Contacts of the strand formed by residues 87 - 98 (chain A) in PDB entry 5J6Y


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 ASP 87 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  GLY*     3.4     3.1    -      -       -      -
     24A  THR*     2.9    36.8    +      -       +      +
     26A  SER      3.2    19.5    -      -       -      +
     27A  GLN*     3.0     1.7    -      -       -      +
     28A  LEU*     3.0    26.6    +      -       +      -
     62A  ALA*     3.5    10.2    -      -       -      +
     86A  THR*     1.3   100.0    +      -       -      +
     88A  GLY*     1.3    58.2    +      -       -      +
    155A  ASP*     3.5     8.7    -      -       -      +
    156A  GLN*     3.2    13.8    -      -       -      +
    302A   CA      2.4    31.6    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  TYR*     4.0    13.5    -      -       -      -
     22A  TYR      3.1    13.2    -      -       -      -
     23A  GLY*     4.0     0.4    -      -       -      -
     24A  THR      4.7     0.2    -      -       -      -
     28A  LEU*     3.9    10.5    -      -       -      +
     61A  VAL*     4.0     7.1    -      -       -      +
     62A  ALA*     4.1     3.4    -      -       -      +
     87A  ASP*     1.3    76.3    -      -       -      +
     89A  GLY*     1.3    58.5    +      -       -      -
    154A  TRP*     3.4     1.2    -      -       -      +
    155A  ASP*     2.8    34.7    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  TYR*     3.2    10.5    -      -       -      -
     22A  TYR      2.9    31.7    +      -       -      -
     34A  PHE*     3.3    15.8    -      -       -      -
     88A  GLY*     1.3    74.6    -      -       -      -
     90A  ILE*     1.3    63.9    +      -       -      -
    153A  TRP*     3.1    21.5    -      -       -      -
    154A  TRP*     3.8     2.0    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 90 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20A  GLU      3.2     9.0    -      -       -      +
     21A  TYR*     4.3    10.3    -      -       +      -
     34A  PHE*     3.3     8.0    -      -       -      -
     47A  PHE*     4.0    22.2    -      -       +      -
     54A  TYR*     3.9    33.9    -      -       +      -
     67A  LEU*     4.8     5.2    -      -       +      -
     70A  PHE*     4.5     7.4    -      -       +      -
     71A  LEU*     4.9     0.2    -      -       +      -
     89A  GLY*     1.3    79.3    -      -       -      +
     91A  TYR*     1.3    59.5    +      -       -      +
     92A  LEU*     4.1    22.4    -      -       +      -
    151A  MET*     6.2     0.2    -      -       +      -
    152A  ILE*     3.2     5.8    -      -       -      -
    153A  TRP*     2.9    60.5    +      -       +      +
    162A  PHE*     4.4     9.9    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 91 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  VAL      3.6     2.4    -      -       -      +
     19A  GLY*     3.6     0.2    -      -       -      -
     20A  GLU*     2.9    62.6    +      -       +      +
     22A  TYR*     4.7     0.7    -      -       +      -
     34A  PHE*     4.3     0.2    -      -       -      -
     35A  ARG*     5.4     4.7    -      -       -      -
     38A  VAL*     4.2    29.6    -      -       +      -
     90A  ILE*     1.3    73.4    -      -       -      +
     92A  LEU*     1.3    74.2    +      -       -      +
     93A  GLN*     3.7    27.5    -      -       +      +
    150A  ASP*     4.1    17.4    +      -       +      +
    151A  MET      3.3    10.3    -      -       -      -
    152A  ILE*     3.9    17.3    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 92 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  LEU*     3.9    14.8    -      -       +      -
     18A  VAL      3.2     3.8    -      -       -      +
     19A  GLY*     3.7    18.2    -      -       -      -
     47A  PHE*     3.7    19.7    -      -       +      -
     49A  ALA*     3.9    12.8    -      -       +      -
     52A  ILE*     3.9    34.5    -      -       +      -
     54A  TYR*     4.6     1.6    -      -       +      -
     90A  ILE*     4.1    22.0    -      -       +      -
     91A  TYR*     1.3    82.5    -      -       -      +
