.01 1.18 1.02 0.94 0.86 0.95 - 0.90 0.88 0.96 0.72 0.80 0.87 0.85
+ 0.90 0.63 0.88 0.87 0.78 0.95 0.86 0.58 0.92 0.53 0.72 0.74 0.75 0.66 0.40 0.69 0.74 0.91
+ 0.86 0.75 0.83 0.73 1.00 0.85 0.76 0.58 0.81 0.68 0.79 0.79 0.86 0.71 0.54 0.63 0.65 0.66 0.80
+ 1.09 0.98 0.96 1.01 1.33 1.06 1.04 0.95 1.01 0.83 0.88 0.99 1.02 0.76 0.77 0.93 0.84 0.60 0.67 0.83
+//
+H MEHP950102
+D (Mehta et al., 1995)
+R PMID:8580842
+A Mehta, P.K., Heringa, J. and Argos, P.
+T A simple and fast approach to prediction of protein secondary structure from
+ multiply aligned sequences with accuracy above 70%
+J Protein Science 4, 2517-2525 (1995)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 0.75
+ 0.80 0.90
+ 0.71 0.88 0.80
+ 0.56 0.63 0.69 0.66
+ 0.75 0.84 0.72 0.67 1.07
+ 0.68 0.83 0.71 0.64 0.65 0.80
+ 0.63 0.82 0.74 0.58 0.69 0.73 0.74
+ 0.83 0.84 0.71 0.61 0.80 0.78 0.87 0.97
+ 0.79 0.92 0.78 0.68 0.69 0.79 0.78 0.71 0.99
+ 1.11 1.23 1.12 1.06 0.96 1.10 1.15 1.25 1.24 1.33
+ 0.97 1.05 0.97 0.96 0.84 1.07 1.12 1.09 1.07 1.21 1.12
+ 0.65 0.84 0.72 0.64 0.79 0.75 0.78 0.76 0.82 1.11 0.99 0.78
+ 0.97 1.14 0.92 0.93 0.97 0.97 0.96 1.18 0.96 1.16 1.06 1.03 1.05
+ 1.16 1.26 1.11 1.17 1.04 1.07 1.17 1.30 1.05 1.54 1.27 1.11 1.21 1.33
+ 0.77 1.03 0.91 0.75 0.67 0.83 0.75 0.75 0.83 1.30 1.21 0.92 1.34 1.07 0.82
+ 0.80 0.99 0.84 0.77 0.81 0.85 0.92 0.91 0.85 1.24 1.09 0.89 1.15 1.28 0.87 0.96
+ 0.97 1.08 0.99 0.88 0.93 1.02 1.11 1.03 0.91 1.27 1.18 1.09 1.11 1.32 0.93 1.10 1.16
+ 1.18 1.33 0.95 1.04 1.47 1.17 1.33 1.28 1.18 1.71 1.37 1.11 1.35 1.31 1.09 1.34 1.42 1.22
+ 1.23 1.25 1.08 1.12 1.22 1.11 1.31 1.27 1.23 1.51 1.41 1.18 1.23 1.34 1.29 1.41 1.46 1.29 1.31
+ 1.05 1.08 1.05 0.99 0.91 1.03 1.08 1.09 1.13 1.42 1.35 1.06 1.22 1.51 1.13 1.21 1.27 1.63 1.60 1.41
+//
+H MEHP950103
+D (Mehta et al., 1995)
+R PMID:8580842
+A Mehta, P.K., Heringa, J. and Argos, P.
+T A simple and fast approach to prediction of protein secondary structure from
+ multiply aligned sequences with accuracy above 70%
+J Protein Science 4, 2517-2525 (1995)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 0.86
+ 1.02 1.06
+ 0.95 1.19 1.36
+ 1.23 1.41 1.52 1.43
+ 0.49 0.82 0.70 0.60 0.71
+ 0.92 1.13 1.13 1.17 0.51 0.96
+ 0.96 1.02 1.04 1.17 0.57 0.96 1.01
+ 1.11 1.41 1.80 1.88 0.51 1.22 1.15 1.50
+ 1.04 1.02 1.18 1.63 0.39 0.92 0.91 1.40 1.05
+ 0.51 0.69 1.00 1.04 0.43 0.70 0.74 0.98 0.81 0.58
+ 0.57 0.82 1.13 1.09 0.28 0.80 0.69 1.10 0.62 - 0.61
+ 1.06 1.08 1.30 1.38 0.68 1.02 0.93 1.43 1.15 0.91 0.84 1.10
+ 0.53 0.74 1.17 1.34 0.10 0.79 1.02 1.07 0.88 0.59 0.63 0.97 0.77
+ 0.79 1.09 1.19 1.17 0.46 1.16 0.85 1.16 1.05 0.42 0.63 1.33 0.74 0.83
+ 1.69 1.76 1.91 2.04 0.96 1.63 1.71 1.80 1.96 1.18 1.19 2.08 1.28 1.66 2.13
+ 1.04 1.29 1.35 1.63 0.55 1.12 1.13 1.37 1.29 0.74 0.74 1.32 0.79 0.94 1.87 1.29
+ 0.92 1.13 1.23 1.27 0.68 0.89 0.89 1.30 1.33 0.79 0.84 1.12 0.83 0.97 1.71 1.11 1.08
+ 0.86 1.22 1.46 1.24 0.47 0.73 0.61 1.46 0.78 0.56 0.88 1.44 0.83 1.19 2.39 1.01 0.69 0.78
+ 0.84 1.10 1.27 1.46 0.48 1.14 0.91 1.51 0.97 0.65 0.57 1.13 0.84 0.99 1.54 1.03 0.85 1.22 0.83
+ 0.65 0.86 0.99 0.99 0.32 0.77 0.71 0.90 0.66 0.45 0.49 0.89 0.44 0.44 1.32 0.70 0.78 0.57 0.48 0.63
+//
+H KAPO950101
+D (Kapp et al., 1995)
+R PMID:8535255
+A Kapp, O.H., Moens, L., Vanfleteren, J., Trotman, C.N., Suzuki, T. and
+ Vinogradov, S.N.
+T Alignment of 700 globin sequences: extent of amino acid substitution and its
+ correlation with variation in volume
+J Protein Science 4, 2179-2190 (1995)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 23.40
+ 16.80 29.50
+ 17.10 17.10 27.40
+ 18.20 18.20 21.40 25.90
+ 21.50 14.40 14.70 14.00 31.90
+ 17.20 19.60 18.60 22.20 13.80 96.50
+ 18.10 18.70 20.00 22.80 12.20 20.40 26.50
+ 19.90 16.10 18.10 18.70 15.00 16.30 19.30 26.80
+ 11.50 13.70 18.90 17.20 13.50 21.20 15.70 12.20 30.80
+ 17.20 14.30 14.80 13.70 20.90 15.80 14.90 14.70 12.40 24.70
+ 13.60 12.20 11.70 12.50 15.50 13.30 11.40 11.50 9.07 21.00 24.80
+ 17.10 21.90 17.70 18.20 9.83 22.00 19.20 15.60 15.50 14.20 12.10 26.40
+ 16.20 15.50 13.70 15.50 19.80 17.80 15.20 15.00 11.40 20.90 22.40 15.40 25.90
+ 11.90 10.10 11.40 9.04 13.50 11.50 9.24 9.84 10.70 18.40 20.60 9.68 20.20 27.10
+ 17.70 15.70 14.60 19.40 5.43 18.00 19.10 17.00 11.70 9.35 7.28 16.80 11.60 3.14 32.20
+ 20.40 17.50 20.90 19.10 17.70 17.60 17.70 20.20 13.80 14.60 12.20 16.60 14.70 9.65 17.90 25.40
+ 18.10 20.60 20.20 19.00 16.20 17.40 18.80 18.20 14.80 17.50 14.30 17.60 16.90 12.80 14.90 19.50 26.10
+ 10.10 9.94 7.74 9.08 9.56 16.60 15.30 7.20 0.00 10.40 14.70 7.79 18.50 19.30 9.85 9.70 17.20 33.80
+ 15.30 13.80 20.10 14.90 17.30 14.60 12.70 13.70 19.40 17.60 17.90 14.70 20.00 22.60 6.99 14.40 17.70 19.50 29.20
+ 16.70 14.40 14.80 15.10 21.40 15.20 15.10 14.50 12.90 22.20 18.90 13.50 19.10 17.20 11.10 15.10 17.90 11.60 16.50 25.00
+//
+H VOGG950101
+D (Vogt et al., 1995)
+R PMID:7602593
+A Vogt G, Etzold T, Argos P
+T An assessment of amino acid exchange matrices in aligning protein sequences:
+ the twilight zone revisited
+J J. Mol. Biol. 249, 816-831 (1995)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 7.6
+ 4.6 9.9
+ 4.9 5.5 9.0
+ 4.9 4.9 7.4 9.9
+ 5.7 3.0 3.4 2.0 16.7
+ 5.0 6.7 5.9 6.1 2.8 7.9
+ 5.2 5.6 6.1 7.9 2.2 6.9 8.8
+ 5.7 4.2 5.6 5.3 3.2 4.2 4.4 11.8
+ 4.4 5.8 6.4 5.6 3.9 6.4 5.6 3.8 11.2
+ 4.4 2.8 2.4 1.4 4.1 3.3 2.5 0.7 3.0 9.2
+ 4.0 3.0 2.2 1.2 3.7 3.6 2.4 0.8 3.3 8.0 9.2
+ 4.8 7.9 6.0 5.7 2.4 6.7 6.4 4.1 5.8 3.1 3.1 8.4
+ 4.5 3.5 3.0 2.2 4.3 4.2 3.2 1.7 3.9 7.7 8.0 3.8 9.5
+ 2.9 2.0 2.1 0.7 4.4 2.6 1.3 0.0 5.1 6.2 7.2 1.9 6.8 12.2
+ 5.5 4.3 4.3 4.5 2.1 5.0 4.7 3.6 4.1 2.6 2.9 4.6 2.8 1.4 12.8
+ 6.3 5.0 6.1 5.7 5.3 5.4 5.4 5.6 5.0 3.4 3.1 5.3 3.8 2.4 5.6 7.4
+ 5.8 5.0 5.7 5.2 4.7 5.2 5.1 4.1 4.9 4.6 3.9 5.3 4.6 3.0 5.3 6.7 7.7
+ 1.6 3.6 1.6 0.0 4.2 2.5 0.9 1.2 4.4 3.4 4.5 1.7 4.2 8.8 0.2 1.9 1.7 19.4
+ 3.0 3.4 3.8 2.4 4.7 3.5 2.5 1.2 7.4 4.5 5.2 3.1 5.0 10.3 2.1 3.3 3.3 9.3 13.0
+ 5.3 3.2 3.0 2.3 5.2 3.7 3.3 1.9 3.2 8.3 7.0 3.5 6.8 5.3 3.4 4.2 5.2 2.6 4.1 8.6
+//
+H KOSJ950101
+D Context-dependent optimal substitution matrices for exposed helix
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 55.7 3.0 3.0 3.0 3.0 0.4 0.1 3.0 3.0 2.1 3.0 3.0 3.0 0.1 1.9 2.2 2.4 3.0 0.8 1.3 3.0
+ 25.6 47.2 1.5 1.0 0.7 0.3 1.9 2.3 4.3 0.6 0.2 2.0 0.8 0.1 0.3 3.1 2.8 3.7 0.4 0.1 2.0
+ 14.8 0.9 62.7 1.3 0.4 0.3 4.6 0.3 0.1 1.9 0.5 2.2 5.1 0.6 0.2 0.4 1.9 1.5 0.4 0.2 0.3
+ 15.2 0.2 0.5 48.2 3.3 0.1 3.2 4.9 0.1 1.7 1.7 1.4 3.0 0.6 1.0 0.1 9.7 2.7 0.7 1.1 1.5
+ 15.9 3.9 1.4 7.3 52.1 0.3 0.9 11.0 2.0 0.4 0.6 0.1 0.6 0.5 0.1 0.6 2.9 0.1 0.1 0.1 0.1
+ 9.4 1.5 0.1 1.5 1.6 73.6 0.1 2.6 0.1 0.1 2.1 4.0 0.1 0.1 0.8 0.7 0.3 2.2 0.1 0.1 0.1
+ 0.1 8.4 5.7 2.0 4.5 0.3 47.5 8.2 0.9 1.6 0.1 3.4 7.8 0.5 0.1 0.7 5.3 2.2 0.2 0.7 0.5
+ 5.2 5.3 1.0 1.5 8.6 0.1 4.9 56.8 1.5 1.0 0.3 0.9 5.8 0.1 0.2 1.6 2.1 2.4 0.2 0.1 1.1
+ 20.2 2.0 1.2 2.3 3.3 0.1 0.4 0.1 6 4.8 0.8 0.1 0.1 1.4 0.3 0.6 0.1 1.2 0.6 0.1 0.5
+ 13.3 0.3 4.7 7.5 1.8 0.1 4.4 0.7 0.1 56.9 0.6 0.1 2.3 1.2 2.2 0.1 0.1 0.1 0.1 4.4 0.1
+ 18.4 0.1 0.1 0.1 0.1 0.1 0.4 0.1 0.1 0.1 5 2.6 10.8 1.2 3.5 1.3 0.1 0.1 3.4 0.1 0.1
+ 15.4 0.8 0.6 0.1 0.1 0.1 1.1 0.1 0.2 0.2 3.4 67.3 0.6 3.5 3.5 0.1 0.1 0.7 0.1 0.1 2.9
+ 5.5 4.1 8.3 3.5 1.3 0.1 3.7 5.8 1.1 1.2 0.3 1.0 55.3 0.4 0.1 0.2 2.7 3.7 0.1 0.2 1.9
+ 0.7 5.2 4.3 3.2 0.1 0.5 2.0 5.4 1.5 0.1 7.4 9.3 3.0 44.0 1.3 0.1 2.4 4.3 0.1 0.1 6.0
+ 14.3 1.7 0.1 0.3 0.5 1.0 0.8 0.5 0.1 0.1 0.7 1.5 0.1 0.4 67.6 0.1 2.1 1.8 0.1 7.1 0.1
+ 13.6 1.7 1.0 0.5 3.1 0.1 0.6 0.6 0.1 1.0 0.8 1.5 2.7 0.1 0.1 65.9 5.2 1.8 0.1 0.3 0.2
+ 6.0 18.1 1.2 1.6 2.7 0.9 0.4 2.4 5.0 1.1 0.6 0.2 3.5 0.1 0.1 0.5 46.8 7.5 0.1 0.5 1.4
+ 18.4 7.5 0.3 2.5 0.7 0.1 0.4 0.2 1.8 0.8 2.4 4.8 1.2 1.0 0.1 0.2 6.3 48.8 0.1 0.6 2.7
+ 21.7 0.3 0.1 0.1 0.1 0.1 1.8 0.1 0.1 0.1 0.1 2.1 2.5 0.1 4.3 0.1 0.1 0.6 64.6 2.3 0.1
+ 8.3 0.5 0.1 0.1 0.1 0.1 0.1 1.1 0.1 3.4 2.4 6.6 0.9 0.2 8.7 0.3 0.9 1.5 1.0 60.8 3.8
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+//
+H KOSJ950102
+D Context-dependent optimal substitution matrices for exposed beta
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 72.6 0.8 3.0 0.1 2.3 0.3 1.9 1.3 0.8 0.1 0.3 2.3 3.0 0.5 0.8 1.6 3.0 1.5 0.1 0.8 3.0
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+ 3.0 2.1 3.0 53.5 11.8 0.1 2.9 0.1 1.8 2.5 0.1 1.3 4.4 0.1 0.3 1.2 9.0 1.6 0.1 1.9 0.1
+ 14.6 1.9 0.1 6.1 58.5 0.1 2.8 5.8 4.0 0.1 0.9 0.1 1.7 0.3 0.5 0.9 1.9 0.1 0.1 0.8 0.1
+ 20.4 1.9 0.1 0.1 1.7 49.5 1.6 0.1 1.7 0.1 4.0 0.1 0.1 0.1 8.4 0.1 2.0 1.9 0.1 3.9 3.5
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+ 5.0 1.5 0.6 1.7 8.4 0.1 2.0 66.4 0.6 1.1 0.5 0.7 4.2 0.1 0.1 0.6 3.3 1.5 0.4 0.1 2.0
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+ 0.1 1.2 10.0 5.7 0.1 0.7 0.3 4.2 0.8 45.8 0.1 1.7 1.8 1.3 0.1 0.1 8.3 10.8 0.1 4.6 2.8
+ 0.1 0.1 2.5 0.5 0.1 0.5 0.1 0.1 0.1 0.1 54.4 5.4 1.1 2.9 4.5 0.3 0.1 3.9 0.1 1.5 22.8
+ 14.2 1.0 0.6 0.7 0.1 0.1 2.1 0.5 0.1 1.8 5.7 60.3 0.9 2.6 2.9 1.7 1.2 0.1 0.1 0.7 3.4
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+ 12.6 6.3 3.2 0.1 0.1 0.1 2.7 2.6 0.1 0.1 4.9 2.3 7.8 46.5 1.0 0.1 3.9 2.2 0.1 0.1 4.2
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+ 16.8 6.2 0.1 0.6 0.7 0.1 0.7 0.1 0.8 0.1 0.1 1.3 0.5 0.1 0.1 67.1 2.7 2.5 0.1 0.3 0.1
+ 30.0 2.0 0.1 1.7 0.1 0.1 0.1 1.0 4.6 0.5 0.2 0.7 0.9 0.1 0.1 2.8 49.8 4.5 0.1 0.1 1.5
+ 4.7 3.4 1.5 2.0 2.6 0.1 0.4 3.9 0.6 0.1 1.8 1.4 4.7 0.1 0.1 0.1 8.4 59.0 0.3 0.5 5.0
+ 5.9 0.1 0.1 0.1 0.1 0.1 0.1 2.3 2.0 0.1 0.8 2.9 0.1 0.1 4.7 0.1 1.0 0.1 75.5 2.9 2.5
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+//
+H KOSJ950103
+D Context-dependent optimal substitution matrices for exposed turn
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 69.2 3.0 1.3 3.0 0.9 0.7 1.9 3.0 3.0 1.6 0.9 1.3 0.8 0.6 1.1 1.4 1.0 3.0 0.1 1.4 0.8
