Contacts of the strand formed by residues 131 - 137 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19B  GLU*     5.2     0.2    -      -       -      +
     29B  LEU*     3.6    27.6    -      -       +      +
     65B  HIS      4.8    12.2    +      -       -      +
    123B  LEU*     4.3     7.4    -      -       +      -
    124B  PHE      3.3     9.0    -      -       -      +
    125B  PHE*     3.8     6.7    -      -       +      -
    130B  SER*     1.3    74.9    +      -       -      +
    132B  MET*     1.3    64.2    +      -       -      +
    133B  LEU      3.5     2.4    +      -       -      +
    134B  LYS*     3.9    29.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64B  VAL*     3.8    14.9    -      -       -      +
     99B  ILE*     3.5    28.5    -      -       +      -
    100B  LYS      3.8     7.9    -      -       -      +
    103B  ASN      4.0     5.2    -      -       -      +
    104B  CYS*     3.2    48.9    -      -       -      -
    124B  PHE*     2.7    17.1    +      -       +      +
    125B  PHE      4.0     1.3    -      -       -      -
    126B  ASN*     3.7    20.6    -      -       +      +
    130B  SER*     3.3     0.4    +      -       -      -
    131B  ALA*     1.3    73.5    -      -       -      +
    133B  LEU*     1.3    61.0    +      -       +      +
     66C  THR*     5.0     3.8    +      -       -      +
     68C  ASP*     3.7    37.7    -      -       +      +
     69C  VAL*     3.5    16.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  TRP*     3.7    36.3    -      -       +      -
     62B  THR*     4.1    15.7    -      -       +      -
     63B  LEU      3.6     8.5    -      -       -      +
     64B  VAL*     3.6    12.1    -      -       +      +
     99B  ILE*     3.9    11.9    -      -       +      -
    123B  LEU*     3.7     0.3    -      -       -      -
    124B  PHE*     3.0    41.8    +      -       +      +
    131B  ALA*     3.2     2.0    -      -       -      +
    132B  MET*     1.3    86.8    -      -       +      +
    134B  LYS*     1.3    69.9    +      -       -      +
    135B  ILE*     4.4     5.6    -      -       +      -
     69C  VAL*     4.6     8.5    -      -       +      -
     71C  LEU*     3.5    38.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18B  LEU*     5.8     2.0    -      -       -      +
     19B  GLU*     2.5    37.1    +      -       -      -
     29B  LEU*     4.4     3.4    -      -       -      +
     61B  THR      3.8     0.6    -      -       -      +
     62B  THR*     4.0     0.2    -      -       -      +
     63B  LEU*     2.8    53.4    +      -       +      +
     65B  HIS*     3.8    24.4    +      -       +      +
    122B  ILE      3.3     8.7    -      -       -      +
    123B  LEU*     3.7    27.6    -      -       +      +
    131B  ALA*     3.9    19.7    -      -       +      -
    133B  LEU*     1.3    79.9    -      -       -      +
    135B  ILE*     1.3    68.5    +      -       -      +
    136B  PHE*     3.8    27.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51B  TRP*     5.0     0.4    -      -       +      -
     54B  VAL*     5.4     8.3    -      -       +      -
     57B  TRP*     6.4     0.4    -      -       +      -
     60B  VAL*     3.7    32.5    -      -       +      -
     61B  THR      3.3     2.2    -      -       -      +
     62B  THR*     2.9    47.1    -      -       +      +
     77B  LEU*     3.6    18.4    -      -       +      -
    121B  SER*     3.2     3.6    -      -       -      -
    122B  ILE*     2.8    55.0    +      -       +      +
    124B  PHE*     4.1    22.0    -      -       +      -
    133B  LEU*     4.4     5.8    -      -       +      -
    134B  LYS*     1.3    76.4    -      -       -      +
    136B  PHE*     1.3    66.8    +      -       -      +
    137B  LEU*     4.2     3.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     60B  VAL*     3.5     4.3    -      -       -      +
     61B  THR*     2.7    45.8    +      -       +      +
     63B  LEU*     3.8    31.9    -      -       +      -
    114B  PHE*     5.7     9.6    -      +       +      -
    119B  THR*     3.6    29.2    -      -       +      -
    120B  ALA      3.5     3.8    -      -       -      -
    121B  SER*     3.6    24.0    -      -       -      -
    123B  LEU*     5.3     0.4    -      -       +      -
    134B  LYS*     3.8    34.1    -      -       +      -
    135B  ILE*     1.3    79.5    -      -       -      +
    137B  LEU*     1.3    67.8    +      -       -      +
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Residues in contact with LEU 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57B  TRP*     4.1    14.8    -      -       +      -
     60B  VAL*     4.8     2.7    -      -       +      -
     61B  THR*     5.1     2.1    +      -       -      -
    120B  ALA*     3.0    37.4    +      -       +      +
    121B  SER*     4.7     2.2    -      -       -      +
    122B  ILE*     5.1     3.4    -      -       +      -
    135B  ILE*     5.0     4.0    -      -       +      +
    136B  PHE*     1.3    80.2    -      -       -      +
    138B  GLY*     1.3    66.2    +      -       -      +
    139B  ARG*     4.4     4.7    +      -       -      +
    145B  LEU*     3.9    20.9    -      -       +      +
    146B  LEU      5.0     0.4    -      -       -      +
    149B  GLN*     3.4    20.6    -      -       +      +
    150B  VAL*     3.6    42.4    -      -       +      +
    153B  PHE*     3.7    28.5    -      -       +      -
----------------------------------------------------------
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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