Contacts of the strand formed by residues 979 - 981 (chain B) in PDB entry 4V1M


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 LYS 979 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    483A  ASP      3.3    24.2    +      -       -      +
    484A  GLY*     4.5     5.6    -      -       -      -
    773B  MET*     5.3     2.7    -      -       -      -
    776B  GLN*     5.3     3.5    -      -       -      +
    977B  GLY      3.4     1.8    +      -       -      -
    978B  ASP*     1.4    71.7    -      -       -      +
    980B  PHE*     1.4    71.0    +      -       -      +
    987B  LYS*     3.9    15.3    -      -       -      -
    988B  GLY      3.2    14.8    -      -       -      +
    989B  THR*     4.1     9.0    -      -       +      +
   1094B  ARG*     4.9     0.5    +      -       -      +
   1095B  LEU*     3.2    46.0    +      -       +      +
   1097B  HIS*     3.1    49.5    +      -       +      +
   1098B  MET*     5.4     0.4    -      -       -      +
   1102B  LYS*     5.3     0.2    -      -       -      +
      9P    G      3.1    17.2    +      -       -      -
     10P    A      3.0    25.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 980 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    839B  MET*     3.4    25.5    -      -       +      +
    841B  MET*     3.7    16.6    -      -       +      -
    851B  PHE*     3.7    21.5    -      +       -      -
    974B  PRO*     4.0    13.0    -      -       +      -
    978B  ASP*     3.4    22.7    -      -       +      -
    979B  LYS*     1.4    68.7    -      -       -      +
    981B  ALA*     1.4    59.5    +      -       -      +
    986B  GLN      4.2     0.5    -      -       -      +
    987B  LYS*     3.4     1.4    -      -       -      +
    988B  GLY*     2.8    34.9    +      -       -      +
    990B  ILE*     3.4    32.3    -      -       +      -
   1092B  TYR*     4.3     6.1    -      -       +      -
   1093B  GLN      3.2    22.2    -      -       -      +
   1094B  ARG*     3.4    43.1    -      -       +      -
   1095B  LEU*     3.7     5.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 981 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    770B  GLN*     4.9     0.7    -      -       -      +
    773B  MET*     3.7    15.9    -      -       +      -
    980B  PHE*     1.4    77.4    -      -       -      +
    982B  SER*     1.3    67.1    +      -       -      +
    986B  GLN      3.3     8.1    -      -       -      +
    987B  LYS*     3.7    17.5    -      -       -      +
   1092B  TYR*     3.4     9.0    -      -       -      -
   1093B  GLN*     2.7    42.8    +      -       -      +
   1095B  LEU*     3.7    16.7    -      -       +      +
----------------------------------------------------------
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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