Contacts of the strand formed by residues 566 - 571 (chain A) in PDB entry 3HR4


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 ASN 566 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    533A  MET*     3.6    41.0    +      -       +      +
    534A  ALA*     4.6     6.5    -      -       -      +
    536A  ARG*     4.2     3.8    +      -       +      +
    537A  VAL      3.0    15.2    +      -       -      +
    538A  ARG*     3.6    24.3    -      -       -      +
    539A  VAL      3.3    15.8    +      -       -      +
    565A  PHE*     1.3    75.1    -      -       -      +
    567A  PRO*     1.3    66.3    -      -       -      +
    568A  LYS*     4.8     5.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 567 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    533A  MET*     5.9     1.1    -      -       -      -
    539A  VAL*     3.3    15.0    -      -       +      +
    541A  ILE*     4.3    14.4    -      -       +      -
    558A  GLY*     3.6    16.6    -      -       -      +
    561A  PHE*     4.0    20.2    -      -       +      +
    562A  SER*     3.6    25.1    -      -       -      +
    565A  PHE*     2.9    17.3    -      -       +      +
    566A  ASN*     1.3    91.5    -      -       -      +
    568A  LYS*     1.3    71.3    +      -       -      +
    569A  VAL*     5.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 568 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    539A  VAL      2.9    10.8    +      -       -      +
    540A  THR*     3.8     4.7    -      -       +      +
    541A  ILE*     2.8    27.3    +      -       -      +
    555A  TRP*     5.4     7.9    -      -       -      +
    566A  ASN*     4.8     6.3    -      -       -      +
    567A  PRO*     1.3    83.3    +      -       -      +
    569A  VAL*     1.3    76.2    +      -       -      +
    570A  VAL*     3.8    16.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 569 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    541A  ILE*     3.4    16.2    -      -       +      +
    543A  PHE*     3.9    16.6    -      -       +      -
    554A  ALA*     3.6    29.4    -      -       +      +
    555A  TRP*     3.5    68.1    -      -       +      +
    558A  GLY*     4.6     6.1    -      -       -      -
    567A  PRO      5.9     0.2    -      -       -      -
    568A  LYS*     1.3    83.4    +      -       -      +
    570A  VAL*     1.3    71.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 570 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    540A  THR*     4.8     7.6    -      -       +      -
    541A  ILE      2.7     9.6    +      -       -      +
    542A  LEU*     3.1    40.7    -      -       +      +
    543A  PHE*     3.3     5.5    +      -       -      -
    568A  LYS*     4.3    18.2    -      -       +      +
    569A  VAL*     1.3    86.6    -      -       -      +
    571A  CYS*     1.3    76.9    +      -       -      +
    574A  LYS*     4.2    24.5    -      -       +      +
    575A  TYR*     4.3     6.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 571 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    543A  PHE*     3.4    40.6    -      -       +      -
    570A  VAL*     1.3    83.7    -      -       -      +
    572A  MET*     1.3    69.4    +      -       -      +
    573A  ASP*     3.5    32.5    -      -       -      +
    574A  LYS*     3.0    20.1    +      -       +      +
    575A  TYR*     3.5     2.1    +      -       -      +
    601A  ASN*     3.8    21.8    -      -       -      -
----------------------------------------------------------
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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