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Commit ba19c9a0 authored by Valerio Mariani's avatar Valerio Mariani
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New helper functions and updated stereo chemical parameter file

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modules/mol/alg/pymod/__init__.py
+ 41
− 0
View file @ ba19c9a0
import os.path
from _ost_mol_alg import * from _ost_mol_alg import *
from ost.mol.alg.superpose import * from ost.mol.alg.superpose import *
import ost.mol.alg.trajectory_analysis import ost.mol.alg.trajectory_analysis
...@@ -10,3 +11,43 @@ def FillClashingDistancesFromFile(filename,default_clashing_distance,default_tol ...@@ -10,3 +11,43 @@ def FillClashingDistancesFromFile(filename,default_clashing_distance,default_tol
lines=fh.readlines() lines=fh.readlines()
fh.close() fh.close()
return FillClashingDistances(lines,default_clashing_distance,default_tolerance) return FillClashingDistances(lines,default_clashing_distance,default_tolerance)
def FillBondStereoChemicalParamsFromFile(filename):
fh=open(filename,'r')
lines=fh.readlines()
fh.close()
return FillBondStereoChemicalParams("Bond",lines)
def FillAngleStereoChemicalParamsFromFile(filename):
fh=open(filename,'r')
lines=fh.readlines()
fh.close()
return FillAngleStereoChemicalParams("Angle",lines)
def DefaultClashingDistances():
shared_path=ost.GetSharedDataPath()
filename=os.path.join(shared_path,'stereo_chemical_props.txt')
fh=open(filename,'r')
lines=fh.readlines()
fh.close()
return FillClashingDistances(lines,1.5,0.0)
def DefaultBondStereoChemicalParams():
shared_path=ost.GetSharedDataPath()
filename=os.path.join(shared_path,'stereo_chemical_props.txt')
fh=open(filename,'r')
lines=fh.readlines()
fh.close()
return FillStereoChemicalParams("Bond",lines)
def DefaultAngleStereoChemicalParams():
shared_path=ost.GetSharedDataPath()
filename=os.path.join(shared_path,'stereo_chemical_props.txt')
fh=open(filename,'r')
lines=fh.readlines()
fh.close()
return FillStereoChemicalParams("Angle",lines)
