Contacts of the strand formed by residues 87 - 89 (chain A) in PDB entry 1JK7


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 87 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  LEU*     3.5     4.2    -      -       -      +
     60A  LYS*     3.3    31.0    -      -       +      -
     62A  CYS*     4.3     7.2    -      -       -      -
     75A  LEU*     5.0     1.6    -      -       +      -
     76A  PHE*     3.6    26.4    -      +       -      -
     79A  GLY*     3.2    20.8    -      -       -      -
     80A  GLY      2.6    31.5    +      -       -      -
     82A  PRO*     4.1    15.5    -      -       +      -
     85A  SER*     3.3    30.5    -      -       -      -
     86A  ASN*     1.3    73.4    -      -       -      +
     88A  LEU*     1.3    60.4    +      -       -      +
     89A  PHE*     3.8    30.1    -      +       +      -
    117A  ASN      3.2     7.7    +      -       -      -
    118A  PHE*     3.6    11.9    -      +       +      -
    119A  PHE*     2.8    32.2    +      -       -      -
    282A  MET*     4.0    13.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 88 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  LEU*     4.8     0.2    -      -       +      -
     55A  LEU*     4.0    19.5    -      -       +      -
     59A  LEU*     4.0    22.9    -      -       +      -
     60A  LYS      2.9     6.7    +      -       -      +
     61A  ILE*     3.2    11.8    -      -       +      +
     62A  CYS      3.0    23.2    +      -       -      -
     87A  TYR*     1.3    76.1    -      -       -      +
     89A  PHE*     1.3    75.9    +      -       -      +
     90A  LEU*     4.3     7.0    -      -       +      -
    119A  PHE*     3.4    22.7    -      -       +      +
    121A  LEU*     3.9    19.5    -      -       +      -
    163A  ALA*     4.1     6.3    -      -       +      -
    165A  VAL*     4.5     1.3    -      -       +      -
    171A  CYS*     3.9    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 89 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     62A  CYS*     3.6    35.9    -      -       +      -
     63A  GLY      4.7     0.7    -      -       -      +
     65A  ILE*     4.0    21.1    -      -       +      -
     72A  LEU*     3.7    19.5    -      -       +      -
     75A  LEU*     4.6     0.9    -      -       +      -
     76A  PHE*     3.8    18.6    -      +       -      -
     87A  TYR*     3.8    18.2    -      +       +      -
     88A  LEU*     1.3    79.3    -      -       -      +
     90A  LEU*     1.3    61.5    +      -       -      +
     91A  GLY      3.4     0.7    -      -       -      -
     93A  TYR*     3.5    22.9    -      +       +      +
    107A  LEU*     3.8    13.2    -      -       +      -
    118A  PHE*     3.7    22.7    -      +       -      -
    119A  PHE      3.0    10.1    +      -       -      -
    120A  LEU*     3.8    18.8    -      -       +      -
    121A  LEU*     3.0    29.8    +      -       -      +
----------------------------------------------------------
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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