Contacts of the strand formed by residues 1111 - 1115 (chain B) in PDB entry 2O8C


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 ASN1111 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    202B  ADP      4.8     4.8    +      -       -      -
   1093B  GLY      3.1     3.1    +      -       -      -
   1094B  SER*     2.7    44.2    +      -       -      +
   1108B  PHE*     5.2     0.4    -      -       -      -
   1109B  ILE      3.6     8.1    +      -       -      +
   1110B  PRO*     1.3    83.2    -      -       -      +
   1112B  ASP*     1.3    67.2    +      -       -      +
   1139B  GLY      5.9     0.4    +      -       -      -
   1143B  LEU*     4.0    22.6    -      -       +      +
   1146B  GLN*     3.4    24.2    -      -       -      +
   1267B  MET*     5.3     1.8    -      -       -      -
   1287B  TYR      3.0    27.4    +      -       -      +
   1288B  LYS*     3.4    13.0    -      -       -      +
   1289B  PHE*     4.1    13.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP1112 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1091B  LEU      3.3     7.6    -      -       -      +
   1092B  LYS*     3.4    11.2    -      -       -      +
   1093B  GLY*     2.7    32.5    +      -       -      -
   1111B  ASN*     1.3    74.8    -      -       -      +
   1113B  ILE*     1.3    63.4    +      -       -      +
   1114B  LEU*     3.6    18.0    +      -       +      +
   1289B  PHE*     3.7    27.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE1113 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1089B  LEU*     4.0     5.8    -      -       +      +
   1090B  GLU      4.0     0.5    -      -       -      -
   1091B  LEU*     3.0    47.0    +      -       +      +
   1094B  SER*     3.6    19.5    -      -       -      +
   1111B  ASN*     3.9     0.8    +      -       +      -
   1112B  ASP*     1.3    72.4    -      -       -      +
   1114B  LEU*     1.3    60.6    +      -       -      +
   1115B  ILE*     4.1    14.8    +      -       +      -
   1143B  LEU*     3.8    34.3    -      -       +      +
   1146B  GLN*     3.9    11.9    -      -       +      -
   1147B  ALA*     3.9    35.2    -      -       +      -
   1150B  LEU*     5.0     0.4    -      -       +      -
   1244B  LEU*     4.4    15.7    -      -       +      -
   1289B  PHE*     4.6     7.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU1114 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1089B  LEU      3.7     1.6    -      -       -      -
   1090B  GLU*     3.7    20.6    -      -       +      -
   1091B  LEU      3.5    35.0    -      -       -      +
   1092B  LYS*     4.4    15.0    -      -       +      -
   1112B  ASP*     3.6    16.9    +      -       +      +
   1113B  ILE*     1.3    73.1    -      -       -      +
   1115B  ILE*     1.3    63.4    +      -       -      +
   1117B  CYS*     3.8    13.2    -      -       -      -
   1130B  VAL*     4.4     8.1    -      -       -      +
   1263B  ARG*     3.2    30.2    +      -       -      +
   1289B  PHE*     5.1     5.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE1115 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1088B  PHE*     3.6     1.3    -      -       -      -
   1089B  LEU*     2.8    67.9    +      -       +      +
   1113B  ILE*     4.4     7.4    -      -       +      -
   1114B  LEU*     1.3    77.3    -      -       -      +
   1116B  GLY*     1.3    60.8    +      -       -      +
   1117B  CYS*     2.9     7.4    +      -       -      -
   1128B  TYR*     3.3    26.5    -      -       -      +
   1130B  VAL*     4.3     4.7    -      -       +      -
   1209B  LEU*     4.3    14.6    -      -       +      -
   1242B  ARG*     3.7    26.9    -      -       +      -
   1243B  THR      4.9     2.7    -      -       -      +
   1244B  LEU*     3.8    40.2    -      -       +      -
----------------------------------------------------------
 Back to top of page


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