modules/mol/alg/src/new_stereo_chemical_props.txt deleted 100644 → 0
+ 0
− 345
View file @ e41e1514
Bond Residue Mean StdDev
CA-CB ALA 1.520 0.021
N-CA ALA 1.459 0.020
CA-C ALA 1.525 0.026
C-O ALA 1.229 0.019
CA-CB ARG 1.535 0.022
CB-CG ARG 1.521 0.027
CG-CD ARG 1.515 0.025
CD-NE ARG 1.460 0.017
NE-CZ ARG 1.326 0.013
CZ-NH1 ARG 1.326 0.013
CZ-NH2 ARG 1.326 0.013
N-CA ARG 1.459 0.020
CA-C ARG 1.525 0.026
C-O ARG 1.229 0.019
CA-CB ASN 1.527 0.026
CB-CG ASN 1.506 0.023
CG-OD1 ASN 1.235 0.022
CG-ND2 ASN 1.324 0.025
N-CA ASN 1.459 0.020
CA-C ASN 1.525 0.026
C-O ASN 1.229 0.019
CA-CB ASP 1.535 0.022
CB-CG ASP 1.513 0.021
CG-OD1 ASP 1.249 0.023
CG-OD2 ASP 1.249 0.023
N-CA ASP 1.459 0.020
CA-C ASP 1.525 0.026
C-O ASP 1.229 0.019
CA-CB CYS 1.526 0.013
CB-SG CYS 1.812 0.016
N-CA CYS 1.459 0.020
CA-C CYS 1.525 0.026
C-O CYS 1.229 0.019
CA-CB GLU 1.535 0.022
CB-CG GLU 1.517 0.019
CG-CD GLU 1.515 0.015
CD-OE1 GLU 1.252 0.011
CD-OE2 GLU 1.252 0.011
N-CA GLU 1.459 0.020
CA-C GLU 1.525 0.026
C-O GLU 1.229 0.019
CA-CB GLN 1.535 0.022
CB-CG GLN 1.521 0.027
CG-CD GLN 1.506 0.023
CD-OE1 GLN 1.235 0.022
CD-NE2 GLN 1.324 0.025
N-CA GLN 1.459 0.020
CA-C GLN 1.525 0.026
C-O GLN 1.229 0.019
N-CA GLY 1.456 0.015
CA-C GLY 1.514 0.016
C-O GLY 1.232 0.016
CA-CB HIS 1.535 0.022
CB-CG HIS 1.492 0.016
CG-ND1 HIS 1.369 0.015
CG-CD2 HIS 1.353 0.017
ND1-CE1 HIS 1.343 0.025
CD2-NE2 HIS 1.415 0.021
CE1-NE2 HIS 1.322 0.023
N-CA HIS 1.459 0.020
CA-C HIS 1.525 0.026
C-O HIS 1.229 0.019
CA-CB ILE 1.544 0.023
CB-CG1 ILE 1.536 0.028
CB-CG2 ILE 1.524 0.031
CG1-CD1 ILE 1.500 0.069
N-CA ILE 1.459 0.020
CA-C ILE 1.525 0.026
C-O ILE 1.229 0.019
CA-CB LEU 1.533 0.023
CB-CG LEU 1.521 0.029
CG-CD1 LEU 1.514 0.037
CG-CD2 LEU 1.514 0.037
N-CA LEU 1.459 0.020
CA-C LEU 1.525 0.026
C-O LEU 1.229 0.019
CA-CB LYS 1.535 0.022
CB-CG LYS 1.521 0.027
CG-CD LYS 1.520 0.034
CD-CE LYS 1.508 0.025
CE-NZ LYS 1.486 0.025
N-CA LYS 1.459 0.020
CA-C LYS 1.525 0.026
C-O LYS 1.229 0.019
CA-CB MET 1.535 0.022
CB-CG MET 1.509 0.032
CG-SD MET 1.807 0.026
SD-CE MET 1.774 0.056
N-CA MET 1.459 0.020
CA-C MET 1.525 0.026
C-O MET 1.229 0.019
CA-CB PHE 1.535 0.022
CB-CG PHE 1.509 0.017
CG-CD1 PHE 1.383 0.015
CG-CD2 PHE 1.383 0.015
CD1-CE1 PHE 1.388 0.020
CD2-CE2 PHE 1.388 0.020
CE1-CZ PHE 1.369 0.019
CE2-CZ PHE 1.369 0.019
N-CA PHE 1.459 0.020
CA-C PHE 1.525 0.026
C-O PHE 1.229 0.019
CA-CB PRO 1.531 0.020
CB-CG PRO 1.495 0.050
CG-CD PRO 1.502 0.033
CD-N PRO 1.474 0.014
N-CA PRO 1.468 0.017
CA-C PRO 1.524 0.020
C-O PRO 1.228 0.020
CA-CB SER 1.525 0.015
CB-OG SER 1.418 0.013
N-CA SER 1.459 0.020
CA-C SER 1.525 0.026
C-O SER 1.229 0.019
CA-CB THR 1.529 0.026
CB-OG1 THR 1.428 0.020
CB-CG2 THR 1.519 0.033
N-CA THR 1.459 0.020
CA-C THR 1.525 0.026
C-O THR 1.229 0.019
CA-CB TRP 1.535 0.022
CB-CG TRP 1.498 0.018
CG-CD1 TRP 1.363 0.014
CG-CD2 TRP 1.432 0.017
CD1-NE1 TRP 1.375 0.017
NE1-CE2 TRP 1.371 0.013
CD2-CE2 TRP 1.409 0.012
CD2-CE3 TRP 1.399 0.015
CE2-CZ2 TRP 1.393 0.017
CE3-CZ3 TRP 1.380 0.017
CZ2-CH2 TRP 1.369 0.019
CZ3-CH2 TRP 1.396 0.016
N-CA TRP 1.459 0.020
CA-C TRP 1.525 0.026
C-O TRP 1.229 0.019
CA-CB TYR 1.535 0.022
CB-CG TYR 1.512 0.015
CG-CD1 TYR 1.387 0.013
CG-CD2 TYR 1.387 0.013
CD1-CE1 TYR 1.389 0.015
CD2-CE2 TYR 1.389 0.015
CE1-CZ TYR 1.381 0.013
CE2-CZ TYR 1.381 0.013
CZ-OH TYR 1.374 0.017
N-CA TYR 1.459 0.020
