Contacts of the strand formed by residues 235 - 237 (chain B) in PDB entry 2QC8


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 ILE 235 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139B  LEU*     3.3     5.4    -      -       -      +
    140B  MET*     2.7    50.0    +      -       +      +
    141B  GLY      4.0    16.4    -      -       -      +
    142B  THR*     4.2    14.1    -      -       -      +
    144B  GLY*     5.7     1.6    -      -       -      +
    229B  CYS*     4.5     3.6    -      -       -      -
    234B  VAL*     1.3    76.6    -      -       -      +
    236B  ALA*     1.3    73.2    -      -       -      +
    237B  THR*     4.3     4.0    -      -       -      +
    166C  GLY*     5.8     1.1    -      -       -      -
    167C  ALA*     4.6     3.4    -      -       +      +
    168C  ASP*     3.4    52.0    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 236 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137B  TYR*     4.3     9.0    -      -       +      -
    138B  THR      3.6     5.4    -      -       -      -
    139B  LEU*     4.5     0.9    -      -       +      -
    225B  LEU*     3.7    31.4    -      -       +      -
    226B  HIS*     3.4    32.1    +      -       +      +
    229B  CYS*     3.9    18.7    -      -       -      +
    235B  ILE*     1.3    78.9    -      -       -      +
    237B  THR*     1.3    60.8    +      -       -      +
    238B  PHE*     4.1     2.8    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR 237 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    137B  TYR*     3.5     6.9    -      -       -      +
    138B  THR*     2.9    50.5    +      -       -      +
    140B  MET*     3.9    19.5    -      -       +      -
    235B  ILE*     4.1     4.2    -      -       -      -
    236B  ALA*     1.3    73.9    -      -       -      +
    238B  PHE*     1.3    60.3    +      -       -      +
    239B  ASP*     3.3    24.2    +      -       -      +
    242B  PRO*     4.1    18.8    -      -       +      +
    250B  ALA*     5.6     0.3    -      -       -      +
----------------------------------------------------------
 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