Contacts of the strand formed by residues 77 - 83 (chain G) in PDB entry 2OV2


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 VAL 77 (chain G).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4G  ILE*     4.1     7.2    -      -       +      -
      5G  LYS      3.1     2.4    +      -       -      +
      6G  CYS*     3.2    26.9    -      -       +      -
      7G  VAL      3.0    23.0    +      -       -      -
     75G  THR*     3.3     7.7    -      -       -      +
     76G  ASP*     1.3    80.8    -      -       -      +
     78G  PHE*     1.3    65.7    +      -       -      +
     79G  LEU*     4.9     1.1    -      -       +      -
    108G  THR*     4.2     0.4    -      -       -      -
    109G  PRO*     3.5    11.2    -      -       +      +
    111G  LEU*     3.7    29.4    -      -       +      -
    172G  ALA*     4.1    22.0    -      -       +      +
    175G  ALA*     4.3     5.6    -      -       +      -
    176G  VAL*     3.6    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 78 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7G  VAL*     3.3    28.5    -      -       +      -
      9G  VAL*     4.5     4.0    -      -       +      -
     72G  TYR*     3.6    31.0    -      +       -      -
     75G  THR*     3.6    22.4    -      -       +      -
     77G  VAL*     1.3    75.4    -      -       -      +
     79G  LEU*     1.3    64.0    +      -       -      +
     80G  ILE*     4.0     3.4    -      -       +      -
    101G  VAL*     3.6    37.7    -      -       +      -
    105G  CYS*     3.6    32.1    -      -       +      -
    108G  THR*     3.8    19.1    -      -       +      -
    109G  PRO      2.9    12.5    +      -       -      +
    110G  ILE*     3.4    13.6    -      -       +      -
    111G  LEU      2.8    31.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 79 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6G  CYS*     3.8    22.2    -      -       -      -
      7G  VAL      3.0     6.9    +      -       -      +
      8G  VAL*     3.5    29.2    -      -       +      +
      9G  VAL*     2.9    29.3    +      -       -      +
     19G  LEU*     4.5     5.6    -      -       +      -
     77G  VAL*     4.9     1.1    -      -       +      -
     78G  PHE*     1.3    80.6    -      -       -      +
     80G  ILE*     1.3    61.8    +      -       -      +
     81G  CYS*     3.8     2.2    +      -       -      -
    111G  LEU*     3.4    24.9    -      -       +      -
    113G  VAL*     4.0    14.6    -      -       +      -
    168G  VAL*     4.0    20.6    -      -       +      -
    169G  PHE*     4.1    17.3    -      -       +      -
    172G  ALA*     4.3    15.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 80 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9G  VAL*     3.4    14.4    -      -       +      +
     78G  PHE*     4.0     3.1    -      -       +      -
     79G  LEU*     1.3    73.7    -      -       -      +
     81G  CYS*     1.3    63.0    +      -       -      +
     93G  VAL*     4.0    24.5    -      -       +      -
     97G  TRP*     3.5    30.7    -      -       +      +
     98G  TYR*     4.1    23.1    -      -       -      +
    101G  VAL*     4.5     6.1    -      -       +      -
    110G  ILE*     3.6    39.3    -      -       +      -
    111G  LEU      3.0     7.6    +      -       -      +
    112G  LEU*     3.5    11.1    -      -       +      +
    113G  VAL      2.9    23.7    +      -       -      -
    149G  ILE*     4.2     8.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with CYS 81 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8G  VAL*     3.6    30.7    -      -       -      -
      9G  VAL      2.8    13.8    +      -       -      +
     10G  GLY*     3.6    18.2    -      -       -      -
     11G  ASP      4.2     1.9    +      -       -      -
     14G  VAL*     4.0    19.2    -      -       +      +
     16G  LYS*     4.2     5.4    -      -       +      -
     19G  LEU*     4.3    12.1    -      -       -      -
     79G  LEU*     4.1     6.5    -      -       -      -
     80G  ILE*     1.3    81.5    -      -       -      +
     82G  PHE*     1.3    62.6    +      -       -      +
     89G  SER      5.1     1.2    -      -       -      +
     93G  VAL*     4.7     1.9    -      -       -      +
     97G  TRP*     5.0     1.6    -      -       -      -
    113G  VAL*     3.3    22.9    -      -       -      +
    115G  THR*     4.1     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 82 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14G  VAL*     4.2     7.2    -      -       -      -
     81G  CYS*     1.3    75.5    -      -       -      +
     83G  SER*     1.3    67.5    +      -       -      +
     84G  LEU*     3.9    10.8    -      -       +      -
     89G  SER*     3.4    25.6    -      -       -      +
     90G  PHE*     3.4    45.8    -      +       +      -
     93G  VAL*     4.0     4.7    -      -       +      -
    112G  LEU*     3.7    28.0    -      -       +      -
    113G  VAL      3.0     9.9    +      -       -      +
    114G  GLY*     3.4    18.8    -      -       -      -
    115G  THR*     2.7    35.0    +      -       -      -
    137G  ILE*     3.8    16.6    -      -       +      -
    154G  TYR*     3.9    24.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 83 (chain G). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13G  ALA      5.1     0.4    -      -       -      -
     14G  VAL*     3.9    15.6    -      -       -      +
     82G  PHE*     1.3    78.2    -      -       -      +
     84G  LEU*     1.3    63.4    +      -       -      +
     85G  VAL*     3.0    27.5    +      -       -      +
     86G  SER*     3.0    38.2    +      -       -      +
     89G  SER*     3.1     6.2    +      -       -      -
    115G  THR*     3.3    13.6    +      -       -      -
    116G  LYS*     3.4    20.0    +      -       -      +
    137G  ILE*     4.6     0.7    -      -       -      +
----------------------------------------------------------
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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