Contacts of the strand formed by residues 116 - 121 (chain C) 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 LEU 116 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63C  LEU*     4.2    16.6    -      -       +      -
     64C  ARG      3.9    21.8    -      -       -      +
     65C  SER*     3.0    13.8    +      -       -      +
     66C  VAL*     6.0     0.7    -      -       +      -
     88C  TRP*     3.6     4.9    -      -       -      -
     89C  LEU*     2.8    55.5    +      -       +      +
    114C  GLY      3.6    11.9    -      -       -      +
    115C  HIS*     1.3    82.7    -      -       -      +
    117C  TRP*     1.3    63.0    +      -       -      +
    135C  LEU*     4.1    23.6    -      -       +      -
    136C  PHE      3.7     1.1    -      -       -      +
    137C  VAL*     3.8    21.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 117 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76C  PHE*     3.7    35.8    -      +       -      -
     86C  PRO*     4.1     3.6    -      -       +      -
     87C  VAL      3.3    12.8    -      -       -      -
     88C  TRP*     3.5    49.9    -      +       +      -
     89C  LEU*     5.6     0.2    -      -       -      -
     98C  TYR*     3.6    44.9    -      +       +      -
    109C  ILE*     4.4    13.7    -      -       +      -
    110C  HIS      5.4     1.3    -      -       -      -
    111C  SER*     3.3    25.7    +      -       -      -
    116C  LEU*     1.3    79.9    -      -       -      +
    118C  LEU*     1.3    65.8    +      -       -      +
    119C  PHE*     4.0    17.4    -      +       +      -
    135C  LEU*     3.4     8.1    -      -       -      +
    136C  PHE*     2.8    40.4    +      +       +      +
    138C  PRO*     3.9    23.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 118 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87C  VAL*     2.7    61.1    +      -       +      +
     89C  LEU*     4.4     9.9    -      -       +      -
    117C  TRP*     1.3    80.9    -      -       -      +
    119C  PHE*     1.3    65.1    +      -       -      +
    120C  ARG*     4.0    30.1    -      -       +      +
    134C  GLU*     4.3     4.9    -      -       +      +
    135C  LEU*     3.6    22.4    -      -       +      -
    194C  VAL*     4.1    20.9    -      -       +      +
    197C  ASP*     6.0     1.6    -      -       +      -
    198C  LEU*     4.0    23.3    -      -       +      -
    201C  LEU*     5.3     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 119 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76C  PHE*     3.7    34.8    -      +       -      -
     84C  VAL*     3.9    14.1    -      -       +      -
     85C  LEU      3.8     2.0    -      -       -      -
     86C  PRO*     3.5    33.7    -      -       +      -
    117C  TRP*     4.0    23.1    -      -       +      -
    118C  LEU*     1.3    75.7    -      -       -      +
    120C  ARG*     1.3    81.4    +      -       -      +
    128C  LEU*     3.2    23.3    +      -       +      +
    129C  LEU      5.6     0.2    -      -       -      -
    130C  VAL*     3.6    42.8    -      -       +      -
    134C  GLU      4.8     1.6    +      -       -      -
    136C  PHE*     4.1     3.1    -      +       +      -
    151C  ILE*     3.6    36.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 120 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84C  VAL*     3.6     4.3    -      -       -      -
     85C  LEU*     2.8    41.9    +      -       +      +
     87C  VAL*     4.8     4.7    -      -       +      -
    118C  LEU*     4.0    31.0    -      -       +      +
    119C  PHE*     1.3    95.2    +      -       -      +
    121C  ASP*     1.3    66.6    +      -       -      +
    125C  HIS*     3.5    24.2    -      -       +      +
    126C  ASP      3.3    10.3    -      -       -      +
    127C  GLY*     3.6    11.5    -      -       -      -
    128C  LEU*     3.5    16.6    +      -       -      +
    134C  GLU*     3.9    31.5    +      -       -      +
    194C  VAL*     4.1    26.7    -      -       +      +
    197C  ASP*     2.7    39.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 121 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82C  ARG*     3.2    40.7    +      -       +      +
     83C  VAL*     3.7     8.2    +      -       -      +
     85C  LEU*     4.6     0.3    -      -       -      +
    120C  ARG*     1.3    72.1    -      -       -      +
    122C  ALA*     1.3    59.3    +      -       -      +
    123C  GLY*     2.8    26.9    +      -       -      -
    124C  THR*     2.9    31.3    +      -       -      +
    125C  HIS*     2.8    28.8    +      -       -      -
    126C  ASP*     2.9    23.6    +      -       +      +
    128C  LEU*     3.7     8.1    -      -       +      +
----------------------------------------------------------
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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