Contacts of the strand formed by residues 52 - 60 (chain J) in PDB entry 1JJ2


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 LYS 52 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1J  MET*     4.9    11.5    -      -       +      +
     34J  VAL*     3.8     1.9    -      -       -      +
     35J  HIS*     2.8    68.0    +      -       +      +
     50J  GLY      3.9     1.6    +      -       -      -
     51J  ASP*     1.3    72.5    -      -       -      +
     53J  ILE*     1.3    60.1    +      -       -      +
     70J  GLU*     4.1    31.6    +      -       +      -
     71J  ALA      3.3    15.3    -      -       -      +
     72J  VAL*     4.3    11.9    -      -       +      -
     98J  VAL*     4.5    13.2    -      -       +      -
     99J  ASP      5.6     0.4    +      -       -      -
    100J  GLU      5.0     5.3    +      -       -      -
    102J  GLU*     3.1    32.8    +      -       +      +
    121J  PHE*     4.5     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 53 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12J  LEU*     5.5     0.4    -      -       +      -
     18J  ILE*     4.1    12.1    -      -       +      -
     31J  VAL*     4.0    24.2    -      -       +      -
     33J  SER      3.1    13.9    -      -       -      +
     34J  VAL*     4.4     2.5    -      -       +      -
     35J  HIS*     4.4     0.9    -      -       -      +
     47J  ALA*     3.7    28.9    -      -       +      -
     51J  ASP*     4.1     5.6    -      -       +      +
     52J  LYS*     1.3    79.0    -      -       -      +
     54J  THR*     1.3    61.2    +      -       -      +
     55J  VAL*     3.4    23.8    -      -       +      -
     70J  GLU*     3.6     5.2    -      -       -      +
     71J  ALA      2.9    37.0    +      -       -      +
     73J  VAL*     3.8    26.7    -      -       +      -
     95J  ALA*     4.6     4.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 54 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   25960    A      3.7    32.3    -      -       -      +
   25970    U      2.9    27.1    +      -       -      +
     31J  VAL*     3.9     1.0    -      -       -      -
     32J  ILE*     3.0    27.1    +      -       +      -
     33J  SER*     2.7    15.1    +      -       -      +
     35J  HIS      5.1     0.8    +      -       -      +
     53J  ILE*     1.3    70.9    -      -       -      +
     55J  VAL*     1.3    73.2    +      -       -      +
     68J  VAL*     3.7    19.5    -      -       +      -
     69J  LEU      3.5    11.7    -      -       -      +
     70J  GLU*     4.4    10.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 55 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29J  LEU*     3.3    39.9    -      -       +      -
     30J  LYS      2.9    21.3    -      -       -      +
     31J  VAL*     4.5     1.1    -      -       +      -
     32J  ILE*     4.0     5.2    -      -       -      -
     53J  ILE*     3.4    35.9    -      -       +      +
     54J  THR*     1.3    83.8    -      -       -      +
     56J  SER*     1.3    72.0    +      -       -      +
     57J  VAL*     6.0     0.4    -      -       -      -
     68J  VAL*     3.2     6.9    -      -       -      +
     69J  LEU*     2.6    42.2    +      -       +      +
     71J  ALA*     4.1    13.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 56 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19930    C      2.8    39.2    +      -       -      -
     29J  LEU*     3.5     0.9    -      -       -      -
     30J  LYS*     2.9    44.3    +      -       -      +
     32J  ILE*     3.6    16.6    -      -       -      -
     55J  VAL*     1.3    81.4    -      -       -      +
     57J  VAL*     1.3    63.2    +      -       -      +
     58J  THR*     3.5     1.4    +      -       -      -
     66J  ARG      5.0     0.9    -      -       -      -
     67J  GLN      3.3     9.2    -      -       -      -
     68J  VAL*     4.5     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 57 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19930    C      5.0     3.9    +      -       -      -
     26J  ALA*     3.7    22.4    -      -       +      -
     28J  GLU      3.7     4.7    -      -       -      +
     29J  LEU*     3.7    19.1    -      -       +      -
     55J  VAL      6.0     0.2    -      -       -      -
     56J  SER*     1.3    72.9    +      -       -      +
     58J  THR*     1.3    60.5    +      -       -      +
     59J  LYS      3.2    29.2    -      -       -      +
     64J  MET*     3.3    29.2    -      -       +      +
     65J  ARG*     3.9     7.8    -      -       -      +
     66J  ARG*     3.0    25.1    +      -       -      +
     67J  GLN      3.1    13.0    +      -       -      +
     69J  LEU*     4.2    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 58 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19930    C      4.7     1.7    +      -       -      -
     17J  LEU*     4.1     5.6    -      -       +      +
     28J  GLU*     2.9    41.5    +      -       -      +
     30J  LYS*     3.7    33.8    +      -       -      +
     56J  SER*     3.5     2.7    +      -       -      -
     57J  VAL*     1.3    74.5    -      -       -      +
     59J  LYS*     1.3    68.8    +      -       +      +
     65J  ARG*     3.9    14.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 59 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27J  ARG*     2.8    31.4    +      -       +      -
     28J  GLU*     3.3    47.6    +      -       +      +
     57J  VAL*     3.2    14.3    -      -       -      +
     58J  THR*     1.3    89.7    -      -       +      +
     60J  GLY*     1.3    59.2    +      -       -      +
     65J  ARG*     4.4     3.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 60 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25J  GLY      3.3    12.3    -      -       -      -
     26J  ALA*     4.4     0.7    -      -       -      -
     27J  ARG*     4.0    18.0    -      -       -      +
     57J  VAL*     4.9     1.3    -      -       -      -
     59J  LYS*     1.3    76.3    -      -       -      +
     61J  THR*     1.3    66.8    +      -       -      -
     62J  PRO*     3.5     2.9    -      -       -      +
     65J  ARG*     3.4    19.5    +      -       -      +
----------------------------------------------------------
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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