Contacts of the strand formed by residues 609 - 613 (chain B) 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 ALA 609 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    597B  VAL*     3.7     0.3    -      -       -      -
    598B  ILE*     2.7    41.5    +      -       +      +
    608B  VAL*     1.3    81.2    -      -       -      +
    610B  VAL*     1.3    56.5    +      -       -      +
    650B  LEU*     4.3     6.7    -      -       +      -
    651B  ILE      3.7     4.5    -      -       -      +
    652B  GLY*     4.0     3.1    -      -       -      -
    653B  ALA*     3.9    35.0    -      -       +      +
    692B  ILE*     3.3    20.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 610 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295B  PRO*     4.8    19.1    -      -       +      -
    595B  VAL*     3.6    24.0    -      -       +      -
    596B  SER      3.2    13.7    -      -       -      +
    597B  VAL*     4.0    13.7    -      -       +      +
    598B  ILE*     4.2     0.4    -      -       -      -
    608B  VAL      4.4     0.2    +      -       -      -
    609B  ALA*     1.3    75.2    -      -       -      +
    611B  LEU*     1.3    69.7    +      -       -      +
    612B  TYR*     4.5    17.5    -      -       +      +
    638B  THR      5.4     5.4    -      -       -      +
    650B  LEU*     3.1     8.9    -      -       -      +
    651B  ILE*     2.9    51.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 611 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    312B  ILE*     4.6     4.3    -      -       +      -
    595B  VAL*     3.3     6.8    -      -       -      +
    596B  SER*     2.7    52.2    +      -       -      +
    598B  ILE*     3.8    11.9    -      -       +      +
    610B  VAL*     1.3    73.2    -      -       -      +
    612B  TYR*     1.3    67.3    +      -       -      +
    613B  GLN*     3.6    17.0    +      -       -      +
    645B  THR*     4.8     3.1    -      -       +      -
    647B  ALA*     4.9     9.6    -      -       +      +
    648B  GLY      3.9    13.0    -      -       -      +
    649B  CYS      3.3    32.1    -      -       -      +
    650B  LEU*     3.5    13.9    -      -       +      +
    651B  ILE*     4.9     0.4    -      -       -      +
    666B  ILE*     3.7    31.9    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 612 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    318B  PHE*     4.4    19.1    -      +       +      -
    594B  GLY      4.2     1.6    -      -       -      -
    595B  VAL*     3.5    30.1    -      -       +      -
    610B  VAL*     4.5    14.2    -      -       +      +
    611B  LEU*     1.3    71.4    -      -       -      +
    613B  GLN*     1.3    66.9    +      -       -      +
    614B  ASP      3.4     2.4    +      -       -      -
    615B  VAL*     3.7    22.5    -      -       +      +
    617B  CYS*     6.0     1.8    -      -       +      -
    620B  VAL*     3.5    37.8    -      -       +      +
    648B  GLY*     3.7     0.3    -      -       -      -
    649B  CYS*     3.1    33.7    +      -       -      +
    651B  ILE*     3.5    34.2    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 613 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    314B  GLN*     5.0    10.7    +      -       -      -
    318B  PHE*     4.1     6.1    -      -       -      -
    592B  PHE      4.8     0.3    -      -       -      +
    593B  GLY*     4.4     6.9    -      -       -      -
    594B  GLY*     2.9    41.3    +      -       -      +
    595B  VAL*     5.1     0.4    -      -       -      -
    596B  SER*     4.5    14.6    +      -       -      +
    611B  LEU*     3.6    18.7    +      -       +      +
    612B  TYR*     1.3    72.3    -      -       -      +
    614B  ASP*     1.3    77.5    +      -       +      +
    615B  VAL*     3.1     6.6    +      -       -      +
    647B  ALA*     4.0    10.7    -      -       +      +
    735C  SER*     5.7     1.2    +      -       -      -
    859C  THR*     4.8    12.7    +      -       -      +
    861C  LEU*     3.2    35.0    -      -       +      +
    862C  PRO*     5.4     5.5    -      -       +      +
----------------------------------------------------------
 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