Contacts of the strand formed by residues 851 - 859 (chain A) in PDB entry 6Q6Q


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 851 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707A  ILE*     4.2     3.5    -      -       -      +
    743A  ILE      4.8     0.4    -      -       -      -
    744A  HIS*     3.8     1.7    +      -       -      +
    745A  MET*     2.9    42.0    +      -       +      +
    849A  HIS*     3.4     6.2    +      -       +      -
    850A  PRO*     1.3    77.7    -      -       -      +
    852A  LEU*     1.3    64.4    +      -       -      +
    872A  HIS*     3.9    34.3    +      +       +      -
    873A  TYR      3.2    11.0    -      -       -      -
    874A  SER*     3.8    15.3    -      -       -      -
    886A  VAL*     3.7    24.5    +      -       +      +
    887A  ILE*     3.3    24.7    -      -       +      +
    890A  GLY*     4.5     7.1    -      -       -      -
    924A  GLY      4.6     3.7    +      -       -      -
    927A  GLN*     3.4    59.0    -      -       +      +
    928A  ALA*     4.5     5.6    -      -       +      -
    931A  ILE*     5.4     7.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 852 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    707A  ILE*     3.7    37.5    -      -       +      -
    708A  GLU*     4.7    12.1    -      -       +      +
    711A  ILE*     6.4     0.7    -      -       +      -
    742A  GLU*     4.0    15.7    -      -       +      +
    743A  ILE      3.7    13.2    -      -       -      +
    744A  HIS*     3.4    39.9    -      -       +      +
    851A  TYR*     1.3    79.0    -      -       -      +
    853A  GLY*     1.3    63.1    +      -       -      +
    854A  LYS*     4.4    16.2    -      -       +      -
    871A  GLU      3.6     0.5    -      -       -      +
    872A  HIS*     3.7     0.7    -      -       -      -
    873A  TYR*     2.8    51.9    +      -       +      -
    931A  ILE*     5.0     0.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 853 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    742A  GLU*     3.2    23.0    -      -       -      -
    743A  ILE*     3.2    17.2    +      -       -      +
    851A  TYR*     5.8     0.2    -      -       -      -
    852A  LEU*     1.3    74.8    -      -       -      +
    854A  LYS*     1.3    62.8    +      -       -      -
    855A  TYR*     3.6     9.4    -      -       -      -
    870A  MET*     5.1     0.7    -      -       -      -
    871A  GLU      3.4     7.6    -      -       -      -
    872A  HIS*     4.9     4.3    -      -       -      -
    931A  ILE*     3.8    22.6    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 854 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    708A  GLU*     3.2    26.3    +      -       -      -
    711A  ILE*     5.5     3.2    -      -       -      +
    741A  GLY      3.7     5.4    -      -       -      +
    742A  GLU*     3.3    30.7    -      -       +      +
    852A  LEU*     4.1    15.7    +      -       +      -
    853A  GLY*     1.3    71.9    -      -       -      -
    855A  TYR*     1.3    64.0    +      -       -      +
    856A  LYS*     4.3    12.3    +      -       -      +
    870A  MET*     3.4     2.6    -      -       -      +
    871A  GLU*     2.8    60.3    +      -       +      +
    873A  TYR*     4.2    15.1    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 855 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    739A  LEU*     4.6    10.8    -      -       +      -
    740A  GLU*     3.5     1.2    -      -       -      +
    741A  GLY*     2.9    56.8    +      -       -      +
    742A  GLU*     3.8    17.0    +      -       -      -
    743A  ILE*     4.4     6.5    -      -       +      -
    853A  GLY      3.6    13.0    -      -       -      -
    854A  LYS*     1.3    74.7    -      -       -      +
    856A  LYS*     1.3    71.8    +      -       -      +
    857A  ALA      5.0     0.2    -      -       -      -
    868A  LEU*     4.2     3.4    -      -       +      -
    869A  ASP      3.2     8.5    -      -       -      +
    870A  MET*     3.5    24.0    -      -       +      -
    931A  ILE*     4.0    19.5    -      -       +      -
    934A  SER*     3.6     8.7    +      -       -      -
    935A  CYS*     3.5    33.7    -      -       +      -
    938A  GLU*     3.3    30.7    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LYS 856 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    732A  PHE*     3.4    19.9    -      -       +      -
    738A  ILE*     5.2     4.3    -      -       +      -
    739A  LEU      3.4     5.4    -      -       -      +
    740A  GLU*     3.6    33.7    -      -       +      +
    854A  LYS*     4.3    11.9    -      -       -      +
    855A  TYR*     1.3    87.1    -      -       -      +
    857A  ALA*     1.3    60.9    +      -       -      +
    868A  LEU*     3.4     2.0    -      -       -      -
    869A  ASP*     2.8    64.1    +      -       +      +
    871A  GLU*     3.6    28.1    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with ALA 857 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    732A  PHE*     3.8     3.3    -      -       -      -
    738A  ILE*     3.4     4.0    -      -       -      -
    739A  LEU*     2.9    36.5    +      -       +      +
    855A  TYR*     4.3     0.4    -      -       +      -
    856A  LYS*     1.3    72.1    -      -       -      +
    858A  GLY*     1.3    58.8    +      -       -      +
    859A  PHE*     3.4     7.0    -      -       +      -
    865A  ILE*     4.6     7.6    -      -       +      -
    867A  ALA      3.3     5.6    -      -       -      +
    868A  LEU*     3.9     7.0    -      -       +      -
    935A  CYS*     3.8    28.3    -      -       -      -
    939A  VAL*     4.2    17.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 858 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    732A  PHE*     3.4    17.2    -      -       -      -
    735A  VAL*     3.7    17.3    -      -       -      -
    737A  GLN      3.5     7.4    -      -       -      -
    738A  ILE*     4.6     0.2    -      -       -      -
    857A  ALA*     1.3    70.6    -      -       -      +
    859A  PHE*     1.3    63.1    +      -       -      +
    865A  ILE*     3.5     2.1    -      -       -      +
    866A  LEU      2.9    24.4    +      -       -      -
    867A  ALA*     2.4    22.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with PHE 859 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    735A  VAL*     3.7     4.1    -      -       -      +
    736A  ASP*     3.2     4.3    +      -       -      +
    737A  GLN*     3.0    61.9    +      -       +      +
    739A  LEU*     3.5    29.6    -      -       +      -
    857A  ALA*     3.4    15.5    -      -       +      -
    858A  GLY*     1.3    74.0    -      -       -      +
    860A  MET*     1.3    66.2    +      -       -      +
    863A  GLY*     5.1     1.1    -      -       -      +
    864A  ARG      3.3    15.9    -      -       -      +
    865A  ILE*     3.9    15.0    -      -       +      -
    866A  LEU      4.4     1.3    -      -       -      +
    939A  VAL*     4.0    24.7    -      -       +      -
    942A  LYS*     4.0    20.2    -      -       +      -
    943A  CYS*     3.5    33.9    -      -       -      -
----------------------------------------------------------
 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