CA-C TYR 1.525 0.026
C-O TYR 1.229 0.019
CA-CB VAL 1.543 0.021
CB-CG1 VAL 1.524 0.021
CB-CG2 VAL 1.524 0.021
N-CA VAL 1.459 0.020
CA-C VAL 1.525 0.026
C-O VAL 1.229 0.019
-
Angle Residue Mean StdDev
N-CA-CB ALA 110.1 1.4
CB-CA-C ALA 110.1 1.5
N-CA-C ALA 111.0 2.7
CA-C-O ALA 120.1 2.1
N-CA-CB ARG 110.6 1.8
CB-CA-C ARG 110.4 2.0
CA-CB-CG ARG 113.4 2.2
CB-CG-CD ARG 111.6 2.6
CG-CD-NE ARG 111.8 2.1
CD-NE-CZ ARG 123.6 1.4
NE-CZ-NH1 ARG 120.3 0.5
NE-CZ-NH2 ARG 120.3 0.5
NH1-CZ-NH2 ARG 119.4 1.1
N-CA-C ARG 111.0 2.7
CA-C-O ARG 120.1 2.1
N-CA-CB ASN 110.6 1.8
CB-CA-C ASN 110.4 2.0
CA-CB-CG ASN 113.4 2.2
CB-CG-ND2 ASN 116.7 2.4
CB-CG-OD1 ASN 121.6 2.0
ND2-CG-OD1 ASN 121.9 2.3
N-CA-C ASN 111.0 2.7
CA-C-O ASN 120.1 2.1
N-CA-CB ASP 110.6 1.8
CB-CA-C ASP 110.4 2.0
CA-CB-CG ASP 113.4 2.2
CB-CG-OD1 ASP 118.3 0.9
CB-CG-OD2 ASP 118.3 0.9
OD1-CG-OD2 ASP 123.3 1.9
N-CA-C ASP 111.0 2.7
CA-C-O ASP 120.1 2.1
N-CA-CB CYS 110.8 1.5
CB-CA-C CYS 111.5 1.2
CA-CB-SG CYS 114.2 1.1
N-CA-C CYS 111.0 2.7
CA-C-O CYS 120.1 2.1
N-CA-CB GLU 110.6 1.8
CB-CA-C GLU 110.4 2.0
CA-CB-CG GLU 113.4 2.2
CB-CG-CD GLU 114.2 2.7
CG-CD-OE1 GLU 118.3 2.0
CG-CD-OE2 GLU 118.3 2.0
OE1-CD-OE2 GLU 123.3 1.2
N-CA-C GLU 111.0 2.7
CA-C-O GLU 120.1 2.1
N-CA-CB GLN 110.6 1.8
CB-CA-C GLN 110.4 2.0
CA-CB-CG GLN 113.4 2.2
CB-CG-CD GLN 111.6 2.6
CG-CD-OE1 GLN 121.6 2.0
CG-CD-NE2 GLN 116.7 2.4
OE1-CD-NE2 GLN 121.9 2.3
N-CA-C GLN 111.0 2.7
CA-C-O GLN 120.1 2.1
N-CA-C GLY 113.1 2.5
CA-C-O GLY 120.6 1.8
N-CA-CB HIS 110.6 1.8
CB-CA-C HIS 110.4 2.0
CA-CB-CG HIS 113.6 1.7
CB-CG-ND1 HIS 123.2 2.5
CB-CG-CD2 HIS 130.8 3.1
CG-ND1-CE1 HIS 108.2 1.4
ND1-CE1-NE2 HIS 109.9 2.2
CE1-NE2-CD2 HIS 106.6 2.5
NE2-CD2-CG HIS 109.2 1.9
CD2-CG-ND1 HIS 106.0 1.4
N-CA-C HIS 111.0 2.7
CA-C-O HIS 120.1 2.1
N-CA-CB ILE 110.8 2.3
CB-CA-C ILE 111.6 2.0
CA-CB-CG1 ILE 111.0 1.9
CB-CG1-CD1 ILE 113.9 2.8
CA-CB-CG2 ILE 110.9 2.0
CG1-CB-CG2 ILE 111.4 2.2
N-CA-C ILE 111.0 2.7
CA-C-O ILE 120.1 2.1
N-CA-CB LEU 110.4 2.0
CB-CA-C LEU 110.2 1.9
CA-CB-CG LEU 115.3 2.3
CB-CG-CD1 LEU 111.0 1.7
CB-CG-CD2 LEU 111.0 1.7
CD1-CG-CD2 LEU 110.5 3.0
N-CA-C LEU 111.0 2.7
CA-C-O LEU 120.1 2.1
N-CA-CB LYS 110.6 1.8
CB-CA-C LYS 110.4 2.0
CA-CB-CG LYS 113.4 2.2
CB-CG-CD LYS 111.6 2.6
CG-CD-CE LYS 111.9 3.0
CD-CE-NZ LYS 111.7 2.3
N-CA-C LYS 111.0 2.7
CA-C-O LYS 120.1 2.1
N-CA-CB MET 110.6 1.8
CB-CA-C MET 110.4 2.0
CA-CB-CG MET 113.3 1.7
CB-CG-SD MET 112.4 3.0
CG-SD-CE MET 100.2 1.6
N-CA-C MET 111.0 2.7
CA-C-O MET 120.1 2.1
N-CA-CB PHE 110.6 1.8
CB-CA-C PHE 110.4 2.0
CA-CB-CG PHE 113.9 2.4
CB-CG-CD1 PHE 120.8 0.7
CB-CG-CD2 PHE 120.8 0.7
CD1-CG-CD2 PHE 118.3 1.3
CG-CD1-CE1 PHE 120.8 1.1
CG-CD2-CE2 PHE 120.8 1.1
CD1-CE1-CZ PHE 120.1 1.2
CD2-CE2-CZ PHE 120.1 1.2
CE1-CZ-CE2 PHE 120.0 1.8
N-CA-C PHE 111.0 2.7
CA-C-O PHE 120.1 2.1
N-CA-CB PRO 103.3 1.2
CB-CA-C PRO 111.7 2.1
CA-CB-CG PRO 104.8 1.9
CB-CG-CD PRO 106.5 3.9
CG-CD-N PRO 103.2 1.5
CA-N-CD PRO 111.7 1.4
N-CA-C PRO 112.1 2.6
CA-C-O PRO 120.2 2.4
N-CA-CB SER 110.5 1.5
CB-CA-C SER 110.1 1.9
CA-CB-OG SER 111.2 2.7
N-CA-C SER 111.0 2.7
CA-C-O SER 120.1 2.1
N-CA-CB THR 110.3 1.9
CB-CA-C THR 111.6 2.7
CA-CB-OG1 THR 109.0 2.1
CA-CB-CG2 THR 112.4 1.4
OG1-CB-CG2 THR 110.0 2.3
N-CA-C THR 111.0 2.7
CA-C-O THR 120.1 2.1
N-CA-CB TRP 110.6 1.8
CB-CA-C TRP 110.4 2.0
CA-CB-CG TRP 113.7 1.9
CB-CG-CD1 TRP 127.0 1.3
CB-CG-CD2 TRP 126.6 1.3
