Contacts of the strand formed by residues 797 - 806 (chain A) 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 VAL 797 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    662A  GLN*     4.6     0.8    -      -       -      +
    664A  PHE*     3.4    20.0    -      -       +      +
    666A  ILE*     3.7    33.7    -      -       +      -
    771A  ALA*     3.9     9.6    -      -       +      -
    790A  LEU*     4.1    14.4    -      -       +      +
    791A  ALA*     3.4    37.9    -      -       +      +
    794A  ILE*     3.6    33.8    -      -       +      +
    795A  PRO      3.2     7.2    -      -       -      +
    796A  THR*     1.3    81.8    -      -       -      +
    798A  ASN*     1.3    62.0    +      -       -      +
    799A  ASN*     4.3     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 798 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    662A  GLN*     3.1    40.2    +      -       -      +
    664A  PHE      2.9    11.0    +      -       -      +
    665A  HIS*     3.4    17.0    +      -       -      +
    666A  ILE*     2.8    27.0    +      -       -      +
    791A  ALA*     4.7     0.4    -      -       -      -
    796A  THR      4.0     0.2    +      -       -      -
    797A  VAL*     1.3    73.1    +      -       -      +
    799A  ASN*     1.3    79.5    +      -       -      +
    800A  LEU*     3.4    21.7    +      -       -      +
    819A  LYS*     4.9    11.2    -      -       -      +
    820A  GLY      5.4     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 799 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    666A  ILE*     3.5    23.0    -      -       -      +
    788A  THR*     2.6    42.7    +      -       -      +
    791A  ALA*     3.5    18.6    -      -       -      +
    792A  ASN*     5.7     0.6    +      -       -      -
    798A  ASN*     1.3    86.2    +      -       -      +
    800A  LEU*     1.3    63.7    +      -       -      +
    820A  GLY*     2.7    32.2    +      -       -      -
    821A  VAL*     3.8    18.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 800 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    665A  HIS*     3.6    33.2    -      -       +      +
    666A  ILE      2.7    17.5    +      -       -      +
    667A  ILE*     3.2    10.1    -      -       +      -
    668A  THR*     2.9    26.2    +      -       -      -
    678A  TYR*     4.2    21.5    -      -       +      +
    779A  MET*     5.7     0.2    -      -       +      -
    798A  ASN*     3.4    16.6    -      -       -      +
    799A  ASN*     1.3    81.7    -      -       -      +
    801A  HIS*     1.3    59.5    +      -       -      +
    817A  VAL*     3.6    25.4    -      -       +      +
    818A  LYS      3.6    14.1    -      -       -      +
    819A  LYS*     3.9    17.0    -      -       +      -
    820A  GLY      3.3     5.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 801 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    668A  THR*     3.3    14.6    -      -       -      +
    669A  GLY*     5.4     0.2    -      -       -      -
    800A  LEU*     1.3    74.1    -      -       -      +
    802A  VAL*     1.3    68.9    +      -       -      +
    803A  THR*     3.6    29.2    -      -       +      +
    817A  VAL*     3.4    20.4    -      -       -      +
    818A  LYS*     3.3    39.8    +      -       +      +
    819A  LYS      3.7    14.4    +      -       -      -
    820A  GLY      2.6    29.4    +      -       -      +
    821A  VAL*     3.7    13.4    +      -       +      -
    822A  CYS*     4.0    29.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 802 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    667A  ILE*     4.5     7.0    -      -       +      -
    668A  THR      3.2    15.8    +      -       -      +
    669A  GLY*     4.1     8.6    -      -       -      -
    670A  PRO*     3.6    17.9    -      -       +      +
    673A  GLY*     3.3    37.0    -      -       -      +
    674A  GLY      4.6     3.1    -      -       -      +
    675A  LYS*     3.8    26.9    -      -       +      +
    801A  HIS*     1.3    85.5    -      -       -      +
    803A  THR*     1.3    73.3    +      -       -      +
    804A  ALA      4.2     0.2    +      -       -      -
    815A  TYR*     5.3     3.6    -      -       -      +
    816A  GLN      4.3     6.5    -      -       -      +
    817A  VAL*     5.1     8.1    -      -       +      -
    822A  CYS*     5.0     2.6    -      -       -      -
    826A  PHE*     4.5     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 803 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    801A  HIS*     3.6    27.1    -      -       +      +
    802A  VAL*     1.3    86.9    -      -       -      +
    804A  ALA*     1.3    65.7    +      -       -      +
    813A  MET*     4.2     2.3    -      -       -      +
    814A  LEU*     3.4    44.6    +      -       -      +
    815A  TYR      4.4     0.5    +      -       -      -
    816A  GLN*     3.6    13.9    +      -       -      +
    818A  LYS*     3.8    30.0    -      -       +      +
    822A  CYS*     5.6     2.5    -      -       -      -
    826A  PHE*     5.2     1.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 804 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    670A  PRO*     4.5     4.0    -      -       +      -
    803A  THR*     1.3    78.1    -      -       -      +
    805A  LEU*     1.3    68.7    +      -       -      +
    806A  THR      4.3     0.2    +      -       -      -
    811A  LEU*     4.1     9.2    -      -       +      -
    812A  THR      3.3    14.6    -      -       -      +
    813A  MET*     3.9    17.5    -      -       -      -
    814A  LEU*     4.4     5.1    -      -       -      +
    824A  GLN*     4.2     4.5    -      -       -      +
    826A  PHE*     3.4    40.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 805 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    804A  ALA*     1.3    78.0    -      -       -      +
    806A  THR*     1.3    64.2    +      -       -      +
    807A  THR*     5.2     0.6    +      -       -      -
    810A  THR*     3.7     1.4    -      -       -      +
    811A  LEU*     3.4     8.3    -      -       -      +
    812A  THR*     2.9    41.7    +      -       +      +
    814A  LEU*     3.8    34.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 806 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    804A  ALA      4.3     0.2    +      -       -      -
    805A  LEU*     1.3    78.0    -      -       -      +
    807A  THR*     1.3    69.0    +      -       -      +
    810A  THR      3.6     3.4    -      -       -      -
    811A  LEU*     3.8    10.3    -      -       +      -
    824A  GLN*     5.1     5.1    +      -       -      +
    826A  PHE*     3.6    33.4    -      -       +      -
    829A  HIS*     4.1    22.7    -      -       +      +
----------------------------------------------------------
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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