Contacts of the strand formed by residues 670 - 675 (chain A) in PDB entry 6ZGI


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 670 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    643A  PHE*     4.8    11.2    -      -       +      -
    645A  THR*     4.1    33.2    -      -       +      -
    646A  ARG      5.7     0.4    -      -       -      +
    650A  LEU*     5.3     1.6    -      -       +      -
    655A  HIS*     6.0     1.8    -      -       +      -
    665A  PRO*     4.3     0.3    -      -       -      +
    666A  ILE*     3.0    36.1    +      -       +      -
    667A  GLY      2.9    21.1    +      -       -      +
    668A  ALA*     4.1     8.7    -      -       +      +
    669A  GLY*     1.3    79.7    -      -       -      +
    671A  CYS*     1.3    71.3    +      -       -      +
    694A  ALA*     4.5    14.6    -      -       +      -
    695A  TYR      3.4    10.8    -      -       -      +
    696A  THR*     3.7    23.8    -      -       +      +
    864B  LEU*     5.9     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 671 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    662A  CYS*     2.0    53.2    -      -       -      -
    663A  ASP      4.4     0.4    -      -       -      +
    664A  ILE      3.3     5.8    -      -       -      +
    665A  PRO*     4.3     0.7    -      -       -      -
    666A  ILE*     4.0     4.0    -      -       -      -
    669A  GLY      5.0     0.2    -      -       -      -
    670A  ILE*     1.3    78.5    -      -       -      +
    672A  ALA*     1.3    61.5    +      -       -      +
    694A  ALA*     3.4     3.6    -      -       -      -
    695A  TYR*     2.9    53.0    +      -       +      +
    697A  MET*     3.6    25.6    -      -       +      -
    864B  LEU*     5.1     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 672 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    598A  ILE*     4.6    15.0    -      -       +      -
    650A  LEU*     5.8     2.7    -      -       +      -
    653A  ALA*     6.0     0.2    -      -       +      -
    663A  ASP*     3.3     5.2    -      -       -      +
    664A  ILE*     2.9    37.3    +      -       +      +
    666A  ILE*     3.9    22.7    -      -       +      -
    671A  CYS*     1.3    77.3    -      -       -      +
    673A  SER*     1.3    62.5    +      -       -      +
    692A  ILE*     4.6     8.7    -      -       +      -
    693A  ILE      3.2    11.7    -      -       -      +
    694A  ALA*     4.7     4.7    -      -       +      -
    695A  TYR*     4.0     2.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 673 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    663A  ASP*     3.1    21.7    +      -       -      +
    664A  ILE*     4.7     6.5    -      -       -      -
    672A  ALA*     1.3    76.6    -      -       -      +
    674A  TYR*     1.3    61.2    +      -       -      +
    675A  GLN*     2.7    33.4    +      -       -      -
    692A  ILE*     3.3     9.2    -      -       -      +
    693A  ILE*     2.9    33.5    +      -       -      +
    695A  TYR*     3.8    22.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 674 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    600A  PRO*     4.0    26.0    -      -       +      -
    604A  THR*     3.7    29.3    +      -       +      +
    605A  SER*     3.8    21.0    +      -       -      -
    607A  GLN*     4.4    11.5    +      -       +      -
    663A  ASP*     4.6     1.8    +      -       -      -
    664A  ILE*     5.6     1.3    -      -       +      +
    673A  SER*     1.3    76.7    +      -       -      +
    675A  GLN*     1.3    71.9    +      -       -      +
    690A  GLN*     3.2    38.9    +      -       +      +
    691A  SER*     3.5    30.7    -      -       -      -
    692A  ILE*     4.0    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 675 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    660A  TYR*     5.9     2.2    -      -       +      -
    663A  ASP*     5.0     0.2    -      -       -      +
    673A  SER*     2.7    25.8    +      -       -      +
    674A  TYR*     1.3    83.1    -      -       -      +
    676A  THR*     1.3    65.5    +      -       -      +
    690A  GLN*     3.1    14.2    +      -       -      +
    691A  SER      2.9    32.1    +      -       -      +
    693A  ILE*     3.7    35.7    -      -       +      -
----------------------------------------------------------
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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