Contacts of the strand formed by residues 879 - 881 (chain A) in PDB entry 5ZR1


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 LEU 879 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    804A  PHE*     3.6    25.6    -      -       +      -
    805A  ILE*     4.5     8.5    -      -       +      -
    808A  LEU*     3.7    19.1    -      -       +      -
    870A  LEU*     3.8     9.4    -      -       +      -
    873A  LEU*     3.1    31.3    +      -       +      +
    874A  LEU*     3.7    40.0    -      -       +      +
    877A  GLY*     3.2     2.1    -      -       -      -
    878A  ILE*     1.3    80.6    -      -       +      +
    880A  PHE*     1.3    58.4    +      -       -      +
    892A  VAL*     3.7    15.9    -      -       +      -
    893A  LYS      3.3    17.5    -      -       -      +
    894A  LEU*     3.8    11.0    -      -       +      -
    895A  ASN*     3.7     6.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 880 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    819A  GLU*     6.2     0.2    -      -       -      -
    874A  LEU*     4.8     0.7    -      -       -      -
    879A  LEU*     1.3    72.6    -      -       -      +
    881A  LYS*     1.3    80.0    +      -       -      +
    882A  GLN*     4.4    12.1    -      -       +      -
    892A  VAL*     3.3     6.6    -      -       -      +
    893A  LYS*     2.9    62.0    +      -       +      +
    895A  ASN*     3.4    30.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 881 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    822A  LEU*     4.3    12.8    -      -       +      -
    870A  LEU*     3.8    26.5    -      -       +      -
    871A  ASN*     5.8     0.7    -      -       -      -
    874A  LEU*     3.7    35.7    -      -       +      +
    879A  LEU      4.2     0.6    +      -       -      -
    880A  PHE*     1.3    89.5    -      -       -      +
    882A  GLN*     1.3    79.3    +      -       -      +
    883A  THR*     4.8     2.5    +      -       -      +
    884A  MET      4.9     6.9    +      -       -      +
    887A  ASP*     5.8     2.0    +      -       -      -
    890A  CYS*     3.6    21.0    -      -       -      -
    891A  CYS      3.6     7.4    -      -       -      +
    892A  VAL*     4.0     9.0    -      -       +      -
----------------------------------------------------------
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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