+ 31.5 46.2 1.1 0.8 0.8 0.1 0.3 0.3 2.5 0.1 2.0 2.3 0.9 0.4 0.3 0.2 4.4 2.0 0.4 0.1 4.1
+ 5.9 1.3 64.3 2.5 1.7 0.5 2.6 0.1 2.4 2.1 0.2 0.2 8.7 0.4 0.4 0.6 3.5 1.2 0.6 0.5 1.1
+ 9.3 1.7 1.2 55.1 6.4 0.5 1.3 1.7 4.4 0.8 0.1 0.4 3.8 0.7 0.3 0.2 8.9 1.3 0.3 1.4 1.0
+ 2.1 2.9 0.2 9.4 61.5 0.1 1.9 9.2 3.4 0.4 0.1 0.6 3.1 0.1 0.1 1.4 2.5 1.4 0.1 0.2 0.3
+ 17.0 7.1 0.1 0.1 0.1 66.1 0.1 0.1 2.0 0.8 0.4 0.7 0.1 0.3 3.0 0.1 2.6 0.1 0.1 0.3 0.1
+ 9.0 4.9 3.9 3.3 2.3 0.1 48.8 4.8 1.7 2.0 1.6 4.3 4.7 0.8 0.4 2.1 1.6 3.3 0.1 0.1 0.9
+ 7.8 3.8 1.0 1.1 7.0 0.1 3.5 57.8 1.1 1.5 1.1 1.7 4.5 0.4 0.4 1.7 3.3 1.0 0.4 0.3 1.0
+ 6.5 2.8 0.4 2.9 2.8 0.1 0.8 1.9 74.8 0.4 0.1 0.1 1.7 0.1 0.4 0.3 2.2 1.9 0.1 0.1 0.3
+ 14.9 1.8 0.1 4.0 0.1 0.6 2.9 1.4 0.7 56.0 0.6 0.4 2.9 0.2 2.8 2.2 2.2 0.1 0.9 5.9 0.1
+ 10.4 0.1 0.1 0.1 0.1 0.5 0.1 0.1 0.1 0.1 65.5 7.0 0.1 2.4 0.8 0.5 0.1 2.7 0.7 0.9 8.8
+ 9.1 0.7 3.1 0.3 0.1 0.1 0.1 0.7 0.3 0.4 3.7 68.3 0.8 4.4 1.7 0.6 0.3 1.0 1.0 1.3 2.8
+ 2.5 4.7 8.1 2.6 1.3 0.1 5.9 4.4 1.3 1.6 0.1 1.4 58.1 0.5 0.5 0.5 2.9 2.0 0.1 0.5 1.5
+ 15.2 1.3 0.8 0.1 0.1 0.4 0.1 0.1 0.1 0.6 4.7 6.8 0.8 61.0 2.9 0.1 0.1 1.1 0.1 2.8 1.8
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+ 4.4 7.5 1.7 1.0 1.2 0.1 0.4 2.2 0.7 0.4 0.9 0.8 2.3 0.4 0.1 70.2 3.0 2.4 0.1 0.2 0.6
+ 2.5 10.8 1.1 2.5 5.3 0.9 1.7 1.8 5.1 1.0 0.4 1.4 3.1 0.4 0.6 1.8 49.6 8.8 0.1 0.8 0.7
+ 15.3 2.9 1.3 2.9 1.5 0.1 1.5 1.5 0.9 0.2 2.0 1.0 1.9 0.6 0.1 0.5 9.5 54.0 0.3 0.1 2.8
+ 10.5 0.1 0.1 0.1 0.1 0.7 0.1 0.1 0.1 0.1 0.1 0.3 0.1 0.1 0.1 1.0 0.1 0.1 77.0 10.5 0.1
+ 13.0 0.1 0.4 0.1 0.1 0.1 0.1 0.7 0.1 0.9 1.2 2.8 0.5 0.1 8.4 0.3 0.1 0.4 0.1 71.2 0.5
+ 8.1 2.7 0.2 0.3 0.1 1.8 0.8 0.1 1.0 0.5 10.3 4.5 1.3 1.1 2.7 0.1 0.7 2.1 0.3 1.9 60.1
+//
+H KOSJ950104
+D Context-dependent optimal substitution matrices for exposed coil
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 50.4 3.0 3.0 2.5 3.0 1.1 3.0 3.0 3.0 1.8 3.0 3.0 3.1 1.4 1.5 3.0 3.0 3.0 0.5 1.8 3.0
+ 29.8 49.8 0.1 0.5 0.8 0.1 2.1 0.3 4.1 0.6 0.5 1.1 0.3 0.1 0.1 2.2 3.7 1.4 0.2 0.1 3.1
+ 15.0 1.2 60.3 1.2 0.1 0.1 1.2 0.7 0.1 2.5 0.9 0.9 6.6 0.1 0.1 2.1 2.5 3.1 0.6 0.9 0.7
+ 8.3 1.6 2.6 50.6 5.5 0.5 2.0 3.2 2.2 2.7 0.9 1.0 4.7 0.9 0.3 0.1 6.8 3.9 0.1 1.2 1.4
+ 9.1 1.6 0.6 7.8 62.7 0.1 2.5 6.1 1.3 0.1 0.4 0.5 1.4 0.3 0.2 1.4 1.8 1.4 0.1 1.1 0.3
+ 23.2 12.9 0.2 0.1 1.5 58.1 0.1 1.2 0.1 0.1 2.0 0.1 0.1 0.8 0.1 0.1 0.1 0.3 0.1 0.1 0.1
+ 28.1 0.1 2.2 2.0 0.1 0.1 44.4 9.2 0.1 1.4 0.6 0.4 3.1 1.5 0.1 0.1 1.6 3.6 0.1 0.7 1.6
+ 22.2 5.1 0.5 0.5 4.3 0.1 3.0 57.1 1.4 0.7 0.5 0.6 1.1 0.1 0.1 0.1 1.6 0.9 0.1 0.1 1.0
+ 18.4 1.5 0.3 1.4 1.7 0.4 0.3 0.9 70.2 0.4 0.1 0.2 0.4 0.2 0.3 0.2 2.1 0.8 0.1 0.3 0.4
+ 27.6 1.2 0.5 0.1 4.2 0.1 2.6 1.0 0.1 50.8 0.1 0.1 1.9 0.3 0.9 3.9 4.8 0.1 0.1 0.9 0.1
+ 30.9 1.2 0.1 0.1 0.1 0.1 0.1 0.7 1.6 0.9 41.7 3.8 2.2 0.1 0.4 1.3 0.1 0.8 0.7 0.5 13.6
+ 18.9 0.7 1.0 0.4 0.2 0.3 2.1 0.4 0.4 0.6 6.0 57.6 0.1 3.3 3.8 1.3 0.1 0.5 0.1 0.1 2.9
+ 9.3 3.5 6.0 2.2 3.3 0.1 3.9 4.4 1.8 0.8 0.1 2.5 52.1 0.5 0.8 2.6 3.2 2.6 0.1 0.1 1.0
+ 22.9 0.1 0.1 0.1 0.1 0.1 0.1 0.3 0.1 1.0 7.9 9.1 1.0 45.8 2.2 1.7 0.1 6.3 0.1 0.1 2.2
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+ 15.4 6.7 0.8 0.2 0.3 0.1 1.3 2.0 1.3 0.2 0.1 0.6 0.4 0.1 0.1 64.2 3.6 0.6 0.1 0.7 1.9
+ 13.4 5.0 0.9 3.6 3.5 1.8 1.0 1.6 3.3 0.1 0.3 0.3 0.8 0.1 0.6 3.5 48.7 8.7 0.4 0.3 2.6
+ 16.3 4.5 0.1 2.3 0.6 0.4 1.7 0.5 0.6 0.4 2.4 1.9 1.0 0.1 0.6 2.6 8.9 51.4 0.1 0.4 4.0
+ 15.9 0.1 0.1 1.1 0.1 0.1 0.1 0.1 0.1 0.1 3.2 0.1 0.6 1.8 2.7 0.1 0.2 0.1 73.5 1.4 0.1
+ 15.5 0.4 0.1 0.1 0.1 0.1 0.1 0.1 0.6 0.6 0.1 2.5 0.1 0.6 8.4 0.1 0.1 0.6 1.0 68.7 1.6
+ 25.4 1.4 0.1 0.7 0.4 0.4 0.6 0.1 0.1 0.1 8.0 4.3 1.3 1.1 1.5 0.1 0.9 2.5 0.1 0.1 51.9
+//
+H KOSJ950105
+D Context-dependent optimal substitution matrices for buried helix
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 61.0 3.0 1.8 4.0 1.7 3.0 2.3 0.5 3.0 0.1 3.0 3.6 0.5 3.0 1.7 0.9 1.9 3.0 0.5 0.8 0.6
+ 1.3 76.5 0.6 0.1 0.2 0.4 0.7 1.8 2.5 0.1 0.6 1.7 0.8 0.5 0.4 0.7 6.6 1.6 0.1 0.8 2.8
+ 2.6 1.3 79.9 0.6 0.1 0.3 3.1 1.3 0.1 1.2 0.1 0.9 4.6 0.1 0.4 0.5 2.6 0.9 0.1 0.3 0.1
+ 7.6 3.2 0.1 70.8 3.8 0.6 0.1 2.5 1.4 0.1 0.9 0.1 1.0 0.1 0.1 0.5 3.2 3.5 0.1 1.4 0.1
+ 3.1 2.9 0.4 1.2 78.5 0.1 0.1 5.6 0.1 0.1 0.4 0.6 2.0 0.1 0.3 1.1 2.3 0.9 0.1 0.8 0.1
+ 7.9 7.5 0.9 0.1 1.4 56.1 1.5 0.7 4.2 0.1 2.3 0.8 0.1 1.8 1.1 0.1 4.4 2.1 0.9 0.1 6.6
+ 4.3 2.9 1.7 2.6 2.8 0.1 74.3 1.5 0.3 3.4 0.1 0.1 3.2 0.9 0.1 0.5 0.5 1.1 0.5 0.1 0.1
+ 2.4 1.4 0.1 0.2 1.5 0.2 4.4 80.7 1.3 0.1 1.1 2.8 2.5 0.1 0.1 0.1 0.7 0.1 0.1 0.6 0.6
+ 2.3 7.0 0.8 1.3 0.5 0.2 1.3 1.8 80.3 0.3 0.1 0.3 0.7 0.1 0.1 0.1 1.6 1.1 0.1 0.1 0.9
+ 0.1 0.9 1.9 1.0 0.4 0.1 2.9 1.0 0.1 85.0 0.1 0.1 2.2 0.6 1.6 0.5 0.9 1.1 0.1 0.1 0.6
+ 1.9 1.1 0.7 0.3 0.2 0.1 0.1 0.2 0.5 0.1 75.2 7.3 0.3 2.3 1.3 0.1 0.5 1.8 0.2 0.4 6.3
+ 1.0 0.7 0.2 0.5 0.1 0.4 0.6 0.2 0.1 0.4 5.5 78.6 0.7 3.0 3.3 0.1 0.6 0.2 0.1 0.6 3.7
+ 1.5 0.1 5.3 3.4 0.1 0.1 0.9 2.8 0.8 0.1 0.1 4.2 73.1 2.3 0.1 0.1 1.1 1.5 0.1 1.4 2.0
+ 2.9 2.6 0.1 0.5 0.1 0.4 1.1 0.1 0.6 0.1 5.6 11.9 0.1 65.8 2.6 0.1 0.1 2.7 0.9 0.1 2.9
+ 1.2 0.4 0.1 0.1 0.3 0.1 0.1 0.2 0.2 0.4 0.5 6.5 0.1 0.5 78.0 0.3 0.3 0.5 2.9 7.1 1.0
+ 3.1 0.1 0.1 0.8 0.1 0.1 1.1 1.2 0.8 1.0 0.7 0.1 0.2 0.1 0.1 85.9 1.8 1.9 0.1 0.1 1.8
+ 2.2 4.9 1.0 2.7 0.1 2.1 1.8 0.1 2.7 0.1 0.6 0.6 0.1 0.6 0.8 0.3 73.5 5.8 0.1 0.1 0.6
+ 4.3 4.1 1.6 0.1 0.3 0.4 0.4 0.9 0.7 0.1 0.1 2.2 1.0 0.5 0.5 1.1 5.2 72.1 0.1 0.1 5.0
+ 1.0 0.3 0.4 0.1 1.1 0.1 0.1 0.1 0.1 0.1 0.1 1.2 1.7 0.1 0.1 0.4 0.7 0.1 91.3 1.2 1.2
+ 0.9 1.4 0.8 0.8 0.1 0.6 0.2 0.6 0.1 2.3 0.5 4.3 0.7 1.4 8.2 0.1 0.6 0.3 0.4 76.6 0.1
+ 0.3 7.2 0.6 0.2 0.4 0.8 0.4 0.5 0.1 0.4 13.4 5.9 0.1 2.2 0.6 0.1 0.1 3.1 0.1 0.1 64.2
+//
+H KOSJ950106
+D Context-dependent optimal substitution matrices for buried beta
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 56.4 3.0 2.1 1.7 1.6 3.0 1.7 2.1 3.0 0.9 3.0 3.0 1.1 1.1 2.0 3.0 3.0 3.0 0.7 1.7 3.0
+ 5.8 66.6 0.5 0.9 1.5 0.3 0.6 1.7 3.7 1.0 0.4 0.3 1.0 0.1 0.1 2.6 7.3 3.7 0.1 0.2 2.4
+ 16.1 0.1 72.6 0.1 0.1 0.1 0.8 0.1 2.5 0.1 0.7 1.0 3.0 0.8 0.1 0.9 0.1 2.0 0.1 0.1 0.1
+ 9.5 0.1 1.5 70.8 4.2 0.1 1.3 0.1 1.2 1.6 0.5 0.1 2.8 0.1 0.1 1.1 2.6 1.9 0.7 0.1 0.8
+ 11.0 0.1 0.2 2.9 80.8 0.1 0.2 1.0 1.2 0.1 0.6 0.9 0.1 0.1 0.1 0.1 0.6 1.3 0.1 0.1 0.1
+ 12.4 5.9 0.4 0.4 0.8 65.6 0.1 0.8 1.2 0.7 2.5 3.0 0.1 0.4 1.2 0.5 3.0 1.9 0.1 0.1 0.1
+ 10.9 0.1 3.1 1.9 0.1 0.1 71.6 3.3 0.1 0.1 0.1 3.0 2.6 1.4 0.4 0.6 0.1 0.6 0.1 0.7 0.5
+ 14.3 0.9 1.2 1.0 4.4 0.1 2.3 67.9 2.3 0.1 0.1 0.7 1.7 0.1 0.4 0.1 0.2 0.1 0.1 1.0 2.3
+ 5.8 2.8 0.1 0.1 0.7 0.1 0.1 0.1 87.6 0.6 0.1 0.1 0.1 0.1 0.1 0.3 1.4 0.3 0.1 0.1 0.4
+ 6.3 0.1 5.0 1.3 2.2 0.6 3.0 2.5 0.1 70.9 0.1 1.6 0.5 0.9 1.0 0.5 2.3 0.1 0.9 1.1 0.1
+ 3.2 0.4 0.4 0.3 0.1 0.4 0.1 0.1 0.1 0.1 64.4 8.9 0.2 2.0 2.3 0.4 0.7 1.6 0.4 0.3 14.4
+ 5.8 0.6 0.1 0.1 0.1 0.2 0.1 0.3 0.3 0.1 4.4 77.6 0.1 2.8 2.2 0.2 0.1 0.3 0.3 0.8 4.4
+ 11.0 0.6 10.7 0.1 0.1 0.1 2.2 0.2 0.1 1.5 1.5 0.7 67.7 0.1 0.1 0.4 0.7 1.7 0.1 0.4 0.9
+ 4.9 3.1 0.1 0.6 0.4 0.6 2.8 0.1 0.5 0.1 4.4 9.4 0.1 63.4 3.1 0.7 0.1 2.5 0.1 0.5 3.6
+ 3.4 0.2 0.1 0.1 0.1 0.3 0.1 0.1 0.3 0.4 2.4 3.0 0.2 1.1 79.7 0.1 0.6 0.7 1.2 5.2 1.7
+ 16.2 1.8 0.5 0.1 0.1 0.1 1.3 0.7 0.5 0.1 0.1 0.3 0.7 0.1 0.1 73.3 4.4 0.8 0.1 0.1 0.1
+ 13.9 2.5 3.0 2.8 1.1 0.3 1.1 1.4 3.7 0.5 0.1 0.1 0.8 0.5 0.8 0.9 63.3 3.4 0.1 0.1 0.5
+ 8.9 2.9 0.4 0.7 0.1 0.4 1.0 1.8 0.6 0.3 2.0 0.6 1.6 0.7 0.1 0.4 4.6 70.2 0.1 0.7 2.5
+ 4.6 0.1 0.6 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0.1 0.1 0.1 0.6 1.2 0.1 0.5 0.1 90.5 2.2 0.1
+ 4.0 0.1 0.6 1.5 0.1 1.0 0.3 0.1 0.1 1.3 0.5 0.7 0.4 0.1 6.3 0.6 1.1 0.6 0.8 80.9 0.1
+ 3.9 2.4 0.3 0.1 0.4 0.8 0.2 0.1 0.1 0.1 9.6 3.0 0.1 0.2 0.6 0.3 1.1 2.1 0.1 0.3 75.0
+//
+H KOSJ950107
+D Context-dependent optimal substitution matrices for buried turn
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 86.4 1.4 0.7 0.4 1.5 0.5 0.6 0.1 2.5 0.1 0.1 0.5 0.2 0.2 0.8 0.6 0.5 0.7 0.1 0.5 1.7
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+//
+H KOSJ950108
+D Context-dependent optimal substitution matrices for buried coil
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 74.9 3.0 0.2 0.6 2.2 1.2 1.5 1.4 1.5 0.4 0.8 2.5 0.7 0.5 1.0 1.6 1.7 0.9 0.1 0.7 2.5
+ 7.2 68.0 0.6 0.5 0.5 1.0 0.2 0.1 5.5 0.1 0.4 0.5 0.9 0.5 0.4 1.8 5.7 4.4 0.1 0.1 2.1
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+ 7.4 1.7 0.4 4.7 75.7 0.1 0.1 3.0 0.2 0.5 1.0 0.3 0.5 0.1 0.1 0.9 1.9 0.4 0.1 1.8 0.1
+ 5.3 9.2 0.1 1.2 0.1 64.4 0.7 1.4 1.4 0.1 1.4 1.3 0.1 3.2 2.0 0.1 3.5 0.8 1.2 2.1 1.4
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+ 2.2 1.4 0.4 2.6 0.8 0.8 1.3 0.8 1.3 0.7 0.9 0.1 0.9 0.7 0.1 0.7 5.3 76.9 0.1 0.5 2.3
+ 0.1 0.1 0.9 0.1 0.1 0.1 0.1 0.1 0.1 0.1 2.2 1.7 0.9 0.1 6.9 0.1 0.1 0.1 82.1 4.2 1.5
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+//
+H KOSJ950109
+D Context-dependent optimal substitution matrices for alpha helix
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 70.7 1.7 2.1 2.5 2.0 2.2 1.8 0.7 2.7 1.7 1.9 1.1 0.3 0.8 1.0 2.4 0.2 2.6 1.1 0.3 0.1
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+ 13.8 1.8 0.6 60.2 3.7 0.2 1.4 3.7 0.9 1.2 0.9 0.4 2.0 0.7 0.5 0.1 4.0 1.8 0.3 1.1 0.8
+ 11.0 2.7 1.1 4.1 61.0 0.3 0.5 9.8 1.4 0.5 0.4 0.4 1.6 0.3 0.3 1.2 2.0 1.0 0.2 0.3 0.0
+ 12.3 3.5 0.0 0.7 1.3 66.6 0.1 1.8 1.5 0.0 1.2 1.3 0.0 0.9 0.9 0.4 2.6 1.7 0.3 0.1 2.8
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+ 3.9 4.0 1.1 1.5 6.6 0.4 6.0 61.5 1.4 0.8 0.4 1.1 4.8 0.3 0.1 1.1 2.2 1.7 0.1 0.2 0.9
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+ 6.1 0.7 0.2 0.1 0.9 0.1 0.1 0.0 0.0 0.0 0.0 1.0 2.2 0.2 0.5 0.1 0.6 0.0 84.5 1.7 1.1
+ 1.9 1.1 0.4 0.6 0.1 0.6 0.1 1.0 0.1 3.0 1.1 4.6 0.9 1.0 9.0 0.0 0.9 0.6 0.5 71.7 0.9