CD1-CG-CD2 TRP 106.3 0.8
CG-CD1-NE1 TRP 110.1 1.0
CD1-NE1-CE2 TRP 109.0 0.9
NE1-CE2-CD2 TRP 107.3 1.0
CE2-CD2-CG TRP 107.3 0.8
CG-CD2-CE3 TRP 133.9 0.9
NE1-CE2-CZ2 TRP 130.4 1.1
CE3-CD2-CE2 TRP 118.7 1.2
CD2-CE2-CZ2 TRP 122.3 1.2
CE2-CZ2-CH2 TRP 117.4 1.0
CZ2-CH2-CZ3 TRP 121.6 1.2
CH2-CZ3-CE3 TRP 121.2 1.1
CZ3-CE3-CD2 TRP 118.8 1.3
N-CA-C TRP 111.0 2.7
CA-C-O TRP 120.1 2.1
N-CA-CB TYR 110.6 1.8
CB-CA-C TYR 110.4 2.0
CA-CB-CG TYR 113.4 1.9
CB-CG-CD1 TYR 121.0 0.6
CB-CG-CD2 TYR 121.0 0.6
CD1-CG-CD2 TYR 117.9 1.1
CG-CD1-CE1 TYR 121.3 0.8
CG-CD2-CE2 TYR 121.3 0.8
CD1-CE1-CZ TYR 119.8 0.9
CD2-CE2-CZ TYR 119.8 0.9
CE1-CZ-CE2 TYR 119.8 1.6
CE1-CZ-OH TYR 120.1 2.7
CE2-CZ-OH TYR 120.1 2.7
N-CA-C TYR 111.0 2.7
CA-C-O TYR 120.1 2.1
N-CA-CB VAL 111.5 2.2
CB-CA-C VAL 111.4 1.9
CA-CB-CG1 VAL 110.9 1.5
CA-CB-CG2 VAL 110.9 1.5
CG1-CB-CG2 VAL 110.9 1.6
N-CA-C VAL 111.0 2.7
CA-C-O VAL 120.1 2.1
-
Non-bonded distance Minimum Dist Tolerance
C-C 3.4 1.5
C-N 3.25 1.5
C-S 3.5 1.5
C-O 3.22 1.5
N-N 3.1 1.5
N-S 3.35 1.5
N-O 3.07 1.5
O-S 3.32 1.5
O-O 3.04 1.5
S-S 2.03 1.0
-
modules/mol/alg/src/stereo_chemical_props.txt
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View file @ ba19c9a0
# This file contains stereochemical parameters used to evaluate the quality of models.
# Bond distances and Angles come from Engh,Huber (1991). Non bonded distances come from
Bond Residue Mean StdDev Bond Residue Mean StdDev
N-CA ALA 1.458 0.019 CA-CB ALA 1.520 0.021
CA-C ALA 1.525 0.021 N-CA ALA 1.459 0.020
C-O ALA 1.231 0.02 CA-C ALA 1.525 0.026
CA-CB ALA 1.521 0.033 C-O ALA 1.229 0.019
N-CA CYS 1.458 0.019 CA-CB ARG 1.535 0.022
CA-C CYS 1.525 0.021 CB-CG ARG 1.521 0.027
C-O CYS 1.231 0.02 CG-CD ARG 1.515 0.025
CA-CB CYS 1.53 0.02 CD-NE ARG 1.460 0.017
CB-SG CYS 1.808 0.033 NE-CZ ARG 1.326 0.013
N-CA ASP 1.458 0.019 CZ-NH1 ARG 1.326 0.013
CA-C ASP 1.525 0.021 CZ-NH2 ARG 1.326 0.013
C-O ASP 1.231 0.02 N-CA ARG 1.459 0.020
CA-CB ASP 1.53 0.02 CA-C ARG 1.525 0.026
CB-CG ASP 1.516 0.025 C-O ARG 1.229 0.019
CG-OD1 ASP 1.249 0.019 CA-CB ASN 1.527 0.026
CG-OD2 ASP 1.249 0.019 CB-CG ASN 1.506 0.023
N-CA GLU 1.458 0.019 CG-OD1 ASN 1.235 0.022
CA-C GLU 1.525 0.021 CG-ND2 ASN 1.324 0.025
C-O GLU 1.231 0.02 N-CA ASN 1.459 0.020
CA-CB GLU 1.53 0.02 CA-C ASN 1.525 0.026
CB-CG GLU 1.52 0.03 C-O ASN 1.229 0.019
CG-CD GLU 1.516 0.025 CA-CB ASP 1.535 0.022
CD-OE1 GLU 1.249 0.019 CB-CG ASP 1.513 0.021
CD-OE2 GLU 1.249 0.019 CG-OD1 ASP 1.249 0.023
N-CA PHE 1.458 0.019 CG-OD2 ASP 1.249 0.023
CA-C PHE 1.525 0.021 N-CA ASP 1.459 0.020
C-O PHE 1.231 0.02 CA-C ASP 1.525 0.026
CA-CB PHE 1.53 0.02 C-O ASP 1.229 0.019
CB-CG PHE 1.502 0.023 CA-CB CYS 1.526 0.013
CG-CD1 PHE 1.384 0.021 CB-SG CYS 1.812 0.016
CG-CD2 PHE 1.384 0.021 N-CA CYS 1.459 0.020
CD1-CE1 PHE 1.382 0.03 CA-C CYS 1.525 0.026
CD2-CE2 PHE 1.382 0.03 C-O CYS 1.229 0.019
CE1-CZ PHE 1.382 0.03 CA-CB GLU 1.535 0.022
CE2-CZ PHE 1.382 0.03 CB-CG GLU 1.517 0.019
N-CA GLY 1.451 0.016 CG-CD GLU 1.515 0.015
CA-C GLY 1.516 0.018 CD-OE1 GLU 1.252 0.011
C-O GLY 1.231 0.02 CD-OE2 GLU 1.252 0.011
N-CA HIS 1.458 0.019 N-CA GLU 1.459 0.020
CA-C HIS 1.525 0.021 CA-C GLU 1.525 0.026
C-O HIS 1.231 0.02 C-O GLU 1.229 0.019
CA-CB HIS 1.53 0.02 CA-CB GLN 1.535 0.022
CB-CG HIS 1.497 0.014 CB-CG GLN 1.521 0.027
CG-ND1 HIS 1.378 0.011 CG-CD GLN 1.506 0.023
