Contacts of the strand formed by residues 456 - 462 (chain B) in PDB entry 2V3D


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 456 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  LEU*     4.7     3.8    -      -       +      -
    449B  LEU      3.6     5.2    -      -       -      +
    450B  MET*     3.9    15.3    -      -       +      -
    455B  SER*     1.3    76.4    +      -       -      +
    457B  VAL*     1.3    65.8    +      -       -      +
    492B  TYR      4.3     0.9    -      -       -      -
    493B  LEU*     3.4     8.0    -      -       -      +
    494B  TRP*     2.9    70.0    +      -       +      +
    496B  ARG*     4.3     5.5    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 457 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  LEU*     5.7     0.2    -      -       -      +
    426B  PHE*     3.5    20.2    -      -       +      +
    427B  ILE*     4.1    21.1    -      -       +      -
    431B  SER*     5.9     1.1    -      -       -      +
    447B  VAL      3.9     0.7    -      -       -      +
    448B  ALA*     3.3     2.8    -      -       -      +
    449B  LEU*     2.7    54.9    +      -       +      +
    451B  HIS*     4.6    19.7    -      -       +      +
    455B  SER*     5.5     0.7    -      -       -      +
    456B  ALA*     1.3    78.1    -      -       -      +
    458B  VAL*     1.3    66.5    +      -       -      +
    459B  VAL*     4.6     4.0    -      -       +      -
    491B  THR*     3.7    26.7    -      -       +      -
    492B  TYR      3.3     3.6    -      -       -      -
    493B  LEU*     3.8    12.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 458 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  LEU*     5.3     1.1    -      -       +      -
     69B  LEU*     4.6     4.9    -      -       +      -
    436B  LEU*     4.4    16.6    -      -       +      -
    447B  VAL      3.3     9.9    -      -       -      +
    448B  ALA*     4.0    15.7    -      -       +      -
    457B  VAL*     1.3    79.2    -      -       -      +
    459B  VAL*     1.3    66.3    +      -       -      +
    460B  VAL*     3.8    22.0    -      -       +      -
    472B  ILE*     4.2    17.0    -      -       +      -
    490B  HIS      3.8     0.7    -      -       -      +
    491B  THR*     3.3     2.6    -      -       -      +
    492B  TYR*     2.7    47.5    +      -       +      +
    494B  TRP*     3.5    29.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 459 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    368B  ILE*     4.5     5.6    -      -       +      +
    422B  HIS*     3.8    18.2    -      -       +      +
    423B  PHE*     3.7    44.6    -      -       +      -
    427B  ILE*     4.4    10.5    -      -       +      -
    445B  ASP      3.8     0.5    -      -       -      +
    446B  ALA*     3.2     6.9    -      -       -      +
    447B  VAL*     3.0    36.4    +      -       +      +
    449B  LEU*     5.4     0.7    -      -       +      -
    457B  VAL*     4.6     2.9    -      -       +      -
    458B  VAL*     1.3    76.7    -      -       -      +
    460B  VAL*     1.3    64.6    -      -       -      +
    461B  LEU      4.2     0.2    -      -       -      -
    489B  ILE*     3.8    20.0    -      -       +      -
    490B  HIS      3.3    10.1    -      -       -      +
    491B  THR*     3.9    12.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 460 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67B  LEU*     4.6     7.4    -      -       +      -
    444B  LEU*     3.8    31.0    -      -       +      -
    445B  ASP      3.5     5.6    -      -       -      +
    446B  ALA*     4.4     8.7    -      -       +      -
    458B  VAL*     3.8    19.7    -      -       +      -
    459B  VAL*     1.3    78.8    -      -       -      +
    461B  LEU*     1.3    61.3    +      -       -      +
    462B  ASN      4.2     0.2    +      -       -      -
    470B  LEU*     4.7     9.2    -      -       +      -
    472B  ILE*     4.9     1.3    -      -       +      -
    484B  SER*     4.0    17.9    +      -       -      +
    488B  SER*     4.1     1.2    +      -       -      +
    489B  ILE*     3.3     5.4    -      -       -      -
    490B  HIS*     2.8    40.4    +      -       +      +
    492B  TYR*     4.1    22.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 461 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361B  MET*     3.9    16.6    -      -       +      +
    364B  SER*     3.4    28.3    -      -       -      +
    365B  HIS*     3.5    19.1    -      -       -      +
    368B  ILE*     3.8    15.0    -      -       +      -
    419B  HIS*     3.8    17.5    -      -       +      -
    444B  LEU*     3.4     9.2    -      -       -      +
    445B  ASP*     2.7    47.1    +      -       +      +
    459B  VAL      4.2     0.4    -      -       -      -
    460B  VAL*     1.3    73.4    -      -       -      +
    462B  ASN*     1.3    60.3    +      -       -      +
    463B  ARG*     3.6    30.8    +      -       +      -
    488B  SER      3.6    15.5    -      -       -      +
    489B  ILE*     4.0     7.4    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 462 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    361B  MET*     3.2    11.4    -      -       -      +
    443B  ASP*     4.9     1.9    -      -       -      +
    444B  LEU*     3.5    18.3    -      -       +      +
    460B  VAL      4.2     0.4    +      -       -      -
    461B  LEU*     1.3    71.5    -      -       -      +
    463B  ARG*     1.3    57.0    +      -       -      +
    464B  SER*     2.7    29.9    +      -       -      -
    466B  LYS      3.0    19.2    +      -       -      -
    468B  VAL*     3.8     4.0    -      -       -      +
    484B  SER*     2.8    43.0    +      -       -      +
    485B  PRO      3.4    14.6    +      -       -      +
    487B  TYR*     3.1    20.4    +      -       -      -
    488B  SER      3.0    11.5    +      -       -      +
----------------------------------------------------------
 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