+ 0.8 8.5 0.7 0.4 0.1 0.8 0.3 0.9 0.2 0.3 15.1 5.9 0.4 1.7 0.8 0.2 0.2 2.8 0.3 0.8 58.9
+//
+H KOSJ950110
+D Context-dependent optimal substitution matrices for beta sheet
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 68.7 1.0 2.7 1.2 2.0 3.0 2.1 1.7 1.1 1.0 0.7 1.4 1.4 1.3 0.7 2.9 2.9 1.3 1.0 0.8 1.1
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+ 6.7 0.2 1.8 63.9 7.6 0.1 1.9 0.3 1.3 2.1 0.3 0.9 3.4 0.2 0.1 1.4 4.8 1.4 0.0 0.9 0.7
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+ 9.6 1.3 0.8 1.4 5.6 0.1 2.2 66.1 1.3 0.8 0.4 0.7 3.1 0.2 0.1 0.5 2.6 1.0 0.3 0.2 1.8
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+ 5.9 0.2 4.9 3.0 1.0 0.8 2.7 2.3 2.1 60.3 0.0 2.3 0.3 1.0 0.9 1.7 4.4 3.6 0.6 1.6 0.7
+ 4.2 0.4 0.5 0.4 0.1 0.6 0.1 0.1 0.0 0.1 62.0 8.3 0.3 2.2 2.6 0.3 0.4 1.5 0.3 0.5 15.1
+ 8.1 0.8 0.2 0.2 0.1 0.5 0.7 0.3 0.3 0.6 4.4 72.2 0.3 2.8 2.3 0.5 0.3 0.3 0.2 0.8 4.2
+ 8.3 1.6 9.8 1.5 0.4 0.4 3.2 2.2 0.3 1.2 1.0 1.1 60.9 0.3 0.4 0.5 1.7 3.4 0.4 0.6 0.9
+ 7.3 4.4 1.9 0.4 0.2 0.8 2.7 1.0 1.0 0.2 4.4 7.5 1.4 56.2 2.4 0.5 1.9 2.5 0.1 0.1 3.2
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+ 16.8 3.6 0.2 0.3 0.3 0.0 1.1 0.3 1.1 0.4 0.1 0.8 0.4 0.1 0.0 69.9 3.1 1.2 0.0 0.1 0.1
+ 16.3 2.3 1.7 2.4 0.8 0.7 0.7 0.9 4.0 1.1 0.3 0.1 1.0 0.5 0.6 1.8 59.3 4.6 0.1 0.3 0.7
+ 7.7 2.9 1.3 1.4 1.4 0.4 0.7 2.6 0.6 0.9 2.1 1.0 3.4 0.6 0.2 0.3 5.2 64.0 0.2 0.7 2.7
+ 5.5 0.0 0.5 0.0 0.0 0.0 0.1 0.1 0.0 0.1 0.1 0.8 0.1 0.5 1.8 0.0 0.5 0.0 87.5 2.3 0.0
+ 4.4 0.5 0.8 1.2 0.1 0.9 0.5 0.2 0.0 1.9 1.3 1.2 0.6 0.0 6.1 0.4 1.2 0.6 0.7 77.2 0.3
+ 6.3 2.2 0.7 0.2 0.3 0.6 0.6 0.7 0.1 0.2 8.7 3.1 0.3 0.8 0.7 0.4 1.2 2.5 0.2 0.3 70.1
+//
+H KOSJ950111
+D Context-dependent optimal substitution matrices for turn
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 74.2 3.1 1.1 1.3 0.6 1.7 2.1 1.0 1.0 1.2 1.5 1.0 0.4 1.5 1.5 0.7 1.1 1.3 1.0 1.7 1.2
+ 15.8 54.3 1.1 1.3 1.6 2.1 0.8 0.9 3.4 0.6 1.6 2.4 1.2 0.4 0.2 1.8 4.2 2.3 0.3 0.1 3.6
+ 5.5 1.1 68.1 2.3 1.3 0.3 2.8 0.2 1.7 1.9 0.4 0.5 6.9 0.4 0.3 0.7 2.5 1.1 0.5 0.5 1.1
+ 6.7 1.5 1.4 60.1 6.7 0.4 1.4 1.6 4.2 1.3 0.0 0.8 3.6 0.5 0.2 0.3 6.4 1.0 0.2 1.1 0.7
+ 3.2 1.9 0.3 7.5 64.1 0.6 1.5 8.3 3.3 0.6 0.1 0.2 2.4 0.0 0.0 1.3 2.9 1.2 0.0 0.3 0.4
+ 9.1 8.6 0.1 0.1 2.6 67.0 0.0 1.3 2.3 1.1 0.4 0.0 0.0 0.2 2.3 0.3 2.6 0.0 0.2 1.2 0.6
+ 10.9 3.2 3.5 2.1 1.8 0.0 52.5 4.0 1.6 2.5 1.4 3.9 4.7 0.9 0.2 2.3 0.7 2.2 0.4 0.0 1.4
+ 5.1 3.8 1.0 1.3 7.4 0.3 4.1 60.0 0.9 1.2 0.8 1.2 4.7 0.3 0.3 2.0 2.9 1.5 0.2 0.2 1.0
+ 5.1 2.7 0.4 2.2 2.1 0.6 0.6 1.5 78.5 0.3 0.0 0.2 1.5 0.1 0.3 0.2 1.9 1.5 0.1 0.1 0.2
+ 6.2 2.5 0.5 3.1 0.1 0.7 1.8 2.4 0.7 64.6 0.6 0.7 2.6 1.0 2.2 2.6 2.0 0.8 0.0 5.1 0.0
+ 7.6 0.4 0.1 0.2 0.0 0.4 0.3 0.4 0.0 0.1 68.5 6.5 0.3 3.1 1.1 0.4 0.1 2.2 0.1 0.5 7.7
+ 5.3 1.3 2.2 0.2 0.7 0.2 1.0 0.8 0.4 0.4 4.9 70.1 0.4 3.9 2.3 0.3 0.3 0.8 0.6 1.0 3.1
+ 2.3 3.8 8.2 2.7 1.2 0.0 5.4 3.6 1.4 1.3 0.1 1.5 60.8 0.6 0.5 0.4 2.8 2.1 0.0 0.4 1.1
+ 7.7 0.4 1.2 0.1 0.0 0.9 0.2 1.3 0.0 0.2 3.3 7.8 0.9 67.3 3.3 0.0 0.1 0.7 0.4 1.3 2.9
+ 7.8 0.0 0.6 0.9 0.0 0.6 0.7 0.1 0.1 0.8 0.6 3.1 0.6 0.9 73.1 0.4 0.5 0.0 1.8 5.7 1.8
+ 3.5 4.6 1.4 1.1 0.8 0.1 0.6 1.5 0.7 0.6 0.7 1.0 1.6 0.2 0.4 76.2 2.7 1.8 0.1 0.2 0.4
+ 6.0 8.2 1.5 2.7 4.2 1.1 1.8 1.6 4.5 0.8 0.3 1.2 2.6 0.3 0.6 1.2 52.9 6.9 0.3 0.8 0.7
+ 7.0 2.9 0.9 3.1 1.5 0.2 1.3 1.5 1.0 0.2 2.0 0.6 1.9 1.0 0.1 1.2 10.0 60.7 0.2 0.2 2.6
+ 5.2 0.1 0.1 0.0 0.0 0.9 0.1 0.0 0.4 0.0 0.5 0.1 0.0 1.5 1.3 0.3 1.1 0.7 82.1 4.9 0.7
+ 8.8 0.5 0.3 0.3 0.1 0.3 0.2 0.8 0.0 2.1 0.9 2.0 0.7 0.3 6.8 0.0 0.2 0.8 1.2 73.4 0.4
+ 6.4 3.9 0.3 0.7 0.2 0.8 0.8 0.2 0.8 0.1 8.4 4.8 0.7 0.7 2.2 0.8 0.7 2.8 0.5 1.5 62.8
+//
+H KOSJ950112
+D Context-dependent optimal substitution matrices for coil
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 60.6 3.0 2.1 1.0 1.3 2.0 2.9 3.2 1.8 2.0 2.7 1.5 1.5 2.4 1.6 1.8 1.5 1.8 1.3 1.7 2.4
+ 19.0 55.6 0.4 0.5 0.8 2.7 1.2 0.8 4.3 0.3 0.6 0.8 0.8 0.2 0.3 2.3 4.7 2.6 0.0 0.1 2.0
+ 13.6 0.5 64.3 1.3 0.1 0.1 1.3 0.6 0.2 2.0 0.2 1.3 5.8 0.0 0.1 1.6 2.7 2.9 0.4 0.7 0.5
+ 6.4 1.0 1.9 59.8 4.8 0.7 1.6 2.8 2.3 2.2 0.7 0.9 3.6 0.8 0.2 0.1 5.4 2.6 0.1 1.0 1.3
+ 8.6 1.5 0.5 6.2 66.7 0.3 1.8 5.0 1.2 0.6 0.6 0.5 1.3 0.1 0.1 1.2 1.6 1.1 0.0 1.1 0.2
+ 13.0 11.3 0.4 0.2 1.1 59.3 0.0 1.6 0.9 0.1 2.3 0.1 0.0 1.5 1.0 0.0 2.9 1.0 0.9 0.6 2.0
+ 19.2 1.5 2.5 1.7 1.3 0.0 51.2 7.4 0.9 0.9 0.3 0.7 3.1 1.3 0.7 0.3 2.3 3.2 0.0 0.5 1.1
+ 20.4 3.3 1.0 0.7 3.4 0.4 2.9 60.6 1.2 0.8 0.2 0.5 1.2 0.1 0.0 0.4 1.3 0.7 0.0 0.3 0.6
+ 11.7 1.2 0.2 1.0 1.3 0.3 0.4 0.8 77.9 0.3 0.1 0.1 0.5 0.1 0.1 0.5 2.0 0.8 0.1 0.3 0.4
+ 12.9 1.4 1.2 1.9 2.3 0.6 1.4 0.5 0.3 68.2 0.9 0.8 0.3 0.2 1.3 0.7 2.1 0.1 0.4 2.6 0.0
+ 17.1 0.6 0.4 0.2 0.1 0.6 0.3 1.0 0.4 0.2 55.0 5.2 1.1 1.6 1.6 0.9 0.4 1.0 0.7 0.3 11.5
+ 10.2 0.8 0.6 0.2 0.1 0.3 1.5 0.2 0.3 0.6 4.9 68.2 0.7 3.0 3.0 0.9 0.1 0.7 0.2 0.8 2.7
+ 9.7 3.4 6.0 1.7 2.7 0.0 3.2 3.9 2.0 1.3 0.4 1.3 55.4 0.4 0.6 1.9 2.8 1.9 0.2 0.2 1.3
+ 15.4 0.0 0.0 0.2 0.4 0.4 0.3 0.6 0.0 0.8 6.5 9.4 0.1 56.8 0.6 0.1 0.5 3.0 0.2 0.1 4.5
+ 10.2 0.2 0.4 0.2 0.0 0.2 0.5 0.0 0.3 0.4 1.2 3.6 0.1 0.6 70.9 1.1 0.8 0.7 1.1 5.9 1.7
+ 11.9 5.1 0.8 0.5 0.3 0.0 1.4 1.7 0.8 0.4 0.3 0.8 0.5 0.4 0.3 69.9 2.7 0.5 0.0 0.5 1.4
+ 9.9 4.4 0.7 3.4 3.2 1.3 0.9 1.3 2.5 0.5 0.4 0.4 1.2 0.1 0.3 3.6 57.1 6.9 0.3 0.5 1.2
+ 11.7 3.2 0.7 2.7 0.8 0.5 1.6 0.5 1.0 0.6 1.7 0.9 1.2 0.8 0.2 2.0 7.5 58.8 0.0 0.6 3.3
+ 8.4 0.0 0.4 0.5 0.0 0.2 0.0 0.0 0.0 0.1 2.9 0.9 0.9 0.7 4.3 0.0 1.4 0.0 76.5 2.1 0.7
+ 10.9 0.3 0.3 0.3 0.3 0.1 0.1 0.1 0.6 0.9 0.1 0.7 0.7 0.5 8.4 0.1 0.1 0.4 0.9 73.3 0.9
+ 15.5 3.3 0.1 0.9 0.3 0.7 0.3 0.8 0.3 0.1 6.3 3.9 0.8 1.1 1.0 0.5 1.6 3.0 0.3 0.5 58.8
+//
+H KOSJ950113
+D Context-dependent optimal substitution matrices for exposed residues
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 60.2 3.3 1.7 1.1 1.1 2.8 2.1 1.2 1.8 2.2 2.6 2.3 0.7 2.2 2.2 2.1 1.7 2.1 2.1 1.8 2.7
+ 21.5 51.3 0.7 0.6 1.1 1.0 1.2 1.2 3.0 0.4 1.2 2.1 1.2 0.7 0.2 2.1 4.2 2.8 0.3 0.2 3.2
+ 11.4 1.2 62.9 1.6 0.7 0.1 2.9 0.9 0.7 1.6 0.6 1.1 7.3 0.5 0.4 0.6 2.2 1.6 0.6 0.4 0.8
+ 7.5 1.8 1.5 52.6 6.4 0.4 2.3 2.7 2.8 1.7 0.4 1.0 4.8 0.8 0.4 0.1 7.9 2.7 0.3 1.2 0.9
+ 7.4 2.8 0.7 8.0 59.2 0.3 1.7 8.3 2.3 0.3 0.4 0.4 2.3 0.2 0.1 1.4 2.6 1.2 0.0 0.4 0.2
+ 18.1 4.2 0.0 0.3 1.3 64.7 0.0 0.9 1.1 0.5 1.1 1.0 0.0 1.5 2.2 0.0 1.7 0.9 0.0 0.1 0.3
+ 13.9 3.1 3.7 1.8 1.7 0.1 51.0 5.9 1.0 1.7 0.5 3.0 3.9 0.8 0.1 1.0 2.3 2.6 0.1 0.6 1.4
+ 7.8 4.3 0.9 1.3 6.7 0.2 4.5 58.3 1.1 1.1 0.6 1.0 4.2 0.5 0.3 1.4 2.5 1.8 0.2 0.1 1.3
+ 11.8 2.6 0.4 2.2 2.3 0.3 0.6 1.6 71.0 0.3 0.0 0.1 1.2 0.3 0.5 0.3 2.2 1.7 0.2 0.2 0.4
+ 14.1 0.9 3.3 5.0 1.0 0.1 2.2 1.7 0.8 54.8 0.6 1.1 1.3 0.5 1.9 1.4 2.6 0.1 0.0 4.4 2.4
+ 17.2 0.3 0.3 0.2 0.1 0.3 0.2 0.3 0.0 0.1 54.4 7.6 0.7 2.0 1.5 0.6 0.0 2.1 0.3 0.6 11.3
+ 15.0 0.7 1.2 0.4 0.1 0.2 0.8 0.4 0.3 0.6 3.8 64.4 0.8 3.5 2.8 0.5 0.3 0.6 0.5 0.7 2.6
+ 4.8 3.8 7.9 2.3 1.6 0.2 4.6 4.9 1.2 1.3 0.4 1.4 56.0 0.4 0.4 0.9 3.0 3.2 0.1 0.3 1.4
+ 14.4 2.8 0.7 0.2 0.0 0.4 1.1 1.9 1.1 0.1 6.6 7.7 1.8 49.9 2.1 0.1 1.4 2.7 0.8 0.8 3.5
+ 14.2 0.6 0.5 0.5 0.2 0.5 0.4 0.2 0.1 0.5 1.7 2.8 0.7 0.6 66.6 0.4 0.8 0.5 1.1 5.9 1.2
+ 13.8 4.9 1.3 0.6 0.8 0.0 0.8 1.3 0.9 0.4 0.4 1.0 1.3 0.3 0.1 66.0 3.5 1.3 0.1 0.4 0.9
+ 11.3 7.4 1.3 2.7 3.0 0.9 1.1 1.9 4.3 0.8 0.1 0.5 1.8 0.3 0.3 2.3 50.1 8.1 0.0 0.5 1.3
+ 13.7 4.0 0.9 2.5 1.2 0.2 1.3 1.2 0.6 0.6 2.8 2.3 2.0 0.7 0.2 1.3 7.4 53.0 0.3 0.4 3.6
+ 13.7 0.1 0.1 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.6 2.0 0.5 0.2 2.5 0.4 0.0 0.1 75.4 4.2 0.1
+ 11.6 0.6 0.4 0.4 0.2 0.5 0.1 0.6 0.2 1.5 1.6 3.0 0.6 0.4 7.8 0.1 0.7 0.7 1.0 66.8 1.2
+ 17.5 2.5 0.4 0.5 0.4 0.6 0.8 0.6 0.6 0.6 10.4 3.7 0.7 0.9 1.6 0.3 0.7 1.6 0.3 0.7 54.8
+//
+H KOSJ950114
+D Context-dependent optimal substitution matrices for buried residues
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 79.2 0.2 1.6 1.2 1.9 1.2 1.2 2.0 0.7 0.2 0.4 0.2 4.0 0.4 0.4 1.6 1.8 0.7 0.4 0.4 0.3
+ 1.0 76.3 0.6 0.5 0.6 1.7 0.6 1.0 2.8 0.2 0.9 1.5 0.4 0.5 0.3 1.1 4.4 1.7 0.0 0.4 3.7
+ 8.2 0.7 72.9 0.9 0.1 0.4 2.4 0.4 0.9 1.7 1.1 1.4 3.7 0.2 0.3 0.6 1.7 1.9 0.1 0.4 0.1
+ 6.2 2.0 1.1 65.7 3.1 0.6 1.3 0.9 2.5 1.6 1.2 1.5 1.6 0.4 0.1 0.5 4.8 2.6 0.1 1.0 1.3
+ 9.7 2.5 0.6 3.0 66.9 0.4 0.6 4.2 2.0 0.7 0.8 0.8 0.9 0.0 0.2 1.0 2.7 1.5 0.2 1.0 0.5
+ 5.7 6.9 0.1 0.1 1.5 71.6 0.1 0.6 1.4 0.3 1.8 2.0 0.0 0.5 1.3 0.0 2.0 0.7 0.1 0.1 3.2
+ 6.1 2.4 1.7 1.3 0.9 0.4 67.3 2.0 0.8 1.9 0.6 3.6 2.9 2.3 1.0 0.9 1.3 1.1 0.8 0.4 0.5
+ 9.9 4.0 1.8 0.6 2.5 0.4 3.8 62.5 1.8 0.5 0.1 2.5 1.6 0.3 0.0 0.5 2.5 1.0 0.0 1.3 2.5
+ 3.6 3.6 0.3 0.6 0.5 0.3 0.4 0.4 85.7 0.2 0.1 0.3 0.5 0.1 0.1 0.2 1.7 0.7 0.2 0.1 0.4
+ 1.0 0.6 0.8 0.9 0.6 0.4 1.4 0.5 0.0 84.1 0.6 1.0 0.6 0.8 2.0 0.3 0.5 0.5 0.6 2.6 0.2
+ 1.8 0.4 0.3 0.3 0.2 0.4 0.1 0.2 0.0 0.1 73.9 7.7 0.4 2.2 1.5 0.2 0.3 0.8 0.2 0.2 8.8
+ 1.1 0.6 0.3 0.4 0.2 0.5 0.9 0.6 0.2 0.2 5.0 78.6 1.1 3.0 2.4 0.3 0.1 0.4 0.2 0.5 3.4
+ 20.3 1.8 5.4 1.6 0.5 0.0 1.3 1.8 1.7 1.5 1.6 4.8 46.8 1.1 0.6 0.4 1.1 2.8 0.2 1.1 3.7
+ 2.2 1.2 0.2 0.3 0.2 0.7 0.6 0.3 0.4 0.2 5.1 12.2 0.3 68.7 2.2 0.1 0.1 0.4 0.4 0.1 4.2
+ 1.9 0.2 0.1 0.1 0.1 0.3 0.2 0.0 0.4 0.5 1.5 4.7 0.1 1.0 80.2 0.1 0.5 0.4 1.6 4.6 1.4
+ 7.8 4.6 0.4 1.0 0.2 0.1 1.2 0.8 0.9 0.8 1.0 1.3 0.3 0.5 0.4 73.3 2.9 1.5 0.0 0.0 1.0
+ 8.8 7.1 1.1 1.5 0.8 1.6 0.9 0.6 2.2 0.8 0.5 0.4 0.7 0.4 1.1 1.2 62.2 5.9 0.1 0.9 1.2
+ 3.5 3.8 0.5 0.8 0.4 0.9 0.8 0.9 0.6 0.3 3.1 1.7 0.9 1.7 0.2 0.6 4.5 68.2 0.0 0.4 6.4
+ 1.9 0.0 0.6 0.0 0.0 0.4 0.2 0.0 0.2 0.1 0.7 0.8 0.7 0.7 1.4 0.0 0.5 0.2 89.0 1.7 0.8
+ 2.0 0.4 0.4 0.6 0.2 0.6 0.2 0.3 0.0 1.5 0.9 2.0 0.5 0.5 9.7 0.2 0.2 0.5 0.7 78.0 0.6
+ 1.4 2.5 0.2 0.3 0.2 0.8 0.1 0.6 0.1 0.1 11.1 3.8 0.9 1.0 1.2 0.3 0.5 1.6 0.2 0.1 73.0
+//
+H KOSJ950115
+D Context-dependent optimal substitution matrices for all residues
+ (Koshi-Goldstein, 1995)
+R PMID:8577693
+A Koshi, J.M. and Goldstein, R.A.
