Contacts of the strand formed by residues 1156 - 1167 (chain A) in PDB entry 6O0Z


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with LYS1156 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1149A  VAL      3.0     4.5    -      -       -      +
   1150A  GLU*     3.3     2.3    -      -       -      -
   1151A  LYS*     2.5    52.7    +      -       +      +
   1154A  SER*     3.3     8.4    -      -       -      -
   1155A  LYS*     1.3    77.3    -      -       -      +
   1157A  LEU*     1.3    61.5    +      -       -      +
   1158A  LYS*     3.3     3.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1148A  LYS*     4.0    37.4    +      -       +      +
   1149A  VAL      3.6     6.1    -      -       -      +
   1150A  GLU*     3.3    36.8    -      -       -      +
   1155A  LYS      4.0     5.8    -      -       -      +
   1156A  LYS*     1.3    71.2    -      -       -      +
   1158A  LYS*     1.3    62.5    +      -       -      +
   1159A  SER*     3.5     3.3    +      -       -      -
   1188A  LYS*     5.6     5.6    -      -       +      -
   1189A  GLU*     6.4     0.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1148A  LYS*     4.0     0.7    -      -       -      -
   1149A  VAL*     3.2    29.0    +      -       +      +
   1151A  LYS*     3.8    22.0    -      -       +      -
   1156A  LYS*     3.3     6.6    +      -       +      +
   1157A  LEU*     1.3    74.5    -      -       -      +
   1159A  SER*     1.3    67.3    +      -       -      +
   1160A  VAL*     4.3     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER1159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1146A  VAL*     4.9     7.1    -      -       -      +
   1147A  ALA      3.4    13.7    +      -       -      -
   1148A  LYS*     3.8    15.0    -      -       -      -
   1157A  LEU      3.5     4.0    +      -       -      -
   1158A  LYS*     1.3    79.0    -      -       -      +
   1160A  VAL*     1.3    65.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1145A  VAL      4.1     1.0    -      -       -      +
   1146A  VAL*     3.6     2.9    -      -       -      +
   1147A  ALA      2.7    47.0    +      -       -      +
   1149A  VAL*     4.2    30.5    -      -       +      +
   1158A  LYS      4.5     0.9    -      -       -      +
   1159A  SER*     1.3    81.4    +      -       -      +
   1161A  LYS*     1.3    70.4    +      -       -      +
   1162A  GLU*     4.0    19.2    -      -       +      +
   1187A  TYR*     4.5    15.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1161 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1144A  LEU*     3.9    30.1    -      -       +      -
   1145A  VAL      3.7     5.4    -      -       -      +
   1146A  VAL*     4.4    17.0    -      -       +      +
   1160A  VAL*     1.3    74.8    -      -       -      +
   1162A  GLU*     1.3    66.4    +      -       -      +
   1343A  LEU*     3.4    45.7    +      -       +      +
   1344A  ASP*     4.5     7.2    +      -       -      -
   1362A  LEU*     3.2    25.6    +      -       +      +
   1363A  SER      4.6     4.6    +      -       -      -
   1365A  LEU*     3.5    17.6    +      -       +      +
   1366A  GLY      4.3     6.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1162 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1144A  LEU*     3.5     7.1    -      -       -      +
   1145A  VAL*     2.9    40.0    +      -       +      +
   1160A  VAL*     4.0    19.6    -      -       +      +
   1161A  LYS*     1.3    79.0    -      -       -      +
   1163A  LEU*     1.3    80.9    +      -       -      +
   1164A  LEU*     4.1     1.1    -      -       +      -
   1187A  TYR*     3.6    28.0    -      -       +      +
   1339A  THR*     5.5     2.3    +      -       -      -
   1343A  LEU*     4.8     6.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1142A  SER*     3.9    24.2    -      -       -      +
   1143A  VAL      3.8    10.1    -      -       -      +
   1144A  LEU*     4.8     5.2    -      -       +      +
   1162A  GLU*     1.3    92.5    +      -       -      +
   1164A  LEU*     1.3    61.5    +      -       -      +
   1198A  LEU*     4.2    21.8    -      -       +      -
   1204A  PHE*     5.5     0.2    -      -       +      -
   1214A  LEU*     4.7    14.6    -      -       +      -
   1216A  SER      4.8     2.7    -      -       -      +
   1217A  ALA*     3.7    34.7    -      -       +      +
   1339A  THR*     4.7    13.6    +      -       -      +
   1342A  VAL*     4.8    11.7    -      -       +      -
   1343A  LEU*     4.3    23.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU1164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1142A  SER*     3.4     5.9    -      -       -      -
   1143A  VAL*     3.1    39.7    +      -       +      +
   1145A  VAL*     4.6     9.4    -      -       +      -
   1162A  GLU*     4.1     0.9    -      -       +      -
   1163A  LEU*     1.3    75.1    -      -       -      +
   1165A  GLY*     1.3    83.9    +      -       -      +
   1166A  ILE*     3.7    17.9    -      -       +      -
   1181A  PHE*     5.3     0.9    -      -       +      -
   1182A  LEU*     4.9    11.9    -      -       +      -
   1185A  LYS*     4.3    27.1    -      -       +      +
   1187A  TYR*     3.7    36.8    -      -       +      +
   1217A  ALA*     4.5     2.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY1165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1139A  VAL*     3.8    12.8    -      -       -      -
   1141A  TYR      4.0     2.2    -      -       -      -
   1142A  SER*     4.2     0.7    -      -       -      -
   1164A  LEU*     1.3    89.6    -      -       -      +
   1166A  ILE*     1.3    63.0    +      -       -      +
   1167A  THR*     4.0     2.7    +      -       -      -
   1170A  GLU*     4.2     5.7    -      -       -      +
   1185A  LYS*     5.4     0.3    +      -       -      -
   1217A  ALA*     3.8    24.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE1166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1139A  VAL*     3.4     5.0    -      -       -      +
   1140A  ALA*     2.9    25.8    +      -       -      +
   1141A  TYR*     3.1    28.4    +      -       +      +
   1143A  VAL*     4.2    22.9    -      -       +      -
   1164A  LEU*     3.7    24.9    -      -       +      +
   1165A  GLY*     1.3    72.1    -      -       -      -
   1167A  THR*     1.3    72.8    +      -       -      +
   1170A  GLU*     3.7    11.7    -      -       +      +
   1171A  ARG*     3.6    21.8    -      -       +      +
   1174A  PHE*     4.4    18.6    -      -       +      -
   1181A  PHE*     3.9    22.4    -      -       +      -
   1182A  LEU*     5.8     0.9    -      -       +      -
   1185A  LYS*     5.7     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR1167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1105A  PHE*     4.5     6.1    -      -       +      +
   1120A  ILE*     6.0     0.4    -      -       +      -
   1137A  PRO*     3.6    30.9    -      -       +      +
   1138A  THR      3.4    20.6    -      -       -      +
   1139A  VAL*     4.5     3.1    -      -       -      +
   1140A  ALA      4.6     0.2    -      -       -      -
   1165A  GLY      4.8     1.7    +      -       -      -
   1166A  ILE*     1.3    76.8    -      -       -      +
   1168A  ILE*     1.3    63.6    +      -       +      +
   1169A  MET*     3.4    14.1    -      -       +      +
   1170A  GLU*     2.8    32.0    +      -       -      -
   1171A  ARG*     2.5    34.1    +      -       -      +
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il