Contacts of the strand formed by residues 12 - 19 (chain D) 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 THR 12 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7D  ILE      4.5     0.7    -      -       -      +
      8D  ARG*     3.6     3.1    +      -       -      +
      9D  ARG*     2.8    40.9    +      -       +      +
     10D  HIS*     2.4    20.7    +      -       -      +
     11D  LYS*     1.3    69.8    +      -       -      +
     13D  THR*     1.3    72.9    +      -       -      +
     14D  ILE*     4.8     3.4    -      -       +      -
     35D  LEU*     4.3    28.0    -      -       +      -
     28E  GLU*     3.6    11.7    +      -       +      +
     30E  ILE*     4.0    20.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 13 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6D  MET*     3.6    23.2    -      -       -      +
      7D  ILE      3.2     6.3    -      -       -      -
      8D  ARG*     3.6    16.8    -      -       -      +
     11D  LYS      4.3     5.6    -      -       -      +
     12D  THR*     1.3    85.5    -      -       -      +
     14D  ILE*     1.3    61.8    +      -       -      +
     15D  PHE*     4.1     4.5    +      -       -      -
     93D  PHE*     4.1    12.1    -      -       +      -
     27E  HIS*     4.5     1.3    -      -       +      -
     28E  GLU      3.1    12.0    +      -       -      +
     29E  PHE*     3.4    41.1    -      -       +      +
     30E  ILE      3.1    21.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 14 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  LEU      3.5     1.2    -      -       -      +
      6D  MET*     3.1     5.2    -      -       -      -
      7D  ILE*     2.7    56.6    +      -       +      +
     12D  THR*     4.8     4.5    -      -       +      -
     13D  THR*     1.3    74.5    -      -       -      +
     15D  PHE*     1.3    74.3    +      -       -      +
     16D  THR*     3.8    13.4    +      -       +      -
     31D  VAL*     5.0    10.8    -      -       +      -
     34D  ILE*     3.6    46.0    -      -       +      -
     35D  LEU*     3.9    23.3    -      -       +      -
     18E  TYR*     5.0     1.1    -      -       +      -
     30E  ILE*     3.8    25.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 15 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5D  LEU      3.4    11.7    -      -       -      +
      6D  MET*     3.7    30.5    -      -       +      -
     13D  THR*     4.1     8.7    -      -       -      -
     14D  ILE*     1.3    76.3    -      -       -      +
     16D  THR*     1.3    63.4    +      -       -      +
     72D  PRO*     4.2     8.5    -      -       +      -
     18E  TYR*     4.3    10.2    -      -       -      -
     29E  PHE*     3.6    26.5    -      +       +      -
     30E  ILE      3.2    16.1    +      -       -      +
     31E  VAL*     4.2    20.4    -      -       +      +
     32E  LYS*     4.9     5.2    +      -       -      +
     71E  SER*     3.9    11.7    -      -       -      -
     74E  CYS*     3.6    33.9    -      -       +      -
     75E  MET*     3.9    20.0    -      -       +      -
     78E  THR*     4.6    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 16 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4D  PHE*     3.7     3.1    -      -       -      +
      5D  LEU*     2.7    42.4    +      -       +      +
      7D  ILE*     3.9    30.7    -      -       +      -
     14D  ILE*     4.2    10.3    -      -       +      -
     15D  PHE*     1.3    75.5    -      -       -      +
     17D  ASP*     1.3    75.4    +      -       -      +
     27D  LEU*     4.5    10.1    -      -       +      -
     30D  ILE*     4.3    16.1    -      -       +      +
     18E  TYR*     4.1    15.9    +      -       -      -
     32E  LYS*     4.6     8.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 17 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2D  ASP*     3.5    17.5    -      -       +      +
      3D  VAL      3.1    16.2    -      -       -      +
      4D  PHE*     3.8    26.5    -      -       +      -
      5D  LEU*     4.5     1.8    -      -       -      +
     16D  THR*     1.3    88.4    +      -       -      +
     18D  ALA*     1.3    69.5    +      -       -      +
     30D  ILE*     4.5     6.8    -      -       -      +
     32E  LYS*     3.0    29.6    +      -       -      -
     35E  HIS*     5.7     1.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 18 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      2D  ASP*     3.3     4.3    -      -       -      -
      3D  VAL*     2.7    33.2    +      -       -      +
      5D  LEU*     4.9     5.6    -      -       +      -
     17D  ASP*     1.3    83.4    +      -       -      +
     19D  LYS*     1.3    65.0    +      -       -      +
     22D  SER*     4.1     9.4    -      -       -      +
     27D  LEU*     5.4     5.4    -      -       +      -
     30D  ILE*     5.1    10.3    -      -       +      -
     57D  LEU*     3.9    24.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 19 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1D  MET*     3.3    16.6    -      -       -      +
      2D  ASP*     2.9    37.0    +      -       -      +
      3D  VAL*     4.8     0.2    -      -       -      -
     18D  ALA*     1.3    77.3    -      -       -      +
     20D  GLU*     1.3    60.3    +      -       -      +
     21D  SER*     3.8    18.4    -      -       -      +
     22D  SER*     2.8    31.4    +      -       -      +
     57D  LEU*     3.7     8.5    -      -       -      +
----------------------------------------------------------
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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