Contacts of the strand formed by residues 863 - 870 (chain A) in PDB entry 4YOC


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 TYR 863 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    774A  LEU*     4.9    14.3    -      -       +      +
    776A  LEU*     3.8    29.5    -      -       +      +
    811A  PRO      4.1    17.3    -      -       -      -
    812A  LEU*     3.4    24.0    -      -       +      +
    814A  LEU*     3.9    21.1    -      -       +      -
    832A  VAL*     4.7    15.5    -      -       +      -
    833A  LYS      3.3    16.7    +      -       -      +
    834A  VAL*     3.3    16.7    -      -       +      -
    835A  ILE*     2.9    25.2    +      -       -      +
    862A  THR*     1.3    81.7    -      -       +      +
    864A  PHE*     1.3    60.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 864 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    810A  ASP*     3.7    21.1    -      -       +      -
    812A  LEU*     2.9    34.6    +      -       +      +
    813A  GLU*     3.5    37.9    -      -       +      -
    814A  LEU*     2.8    25.8    +      -       -      +
    834A  VAL*     4.5     2.5    -      -       -      -
    835A  ILE*     3.2    28.5    -      -       +      +
    837A  LYS*     4.2    41.5    -      -       +      -
    862A  THR      3.7    11.2    -      -       -      +
    863A  TYR*     1.3    75.2    -      -       -      +
    865A  TYR*     1.3    68.9    +      -       -      +
    866A  GLN*     4.8     3.4    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 865 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    778A  ARG*     4.6    23.7    +      -       -      -
    797A  PHE*     4.6     4.0    -      +       +      -
    813A  GLU*     5.1     0.7    -      -       -      -
    814A  LEU*     3.2    28.5    -      -       +      +
    815A  PHE*     4.7     0.7    -      -       -      +
    816A  LEU*     3.5    47.4    -      -       +      +
    834A  VAL*     3.8    16.8    -      -       +      -
    835A  ILE      2.9    26.1    +      -       -      -
    836A  TYR*     3.3    50.3    -      +       +      +
    837A  LYS      2.9    23.9    +      -       -      -
    864A  PHE*     1.3    77.8    -      -       -      +
    866A  GLN*     1.3    67.1    +      -       -      +
    867A  LEU      4.6     0.7    -      -       -      +
    879A  PRO*     4.8     1.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 866 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    813A  GLU*     3.0    27.4    +      -       -      +
    814A  LEU      4.3     1.8    +      -       -      -
    836A  TYR*     4.0    10.5    +      -       -      -
    837A  LYS*     3.4    37.9    -      -       +      +
    839A  PRO*     5.8     6.1    -      -       +      +
    864A  PHE*     4.8     5.5    -      -       +      -
    865A  TYR*     1.3    76.2    -      -       -      +
    867A  LEU*     1.3    81.2    +      -       +      +
    879A  PRO*     3.4    23.0    -      -       -      +
   1288A  VAL*     3.1    28.4    +      -       -      +
   1289A  ARG*     4.7     5.9    +      -       -      +
   1291A  GLY*     3.8    17.5    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 867 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    814A  LEU      4.4     0.2    -      -       -      +
    815A  PHE*     3.3    26.4    -      -       +      -
    816A  LEU*     3.2    24.8    +      -       -      +
    865A  TYR*     4.6     1.0    -      -       -      -
    866A  GLN*     1.3   100.9    -      -       +      +
    868A  TRP*     1.3    62.5    +      -       -      +
    876A  PHE*     4.0    18.2    -      -       +      -
    877A  GLU*     3.3    24.9    -      -       -      +
    878A  SER*     4.1     5.6    -      -       -      +
    879A  PRO*     4.6     0.9    -      -       +      -
   1288A  VAL*     4.0    27.6    -      -       +      +
   1291A  GLY      4.6     9.0    -      -       -      +
   1292A  TYR      3.3    26.7    -      -       -      +
   1293A  GLN*     4.6     5.8    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TRP 868 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    816A  LEU*     3.3    38.7    -      -       +      +
    817A  VAL*     3.8     9.0    -      -       -      +
    818A  ASP*     3.3    39.4    +      -       -      -
    867A  LEU*     1.3    73.8    -      -       -      +
    869A  TYR*     1.3    65.1    +      -       -      +
    870A  ASP*     3.6    42.0    -      -       +      -
    875A  ARG      3.5     0.5    -      -       -      +
    876A  PHE*     3.4     4.5    -      -       -      -
    877A  GLU*     2.9    68.1    +      -       +      +
    878A  SER      4.3     2.5    -      -       -      +
    879A  PRO*     4.4     4.1    -      -       +      -
    880A  PRO*     3.9    32.5    -      -       +      -
    898A  ARG*     3.5    21.9    -      -       -      +
    902A  MET*     5.6     3.6    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 869 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    798A  CYS*     4.5     2.7    -      -       -      -
    802A  ASP      4.8     1.6    +      -       -      -
    803A  THR*     3.6    29.1    -      -       +      -
    804A  VAL*     3.2    29.4    +      -       +      +
    815A  PHE*     3.8    21.3    -      -       +      -
    816A  LEU      2.7    11.8    +      -       -      +
    817A  VAL*     3.8    23.1    -      -       +      +
    868A  TRP*     1.3    82.6    -      -       -      +
    870A  ASP*     1.3    75.0    +      -       -      +
    871A  GLN*     3.6    35.5    +      -       +      +
    874A  ALA*     4.2     2.7    -      -       -      -
    875A  ARG      3.4     2.7    -      -       -      -
    876A  PHE*     3.5    42.8    -      +       +      -
   1348A  LYS*     5.9     0.2    -      -       -      +
   1350A  PHE*     3.5    15.8    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ASP 870 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    868A  TRP*     3.6    31.8    -      -       +      -
    869A  TYR*     1.3    74.8    -      -       -      +
    871A  GLN*     1.3    61.5    +      -       -      +
    872A  ASP*     3.2    19.4    +      -       -      +
    873A  TYR*     3.4    28.1    +      -       -      -
    874A  ALA*     3.0     9.7    +      -       -      -
    875A  ARG*     2.9    47.9    +      -       +      +
    877A  GLU*     5.2     0.2    -      -       -      +
    902A  MET*     6.0     1.7    -      -       -      +
----------------------------------------------------------
 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