Contacts of the strand formed by residues 326 - 333 (chain A) in PDB entry 2ZH2


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 PHE 326 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  LYS*     3.4    43.5    -      -       +      -
    283A  PHE      3.1    20.9    -      -       -      +
    284A  ARG*     3.5    46.9    -      -       +      -
    285A  LYS*     3.9     4.0    -      -       -      +
    321A  LYS      4.0     0.3    -      -       -      +
    322A  ALA*     3.6     1.0    -      -       -      -
    323A  SER*     2.7    35.5    +      -       -      +
    325A  GLU*     1.3   110.4    -      -       +      +
    327A  CYS*     1.3    68.0    +      -       -      +
    328A  TYR*     4.2    11.4    -      -       +      -
    411A  TYR*     4.4     7.6    -      +       -      -
----------------------------------------------------------
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Residues in contact with CYS 327 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    281A  VAL      3.5     0.7    -      -       -      +
    282A  LYS*     3.4     5.9    -      -       -      +
    283A  PHE*     3.0    57.2    +      -       +      -
    285A  LYS*     3.5    33.4    -      -       -      -
    293A  LEU*     4.2     7.9    -      -       -      -
    297A  LEU*     4.1    15.5    -      -       +      -
    321A  LYS      3.2     5.6    -      -       -      +
    322A  ALA*     4.0    17.9    -      -       -      -
    326A  PHE*     1.3    73.1    -      -       -      +
    328A  TYR*     1.3    66.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 328 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280A  ALA*     4.7    10.1    -      -       +      -
    281A  VAL      3.2     4.5    -      -       -      +
    282A  LYS*     3.8    33.6    +      -       +      -
    297A  LEU*     5.3     0.3    -      -       -      +
    320A  PHE*     2.9     8.8    -      -       -      +
    321A  LYS*     2.7    45.4    +      -       +      +
    323A  SER*     3.9    19.5    -      -       -      -
    325A  GLU*     3.9     9.0    +      -       -      -
    326A  PHE*     4.2    14.4    -      -       +      -
    327A  CYS*     1.3    79.4    -      -       -      +
    329A  LEU*     1.3    65.2    +      -       -      +
    330A  LEU*     3.5    17.5    -      -       +      -
    415A  ILE*     5.9     1.3    -      -       +      -
    420A  LEU*     5.5     0.4    -      -       +      -
    423A  GLU*     2.7    41.9    +      -       +      -
    424A  PRO*     3.1    21.0    -      -       +      +
    425A  VAL*     3.5    19.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 329 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280A  ALA*     3.0     5.0    -      -       -      -
    281A  VAL*     2.8    42.3    +      -       +      +
    283A  PHE*     3.9    19.7    -      -       +      -
    297A  LEU*     4.0    24.5    -      -       +      +
    300A  ALA*     3.8    19.5    -      -       +      -
    301A  SER*     3.6    18.4    -      -       -      +
    304A  ILE*     3.7    27.4    -      -       +      -
    319A  ALA      3.5     3.6    -      -       -      -
    320A  PHE*     3.8     7.9    -      -       +      -
    328A  TYR*     1.3    80.2    -      -       -      +
    330A  LEU*     1.3    62.4    +      -       -      +
    331A  PHE*     3.7    19.5    -      -       +      -
    408A  ILE*     4.6     3.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 330 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  PHE      3.6     3.1    -      -       -      +
    280A  ALA*     3.9    10.5    -      -       +      -
    318A  SER*     3.2     1.4    -      -       -      -
    319A  ALA*     2.8    41.5    +      -       +      +
    320A  PHE*     4.3     4.9    -      -       -      +
    321A  LYS      4.8     0.7    -      -       -      +
    328A  TYR*     3.5    31.6    -      -       +      +
    329A  LEU*     1.3    79.7    -      -       -      +
    331A  PHE*     1.3    79.3    +      -       -      +
    420A  LEU*     5.6     0.2    -      -       +      -
    425A  VAL*     4.0    13.0    -      -       +      -
    428A  GLU*     3.6    30.5    -      -       +      -
    429A  LEU*     3.5    32.1    -      -       +      +
    432A  MET*     4.0     7.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 331 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277A  ALA      3.6     1.1    -      -       -      +
    278A  VAL*     3.3     7.6    -      -       -      +
    279A  PHE*     2.9    66.9    +      +       +      +
    281A  VAL*     4.1     8.7    -      -       +      -
    301A  SER*     3.7    20.6    -      -       -      -
    304A  ILE*     3.4    34.1    -      -       +      -
    305A  PHE*     4.1     7.4    -      +       -      -
    308A  LEU*     3.9    19.5    -      -       +      -
    315A  PRO*     6.1     0.2    -      -       +      -
    317A  ARG      3.8     6.3    -      -       -      +
    318A  SER*     3.5    25.6    -      -       -      -
    329A  LEU*     3.7    34.3    -      -       +      -
    330A  LEU*     1.3    83.4    -      -       -      +
    332A  GLU*     1.3    61.0    +      -       -      +
    333A  CYS*     5.0     0.2    -      -       -      -
    432A  MET*     4.0     3.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 332 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    274A  ARG*     2.7    45.1    +      -       -      -
    276A  THR*     2.8    33.3    +      -       -      +
    277A  ALA      3.1     3.6    -      -       -      -
    278A  VAL*     3.8     6.2    -      -       +      +
    315A  PRO*     3.5     3.1    -      -       -      +
    316A  LEU*     2.7    53.1    +      -       +      +
    317A  ARG*     3.5    11.2    +      -       -      +
    331A  PHE*     1.3    76.2    -      -       -      +
    333A  CYS*     1.3    56.6    +      -       -      +
    432A  MET*     3.9    18.7    -      -       +      +
    433A  MET*     3.7    17.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS 333 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    276A  THR*     2.8    25.9    -      -       -      -
    277A  ALA*     2.9    19.2    +      -       +      +
    279A  PHE*     4.3     5.8    -      -       -      -
    308A  LEU*     3.8    28.3    -      -       -      -
    313A  PHE*     3.3    15.7    -      -       -      +
    314A  MET      3.6     4.5    -      -       -      -
    315A  PRO*     3.7    22.4    -      -       -      -
    316A  LEU*     4.3     1.3    -      -       -      +
    332A  GLU*     1.3    77.3    -      -       -      +
    334A  GLN*     1.3    62.8    +      -       -      +
    335A  ILE      4.1     3.6    -      -       -      +
    385A  PRO*     4.3    22.2    -      -       +      -
----------------------------------------------------------
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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