Contacts of the strand formed by residues 83 - 89 (chain B) in PDB entry 3VAS


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 CYS 83 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9B  VAL*     3.3    20.4    -      -       -      +
     70B  VAL*     3.6    14.4    -      -       +      -
     73B  ILE*     3.7    17.9    -      -       -      -
     74B  GLN*     2.9    41.4    +      -       +      +
     81B  PHE      4.0     3.2    -      -       -      +
     82B  VAL*     1.3    82.9    -      -       -      +
     84B  SER*     1.3    63.7    +      -       -      +
    107B  LEU*     3.2    19.7    -      -       +      +
    108B  VAL*     3.1    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 84 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7B  GLY*     3.7    19.4    +      -       -      -
      9B  VAL      2.8     8.6    +      -       -      -
     10B  PHE*     3.5    22.3    -      -       -      -
     11B  GLY*     2.8    25.7    +      -       -      -
     70B  VAL*     3.8     5.2    -      -       -      +
     83B  CYS*     1.3    76.7    +      -       -      +
     85B  TYR*     1.3    62.9    +      -       -      +
    107B  LEU*     4.0     1.8    -      -       -      -
    108B  VAL*     3.2    18.5    -      -       -      +
    157B  LEU*     4.2    23.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 85 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11B  GLY*     3.1    18.8    -      -       -      -
     13B  GLY      3.1    37.6    +      -       -      -
     14B  ASN      3.4     3.1    +      -       -      -
     15B  PRO*     3.2    19.1    -      -       +      +
     66B  THR*     4.0     6.7    -      -       +      -
     67B  LEU*     3.7    48.8    +      -       +      +
     70B  VAL*     4.6     4.9    -      -       +      -
     84B  SER*     1.3    76.8    -      -       -      +
     86B  VAL*     1.3    77.4    +      -       -      +
     87B  GLY*     3.9     2.0    -      -       -      -
    107B  LEU*     4.1    20.0    -      -       +      -
    108B  VAL      2.9     5.9    +      -       -      -
    109B  THR*     3.3     7.4    -      -       +      -
    110B  GLU      3.2    24.3    +      -       -      -
    111B  PHE*     3.7    32.5    -      +       -      -
    157B  LEU*     5.4     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 86 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10B  PHE*     3.5    33.4    -      -       +      -
     11B  GLY      2.9     7.2    +      -       -      +
     12B  MET*     3.2     8.1    -      -       +      +
     13B  GLY      3.0    24.9    +      -       -      -
     85B  TYR*     1.3    83.7    -      -       -      +
     87B  GLY*     1.3    61.6    +      -       -      +
    110B  GLU*     3.8    15.7    -      -       +      +
    144B  LEU*     4.2    11.2    -      -       +      -
    148B  HIS*     3.8    26.9    -      -       +      -
    149B  ILE*     4.6     9.9    -      -       +      -
    154B  VAL*     3.9    20.9    -      -       +      -
    157B  LEU*     4.8     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 87 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  GLY      3.4    15.7    -      -       -      -
     15B  PRO*     3.9     9.4    -      -       -      -
     85B  TYR*     3.9     6.4    -      -       -      -
     86B  VAL*     1.3    78.5    -      -       -      +
     88B  CYS*     1.3    61.7    +      -       -      -
    110B  GLU      4.1     1.6    +      -       -      +
    111B  PHE*     3.3    11.0    -      -       -      -
    112B  GLN*     2.8    22.9    +      -       -      +
    144B  LEU*     4.1    11.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 88 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  GLY      4.3     0.8    +      -       -      -
     15B  PRO*     3.3    19.9    -      -       -      +
     87B  GLY*     1.3    71.7    -      -       -      -
     89B  ILE*     1.3    59.4    +      -       -      +
    112B  GLN*     3.3    28.9    -      -       +      -
    114B  ALA*     3.6    24.5    -      -       -      -
    121B  GLY      5.6     0.3    +      -       -      -
    140B  ALA*     3.2    24.9    -      -       -      +
    141B  ALA*     3.4    21.6    +      -       -      +
    143B  ASP*     3.9    11.0    -      -       -      -
    144B  LEU*     3.7    23.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 89 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15B  PRO*     3.6    29.6    -      -       +      +
     87B  GLY      4.1     0.2    +      -       -      -
     88B  CYS*     1.3    73.8    -      -       -      +
     90B  GLY*     1.3    62.6    +      -       -      +
     95B  GLY*     3.6    33.9    -      -       -      +
     98B  ILE*     4.4    11.2    -      -       +      -
     99B  LYS*     3.8    24.2    -      -       -      -
    111B  PHE*     4.0    23.6    -      -       +      -
    112B  GLN      3.0    11.4    +      -       -      +
    113B  ILE*     3.5    17.1    -      -       +      -
    114B  ALA      3.0    23.6    +      -       -      -
    120B  THR*     3.8     9.4    -      -       +      +
    140B  ALA*     3.5     8.0    -      -       -      +
----------------------------------------------------------
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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