Contacts of the strand formed by residues 526 - 531 (chain B) in PDB entry 5ZF6


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 ASP 526 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353B  LEU*     4.5     5.0    -      -       +      +
    356B  TYR*     4.6     1.0    +      -       -      -
    515B  THR*     3.4     0.7    -      -       -      -
    516B  LYS*     2.9    42.3    +      -       +      +
    524B  ILE*     3.4     7.1    +      -       -      +
    525B  GLU*     1.3    79.6    -      -       -      +
    527B  TYR*     1.3    79.1    +      -       -      +
    528B  ARG*     2.7    39.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 527 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    353B  LEU*     4.5     0.9    -      -       -      -
    513B  LEU*     3.8    10.3    -      -       +      -
    514B  VAL      3.3     7.6    -      -       -      -
    515B  THR*     3.7    22.4    -      -       +      -
    524B  ILE*     4.3     7.6    -      -       +      -
    526B  ASP*     1.3    86.9    +      -       -      +
    528B  ARG*     1.3    81.4    +      -       -      +
    529B  LEU*     4.4    14.8    -      -       +      -
    569B  LYS*     3.3    22.3    +      -       -      -
    570B  ILE*     3.7    34.9    -      -       +      +
    573B  GLU*     2.7    41.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 528 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352B  VAL*     3.2    38.9    +      -       +      +
    353B  LEU*     2.7    45.9    +      -       +      +
    356B  TYR*     3.1    36.5    +      -       -      -
    364B  LEU*     3.7    24.0    -      -       +      -
    513B  LEU*     3.3     8.2    -      -       -      +
    514B  VAL*     2.8    35.6    +      -       +      +
    526B  ASP*     2.7    35.5    +      -       -      -
    527B  TYR*     1.3    92.5    +      -       -      +
    529B  LEU*     1.3    61.6    +      -       -      +
    530B  LEU*     3.8     6.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 529 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364B  LEU*     3.2    20.4    -      -       -      +
    511B  ILE*     4.1     5.2    -      -       +      -
    512B  GLY      3.4    14.8    -      -       -      +
    513B  LEU*     3.9     5.4    -      -       +      -
    527B  TYR*     4.3    14.9    +      -       +      -
    528B  ARG*     1.3    71.9    -      -       -      +
    530B  LEU*     1.3    60.9    +      -       -      +
    543B  MET*     3.6    21.3    -      -       +      -
    570B  ILE*     3.9    17.3    -      -       +      +
    573B  GLU*     3.6    40.2    -      -       +      +
    574B  ALA*     3.8    13.7    -      -       +      +
    577B  GLN*     3.1    34.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 530 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352B  VAL*     3.7    30.1    -      -       +      -
    358B  ARG*     3.8    16.4    -      -       +      +
    364B  LEU*     3.5    16.2    -      -       +      -
    511B  ILE*     3.3     7.9    -      -       -      +
    512B  GLY*     2.7    35.6    +      -       -      +
    513B  LEU      4.5     4.0    -      -       -      +
    514B  VAL*     3.7    22.9    -      -       +      -
    528B  ARG*     4.1    11.0    -      -       +      +
    529B  LEU*     1.3    77.2    -      -       -      +
    531B  THR*     1.3    61.1    +      -       -      +
    532B  ASP      3.7     0.2    +      -       -      -
    533B  ILE*     3.6    18.9    -      -       +      +
    537B  GLU*     3.6    32.8    -      -       +      +
    577B  GLN*     4.1     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 531 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358B  ARG*     2.8    27.7    +      -       -      +
    362B  ARG*     3.3     2.1    +      -       -      -
    364B  LEU      2.6    16.3    +      -       -      -
    365B  THR*     3.4    24.7    +      -       -      +
    366B  SER      3.3     6.7    -      -       -      +
    367B  LEU*     4.4     3.6    -      -       +      +
    509B  VAL*     4.7     0.2    -      -       +      -
    511B  ILE*     3.9     8.3    -      -       +      +
    530B  LEU*     1.3    68.6    -      -       -      +
    532B  ASP*     1.3    75.6    +      -       +      +
    577B  GLN*     2.7    36.4    +      -       -      +
    581B  ALA*     3.7    28.7    -      -       +      -
----------------------------------------------------------
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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