Contacts of the strand formed by residues 815 - 821 (chain W) in PDB entry 5O9G


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 MET 815 (chain W).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    610W  THR*     3.8    28.5    -      -       +      +
    612W  ARG*     5.3     4.5    -      -       -      -
    707W  LEU*     6.0     4.7    -      -       +      -
    784W  ASP*     3.4     5.1    +      -       -      +
    785W  THR*     3.3    20.5    +      -       +      +
    786W  VAL      3.1    22.5    +      -       -      -
    814W  VAL*     1.3    73.6    -      -       -      +
    816W  VAL*     1.3    65.0    +      -       -      +
    817W  TYR*     3.5    46.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 816 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    610W  THR      4.0    12.1    +      -       -      +
    611W  GLU*     3.7    21.3    -      -       +      +
    612W  ARG      3.0    26.9    +      -       -      -
    786W  VAL*     3.3    22.4    -      -       +      +
    788W  ILE*     5.0     7.2    -      -       +      -
    802W  MET*     3.6    35.4    -      -       +      -
    814W  VAL*     3.8    20.6    -      -       +      -
    815W  MET*     1.3    79.6    -      -       -      +
    817W  TYR*     1.3    75.9    +      -       -      +
    818W  ARG*     4.9     3.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 817 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    612W  ARG*     3.3    49.4    +      -       +      +
    614W  LEU*     5.9     2.7    -      -       +      -
    703W  LEU*     3.8    33.0    -      -       +      -
    706W  ARG*     4.6    14.6    +      -       -      -
    707W  LEU*     5.2    16.9    -      -       +      +
    785W  THR*     5.3     4.0    -      -       +      -
    786W  VAL      3.2     6.9    +      -       -      +
    787W  VAL*     3.6    25.0    -      -       +      +
    788W  ILE*     3.1    26.5    +      -       -      +
    815W  MET*     3.5    40.6    +      -       +      +
    816W  VAL*     1.3    84.0    -      -       -      +
    818W  ARG*     1.3    60.9    +      -       -      +
    819W  LEU*     4.0     7.6    +      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 818 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    611W  GLU*     2.5    48.0    +      -       -      +
    612W  ARG      3.2     7.5    +      -       -      -
    613W  ILE*     3.4    14.1    -      -       +      +
    614W  LEU*     2.8    32.3    +      -       -      +
    788W  ILE*     3.9    21.2    -      -       +      +
    790W  ASP*     5.7     1.8    -      -       -      -
    791W  SER*     4.3    16.4    +      -       -      +
    798W  ASP*     3.9    29.3    +      -       -      +
    799W  LEU*     6.3     0.6    -      -       -      +
    802W  MET*     5.6     6.9    -      -       -      +
    816W  VAL*     5.6     2.8    -      -       +      +
    817W  TYR*     1.3    72.1    -      -       -      +
    819W  LEU*     1.3    61.1    +      -       -      +
    820W  VAL*     3.0    25.6    +      -       +      +
    830W  LEU*     4.5    12.5    -      -       -      +
    834W  ARG*     3.9    25.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 819 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    614W  LEU*     3.5    32.1    -      -       +      -
    616W  VAL*     4.4     5.8    -      -       +      -
    696W  LYS*     3.4    43.5    +      -       +      +
    699W  LEU*     5.5     3.6    -      -       +      -
    700W  LEU*     5.0     5.6    -      -       +      +
    703W  LEU*     5.3     5.2    -      -       +      -
    787W  VAL*     4.4    15.9    -      -       +      -
    788W  ILE      3.1    12.0    +      -       -      +
    789W  PHE*     2.8    60.3    -      -       +      +
    790W  ASP*     4.6     2.5    -      -       -      -
    817W  TYR*     5.1     7.2    -      -       +      -
    818W  ARG*     1.3    72.9    -      -       -      +
    820W  VAL*     1.3    65.0    +      -       -      +
    821W  SER      3.4     2.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 820 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    613W  ILE*     4.1    19.5    -      -       +      -
    614W  LEU      2.8    14.5    +      -       -      +
    615W  ARG*     3.2    27.1    -      -       +      +
    616W  VAL*     2.7    33.2    +      -       -      +
    790W  ASP*     6.2     0.4    -      -       -      +
    818W  ARG*     3.0    35.8    +      -       +      +
    819W  LEU*     1.3    71.2    -      -       -      +
    821W  SER*     1.3    67.4    +      -       -      +
    826W  GLU*     6.0     0.9    -      -       +      -
    827W  GLU*     4.9    11.4    -      -       +      +
    830W  LEU*     4.4    19.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 821 (chain W). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    616W  VAL      3.8     5.8    -      -       -      -
    618W  LEU*     5.4     2.0    -      -       -      +
    659W  SER      4.8     3.4    -      -       -      -
    660W  ASN*     4.3     7.6    -      -       -      +
    696W  LYS*     3.1    30.1    +      -       -      +
    790W  ASP*     5.3     0.7    -      -       -      +
    819W  LEU      3.4     1.0    +      -       -      -
    820W  VAL*     1.3    78.9    -      -       -      +
    822W  LYS*     1.3    60.2    +      -       -      +
    824W  THR*     2.9    38.2    +      -       -      -
    826W  GLU*     3.7    21.9    +      -       -      +
    827W  GLU*     3.0    13.7    +      -       -      +
----------------------------------------------------------
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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