+T Context-dependent optimal substitution matrices.
+J Protein Engineering 8, 641-645 (1995)
+M rows = -ARNDCQEGHILKMFPSTWYV, cols = -ARNDCQEGHILKMFPSTWYV
+ 69.2 1.6 2.0 1.1 1.3 2.4 2.0 1.4 1.5 1.7 1.2 1.3 0.9 1.7 1.1 2.1 2.1 1.5 1.0 1.3 1.7
+ 8.9 61.9 0.8 0.6 1.3 1.6 1.0 1.6 3.7 0.3 0.6 1.6 1.3 0.5 0.2 1.9 5.9 3.2 0.2 0.4 2.6
+ 11.3 1.3 67.2 1.4 0.7 0.2 2.4 0.7 0.6 1.3 0.6 1.0 5.7 0.3 0.2 0.7 1.9 1.4 0.3 0.5 0.4
+ 6.4 1.8 1.5 60.9 5.4 0.3 1.8 2.0 2.5 1.6 0.5 0.8 3.5 0.7 0.1 0.4 5.6 2.0 0.4 1.0 1.0
+ 7.3 2.0 0.5 6.1 65.0 0.4 1.2 6.9 1.9 0.3 0.4 0.4 1.9 0.3 0.2 1.1 2.4 1.0 0.0 0.5 0.2
+ 13.8 6.6 0.0 0.3 1.6 64.4 0.0 1.2 1.3 0.5 1.8 1.2 0.0 0.5 1.6 0.0 2.6 1.0 0.2 0.2 1.2
+ 11.4 2.4 3.3 1.6 1.7 0.2 58.4 4.9 1.0 1.8 0.5 2.0 3.5 0.8 0.3 1.0 1.9 1.9 0.5 0.5 0.6
+ 7.9 3.2 1.0 1.4 5.8 0.3 4.3 62.1 1.2 0.9 0.4 1.1 4.0 0.2 0.1 1.2 2.2 1.3 0.2 0.1 1.2
+ 8.4 2.5 0.4 1.4 1.6 0.4 0.5 1.1 77.8 0.3 0.0 0.2 1.0 0.1 0.2 0.3 1.9 1.1 0.1 0.2 0.4
+ 9.5 0.9 2.7 2.8 1.1 0.3 2.4 1.4 0.8 65.4 0.5 1.5 1.5 0.8 1.5 1.0 1.9 0.5 0.4 2.9 0.3
+ 6.9 0.8 0.3 0.4 0.1 0.4 0.1 0.4 0.2 0.1 64.8 7.7 0.4 2.0 1.7 0.3 0.3 1.6 0.3 0.3 10.9
+ 7.1 0.9 0.7 0.2 0.1 0.3 1.0 0.3 0.1 0.4 4.7 71.7 0.8 3.2 2.8 0.3 0.2 0.6 0.2 0.8 3.7
+ 5.0 2.9 8.1 2.3 1.4 0.1 4.1 4.3 1.1 1.2 0.4 1.4 58.7 0.5 0.5 1.2 2.5 2.6 0.1 0.3 1.4
+ 9.4 2.0 0.8 0.2 1.3 0.4 1.0 0.9 0.6 0.2 5.5 9.2 0.8 59.4 2.2 0.1 0.6 1.7 0.2 0.2 3.4
+ 6.4 0.3 0.2 0.4 0.2 0.4 0.4 0.2 0.3 0.4 1.4 3.7 0.1 0.9 73.8 0.3 0.9 0.6 1.4 6.4 1.5
+ 12.0 3.5 0.9 0.6 0.6 0.0 0.8 1.0 0.7 0.4 0.5 0.9 0.9 0.6 0.1 71.2 2.8 1.4 0.0 0.5 0.7
+ 11.7 5.1 1.4 3.0 2.2 0.9 1.1 1.5 3.3 0.6 0.4 0.5 1.4 0.3 0.5 1.8 56.8 6.1 0.3 0.5 0.8
+ 8.8 3.1 0.9 2.2 1.1 0.4 1.1 1.2 0.9 0.6 2.0 1.4 2.0 0.8 0.1 1.1 6.9 61.8 0.1 0.4 3.2
+ 6.0 0.1 0.4 0.1 0.0 0.7 0.1 0.0 0.5 0.1 0.4 1.0 0.6 0.8 2.3 0.0 1.3 0.2 82.3 2.5 0.7
+ 7.4 0.6 0.5 0.6 0.4 0.7 0.2 0.5 0.3 1.7 0.9 2.0 0.6 0.4 7.1 0.1 0.6 0.9 0.7 73.2 0.7
+ 9.8 3.7 0.5 0.4 0.2 0.8 0.5 0.4 0.3 0.1 8.8 3.6 0.4 0.8 1.2 0.4 0.9 2.5 0.2 0.5 64.0
+//
+H OVEJ920102
+D Environment-specific amino acid substitution matrix for alpha residues
+ (Overington et al., 1992)
+R PMID:1304904
+A Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L.
+T Environment-specific amino acid substitution tables: tertiary templates
+ and prediction of protein folds
+J Protein Science 1, 216-226 (1992)
+M rows = ACDEFGHIKLMNPQRSTVWYJ-, cols = ACDEFGHIKLMNPQRSTVWYJ
+ 0.355 0.007 0.090 0.100 0.050 0.177 0.037 0.077 0.096 0.056 0.081 0.103 0.106 0.090 0.088 0.163 0.120 0.098 0.065 0.036 0.252
+ 0.001 0.901 0.000 0.000 0.000 0.000 0.000 0.004 0.001 0.000 0.000 0.003 0.000 0.006 0.006 0.004 0.002 0.000 0.007 0.000 0.000
+ 0.038 0.000 0.315 0.109 0.006 0.041 0.027 0.009 0.033 0.004 0.009 0.088 0.051 0.089 0.023 0.065 0.048 0.013 0.012 0.011 0.009
+ 0.044 0.011 0.111 0.305 0.011 0.048 0.026 0.011 0.059 0.013 0.009 0.068 0.069 0.086 0.053 0.033 0.045 0.017 0.012 0.018 0.000
+ 0.017 0.000 0.005 0.007 0.415 0.004 0.009 0.039 0.025 0.097 0.042 0.013 0.006 0.011 0.009 0.009 0.014 0.041 0.053 0.085 0.009
+ 0.065 0.000 0.070 0.042 0.006 0.370 0.017 0.022 0.029 0.013 0.015 0.036 0.043 0.031 0.013 0.068 0.049 0.014 0.009 0.021 0.045
+ 0.010 0.000 0.012 0.011 0.010 0.007 0.571 0.003 0.022 0.005 0.015 0.043 0.006 0.035 0.021 0.016 0.008 0.017 0.009 0.037 0.009
+ 0.029 0.014 0.009 0.008 0.048 0.021 0.004 0.325 0.017 0.076 0.107 0.018 0.007 0.007 0.015 0.014 0.033 0.112 0.016 0.030 0.018
+ 0.053 0.007 0.044 0.081 0.020 0.041 0.044 0.026 0.336 0.029 0.059 0.073 0.045 0.094 0.163 0.041 0.054 0.026 0.041 0.028 0.036
+ 0.038 0.000 0.006 0.018 0.210 0.019 0.004 0.139 0.033 0.415 0.225 0.033 0.016 0.041 0.028 0.029 0.026 0.133 0.037 0.057 0.036
+ 0.013 0.000 0.004 0.003 0.016 0.007 0.000 0.043 0.014 0.053 0.197 0.010 0.000 0.018 0.004 0.003 0.010 0.018 0.021 0.021 0.018
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+ 0.022 0.000 0.036 0.035 0.005 0.026 0.011 0.009 0.020 0.006 0.000 0.013 0.424 0.013 0.016 0.039 0.011 0.009 0.002 0.000 0.000
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+ 0.019 0.011 0.012 0.023 0.005 0.008 0.019 0.010 0.069 0.009 0.004 0.018 0.013 0.028 0.348 0.030 0.019 0.005 0.007 0.018 0.018
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+ 0.043 0.007 0.039 0.033 0.020 0.038 0.014 0.026 0.032 0.015 0.026 0.057 0.028 0.046 0.035 0.065 0.266 0.037 0.016 0.034 0.000
+ 0.055 0.000 0.018 0.021 0.069 0.022 0.044 0.178 0.025 0.111 0.016 0.018 0.025 0.017 0.015 0.129 0.060 0.350 0.012 0.043 0.162
+ 0.009 0.000 0.003 0.004 0.022 0.004 0.007 0.006 0.012 0.006 0.020 0.001 0.001 0.006 0.004 0.002 0.007 0.003 0.588 0.064 0.000
+ 0.009 0.000 0.006 0.006 0.046 0.006 0.029 0.014 0.007 0.013 0.031 0.033 0.003 0.020 0.010 0.007 0.017 0.016 0.078 0.377 0.027
+ 0.009 0.000 0.001 0.000 0.001 0.004 0.001 0.002 0.002 0.002 0.004 0.000 0.000 0.004 0.003 0.006 0.004 0.010 0.000 0.005 0.297
+ 0.028 0.004 0.041 0.074 0.010 0.029 0.017 0.022 0.050 0.031 0.033 0.031 0.045 0.039 0.028 0.047 0.034 0.032 0.002 0.021 0.000
+//
+H OVEJ920103
+D Environment-specific amino acid substitution matrix for beta residues
+ (Overington et al., 1992)
+R PMID:1304904
+A Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L.
+T Environment-specific amino acid substitution tables: tertiary templates
+ and prediction of protein folds
+J Protein Science 1, 216-226 (1992)
+M rows = ACDEFGHIKLMNPQRSTVWYJ-, cols = ACDEFGHIKLMNPQRSTVWYJ
+ 0.275 0.000 0.025 0.047 0.023 0.086 0.007 0.029 0.036 0.031 0.074 0.041 0.035 0.050 0.050 0.057 0.055 0.065 0.014 0.031 0.080
+ 0.000 0.910 0.000 0.016 0.014 0.000 0.000 0.003 0.008 0.000 0.000 0.000 0.000 0.008 0.015 0.002 0.001 0.000 0.000 0.000 0.020
+ 0.008 0.000 0.350 0.059 0.008 0.011 0.014 0.017 0.018 0.006 0.000 0.095 0.040 0.020 0.010 0.026 0.020 0.013 0.006 0.012 0.000
+ 0.018 0.016 0.054 0.192 0.004 0.015 0.021 0.012 0.071 0.009 0.037 0.039 0.028 0.056 0.053 0.018 0.036 0.018 0.002 0.015 0.000
+ 0.020 0.022 0.013 0.005 0.398 0.008 0.021 0.049 0.017 0.046 0.023 0.006 0.012 0.006 0.015 0.020 0.012 0.021 0.071 0.096 0.020
+ 0.092 0.000 0.021 0.033 0.015 0.623 0.007 0.016 0.018 0.016 0.042 0.019 0.017 0.033 0.017 0.036 0.028 0.013 0.049 0.021 0.020
+ 0.003 0.000 0.006 0.010 0.008 0.002 0.332 0.006 0.022 0.004 0.000 0.035 0.014 0.021 0.023 0.009 0.010 0.009 0.000 0.008 0.020
+ 0.040 0.010 0.044 0.021 0.089 0.020 0.017 0.358 0.022 0.105 0.077 0.025 0.012 0.010 0.015 0.021 0.026 0.119 0.041 0.034 0.020
+ 0.024 0.011 0.021 0.099 0.015 0.007 0.070 0.013 0.299 0.017 0.012 0.060 0.052 0.060 0.139 0.026 0.051 0.010 0.004 0.017 0.040
+ 0.057 0.000 0.027 0.031 0.111 0.023 0.031 0.143 0.051 0.459 0.169 0.031 0.038 0.026 0.031 0.025 0.028 0.119 0.096 0.044 0.060
+ 0.026 0.000 0.006 0.021 0.011 0.013 0.021 0.021 0.007 0.031 0.244 0.010 0.002 0.031 0.002 0.007 0.013 0.019 0.006 0.006 0.000
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+//
+H OVEJ920104
+D Environment-specific amino acid substitution matrix for accessible
+ residues (Overington et al., 1992)
+R PMID:1304904
+A Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L.
+T Environment-specific amino acid substitution tables: tertiary templates
+ and prediction of protein folds
+J Protein Science 1, 216-226 (1992)
+M rows = ACDEFGHIKLMNPQRSTVWYJ-, cols = ACDEFGHIKLMNPQRSTVWYJ
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+//
+H OVEJ920105
+D Environment-specific amino acid substitution matrix for inaccessible residues
+ (Overington et al., 1992)
+R PMID:1304904
+A Overington, J., Donnelly, D., Johnson, M.S., Sali, A. and Blundell, T.L.
+T Environment-specific amino acid substitution tables: tertiary templates
+ and prediction of protein folds
+J Protein Science 1, 216-226 (1992)
+M rows = ACDEFGHIKLMNPQRSTVWYJ-, cols = ACDEFGHIKLMNPQRSTVWYJ
+ 0.426 0.022 0.025 0.095 0.036 0.075 0.009 0.039 0.000 0.029 0.061 0.036 0.041 0.053 0.015 0.149 0.103 0.071 0.020 0.032 0.112
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+ 0.011 0.000 0.071 0.011 0.005 0.007 0.028 0.006 0.000 0.002 0.013 0.398 0.007 0.005 0.008 0.035 0.012 0.003 0.006 0.009 0.009
+ 0.014 0.002 0.005 0.000 0.011 0.013 0.004 0.005 0.000 0.002 0.000 0.015 0.764 0.008 0.008 0.005 0.012 0.007 0.000 0.001 0.000
+ 0.017 0.009 0.002 0.101 0.002 0.009 0.039 0.001 0.088 0.003 0.039 0.018 0.000 0.560 0.122 0.008 0.001 0.007 0.006 0.005 0.004
+ 0.013 0.009 0.000 0.058 0.003 0.004 0.015 0.004 0.294 0.003 0.001 0.000 0.002 0.040 0.588 0.013 0.002 0.004 0.003 0.007 0.009
+ 0.074 0.010 0.023 0.016 0.011 0.039 0.017 0.009 0.015 0.007 0.016 0.103 0.020 0.013 0.000 0.450 0.111 0.017 0.005 0.004 0.052
+ 0.044 0.006 0.012 0.000 0.006 0.018 0.006 0.015 0.015 0.009 0.025 0.024 0.025 0.005 0.008 0.081 0.504 0.025 0.002 0.005 0.034
+ 0.116 0.001 0.012 0.053 0.073 0.015 0.054 0.205 0.000 0.134 0.118 0.033 0.031 0.027 0.015 0.043 0.079 0.476 0.014 0.047 0.082
+ 0.006 0.003 0.007 0.000 0.024 0.001 0.011 0.011 0.000 0.009 0.013 0.003 0.000 0.005 0.000 0.003 0.001 0.005 0.731 0.031 0.000
+ 0.015 0.001 0.005 0.000 0.071 0.006 0.034 0.021 0.029 0.013 0.023 0.024 0.007 0.008 0.000 0.014 0.012 0.017 0.037 0.561 0.009
+ 0.013 0.002 0.000 0.000 0.002 0.002 0.000 0.002 0.000 0.002 0.003 0.006 0.000 0.003 0.000 0.008 0.007 0.003 0.000 0.004 0.547
+ 0.006 0.010 0.012 0.005 0.007 0.013 0.006 0.011 0.074 0.010 0.009 0.018 0.016 0.000 0.000 0.011 0.018 0.016 0.002 0.012 0.017
+//
+H LINK010101
+D Substitution matrices from an neural network model (Lin et al., 2001)
+R PMID:11694178
+A Lin, K., May, A.C. and Taylor, W.R.
+T Amino acid substitution matrices from an artificial neural network
+ model
+J J Comput Biol. 8, 471-481 (2001)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 0.441 0.030 0.020 0.033 0.000 0.029 0.045 0.064 0.011 0.021 0.043 0.032 0.010 0.015 0.029 0.069 0.041 0.003 0.009 0.055
+ 0.034 0.519 0.026 0.012 0.001 0.047 0.033 0.022 0.014 0.020 0.029 0.134 0.007 0.005 0.019 0.041 0.013 0.004 0.015 0.004
+ 0.029 0.036 0.396 0.097 0.001 0.034 0.046 0.051 0.015 0.014 0.021 0.053 0.006 0.008 0.009 0.088 0.054 0.002 0.017 0.025
+ 0.039 0.012 0.070 0.522 0.000 0.031 0.102 0.042 0.008 0.003 0.006 0.036 0.002 0.007 0.014 0.047 0.031 0.002 0.011 0.016
+ 0.035 0.012 0.007 0.006 0.757 0.007 0.003 0.012 0.007 0.021 0.031 0.008 0.003 0.009 0.004 0.023 0.023 0.001 0.015 0.019
+ 0.055 0.061 0.031 0.043 0.001 0.395 0.121 0.022 0.022 0.014 0.011 0.092 0.013 0.005 0.013 0.036 0.044 0.004 0.006 0.014
+ 0.056 0.029 0.026 0.091 0.000 0.072 0.474 0.021 0.010 0.009 0.015 0.065 0.008 0.004 0.018 0.029 0.036 0.000 0.016 0.021
+ 0.060 0.023 0.027 0.036 0.001 0.016 0.007 0.691 0.008 0.007 0.017 0.022 0.000 0.001 0.017 0.038 0.015 0.000 0.002 0.012
+ 0.019 0.038 0.041 0.039 0.000 0.044 0.040 0.012 0.572 0.005 0.036 0.044 0.006 0.014 0.011 0.006 0.011 0.001 0.047 0.015
+ 0.024 0.011 0.006 0.003 0.000 0.009 0.010 0.011 0.003 0.464 0.157 0.015 0.028 0.016 0.011 0.008 0.039 0.001 0.009 0.175
+ 0.027 0.011 0.011 0.003 0.007 0.002 0.008 0.006 0.004 0.096 0.603 0.011 0.042 0.039 0.013 0.010 0.017 0.002 0.011 0.077
+ 0.050 0.107 0.034 0.039 0.001 0.057 0.070 0.019 0.013 0.018 0.019 0.411 0.004 0.008 0.022 0.044 0.057 0.002 0.010 0.019
+ 0.020 0.019 0.013 0.005 0.000 0.005 0.023 0.020 0.012 0.092 0.243 0.031 0.337 0.037 0.016 0.017 0.023 0.001 0.014 0.073
+ 0.027 0.005 0.004 0.010 0.003 0.003 0.001 0.010 0.011 0.009 0.088 0.011 0.015 0.605 0.009 0.014 0.023 0.017 0.111 0.024
+ 0.056 0.016 0.004 0.025 0.000 0.013 0.038 0.020 0.010 0.009 0.009 0.024 0.004 0.009 0.688 0.043 0.003 0.000 0.004 0.024
+ 0.104 0.030 0.052 0.033 0.001 0.027 0.043 0.039 0.004 0.020 0.015 0.032 0.004 0.012 0.027 0.408 0.111 0.002 0.017 0.022
+ 0.065 0.016 0.036 0.028 0.000 0.024 0.035 0.012 0.004 0.039 0.032 0.053 0.009 0.018 0.008 0.126 0.424 0.002 0.015 0.056
+ 0.018 0.010 0.014 0.014 0.000 0.014 0.016 0.008 0.005 0.015 0.031 0.018 0.011 0.037 0.000 0.019 0.011 0.688 0.049 0.022
+ 0.027 0.012 0.010 0.018 0.000 0.007 0.011 0.020 0.028 0.004 0.028 0.004 0.010 0.128 0.003 0.021 0.024 0.000 0.635 0.011
+ 0.056 0.004 0.015 0.011 0.007 0.006 0.017 0.007 0.005 0.146 0.112 0.018 0.017 0.022 0.015 0.023 0.048 0.003 0.007 0.463
+//
+H BLAJ010101
+D Matrix built from structural superposition data for identifying potential
+ remote homologues (Blake-Cohen, 2001)
+R PMID:11254392
+A Blake, J.D. and Cohen, F.E.
