Contacts of the strand formed by residues 582 - 585 (chain A) in PDB entry 2HAZ


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 582 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    496A  ILE*     3.8    34.6    -      -       -      +
    497A  ASP      5.8     0.2    +      -       -      -
    498A  GLN*     5.4     1.6    -      -       -      -
    499A  VAL*     3.9    14.3    +      -       -      +
    563A  TYR      3.8     0.3    -      -       -      +
    564A  ALA*     3.5     0.3    -      -       -      -
    565A  VAL*     2.8    39.5    +      -       -      +
    580A  ALA      3.6     0.8    +      -       -      -
    581A  ALA*     1.3    74.2    -      -       -      +
    583A  GLU*     1.3    68.8    +      -       -      +
    584A  PHE*     4.0     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 583 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    531A  VAL*     4.4    12.3    -      -       +      -
    562A  THR*     4.8     8.5    -      -       +      -
    563A  TYR      3.2    11.4    -      -       -      +
    564A  ALA*     3.9    12.7    -      -       +      +
    581A  ALA*     3.5    33.4    -      -       -      +
    582A  SER*     1.3    79.6    +      -       -      +
    584A  PHE*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 584 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    499A  VAL*     3.6    31.2    -      -       +      +
    501A  PRO*     3.8    22.2    -      -       +      -
    506A  ALA*     3.9    13.5    -      -       +      -
    528A  TRP*     5.5     0.7    -      -       +      -
    554A  ILE*     3.5    27.4    -      -       +      -
    557A  LEU*     4.0    12.8    -      -       +      -
    562A  THR*     3.2     8.3    -      -       -      +
    563A  TYR*     2.7    71.1    +      +       +      -
    565A  VAL*     3.7    29.4    -      -       +      -
    583A  GLU*     1.3    76.3    -      -       -      +
    585A  LYS*     1.3    62.5    +      -       -      +
    586A  THR*     4.2     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 585 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    501A  PRO*     3.1    22.6    -      -       -      +
    560A  GLU*     3.7    24.7    +      -       -      +
    561A  THR      3.4     9.0    -      -       -      +
    562A  THR*     3.6    25.4    -      -       +      +
    584A  PHE*     1.3    77.8    -      -       -      +
    586A  THR*     1.3    73.8    +      -       -      +
    587A  GLN*     3.6     1.7    +      -       -      +
----------------------------------------------------------
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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