Contacts of the strand formed by residues 438 - 442 (chain A) in PDB entry 5A63


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 GLY 438 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362A  PHE*     3.3    16.2    -      -       -      -
    380A  THR*     3.6    18.9    -      -       -      +
    381A  ASP      5.0     2.1    +      -       -      -
    394A  VAL*     4.5     3.9    -      -       -      +
    427A  LEU*     3.5    25.2    -      -       -      +
    436A  ILE      2.9    11.8    +      -       -      -
    437A  SER*     1.3    71.4    -      -       -      +
    439A  VAL*     1.3    68.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 439 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    362A  PHE      2.8     6.9    +      -       -      +
    363A  VAL*     3.4     8.2    -      -       +      +
    364A  GLU      3.0    22.3    +      -       -      -
    378A  MET*     3.9    22.4    -      -       +      -
    379A  HIS      4.0     5.6    -      -       -      +
    380A  THR*     4.5     2.9    -      -       +      -
    394A  VAL*     5.0     1.1    -      -       +      +
    397A  LEU*     2.7    46.9    -      -       +      -
    398A  LEU*     4.4    13.0    -      -       +      -
    401A  LEU*     3.5    24.5    -      -       +      -
    427A  LEU*     3.6     2.2    -      -       -      +
    438A  GLY*     1.3    77.6    -      -       -      +
    440A  VAL*     1.3    72.1    +      -       -      +
    441A  LEU*     4.1     6.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 440 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    364A  GLU*     2.9    16.2    -      -       +      +
    366A  GLY*     4.0    15.9    -      -       -      +
    377A  TRP      3.6     0.5    -      -       -      +
    378A  MET*     3.1     7.6    -      -       -      -
    379A  HIS*     3.1    46.9    +      -       +      +
    422A  LEU*     4.1     9.2    -      -       +      -
    423A  PRO*     4.4    11.7    -      -       +      -
    425A  SER*     3.9    22.4    -      -       -      +
    427A  LEU*     3.7    25.8    -      -       +      -
    439A  VAL*     1.3    79.8    -      -       -      +
    441A  LEU*     1.3    65.0    +      -       -      +
    442A  ALA*     3.7     2.6    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 441 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    363A  VAL*     3.7    18.4    -      -       +      -
    364A  GLU      2.9     6.9    +      -       -      -
    365A  LEU*     3.1    14.2    -      -       +      +
    366A  GLY      2.8    26.8    +      -       -      +
    368A  VAL*     4.1     4.6    -      -       +      +
    376A  LEU*     4.3    25.8    -      -       +      -
    377A  TRP      3.7     1.1    -      -       -      +
    378A  MET*     3.6    28.3    -      -       +      -
    401A  LEU*     4.0    27.8    -      -       +      -
    413A  LEU*     4.5     2.9    -      -       +      -
    439A  VAL*     4.1     6.1    -      -       +      -
    440A  VAL*     1.3    71.9    -      -       -      +
    442A  ALA*     1.3    60.0    +      -       -      +
    490A  VAL*     5.8     2.2    -      -       +      -
    493A  VAL*     5.9     1.8    -      -       +      -
    494A  LEU*     3.6    34.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 442 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    366A  GLY      3.1    11.9    -      -       -      +
    368A  VAL*     5.1     0.9    -      -       -      -
    376A  LEU*     3.7    11.6    -      -       -      +
    377A  TRP*     2.9    29.3    +      -       -      -
    379A  HIS*     3.2    35.2    -      -       +      +
    440A  VAL*     4.5     4.5    -      -       +      -
    441A  LEU*     1.3    76.2    -      -       -      +
    443A  ASP*     1.3    65.8    +      -       -      +
    444A  HIS*     3.4    17.4    +      -       +      +
----------------------------------------------------------
 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