Contacts of the strand formed by residues 3086 - 3087 (chain C) in PDB entry 2H7C


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 MET3086 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3084C  PRO      3.8     0.4    +      -       -      -
   3085C  PRO*     1.3    74.3    -      -       -      +
   3087C  CYS*     1.3    66.9    +      -       -      +
   3089C  GLN*     3.5    33.9    -      -       +      +
   3091C  PRO*     4.7     7.4    -      -       +      +
   3094C  GLY*     4.2    19.7    -      -       -      +
   3095C  GLN*     4.6     3.4    -      -       +      +
   3098C  SER*     6.2     2.5    -      -       -      -
   3110C  LEU*     4.1    31.8    -      -       +      +
   3111C  LYS      2.8    15.8    +      -       -      +
   3112C  LEU*     3.2    26.6    -      -       +      -
   3113C  SER      3.1    19.1    +      -       -      -
   3116C  CYS*     4.0     2.0    -      -       -      -
   3147C  GLY      4.0     1.1    -      -       -      +
   3148C  ALA*     3.6    26.0    -      -       +      -
   3169C  GLN*     3.9     6.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with CYS3087 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   3086C  MET*     1.3    73.8    -      -       -      +
   3088C  THR*     1.3    67.0    +      -       -      +
   3089C  GLN*     2.8    27.3    +      -       -      +
   3112C  LEU*     4.2     0.2    -      -       -      +
   3113C  SER      3.3     8.1    -      -       -      -
   3116C  CYS*     2.0    49.9    -      -       -      +
   3147C  GLY      4.9     0.8    +      -       -      -
   3169C  GLN*     4.4     5.0    -      -       -      +
   3170C  TYR      3.2    32.1    -      -       -      +
   3171C  ARG*     4.0     1.6    -      -       +      -
   3172C  LEU*     3.9    25.3    -      -       +      +
   3175C  TRP*     6.4     1.1    -      -       +      -
----------------------------------------------------------
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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