Contacts of the strand formed by residues 2 - 9 (chain J) in PDB entry 1VCB


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 ASP 2 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1J  MET*     1.3    82.2    -      -       -      +
      3J  VAL*     1.3    61.4    +      -       -      +
      4J  PHE*     3.8    31.5    -      -       +      -
     17J  ASP*     3.6    19.3    -      -       -      +
     18J  ALA      3.4     6.3    -      -       -      +
     19J  LYS*     2.9    35.7    +      -       -      +
     64J  SER*     3.5    18.2    +      -       -      -
     82K  ARG*     5.5     5.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 3 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2J  ASP*     1.3    76.2    -      -       -      +
      4J  PHE*     1.3    63.4    +      -       -      +
      5J  LEU*     3.7    33.4    -      -       +      -
     17J  ASP*     3.1    25.8    -      -       -      +
     18J  ALA      2.7    16.7    +      -       -      +
     20J  GLU*     4.4    15.0    -      -       +      +
     57J  LEU*     4.1    12.8    -      -       +      -
     62J  PHE*     3.4    36.6    -      -       +      +
     63J  THR*     3.6    17.7    -      -       -      -
     64J  SER      4.1     0.7    -      -       -      +
     67J  ALA*     3.6     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 4 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2J  ASP*     3.8    32.5    -      -       +      -
      3J  VAL*     1.3    70.8    -      -       -      +
      5J  LEU*     1.3    62.6    +      -       -      +
     16J  THR      3.9     3.1    -      -       -      +
     17J  ASP*     3.7    24.5    -      -       +      -
     67J  ALA*     2.9    33.0    +      -       -      +
     68J  ARG      4.0    11.2    -      -       -      +
     69J  PRO*     3.5    39.5    -      -       +      -
     72J  PRO*     3.1     8.3    -      -       +      +
     73J  ALA      2.8    23.7    +      -       -      -
     35K  HIS*     6.3     0.9    -      -       -      -
     78K  THR*     4.7    15.7    -      -       +      +
     82K  ARG*     4.1    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 5 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3J  VAL*     3.7    25.8    -      -       +      +
      4J  PHE*     1.3    81.9    -      -       -      +
      6J  MET*     1.3    65.3    +      -       -      +
      7J  ILE*     4.0     8.7    -      -       +      -
     14J  ILE      4.1     0.4    -      -       -      -
     15J  PHE*     3.5     6.6    -      -       -      +
     16J  THR*     2.8    41.3    +      -       +      +
     17J  ASP      5.3     0.2    -      -       -      -
     18J  ALA*     4.9     5.6    -      -       +      -
     27J  LEU*     4.0    27.6    -      -       +      -
     57J  LEU*     4.0    17.9    -      -       +      -
     62J  PHE*     3.7    33.2    -      -       +      -
     67J  ALA*     4.3     0.4    -      -       +      -
     72J  PRO*     4.0     5.8    -      -       -      +
     73J  ALA*     3.3    12.1    -      -       +      +
     75J  VAL*     4.3     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 6 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5J  LEU*     1.3    75.5    -      -       -      +
      7J  ILE*     1.3    61.3    +      -       -      +
      8J  ARG*     3.4    19.8    +      -       +      +
     13J  THR*     3.6    20.6    -      -       -      +
     14J  ILE      3.1     5.8    -      -       -      +
     15J  PHE*     3.7    31.2    -      -       +      +
     72J  PRO*     4.1    17.9    -      -       +      +
     73J  ALA      2.8    10.8    +      -       -      +
     74J  THR*     3.4    24.5    -      -       -      +
     75J  VAL      3.1    20.5    +      -       -      -
     93J  PHE*     4.8    13.5    -      -       +      -
     75K  MET*     4.0    22.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 7 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5J  LEU*     4.6     5.6    -      -       +      -
      6J  MET*     1.3    69.3    -      -       -      +
      8J  ARG*     1.3    61.5    +      -       -      +
      9J  ARG      4.3     0.5    +      -       -      -
     12J  THR*     4.5     0.5    -      -       -      +
     13J  THR*     3.3     2.4    -      -       -      -
     14J  ILE*     2.7    55.1    +      -       +      +
     16J  THR*     3.9    16.8    -      -       +      -
     27J  LEU*     3.4    34.8    -      -       +      -
     30J  ILE*     5.8     1.6    -      -       +      -
     31J  VAL*     3.8    26.9    -      -       +      -
     44J  LEU*     4.6     9.4    -      -       +      -
     75J  VAL*     3.4    22.0    -      -       +      +
     77J  LEU*     4.3    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 8 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6J  MET*     3.5    27.3    -      -       -      +
      7J  ILE*     1.3    78.6    -      -       -      +
      9J  ARG*     1.3    61.3    +      -       -      +
     11J  LYS      5.6     1.6    -      -       -      +
     12J  THR      3.6     3.9    +      -       -      +
     13J  THR*     3.6    26.3    -      -       -      +
     74J  THR*     3.9    17.8    +      -       +      +
     75J  VAL      2.6    16.1    +      -       -      +
     76J  GLY*     3.5     4.9    -      -       -      -
     77J  LEU*     2.9    26.5    +      -       -      -
     90J  ILE*     3.4    36.2    -      -       +      +
     91J  GLU      2.7    29.7    +      -       -      -
     92J  PRO*     4.4     4.0    -      -       -      +
     93J  PHE*     3.3    40.2    -      -       -      +
     27K  HIS*     3.9     3.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 9 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8J  ARG*     1.3    75.6    -      -       -      +
     10J  HIS*     1.3   114.4    +      -       -      +
     11J  LYS      3.7     0.4    -      -       -      -
     12J  THR*     2.8    30.6    +      -       +      -
     35J  LEU*     5.7     1.1    -      -       +      +
     77J  LEU*     3.4    38.8    -      -       +      +
     79J  PHE*     3.1    38.5    -      -       -      +
     86J  GLU*     2.5    43.1    +      -       -      -
     89J  CYS      3.9     6.5    -      -       -      +
     90J  ILE*     4.7     1.5    -      -       -      +
----------------------------------------------------------
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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