Contacts of the strand formed by residues 565 - 569 (chain A) in PDB entry 3I7K


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 SER 565 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    558A  ILE      3.8     0.7    -      -       -      +
    559A  GLY*     3.5     2.6    -      -       -      -
    560A  LEU*     2.9    29.3    +      -       -      +
    563A  ASP*     2.6    33.7    +      -       -      -
    564A  ILE*     1.3    78.0    -      -       -      +
    566A  ALA*     1.3    61.0    +      -       -      +
    567A  ARG*     2.7    26.0    +      -       -      -
    579A  LYS*     4.7     0.2    -      -       -      -
    580A  GLU      3.2    16.2    -      -       -      -
    581A  MET*     3.7    11.9    -      -       -      -
    582A  LEU*     4.7     2.0    -      -       -      -
    588A  PRO*     4.4     4.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 566 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    558A  ILE      3.1     4.5    -      -       -      +
    559A  GLY*     5.0     0.7    -      -       -      -
    565A  SER*     1.3    74.6    -      -       -      +
    567A  ARG*     1.3    61.1    +      -       -      +
    568A  ILE*     5.9     0.4    -      -       -      -
    578A  HIS      4.2     0.2    -      -       -      +
    579A  LYS*     3.3     1.2    -      -       -      -
    580A  GLU*     2.7    43.9    +      -       +      +
    582A  LEU*     4.9     7.2    -      -       +      +
    591A  ILE*     3.6    26.7    -      -       +      -
    604A  CYS*     4.5    15.0    -      -       +      -
    614A  PHE*     6.3     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 567 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    534A  MET*     3.5    23.9    -      -       +      +
    535A  GLU*     3.9    15.2    +      -       -      +
    556A  CYS      3.5     3.3    -      -       -      +
    557A  ALA*     3.6     3.1    -      -       -      +
    558A  ILE*     2.8    59.7    +      -       +      +
    560A  LEU*     3.5    19.1    -      -       +      +
    563A  ASP*     2.6    29.9    +      -       -      -
    565A  SER*     2.7    27.8    +      -       -      -
    566A  ALA*     1.3    73.7    -      -       -      +
    568A  ILE*     1.3    69.9    +      -       -      +
    569A  LEU*     4.5     1.8    -      -       +      -
    576A  LEU*     3.8    20.4    -      -       +      +
    578A  HIS      3.3    12.6    -      -       -      +
    579A  LYS*     3.2    43.3    -      -       +      +
    591A  ILE*     5.1     1.0    -      -       -      +
    602A  LEU*     5.0     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 568 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    555A  LEU*     3.8    30.5    -      -       +      -
    556A  CYS      3.3     6.5    -      -       -      +
    567A  ARG*     1.3    77.9    -      -       -      +
    569A  LEU*     1.3    69.5    +      -       -      +
    576A  LEU*     4.4     0.2    -      -       -      +
    577A  LEU*     3.4    32.1    +      -       +      +
    578A  HIS*     3.0    30.9    +      -       +      +
    593A  MET*     5.2     0.4    -      -       +      -
    602A  LEU*     3.7    23.3    -      -       +      -
    616A  LEU*     3.6    38.1    -      -       +      -
    620A  THR      4.4     6.5    -      -       -      +
    621A  GLY*     4.7     3.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 569 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    516A  LEU*     4.4    22.2    -      -       +      -
    532A  THR*     6.5     0.2    -      -       +      -
    534A  MET*     4.6    14.4    -      -       -      -
    541A  LEU*     6.2     0.4    -      -       +      -
    555A  LEU*     3.5    13.2    -      -       -      +
    556A  CYS*     2.8    48.1    +      -       +      +
    558A  ILE*     4.0    27.6    -      -       +      -
    567A  ARG*     4.5     1.3    -      -       +      -
    568A  ILE*     1.3    85.6    -      -       -      +
    570A  LYS*     1.3    60.7    +      -       -      +
    571A  LEU      4.0     0.2    -      -       -      -
    574A  PHE*     3.6    28.7    -      -       +      +
    575A  GLU      3.9     0.2    -      -       -      -
    576A  LEU*     3.9    34.3    -      -       +      -
    577A  LEU*     3.6     7.1    -      -       -      +
----------------------------------------------------------
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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