+T Pairwise sequence alignment below the twilight zone
+J J Mol Biol. 307, 721-735 (2001)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 9
+ 0 14
+ 0 1 11
+ 0 -2 5 17
+ -5 -16 -13 -13 39
+ 1 7 1 1 -14 13
+ 0 3 1 5 -20 5 12
+ 1 -2 1 2 -15 -3 0 16
+ -2 2 5 1 -18 2 0 -2 23
+ 0 -7 -8 -9 -3 -7 -8 -3 -4 10
+ -2 -4 -7 -10 -11 -10 -8 -6 -4 7 10
+ 0 7 2 0 -23 4 6 0 1 -7 -4 9
+ -2 -8 -6 -7 -9 -8 -6 -7 -5 10 11 -4 13
+ -1 -6 -3 -6 -12 -4 -10 -8 -1 3 3 -8 0 16
+ -1 -3 -1 2 -18 -4 -1 0 -4 -3 1 1 -4 -4 19
+ 0 2 3 0 -18 0 0 0 0 -6 -4 1 -7 -4 1 9
+ -3 0 2 0 -19 2 3 -4 0 -3 -5 1 -3 -2 -1 5 7
+ -11 -6 -9 -7 -24 -12 -3 -10 -9 -6 2 -7 -4 9 -5 -7 0 32
+ -3 -1 1 -6 -1 -5 -5 -10 1 -2 -4 -5 -3 8 -8 -1 3 0 19
+ 0 -4 -4 -10 0 -2 -6 -5 -6 8 6 -6 6 1 -4 -5 -1 -5 -1 9
+//
+H PRLA000101
+D Structure derived matrix (SDM) for alignment of distantly related sequences
+ (Prlic et al., 2000)
+R PMID:10964983
+A Prlic, A., Domingues, F.S. and Sippl, M.J.
+T Structure-derived substitution matrices for alignment of distantly
+ related sequences
+J Protein Eng. 13, 545-550 (2000)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 2.09
+ -0.50 2.87
+ -0.57 0.60 3.60
+ -0.73 0.13 1.78 4.02
+ 0.33 -1.30 -2.08 -2.51 6.99
+ -0.75 0.13 0.33 0.34 -0.83 2.60
+ -0.12 0.99 -0.16 1.20 -1.97 1.23 2.97
+ 0.27 -0.96 0.79 -1.20 -2.11 -0.12 -0.41 4.36
+ -1.42 0.54 0.76 -0.01 -1.50 -0.46 -0.62 -0.40 5.89
+ -0.97 -1.40 -2.43 -2.77 0.13 -1.47 -1.81 -2.93 -1.76 2.76
+ -0.39 -1.19 -2.10 -2.65 -0.31 -1.49 -2.11 -1.98 -0.93 1.56 2.43
+ -0.38 1.42 0.83 0.66 -2.19 0.92 1.11 -0.71 0.31 -1.81 -1.96 2.91
+ -0.04 -0.63 -2.01 -2.58 1.04 -0.13 -1.86 -1.86 -1.04 0.99 1.61 -1.62 3.75
+ -0.76 -1.40 -2.25 -2.19 1.13 -2.31 -1.61 -2.67 -0.22 0.76 1.23 -2.41 0.80 3.28
+ -0.53 0.21 -1.10 0.72 -2.19 0.24 -0.26 -0.04 -1.44 -2.00 -1.56 -0.19 -1.09 -0.91 5.45
+ 0.34 -0.06 0.40 0.71 0.31 1.04 0.31 0.29 -0.74 -1.75 -2.30 -0.06 -1.34 -1.11 -0.29 2.36
+ 0.13 -0.15 0.30 -0.75 -0.59 0.60 -0.21 -0.81 -0.52 -0.96 -0.86 -0.10 -1.58 -0.69 0.93 1.20 2.04
+ -0.66 -0.04 -2.89 -1.91 -0.76 -0.81 -2.70 -1.21 -1.48 0.25 -0.14 -1.94 0.87 2.29 -5.34 -1.18 -0.57 6.96
+ -1.25 -0.75 -0.36 -1.21 0.13 -0.61 -1.64 -1.62 -0.12 0.08 0.70 -1.72 -0.41 1.96 -1.98 -1.56 -0.41 2.15 3.95
+ 0.02 -1.52 -2.17 -2.02 0.34 -1.38 -1.84 -1.96 -0.35 1.94 0.81 -1.27 0.61 0.51 -1.11 -1.11 0.05 -1.09 0.21 2.05
+//
+H PRLA000102
+D Homologous structure dereived matrix (HSDM) for alignment of distantly
+ related sequences (Prlic et al., 2000)
+R PMID:10964983
+A Prlic, A., Domingues, F.S. and Sippl, M.J.
+T Structure-derived substitution matrices for alignment of distantly
+ related sequences
+J Protein Eng. 13, 545-550 (2000)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 5.50
+ -2.24 8.59
+ -1.77 0.24 10.00
+ -2.38 -0.33 4.07 11.01
+ 0.45 -6.29 -6.53 -6.98 19.05
+ -2.16 -0.74 1.42 1.10 -2.47 7.85
+ -0.47 2.83 -0.39 2.41 -4.70 3.16 8.43
+ 0.63 -3.39 1.16 -3.91 -5.70 -0.24 -1.80 11.64
+ -3.01 0.70 1.77 0.32 -5.95 -2.24 -1.29 -1.24 15.72
+ -1.72 -3.93 -5.78 -6.18 -0.13 -3.26 -5.89 -8.58 -4.44 6.74
+ -1.09 -2.83 -5.64 -7.41 -0.82 -4.56 -5.62 -6.55 -2.49 3.86 6.38
+ -1.22 3.89 1.64 1.53 -6.65 3.24 3.08 -1.82 -0.17 -4.82 -5.91 8.23
+ 0.16 -1.43 -4.67 -7.88 3.50 -1.76 -3.94 -5.29 -3.66 2.94 4.32 -5.47 10.21
+ -2.42 -4.36 -6.22 -5.06 1.72 -5.54 -4.44 -7.46 0.25 2.30 3.90 -6.19 2.66 9.14
+ -1.11 1.31 -3.23 0.81 -6.70 1.30 -0.43 -1.79 -3.55 -4.04 -2.88 -1.21 -2.02 -2.96 13.32
+ 1.27 -0.50 1.54 2.34 1.08 2.59 0.42 0.63 -2.38 -4.67 -6.22 -0.27 -3.92 -5.03 -1.28 6.35
+ 0.60 0.34 1.14 -1.36 -1.89 1.08 -0.61 -2.24 -1.14 -3.03 -2.40 -0.37 -5.18 -4.00 2.44 3.09 6.33
+ -2.61 1.02 -6.29 -5.63 -3.01 -4.30 -6.28 -4.77 -5.71 -0.26 -0.58 -5.45 4.28 6.49 -11.46 -4.44 -3.55 18.08
+ -4.22 -1.01 -0.93 -3.85 -0.44 -1.73 -4.50 -4.34 1.17 -0.08 1.81 -4.03 -4.95 5.38 -7.41 -4.17 -2.92 6.79 10.92
+ 0.16 -3.80 -5.65 -6.10 1.32 -4.97 -4.23 -5.32 -1.63 5.23 2.28 -3.57 1.18 0.52 -2.31 -2.69 -0.23 -2.13 0.66 5.28
+//
+H DOSZ010101
+D Amino acid similarity matrix based on the sausage force
+ field (Dosztanyi-Torda, 2001)
+R PMID:11524370
+A Dosztanyi, Z. and Torda, A.E.
+T Amino acid similarity matrices based on force fields
+J Bioinformatics. 17, 686-699 (2001)
+* #SM_SAUSAGE
+* #Amino acid similarity matrix based on the sausage force field
+* #Supplementary material
+* #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_SAUSAGE
+* #Zsuzsanna Doszt?yi and Andrew E. Torda
+* #Amino acid similarity matrices based on force fields
+* #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix.
+* #The native cysteine residues were devided into two subsets depending on their covalent state.
+* #Three rows correspond to cysteines: disulfide bonded (O), free cysteines (J) and all cysteines (C).
+M rows = ARNDCQEGHILKMFPSTWYVJO, cols = ARNDCQEGHILKMFPSTWYV
+ 15.4 -4.9 -8.1 -10.7 38.6 -7.4 -10.7 -6.0 0.2 23.0 20.9 -10.9 17.8 18.9 -9.3 -1.6 -5.2 17.6 18.9 23.7
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+ 9.9 -6.9 -8.8 -10.7 37.4 -8.6 -11.7 -9.0 -0.3 23.2 19.7 -12.1 16.2 18.4 -7.4 -3.8 -5.5 17.0 19.1 23.8
+ 10.2 -6.5 -8.6 -10.7 37.4 -8.4 -11.6 -8.8 -0.0 23.7 19.9 -11.7 16.6 19.1 -7.7 -3.9 -5.3 16.9 19.8 24.6
+ 13.4 -5.4 -10.7 -14.8 41.3 -8.6 -13.4 -11.4 1.0 35.9 29.2 -12.6 23.0 26.0 -8.4 -5.5 -3.9 22.1 25.1 36.7
+ 14.8 -7.1 -10.4 -13.9 48.4 -9.3 -13.4 -8.9 1.0 30.8 27.0 -13.5 23.1 25.1 -10.1 -3.1 -4.6 21.6 24.9 31.8
+ 24.8 -4.6 -3.2 -1.4 166.7 -1.7 -10.1 4.6 20.6 31.6 28.3 -9.3 29.4 44.3 10.4 8.8 7.5 30.9 36.2 32.3
+//
+H DOSZ010102
+D Normalised version of SM_SAUSAGE (Dosztanyi-Torda, 2001)
+R PMID:11524370
+A Dosztanyi, Z. and Torda, A.E.
+T Amino acid similarity matrices based on force fields
+J Bioinformatics. 17, 686-699 (2001)
+* #SM_SAUS_NORM
+* #Normalised version of SM_SAUSAGE
+* #For each matrix element of SM_SAUSAGE, the average over its column and row were subtracted.
+* #Supplementary material
+* #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_SAUS_NORM
+* #Zsuzsanna Doszt?yi and Andrew E. Torda
+* #Amino acid similarity matrices based on force fields
+* #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix.
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
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+ -2.74 -6.81 -9.98 -11.26 0.73 -7.44 -8.85 -10.47 -5.34 6.58 5.26 -8.48 1.62 1.91 -8.38 -9.58 -7.08 0.30 0.07 4.19
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+ -3.42 -6.69 -8.26 -8.93 1.34 -7.06 -8.01 -7.42 -4.96 2.74 1.57 -7.53 -0.35 0.74 -6.23 -7.68 -6.23 -0.50 -0.36 1.52
+ -5.95 -3.94 -2.26 -0.52 -7.12 -2.87 -1.51 -0.20 -2.55 -7.90 -8.52 -1.66 -7.10 -6.65 7.75 -1.58 -2.20 -5.96 -7.30 -7.69
+ -3.67 -2.18 0.63 1.90 -5.80 -1.63 -0.97 0.58 -3.10 -11.75 -9.84 -1.38 -7.62 -8.02 -1.44 3.35 -0.07 -7.36 -6.95 -10.43
+ -4.77 -2.16 -0.75 -0.62 -7.27 -2.26 -2.25 -2.58 -3.43 -7.48 -7.34 -1.98 -6.61 -6.42 -2.08 0.71 -0.11 -6.41 -5.58 -6.35
+ -3.91 -6.07 -6.74 -6.70 0.60 -5.95 -6.26 -5.99 -4.57 -0.27 -0.92 -6.32 -2.01 -1.37 -4.55 -6.28 -5.42 -0.78 -1.14 -1.09
+ -3.88 -5.94 -6.73 -6.96 0.33 -5.99 -6.32 -6.07 -4.56 0.05 -0.99 -6.20 -1.90 -0.88 -5.16 -6.67 -5.43 -1.14 -0.77 -0.54
+ -3.35 -7.47 -11.62 -13.79 1.58 -8.92 -10.84 -11.38 -6.24 9.49 5.63 -9.80 1.76 3.32 -8.51 -10.91 -6.70 1.31 1.87 8.82
+//
+H DOSZ010103
+D An amino acid similarity matrix based on the THREADER force field
+ (Dosztanyi-Torda, 2001)
+R PMID:11524370
+A Dosztanyi, Z. and Torda, A.E.
+T Amino acid similarity matrices based on force fields
+J Bioinformatics. 17, 686-699 (2001)
+* #SM_THREADER
+* #An amino acid similarity matrix based on the THREADER force field (Jones, DT et al.Nature, 358,86-89).
+* #Supplementary material
+* #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_THREADER
+* #Zsuzsanna Doszt?yi and Andrew E. Torda
+* #Amino acid similarity matrices based on force fields
+* #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix.
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 10.0 -0.2 -1.2 -2.8 3.8 0.6 -1.0 0.9 0.2 5.1 4.5 -1.4 3.9 1.9 -0.9 1.8 1.6 0.5 1.8 5.5
+ 2.3 8.1 -0.4 -1.6 -0.6 2.9 1.0 -1.9 1.8 0.5 1.8 3.6 1.7 0.4 -2.1 0.2 0.7 -0.5 1.7 1.0
+ 1.5 0.3 6.4 1.9 -0.3 1.2 0.6 0.5 2.0 -0.4 -1.1 0.5 0.2 -1.9 -1.3 1.6 1.0 -2.4 -0.4 -0.6
+ 0.7 -0.4 2.2 7.3 -2.3 1.5 2.7 -0.4 0.2 -1.6 -1.3 -0.1 -1.7 -3.0 -0.4 0.9 0.2 -3.4 -1.4 -1.8
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+ 2.0 -2.2 -0.1 -1.3 -1.0 -1.3 -3.0 7.8 -0.9 -1.2 -1.4 -2.2 -0.9 -1.9 -1.5 0.6 -0.9 -1.7 -1.3 -1.3
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+ 2.7 4.6 0.8 -0.3 -0.7 3.9 2.4 -1.0 1.6 0.4 0.8 6.5 1.0 -1.3 -0.2 1.2 0.6 -1.1 0.2 0.0
+ 4.3 -0.4 -2.2 -4.9 3.6 1.2 -2.5 -1.7 1.3 8.7 9.7 -2.5 11.4 5.2 -2.8 -1.0 0.9 2.7 4.1 7.2
+ 1.8 -2.0 -4.4 -6.3 3.8 -3.1 -4.3 -2.6 1.1 7.0 7.6 -5.1 4.8 12.4 -3.8 -2.2 -0.1 4.4 7.6 5.8
+ 0.3 -2.1 -1.5 -0.8 -2.9 -0.4 -0.7 -1.2 -1.1 -1.5 -2.4 -0.9 -1.7 -2.7 8.7 -0.4 -0.2 -3.1 -1.9 -1.5
+ 3.5 0.0 0.9 -0.3 1.3 0.9 -0.8 0.6 0.3 0.4 0.4 -0.1 0.6 -0.4 -0.6 4.9 2.8 -2.0 0.1 1.1
+ 2.9 0.1 -0.1 -1.4 2.1 -0.0 -1.1 -1.0 -0.3 3.2 2.9 -1.1 2.0 1.1 -0.6 2.4 5.8 -0.7 0.7 3.9
+ 1.5 -1.8 -4.2 -5.9 0.6 -0.3 -3.8 -2.0 -0.7 3.5 4.3 -3.9 3.5 5.5 -3.7 -3.0 -1.2 16.0 5.4 3.1
+ 2.2 -0.1 -2.5 -4.2 2.4 -0.4 -3.1 -1.9 3.6 5.4 5.1 -3.0 4.3 8.2 -2.9 -1.3 -0.2 4.9 10.8 5.1
+ 4.6 -2.2 -3.8 -5.9 5.4 -2.6 -4.9 -2.5 -1.4 11.9 8.4 -4.8 6.1 5.1 -3.0 -1.4 2.0 1.3 3.8 12.7
+//
+H DOSZ010104
+D Normalised version of SM_THREADER (Dosztanyi-Torda, 2001)
+R PMID:11524370
+A Dosztanyi, Z. and Torda, A.E.
+T Amino acid similarity matrices based on force fields
+J Bioinformatics. 17, 686-699 (2001)
+* #SM_THREAD_NORM
+* #Normalised version of SM_THREADER
+* #based on the THREADER force field (Jones, DT et al.Nature, 358,86-89)
+* #For each matrix element of SM_THREADER, the average over its column and row were subtracted.
+* #Supplementary material
+* #http://www.rsc.anu.edu.au/~zsuzsa/suppl/matrices/SM_THREAD_NORM
+* #Zsuzsanna Doszt?yi and Andrew E. Torda
+* #Amino acid similarity matrices based on force fields
+* #The amino acids are ordered according to the first principal component of the SM_SAUSAGE matrix.
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 5.34 -2.01 -2.01 -2.43 0.01 -1.75 -1.66 -0.02 -2.48 -0.08 -0.70 -1.99 -0.84 -2.14 -1.29 0.01 -0.96 -2.08 -2.19 0.48
+ -1.67 7.03 -0.49 -0.60 -3.62 1.22 1.10 -2.07 -0.20 -3.98 -2.76 3.65 -2.34 -2.93 -1.78 -0.86 -1.15 -2.34 -1.64 -3.36
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+ -2.11 -0.33 3.25 9.44 -4.24 0.92 3.93 0.59 -0.65 -4.98 -4.75 1.13 -4.55 -5.14 1.12 0.90 -0.56 -4.19 -3.58 -4.97
+ -0.65 -3.48 -1.98 -3.34 13.84 -3.45 -3.46 -1.20 -2.28 0.06 -0.27 -3.54 -1.22 -0.03 -2.65 -0.95 -0.79 -2.50 -1.78 0.87
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+ -1.02 0.98 0.60 3.37 -3.78 2.32 6.97 -2.17 -0.47 -4.95 -3.65 2.26 -2.97 -3.79 0.06 -0.76 -1.28 -3.04 -3.19 -4.26
+ -0.26 -1.56 1.55 1.48 -2.34 -1.25 -1.17 9.29 -1.15 -4.03 -4.21 -0.44 -3.19 -3.47 0.51 1.17 -1.03 -1.86 -2.90 -3.91
+ -2.56 0.01 0.68 -0.35 -2.57 0.11 -0.10 -1.19 7.89 -3.96 -3.16 -0.08 -1.90 -1.24 -1.20 -1.23 -2.21 -2.46 0.77 -4.03
+ -0.31 -4.43 -4.41 -5.36 1.30 -4.51 -6.08 -3.12 -3.69 8.26 4.84 -5.08 2.88 2.56 -3.16 -3.78 -1.20 -0.79 0.26 7.02
+ -0.88 -3.07 -4.99 -4.92 0.62 -3.02 -4.35 -3.46 -2.92 4.66 7.42 -4.37 3.75 2.96 -4.05 -3.72 -1.49 -0.14 -0.11 3.28
+ -1.38 3.49 0.60 0.70 -3.80 2.13 2.39 -1.25 -0.51 -4.23 -3.83 6.56 -3.10 -4.67 0.10 -0.01 -1.31 -3.05 -3.23 -4.37
+ -0.78 -2.55 -3.44 -4.93 -0.53 -1.56 -3.50 -2.97 -1.76 3.06 4.06 -3.56 6.28 0.83 -3.50 -3.15 -2.07 -0.25 -0.27 1.80
+ -2.29 -3.14 -4.59 -5.31 0.64 -4.86 -4.31 -2.90 -0.99 2.42 2.96 -5.13 0.69 8.98 -3.57 -3.35 -2.07 2.45 4.24 1.36
+ -1.73 -1.24 0.29 2.15 -3.99 -0.11 1.26 0.50 -1.21 -4.07 -4.99 1.11 -3.74 -4.08 11.00 0.46 -0.15 -3.03 -3.33 -3.88
+ -0.12 -0.69 1.10 1.03 -1.37 -0.44 -0.42 0.78 -1.31 -3.73 -3.79 0.30 -3.04 -3.34 0.06 4.20 1.29 -3.55 -2.88 -2.85
+ -1.04 -0.99 -0.21 -0.43 -0.96 -1.67 -1.06 -1.15 -2.26 -1.36 -1.66 -1.06 -2.03 -2.16 -0.27 1.33 3.91 -2.63 -2.66 -0.44
+ -2.06 -2.46 -3.91 -4.46 -2.06 -1.62 -3.37 -1.76 -2.37 -0.62 0.12 -3.41 -0.13 2.53 -2.97 -3.71 -2.67 14.53 2.44 -0.84
+ -2.32 -1.76 -3.17 -3.78 -1.25 -2.67 -3.59 -2.64 0.97 0.27 -0.02 -3.54 -0.32 4.28 -3.11 -2.98 -2.64 2.44 6.90 0.15
+ 0.27 -3.71 -4.37 -5.30 1.94 -4.67 -5.26 -3.06 -3.82 7.00 3.43 -5.11 1.69 1.39 -3.05 -2.86 -0.24 -1.03 0.05 7.93
+//
+H GIAG010101
+D Residue substitutions matrix from thermo/mesophilic to psychrophilic
+ enzymes (Gianese et al., 2001)
+R PMID:11342709
+A Gianese, G., Argos, P. and Pascarella, S.