CG-CD2 HIS 1.354 0.011 CD-OE1 GLN 1.235 0.022
ND1-CE1 HIS 1.321 0.01 CD-NE2 GLN 1.324 0.025
CD2-NE2 HIS 1.374 0.011 N-CA GLN 1.459 0.020
CE1-NE2 HIS 1.321 0.01 CA-C GLN 1.525 0.026
N-CA ILE 1.458 0.019 C-O GLN 1.229 0.019
CA-C ILE 1.525 0.021 N-CA GLY 1.456 0.015
C-O ILE 1.231 0.02 CA-C GLY 1.514 0.016
CA-CB ILE 1.54 0.027 C-O GLY 1.232 0.016
CB-CG1 ILE 1.53 0.02 CA-CB HIS 1.535 0.022
CB-CG2 ILE 1.521 0.033 CB-CG HIS 1.492 0.016
CG1-CD1 ILE 1.513 0.039 CG-ND1 HIS 1.369 0.015
N-CA LYS 1.458 0.019 CG-CD2 HIS 1.353 0.017
CA-C LYS 1.525 0.021 ND1-CE1 HIS 1.343 0.025
C-O LYS 1.231 0.02 CD2-NE2 HIS 1.415 0.021
CA-CB LYS 1.53 0.02 CE1-NE2 HIS 1.322 0.023
CB-CG LYS 1.52 0.03 N-CA HIS 1.459 0.020
CG-CD LYS 1.52 0.03 CA-C HIS 1.525 0.026
CD-CE LYS 1.52 0.03 C-O HIS 1.229 0.019
CE-NZ LYS 1.489 0.03 CA-CB ILE 1.544 0.023
N-CA LEU 1.458 0.019 CB-CG1 ILE 1.536 0.028
CA-C LEU 1.525 0.021 CB-CG2 ILE 1.524 0.031
C-O LEU 1.231 0.02 CG1-CD1 ILE 1.500 0.069
CA-CB LEU 1.53 0.02 N-CA ILE 1.459 0.020
CB-CG LEU 1.53 0.02 CA-C ILE 1.525 0.026
CG-CD1 LEU 1.521 0.033 C-O ILE 1.229 0.019
CG-CD2 LEU 1.521 0.033 CA-CB LEU 1.533 0.023
N-CA MET 1.458 0.019 CB-CG LEU 1.521 0.029
CA-C MET 1.525 0.021 CG-CD1 LEU 1.514 0.037
C-O MET 1.231 0.02 CG-CD2 LEU 1.514 0.037
CA-CB MET 1.53 0.02 N-CA LEU 1.459 0.020
CB-CG MET 1.52 0.03 CA-C LEU 1.525 0.026
CG-SD MET 1.803 0.034 C-O LEU 1.229 0.019
SD-CE MET 1.791 0.059 CA-CB LYS 1.535 0.022
N-CA ASN 1.458 0.019 CB-CG LYS 1.521 0.027
CA-C ASN 1.525 0.021 CG-CD LYS 1.520 0.034
C-O ASN 1.231 0.02 CD-CE LYS 1.508 0.025
CA-CB ASN 1.53 0.02 CE-NZ LYS 1.486 0.025
CB-CG ASN 1.516 0.025 N-CA LYS 1.459 0.020
CG-OD1 ASN 1.231 0.02 CA-C LYS 1.525 0.026
CG-ND2 ASN 1.328 0.021 C-O LYS 1.229 0.019
N-CA PRO 1.466 0.015 CA-CB MET 1.535 0.022
CA-C PRO 1.525 0.021 CB-CG MET 1.509 0.032
C-O PRO 1.231 0.02 CG-SD MET 1.807 0.026
CA-CB PRO 1.53 0.02 SD-CE MET 1.774 0.056
CB-CG PRO 1.492 0.05 N-CA MET 1.459 0.020
CG-CD PRO 1.503 0.034 CA-C MET 1.525 0.026
CD-N PRO 1.473 0.014 C-O MET 1.229 0.019
N-CA GLN 1.458 0.019 CA-CB PHE 1.535 0.022
CA-C GLN 1.525 0.021 CB-CG PHE 1.509 0.017
C-O GLN 1.231 0.02 CG-CD1 PHE 1.383 0.015
CA-CB GLN 1.53 0.02 CG-CD2 PHE 1.383 0.015
CB-CG GLN 1.52 0.03 CD1-CE1 PHE 1.388 0.020
CG-CD GLN 1.516 0.025 CD2-CE2 PHE 1.388 0.020
CD-OE1 GLN 1.231 0.02 CE1-CZ PHE 1.369 0.019
CD-NE2 GLN 1.328 0.021 CE2-CZ PHE 1.369 0.019
N-CA ARG 1.458 0.019 N-CA PHE 1.459 0.020
CA-C ARG 1.525 0.021 CA-C PHE 1.525 0.026
C-O ARG 1.231 0.02 C-O PHE 1.229 0.019
CA-CB ARG 1.53 0.02 CA-CB PRO 1.531 0.020
CB-CG ARG 1.52 0.03 CB-CG PRO 1.495 0.050
CG-CD ARG 1.52 0.03 CG-CD PRO 1.502 0.033
CD-NE ARG 1.46 0.018 CD-N PRO 1.474 0.014
NE-CZ ARG 1.329 0.014 N-CA PRO 1.468 0.017
CZ-NH1 ARG 1.326 0.018 CA-C PRO 1.524 0.020
CZ-NH2 ARG 1.326 0.018 C-O PRO 1.228 0.020
N-CA SER 1.458 0.019 CA-CB SER 1.525 0.015
CA-C SER 1.525 0.021 CB-OG SER 1.418 0.013
C-O SER 1.231 0.02 N-CA SER 1.459 0.020
CA-CB SER 1.53 0.02 CA-C SER 1.525 0.026
CB-OG SER 1.417 0.02 C-O SER 1.229 0.019
N-CA THR 1.458 0.019 CA-CB THR 1.529 0.026
CA-C THR 1.525 0.021 CB-OG1 THR 1.428 0.020
C-O THR 1.231 0.02 CB-CG2 THR 1.519 0.033
CA-CB THR 1.54 0.027 N-CA THR 1.459 0.020
CB-OG1 THR 1.433 0.016 CA-C THR 1.525 0.026
CB-CG2 THR 1.521 0.033 C-O THR 1.229 0.019
N-CA VAL 1.458 0.019 CA-CB TRP 1.535 0.022
CA-C VAL 1.525 0.021 CB-CG TRP 1.498 0.018
