Contacts of the strand formed by residues 605 - 610 (chain D) 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 LYS 605 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    686A  HIS*     4.9    16.1    +      -       +      +
    688A  VAL*     6.3     2.7    -      -       +      -
    594C  LYS*     5.2    14.8    -      -       +      +
    603D  ALA      5.2     0.8    +      -       -      -
    604D  PRO*     1.3    75.7    +      -       -      +
    606D  LEU*     1.3    62.7    +      -       -      +
    620D  ASN      3.6     2.1    -      -       -      +
    621D  LEU*     3.8     2.4    -      -       -      -
    622D  ILE*     2.8    58.5    +      -       +      +
    624D  GLN*     3.1    36.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 606 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    688A  VAL*     4.0    17.0    +      -       -      +
    604D  PRO*     3.7     5.6    +      -       +      -
    605D  LYS*     1.3    76.8    -      -       -      +
    607D  GLU*     1.3    61.2    -      -       -      +
    608D  GLY      4.5     0.2    +      -       -      -
    619D  VAL*     4.0    15.0    -      -       +      -
    620D  ASN      3.5     1.1    -      -       -      -
    621D  LEU*     3.3    32.8    -      -       +      -
    622D  ILE*     5.3     0.7    -      -       -      -
    671D  VAL*     4.9     2.0    -      -       +      +
    673D  VAL*     3.7    28.3    -      -       +      -
    685D  ALA*     3.6    35.0    -      -       +      +
    686D  HIS      4.1     3.8    -      -       -      +
    687D  PHE*     3.9    36.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 607 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    641A  LEU*     5.0     0.2    -      -       -      +
    668A  GLU*     2.4    40.6    -      -       -      +
    688A  VAL*     3.3    30.1    -      -       +      +
    689A  PHE      3.8    12.3    -      -       -      -
    690A  ARG*     3.5    15.7    +      -       +      +
    592C  GLU*     4.1     4.5    -      -       -      +
    606D  LEU*     1.3    76.0    -      -       -      +
    608D  GLY*     1.3    65.5    +      -       -      +
    619D  VAL*     3.5     3.7    -      -       -      +
    620D  ASN*     2.7    67.2    +      -       +      +
    622D  ILE*     4.1    11.6    -      -       +      +
    687D  PHE*     4.5     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 608 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    687A  PHE*     5.4     0.4    -      -       -      -
    688A  VAL      2.9    12.4    +      -       -      -
    689A  PHE*     3.2     8.5    -      -       -      +
    690A  ARG      2.9    26.3    +      -       -      +
    607D  GLU*     1.3    73.4    -      -       -      +
    609D  GLN*     1.3    60.2    +      -       -      +
    617D  ILE*     4.7     2.2    -      -       -      -
    618D  LYS      3.7     4.3    -      -       -      -
    619D  VAL*     4.9     0.7    -      -       -      -
    687D  PHE*     3.5    29.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 609 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    690A  ARG*     3.4    42.5    +      -       +      +
    691A  THR      4.7     6.0    +      -       -      +
    692A  ALA*     5.4     1.9    -      -       -      +
   1697A  SO4      4.7    16.2    +      -       -      -
    608D  GLY*     1.3    73.9    -      -       -      +
    610D  ARG*     1.3    67.8    +      -       +      +
    617D  ILE*     3.3    10.0    -      -       -      +
    618D  LYS*     2.7    68.6    +      -       +      +
    620D  ASN*     2.7    30.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 610 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    610A  ARG*     3.4    56.2    -      -       +      +
    611A  GLY      3.3    25.3    +      -       -      +
    612A  GLU      4.2     2.8    +      -       -      -
    613A  ASP*     3.5    15.4    +      -       -      +
    614A  GLY*     3.4    37.0    -      -       -      +
    616A  SER      5.2     1.8    +      -       -      -
    690A  ARG      4.6     3.2    +      -       -      +
    692A  ALA*     4.8    12.8    -      -       +      +
   1697A  SO4      4.7    10.9    +      -       -      +
    609D  GLN*     1.3    85.5    +      -       +      +
    611D  GLY*     1.3    68.8    +      -       -      +
    616D  SER      5.1     0.9    -      -       -      -
    617D  ILE*     5.0     1.6    -      -       -      +
    618D  LYS*     4.0     8.8    -      -       -      +
----------------------------------------------------------
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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