Contacts of the strand formed by residues 76 - 83 (chain A) in PDB entry 1JNK


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 GLY 76 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72A  SER*     3.8     0.9    -      -       -      -
     73A  GLY*     3.0    26.5    +      -       -      -
     74A  ALA      3.5     2.8    -      -       -      +
     75A  GLN*     1.3    81.4    -      -       -      +
     77A  ILE*     1.3    65.2    +      -       -      -
     78A  VAL*     4.0     1.7    +      -       -      +
     93A  LYS*     4.6     9.4    -      -       -      -
     94A  LYS      3.1    14.6    -      -       -      -
     96A  SER*     5.1     1.6    -      -       -      -
   1001A  ANP      3.6     8.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 77 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  VAL*     5.3     6.3    -      -       +      +
     55A  ASP*     6.1     0.7    -      -       +      +
     56A  SER*     3.3    31.6    -      -       -      +
     58A  PHE*     3.4    24.5    -      -       +      -
     69A  PRO*     5.4     4.9    -      -       +      -
     71A  GLY      3.6    12.6    -      -       -      +
     72A  SER*     4.3    13.9    -      -       -      +
     76A  GLY*     1.3    75.6    -      -       -      -
     78A  VAL*     1.3    69.2    +      -       -      +
     79A  CYS*     5.2     4.3    -      -       -      -
     94A  LYS*     2.9    33.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 78 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     69A  PRO*     3.9     3.1    -      -       -      +
     70A  ILE*     3.0    34.0    +      -       +      -
     71A  GLY      2.9    23.8    +      -       -      +
     76A  GLY      4.4     3.8    -      -       -      +
     77A  ILE*     1.3    76.6    -      -       -      +
     79A  CYS*     1.3    66.3    +      -       -      +
     91A  ALA*     4.4     4.9    -      -       +      -
     92A  ILE      3.5    13.5    -      -       -      +
     93A  LYS*     3.7    22.2    -      -       +      -
    146A  MET*     4.5     0.7    -      -       +      -
   1001A  ANP      3.4    63.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 79 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53A  VAL*     3.2    44.4    -      -       -      -
     58A  PHE*     4.2    19.1    -      -       +      -
     67A  LEU*     4.0    14.4    -      -       +      -
     68A  LYS      3.3     4.7    -      -       -      +
     69A  PRO*     3.8    15.3    -      -       -      -
     70A  ILE*     4.0     4.0    -      -       -      -
     77A  ILE*     4.1     2.0    +      -       -      -
     78A  VAL*     1.3    74.3    -      -       -      +
     80A  ALA*     1.3    64.1    +      -       -      +
     91A  ALA*     3.4     4.0    -      -       -      +
     92A  ILE*     2.7    41.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 80 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     66A  ASN      3.4     1.6    -      -       -      +
     67A  LEU*     3.3     3.5    -      -       -      -
     68A  LYS*     2.7    38.0    +      -       +      +
     70A  ILE*     3.5    28.4    -      -       +      +
     79A  CYS*     1.3    73.3    -      -       -      +
     81A  ALA*     1.3    65.2    +      -       -      +
     89A  ASN*     5.4     1.1    -      -       -      +
     90A  VAL      3.5     5.4    -      -       -      -
    148A  LEU*     3.9    24.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 81 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64A  TYR*     4.5     2.0    -      -       +      -
     65A  GLN      3.6     3.6    -      -       -      +
     66A  ASN      3.5     6.1    -      -       -      -
     67A  LEU*     3.2    30.5    -      -       +      -
     80A  ALA*     1.3    75.8    -      -       -      +
     82A  TYR*     1.3    62.8    +      -       -      +
     89A  ASN*     3.0    13.0    +      -       -      +
     90A  VAL*     2.7    46.1    +      -       +      +
     92A  ILE*     3.8    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 82 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  ARG      3.1     2.6    -      -       -      +
     64A  TYR*     3.3     4.7    -      -       -      -
     65A  GLN*     2.7    75.3    +      -       +      +
     66A  ASN*     4.2     3.8    +      -       +      -
     81A  ALA*     1.3    74.0    -      -       -      +
     83A  ASP*     1.3    64.0    +      -       -      +
     84A  ALA*     3.8    21.7    +      -       +      -
     87A  ASP*     2.8    27.6    +      -       -      +
     88A  ARG*     3.6    30.1    -      -       -      -
     89A  ASN*     3.7    17.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 83 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     63A  ARG*     2.7    50.3    +      -       -      +
     64A  TYR*     3.6    18.8    +      -       +      -
     81A  ALA      4.1     0.4    +      -       -      -
     82A  TYR*     1.3    74.8    -      -       -      +
     84A  ALA*     1.3    51.6    +      -       -      +
     85A  VAL      3.2     8.8    +      -       -      -
     86A  LEU*     3.2    21.7    -      -       +      +
     87A  ASP*     2.7    36.2    +      -       -      -
     88A  ARG      2.8    19.8    +      -       -      +
     90A  VAL*     4.2    13.4    -      -       +      +
    127A  LEU*     5.6     0.3    -      -       -      +
    145A  VAL*     5.8     0.2    -      -       -      +
----------------------------------------------------------
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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