Contacts of the strand formed by residues 692 - 696 (chain C) in PDB entry 6VSB


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 ILE 692 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598C  ILE*     4.6     7.9    -      -       +      +
    599C  THR      5.0     1.3    -      -       -      -
    600C  PRO*     3.5    38.4    -      -       +      -
    607C  GLN*     4.0    23.2    -      -       +      +
    608C  VAL      4.8     0.9    -      -       -      -
    609C  ALA*     4.1    22.0    -      -       +      +
    652C  GLY      4.7     3.8    -      -       -      +
    653C  ALA*     3.8    28.0    -      -       +      -
    654C  GLU*     3.2    23.9    +      -       -      +
    664C  ILE*     6.2     1.3    -      -       +      -
    672C  ALA*     4.3    13.9    -      -       +      +
    687C  VAL*     3.9    14.8    -      -       +      +
    691C  SER*     1.3    76.7    +      -       -      +
    693C  ILE*     1.3    72.4    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 693 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    654C  GLU*     3.1    17.5    -      -       -      +
    656C  VAL*     3.7    28.0    -      -       +      -
    660C  TYR*     4.6    17.5    -      -       +      -
    671C  CYS      3.8     0.5    -      -       -      +
    672C  ALA*     3.1    33.6    +      -       -      +
    687C  VAL*     4.7     2.7    -      -       -      +
    688C  ALA*     3.7    43.7    -      -       +      +
    689C  SER*     5.1     2.7    -      -       -      +
    691C  SER      4.4     0.2    -      -       -      +
    692C  ILE*     1.3    85.8    -      -       -      +
    694C  ALA*     1.3    59.7    +      -       -      +
    695C  TYR*     4.0    18.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 694 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    643C  PHE*     4.3    13.5    -      -       +      -
    650C  LEU*     4.0    27.4    -      -       +      -
    653C  ALA*     4.0     8.7    -      -       +      +
    654C  GLU      3.0     8.7    +      -       -      +
    655C  HIS*     3.6    12.4    -      -       -      -
    656C  VAL*     3.3    21.7    +      -       -      -
    666C  ILE*     4.9     2.0    -      -       +      -
    670C  ILE*     4.2    12.8    -      -       +      -
    671C  CYS      3.5     4.9    -      -       -      +
    672C  ALA*     4.5     0.4    -      -       +      +
    693C  ILE*     1.3    72.5    -      -       -      +
    695C  TYR*     1.3    61.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 695 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    655C  HIS*     5.2     2.9    -      -       -      -
    656C  VAL*     3.8    13.0    -      -       +      +
    658C  ASN      3.6    17.3    -      -       -      +
    660C  TYR*     3.2    51.6    -      +       +      +
    661C  GLU      2.4    30.7    +      -       -      -
    662C  CYS      4.5     0.7    -      -       -      -
    663C  ASP*     3.5    17.1    +      -       -      -
    670C  ILE*     3.2    10.1    -      -       -      +
    671C  CYS*     2.8    55.2    +      -       +      +
    672C  ALA      4.0    11.2    -      -       -      -
    693C  ILE*     4.0    18.4    -      -       +      -
    694C  ALA*     1.3    77.2    -      -       -      +
    696C  THR*     1.3    73.0    +      -       -      +
    697C  MET*     4.5     3.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 696 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    869A  MET*     4.4    13.0    -      -       +      -
    655C  HIS*     5.7     4.1    +      -       -      -
    656C  VAL      5.5     0.2    +      -       -      -
    657C  ASN      5.7     3.0    +      -       -      -
    658C  ASN      5.1     0.8    +      -       -      -
    659C  SER*     2.7    34.9    +      -       -      -
    669C  GLY      3.5    11.4    -      -       -      +
    670C  ILE*     4.5    10.5    -      -       +      +
    695C  TYR*     1.3    78.2    -      -       -      +
    697C  MET*     1.3    64.2    +      -       -      +
----------------------------------------------------------
 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