Contacts of the strand formed by residues 110 - 112 (chain A) in PDB entry 1YGK


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 TYR 110 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80A  VAL*     3.2    23.6    -      -       +      +
     82A  THR*     2.6    43.5    +      -       +      +
     91A  LEU*     5.0     4.2    -      -       -      +
     94A  VAL*     4.3     8.2    -      -       +      +
     95A  VAL*     5.7     2.8    -      -       +      +
     98A  VAL*     3.7    30.5    -      -       +      -
    102A  LYS*     4.7     1.3    -      -       -      -
    108A  LEU*     3.7     1.8    +      -       -      +
    109A  VAL*     1.3    70.6    -      -       -      +
    111A  VAL*     1.3    68.5    +      -       -      +
    112A  CYS*     3.5    20.2    -      -       +      +
    140A  VAL*     3.8    16.1    -      -       +      +
    143A  VAL*     3.7    26.5    -      -       +      +
    144A  ALA*     3.4    26.6    -      -       +      -
    145A  ASP*     2.7    38.5    +      -       -      +
    146A  ILE      3.4     4.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 111 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79A  TYR*     4.8     1.6    -      -       +      -
     80A  VAL      2.6    17.9    +      -       -      +
     81A  LEU*     3.3    33.5    -      -       +      +
     82A  THR      3.4     7.3    +      -       -      -
    109A  VAL*     3.4     7.8    +      -       +      +
    110A  TYR*     1.3    73.5    -      -       -      +
    112A  CYS*     1.3    63.3    +      -       -      +
    146A  ILE*     3.4    39.7    -      -       +      +
    148A  THR*     5.6     3.4    -      -       +      +
    238A  ALA*     4.5    20.4    -      -       +      +
    241A  LEU*     6.0     0.9    -      -       +      -
    242A  LEU*     3.4    32.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 112 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  THR*     4.1     5.2    -      -       -      -
    110A  TYR*     3.5    23.7    +      -       +      +
    111A  VAL*     1.3    75.7    -      -       -      +
    113A  ASP*     1.3    69.5    +      -       -      +
    114A  PRO*     3.2    12.9    -      -       -      +
    136A  TYR*     4.2     9.9    -      -       -      -
    140A  VAL*     3.7    28.0    -      -       -      -
    141A  VAL*     5.6     2.2    -      -       -      -
    144A  ALA*     3.8    15.5    -      -       +      -
    146A  ILE      2.7    11.1    +      -       -      -
    147A  ILE*     3.1    28.9    -      -       +      +
    148A  THR*     4.4     1.1    -      -       -      -
----------------------------------------------------------
 Back to top of page


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