Contacts of the strand formed by residues 593 - 597 (chain A) in PDB entry 2VWJ


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 LYS 593 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    538A  TYR*     4.2     0.5    -      -       -      -
    588A  PHE      3.7     0.3    -      -       -      -
    589A  VAL*     2.8    35.9    +      -       +      -
    590A  THR*     3.3    32.0    +      -       +      +
    592A  LYS*     1.3    90.6    -      -       +      +
    594A  TYR*     1.3    60.5    +      -       -      +
    606A  ARG      3.1    13.0    -      -       -      +
    607A  GLY*     3.2    29.8    -      -       -      +
    608A  LEU*     4.1    13.5    -      -       +      -
    743A  ARG*     5.4    12.4    -      -       +      +
      9B    A      5.7     4.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 594 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    402A  TYR*     5.7     1.4    -      -       -      -
    538A  TYR*     3.7    42.4    -      +       -      -
    540A  ASP*     5.1     2.0    +      -       -      -
    545A  PHE*     3.6    27.8    -      +       -      -
    587A  PHE      3.3    15.5    -      -       -      +
    588A  PHE*     3.3    18.2    -      +       +      +
    589A  VAL*     4.2     2.5    -      -       -      +
    592A  LYS      4.6     0.4    -      -       -      -
    593A  LYS*     1.3    77.9    -      -       -      +
    595A  ALA*     1.3    68.7    +      -       -      +
    596A  VAL*     4.3    14.8    -      -       +      -
    604A  THR*     5.3     5.2    -      -       +      -
    605A  THR*     3.5     3.4    -      -       -      -
    606A  ARG*     3.0    74.6    +      -       +      -
    608A  LEU*     3.5    11.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 595 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    586A  GLY*     3.1     2.1    -      -       -      -
    587A  PHE*     2.8    48.2    +      -       +      +
    594A  TYR*     1.3    78.7    -      -       -      +
    596A  VAL*     1.3    62.8    +      -       -      +
    604A  THR      3.4    10.3    -      -       -      +
    605A  THR*     4.6     5.2    -      -       +      -
    608A  LEU*     4.0    12.7    -      -       +      +
    627A  LEU*     4.5     5.2    -      -       +      -
    631A  LEU*     3.7    24.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 596 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    400A  ILE*     4.9     0.9    -      -       +      -
    545A  PHE*     3.7    28.0    -      -       +      -
    583A  TYR*     3.6    37.9    -      -       +      -
    585A  ARG      3.6     7.0    -      -       -      +
    586A  GLY*     3.9     4.9    -      -       -      -
    588A  PHE*     3.9    19.3    -      -       +      -
    594A  TYR*     4.3     9.6    -      -       +      -
    595A  ALA*     1.3    79.4    -      -       -      +
    597A  ILE*     1.3    59.7    +      -       -      +
    603A  ILE*     3.6     2.9    -      -       -      +
    604A  THR*     2.9    46.3    +      -       +      +
    631A  LEU*     4.4     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 597 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    583A  TYR*     3.5     5.9    -      -       -      +
    584A  LYS*     2.8    30.1    +      -       +      -
    585A  ARG*     3.0    26.1    +      -       +      +
    596A  VAL*     1.3    76.0    -      -       -      +
    598A  ASP*     1.3    64.0    +      -       -      +
    601A  ASP*     3.5    49.4    -      -       -      +
    602A  LYS      3.7     2.9    -      -       -      +
    603A  ILE*     3.8    17.5    -      -       +      -
    631A  LEU*     3.4    30.3    -      -       +      +
    632A  LYS*     3.9    24.5    -      -       +      -
----------------------------------------------------------
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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