Contacts of the strand formed by residues 808 - 811 (chain A) in PDB entry 3K72


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 808 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    782A  LEU*     4.7    14.8    -      -       +      -
    804A  HIS*     3.0    48.3    -      -       +      -
    805A  PRO*     3.9    20.9    -      -       +      +
    806A  ALA      2.8    10.9    +      -       -      +
    807A  GLY*     1.3    75.5    -      -       -      +
    809A  SER*     1.3    66.9    +      -       -      +
    840A  TRP*     3.7     0.2    -      -       -      -
    863A  PHE*     3.3    35.4    -      -       +      +
    864A  ASP      3.0    23.1    -      -       -      +
    865A  VAL*     4.1    13.9    -      -       +      -
    871A  LEU*     5.9     1.8    -      -       +      -
    875A  LEU*     5.0    12.1    -      -       +      -
    877A  LEU*     5.8     4.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 809 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    804A  HIS*     4.4     5.6    -      -       -      -
    808A  LEU*     1.3    80.7    +      -       -      +
    810A  TYR*     1.3    66.3    +      -       -      +
    831A  SER*     4.7     8.7    +      -       -      -
    840A  TRP*     3.5    22.2    -      -       -      -
    842A  THR*     5.0     4.5    -      -       -      -
    863A  PHE*     3.1    13.7    -      -       -      -
    864A  ASP*     3.1    30.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 810 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    809A  SER*     1.3    78.8    -      -       -      +
    811A  ARG*     1.3    75.3    +      -       -      +
    812A  TYR*     3.8    21.7    -      +       +      -
    813A  VAL*     4.0     1.5    +      -       +      +
    823A  ARG*     3.6    24.3    +      -       -      -
    827A  LEU*     3.7    14.4    -      -       +      +
    829A  CYS*     3.6    39.7    -      -       +      -
    831A  SER*     5.6     0.6    -      -       -      -
    842A  THR*     4.5    14.6    -      -       +      +
    844A  CYS*     4.8     3.4    -      -       -      -
    860A  LEU      4.5     1.4    +      -       -      -
    861A  ALA*     3.6    19.6    -      -       +      +
    862A  THR      3.3    32.3    -      -       -      -
    863A  PHE*     3.8    20.0    -      +       +      -
----------------------------------------------------------
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Residues in contact with ARG 811 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    780A  LEU*     5.7     2.3    -      -       -      +
    781A  GLU*     3.0    37.8    +      -       -      +
    809A  SER      3.8     0.4    +      -       -      -
    810A  TYR*     1.3    88.4    -      -       -      +
    812A  TYR*     1.3    71.5    +      -       -      +
    813A  VAL*     3.4     6.6    +      -       -      +
    862A  THR*     3.0    26.4    +      -       +      +
    864A  ASP*     3.0    39.6    +      -       -      +
----------------------------------------------------------
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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