C-O VAL 1.231 0.02 CG-CD1 TRP 1.363 0.014
CA-CB VAL 1.54 0.027 CG-CD2 TRP 1.432 0.017
CB-CG1 VAL 1.521 0.033 CD1-NE1 TRP 1.375 0.017
CB-CG2 VAL 1.521 0.033 NE1-CE2 TRP 1.371 0.013
N-CA TRP 1.458 0.019 CD2-CE2 TRP 1.409 0.012
CA-C TRP 1.525 0.021 CD2-CE3 TRP 1.399 0.015
C-O TRP 1.231 0.02 CE2-CZ2 TRP 1.393 0.017
CA-CB TRP 1.53 0.02 CE3-CZ3 TRP 1.380 0.017
CB-CG TRP 1.498 0.031 CZ2-CH2 TRP 1.369 0.019
CG-CD1 TRP 1.365 0.025 CZ3-CH2 TRP 1.396 0.016
CG-CD2 TRP 1.433 0.018 N-CA TRP 1.459 0.020
CD1-NE1 TRP 1.374 0.021 CA-C TRP 1.525 0.026
NE1-CE2 TRP 1.37 0.011 C-O TRP 1.229 0.019
CD2-CE2 TRP 1.409 0.017 CA-CB TYR 1.535 0.022
CD2-CE3 TRP 1.398 0.016 CB-CG TYR 1.512 0.015
CE2-CZ2 TRP 1.394 0.021 CG-CD1 TYR 1.387 0.013
CE3-CZ3 TRP 1.382 0.03 CG-CD2 TYR 1.387 0.013
CZ2-CH2 TRP 1.368 0.019 CD1-CE1 TYR 1.389 0.015
CZ3-CH2 TRP 1.4 0.025 CD2-CE2 TYR 1.389 0.015
N-CA TYR 1.458 0.019 CE1-CZ TYR 1.381 0.013
CA-C TYR 1.525 0.021 CE2-CZ TYR 1.381 0.013
C-O TYR 1.231 0.02 CZ-OH TYR 1.374 0.017
CA-CB TYR 1.53 0.02 N-CA TYR 1.459 0.020
CB-CG TYR 1.512 0.022 CA-C TYR 1.525 0.026
CG-CD1 TYR 1.389 0.021 C-O TYR 1.229 0.019
CG-CD2 TYR 1.389 0.021 CA-CB VAL 1.543 0.021
CD1-CE1 TYR 1.382 0.03 CB-CG1 VAL 1.524 0.021
CD2-CE2 TYR 1.382 0.03 CB-CG2 VAL 1.524 0.021
CE1-CZ TYR 1.378 0.024 N-CA VAL 1.459 0.020
CE2-CZ TYR 1.378 0.024 CA-C VAL 1.525 0.026
CZ-OH TYR 1.376 0.021 C-O VAL 1.229 0.019
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Angle Residue Mean StdDev Angle Residue Mean StdDev
N-CA-C ALA 111.2 2.8 N-CA-CB ALA 110.1 1.4
CA-C-O ALA 120.8 1.7 CB-CA-C ALA 110.1 1.5
N-CA-CB ALA 110.4 1.5 N-CA-C ALA 111.0 2.7
C-CA-CB ALA 110.5 1.5 CA-C-O ALA 120.1 2.1
N-CA-C CYS 111.2 2.8 N-CA-CB ARG 110.6 1.8
CA-C-O CYS 120.8 1.7 CB-CA-C ARG 110.4 2.0
N-CA-CB CYS 110.5 1.7 CA-CB-CG ARG 113.4 2.2
C-CA-CB CYS 110.1 1.9 CB-CG-CD ARG 111.6 2.6
N-CA-C ASP 111.2 2.8 CG-CD-NE ARG 111.8 2.1
CA-C-O ASP 120.8 1.7 CD-NE-CZ ARG 123.6 1.4
N-CA-CB ASP 110.5 1.7 NE-CZ-NH1 ARG 120.3 0.5
C-CA-CB ASP 110.1 1.9 NE-CZ-NH2 ARG 120.3 0.5
CA-CB-CG ASP 112.6 1.0 NH1-CZ-NH2 ARG 119.4 1.1
CB-CG-OD2 ASP 118.4 2.3 N-CA-C ARG 111.0 2.7
CB-CG-OD1 ASP 118.4 2.3 CA-C-O ARG 120.1 2.1
OD2-CG-OD1 ASP 122.9 2.4 N-CA-CB ASN 110.6 1.8
N-CA-C GLU 111.2 2.8 CB-CA-C ASN 110.4 2.0
CA-C-O GLU 120.8 1.7 CA-CB-CG ASN 113.4 2.2
N-CA-CB GLU 110.5 1.7 CB-CG-ND2 ASN 116.7 2.4
C-CA-CB GLU 110.1 1.9 CB-CG-OD1 ASN 121.6 2.0
CA-CB-CG GLU 114.1 2.0 ND2-CG-OD1 ASN 121.9 2.3
CB-CG-CD GLU 112.6 1.7 N-CA-C ASN 111.0 2.7
CG-CD-OE2 GLU 118.4 2.3 CA-C-O ASN 120.1 2.1
CG-CD-OE1 GLU 118.4 2.3 N-CA-CB ASP 110.6 1.8
OE2-CD-OE1 GLU 122.9 2.4 CB-CA-C ASP 110.4 2.0
N-CA-C PHE 111.2 2.8 CA-CB-CG ASP 113.4 2.2
CA-C-O PHE 120.8 1.7 CB-CG-OD1 ASP 118.3 0.9
N-CA-CB PHE 110.5 1.7 CB-CG-OD2 ASP 118.3 0.9
C-CA-CB PHE 110.1 1.9 OD1-CG-OD2 ASP 123.3 1.9
CA-CB-CG PHE 113.8 1.0 N-CA-C ASP 111.0 2.7
CB-CG-CD1 PHE 120.7 1.7 CA-C-O ASP 120.1 2.1
CB-CG-CD2 PHE 120.7 1.7 N-CA-CB CYS 110.8 1.5
CG-CD1-CE1 PHE 120.7 1.7 CB-CA-C CYS 111.5 1.2
CG-CD2-CE2 PHE 120.7 1.7 CA-CB-SG CYS 114.2 1.1
CD1-CE1-CZ PHE 120.0 1.8 N-CA-C CYS 111.0 2.7
CD2-CE2-CZ PHE 120.0 1.8 CA-C-O CYS 120.1 2.1
N-CA-CB GLU 110.6 1.8
CB-CA-C GLU 110.4 2.0
CA-CB-CG GLU 113.4 2.2
CB-CG-CD GLU 114.2 2.7
CG-CD-OE1 GLU 118.3 2.0
CG-CD-OE2 GLU 118.3 2.0
OE1-CD-OE2 GLU 123.3 1.2
N-CA-C GLU 111.0 2.7
