Contacts of the strand formed by residues 61 - 66 (chain B) in PDB entry 2H6C


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 ILE 61 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43B  ILE*     3.2    30.1    -      -       +      -
     54B  ILE*     5.5     0.4    -      -       +      -
     56B  LEU*     3.3    31.6    -      -       +      -
     60B  LYS*     1.3    81.3    -      -       -      +
     62B  LYS*     1.3    67.8    +      -       -      +
     63B  LEU*     3.4    22.2    -      -       +      -
     76B  TYR      3.9     0.5    -      -       -      +
     77B  TYR*     3.1     9.7    -      -       -      -
     78B  ALA*     2.6    36.9    +      -       +      +
     84B  ILE*     4.1     7.9    -      -       +      -
     96B  ALA*     4.0    11.7    -      -       +      -
     97B  THR      3.5    10.8    -      -       -      +
     98B  ALA*     4.6     4.5    -      -       +      -
     99B  MET*     4.2     4.3    -      -       -      -
    102B  THR*     4.2    13.0    -      -       +      -
    104B  THR*     4.6     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 62 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61B  ILE*     1.3    73.1    -      -       -      +
     63B  LEU*     1.3    61.5    +      -       -      +
     64B  ASP*     2.6    41.6    +      -       -      +
     74B  LEU*     4.3    15.9    -      -       +      +
     77B  TYR*     3.9    27.0    +      -       +      -
     95B  TYR      3.5     1.6    -      -       -      +
     96B  ALA*     3.1     6.9    -      -       -      +
     97B  THR*     2.8    57.2    +      -       +      +
     99B  MET*     3.7    17.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 63 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44B  ILE*     5.6     1.1    -      -       +      -
     61B  ILE*     3.4    25.1    -      -       +      +
     62B  LYS*     1.3    73.8    -      -       -      +
     64B  ASP*     1.3    58.9    -      -       -      +
     74B  LEU*     3.9     2.3    -      -       -      +
     75B  LEU*     2.8    40.2    +      -       +      +
     76B  TYR*     2.8    57.7    +      -       +      +
     78B  ALA*     4.2     2.0    -      -       +      -
     84B  ILE*     4.0    31.9    -      -       +      -
     94B  ILE*     3.8    26.9    -      -       +      -
     95B  TYR      3.6     2.5    -      -       -      -
     96B  ALA*     4.1    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 64 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62B  LYS*     2.6    42.2    +      -       -      +
     63B  LEU*     1.3    75.5    -      -       -      +
     65B  ILE*     1.3    59.9    +      -       -      +
     72B  GLU*     3.3    32.9    -      -       +      +
     73B  LYS      3.1    11.2    -      -       -      +
     74B  LEU*     3.3    15.9    +      -       -      -
     75B  LEU*     4.3     1.3    -      -       -      -
     94B  ILE*     3.6     5.9    -      -       -      +
     95B  TYR*     3.1    47.0    +      -       +      +
     97B  THR*     4.6     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 65 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  ARG*     4.0    25.6    -      -       +      +
    142A  ALA*     4.0    17.9    -      -       +      -
     64B  ASP*     1.3    74.4    -      -       -      +
     66B  ILE*     1.3    74.5    +      -       -      +
     67B  PHE*     3.8    27.5    -      -       +      -
     71B  SER      3.9     0.7    -      -       -      +
     72B  GLU*     3.5     3.5    -      -       -      -
     73B  LYS*     3.0    30.6    +      -       +      +
     75B  LEU*     4.0    21.7    -      -       +      +
     92B  ASN*     3.7    37.9    -      -       +      +
     93B  ASN      3.4    11.4    -      -       -      +
     94B  ILE*     4.6     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 66 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  ARG*     4.7     2.8    +      -       -      -
     46B  PRO*     4.0    15.9    -      -       +      -
     64B  ASP      4.7     0.2    -      -       -      +
     65B  ILE*     1.3    84.2    -      -       -      +
     67B  PHE*     1.3    72.0    +      -       -      +
     70B  GLY*     4.3    17.3    -      -       -      +
     71B  SER      3.6     8.3    -      -       -      +
     72B  GLU*     4.3    20.0    -      -       +      +
     93B  ASN*     2.9    52.2    +      -       -      +
     95B  TYR*     3.9    31.0    -      -       +      -
----------------------------------------------------------
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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