Contacts of the strand formed by residues 31 - 36 (chain A) in PDB entry 2GDZ


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 31 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  GLY*     4.3    20.9    -      -       -      +
      6A  LYS      2.9    10.3    +      -       -      +
      7A  VAL*     3.5    13.9    -      -       +      -
      8A  ALA*     2.8    26.5    +      -       -      +
     29A  GLY      5.1     1.7    +      -       -      +
     30A  ALA*     1.3    76.8    -      -       -      +
     32A  VAL*     1.3    61.9    +      -       -      +
     56A  GLN*     4.3    16.4    +      -       -      +
     57A  LYS*     3.3    30.2    -      -       +      +
     82A  PHE*     3.7    37.0    -      -       +      +
     84A  ARG*     6.4     0.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 32 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ALA*     3.3     7.2    -      -       +      +
     10A  VAL*     4.1    18.6    -      -       +      -
     22A  ALA*     4.0    12.8    -      -       +      +
     25A  LEU*     3.7    31.4    -      -       +      -
     26A  LEU*     3.9    26.2    -      -       +      +
     30A  ALA      4.4     2.0    -      -       -      +
     31A  LYS*     1.3    80.1    -      -       -      +
     33A  ALA*     1.3    73.4    +      -       -      +
     34A  LEU*     3.6    17.0    -      -       +      +
     57A  LYS      2.8    10.7    +      -       -      -
     58A  THR*     3.3     5.9    -      -       +      -
     59A  LEU      3.1    21.8    +      -       -      -
     82A  PHE*     4.0     4.7    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 33 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ALA      2.7    12.6    +      -       -      +
      9A  LEU*     3.5     5.6    -      -       +      -
     10A  VAL      2.9    29.3    +      -       -      -
     32A  VAL*     1.3    72.3    -      -       -      +
     34A  LEU*     1.3    62.9    +      -       -      +
     35A  VAL*     3.6     4.9    +      -       +      +
     59A  LEU*     3.4    10.8    -      -       +      +
     61A  ILE*     5.4     1.1    -      -       +      -
     78A  VAL*     3.5    43.3    -      -       +      -
     82A  PHE*     3.9    11.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 34 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13A  ALA*     3.6    29.2    -      -       +      +
     14A  ALA*     5.3     0.9    -      -       -      +
     22A  ALA*     4.0    12.3    -      -       +      -
     32A  VAL*     3.6    22.2    -      -       +      +
     33A  ALA*     1.3    71.3    -      -       -      +
     35A  VAL*     1.3    60.4    +      -       -      +
     42A  GLY      5.5     0.7    -      -       -      +
     45A  CYS*     3.4    33.9    -      -       +      -
     46A  LYS*     5.1     7.2    -      -       +      +
     49A  LEU*     4.0    10.8    -      -       +      -
     58A  THR*     3.9    24.2    -      -       +      -
     59A  LEU      2.7    16.0    +      -       -      +
     60A  PHE*     3.2    18.1    -      -       +      -
     61A  ILE      3.0    25.3    +      -       -      -
----------------------------------------------------------
 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
----------------------------------------------------------
      9A  LEU*     3.6    29.8    -      -       +      -
     10A  VAL      2.9    13.4    +      -       -      +
     11A  THR*     4.2    14.8    -      -       +      -
     12A  GLY      2.7    31.9    +      -       -      -
     13A  ALA*     3.2     5.3    +      -       -      +
     33A  ALA*     4.1     8.1    -      -       +      +
     34A  LEU*     1.3    78.9    -      -       -      +
     36A  ASP*     1.3    58.9    +      -       -      +
     61A  ILE*     3.4     9.6    -      -       +      +
     63A  CYS*     3.7    30.1    -      -       +      +
     65A  VAL*     4.8     4.3    -      -       +      -
     71A  LEU*     5.4     1.6    -      -       +      -
     74A  THR*     3.7    21.8    -      -       +      -
     78A  VAL*     4.8     0.7    -      -       +      -
    300A  NAD      5.3     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 36 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  GLY*     3.1    12.5    -      -       -      -
     14A  ALA*     3.0    32.7    +      -       +      +
     35A  VAL*     1.3    75.4    -      -       -      +
     37A  TRP*     1.3    62.1    +      -       -      +
     38A  ASN*     3.0    23.7    +      -       -      +
     60A  PHE*     3.8    15.3    -      -       +      -
     61A  ILE      3.3     6.1    +      -       -      -
     62A  GLN*     3.3     9.9    -      -       -      -
     63A  CYS      2.9    20.6    +      -       -      -
    300A  NAD      2.6    55.2    +      -       -      -
----------------------------------------------------------
 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