Contacts of the strand formed by residues 584 - 588 (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 584 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    554A  GLU*     4.3     1.0    -      -       -      +
    555A  SER*     3.4    41.6    +      -       -      +
    557A  LYS*     3.7    22.9    -      -       +      +
    558A  LYS*     5.1     0.4    -      -       +      -
    559A  PHE*     3.6    59.5    -      -       +      +
    575A  ALA*     4.5     2.5    -      -       +      -
    576A  VAL      3.5     3.1    -      -       -      +
    577A  ARG*     3.7    31.4    -      -       +      +
    582A  LEU      5.1     0.7    -      -       -      +
    583A  GLU*     1.3    77.5    -      -       -      +
    585A  LEU*     1.3    71.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 585 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    533A  LEU*     4.1    30.3    -      -       +      -
    535A  LYS*     4.2    14.4    -      -       +      -
    543A  PHE*     4.3    17.7    -      -       +      -
    552A  LEU*     4.5    12.6    -      -       +      -
    553A  THR      3.3    21.1    -      -       -      +
    554A  GLU*     4.4     3.4    -      -       -      -
    555A  SER*     4.1     0.7    -      -       -      -
    575A  ALA*     3.2     5.9    -      -       -      +
    576A  VAL*     2.9    42.6    +      -       +      +
    578A  ASP*     4.3    11.0    -      -       +      +
    583A  GLU*     4.0    25.8    -      -       +      +
    584A  ILE*     1.3    80.8    -      -       -      +
    586A  ASP*     1.3    67.5    +      -       -      +
    587A  ILE      4.1     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 586 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    551A  VAL      3.4     1.0    -      -       -      +
    552A  LEU*     3.3     7.6    -      -       -      +
    553A  THR*     2.9    45.3    +      -       -      +
    554A  GLU      4.2     3.1    -      -       -      +
    555A  SER*     2.9    36.9    +      -       -      -
    556A  ASN      4.9     0.3    +      -       -      -
    557A  LYS*     3.8    22.1    +      -       -      +
    574A  ASP      3.5     6.9    -      -       -      +
    575A  ALA*     4.1     1.0    -      -       -      +
    585A  LEU*     1.3    75.4    -      -       -      +
    587A  ILE*     1.3    62.3    +      -       -      +
    842B  GLY*     4.0    14.4    -      -       -      +
    843B  ASP*     3.7    23.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 587 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541A  PHE*     3.8    42.4    -      -       +      -
    543A  PHE*     5.7     0.4    -      -       +      -
    546A  LEU*     6.0     1.3    -      -       +      -
    549A  THR      4.6     6.1    -      -       -      +
    550A  GLY*     4.7     1.1    -      -       -      -
    551A  VAL      3.4     5.6    -      -       -      +
    552A  LEU*     3.9    14.4    -      -       +      -
    573A  THR*     4.3    23.3    -      -       +      +
    574A  ASP*     2.9    35.6    +      -       -      +
    575A  ALA      4.6     0.7    -      -       -      +
    576A  VAL*     4.1    27.8    -      -       +      -
    585A  LEU      4.5     0.2    -      -       -      +
    586A  ASP*     1.3    76.8    -      -       -      +
    588A  THR*     1.3    72.5    +      -       -      +
    589A  PRO*     4.4     3.2    -      -       +      +
    842B  GLY      5.6     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with THR 588 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    549A  THR      5.4     0.2    -      -       -      -
    550A  GLY*     3.4     4.5    -      -       -      -
    551A  VAL*     2.9    39.7    +      -       -      +
    553A  THR*     4.8     4.1    +      -       -      +
    587A  ILE*     1.3    79.8    +      -       -      +
    589A  PRO*     1.3    85.2    -      -       +      +
    837B  TYR*     4.1     0.2    -      -       -      +
    841B  LEU*     3.5    27.9    -      -       +      +
    842B  GLY*     3.3    29.9    +      -       -      +
    845B  ALA*     5.1     4.0    -      -       +      +
    855B  PHE*     3.9    17.7    -      -       +      -
----------------------------------------------------------
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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