Contacts of the strand formed by residues 617 - 622 (chain E) 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 617 (chain E).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    608E  GLY*     4.4     6.1    -      -       -      -
    609E  GLN      3.1    17.3    -      -       -      +
    611E  GLY*     4.1     3.4    -      -       -      +
    616E  SER*     1.3    77.4    -      -       -      +
    618E  LYS*     1.3    69.0    +      -       -      +
    619E  VAL*     3.9    15.5    +      -       +      -
    659E  MET*     3.4     7.2    -      -       -      +
    660E  LEU*     2.9    47.2    +      -       +      -
    687E  PHE*     3.6    31.9    -      -       +      -
    689E  PHE*     3.6    46.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 618 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    690B  ARG*     5.8     2.2    -      -       -      +
    609E  GLN*     3.0    70.4    +      -       +      +
    610E  ARG      4.3     8.7    -      -       -      +
    611E  GLY      4.2     1.2    -      -       -      +
    617E  ILE*     1.3    77.1    -      -       -      +
    619E  VAL*     1.3    62.1    +      -       -      +
    620E  ASN*     3.2    23.6    +      -       -      +
    657E  HIS*     3.9    29.5    +      -       +      -
    658E  VAL      4.0     1.8    -      -       -      +
    659E  MET*     3.5    30.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 619 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    606E  LEU*     4.1    35.2    -      -       +      -
    607E  GLU      3.5    10.5    -      -       -      +
    608E  GLY*     4.8     0.2    -      -       -      -
    617E  ILE*     3.9    29.8    -      -       +      -
    618E  LYS*     1.3    72.3    -      -       -      +
    620E  ASN*     1.3    64.5    +      -       -      +
    621E  LEU*     4.8     1.5    -      -       +      +
    657E  HIS*     3.1     3.2    -      -       -      -
    658E  VAL*     2.9    53.9    +      -       +      +
    660E  LEU*     4.7     8.7    -      -       +      -
    671E  VAL*     4.7     8.1    -      -       +      -
    673E  VAL*     5.3     2.5    -      -       +      -
    687E  PHE*     4.6    13.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 620 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    690B  ARG*     4.2     6.2    +      -       -      -
    605E  LYS      3.5     3.3    -      -       -      +
    606E  LEU*     3.6     2.9    -      -       -      -
    607E  GLU*     2.7    65.5    +      -       +      +
    609E  GLN*     3.0    22.2    -      -       -      +
    618E  LYS*     3.2    36.8    +      -       -      +
    619E  VAL*     1.3    73.2    -      -       -      +
    621E  LEU*     1.3    64.9    +      -       -      +
    622E  ILE*     5.5     0.9    -      -       +      -
    656E  ASP      3.7     6.3    +      -       -      +
    657E  HIS*     3.4    10.9    +      -       -      +
    592F  GLU*     5.4     5.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 621 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    604E  PRO*     4.1    10.5    -      -       +      -
    605E  LYS      3.7     0.7    -      -       -      -
    606E  LEU*     3.6    26.5    -      -       +      -
    619E  VAL*     4.8     3.4    -      -       +      +
    620E  ASN*     1.3    74.5    -      -       -      +
    622E  ILE*     1.3    63.3    +      -       -      +
    623E  LYS*     3.8    14.5    +      -       +      +
    634E  TYR*     3.7    42.4    -      -       +      -
    636E  VAL*     6.2     0.2    -      -       +      -
    651E  LEU*     5.1     5.8    -      -       +      -
    655E  SER*     4.0    22.2    -      -       -      +
    656E  ASP*     3.1    19.6    +      -       -      +
    657E  HIS*     4.2    11.0    -      -       -      +
    658E  VAL*     5.4     4.3    -      -       +      -
    673E  VAL*     3.8    19.3    -      -       +      -
    592F  GLU*     4.1    10.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 622 (chain E). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    641B  LEU*     4.7     4.3    -      -       +      -
    688B  VAL*     4.5     9.6    -      -       +      -
    604E  PRO*     3.6     2.8    -      -       -      +
    605E  LYS*     2.8    64.3    +      -       +      +
    607E  GLU*     4.0    33.4    -      -       +      +
    620E  ASN*     4.7     1.8    -      -       +      +
    621E  LEU*     1.3    75.6    -      -       -      +
    623E  LYS*     1.3    63.9    +      -       -      +
    624E  GLN*     3.5     3.1    -      -       -      +
    571F  THR*     4.1    15.9    -      -       +      +
    592F  GLU*     3.9    24.0    -      -       -      +
    593F  PHE*     4.0    24.0    -      -       -      +
    594F  LYS*     4.2     8.7    -      -       +      +
----------------------------------------------------------
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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