Contacts of the strand formed by residues 1089 - 1094 (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 LEU1089 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1088B  PHE*     1.3    80.5    -      -       -      +
   1090B  GLU*     1.3    62.7    +      -       -      +
   1091B  LEU*     3.9    35.0    -      -       +      -
   1113B  ILE*     3.1    10.7    -      -       +      +
   1114B  LEU*     3.5     1.2    -      -       -      -
   1115B  ILE*     3.0    56.5    +      -       +      +
   1116B  GLY      4.9     1.2    -      -       -      +
   1147B  ALA*     4.9     7.6    -      -       +      +
   1150B  LEU      6.4     0.4    -      -       -      -
   1151B  ALA*     5.5     4.5    -      -       +      -
   1165B  CYS*     5.1     2.2    -      -       -      -
   1166B  ARG      3.7     2.9    -      -       -      +
   1167B  LEU*     3.8    31.6    -      -       +      -
   1170B  ILE*     5.3     2.9    -      -       +      -
   1209B  LEU*     4.5    21.1    -      -       +      -
   1242B  ARG*     4.3     9.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU1090 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1088B  PHE*     4.0     8.5    -      -       +      -
   1089B  LEU*     1.3    71.7    -      -       -      +
   1091B  LEU*     1.3    68.0    +      -       -      +
   1092B  LYS*     3.4    29.4    +      -       +      -
   1113B  ILE      3.7     1.3    -      -       -      -
   1114B  LEU*     3.7    17.7    -      -       +      +
   1118B  GLU*     3.5    14.4    -      -       +      +
   1164B  VAL*     3.3    28.2    -      -       +      +
   1165B  CYS*     3.3    15.6    -      -       -      -
   1166B  ARG*     2.9    44.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU1091 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1089B  LEU*     3.9    26.7    -      -       +      -
   1090B  GLU*     1.3    76.6    -      -       -      +
   1092B  LYS*     1.3    64.2    +      -       -      +
   1094B  SER*     3.8    12.3    +      -       -      -
   1111B  ASN      3.5     3.5    -      -       -      +
   1112B  ASP*     3.2     7.3    -      -       -      -
   1113B  ILE*     2.9    55.7    +      -       +      +
   1114B  LEU*     3.9     1.9    -      -       -      +
   1147B  ALA      5.0     2.7    -      -       -      +
   1150B  LEU*     3.8    43.1    -      -       +      -
   1160B  VAL*     5.2     0.9    -      -       +      -
   1162B  ALA*     4.5     6.7    -      -       +      -
   1164B  VAL      3.4     1.6    -      -       -      +
   1165B  CYS*     3.7    33.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS1092 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1090B  GLU*     3.4    30.6    +      -       +      +
   1091B  LEU*     1.3    71.0    -      -       -      +
   1093B  GLY*     1.3    57.8    +      -       -      +
   1112B  ASP*     3.5    13.7    -      -       -      +
   1114B  LEU*     4.6    16.2    -      -       +      -
   1162B  ALA*     3.5     1.6    -      -       -      +
   1163B  GLU*     2.8    41.0    +      -       +      +
   1164B  VAL*     3.0    31.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY1093 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1073B  PRO*     4.7     5.1    -      -       -      +
   1092B  LYS*     1.3    73.6    -      -       -      +
   1094B  SER*     1.3    63.5    +      -       -      +
   1095B  ARG*     3.6     8.7    +      -       -      +
   1110B  PRO*     3.8    19.6    -      -       -      +
   1111B  ASN      3.8     3.1    -      -       -      -
   1112B  ASP*     3.2    12.9    +      -       -      -
   1161B  PRO      3.2    12.6    -      -       -      +
   1162B  ALA*     3.4     6.5    -      -       -      -
   1163B  GLU*     4.4    15.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER1094 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1091B  LEU*     3.8    20.8    +      -       -      -
   1092B  LYS      3.3     1.4    -      -       -      -
   1093B  GLY*     1.3    77.6    -      -       -      +
   1095B  ARG*     1.3    62.0    +      -       -      +
   1109B  ILE      5.1     0.2    -      -       -      +
   1110B  PRO*     3.7     0.9    -      -       -      +
   1111B  ASN      2.8    42.1    +      -       -      -
   1113B  ILE*     3.7    10.6    -      -       -      +
   1146B  GLN*     3.6    15.2    +      -       -      -
   1150B  LEU*     3.5    24.9    -      -       -      -
   1161B  PRO      3.8     4.7    -      -       -      -
   1162B  ALA*     3.9     3.8    -      -       -      -
----------------------------------------------------------
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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