Contacts of the strand formed by residues 79 - 85 (chain C) in PDB entry 2WJ7


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 VAL 79 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15C  ASN*     3.6    30.7    -      -       +      +
     16C  LEU      3.2    12.3    -      -       -      +
     17C  ASP*     5.4     5.4    -      -       +      +
     73C  SER*     4.0     1.0    +      -       -      +
     74C  LEU*     3.3     3.4    -      -       -      +
     75C  SER*     3.0    38.9    +      -       -      +
     77C  ASP*     4.3    12.1    -      -       -      +
     78C  GLY*     1.3    77.8    -      -       -      +
     80C  LEU*     1.3    69.6    +      -       -      +
     81C  THR*     4.0     4.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 80 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14C  VAL      3.7     0.7    -      -       -      +
     15C  ASN*     3.3     3.6    -      -       -      -
     16C  LEU*     2.8    43.4    +      -       +      +
     18C  VAL*     3.8    22.0    -      -       +      -
     26C  LEU*     5.1    11.2    -      -       +      -
     28C  VAL*     4.0    28.3    -      -       +      -
     37C  VAL*     4.1    24.5    -      -       +      -
     72C  SER*     4.9     3.4    -      -       -      +
     73C  SER      3.2    24.7    -      -       -      +
     74C  LEU*     3.7    15.3    -      -       +      -
     78C  GLY      3.7     1.8    +      -       -      -
     79C  VAL*     1.3    73.8    -      -       -      +
     81C  THR*     1.3    69.0    +      -       -      +
     82C  VAL*     4.8     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 81 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13C  SER*     4.2     2.5    -      -       -      +
     14C  VAL      3.2     3.8    -      -       -      -
     15C  ASN*     3.5    29.8    +      -       -      +
     72C  SER*     3.3     4.7    -      -       -      -
     73C  SER*     2.8    47.5    +      -       -      +
     79C  VAL*     4.2     5.0    +      -       -      +
     80C  LEU*     1.3    75.8    -      -       -      +
     82C  VAL*     1.3    72.9    +      -       -      +
     83C  ASN*     3.2    31.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 82 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12C  PHE*     4.0     5.4    -      -       +      -
     13C  SER*     3.4     1.4    -      -       -      -
     14C  VAL*     2.9    40.8    +      -       +      +
     16C  LEU*     5.4     4.5    -      -       +      -
     28C  VAL*     4.4    27.6    -      -       +      -
     30C  VAL*     6.2     0.9    -      -       +      -
     35C  ILE*     4.0    39.5    -      -       +      -
     37C  VAL*     4.8     6.7    -      -       +      -
     59C  TYR*     5.9     1.8    -      -       +      -
     70C  ILE*     4.9     6.7    -      -       +      -
     71C  THR      3.4    12.6    -      -       -      +
     72C  SER*     4.4     4.3    -      -       -      -
     80C  LEU*     4.8     7.0    -      -       +      -
     81C  THR*     1.3    82.1    -      -       -      +
     83C  ASN*     1.3    67.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 83 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11C  ARG*     5.8     1.8    -      -       +      -
     12C  PHE*     2.8    30.5    -      -       -      +
     13C  SER*     4.1     8.0    +      -       -      -
     70C  ILE*     3.3     7.6    -      -       -      +
     71C  THR*     2.8    53.1    +      -       -      +
     72C  SER*     5.1     1.7    -      -       -      -
     73C  SER*     5.9     1.4    -      -       -      -
     81C  THR*     3.2    24.3    -      -       -      +
     82C  VAL*     1.3    72.9    -      -       -      +
     84C  GLY*     1.3    61.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 84 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11C  ARG*     3.2     6.9    -      -       -      +
     12C  PHE*     3.0    37.6    +      -       -      -
     65C  VAL*     5.3     0.7    -      -       -      -
     69C  THR      4.1     5.4    -      -       -      -
     70C  ILE*     4.4     2.5    -      -       -      -
     71C  THR*     4.9     1.3    +      -       -      -
     83C  ASN*     1.3    82.2    -      -       -      +
     85C  PRO*     1.3    74.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 85 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     10C  ASP      3.1    12.6    -      -       -      +
     11C  ARG*     4.2     2.0    -      -       +      -
     64C  ASP      4.4     0.3    -      -       -      +
     65C  VAL*     3.8    17.2    -      -       -      +
     66C  ASP      5.1     0.3    +      -       -      -
     69C  THR*     3.3    34.4    +      -       +      +
     84C  GLY*     1.3    89.8    -      -       -      +
     86C  ARG*     1.3    61.7    +      -       -      +
     87C  LYS      4.7     2.9    -      -       -      +
----------------------------------------------------------
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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