     93A  GLN*     1.3    60.3    +      -       -      +
    150A  ASP*     3.1     7.0    -      -       -      +
    151A  MET*     2.8    55.4    +      -       +      +
    162A  PHE*     4.9     0.7    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with GLN 93 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  LEU*     4.0     5.1    -      -       -      +
     18A  VAL*     2.8    63.8    +      -       +      +
     91A  TYR*     3.7    32.8    -      -       +      +
     92A  LEU*     1.3    77.4    -      -       -      +
     94A  GLY*     1.3    64.9    +      -       -      +
     95A  TYR*     5.6     2.1    -      -       -      -
    149A  ILE      3.5     5.6    -      -       -      +
    150A  ASP*     4.0     8.5    -      -       +      -
    184A  SER      4.9     2.6    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with GLY 94 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  LEU*     3.6     9.5    -      -       -      +
     93A  GLN*     1.3    83.2    +      -       -      +
     95A  TYR*     1.3    81.2    +      -       -      -
    148A  ALA*     3.6     3.5    -      -       -      +
    149A  ILE*     2.9    27.3    +      -       -      +
    183A  SER      3.9     4.0    -      -       -      -
    184A  SER*     3.9     7.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 95 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4A  ALA      3.6    19.3    +      -       -      -
     17A  LEU*     3.5     8.0    -      -       -      +
     93A  GLN*     5.6     2.0    -      -       -      -
     94A  GLY*     1.3    83.9    -      -       -      -
     96A  VAL*     1.3    61.6    +      -       -      +
    146A  TYR*     4.0    25.6    -      -       +      -
    147A  GLN      3.1    19.5    -      -       -      +
    148A  ALA*     3.8    18.7    -      -       +      +
    149A  ILE*     3.9     3.4    -      -       -      -
    182A  LEU*     3.4     4.7    -      -       -      -
    183A  SER      2.9    35.8    +      -       -      +
    184A  SER      3.9     3.6    -      -       -      -
    185A  THR*     3.4    22.2    -      -       -      -
    186A  GLY*     3.3    26.2    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 96 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  TYR*     1.3    75.3    -      -       -      +
     97A  TYR*     1.3    68.6    +      -       -      +
     98A  LEU*     3.3    25.1    +      -       +      -
    117A  ILE*     4.8     3.1    -      -       +      -
    146A  TYR*     3.9     2.5    -      -       -      -
    147A  GLN*     2.8    45.1    +      -       +      +
    149A  ILE*     3.9    27.1    -      -       +      -
    166A  LEU*     5.6     0.4    -      -       +      -
    177A  LEU*     4.2     9.6    -      -       +      -
    181A  ILE*     3.5    36.1    -      -       +      +
    182A  LEU*     4.0    13.2    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 97 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  VAL*     1.3    70.2    -      -       -      +
     98A  LEU*     1.3    81.5    +      -       -      +
     99A  GLU*     4.3    16.2    -      -       +      +
    144A  SER*     4.5     8.0    -      -       -      -
    145A  GLY*     3.5    34.5    +      -       -      -
    146A  TYR*     3.6    31.9    -      +       +      +
    181A  ILE*     2.8    44.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 98 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  VAL*     3.3    25.5    +      -       +      +
     97A  TYR*     1.3    85.9    -      -       -      +
     99A  GLU*     1.3    64.2    +      -       -      +
    103A  TYR*     3.7    32.3    -      -       +      +
    117A  ILE*     4.4    13.2    -      -       +      -
    139A  PHE*     4.8     0.7    -      -       +      -
    141A  ILE*     4.0    22.9    -      -       +      -
    145A  GLY      3.0    30.5    +      -       -      +
    147A  GLN*     3.4    22.0    +      -       +      -
    166A  LEU*     3.9    22.7    -      -       +      -
    175A  PHE*     4.9     3.6    -      -       +      -
    181A  ILE*     4.7     5.4    -      -       +      -
----------------------------------------------------------
 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