CA-C-O GLU 120.1 2.1
N-CA-CB GLN 110.6 1.8
CB-CA-C GLN 110.4 2.0
CA-CB-CG GLN 113.4 2.2
CB-CG-CD GLN 111.6 2.6
CG-CD-OE1 GLN 121.6 2.0
CG-CD-NE2 GLN 116.7 2.4
OE1-CD-NE2 GLN 121.9 2.3
N-CA-C GLN 111.0 2.7
CA-C-O GLN 120.1 2.1
N-CA-C GLY 113.1 2.5
CA-C-O GLY 120.6 1.8
N-CA-CB HIS 110.6 1.8
CB-CA-C HIS 110.4 2.0
CA-CB-CG HIS 113.6 1.7
CB-CG-ND1 HIS 123.2 2.5
CB-CG-CD2 HIS 130.8 3.1
CG-ND1-CE1 HIS 108.2 1.4
ND1-CE1-NE2 HIS 109.9 2.2
CE1-NE2-CD2 HIS 106.6 2.5
NE2-CD2-CG HIS 109.2 1.9
CD2-CG-ND1 HIS 106.0 1.4
N-CA-C HIS 111.0 2.7
CA-C-O HIS 120.1 2.1
N-CA-CB ILE 110.8 2.3
CB-CA-C ILE 111.6 2.0
CA-CB-CG1 ILE 111.0 1.9
CB-CG1-CD1 ILE 113.9 2.8
CA-CB-CG2 ILE 110.9 2.0
CG1-CB-CG2 ILE 111.4 2.2
N-CA-C ILE 111.0 2.7
CA-C-O ILE 120.1 2.1
N-CA-CB LEU 110.4 2.0
CB-CA-C LEU 110.2 1.9
CA-CB-CG LEU 115.3 2.3
CB-CG-CD1 LEU 111.0 1.7
CB-CG-CD2 LEU 111.0 1.7
CD1-CG-CD2 LEU 110.5 3.0
N-CA-C LEU 111.0 2.7
CA-C-O LEU 120.1 2.1
N-CA-CB LYS 110.6 1.8
CB-CA-C LYS 110.4 2.0
CA-CB-CG LYS 113.4 2.2
CB-CG-CD LYS 111.6 2.6
CG-CD-CE LYS 111.9 3.0
CD-CE-NZ LYS 111.7 2.3
N-CA-C LYS 111.0 2.7
CA-C-O LYS 120.1 2.1
N-CA-CB MET 110.6 1.8
CB-CA-C MET 110.4 2.0
CA-CB-CG MET 113.3 1.7
CB-CG-SD MET 112.4 3.0
CG-SD-CE MET 100.2 1.6
N-CA-C MET 111.0 2.7
CA-C-O MET 120.1 2.1
N-CA-CB PHE 110.6 1.8
CB-CA-C PHE 110.4 2.0
CA-CB-CG PHE 113.9 2.4
CB-CG-CD1 PHE 120.8 0.7
CB-CG-CD2 PHE 120.8 0.7
CD1-CG-CD2 PHE 118.3 1.3
CG-CD1-CE1 PHE 120.8 1.1
CG-CD2-CE2 PHE 120.8 1.1
CD1-CE1-CZ PHE 120.1 1.2
CD2-CE2-CZ PHE 120.1 1.2
CE1-CZ-CE2 PHE 120.0 1.8 CE1-CZ-CE2 PHE 120.0 1.8
CD1-CG-CD2 PHE 118.6 1.5 N-CA-C PHE 111.0 2.7
N-CA-C GLY 112.5 2.9 CA-C-O PHE 120.1 2.1
CA-C-O GLY 120.8 2.1 N-CA-CB PRO 103.3 1.2
N-CA-C HIS 111.2 2.8 CB-CA-C PRO 111.7 2.1
CA-C-O HIS 120.8 1.7 CA-CB-CG PRO 104.8 1.9
N-CA-CB HIS 110.5 1.7 CB-CG-CD PRO 106.5 3.9
C-CA-CB HIS 110.1 1.9
CA-CB-CG HIS 113.8 1.0
CB-CG-ND1 HIS 122.7 1.5
CG-ND1-CE1 HIS 109.3 1.7
ND1-CE1-NE2 HIS 108.4 1.0
CE1-NE2-CD2 HIS 109.0 1.0
NE2-CD2-CG HIS 107.2 1.0
CD2-CG-ND1 HIS 106.1 1.0
CB-CG-CD2 HIS 131.2 1.3
N-CA-C ILE 111.2 2.8
CA-C-O ILE 120.8 1.7
N-CA-CB ILE 111.5 1.7
C-CA-CB ILE 109.1 2.2
CA-CB-CG2 ILE 110.5 1.7
CA-CB-CG1 ILE 110.4 1.7
CG2-CB-CG1 ILE 110.7 3.0
CB-CG1-CD1 ILE 113.8 2.1
N-CA-C LYS 111.2 2.8
CA-C-O LYS 120.8 1.7
N-CA-CB LYS 110.5 1.7
C-CA-CB LYS 110.1 1.9
CA-CB-CG LYS 114.1 2.0
CB-CG-CD LYS 111.3 2.3
CG-CD-CE LYS 111.3 2.3
CD-CE-NZ LYS 111.9 3.2
N-CA-C LEU 111.2 2.8
CA-C-O LEU 120.8 1.7
N-CA-CB LEU 110.5 1.7
C-CA-CB LEU 110.1 1.9
CA-CB-CG LEU 116.3 3.5
CB-CG-CD1 LEU 110.7 3.0
CB-CG-CD2 LEU 110.7 3.0
CD1-CG-CD2 LEU 110.8 2.2
N-CA-C MET 111.2 2.8
CA-C-O MET 120.8 1.7
N-CA-CB MET 110.5 1.7
C-CA-CB MET 110.1 1.9
CA-CB-CG MET 114.1 2.0
CB-CG-SD MET 112.7 3.0
CG-SD-CE MET 100.9 2.2
N-CA-C ASN 111.2 2.8
CA-C-O ASN 120.8 1.7
N-CA-CB ASN 110.5 1.7
C-CA-CB ASN 110.1 1.9
CA-CB-CG ASN 112.6 1.0
CB-CG-ND2 ASN 116.4 1.5
CB-CG-OD1 ASN 120.8 2.0
ND2-CG-OD1 ASN 122.6 1.0
N-CA-C PRO 111.8 2.5
CA-C-O PRO 120.8 1.7
N-CA-CB PRO 103.0 1.1
C-CA-CB PRO 110.1 1.9
CA-CB-CG PRO 104.5 1.9
CB-CG-CD PRO 106.1 3.2
CG-CD-N PRO 103.2 1.5 CG-CD-N PRO 103.2 1.5
CD-N-CA PRO 112.0 1.4 CA-N-CD PRO 111.7 1.4
N-CA-C GLN 111.2 2.8 N-CA-C PRO 112.1 2.6
CA-C-O GLN 120.8 1.7 CA-C-O PRO 120.2 2.4
N-CA-CB GLN 110.5 1.7 N-CA-CB SER 110.5 1.5
C-CA-CB GLN 110.1 1.9 CB-CA-C SER 110.1 1.9
