Contacts of the strand formed by residues 631 - 640 (chain B) in PDB entry 2VKX


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 631 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    507A  GLN*     2.9    29.2    +      -       -      +
    601B  PRO*     4.7     6.7    -      -       +      -
    602B  SER      6.0     0.2    -      -       -      +
    623B  LYS*     6.1     1.1    -      -       +      -
    624B  GLN      4.9     6.7    -      -       -      +
    626B  ASP*     3.8    27.6    -      -       +      +
    629B  SER      3.6     0.2    +      -       -      -
    630B  PRO*     1.3    73.1    -      -       -      +
    632B  ARG*     1.3    59.9    +      -       -      +
    633B  HIS      3.5    27.4    -      -       -      +
    634B  TYR*     3.2    37.9    -      -       +      +
    653B  SER*     3.3    25.7    -      -       -      -
    675B  ALA*     4.3    12.3    -      -       +      -
    676B  GLU      3.6     7.4    -      -       -      +
    677B  ASN*     4.3     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 632 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    630B  PRO      3.4     3.1    +      -       -      +
    631B  ILE*     1.3    75.8    -      -       -      +
    633B  HIS*     1.3   115.9    +      -       +      +
    650B  ARG*     4.8     6.1    -      -       -      +
    651B  LEU      4.6     0.2    -      -       -      +
    652B  PRO*     4.6     2.1    -      -       -      +
    653B  SER*     4.2     9.2    +      -       -      -
    676B  GLU*     2.7    31.1    +      -       -      +
    677B  ASN*     4.3     8.2    +      -       -      -
    678B  GLN*     3.0    48.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 633 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    631B  ILE*     3.5    10.4    -      -       -      +
    632B  ARG*     1.3   136.7    +      -       +      +
    634B  TYR*     1.3    63.8    +      -       -      +
    635B  LEU*     3.9    17.0    -      -       +      -
    650B  ARG*     3.4    46.1    +      -       +      +
    651B  LEU      3.3    13.9    +      -       -      +
    652B  PRO*     5.1     2.4    -      -       -      +
    653B  SER      4.9     0.4    -      -       -      +
    675B  ALA*     3.8     0.9    -      -       -      -
    676B  GLU*     3.1    38.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 634 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    604B  PRO*     4.0    17.3    -      -       +      +
    621B  LEU*     3.9    24.7    -      -       +      -
    623B  LYS*     3.8    26.8    -      -       +      +
    624B  GLN      5.0     1.0    +      -       -      -
    631B  ILE*     3.2    29.4    -      -       +      +
    633B  HIS*     1.3    71.8    -      -       -      +
    635B  LEU*     1.3    65.0    +      -       -      +
    636B  VAL*     3.5     1.4    +      -       -      +
    649B  ILE      3.5     2.6    -      -       -      +
    651B  LEU*     2.8    51.3    +      -       +      +
    652B  PRO      4.1    15.0    -      -       -      -
    653B  SER*     4.0    19.1    -      -       -      -
    655B  SER*     4.5     4.3    -      -       -      -
    673B  VAL*     4.4    14.1    -      -       +      -
    674B  VAL      3.4     4.3    -      -       -      -
    675B  ALA*     3.5    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 635 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    633B  HIS*     4.2    12.3    -      -       +      -
    634B  TYR*     1.3    69.5    -      -       -      +
    636B  VAL*     1.3    60.4    +      -       -      +
    637B  ARG*     5.6     0.4    -      -       -      -
    648B  GLU*     3.6    30.5    -      -       -      +
    649B  ILE      3.6     2.9    -      -       -      -
    650B  ARG*     3.5    33.7    -      -       +      +
    672B  TYR      3.6     1.2    -      -       -      +
    673B  VAL*     3.3     3.1    -      -       -      -
    674B  VAL*     2.7    54.1    +      -       +      +
    676B  GLU*     4.2    19.5    -      -       +      +
    681B  LYS*     3.7    31.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 636 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    634B  TYR      4.0     3.1    -      -       -      +
    635B  LEU*     1.3    77.4    -      -       -      +
    637B  ARG*     1.3    73.8    +      -       -      +
    638B  TYR*     4.9     3.1    -      -       +      +
    648B  GLU*     3.4     0.3    -      -       -      +
    649B  ILE*     2.9    50.9    +      -       +      +
    651B  LEU*     3.7    30.3    -      -       +      -
    658B  VAL*     4.1    21.5    -      -       +      -
    660B  LEU*     5.5     0.7    -      -       +      -
    671B  VAL*     3.8    20.9    -      -       +      -
    672B  TYR      3.2     7.2    -      -       -      +
    673B  VAL*     4.0    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 637 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    635B  LEU      5.6     0.4    -      -       -      -
    636B  VAL*     1.3    83.5    -      -       -      +
    638B  TYR*     1.3    61.0    +      -       -      +
    645B  TRP*     3.7    54.6    -      -       +      +
    646B  LYS      4.6    10.1    -      -       -      +
    647B  PRO      5.1     2.0    -      -       -      -
    648B  GLU*     3.5    39.3    +      -       +      +
    671B  VAL*     3.4     0.9    -      -       -      -
    672B  TYR*     2.6    56.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 638 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    636B  VAL*     5.4     1.6    -      -       +      -
    637B  ARG*     1.3    78.1    -      -       -      +
    639B  ARG*     1.3    73.0    +      -       -      +
    645B  TRP*     3.3     4.3    -      -       -      -
    646B  LYS*     3.0    65.3    +      -       +      +
    647B  PRO*     4.8     4.8    -      -       +      +
    649B  ILE*     4.4    16.8    -      -       +      -
    660B  LEU*     3.8    44.2    -      -       +      -
    661B  LYS      5.6     1.6    +      -       -      -
    663B  LEU*     4.2    21.3    -      -       +      +
    669B  TYR*     4.3    14.1    -      +       +      -
    670B  GLU      3.2    15.0    -      -       -      +
    671B  VAL*     4.3     4.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 639 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    638B  TYR*     1.3    83.9    -      -       -      +
    640B  ALA*     1.3    67.2    +      -       -      +
    641B  LEU*     4.9     3.6    -      -       -      +
    642B  SER      5.4     5.8    -      -       -      +
    643B  SER      3.7    22.8    +      -       -      -
    644B  GLU      3.6    17.3    -      -       -      +
    645B  TRP*     3.5    52.1    -      -       +      +
    646B  LYS*     4.3     6.7    -      -       -      +
    669B  TYR*     3.1    11.3    -      -       -      -
    670B  GLU*     2.5    57.9    +      -       +      -
    672B  TYR*     4.9     3.2    +      -       -      -
    569F  GLU      5.8     2.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 640 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    639B  ARG*     1.3    82.1    -      -       -      +
    641B  LEU*     1.3    70.7    +      -       -      +
    643B  SER*     3.4    25.5    +      -       -      -
    644B  GLU      5.1     0.2    +      -       -      -
    646B  LYS*     5.5     4.3    -      -       -      +
    664B  ASP*     5.6     2.9    -      -       -      +
    667B  ALA*     5.6     3.4    -      -       +      -
    668B  GLU      3.3    11.0    -      -       -      +
    669B  TYR*     3.3    26.1    -      -       +      +
    541F  GLY*     6.4     0.9    -      -       -      -
----------------------------------------------------------
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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