Contacts of the strand formed by residues 92 - 95 (chain C) in PDB entry 1HYH


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 92 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23C  LYS      3.7     1.9    +      -       -      +
     24C  ILE*     3.5    15.4    -      -       +      +
     25C  GLY      3.0    22.1    +      -       -      +
     90C  ALA*     4.0     1.4    -      -       -      +
     91C  ASP*     1.3    82.6    -      -       -      +
     93C  VAL*     1.3    72.2    +      -       -      +
     94C  ILE*     4.2    11.2    -      -       +      -
    134C  PHE*     4.3     1.3    -      -       -      -
    137C  VAL*     3.3    12.6    -      -       +      +
    139C  VAL*     3.8    24.9    -      -       +      -
    260C  ALA*     3.9    27.8    -      -       +      +
    263C  VAL*     3.7    24.9    -      -       +      -
    264C  MET*     4.1    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 93 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25C  GLY*     3.3     9.6    -      -       -      +
     27C  ILE*     3.6    33.9    -      -       +      -
     87C  LEU*     4.0    23.8    -      -       +      -
     90C  ALA*     4.3     1.8    -      -       +      -
     92C  VAL*     1.3    77.9    -      -       -      +
     94C  ILE*     1.3    64.7    -      -       -      +
    129C  LEU*     4.3     9.6    -      -       +      -
    134C  PHE*     3.6    34.8    -      -       +      -
    137C  VAL      3.0     6.1    +      -       -      -
    138C  LEU*     3.4    17.8    -      -       +      +
    139C  VAL      2.8    25.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 94 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24C  ILE*     4.3    19.1    -      -       +      -
     25C  GLY      2.8    12.2    +      -       -      +
     26C  ILE*     3.3     8.3    -      -       +      +
     27C  ILE*     2.8    25.8    +      -       -      +
     36C  VAL*     3.8    28.3    -      -       +      -
     40C  LEU*     4.9     2.7    -      -       +      -
     92C  VAL*     4.2    10.8    -      -       +      -
     93C  VAL*     1.3    79.6    -      -       -      +
     95C  SER*     1.3    62.3    +      -       -      +
     96C  THR*     4.3     9.4    -      -       +      -
    139C  VAL*     3.3    17.7    -      -       +      +
    141C  ILE*     4.1    26.2    -      -       +      -
    256C  ALA*     4.3    15.5    -      -       +      +
    257C  ILE*     5.6     0.4    -      -       -      -
    260C  ALA*     4.5    17.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 95 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27C  ILE*     3.6    16.5    -      -       -      +
     93C  VAL      4.1     1.0    +      -       -      -
     94C  ILE*     1.3    73.0    -      -       -      +
     96C  THR*     1.3    61.5    +      -       -      +
     97C  LEU*     3.5    17.5    +      -       -      +
    138C  LEU*     4.3    15.7    -      -       -      -
    139C  VAL      2.9    11.2    +      -       -      -
    140C  VAL*     4.6     4.8    -      -       -      +
    141C  ILE*     2.9    30.0    +      -       -      +
    152C  PHE*     3.7    30.5    -      -       -      -
----------------------------------------------------------
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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