+T Structural adaptation of enzymes to low temperatures
+J Protein Eng. 14, 141-148 (2001)
+* (rows = WARM, cols = COLD)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 0.0 -2.4 0.5 -1.0 -0.4 -0.1 -5.7 1.8 -0.2 -0.8 0.5 -1.8 0.2 -0.2 -2.0 -0.4 0.9 -0.4 -0.4 -3.9
+ 2.4 0.0 2.1 0.9 0.2 2.0 0.9 0.8 0.1 0.2 0.5 3.4 0.1 -0.5 0.5 2.2 1.3 0.2 0.2 0.7
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+ 1.0 -0.9 1.3 0.0 -0.2 -1.2 -2.7 -1.0 -0.2 0.0 -0.8 -0.7 0.1 -0.1 -0.6 -0.3 1.2 -0.2 -0.1 0.1
+ 0.4 -0.2 -0.2 0.2 0.0 0.1 -0.3 -0.3 0.1 -0.1 0.2 0.0 0.0 0.0 0.0 0.0 -0.9 -0.1 0.1 -0.6
+ 0.1 -2.0 0.8 1.2 -0.1 0.0 -1.5 -0.5 0.4 -0.5 -1.4 -1.9 0.5 -0.3 -0.3 0.1 0.7 -0.2 0.0 -0.8
+ 5.7 -0.9 1.9 2.7 0.3 1.5 0.0 0.0 -0.4 0.5 -0.4 -1.7 0.4 -0.1 -0.7 2.7 2.2 -0.2 -0.1 -0.1
+ -1.8 -0.8 0.4 1.0 0.3 0.5 0.0 0.0 0.2 0.0 -0.1 -0.5 0.4 -0.5 -0.2 0.1 -0.1 -0.1 0.3 0.4
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+ -0.5 -0.5 0.5 0.8 -0.2 1.4 0.4 0.1 -0.3 0.3 0.0 -0.7 0.2 -1.0 0.6 -0.1 -0.1 0.1 -0.7 0.1
+ 1.8 -3.4 2.4 0.7 0.0 1.9 1.7 0.5 0.4 0.6 0.7 0.0 0.8 -0.7 0.1 2.6 1.4 0.0 0.1 1.1
+ -0.2 -0.1 0.2 -0.1 0.0 -0.5 -0.4 -0.4 0.0 -1.3 -0.2 -0.8 0.0 0.3 -0.2 -0.2 0.1 0.2 -0.1 -1.0
+ 0.2 0.5 0.4 0.1 0.0 0.3 0.1 0.5 0.5 0.2 1.0 0.7 -0.3 0.0 0.0 0.5 -0.8 -0.7 0.5 0.3
+ 2.0 -0.5 0.8 0.6 0.0 0.3 0.7 0.2 -0.2 -0.2 -0.6 -0.1 0.2 0.0 0.0 1.8 0.5 -0.1 0.1 0.2
+ 0.4 -2.2 1.3 0.3 0.0 -0.1 -2.7 -0.1 -0.3 -0.3 0.1 -2.6 0.2 -0.5 -1.8 0.0 -1.6 -0.1 -0.1 0.0
+ -0.9 -1.3 1.5 -1.2 0.9 -0.7 -2.2 0.1 0.0 -0.8 0.1 -1.4 -0.1 0.8 -0.5 1.6 0.0 -0.4 0.4 -1.5
+ 0.4 -0.2 0.0 0.2 0.1 0.2 0.2 0.1 0.3 0.5 -0.1 0.0 -0.2 0.7 0.1 0.1 0.4 0.0 -0.2 0.1
+ 0.4 -0.2 -0.4 0.1 -0.1 0.0 0.1 -0.3 0.3 0.0 0.7 -0.1 0.1 -0.5 -0.1 0.1 -0.4 0.2 0.0 -0.1
+ 3.9 -0.7 0.9 -0.1 0.6 0.8 0.1 -0.4 -0.1 2.1 -0.1 -1.1 1.0 -0.3 -0.2 0.0 1.5 -0.1 0.1 0.0
+//
+H DAYM780302
+D Log odds matrix for 40 PAMs (Dayhoff et al., 1978)
+R
+A Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C.
+T A model of evolutionary change in proteins
+J In "Atlas of Protein Sequence and Structure", Vol.5, Suppl.3 (Dayhoff,
+ M.O., ed.), National Biomedical Research Foundation, Washington, D.C.,
+ p.352 (1978)
+* #
+* # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93]
+* #
+* # PAM 40 substitution matrix, scale = ln(2)/2 = 0.346574
+* #
+* # Expected score = -4.27, Entropy = 2.26 bits
+* #
+* # Lowest score = -15, Highest score = 13
+* #
+M rows = ARNDCQEGHILKMFPSTWYV-, cols = ARNDCQEGHILKMFPSTWYV
+ 6 -6 -3 -3 -6 -3 -2 -1 -6 -4 -5 -6 -4 -7 -1 0 0 -12 -7 -2
+ -6 8 -5 -9 -7 -1 -8 -8 -1 -5 -8 1 -3 -8 -3 -2 -5 -1 -9 -7
+ -3 -5 7 2 -9 -3 -1 -2 1 -4 -6 0 -7 -8 -5 0 -1 -7 -4 -7
+ -3 -9 2 7 -12 -2 3 -3 -3 -6 -11 -4 -9 -13 -7 -3 -4 -13 -10 -7
+ -6 -7 -9 -12 9 -12 -12 -8 -7 -5 -13 -12 -12 -11 -7 -2 -7 -14 -3 -5
+ -3 -1 -3 -2 -12 8 2 -6 1 -7 -4 -2 -3 -11 -2 -4 -5 -11 -10 -6
+ -2 -8 -1 3 -12 2 7 -3 -4 -5 -8 -4 -6 -12 -5 -4 -5 -15 -8 -6
+ -1 -8 -2 -3 -8 -6 -3 6 -8 -9 -9 -6 -7 -8 -5 -1 -5 -13 -12 -5
+ -6 -1 1 -3 -7 1 -4 -8 9 -8 -5 -5 -9 -5 -3 -5 -6 -6 -3 -6
+ -4 -5 -4 -6 -5 -7 -5 -9 -8 8 -1 -5 0 -2 -7 -6 -2 -12 -5 2
+ -5 -8 -6 -11 -13 -4 -8 -9 -5 -1 7 -7 1 -2 -6 -7 -6 -5 -6 -2
+ -6 1 0 -4 -12 -2 -4 -6 -5 -5 -7 6 -1 -12 -6 -3 -2 -10 -8 -8
+ -4 -3 -7 -9 -12 -3 -6 -7 -9 0 1 -1 11 -3 -7 -5 -3 -11 -10 -1
+ -7 -8 -8 -13 -11 -11 -12 -8 -5 -2 -2 -12 -3 9 -9 -6 -8 -4 2 -7
+ -1 -3 -5 -7 -7 -2 -5 -5 -3 -7 -6 -6 -7 -9 8 -1 -3 -12 -12 -5
+ 0 -2 0 -3 -2 -4 -4 -1 -5 -6 -7 -3 -5 -6 -1 6 1 -4 -6 -5
+ 0 -5 -1 -4 -7 -5 -5 -5 -6 -2 -6 -2 -3 -8 -3 1 7 -11 -6 -2
+ -12 -1 -7 -13 -14 -11 -15 -13 -6 -12 -5 -10 -11 -4 -12 -4 -11 13 -4 -14
+ -7 -9 -4 -10 -3 -10 -8 -12 -3 -5 -6 -8 -10 2 -12 -6 -6 -4 10 -6
+ -2 -7 -7 -7 -5 -6 -6 -5 -6 2 -2 -8 -1 -7 -5 -5 -2 -14 -6 7
+ -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15 -15
+//
+H HENS920104
+D BLOSUM50 substitution matrix (Henikoff-Henikoff, 1992)
+R PMID:1438297
+A Henikoff, S. and Henikoff, J.G.
+T Amino acid substitution matrices from protein blocks
+J Proc. Natl. Acad. Sci. USA 89, 10915-10919 (1992)
+* # Matrix made by matblas from blosum50.iij
+* # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units
+* # Blocks Database = /data/blocks_5.0/blocks.dat
+* # Cluster Percentage: >= 50
+* # Entropy = 0.4808, Expected = -0.3573
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -2 -1 -1 -3 -1 1 0 -3 -2 0
+ -2 7 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -1 -3
+ -1 -1 7 2 -2 0 0 0 1 -3 -4 0 -2 -4 -2 1 0 -4 -2 -3
+ -2 -2 2 8 -4 0 2 -1 -1 -4 -4 -1 -4 -5 -1 0 -1 -5 -3 -4
+ -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1
+ -1 1 0 0 -3 7 2 -2 1 -3 -2 2 0 -4 -1 0 -1 -1 -1 -3
+ -1 0 0 2 -3 2 6 -3 0 -4 -3 1 -2 -3 -1 -1 -1 -3 -2 -3
+ 0 -3 0 -1 -3 -2 -3 8 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4
+ -2 0 1 -1 -3 1 0 -2 10 -4 -3 0 -1 -1 -2 -1 -2 -3 2 -4
+ -1 -4 -3 -4 -2 -3 -4 -4 -4 5 2 -3 2 0 -3 -3 -1 -3 -1 4
+ -2 -3 -4 -4 -2 -2 -3 -4 -3 2 5 -3 3 1 -4 -3 -1 -2 -1 1
+ -1 3 0 -1 -3 2 1 -2 0 -3 -3 6 -2 -4 -1 0 -1 -3 -2 -3
+ -1 -2 -2 -4 -2 0 -2 -3 -1 2 3 -2 7 0 -3 -2 -1 -1 0 1
+ -3 -3 -4 -5 -2 -4 -3 -4 -1 0 1 -4 0 8 -4 -3 -2 1 4 -1
+ -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3
+ 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2
+ 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 2 5 -3 -2 0
+ -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1 1 -4 -4 -3 15 2 -3
+ -2 -1 -2 -3 -3 -1 -2 -3 2 -1 -1 -2 0 4 -3 -2 -2 2 8 -1
+ 0 -3 -3 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -3 -1 5
+//
+H QUIB020101
+D STROMA score matrix for the alignment of known distant homologs
+ (Qian-Goldstein, 2002)
+R PMID:12211027
+A Qian, B. and Goldstein, R.A.
+T Optimization of a new score function for the generation of accurate
+ alignments
+J Proteins. 48, 605-610 (2002)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 2.5
+ 0.2 5.2
+ 1.1 0.7 2.5
+ 1 0.1 3.3 5.3
+ 1.2 -1.3 -1.9 -3.1 11.5
+ -0.1 2 1.9 1.1 -2.5 3.6
+ 1.2 1.9 2.3 3.2 -2.4 1.7 3.7
+ 1.4 -0.2 0.7 0.9 -1.3 -0.3 0.5 7.5
+ -1.4 1.5 1.4 0.5 -1.7 1.4 0.3 -1.7 6.8
+ 0.3 -1.9 -2.4 -2.9 -3.2 -0.9 -3.1 -3.7 -1.8 4.5
+ -0.2 -1.5 -2.4 -3.4 -1.6 -1.2 -1.5 -3.8 -2.4 3.4 5.2
+ -0.2 3.4 1.6 1.4 -3 2.2 1.2 0.4 1.1 -1.5 -2 3.9
+ -0.2 -1.4 -2.1 -2.8 -1.3 -0.6 -2 -3.8 -0.8 2.2 3.1 -0.5 5.4
+ -1.6 -3.2 -2.5 -3.7 -0.8 -1.7 -13.7 -4.7 -0.9 2.2 3.7 -2.8 1.7 7
+ 0.7 -0.6 -0.1 -0.2 -3.6 1 0 -0.8 -2.1 -2.4 -1.4 0.2 -1.9 -4.1 8.1
+ 1.7 0.2 1.4 1.7 0.7 0.9 1.1 1.6 -0.1 -1.1 -0.8 1.4 -1.1 -2.5 2 2.8
+ 1.7 0.2 1.4 0.1 0.3 -0.1 1.6 -0.6 -0.2 0 0.3 1 -0.3 -0.8 1.1 2.6 0.4
+ -3.3 -1.5 -4 -5.7 -0.5 -2.9 -4.7 -4.2 -1.2 -1.8 -1.2 -3 -0.6 3.7 -5 -2.8 -2.9 14.9
+ -1.8 -0.9 -0.8 -2.9 -0.3 -1.5 -2.2 -4.8 2.9 0.2 0.8 -1.5 0.5 5.2 -3.3 -0.9 -0.8 4.9 8.1
+ 1.9 -2.8 -0.9 -2.5 0.7 -1.5 -1.3 -1.4 -2.5 4.5 3.4 -1 1.7 0.9 -1.1 -3 1.5 -2.5 0.3 4.2
+//
+H NAOD960101
+D Substitution matrix derived from the single residue interchanges at spatially
+ conserved regions of proteins (Naor et al., 1996)
+R PMID:8601843
+A Naor, D., Fischer, D., Jernigan, R.L., Wolfson, H.J. and Nussinov, R.
+T Amino Acid Pair Interchanges at Spatially Conserved Locations (Naor et al)
+J Journal of Molecular Biology 256, 924-938 (1996)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 4
+ 0 7
+ 0 4 8
+ 0 4 8 11
+ 2 -5 -5 -4 14
+ 0 5 5 6 -4 7
+ 0 8 6 7 -6 8 11
+ 0 0 5 4 0 0 0 12
+ -1 3 2 3 -2 1 2 3 5
+ -2 -7 -9 -9 4 -7 -9 -7 -3 10
+ 0 -5 -7 -8 2 -5 -6 -6 -3 7 9
+ 0 9 6 7 -7 7 9 0 1 -9 -7 13
+ 0 -2 -3 -4 2 -2 -2 -3 -1 3 5 -4 4
+ -1 -5 -6 -6 3 -5 -6 -3 -2 6 6 -7 3 6
+ 0 1 6 6 -1 1 0 6 2 -8 -8 3 -6 -4 19
+ 0 2 4 4 -3 2 3 4 2 -5 -5 3 -3 -4 3 5
+ 0 1 2 2 -2 1 3 0 0 -3 -3 2 -2 -2 1 2 3
+ 0 -3 -4 -4 0 -2 -3 -1 -1 4 2 -5 1 3 -5 -2 0 9
+ 0 -2 -2 -3 0 -1 -2 -1 0 2 1 -3 1 2 -3 -1 0 2 3
+ -2 -6 -8 -9 4 -8 -9 -5 -2 9 5 -8 2 5 -5 -4 -1 4 2 9
+//
+H RUSR970101
+D Substitution matrix based on structural alignments of analogous proteins
+ (Russell et al., 1997)
+R PMID:9199410
+A Russell, R.B., Saqi, M.A.S., Sayle, R.A., Bates, P.A. and Sternberg, M.J.E.
+T Recognition of analogous and homologous protein folds: Analysis of sequence
+ and structure conservation
+J Journal of Molecular Biology 269, 423-439 (1997)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ -2
+ 1 0
+ 0 2 0
+ 0 3 2 -2
+ 2 -3 -4 0 12
+ 1 -2 2 3 2 0
+ 2 2 2 6 -8 6 -2
+ 1 2 3 3 -1 -1 3 0
+ -1 2 7 2 5 0 -11 -5 -3
+ 1 1 -4 -4 -1 1 -4 0 1 2
+ 3 -2 0 -1 4 -2 -1 -2 3 3 -3
+ 1 4 1 0 -1 3 2 2 2 -4 0 0
+ 4 -5 -1 -1 3 -1 -3 1 3 1 8 1 -9
+ -1 5 1 -3 -1 -6 -4 -1 0 5 3 0 0 -3
+ 2 1 0 3 -1 1 1 0 2 2 0 4 -17 4 -1
+ 0 2 5 3 -5 0 2 4 1 -1 -1 0 -3 -2 5 -10
+ 1 0 1 3 2 3 2 0 5 0 -3 -2 3 3 -1 4 0
+ -4 -5 -3 -4 1 -1 -1 0 2 2 4 3 0 11 2 0 3 5
+ 1 3 -3 0 0 2 -2 1 3 3 3 0 4 0 -3 2 1 -12 -4
+ -1 -4 -1 -2 7 2 -3 -3 0 4 6 0 3 5 -1 1 0 2 3 -1
+//
+H RUSR970102
+D Substitution matrix based on structural alignments of remote homolous proteins
+ (Russell et al., 1997)
+R PMID:919941
+A Russell, R.B., Saqi, M.A.S., Sayle, R.A., Bates, P.A. and Sternberg, M.J.E.
+T Recognition of analogous and homologous protein folds: Analysis of sequence and
+ structure conservation
+J Journal of Molecular Biology 269, 423-439 (1997)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 0
+ 0 4
+ 0 0 3
+ -1 0 5 5
+ 2 -1 0 -1 13
+ -1 3 2 3 -6 4
+ 0 2 0 5 -4 2 3
+ 1 0 1 1 -1 0 -1 6
+ -2 2 4 2 1 4 3 -1 11
+ 0 0 -8 -7 1 -3 -3 -4 -4 1
+ 0 -2 -2 -7 2 -5 -2 -4 0 7 2
+ 1 6 1 1 0 4 4 0 1 -6 -4 2
+ 0 0 -3 -6 1 0 -3 -3 1 5 6 -1 3
+ 0 -3 -1 -6 3 -2 -5 -6 0 4 4 -4 4 5
+ 0 -1 2 1 -1 0 2 0 1 -2 -5 0 -3 -1 7
+ 2 0 3 2 -1 4 1 0 -4 -4 -2 0 -2 0 2 0
+ 0 0 4 1 -2 -2 0 0 1 0 0 2 2 -2 1 4 0
+ -1 2 0 -5 2 -3 -2 -2 0 3 0 -2 3 4 -2 1 -4 16
+ 0 2 0 -2 4 1 -1 -1 2 0 0 0 1 7 0 0 -1 8 3
+ 1 -1 -3 -3 2 -1 -2 -2 -3 7 3 -2 3 3 0 -1 0 -2 1 0
+//
+H RUSR970103
+D Substitution matrix based on structural alignments of analogous and remote homolous
+ proteins (Russell et al., 1997)
+R PMID:9199410
+A Russell, R.B., Saqi, M.A.S., Sayle, R.A., Bates, P.A. and Sternberg, M.J.E.
