Contacts of the strand formed by residues 94 - 102 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  LEU*     3.5    15.9    -      -       -      +
    101A  LYS*     5.8     0.3    -      -       -      +
     55B  VAL*     3.6    21.1    -      -       +      -
     57B  ILE*     3.7    17.9    -      -       +      -
     79B  PHE*     3.7    34.3    -      -       +      -
     88B  TRP*     3.9    21.3    -      -       +      -
     91B  ASP*     3.0    20.9    -      -       -      +
     92B  ALA*     3.1     7.9    -      -       -      +
     93B  GLN*     1.3    72.8    -      -       -      +
     95B  VAL*     1.3    60.3    +      -       -      +
     96B  ASP      4.0     5.4    -      -       -      +
     97B  TYR*     3.7    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 95 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  LEU*     3.3     9.9    -      -       -      +
    101A  LYS*     2.8    56.2    +      -       +      +
     54B  PRO*     3.9    24.2    -      -       +      -
     55B  VAL      3.2    12.0    +      -       -      +
     92B  ALA      4.8     3.6    -      -       -      +
     93B  GLN*     2.9    16.2    +      -       -      +
     94B  VAL*     1.3    74.1    -      -       -      +
     96B  ASP*     1.3    61.5    +      -       +      +
    117B  MET*     4.0    23.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 96 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  LEU*     4.2     0.6    -      -       -      +
     98A  ARG*     3.2    39.5    +      -       -      -
     99A  VAL      3.3     6.4    -      -       -      +
    100A  VAL*     3.5    15.8    -      -       +      +
     55B  VAL      3.7     0.7    +      -       -      +
     56B  LYS*     3.0    29.6    -      -       +      +
     57B  ILE      2.9    22.3    +      -       -      +
     94B  VAL*     3.3     4.7    -      -       -      +
     95B  VAL*     1.3    91.8    -      -       +      +
     97B  TYR*     1.3    66.1    +      -       -      +
     98B  ARG*     5.2     0.2    -      -       -      +
    117B  MET*     4.6     6.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 97 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71A  LEU*     3.8    22.4    -      -       +      -
     72A  ASP*     3.2    28.2    -      -       +      +
     75A  GLN*     3.9     5.0    -      -       -      +
     97A  TYR*     4.1    17.7    -      +       -      -
     98A  ARG*     3.4     2.8    -      -       -      +
     99A  VAL*     3.0    65.0    +      -       +      +
     57B  ILE*     3.3    13.9    -      -       +      +
     59B  ILE*     4.7     1.3    -      -       +      -
     75B  GLN*     3.6    33.6    +      -       +      -
     79B  PHE*     3.9    17.5    -      +       +      -
     94B  VAL*     3.7    21.8    -      -       +      -
     96B  ASP*     1.3    78.1    +      -       -      +
     98B  ARG*     1.3    64.8    +      -       -      +
     99B  VAL*     4.2     8.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 98 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     56A  LYS*     6.0     4.4    -      -       -      +
     96A  ASP*     3.0    39.5    +      -       -      -
     97A  TYR      3.4     8.5    -      -       -      -
     98A  ARG*     3.6    31.6    -      -       +      +
     57B  ILE      2.9    13.9    +      -       -      +
     58B  ARG*     3.2    27.3    -      -       +      +
     59B  ILE*     2.6    33.1    +      -       -      +
     96B  ASP*     5.2     0.4    -      -       -      +
     97B  TYR*     1.3    77.5    -      -       -      +
     99B  VAL*     1.3    57.9    +      -       -      +
    100B  VAL*     3.1    18.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 99 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  ASP*     3.5     1.0    -      -       -      -
     97A  TYR*     3.2    63.8    +      -       +      +
     59B  ILE*     3.3    19.7    -      -       +      +
     61B  CYS*     3.3    30.5    -      -       -      -
     71B  LEU*     3.7    22.9    -      -       +      +
     75B  GLN*     3.8    22.0    -      -       +      +
     97B  TYR*     4.2     4.7    -      -       +      -
     98B  ARG*     1.3    75.6    -      -       -      +
    100B  VAL*     1.3    66.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 100 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  VAL      3.8     5.8    -      -       -      +
     96A  ASP*     3.3    16.8    -      -       +      +
     58B  ARG*     4.5    17.5    -      -       -      +
     59B  ILE      2.9    10.5    +      -       -      +
     60B  GLU*     3.7     3.2    -      -       +      -
     61B  CYS*     2.8    32.1    +      -       -      +
     71B  LEU*     4.4     4.9    -      -       -      -
     98B  ARG*     3.1    39.0    -      -       +      +
     99B  VAL*     1.3    78.5    -      -       -      +
    101B  LYS*     1.3    72.5    +      -       -      +
    102B  MET*     3.7    15.7    +      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 101 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  VAL*     2.9    37.0    +      -       +      +
     61B  CYS*     3.8     3.6    -      -       -      -
     63B  MET*     5.0     7.9    -      -       +      -
     71B  LEU*     4.1    16.7    -      -       +      +
    100B  VAL*     1.3    79.5    -      -       -      +
    102B  MET*     1.3    66.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 102 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58B  ARG*     5.0     2.7    -      -       -      -
     60B  GLU*     3.8    33.9    -      -       +      +
     61B  CYS      2.7    16.9    +      -       -      +
     62B  HIS*     3.1    37.2    -      -       +      +
     63B  MET*     3.7    16.6    +      -       -      +
    100B  VAL*     4.2    14.1    -      -       -      +
    101B  LYS*     1.3    82.1    -      -       -      +
    103B  PRO*     1.3    83.7    -      -       +      +
----------------------------------------------------------
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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