Contacts of the strand formed by residues 1732 - 1736 (chain D) in PDB entry 1GZH


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 TYR1732 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1729D  PHE*     3.0    23.8    +      -       -      +
   1730D  LEU      3.8     8.5    -      -       -      -
   1731D  GLY*     1.3    83.5    +      -       -      +
   1733D  ALA*     1.3    61.1    +      -       -      +
   1734D  PHE*     3.4    21.7    -      +       +      -
   1784D  ALA      4.8     0.2    -      -       -      +
   1785D  GLY*     4.0     0.2    -      -       -      -
   1786D  TYR*     3.0    26.2    +      -       -      +
   1800D  TYR*     4.2     2.4    -      -       -      -
   1801D  GLN*     3.6    37.2    -      -       +      -
   1803D  LEU*     3.9    25.8    -      -       +      -
   1830D  TRP*     4.7     5.5    -      +       -      -
   1840D  LEU*     3.4    33.6    -      -       +      +
   1843D  TYR*     4.4    14.5    -      +       -      -
----------------------------------------------------------
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Residues in contact with ALA1733 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1731D  GLY      4.3     0.4    +      -       -      -
   1732D  TYR*     1.3    73.6    -      -       -      +
   1734D  PHE*     1.3    68.5    +      -       -      +
   1786D  TYR*     3.2    15.7    -      -       +      +
   1788D  LEU*     4.1    17.5    -      -       +      -
   1800D  TYR*     3.8    21.8    -      -       +      -
   1801D  GLN      3.3     5.8    +      -       -      +
   1802D  CYS*     3.4    19.3    -      -       -      -
   1803D  LEU*     3.0    24.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE1734 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1729D  PHE*     4.1    12.3    -      -       +      -
   1732D  TYR*     3.4    35.2    -      -       +      -
   1733D  ALA*     1.3    78.1    -      -       -      +
   1735D  LEU*     1.3    63.0    +      -       -      +
   1736D  LEU*     4.0     9.0    -      -       +      +
   1780D  LEU*     3.6    44.0    -      -       +      -
   1785D  GLY*     4.2     3.1    -      -       -      -
   1786D  TYR      2.8    21.9    +      -       -      +
   1787D  ILE*     4.1     3.2    -      -       +      -
   1788D  LEU*     2.8    37.2    +      -       -      +
   1802D  CYS*     5.9     0.2    -      -       -      -
   1803D  LEU*     3.3    22.4    -      -       +      +
   1805D  ILE*     3.7    22.2    -      -       +      -
   1830D  TRP*     3.4    33.2    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU1735 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1734D  PHE*     1.3    73.6    -      -       -      +
   1736D  LEU*     1.3    60.9    +      -       -      +
   1788D  LEU*     3.4    41.3    -      -       +      +
   1789D  GLU      4.6     1.3    -      -       -      +
   1790D  ASP*     4.0    15.9    -      -       -      -
   1791D  PHE*     4.0    28.7    -      -       +      +
   1802D  CYS*     6.4     0.7    -      -       +      -
   1803D  LEU      3.0     8.8    +      -       -      +
   1804D  LEU*     3.3    12.1    -      -       +      +
   1805D  ILE*     2.6    34.5    +      -       -      +
   1814D  LYS*     4.8    22.4    -      -       +      +
   1818D  CYS*     3.9    22.9    -      -       -      -
   1823D  ILE*     4.7     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU1736 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1734D  PHE*     4.0    14.6    -      -       +      +
   1735D  LEU*     1.3    90.7    -      -       -      +
   1737D  THR*     1.3    62.9    +      -       -      +
   1771D  PHE*     4.6     4.7    -      -       +      -
   1773D  LYS*     4.2    23.0    -      -       +      +
   1776D  THR*     3.7    28.0    -      -       +      -
   1777D  GLU*     3.9    30.1    -      -       +      +
   1780D  LEU*     4.1     5.4    -      -       +      -
   1787D  ILE*     4.7     7.2    -      -       +      -
   1788D  LEU      5.3     1.9    +      -       -      +
   1804D  LEU*     4.7     0.2    -      -       -      -
   1805D  ILE*     3.3    36.1    -      -       +      +
   1814D  LYS*     3.4    16.9    +      -       -      +
   2970D  SO4      3.1    11.1    +      -       -      -
----------------------------------------------------------
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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