+T Recognition of analogous and homologous protein folds: Analysis of sequence and
+ structure conservation
+J Journal of Molecular Biology 269, 423-439 (1997)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ -2
+ 1 0
+ 0 0 0
+ -1 0 1 0
+ 2 -4 -1 0 12
+ 0 1 3 3 -4 0
+ 1 2 0 4 -8 4 0
+ 0 1 2 2 0 0 1 1
+ 0 3 3 3 2 0 -1 -3 1
+ 1 1 -7 -3 -4 0 -3 -1 -1 0
+ 2 -2 0 -3 2 -2 0 -2 2 5 0
+ 1 3 0 2 2 4 3 1 3 -5 -2 -1
+ 2 0 -3 -2 1 0 -1 0 3 4 6 0 -5
+ 0 -1 1 -4 3 -3 -5 -3 0 4 4 -1 0 0
+ 0 0 1 3 0 0 1 1 2 0 -2 1 0 1 0
+ 0 0 4 2 -3 1 2 0 -1 -3 0 0 -4 0 5 -3
+ 0 0 3 2 0 0 1 0 3 0 -1 1 2 0 1 3 -2
+ 0 0 -1 -5 2 -1 -3 -1 0 4 1 0 3 5 2 2 0 7
+ 0 3 0 -1 1 0 -1 0 1 2 0 0 1 5 -1 0 0 4 -1
+ 0 0 0 -1 5 0 -2 -1 -1 5 4 0 1 3 -1 0 0 0 2 -2
+//
+H OGAK980101
+D Substitution matrix derived from structural alignments by maximizing entropy
+ (Ogata et al., 1998)
+R PMID:10522237
+A Ogata, K., Ohya, M. and Umeyama, H.
+T Amino acid similarity matrix for homology modeling derived from structural
+ alignment and optimized by the Monte Carlo method
+J Journal of Molecular Graphics and Modelling 16, 178-254 (1998)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ -4.8
+ -7.0 -6.2
+ -7.1 -7.3 -4.8
+ -6.9 -7.3 -6.3 -5.0
+ -7.7 -8.3 -8.6 -8.3 -3.2
+ -7.0 -7.5 -7.1 -7.3 -8.3 -6.5
+ -6.7 -7.5 -6.5 -6.4 -10.2 -6.8 -5.4
+ -5.8 -7.5 -6.8 -6.3 -7.5 -7.6 -7.4 -4.2
+ -7.7 -8.1 -6.8 -8.1 -9.3 -7.7 -7.8 -7.7 -6.1
+ -7.1 -7.7 -7.6 -8.3 -9.0 -7.9 -8.3 -8.0 -8.2 -5.5
+ -6.7 -7.9 -7.7 -7.1 -7.7 -7.4 -7.4 -8.0 -8.1 -5.5 -4.0
+ -6.7 -6.6 -6.8 -6.9 -8.5 -6.7 -6.7 -6.8 -7.6 -8.1 -7.2 -5.5
+ -8.0 -7.8 -7.4 -8.2 -8.7 -8.5 -8.1 -8.2 -9.7 -7.4 -7.0 -8.2 -6.7
+ -7.9 -8.1 -8.2 -9.5 -8.9 -8.6 -8.2 -8.1 -8.2 -7.2 -6.6 -8.8 -8.5 -5.7
+ -6.8 -7.9 -8.0 -7.3 -8.3 -8.1 -7.8 -7.2 -7.5 -7.2 -6.6 -7.5 -8.8 -8.8 -5.7
+ -5.6 -6.9 -6.5 -5.7 -8.2 -7.0 -6.6 -6.3 -7.0 -7.2 -6.4 -6.6 -7.5 -8.3 -6.8 -4.6
+ -6.2 -6.8 -6.4 -6.5 -7.5 -7.0 -6.8 -6.7 -8.0 -7.1 -6.2 -6.3 -7.3 -7.7 -6.7 -5.5 -5.0
+ -9.0 -9.4 -8.6 -9.8 -12.0 -8.3 -7.9 -7.2 -9.7 -7.7 -6.8 -9.5 -7.2 -6.9 -10.4 -7.6 -7.6 -5.0
+ -7.5 -8.4 -7.0 -7.2 -10.6 -7.3 -7.5 -7.5 -6.8 -7.4 -6.6 -7.3 -7.9 -6.0 -8.1 -7.3 -6.8 -6.5 -4.7
+ -5.9 -7.4 -7.2 -7.1 -8.1 -7.5 -7.3 -7.3 -7.5 -5.7 -5.8 -6.7 -7.2 -7.1 -7.5 -6.8 -6.2 -7.8 -7.2 -4.8
+//
+H KANM000101
+D Substitution matrix (OPTIMA) derived by maximizing discrimination between
+ homologs and non-homologs (Kann et al., 2000)
+R PMID:11056037
+A Kann, M., Qian, B. and Goldstein, R.A.
+T Optimization of a new score function for the detection of remote homologs
+J Proteins: Structure, Function, and Genetics 41, 498-503 (2000)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 36
+ -9 56
+ -19 4 59
+ -20 -18 18 65
+ 6 -29 -30 -30 99
+ -3 12 2 2 -30 46
+ -10 3 3 20 -39 19 40
+ 4 -18 7 -10 -29 -20 -23 67
+ -19 3 12 -7 -29 3 2 -18 86
+ -5 -28 -32 -34 -6 -30 -33 -41 -28 35
+ -7 -20 -32 -43 -6 -23 -31 -42 -27 28 32
+ -10 31 1 -4 -29 15 14 -18 -7 -31 -21 37
+ -9 -10 -19 -30 -8 1 -21 -30 -19 12 24 -12 51
+ -19 -30 -29 -33 -18 -29 -32 -32 -8 8 17 -29 2 57
+ -5 -18 -17 -7 -30 -11 -7 -18 -18 -30 -33 -10 -21 -39 74
+ 12 -11 10 4 -10 0 -1 2 -9 -20 -22 3 -10 -19 -8 36
+ 0 -8 0 -10 -7 -7 -6 -17 -20 -8 -13 -8 -7 -18 -11 18 48
+ -29 -29 -39 -40 -18 -19 -29 -19 -18 -28 -15 -30 -8 14 -38 -29 -19 110
+ -19 -15 -19 -20 -18 -9 -21 -29 20 -8 -2 -17 -9 37 -28 -19 -17 22 69
+ 6 -32 -31 -31 -6 -19 -28 -30 -29 35 18 -23 10 0 -18 -22 6 -28 -9 38
+//
+H NGPC000101
+D Substitution matrix (PHAT) built from hydrophobic and transmembrane regions
+ of the Blocks database (Ng et al., 2000)
+R PMID:11108698
+A Ng, P.C., Henikoff, J.G. and Henikoff, S.
+T PHAT: a transmembrane-specific substitution matrix
+J Bioinformatics 16, 760-766 (2000)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 5
+ -6 9
+ -2 -3 11
+ -5 -7 2 12
+ 1 -8 -2 -7 7
+ -3 -2 2 0 -5 9
+ -5 -6 0 6 -7 1 12
+ 1 -5 -1 -2 -2 -2 -3 9
+ -3 -4 4 -1 -7 2 -1 -4 11
+ 0 -6 -3 -5 -3 -3 -5 -2 -5 5
+ -1 -6 -3 -5 -2 -3 -5 -2 -4 2 4
+ -7 -1 -2 -5 -10 -1 -4 -5 -5 -7 -7 5
+ -1 -6 -2 -5 -2 -1 -5 -1 -4 3 2 -6 6
+ -1 -7 -1 -5 0 -2 -5 -2 -2 0 1 -7 0 6
+ -3 -7 -4 -5 -8 -3 -5 -3 -6 -4 -5 -4 -5 -5 13
+ 2 -6 1 -4 1 -1 -3 1 -2 -2 -2 -5 -2 -2 -3 6
+ 0 -6 -1 -5 -1 -3 -5 -1 -4 -1 -1 -6 0 -2 -4 1 3
+ -4 -7 -5 -7 -4 1 -7 -5 -3 -4 -3 -8 -4 0 -6 -5 -7 11
+ -3 -6 2 -4 -1 0 -2 -3 3 -3 -2 -4 -2 4 -5 -2 -3 1 11
+ 1 -7 -3 -5 -2 -3 -5 -2 -5 3 1 -8 1 -1 -4 -2 0 -4 -3 4
+//
+H MUET010101
+D Non-symmetric substitution matrix (SLIM) for detection of homologous
+ transmembrane proteins (Mueller et al., 2001)
+R PMID:11473008
+A Mueller, T., Rahmann, S. and Rehmsmeier, M.
+T Non-symmetric score matrices and the detection of homologous transmembrane
+ proteins
+J Bioinformatics 17 Suppl 1, S182-S189 (2001)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 5.0
+ -5.5 10.0
+ -3.0 -4.5 8.0
+ -6.5 -9.5 -0.5 9.0
+ 2.5 -5.0 -2.5 -7.5 11.0
+ -4.0 -2.5 -1.0 -2.5 -3.5 7.0
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+ 0.0 -5.5 -2.0 -5.5 2.5 -2.0 -5.5 -1.0 -1.0 1.5 2.5 -5.5 2.5 8.0
+ -4.0 -8.0 -6.0 -7.0 -9.0 -6.0 -7.0 -4.5 -8.0 -4.0 -5.0 -4.5 -5.0 -4.5 11.0
+ 2.0 -6.0 0.5 -5.5 3.0 -2.5 -5.0 0.5 -2.5 -1.5 -1.5 -5.0 -1.0 -0.5 -4.0 6.0
+ 1.5 -5.0 -1.5 -5.5 1.0 -3.5 -6.5 -1.5 -3.5 0.5 0.5 -5.0 1.5 0.0 -3.5 1.5 4.0
+ -2.5 -4.5 -4.0 -6.5 -0.5 1.0 -6.0 -4.0 -1.0 -1.5 -0.5 -5.5 -0.5 3.5 -4.5 -3.0 -4.5 15.0
+ -3.5 -5.5 0.0 -5.5 0.5 -2.0 -5.5 -3.5 2.5 -2.5 -1.5 -3.5 -1.5 5.0 -5.5 -2.0 -2.5 2.0 11.0
+ 1.5 -6.0 -4.5 -6.0 1.0 -3.5 -6.5 -2.5 -4.5 4.5 2.5 -7.0 2.5 1.0 -4.0 -1.0 1.0 -2.0 -2.5 5.0
+//
+H MUET020101
+D Substitution matrix (VTML160) obtained by maximum likelihood estimation
+ (Mueller et al., 2002)
+R PMID:11752185
+A Mueller, T., Spang, R. and Vingron, M.
+T Estimating amino acid substitution models: A comparison of Dayhoff's
+ estimator, the resolvent approach and a maximum likelihood method
+J Molecular Biology and Evolution 19, 8-13 (2002)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 5
+ -2 7
+ -1 0 7
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+ 0 -4 -4 -4 1 -3 -3 -5 -3 4 2 -3 1 -1 -3 -2 0 -5 -3 5
+//
+H MUET020102
+D Substitution matrix (VTML250) obtained by maximum likelihood estimation
+ (Mueller et al., 2002)
+R 11752185
+A Mueller, T., Spang, R. and Vingron, M.
+T Estimating amino acid substitution models: A comparison of Dayhoff's
+ estimator, the resolvent approach and a maximum likelihood method
+J Molecular Biology and Evolution 19, 8-13 (2002)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 2
+ -1 5
+ 0 0 4
+ 0 -1 2 5
+ 1 -2 -1 -3 11
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+ -1 3 1 0 -2 2 1 -1 0 -2 -2 3
+ -1 -1 -2 -3 0 -1 -2 -3 -2 2 3 -1 4
+ -2 -3 -3 -5 -2 -2 -4 -4 0 1 2 -3 1 7
+ 0 -1 -1 0 -2 0 0 -1 -1 -3 -2 0 -2 -3 7
+ 1 0 1 0 1 0 0 0 0 -2 -2 0 -1 -2 0 2
+ 1 -1 0 0 0 0 0 -1 0 0 -1 0 0 -2 0 1 3
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+ -2 -2 -1 -3 0 -2 -2 -4 2 -1 0 -2 -1 5 -4 -1 -2 4 8
+ 0 -2 -2 -3 1 -2 -2 -3 -2 3 2 -2 2 0 -2 -1 0 -3 -1 3
+//
+H CROG050101
+D Substitution matrix computed from the Dirichlet Mixture Model
+ (Crooks-Brenner, 2005)
+R PMID:15531614
+A Crooks, G.E. and Brenner, S.E.
+T An alternative model of amino acid replacement
+J Bioinformatics 21, 975-980 (2005)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 4
+ -2 6
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+ -2 -3 -4 -5 -2 -3 -4 -5 -3 2 5
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+ -1 -2 -3 -4 -1 -2 -3 -4 -2 1 2 -2 7
+ -2 -3 -4 -5 -2 -3 -4 -5 -1 0 1 -4 1 7
+ -1 -2 -2 -1 -3 -1 -1 -2 -2 -4 -3 -1 -3 -3 8
+ 0 -1 0 0 -2 0 -1 -1 -1 -4 -3 -1 -2 -3 -1 4
+ -1 -1 -1 -1 -1 -1 -1 -2 -1 -2 -2 -1 -1 -2 -2 1 5
+ -3 -2 -3 -4 -2 -2 -3 -4 0 -1 -1 -3 0 3 -3 -3 -2 12
+ -2 -2 -2 -3 -2 -2 -3 -4 0 -1 -1 -3 0 3 -3 -2 -2 3 8
+ -1 -3 -4 -5 0 -3 -4 -5 -3 3 1 -3 1 0 -3 -3 -1 -2 -2 5
+//
diff --git a/modules/seq/alg/pymod/aaindex3 b/modules/seq/alg/pymod/aaindex3
new file mode 100644
index 000000000..a455867f4
--- /dev/null
+++ b/modules/seq/alg/pymod/aaindex3
@@ -0,0 +1,1383 @@
+H TANS760101
+D Statistical contact potential derived from 25 x-ray protein structures
+R PMID:1004017
+A Tanaka, S. and Scheraga, H.A.
+T Medium- and long-range interaction parameters between amino acids
+ for predicting three-dimensional structures of proteins
+J Macromolecules 9, 945-950 (1976)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ -2.6
+ -3.4 -4.3
+ -3.1 -4.1 -3.2
+ -2.8 -3.9 -3.1 -2.7
+ -4.2 -5.3 -4.9 -4.2 -7.1
+ -3.5 -4.5 -3.8 -3.2 -5.0 -3.4
+ -3.0 -4.2 -3.4 -3.3 -4.4 -3.6 -2.8
+ -3.8 -4.5 -4.0 -3.7 -5.4 -4.4 -3.8 -3.9
+ -4.0 -4.9 -4.4 -4.3 -5.6 -4.7 -4.5 -4.7 -4.9
+ -5.9 -6.2 -5.8 -5.4 -7.3 -5.9 -5.7 -6.3 -6.6 -8.2
+ -4.8 -5.1 -4.6 -4.3 -6.2 -5.0 -4.6 -5.2 -5.6 -7.5 -6.0
+ -3.1 -3.6 -3.3 -3.2 -4.4 -3.7 -3.8 -3.8 -4.1 -5.6 -4.6 -2.7
+ -4.6 -5.0 -4.2 -4.3 -6.2 -3.5 -4.6 -5.1 -5.4 -7.4 -6.3 -4.7 -5.8
+ -5.1 -5.8 -5.0 -4.9 -6.8 -5.3 -5.0 -5.6 -6.4 -8.0 -7.0 -4.9 -6.6 -7.1
+ -3.4 -4.2 -3.6 -3.3 -5.3 -4.0 -3.5 -4.2 -4.5 -6.0 -4.8 -3.6 -5.1 -5.2 -3.5
+ -2.9 -3.8 -3.1 -2.7 -4.6 -3.6 -3.2 -3.8 -4.3 -5.5 -4.4 -3.0 -4.1 -4.7 -3.4 -2.5
+ -3.3 -4.0 -3.5 -3.1 -4.8 -3.7 -3.3 -4.1 -4.5 -5.9 -4.8 -3.3 -4.6 -5.1 -3.6 -3.3 -3.1
+ -5.2 -5.8 -5.3 -5.1 -6.9 -5.8 -5.2 -5.8 -6.5 -7.8 -6.8 -5.0 -6.9 -7.4 -5.6 -5.0 -5.1 -6.8
+ -4.7 -5.6 -5.0 -4.7 -6.6 -5.2 -4.9 -5.4 -6.1 -7.4 -6.2 -4.9 -6.1 -6.6 -5.2 -4.7 -4.9 -6.8 -6.0
+ -4.3 -4.9 -4.3 -4.0 -6.0 -4.7 -4.2 -5.1 -5.3 -7.3 -6.2 -4.2 -6.0 -6.5 -4.7 -4.2 -4.4 -6.5 -5.9 -5.5
+//
+H TANS760102
+D Number of contacts between side chains derived from 25 x-ray protein structures
+R PMID:1004017
+A Tanaka, S. and Scheraga, H.A.
+T Medium- and long-range interaction parameters between amino acids
+ for predicting three-dimensional structures of proteins
+J Macromolecules 9, 945-950 (1976)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 36
+ 20 14
+ 39 34 22
+ 36 35 31 24
+ 15 13 21 10 48
+ 34 29 30 17 13 7
+ 27 34 27 38 9 19 9
+ 115 58 80 83 53 75 54 75
+ 25 17 25 32 11 17 24 40 8
+ 119 33 51 43 33 29 35 109 27 81
+ 174 47 63 60 49 53 53 155 49 230 167
+ 55 20 39 54 14 32 70 92 21 53 86 20
+ 26 9 7 13 11 1 12 32 7 44 58 21 6
+ 62 32 27 32 32 21 22 67 38 103 175 32 20 53
+ 33 20 22 23 24 23 17 62 15 41 46 34 16 19 11
+ 64 44 42 37 28 44 41 145 43 65 93 51 14 36 38 34
+ 70 36 46 38 22 28 28 116 36 67 110 50 16 39 32 69 29
+ 38 15 21 24 17 22 15 52 23 40 68 20 17 41 19 31 20 7
+ 65 45 50 52 43 32 40 103 44 81 105 64 19 45 42 71 53 32 33
+ 101 44 50 53 53 46 39 183 42 216 306 67 52 114 58 106 79 62 85 152
+//
+H ROBB790102
+D Interaction energies derived from side chain contacts in the interiors of
+ known protein structures
+R PMID:513136
+A Robson, B. and Osguthorpe, D.J.
+T Refined Models for Computer-Simulation of Protein Folding - Applications
+ to the Study of Conserved Secondary Structure and Flexible Hinge Points
+ During the Folding of Pancreatic Trypsin-Inhibitor
+J J. Mol. Biol. 132, 19-51 (1979)
+* (Glu is not available)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ -0.268
+ 0.529 3.717
+ 0.010 1.153 0.130
+ 0.926 5.172 1.921 6.271
+ -0.180 5.014 0.245 10.310 -20.000
+ 0.017 1.212 0.149 2.021 0.296 0.169
+ 0.902 4.911 1.835 6.052 9.050 1.926 5.832
+ NA NA NA NA NA NA NA NA
+ -0.187 1.759 0.088 3.336 -0.099 0.112 3.090 NA -0.106
+ -0.899 1.278 -0.577 3.643 -0.811 -0.547 3.248 NA -0.818 -1.530
+ -0.865 2.952 -0.542 8.760 -0.777 -0.513 7.540 NA -0.784 -1.496 -1.461
+ 0.920 4.514 1.808 5.256 8.223 1.910 5.139 NA 3.084 3.368 7.538 4.533
+ -0.525 6.049 -0.202 14.958 -0.437 -0.173 12.775 NA -0.443 -1.156 -1.121 11.998 -0.781
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+ -1.470 0.099 -1.148 0.322 -1.382 -1.118 0.449 NA -1.389 -2.101 -2.066 0.817 -1.726 -2.162 -2.672
+ 0.022 1.048 0.134 1.660 0.376 0.153 1.603 NA 0.133 -0.476 -0.441 1.554 -0.101 -0.537 -1.047 0.128
+ -0.177 1.054 0.053 1.890 -0.089 0.067 1.792 NA -0.096 -0.808 -0.773 1.786 -0.433 -0.869 -1.379 0.072 -0.085
+ -1.052 2.069 -0.730 7.299 -0.964 -0.700 6.288 NA -0.971 -1.683 -1.649 6.663 -1.308 -1.744 -2.254 -0.629 -0.961 -1.836
+ -0.899 2.657 -0.577 8.069 -0.811 -0.547 6.961 NA -0.818 -1.530 -1.495 7.042 -1.155 -1.591 -2.101 -0.476 -0.807 -1.683 -1.530
+ -0.617 0.944 -0.295 2.100 -0.529 -0.265 1.944 NA -0.536 -1.248 -1.214 2.000 -0.874 -1.310 -1.819 -0.194 -0.526 -1.401 -1.248 -0.966
+//
+H BRYS930101
+D Distance-dependent statistical potential (only energies of contacts within
+ 0-5 Angstrooms are included)
+R PMID:8497488
+A Bryant, S.H. and Lawrence, C.E.