CA-CB-CG GLN 114.1 2.0 CA-CB-OG SER 111.2 2.7
CB-CG-CD GLN 112.6 1.7 N-CA-C SER 111.0 2.7
CG-CD-NE2 GLN 116.4 1.5 CA-C-O SER 120.1 2.1
CG-CD-OE1 GLN 120.8 2.0 N-CA-CB THR 110.3 1.9
NE2-CD-OE1 GLN 122.6 1.0 CB-CA-C THR 111.6 2.7
N-CA-C ARG 111.2 2.8 CA-CB-OG1 THR 109.0 2.1
CA-C-O ARG 120.8 1.7 CA-CB-CG2 THR 112.4 1.4
N-CA-CB ARG 110.5 1.7 OG1-CB-CG2 THR 110.0 2.3
C-CA-CB ARG 110.1 1.9 N-CA-C THR 111.0 2.7
CA-CB-CG ARG 114.1 2.0 CA-C-O THR 120.1 2.1
CB-CG-CD ARG 111.3 2.3 N-CA-CB TRP 110.6 1.8
CG-CD-NE ARG 112.0 2.2 CB-CA-C TRP 110.4 2.0
CD-NE-CZ ARG 124.2 1.5 CA-CB-CG TRP 113.7 1.9
NE-CZ-NH1 ARG 120.0 1.9 CB-CG-CD1 TRP 127.0 1.3
NE-CZ-NH2 ARG 120.0 1.9 CB-CG-CD2 TRP 126.6 1.3
NH1-CZ-NH2 ARG 119.7 1.8 CD1-CG-CD2 TRP 106.3 0.8
N-CA-C SER 111.2 2.8 CG-CD1-NE1 TRP 110.1 1.0
CA-C-O SER 120.8 1.7 CD1-NE1-CE2 TRP 109.0 0.9
N-CA-CB SER 110.5 1.7 NE1-CE2-CD2 TRP 107.3 1.0
C-CA-CB SER 110.1 1.9 CE2-CD2-CG TRP 107.3 0.8
CA-CB-OG SER 111.1 2.0 CG-CD2-CE3 TRP 133.9 0.9
N-CA-C THR 111.2 2.8 NE1-CE2-CZ2 TRP 130.4 1.1
CA-C-O THR 120.8 1.7 CE3-CD2-CE2 TRP 118.7 1.2
N-CA-CB THR 111.5 1.7 CD2-CE2-CZ2 TRP 122.3 1.2
C-CA-CB THR 109.1 2.2 CE2-CZ2-CH2 TRP 117.4 1.0
CA-CB-CG2 THR 110.5 1.7 CZ2-CH2-CZ3 TRP 121.6 1.2
CA-CB-OG1 THR 109.6 1.5 CH2-CZ3-CE3 TRP 121.2 1.1
CG2-CB-OG1 THR 109.3 2.0 CZ3-CE3-CD2 TRP 118.8 1.3
N-CA-C VAL 111.2 2.8 N-CA-C TRP 111.0 2.7
CA-C-O VAL 120.8 1.7 CA-C-O TRP 120.1 2.1
N-CA-CB VAL 111.5 1.7 N-CA-CB TYR 110.6 1.8
C-CA-CB VAL 109.1 2.2 CB-CA-C TYR 110.4 2.0
CA-CB-CG1 VAL 110.5 1.7 CA-CB-CG TYR 113.4 1.9
CA-CB-CG2 VAL 110.5 1.7 CB-CG-CD1 TYR 121.0 0.6
CG1-CB-CG2 VAL 110.8 2.2 CB-CG-CD2 TYR 121.0 0.6
N-CA-C TRP 111.2 2.8 CD1-CG-CD2 TYR 117.9 1.1
CA-C-O TRP 120.8 1.7 CG-CD1-CE1 TYR 121.3 0.8
N-CA-CB TRP 110.5 1.7 CG-CD2-CE2 TYR 121.3 0.8
C-CA-CB TRP 110.1 1.9 CD1-CE1-CZ TYR 119.8 0.9
CA-CB-CG TRP 113.6 1.9 CD2-CE2-CZ TYR 119.8 0.9
CB-CG-CD1 TRP 126.9 1.5 CE1-CZ-CE2 TYR 119.8 1.6
CB-CG-CD2 TRP 126.8 1.4 CE1-CZ-OH TYR 120.1 2.7
CD1-CG-CD2 TRP 106.3 1.6 CE2-CZ-OH TYR 120.1 2.7
CG-CD1-NE1 TRP 110.2 1.3 N-CA-C TYR 111.0 2.7
CD1-NE1-CE2 TRP 108.9 1.8 CA-C-O TYR 120.1 2.1
NE1-CE2-CZ2 TRP 130.1 1.5 N-CA-CB VAL 111.5 2.2
NE1-CE2-CD2 TRP 107.4 1.3 CB-CA-C VAL 111.4 1.9
CZ2-CE2-CD2 TRP 122.4 1.0 CA-CB-CG1 VAL 110.9 1.5
CE2-CZ2-CH2 TRP 117.5 1.3 CA-CB-CG2 VAL 110.9 1.5
CZ2-CH2-CZ3 TRP 121.5 1.3 CG1-CB-CG2 VAL 110.9 1.6
CH2-CZ3-CE3 TRP 121.1 1.3 N-CA-C VAL 111.0 2.7
CZ3-CE3-CD2 TRP 118.6 1.3 CA-C-O VAL 120.1 2.1
CE3-CD2-CG TRP 133.9 1.0
CE3-CD2-CE2 TRP 118.8 1.0
CG-CD2-CE2 TRP 107.2 1.2
N-CA-C TYR 111.2 2.8
CA-C-O TYR 120.8 1.7
N-CA-CB TYR 110.5 1.7
C-CA-CB TYR 110.1 1.9
CA-CB-CG TYR 113.9 1.8
CB-CG-CD1 TYR 120.8 1.5
CB-CG-CD2 TYR 120.8 1.5
CG-CD1-CE1 TYR 121.2 1.5
CG-CD2-CE2 TYR 121.2 1.5
CD1-CE1-CZ TYR 119.6 1.8
CD2-CE2-CZ TYR 119.6 1.8
CE1-CZ-CE2 TYR 120.3 2.0
CD1-CG-CD2 TYR 118.1 1.5
CE1-CZ-OH TYR 119.9 3.0
CE2-CZ-OH TYR 119.9 3.0
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Non-bonded distance Minimum Dist Tolerance Non-bonded distance Minimum Dist Tolerance
C-C 2.10 0.5 C-C 3.4 1.5
C-N 2.10 0.5 C-N 3.25 1.5
C-S 2.45 0.5 C-S 3.5 1.5
C-O 2.25 0.5 C-O 3.22 1.5
N-N 2.05 0.5 N-N 3.1 1.5
N-S 2.55 0.5 N-S 3.35 1.5
N-O 2.10 0.5 N-O 3.07 1.5
O-S 2.45 0.5 O-S 3.32 1.5
O-O 2.05 0.5 O-O 3.04 1.5
S-S 1.80 0.5 S-S 2.03 1.0
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