Contacts of the strand formed by residues 588 - 593 (chain A) in PDB entry 3I7L


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 PRO 588 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    539A  ALA*     3.6    19.8    -      -       +      +
    540A  CYS*     3.9    14.6    -      -       -      -
    559A  GLY*     4.2     3.8    -      -       -      -
    560A  LEU      3.5    22.4    -      -       -      +
    564A  ILE*     4.2     9.6    -      -       +      -
    565A  SER      4.1    16.4    -      -       -      +
    582A  LEU*     4.2    12.3    -      -       +      -
    586A  ILE      3.7     4.5    -      -       -      +
    587A  ILE*     1.4    91.5    -      -       +      +
    589A  ARG*     1.3    60.4    +      -       -      +
    604A  CYS*     3.6    26.0    -      -       -      -
    605A  ALA      3.6     6.5    -      -       -      +
    606A  LEU*     4.1     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 589 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    539A  ALA      4.7     2.8    -      -       -      +
    540A  CYS*     3.7    14.9    -      -       -      +
    587A  ILE*     4.6     2.2    -      -       +      +
    588A  PRO*     1.3    74.2    -      -       -      +
    590A  SER*     1.3    64.7    +      -       -      +
    605A  ALA      2.7    16.0    +      -       -      +
    606A  LEU      4.4     0.4    -      -       -      -
    607A  GLY*     4.4     9.0    -      -       -      +
    635A  PRO*     3.4    42.0    +      -       +      +
    636A  THR      4.1     8.3    -      -       -      +
    637A  VAL*     3.3    32.8    -      -       -      +
    678A  TYR*     4.1    22.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 590 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    540A  CYS*     3.9     6.7    -      -       -      -
    589A  ARG*     1.3    81.6    +      -       -      +
    591A  ILE*     1.3    61.3    +      -       -      +
    604A  CYS*     3.5     7.6    -      -       -      -
    605A  ALA*     3.1    26.5    +      -       -      -
    636A  THR      3.8    12.8    +      -       -      -
    637A  VAL*     3.9    11.4    -      -       -      +
    638A  LEU*     3.8    37.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 591 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    540A  CYS*     4.0    10.2    -      -       -      +
    541A  LEU      3.5    39.5    +      -       -      +
    542A  ASP*     3.3    19.3    -      -       +      +
    557A  ALA*     3.8    12.1    -      -       +      +
    558A  ILE      3.7    22.0    -      -       -      +
    559A  GLY      4.3     0.7    -      -       -      +
    566A  ALA*     3.6    30.5    -      -       +      -
    567A  ARG      5.0     1.1    -      -       -      +
    590A  SER*     1.3    76.0    -      -       -      +
    592A  LEU*     1.3    68.0    +      -       -      +
    602A  LEU*     3.9    19.1    -      -       +      -
    603A  LEU      3.5     9.9    -      -       -      +
    604A  CYS*     4.2     8.7    -      -       -      -
    638A  LEU*     4.6     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 592 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    542A  ASP*     3.0    33.4    -      -       -      +
    544A  THR*     5.6     1.6    -      -       -      +
    591A  ILE*     1.3    76.5    -      -       -      +
    593A  MET*     1.3    66.7    +      -       -      +
    594A  THR*     3.9    13.5    -      -       +      +
    601A  TYR      4.0     0.2    -      -       -      +
    602A  LEU*     3.5     5.4    -      -       -      +
    603A  LEU*     2.8    48.8    +      -       +      +
    638A  LEU*     3.8    25.6    -      -       +      -
    639A  ARG*     4.4     6.5    -      -       -      +
    640A  THR*     4.0    15.0    -      -       -      +
    649A  VAL*     3.9    38.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 593 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    542A  ASP*     3.2    48.9    +      -       -      +
    543A  ILE*     4.3     4.7    -      -       -      -
    544A  THR*     5.3     1.4    +      -       -      -
    546A  LEU*     3.5    35.2    -      -       +      +
    555A  LEU*     4.3    14.1    -      -       +      +
    556A  CYS      4.3    12.3    -      -       -      +
    557A  ALA*     4.0    14.8    -      -       +      +
    568A  ILE*     5.6     2.0    -      -       +      -
    592A  LEU*     1.3    74.8    -      -       -      +
    594A  THR*     1.3    71.6    +      -       -      +
    600A  HIS*     5.0     0.9    -      -       -      +
    601A  TYR      3.3    17.9    -      -       -      +
    602A  LEU*     4.1     9.6    -      -       +      -
    616A  LEU*     3.7    23.3    -      -       +      -
    618A  ILE*     5.0     7.9    -      -       +      -
----------------------------------------------------------
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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