Contacts of the strand formed by residues 1266 - 1267 (chain B) in PDB entry 2O8C


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 HIS1266 (chain B). 
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1132B  VAL*     5.2     0.2    -      -       -      -
   1133B  THR*     3.3    27.8    -      -       -      +
   1265B  GLY*     1.3    73.9    -      -       -      -
   1267B  MET*     1.3    85.3    +      -       -      +
   1268B  ALA*     3.8     5.2    +      -       -      -
   1289B  PHE*     3.3    13.7    -      -       -      -
   1290B  ILE*     3.0    64.8    +      -       +      +
   1291B  LYS      4.3     0.9    -      -       -      -
   1292B  GLY*     3.2    29.5    -      -       -      +
   1293B  ALA      3.4    18.2    +      -       -      -
   1294B  CYS*     3.7    17.2    -      -       -      +
   1295B  PRO*     5.4     4.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with MET1267 (chain B). Click here for Legend to table. 
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1111B  ASN*     5.3     2.5    -      -       -      -
   1132B  VAL*     4.2     6.7    -      -       +      -
   1133B  THR      2.9    14.5    +      -       -      +
   1134B  GLY*     4.5     7.4    -      -       -      -
   1135B  PRO*     4.9     7.0    -      -       +      +
   1138B  GLY*     3.3    33.4    -      -       -      +
   1139B  GLY*     3.4    27.1    -      -       -      +
   1140B  LYS*     3.8    11.7    -      -       +      +
   1143B  LEU*     4.1    22.7    -      -       +      -
   1266B  HIS*     1.3    81.8    -      -       -      +
   1268B  ALA*     1.3    69.0    +      -       -      +
   1269B  CYS*     3.7     4.9    +      -       -      +
   1287B  TYR      4.1    12.1    -      -       -      +
   1288B  LYS      3.6    20.4    -      -       -      +
   1289B  PHE*     4.1    11.2    -      -       +      -
   1294B  CYS*     4.8     4.7    -      -       -      -
   1298B  TYR*     6.0     1.4    -      -       -      -
----------------------------------------------------------
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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