Contacts of the strand formed by residues 1046 - 1055 (chain A) in PDB entry 2OOQ


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 TYR1046 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1043A  LEU*     2.8    71.0    +      -       +      +
   1044A  ALA      3.6     0.6    -      -       -      -
   1045A  GLU*     1.3    89.4    -      -       +      +
   1047A  VAL*     1.3    58.7    +      -       -      +
   1048A  ILE*     4.2    14.6    -      -       +      -
   1068A  HIS      3.1    15.3    -      -       -      +
   1069A  PHE*     3.7     4.0    -      +       +      -
   1070A  THR*     3.8     6.0    +      -       -      -
   1083A  GLY*     4.2     8.3    -      -       -      -
   1086A  GLY*     4.1     5.7    +      -       -      -
   1087A  PHE*     3.5    49.6    -      +       +      -
   1090A  GLN*     2.8    41.4    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1047 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1040A  THR*     3.5    32.3    -      -       +      -
   1041A  GLU      3.4    13.7    -      -       -      +
   1042A  PRO*     4.0     9.2    -      -       +      -
   1046A  TYR*     1.3    74.7    -      -       -      +
   1048A  ILE*     1.3    68.5    +      -       -      +
   1049A  ARG*     3.5    35.0    -      -       +      +
   1066A  LEU      3.5     2.4    -      -       -      +
   1068A  HIS*     2.9    46.4    +      -       +      +
   1070A  THR*     4.5     7.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE1048 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  B3P      3.9    22.1    +      -       -      +
   1039A  GLU*     3.9     1.0    -      -       -      +
   1040A  THR*     3.5     1.6    -      -       -      -
   1041A  GLU*     2.7    58.6    +      -       +      +
   1046A  TYR*     4.2    15.0    -      -       +      -
   1047A  VAL*     1.3    75.2    -      -       -      +
   1049A  ARG*     1.3    66.7    +      -       -      +
   1050A  THR*     4.5     1.5    +      -       -      +
   1065A  ARG*     4.3    16.2    -      -       +      -
   1066A  LEU      3.4     7.9    -      -       -      +
   1067A  PHE*     3.9    35.4    -      -       +      -
   1090A  GLN*     3.9    31.6    -      -       -      +
   1094A  LEU*     4.3     4.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ARG1049 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1023A  TRP*     3.7    45.7    -      -       -      +
   1037A  LEU*     4.0     9.9    -      -       +      -
   1039A  GLU      3.3     5.8    -      -       -      +
   1040A  THR*     4.0    22.1    +      -       +      +
   1047A  VAL*     3.5    26.1    -      -       +      +
   1048A  ILE*     1.3    78.1    -      -       -      +
   1050A  THR*     1.3    63.2    +      -       -      +
   1051A  PHE*     3.8    19.5    -      -       +      -
   1065A  ARG*     3.3     2.9    -      -       -      +
   1066A  LEU*     2.8    45.3    +      -       +      +
   1068A  HIS*     3.5    30.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with THR1050 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    301A  B3P      2.6    37.9    +      -       -      +
   1037A  LEU*     3.6     4.2    -      -       -      +
   1038A  ILE*     2.9    37.5    +      -       +      -
   1039A  GLU*     2.9    21.3    +      -       +      +
   1048A  ILE*     4.5     1.4    +      -       -      +
   1049A  ARG*     1.3    77.5    -      -       -      +
   1051A  PHE*     1.3    63.7    +      -       -      +
   1063A  GLU*     3.7    35.9    -      -       +      +
   1064A  LEU      3.4     5.8    -      -       -      +
   1065A  ARG*     3.8     8.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE1051 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    994A  TRP*     5.3     1.8    -      +       -      -
   1023A  TRP*     3.6    26.9    -      +       +      -
   1024A  PRO*     3.6    21.8    -      -       +      -
   1035A  VAL*     3.5    22.9    -      -       +      -
   1036A  THR      3.1     7.6    -      -       -      +
   1037A  LEU*     3.5    34.1    -      -       +      -
   1038A  ILE*     4.2     5.4    -      -       -      +
   1049A  ARG*     3.8    35.7    -      -       +      -
   1050A  THR*     1.3    73.1    -      -       -      +
   1052A  THR*     1.3    69.9    +      -       -      +
   1053A  VAL*     4.5     5.2    -      -       +      -
   1063A  GLU*     3.4     6.6    -      -       -      +
   1064A  LEU*     2.8    49.8    +      -       +      +
   1066A  LEU*     3.9    16.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with THR1052 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   1034A  LYS      3.6     1.6    +      -       -      +
   1035A  VAL*     3.3     5.0    -      -       -      -
   1036A  THR*     2.9    51.7    +      -       -      +
   1038A  ILE*     4.0    26.3    -      -       +      +
   1051A  PHE*     1.3    76.5    -      -       -      +
   1053A  VAL*     1.3    61.8    +      -       -      +
   1061A  ILE*     3.8    23.5    -      -       +      +
   1062A  ARG      3.2     6.3    -      -       -      +
   1063A  GLU*     5.4     2.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL1053 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    994A  TRP*     4.2    20.0    -      -       +      -
    997A  ILE*     5.2     5.2    -      -       +      -
    998A  TRP*     3.5    22.3    -      -       +      -
   1033A  ILE*     3.3    31.9    -      -       +      -
   1034A  LYS      3.4     3.4    -      -       -      -
   1035A  VAL*     4.3     4.9    -      -       +      -
   1051A  PHE*     4.5     5.8    -      -       +      -
   1052A  THR*     1.3    80.7    -      -       -      +
   1054A  GLN*     1.3    61.6    +      -       -      +
   1061A  ILE*     3.6     1.7    -      -       -      -
   1062A  ARG*     2.8    39.6    +      -       +      +
   1064A  LEU*     3.8    30.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN1054 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    998A  TRP*     3.8     7.6    -      -       -      -
   1033A  ILE*     3.6     2.2    -      -       -      -
   1034A  LYS*     2.8    60.6    +      -       +      +
   1053A  VAL*     1.3    77.0    -      -       -      +
   1055A  LYS*     1.3    72.6    +      -       -      +
   1056A  LYS*     3.5     6.3    +      -       -      +
   1057A  GLY      5.3     1.0    -      -       -      +
   1058A  TYR      2.9    21.3    +      -       -      +
   1059A  HIS*     4.4     5.7    +      -       -      +
   1060A  GLU      3.5    13.9    -      -       -      +
   1061A  ILE*     3.9    29.6    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS1055 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    995A  ARG*     5.7     7.5    -      -       -      +
    998A  TRP*     3.7    48.3    -      -       +      +
   1032A  ASP*     2.7    40.8    +      -       -      +
   1033A  ILE*     3.8    12.9    -      -       +      +
   1054A  GLN*     1.3    71.7    -      -       -      +
   1056A  LYS*     1.3    69.8    +      -       -      +
   1058A  TYR*     3.1    56.6    +      -       +      +
   1060A  GLU      4.5     0.2    +      -       -      -
----------------------------------------------------------
 Back to top of page


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