Contacts of the strand formed by residues 1158 - 1163 (chain B) in PDB entry 2NVX


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 PHE1158 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  GLN*     4.2    13.7    -      -       -      +
     74A  MET      5.7     0.2    -      -       -      -
     75A  ASN*     4.3    15.0    -      -       -      -
     76A  GLU*     3.6    28.5    -      -       -      -
     77A  CYS      5.0     0.9    -      -       -      -
     78A  PRO*     4.5     5.6    -      -       +      -
   1116B  ARG*     4.3    16.8    -      -       +      -
   1152B  MET*     4.9     0.4    -      -       -      +
   1157B  ALA*     1.3    78.8    -      -       -      +
   1159B  ARG*     1.3    68.2    -      -       -      +
   1160B  VAL*     3.3    29.0    +      -       +      +
   1194B  ILE      3.5     3.6    -      -       -      +
   1195B  HIS*     3.7     7.3    +      -       -      -
   1196B  ILE      3.0    36.7    +      -       -      +
   1197B  PRO      5.0     0.2    -      -       -      +
   1198B  TYR*     4.1    28.0    -      +       +      +
   1201B  LYS*     3.2    38.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG1159 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  GLN*     2.4    47.4    +      -       -      +
      5A  GLN*     3.2    44.0    +      -       -      +
      7A  SER*     3.6    14.8    +      -       -      -
     76A  GLU*     2.5    26.4    +      -       -      +
   1158B  PHE*     1.3    85.3    -      -       -      +
   1160B  VAL*     1.3    60.5    +      -       -      +
   1161B  HIS*     3.6    25.0    +      -       -      -
   1175B  LEU*     4.3    11.4    -      -       -      +
   1193B  GLN*     3.2    32.1    -      -       +      +
   1194B  ILE      3.7     3.4    -      -       -      +
   1195B  HIS*     4.2    12.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1160 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78A  PRO*     4.2    24.9    -      -       +      -
   1158B  PHE*     3.3    34.5    -      -       +      +
   1159B  ARG*     1.3    73.6    -      -       -      +
   1161B  HIS*     1.3    92.7    +      -       +      +
   1162B  ILE*     5.8     1.1    -      -       +      -
   1169B  MET*     4.3    29.2    -      -       +      -
   1193B  GLN*     3.7     0.2    -      -       -      -
   1194B  ILE*     3.4    34.4    +      -       +      -
   1196B  ILE*     4.7    15.7    -      -       +      -
   1201B  LYS*     4.3     8.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS1161 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  SER*     4.5     8.0    +      -       -      -
      9A  ALA*     4.6     3.8    -      -       +      -
   1159B  ARG*     3.6    22.6    +      -       -      -
   1160B  VAL*     1.3   110.0    +      -       +      +
   1162B  ILE*     1.3    65.3    +      -       -      +
   1168B  LEU      4.0     5.5    -      -       -      +
   1169B  MET*     4.2     8.8    -      -       -      +
   1171B  VAL*     3.5    33.2    +      -       +      +
   1173B  ALA*     4.4    23.3    -      -       +      -
   1175B  LEU*     5.0     6.2    -      -       +      +
   1180B  PHE*     4.3    28.2    -      +       -      -
   1191B  ILE*     5.0     2.7    -      -       +      -
   1192B  TYR      3.5     3.8    +      -       -      +
   1193B  GLN*     3.4    30.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE1162 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1160B  VAL*     5.8     0.4    -      -       +      -
   1161B  HIS*     1.3    81.2    -      -       -      +
   1163B  CYS*     1.3    74.9    +      -       -      +
   1164B  GLY*     5.4     0.2    -      -       -      -
   1167B  GLY      3.2    25.4    -      -       -      +
   1168B  LEU      3.6     8.7    -      -       -      +
   1169B  MET*     5.0     5.4    -      -       +      -
   1171B  VAL*     3.7     3.1    -      -       -      -
   1191B  ILE*     3.3     4.9    -      -       -      +
   1192B  TYR*     2.9    40.4    +      -       +      +
   1194B  ILE*     3.3    46.4    -      -       +      -
   1216B  LEU*     3.4    38.4    -      -       +      +
   1218B  THR*     5.7     4.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS1163 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1162B  ILE*     1.3    79.0    -      -       -      +
   1164B  GLY*     1.3    67.7    +      -       -      +
   1165B  ILE*     3.6     5.8    -      -       -      -
   1166B  CYS*     3.0    34.5    -      -       -      -
   1167B  GLY*     3.0    21.5    +      -       -      +
   1168B  LEU      3.6     5.2    +      -       -      +
   1171B  VAL*     3.5    17.5    -      -       +      +
   1182B  CYS*     4.2     5.6    -      -       -      -
   1187B  ASN*     3.7    26.5    -      -       -      -
   1191B  ILE*     4.3     3.8    -      -       -      -
   1216B  LEU      5.1     0.2    -      -       -      +
   1307B   ZN      3.0    19.7    -      -       -      -
----------------------------------------------------------
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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