Contacts of the strand formed by residues 198 - 201 (chain A) in PDB entry 1VH7


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 ILE 198 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    168A  ILE*     3.5    10.5    -      -       +      +
    170A  LEU*     4.3    26.2    -      -       +      -
    187A  ILE*     4.8    10.1    -      -       +      +
    190A  VAL*     3.8    25.6    -      -       +      -
    191A  ARG*     3.5    41.7    -      -       +      +
    194A  THR*     4.0     7.2    -      -       +      -
    196A  LEU      3.6    11.2    -      -       -      +
    197A  PRO*     1.3    74.4    -      -       -      +
    199A  ILE*     1.3    69.6    +      -       -      +
    200A  ALA*     4.6     1.8    -      -       -      +
    217A  GLY      4.8     1.1    -      -       -      +
    218A  ALA*     3.7    10.4    -      -       +      -
    219A  ASP*     2.7    40.6    +      -       -      +
    220A  ALA      3.2     5.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5A  ARG*     4.9     0.2    -      -       -      +
      7A  ILE*     4.1    21.8    -      -       +      -
     46A  GLU*     5.7     0.4    -      -       -      +
     48A  VAL*     5.8     4.0    -      -       +      -
     78A  THR*     6.1     0.7    -      -       -      +
     99A  LYS*     5.6     1.1    -      -       -      +
    126A  VAL*     4.6    10.3    -      -       +      -
    167A  GLU*     3.7    31.6    -      -       +      +
    168A  ILE      2.8    15.6    +      -       -      +
    169A  LEU*     3.8    28.9    -      -       +      -
    170A  LEU*     3.0    25.3    +      -       -      +
    198A  ILE*     1.3    74.6    -      -       -      +
    200A  ALA*     1.3    63.3    +      -       -      +
    201A  SER*     4.3     0.7    -      -       -      -
    220A  ALA*     3.5    17.7    -      -       +      -
    222A  LEU*     3.8    31.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    170A  LEU*     4.0     2.9    -      -       -      -
    182A  TYR*     3.5    17.8    -      -       +      -
    187A  ILE*     3.7    33.2    -      -       +      -
    198A  ILE*     3.8     3.7    +      -       -      -
    199A  ILE*     1.3    71.5    -      -       -      +
    201A  SER*     1.3    58.2    +      -       -      +
    213A  ALA*     4.2     6.3    -      -       +      -
    218A  ALA*     3.9     9.6    -      -       +      -
    220A  ALA      2.8    17.3    +      -       -      +
    221A  ALA*     4.5     1.8    -      -       -      -
    222A  LEU*     2.8    32.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169A  LEU*     3.6    18.5    -      -       -      +
    170A  LEU      3.1    10.9    +      -       -      +
    171A  THR*     3.0    43.6    +      -       -      +
    172A  SER*     3.3     7.4    +      -       -      -
    176A  ASP*     5.1     1.2    +      -       -      -
    182A  TYR*     3.8     6.6    -      -       -      -
    199A  ILE      4.3     0.2    -      -       -      -
    200A  ALA*     1.3    76.7    -      -       -      +
    202A  GLY*     1.3    66.2    +      -       -      +
    222A  LEU*     3.9    22.0    -      -       -      +
----------------------------------------------------------
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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