Contacts of the strand formed by residues 785 - 788 (chain W) in PDB entry 5O9G


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 THR 785 (chain W).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707W  LEU*     3.7    27.4    -      -       +      +
    712W  HIS*     4.0    13.0    -      -       -      +
    713W  ARG      2.9    12.8    +      -       -      +
    714W  VAL*     3.4    18.2    -      -       +      -
    715W  LEU*     2.7    34.9    +      -       -      +
    784W  ASP*     1.3    88.9    +      -       -      +
    786W  VAL*     1.3    58.6    +      -       -      +
    787W  VAL*     4.1    10.1    -      -       +      -
    815W  MET*     3.3    24.8    +      -       +      +
    817W  TYR*     5.3     3.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 786 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    715W  LEU*     4.0     3.4    -      -       +      -
    717W  PHE*     3.6    33.2    -      -       +      -
    784W  ASP      4.5     5.6    -      -       -      +
    785W  THR*     1.3    75.5    -      -       -      +
    787W  VAL*     1.3    61.1    +      -       -      +
    788W  ILE*     4.1    11.0    -      -       +      -
    802W  MET*     3.8    31.9    -      -       +      +
    805W  ALA*     3.9    27.6    -      -       +      -
    814W  VAL*     5.0     2.9    -      -       +      -
    815W  MET      3.1     7.3    +      -       -      -
    816W  VAL*     3.3    22.8    -      -       +      +
    817W  TYR      3.2    22.0    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 787 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    700W  LEU*     3.9    26.7    -      -       +      -
    703W  LEU*     6.3     2.2    -      -       +      -
    707W  LEU*     5.6     1.6    -      -       +      -
    714W  VAL*     3.7    24.5    -      -       +      -
    715W  LEU      2.8    15.2    +      -       -      +
    716W  ILE*     3.3     9.0    -      -       +      +
    717W  PHE*     3.1    24.1    +      -       -      +
    785W  THR*     4.1     9.4    -      -       +      -
    786W  VAL*     1.3    76.5    -      -       -      +
    788W  ILE*     1.3    63.8    +      -       -      +
    789W  PHE*     4.2     5.7    +      -       +      -
    817W  TYR*     3.6    27.4    -      -       +      +
    819W  LEU*     4.4    20.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 788 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    717W  PHE*     3.8    21.3    -      -       +      +
    786W  VAL*     4.1    21.8    -      -       +      +
    787W  VAL*     1.3    76.2    -      -       -      +
    789W  PHE*     1.3    63.0    +      -       -      +
    790W  ASP      3.3    29.6    -      -       -      +
    791W  SER*     4.6     0.4    -      -       -      +
    792W  ASP*     5.4     3.6    -      -       -      +
    798W  ASP*     4.2    35.4    -      -       +      +
    801W  ALA*     5.3     4.5    -      -       +      -
    802W  MET*     4.5    13.5    -      -       +      -
    816W  VAL*     5.0     4.9    -      -       +      -
    817W  TYR      3.1    10.5    +      -       -      +
    818W  ARG*     3.9    14.9    -      -       +      +
    819W  LEU*     3.1    29.6    +      -       -      +
----------------------------------------------------------
 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