Contacts of the strand formed by residues 1209 - 1212 (chain B) in PDB entry 2O8F


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 LEU1209 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1089B  LEU*     4.5     9.2    -      -       +      -
   1115B  ILE*     4.1    17.3    -      -       +      -
   1147B  ALA*     4.2    11.7    -      -       +      +
   1148B  GLY*     4.6     3.6    -      -       -      -
   1151B  ALA*     3.9    16.6    -      -       +      -
   1170B  ILE*     3.7    27.8    -      -       +      +
   1172B  ARG      3.1     5.7    +      -       -      -
   1173B  VAL*     3.4    20.8    -      -       +      +
   1174B  PHE*     3.0    25.6    +      -       -      +
   1208B  SER*     1.3    73.4    -      -       -      +
   1210B  VAL*     1.3    60.0    +      -       -      +
   1211B  LEU*     3.9    25.6    -      -       +      -
   1242B  ARG*     3.3    27.4    -      -       +      +
   1243B  THR*     4.6     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL1210 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1174B  PHE*     3.8    15.3    -      -       +      -
   1200B  ILE*     3.8    35.9    -      -       +      -
   1204B  ALA*     4.5     3.4    -      -       +      -
   1208B  SER*     4.8     0.2    -      -       -      -
   1209B  LEU*     1.3    74.8    -      -       -      +
   1211B  LEU*     1.3    68.1    +      -       -      +
   1212B  VAL*     3.7    25.6    -      -       +      -
   1235B  LEU*     4.2     8.5    -      -       +      -
   1241B  CYS*     3.9    24.0    -      -       -      -
   1242B  ARG      2.8     9.7    +      -       -      +
   1243B  THR*     3.3    18.8    -      -       +      -
   1244B  LEU      3.0    25.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU1211 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1144B  MET*     3.3    36.3    -      -       +      +
   1147B  ALA*     4.5     2.5    -      -       +      -
   1148B  GLY*     3.8    20.2    -      -       -      -
   1173B  VAL*     3.9     9.4    -      -       +      -
   1174B  PHE      2.9    12.3    +      -       -      +
   1175B  THR*     3.5    22.6    -      -       +      -
   1176B  ARG      2.9    26.6    +      -       -      +
   1177B  LEU*     4.1     4.4    -      -       +      +
   1209B  LEU*     3.9    22.7    -      -       +      +
   1210B  VAL*     1.3    84.4    -      -       -      +
   1212B  VAL*     1.3    61.5    +      -       -      +
   1244B  LEU*     3.8    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL1212 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1144B  MET*     3.5     3.7    -      -       -      +
   1176B  ARG*     3.6    20.2    -      -       +      -
   1197B  THR*     5.4     6.5    -      -       +      +
   1200B  ILE*     3.9    17.7    -      -       +      -
   1210B  VAL*     3.7    24.1    -      -       +      -
   1211B  LEU*     1.3    73.8    -      -       -      +
   1213B  ASP*     1.3    65.0    +      -       -      +
   1214B  GLU      4.0     0.4    -      -       -      +
   1215B  LEU*     4.3    16.2    -      -       +      -
   1231B  VAL*     5.7     1.3    -      -       +      -
   1235B  LEU*     5.3     4.0    -      -       +      -
   1243B  THR*     5.7     0.6    -      -       +      +
   1244B  LEU      3.2    10.4    +      -       -      +
   1245B  PHE*     3.6    37.5    -      -       +      -
   1246B  SER      3.1    24.6    +      -       -      -
----------------------------------------------------------
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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