Contacts of the strand formed by residues 94 - 102 (chain C) in PDB entry 2H8C


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 94 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55C  VAL*     3.3    25.4    -      -       +      +
     57C  ILE*     4.5     2.9    -      -       +      -
     79C  PHE*     3.9    19.5    -      -       +      -
     88C  TRP*     3.8    22.9    -      -       +      -
     91C  ASP*     2.5    35.3    +      -       +      +
     92C  ALA*     3.9     7.4    -      -       -      +
     93C  GLN*     1.3    67.3    -      -       -      +
     95C  VAL*     1.3    60.9    +      -       -      +
     96C  ASP      3.9     8.5    -      -       -      +
     97C  TYR*     3.7    34.1    -      -       +      -
     71D  LEU*     3.9    14.6    -      -       +      +
    101D  LYS*     4.9     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54C  PRO*     3.5    32.5    -      -       +      -
     55C  VAL      3.2    10.9    +      -       -      +
     92C  ALA      5.6     0.7    -      -       -      +
     93C  GLN      3.0     2.4    +      -       -      +
     94C  VAL*     1.3    74.0    -      -       -      +
     96C  ASP*     1.3    60.1    +      -       +      +
    117C  MET*     4.5    10.1    -      -       +      -
     71D  LEU*     4.5     3.4    -      -       -      -
    100D  VAL*     3.7     2.1    -      -       -      +
    101D  LYS*     2.7    74.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 96 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     55C  VAL      3.9     1.3    +      -       -      +
     56C  LYS*     3.2    29.1    -      -       +      +
     57C  ILE*     2.6    34.3    +      -       -      +
     94C  VAL*     3.3     4.6    -      -       -      +
     95C  VAL*     1.3    85.9    -      -       +      +
     97C  TYR*     1.3    58.0    +      -       -      +
     71D  LEU*     4.9     0.4    -      -       -      +
     98D  ARG*     3.4    40.4    +      -       -      +
     99D  VAL      3.7     4.9    -      -       -      -
    100D  VAL*     3.6    18.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 97 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  ILE*     3.2    22.9    -      -       +      -
     59C  ILE*     4.8     0.4    -      -       +      -
     75C  GLN*     3.3    28.7    +      -       +      -
     79C  PHE*     3.7    17.0    -      +       +      -
     94C  VAL*     3.7    13.5    -      -       +      -
     96C  ASP*     1.3    75.1    +      -       -      +
     98C  ARG*     1.3    57.7    +      -       -      +
     99C  VAL*     3.6    22.2    -      -       +      -
     71D  LEU*     4.1    16.6    -      -       +      -
     72D  ASP*     3.4    26.2    +      -       -      +
     75D  GLN*     3.7    12.6    +      -       -      +
     97D  TYR*     3.7    11.7    -      +       -      +
     98D  ARG*     3.1     4.6    -      -       -      -
     99D  VAL*     2.8    71.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 98 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57C  ILE      2.7    13.6    +      -       -      +
     58C  ARG*     3.0    24.3    -      -       +      +
     59C  ILE*     2.6    33.8    +      -       -      +
     97C  TYR*     1.3    73.6    -      -       -      +
     99C  VAL*     1.3    57.5    +      -       -      +
    100C  VAL*     3.9     7.9    -      -       +      -
     56D  LYS*     4.0    21.3    -      -       -      +
     96D  ASP*     2.7    39.6    +      -       -      +
     97D  TYR      3.3     3.8    -      -       -      -
     98D  ARG*     3.4    52.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 99 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59C  ILE*     3.6    22.0    -      -       +      +
     61C  CYS*     3.9    22.7    -      -       -      -
     71C  LEU*     3.9    29.2    -      -       +      +
     75C  GLN*     3.9     8.7    -      -       +      +
     97C  TYR*     3.6    31.6    -      -       +      -
     98C  ARG*     1.3    76.5    -      -       -      +
    100C  VAL*     1.3    63.0    +      -       -      +
     95D  VAL      3.7     1.6    -      -       -      +
     96D  ASP*     3.3     3.1    -      -       -      -
     97D  TYR*     2.7    49.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 100 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58C  ARG*     3.9    25.4    -      -       +      +
     59C  ILE      2.9    13.5    +      -       -      +
     60C  GLU*     3.7     3.8    -      -       -      -
     61C  CYS*     2.6    38.4    +      -       -      +
     98C  ARG*     3.9    15.0    -      -       +      +
     99C  VAL*     1.3    78.7    -      -       -      +
    101C  LYS*     1.3    72.8    +      -       -      +
    102C  MET*     3.1    12.6    +      -       +      -
     95D  VAL      3.3    10.1    -      -       -      +
     96D  ASP*     3.2    28.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 101 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61C  CYS*     3.7     6.7    -      -       -      -
     63C  MET*     3.8    34.5    -      -       +      -
     71C  LEU*     4.3    12.0    -      -       +      +
    100C  VAL*     1.3    76.9    -      -       -      +
    102C  MET*     1.3    64.0    +      -       -      +
     95D  VAL*     2.8    40.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 102 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58C  ARG*     5.0     2.0    -      -       -      -
     60C  GLU*     3.7    38.4    -      -       +      +
     61C  CYS      2.6    19.9    +      -       -      +
     62C  HIS*     3.4    37.5    -      -       +      +
     63C  MET*     3.3    14.4    +      -       -      +
    100C  VAL*     3.1    13.1    +      -       -      +
    101C  LYS*     1.3    82.6    -      -       -      +
    103C  PRO*     1.3    89.4    -      -       +      +
----------------------------------------------------------
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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