+T An Empirical Energy Function for Threading Protein-Sequence Through the
+ Folding Motif
+J Proteins 16, 92-112 (1993)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 0.230
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+ -0.008 0.222 -0.187 -0.128 0.487 -0.430
+ 0.182 -0.717 -0.262 -0.178 0.121 -0.728 1.060
+ 0.282 -0.037 -0.097 -0.336 -0.187 -0.072 -0.041 -0.068
+ -0.079 0.111 -0.141 -0.270 -0.187 0.247 0.072 0.127 0.392
+ -0.535 -0.014 0.456 0.229 -0.415 0.020 0.385 0.127 -0.062 -0.051
+ -0.245 0.374 0.430 0.316 -0.061 0.391 0.480 -0.004 0.029 -0.223 -0.070
+ 0.063 0.734 0.222 -0.759 1.115 -0.181 -0.782 0.065 -0.235 -0.058 -0.015 0.567
+ -0.364 0.509 0.405 0.097 -0.032 0.013 0.188 0.084 0.293 -0.103 -0.253 0.347 -0.006
+ 0.132 -0.018 0.336 0.118 -0.095 0.283 0.270 0.457 -0.141 -0.348 -0.460 0.259 -0.501 -0.163
+ 0.022 -0.176 0.109 0.175 -0.199 -0.545 -0.064 0.127 0.037 0.382 -0.170 0.068 -0.104 -0.083 0.033
+ 0.115 -0.263 -0.334 -0.565 -0.164 0.298 -0.207 -0.100 0.080 0.254 0.390 -0.246 0.259 0.357 0.057 -0.150
+ 0.002 0.250 -0.018 -0.433 0.021 0.060 -0.006 -0.106 0.061 0.167 0.075 -0.170 0.087 0.058 0.108 -0.430 -0.315
+ 0.117 -0.244 0.538 1.287 0.080 0.459 -0.089 0.036 -0.098 -0.505 -0.635 -0.822 -0.783 -0.185 -0.312 0.298 0.040 0.707
+ -0.030 0.044 -0.491 0.694 0.069 -0.036 -0.004 0.121 -0.305 -0.100 -0.289 -0.294 -0.218 -0.335 0.071 0.442 0.492 -0.105 0.211
+ -0.359 -0.011 0.158 0.442 -0.026 -0.191 0.255 0.141 0.006 -0.253 -0.454 0.253 -0.265 -0.288 0.358 0.316 0.251 -0.034 0.075 -0.641
+//
+H THOP960101
+D Mixed quasichemical and optimization-based protein contact potential
+R PMID:8876187
+A Thomas, P.D. and Dill, K.A.
+T An iterative method for extracting energy-like quantities
+ from protein structures
+J Proc. Natl. Acad. Sci. USA 93, 11628-11633 (1996)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ -0.08
+ 0.07 0.23
+ -0.14 0.04 -0.86
+ 0.10 -0.15 -0.12 0.60
+ -0.30 -0.40 -0.32 0.55 -1.79
+ -0.11 0.62 -0.05 0.46 -0.49 -0.08
+ 0.03 -0.26 -0.25 0.68 0.04 0.62 0.21
+ -0.09 -0.15 -0.18 -0.06 -0.42 0.12 0.40 0.04
+ -0.15 -0.01 0.06 -0.06 -0.82 0.05 -0.53 0.00 0.14
+ -0.64 -0.08 0.39 0.04 -0.48 -0.39 -0.20 0.40 -0.52 -0.71
+ -0.57 -0.10 -0.10 0.50 -0.69 -0.13 -0.05 -0.08 -0.36 -1.04 -1.14
+ 0.00 0.30 0.18 -0.09 0.00 0.04 -0.09 0.10 0.14 -0.26 0.10 1.45
+ 0.05 -0.43 0.31 1.07 -1.23 -0.54 0.02 0.00 -0.35 -0.41 -0.31 0.55 0.36
+ -0.05 -0.22 -0.02 0.20 -0.98 0.10 0.19 0.21 -0.75 -0.66 -1.02 -0.17 -1.03 -0.61
+ 0.41 -0.02 0.11 0.84 0.07 -0.21 0.33 0.40 -0.22 0.25 0.09 0.51 -0.25 -0.43 0.28
+ -0.01 0.61 0.37 -0.09 -0.20 0.40 0.30 -0.04 -0.59 -0.13 -0.07 0.18 -0.47 0.14 0.44 -0.13
+ -0.22 -0.17 -0.27 -0.03 -0.38 -0.17 0.15 0.13 -0.27 -0.29 -0.39 0.09 0.06 -0.19 0.36 0.05 0.26
+ -0.08 -0.78 -0.68 0.24 -0.30 0.40 0.32 -0.14 -0.41 -0.89 -0.97 -0.30 -0.07 -0.89 -0.44 -0.20 0.07 0.02
+ -0.37 0.21 -0.74 0.11 -0.96 -0.39 0.22 -0.32 -0.67 -0.87 -0.60 -0.20 -1.10 -0.82 -0.45 0.25 -0.23 -0.99 0.35
+ -0.60 -0.48 -0.24 0.25 -0.94 -0.09 -0.02 -0.20 -0.35 -0.98 -1.03 -0.08 -0.94 -0.78 -0.08 -0.31 0.06 -0.60 -0.70 -1.15
+//
+H MIRL960101
+D Statistical potential derived by the maximization of the harmonic mean of Z
+ scores
+R PMID:9000638
+A Mirny, L.A. and Shakhnovich, E.I.
+T How to derive a protein folding potential? A new approach
+ to an old problem
+J J. Mol. Biol. 264, 1164-1179 (1996)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ -0.13
+ 0.43 0.11
+ 0.28 -0.14 -0.53
+ 0.12 -0.72 -0.30 0.04
+ 0.00 0.24 0.13 0.03 -1.06
+ 0.08 -0.52 -0.25 -0.17 0.05 0.29
+ 0.26 -0.74 -0.32 -0.15 0.69 -0.17 -0.03
+ -0.07 -0.04 -0.14 -0.22 -0.08 -0.06 0.25 -0.38
+ 0.34 -0.12 -0.24 -0.39 -0.19 -0.02 -0.45 0.20 -0.29
+ -0.22 0.42 0.53 0.59 0.16 0.36 0.35 0.25 0.49 -0.22
+ -0.01 0.35 0.30 0.67 -0.08 0.26 0.43 0.23 0.16 -0.41 -0.27
+ 0.14 0.75 -0.33 -0.76 0.71 -0.38 -0.97 0.11 0.22 0.36 0.19 0.25
+ 0.25 0.31 0.08 0.65 0.19 0.46 0.44 0.19 0.99 -0.28 -0.20 0.00 0.04
+ 0.03 0.41 0.18 0.39 -0.23 -0.29 0.27 -0.38 -0.16 -0.19 -0.30 0.44 -0.42 -0.44
+ 0.10 -0.38 -0.18 0.04 0.00 -0.42 -0.10 -0.11 -0.21 0.25 0.42 0.11 -0.34 0.20 0.26
+ -0.06 0.17 -0.14 -0.31 -0.02 -0.14 -0.26 -0.16 -0.05 0.21 0.25 -0.13 0.14 0.29 0.01 -0.20
+ -0.09 -0.35 -0.11 -0.29 0.19 -0.14 0.00 -0.26 -0.19 0.14 0.20 -0.09 0.19 0.31 -0.07 -0.08 0.03
+ -0.09 -0.16 0.06 0.24 0.08 0.08 0.29 0.18 -0.12 0.02 -0.09 0.22 -0.67 -0.16 -0.28 0.34 0.22 -0.12
+ 0.09 -0.25 -0.20 0.00 0.04 -0.20 -0.10 0.14 -0.34 0.11 0.24 -0.21 -0.13 0.00 -0.33 0.09 0.13 -0.04 0.06
+ -0.10 0.30 0.50 0.58 0.06 0.24 0.34 0.16 0.19 -0.25 -0.29 0.44 -0.14 -0.22 0.09 0.18 0.25 -0.07 0.02 -0.29
+//
+H VENM980101
+D Statistical potential derived by the maximization of the perceptron criterion
+R
+A Vendruscolo, M. and Domany E.
+T Pairwise contact potentials are unsuitable for protein folding
+J J. Chem. Phys. 109, 11101-11108 (1998)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ -0.02808
+ 0.01438 0.0543
+ 0.09084 -0.0321 -0.07726
+ 0.01673 -0.1196 0.07582 0.08769
+ 0.00069 0.1005 0.00943 0.01585 -0.18164
+ 0.02297 -0.1314 0.04386 -0.08755 0.03575 0.0197
+ 0.09398 -0.1873 -0.00720 -0.00952 0.02004 -0.0372 0.0865
+ 0.00253 0.0711 -0.03475 -0.06461 -0.01841 0.0200 0.0860 -0.1748
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+A Bastolla, U., Farwer, J., Knapp, E.W. and Vendruscolo, M.
+T How to guarantee optimal stability for most representative
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+A Miyazawa, S. and Jernigan, R.L.
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+A Miyazawa, S. and Jernigan, R.L.
+T Self-consistent estimation of inter-residue protein contact energies
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+A Miyazawa, S. and Jernigan, R.L.
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+T A united-residue force field for off-lattice protein-structure simulations:
+ 1. Functional forms and parameters of long-range side-chain interaction
+ potentials from protein crystal data.
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+A Betancourt,M.R. and Thirumalai,D.
+T Pair potentials for protein folding: Choice of reference states
+ and sensitivity of predicted native states to variations
+ in the interaction schemes
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+A Park, B. and Levitt, M.
+T Energy functions that discriminate X-ray and near-native folds
+ from well-constructed decoys
+J J. Mol. Biol. 258, 367-392 (1996)
+* (Glu is not available)
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+R PMID:8627632
+A Park, B. and Levitt, M.
+T Energy functions that discriminate X-ray and near-native folds
+ from well-constructed decoys
+J J. Mol. Biol. 258, 367-392 (1996)
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+//
+H KOLA930101
+D Statistical potential derived by the quasichemical approximation
+A Kolinski, A., Godzik, A. and Skolnick, J.
+T A general method for the prediction of the three dimensional structure
+ and folding pathway of globular proteins: Application to designed helical
+ proteins
+J J. Chem. Phys. 98, 7420-7433 (1993)
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+//
+H GODA950101
+D Quasichemical statistical potential derived from buried contacts
+R PMID:8535247
+A Godzik, A., Kolinski, A. and Skolnick, J.
+T Are Proteins Ideal Mixtures of Amino-Acids-Analysis
+ of Energy Parameter Sets
+J Protein Science 4, 2107-2117 (1995)
+* (Glu is not available)
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+//
+H SKOJ970101
+D Statistical potential derived by the quasichemical approximation
+R PMID:9070450
+A Skolnick, J., Jaroszewski, L., Kolinski, A. and Godzik, A.
+T Derivation and testing of pair potentials for protein folding.
+ When is the quasichemical approximation correct?
+J Protein Science 6, 676-688 (1997)
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+H SKOJ000101
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+R PMID:10651034
+A Skolnick, J., Kolinski, A. and Ortiz, A.
+T Derivation of protein-specific pair potentials based on weak sequence
+ fragment similarity
+J Proteins 38, 3-16 (2000)
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+H SKOJ000102
+D Statistical quasichemical potential with the composition-corrected pair scale
+R PMID:10651034
+A Skolnick, J., Kolinski, A. and Ortiz, A.
+T Derivation of protein-specific pair potentials based on weak sequence
+ fragment similarity
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+H BONM030101
+D Quasichemical statistical potential for the antiparallel orientation of
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+R PMID:15072433
+A Boniecki, M., Rotkiewicz, P., Skolnick, J. and Kolinski, A.
+T Protein fragment reconstruction using various modeling techniques
+J J. Comput. Aided Mol. Des. 17, 725-738 (2003)
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+H BONM030102
+D Quasichemical statistical potential for the intermediate orientation of
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+R PMID:15072433
+A Boniecki, M., Rotkiewicz, P., Skolnick, J. and Kolinski, A.
+T Protein fragment reconstruction using various modeling techniques
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+//
+H BONM030103
+D Quasichemical statistical potential for the parallel orientation of interacting
+ side groups
+R PMID:15072433
+A Boniecki, M., Rotkiewicz, P., Skolnick, J. and Kolinski, A.
+T Protein fragment reconstruction using various modeling techniques
+J J. Comput. Aided Mol. Des. 17, 725-738 (2003)
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+A Micheletti, C., Seno, F., Banavar, J.R. and Maritan, A.
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+T Improved recognition of native-like protein structures using
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+T Improved recognition of native-like protein structures using
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+ D.
+T Improved recognition of native-like protein structures using
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+ -0.70 0.03 0.63 0.15 -1.26 0.29 0.35 -0.11 -0.36 -1.73 -1.55 0.71 -0.97 -1.55 -0.28 -0.09 -0.32 -1.23 -0.91 -1.30
+ 0.17 0.50 0.60 0.67 -1.31 0.50 0.94 0.02 -0.45 -1.26 -0.91 1.08 0.83 -0.87 0.63 0.31 0.26 -0.50 -0.55 -0.79
+ -0.06 0.99 0.73 0.86 -0.89 0.85 0.67 0.08 0.06 -0.22 -0.29 0.94 -0.08 -0.41 0.67 0.33 0.13 -1.01 0.13 -0.24
+ 0.26 0.93 0.70 0.87 -0.78 0.58 1.20 0.12 0.52 -0.30 -0.24 1.11 0.01 -0.08 0.65 0.47 0.41 -0.31 0.12 -0.32
+ -0.03 -0.11 0.27 0.66 -1.50 0.65 0.50 -0.12 -0.32 -1.13 -1.01 0.52 -1.08 -1.04 -0.32 -0.03 -0.10 -0.67 -0.73 -0.64
+ -0.44 0.20 0.20 0.20 -1.26 0.16 0.10 -0.21 -0.52 -1.26 -1.30 0.60 -0.76 -1.17 -0.42 0.05 -0.27 -1.20 -0.75 -0.84
+ -0.83 0.20 0.48 0.62 -1.44 0.17 0.73 -0.12 -0.26 -1.64 -1.59 0.52 -0.70 -1.55 -0.28 0.12 -0.17 -1.16 -0.85 -1.42
+//
+H ZHAC000106
+D Environment-dependent residue contact energies (rows = coil, cols = coil)
+R PMID:10706611
+A Zhang, C. and Kim, S.H.
+T Environment-dependent residue contact energies for proteins
+J Proc. Natl. Acad. Sci. USA 97, 2550-2555 (2000)
+M rows = ARNDCQEGHILKMFPSTWYV, cols = ARNDCQEGHILKMFPSTWYV
+ 0.12
+ 0.56 1.18
+ 0.59 0.83 0.83
+ 0.65 0.33 0.61 1.15
+ -0.74 -0.25 -0.07 -0.12 -2.42
+ 0.70 0.94 0.87 0.96 -0.05 1.22
+ 1.32 0.54 1.09 1.48 0.20 1.11 2.18
+ 0.11 0.65 0.79 0.75 -0.56 0.73 1.16 0.35
+ 0.35 0.47 0.91 0.29 -0.83 0.83 0.74 0.53 0.28
+ -0.45 0.05 0.40 0.47 -1.27 0.24 0.70 0.01 -0.21 -1.04
+ -0.25 0.26 0.37 0.57 -1.25 0.38 0.82 0.13 -0.03 -1.15 -1.04
+ 1.06 1.65 1.11 0.58 0.76 1.29 0.93 1.08 1.23 0.48 0.78 2.23
+ 0.29 0.58 0.68 0.75 -0.74 0.65 1.08 0.54 0.19 -0.52 -0.68 1.15 -0.12
+ -0.41 0.24 0.46 0.38 -1.44 0.39 0.55 0.09 -0.28 -1.09 -1.05 0.74 -0.60 -1.09
+ 0.48 0.82 1.09 1.26 -0.23 1.09 1.25 0.74 0.59 0.14 0.10 1.59 0.54 -0.04 1.11
+ 0.45 0.55 0.81 0.54 -0.47 0.75 0.87 0.61 0.46 0.09 0.01 1.24 0.56 0.17 0.94 0.87
+ 0.30 0.80 0.54 0.51 -0.37 0.81 0.81 0.38 0.31 -0.28 -0.05 1.10 0.46 0.08 0.67 0.54 0.69
+ -0.28 -0.04 0.13 0.43 -0.63 -0.01 0.44 -0.17 -0.44 -1.28 -0.98 0.23 -0.50 -1.02 -0.33 0.14 -0.19 -0.46
+ -0.07 0.22 0.40 0.38 -0.58 0.09 0.47 0.28 -0.18 -0.74 -0.56 0.62 -0.26 -0.63 0.04 0.23 0.27 -0.87 -0.18
+ -0.18 0.43 0.54 0.59 -1.22 0.23 0.74 0.04 0.09 -0.90 -0.93 0.81 -0.31 -0.77 0.17 0.20 -0.10 -0.57 -0.38 -0.31
+//
diff --git a/modules/seq/alg/tests/CMakeLists.txt b/modules/seq/alg/tests/CMakeLists.txt
index 9348d402b..1bfc16eed 100644
--- a/modules/seq/alg/tests/CMakeLists.txt
+++ b/modules/seq/alg/tests/CMakeLists.txt
@@ -9,6 +9,7 @@ set(OST_SEQ_ALG_UNIT_TESTS
test_semiglobal_align.py
test_weight_matrix.py
test_alignment_from_chain_view.py
+ test_aaindex.py
)
if (COMPOUND_LIB)
diff --git a/modules/seq/alg/tests/test_aaindex.py b/modules/seq/alg/tests/test_aaindex.py
new file mode 100644
index 000000000..a1915e28e
--- /dev/null
+++ b/modules/seq/alg/tests/test_aaindex.py
@@ -0,0 +1,49 @@
+import sys
+import unittest
+from ost.seq.alg import aaindex
+
+class TestAAIndex(unittest.TestCase):
+
+
+ def testStuff(self):
+ index = aaindex.AAIndex()
+
+ # test some random aaindex annotations from all three files
+ # the files themselves are lazy loaded until the required
+ # annotation is found
+
+ # entry from aaindex1
+ self.assertEqual(index["BHAR880101"].GetScore("C"), 0.346)
+
+ # entries from aaindex2
+ # symmetric one:
+ self.assertEqual(index["HENS920102"].GetPairScore("C", "A"), -1.0)
+ self.assertEqual(index["HENS920102"].GetPairScore("A", "C"), -1.0)
+ # non-symmetric one:
+ self.assertEqual(index["LINK010101"].GetPairScore("C", "A"), 0.035)
+ self.assertEqual(index["LINK010101"].GetPairScore("A", "C"), 0.000)
+
+
+ # entries from aaindex3
+ # symmetric one
+ self.assertEqual(index["TANS760102"].GetPairScore("H", "R"), 17)
+ self.assertEqual(index["TANS760102"].GetPairScore("R", "H"), 17)
+ # non symmetric one
+ self.assertEqual(index["ZHAC000102"].GetPairScore("H", "R"), 2.19)
+ self.assertEqual(index["ZHAC000102"].GetPairScore("R", "H"), 0.94)
+
+ # depending on annotation type (single amino acids or pairs), we need
+ # to call the right functions
+ with self.assertRaises(RuntimeError):
+ index["TANS760102"].GetScore("H")
+
+ with self.assertRaises(RuntimeError):
+ index["BHAR880101"].GetPairScore("H", "R")
+
+
+if __name__ == "__main__":
+ from ost import testutils
+ # the function below indirectly enables GetSharedDataPath when
+ # calling stuff from python which is the case in unit tests
+ testutils.SetDefaultCompoundLib()
+ testutils.RunTests()
--
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