Contacts of the strand formed by residues 32 - 40 (chain A) in PDB entry 3ZWG


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 LYS 32 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LEU*     2.8    42.3    +      -       +      +
     24A  GLU*     4.0     7.3    -      -       -      +
     26A  LEU*     3.6    24.7    -      -       +      -
     27A  GLY      2.8    23.5    +      -       -      +
     28A  ASN*     4.9     0.8    +      -       -      +
     29A  VAL*     3.6    20.2    -      -       +      -
     31A  ARG*     1.3    77.6    -      -       -      +
     33A  ILE*     1.3    59.8    +      -       -      +
     75A  GLY      3.4     6.5    -      -       -      +
     76A  GLN*     4.2     0.9    -      -       +      +
     86A  VAL*     4.5     6.8    -      -       -      +
    106A  VAL*     4.8     0.5    -      -       -      +
    168A  GLY      3.2     7.3    +      -       -      +
    169A  HIS*     3.5    43.5    +      -       +      -
    170A  ALA*     2.8    25.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  LEU*     3.9     4.3    -      -       -      -
     26A  LEU*     4.4     0.7    -      -       -      +
     32A  LYS*     1.3    76.6    -      -       -      +
     34A  ALA*     1.3    70.3    +      -       -      +
     35A  VAL*     4.0    15.9    -      -       +      -
     74A  ASN*     3.2     8.1    -      -       -      +
     75A  GLY*     2.9    41.6    +      -       -      +
     86A  VAL*     4.4     4.7    -      -       +      -
    104A  PHE*     3.8    48.0    -      -       +      -
    106A  VAL*     4.0    10.8    -      -       +      -
    164A  MET*     3.8    22.4    -      -       +      -
    170A  ALA*     3.4    17.3    -      -       +      +
    171A  ILE      4.7     0.2    -      -       -      +
    172A  LEU*     4.3     7.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  LEU*     3.6    26.7    -      -       +      +
     22A  VAL*     3.5    27.1    -      -       +      -
     23A  LEU*     3.6    13.2    -      -       +      +
     33A  ILE*     1.3    75.4    -      -       -      +
     35A  VAL*     1.3    61.3    +      -       -      +
     73A  TYR      3.7     4.5    -      -       -      -
    170A  ALA      2.9     9.6    +      -       -      +
    171A  ILE*     3.7     3.8    -      -       +      -
    172A  LEU      3.1    24.8    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 35 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  LEU*     3.8     8.5    -      -       -      +
     22A  VAL*     5.6     0.2    -      -       -      +
     33A  ILE*     4.0    30.5    -      -       +      -
     34A  ALA*     1.3    78.1    -      -       -      +
     36A  GLY*     1.3    62.1    +      -       -      +
     37A  ILE*     4.1    23.3    -      -       +      -
     71A  LEU*     5.7     0.4    -      -       +      -
     72A  LEU*     3.6     3.1    -      -       -      +
     73A  TYR*     2.9    49.6    +      -       +      +
     90A  ILE*     4.5    13.9    -      -       +      -
    102A  VAL*     5.3     0.9    -      -       +      -
    104A  PHE*     4.8    11.4    -      -       +      -
    172A  LEU*     3.5    26.0    -      -       +      +
    174A  ILE*     5.2     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LEU*     3.7    14.5    -      -       -      +
     19A  LEU*     3.8    13.5    -      -       -      +
     35A  VAL*     1.3    76.9    -      -       -      +
     37A  ILE*     1.3    66.2    +      -       -      +
     71A  LEU      3.3    11.2    -      -       -      -
     72A  LEU*     4.5     0.4    -      -       -      -
    172A  LEU      3.0    12.1    +      -       -      +
    173A  GLU*     3.7     1.2    -      -       -      -
    174A  ILE*     3.0    25.3    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 37 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  LEU*     3.7     4.7    -      -       -      +
     35A  VAL*     4.1    18.8    -      -       +      -
     36A  GLY*     1.3    80.8    -      -       -      +
     38A  ASP*     1.3    63.7    +      -       -      +
     39A  ASN*     3.7     0.9    +      -       -      +
     45A  TRP*     3.5    30.8    -      -       +      -
     69A  LYS      4.2     0.2    -      -       -      +
     70A  ALA*     3.1     2.6    -      -       -      -
     71A  LEU*     3.0    56.1    +      -       +      +
     90A  ILE*     4.9    11.4    -      -       +      -
     92A  TYR*     5.4     1.6    -      -       +      -
    100A  LEU*     4.8     3.8    -      -       +      -
    102A  VAL*     4.1    28.0    -      -       +      -
    174A  ILE*     3.4    22.2    -      -       +      +
    176A  VAL*     4.6     3.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 38 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  GLY*     3.2    30.1    -      -       -      +
     14A  LEU*     3.7     5.9    -      -       +      +
     37A  ILE*     1.3    71.4    -      -       -      +
     39A  ASN*     1.3    64.8    +      -       -      +
     40A  GLU*     2.7    37.4    +      -       -      +
     45A  TRP*     3.8     5.7    -      -       -      -
     69A  LYS      3.9     0.9    -      -       -      +
     70A  ALA*     3.9     6.5    -      -       -      -
    174A  ILE      2.9     7.9    +      -       -      +
    175A  HIS*     3.1    40.6    +      -       +      +
    176A  VAL      3.1    22.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ASN 39 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  ILE      3.7     0.8    +      -       -      -
     38A  ASP*     1.3    72.1    +      -       -      +
     40A  GLU*     1.3    54.9    +      -       -      +
     41A  SER*     2.5    27.5    +      -       -      -
     43A  LYS      3.0    20.8    +      -       -      +
     45A  TRP*     3.0    28.0    -      -       +      +
     65A  VAL*     3.1    33.3    +      -       +      -
     66A  ALA      3.2    10.9    +      -       -      +
     67A  HIS*     3.6     1.2    -      -       -      -
     68A  GLY*     2.6    35.3    +      -       -      -
     69A  LYS      2.8    20.2    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLU 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11A  GLY*     4.1     3.5    -      -       -      -
     38A  ASP*     2.7    35.9    -      -       -      +
     39A  ASN*     1.3    74.1    -      -       -      +
     41A  SER*     1.3    62.2    +      -       -      +
     42A  GLY      3.3     4.1    +      -       -      -
     67A  HIS*     3.4    28.2    +      -       +      -
     68A  GLY*     3.3    20.8    -      -       -      +
    175A  HIS*     5.7     0.4    -      -       -      +
    176A  VAL      2.8    19.0    +      -       -      +
    177A  THR*     3.8    19.3    -      -       +      -
    178A  LYS*     3.3    19.1    +      -       -      -
----------------------------------------------------------
 Back to top of page


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