Contacts of the strand formed by residues 131 - 137 (chain C) in PDB entry 2OVI


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 ALA 131 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19C  GLU*     5.5     0.2    -      -       -      +
     29C  LEU*     3.7    26.1    -      -       +      +
     65C  HIS      5.0     8.5    +      -       -      +
    123C  LEU*     4.6     4.0    -      -       +      -
    124C  PHE      3.4     8.3    -      -       -      +
    125C  PHE*     3.8    10.7    -      -       +      -
    130C  SER*     1.3    74.5    +      -       -      +
    132C  MET*     1.3    65.7    +      -       -      +
    133C  LEU*     4.3    10.0    -      -       -      +
    134C  LYS*     4.1    20.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 132 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66B  THR*     5.1     4.3    +      -       -      +
     68B  ASP*     3.6    44.9    -      -       +      +
     69B  VAL*     3.6    14.6    -      -       +      +
     47C  PHE*     6.0     0.4    -      -       +      -
     64C  VAL*     4.1    13.4    -      -       -      +
     65C  HIS      5.6     0.2    +      -       -      -
     99C  ILE*     3.7    26.0    -      -       +      -
    100C  LYS      3.6    18.8    -      -       -      +
    101C  ALA*     4.5     0.9    -      -       -      +
    103C  ASN      4.1     3.6    -      -       -      -
    104C  CYS*     3.7    38.1    -      -       +      -
    124C  PHE*     2.6    21.4    +      -       +      +
    125C  PHE      4.0     5.6    -      -       -      +
    126C  ASN*     3.8    12.1    -      -       +      +
    131C  ALA*     1.3    73.8    -      -       -      +
    133C  LEU*     1.3    62.2    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 133 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69B  VAL*     4.6     5.4    -      -       +      -
     71B  LEU*     4.0     9.6    -      -       +      -
     47C  PHE*     6.3     0.2    -      -       +      -
     51C  TRP*     3.7    35.9    -      -       +      -
     62C  THR*     3.6    23.1    -      -       +      -
     63C  LEU      3.3    19.7    -      -       -      +
     64C  VAL*     3.6    20.4    -      -       +      +
     99C  ILE*     4.0    18.8    -      -       +      -
    123C  LEU*     3.6     0.3    -      -       -      -
    124C  PHE*     3.0    41.3    +      -       +      +
    131C  ALA*     3.3     2.0    -      -       -      +
    132C  MET*     1.3    83.4    -      -       +      +
    134C  LYS*     1.3    81.8    +      -       -      +
    135C  ILE*     4.8     1.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 134 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18C  LEU*     5.8     1.6    -      -       -      +
     19C  GLU*     2.4    39.1    +      -       -      -
     29C  LEU*     4.4     2.7    -      -       -      +
     62C  THR*     3.4     5.9    -      -       -      +
     63C  LEU*     2.8    52.4    +      -       +      +
     65C  HIS*     4.0    20.4    +      -       +      +
    121C  SER*     5.5     0.2    -      -       -      -
    122C  ILE      3.2     8.5    -      -       -      +
    123C  LEU*     3.9    26.2    -      -       +      +
    124C  PHE*     4.9     0.2    -      -       -      -
    131C  ALA*     4.1    20.2    -      -       +      -
    133C  LEU*     1.3    81.1    -      -       -      +
    135C  ILE*     1.3    67.0    +      -       -      +
    136C  PHE*     3.9    26.1    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 135 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51C  TRP*     4.4     4.0    -      -       +      -
     54C  VAL*     4.3    18.4    -      -       +      -
     57C  TRP*     6.2     0.2    -      -       +      -
     60C  VAL*     3.8    29.4    -      -       +      -
     61C  THR      3.4     3.8    -      -       -      +
     62C  THR*     4.1    13.7    -      -       +      +
     77C  LEU*     3.8    31.4    -      -       +      -
    121C  SER*     3.1     4.2    -      -       -      -
    122C  ILE*     2.7    48.5    +      -       +      +
    124C  PHE*     3.9    27.8    -      -       +      -
    133C  LEU*     4.8     0.9    -      -       +      -
    134C  LYS*     1.3    80.7    -      -       -      +
    136C  PHE*     1.3    68.5    +      -       -      +
    137C  LEU*     4.2     3.8    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 136 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60C  VAL*     3.5     5.4    -      -       -      +
     61C  THR*     2.8    46.7    +      -       +      +
     63C  LEU*     3.4    42.8    -      -       +      -
    114C  PHE*     5.0    17.9    -      +       -      -
    119C  THR*     4.5    23.6    -      -       +      -
    120C  ALA      3.5     6.3    -      -       -      +
    121C  SER*     3.7    23.6    -      -       -      -
    134C  LYS*     3.9    25.4    -      -       +      -
    135C  ILE*     1.3    76.1    -      -       -      +
    137C  LEU*     1.3    68.9    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 137 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  TRP*     3.5    34.3    -      -       +      -
     60C  VAL*     4.7     2.9    -      -       +      -
     61C  THR*     5.3     1.2    +      -       -      -
    120C  ALA*     3.0    38.8    +      -       +      +
    122C  ILE*     5.5     2.9    -      -       +      -
    135C  ILE*     5.4     4.7    -      -       +      +
    136C  PHE*     1.3    79.6    -      -       -      +
    138C  GLY*     1.3    67.4    +      -       -      +
    139C  ARG*     4.9     3.8    +      -       -      +
    145C  LEU*     4.0    15.4    -      -       +      +
    149C  GLN*     3.6    21.8    -      -       +      +
    150C  VAL*     3.5    40.2    -      -       +      +
    153C  PHE*     3.8    15.5    -      -       +      -
----------------------------------------------------------
 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