Contacts of the strand formed by residues 26 - 34 (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 ALA 26 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20J  CYS*     3.0    28.0    -      -       -      +
     22J  ASP*     4.3     5.0    -      -       -      +
     24J  THR*     3.4    14.5    +      -       -      +
     25J  GLY*     1.3    78.9    +      -       -      +
     27J  ARG*     1.3    60.3    +      -       -      +
     29J  LEU*     4.3     2.9    -      -       +      -
     57J  VAL*     3.7    27.8    -      -       +      -
     59J  LYS      3.7     4.9    -      -       -      -
     64J  MET*     4.0     6.7    -      -       +      +
     97J  ILE*     3.8    18.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 27 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19J  THR*     3.8     8.5    -      -       -      +
     20J  CYS*     2.9    26.3    +      -       -      +
     25J  GLY      4.7     3.4    -      -       -      +
     26J  ALA*     1.3    77.0    -      -       -      +
     28J  GLU*     1.3    57.1    +      -       +      +
     59J  LYS*     2.8    21.9    +      -       +      +
     60J  GLY*     4.1    17.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 28 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17J  LEU*     3.5    32.2    -      -       +      +
     18J  ILE      3.6     9.4    -      -       -      +
     19J  THR*     5.0     0.2    -      -       -      +
     27J  ARG*     1.3    80.9    -      -       +      +
     29J  LEU*     1.3    70.3    +      -       -      +
     57J  VAL*     3.7     6.4    -      -       -      +
     58J  THR*     2.9    54.9    +      -       -      +
     59J  LYS*     3.3    44.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 29 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16J  SER      3.6     0.5    -      -       -      +
     17J  LEU*     3.3     4.2    -      -       -      +
     18J  ILE*     2.8    49.3    +      -       +      +
     19J  THR      4.4     1.6    -      -       -      +
     20J  CYS*     3.5    43.1    -      -       +      -
     26J  ALA*     4.3     3.4    -      -       +      -
     28J  GLU*     1.3    81.2    -      -       -      +
     30J  LYS*     1.3    59.3    +      -       -      +
     31J  VAL      4.1     0.2    -      -       -      -
     55J  VAL*     3.3    23.8    -      -       +      -
     56J  SER      3.5     1.6    -      -       -      -
     57J  VAL*     3.7    29.6    -      -       +      -
     58J  THR*     4.8     0.2    -      -       -      -
     69J  LEU*     6.1     0.7    -      -       +      -
     71J  ALA*     4.7     5.2    -      -       +      -
     95J  ALA*     4.0    24.5    -      -       +      +
     97J  ILE*     4.3    12.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 30 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19920    U      3.2    15.8    +      -       -      -
   19930    C      2.8    44.1    +      -       +      +
   19940    A      5.7     0.4    -      -       -      +
     15J  GLY*     4.1    13.9    -      -       -      +
     16J  SER      3.3     4.5    -      -       -      -
     17J  LEU*     3.6    21.1    -      -       +      -
     29J  LEU*     1.3    72.5    -      -       -      +
     31J  VAL*     1.3    74.1    +      -       -      +
     32J  ILE*     3.5     2.2    +      -       +      +
     55J  VAL*     2.9    16.1    -      -       -      +
     56J  SER*     2.9    31.9    +      -       -      +
     58J  THR*     3.7    13.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 31 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19930    C      5.1     1.4    +      -       -      -
     12J  LEU*     4.7     9.2    -      -       +      -
     13J  GLU      3.5    25.1    -      -       -      +
     14J  LYS*     4.2     5.6    -      -       -      +
     15J  GLY*     2.7    27.4    +      -       -      -
     16J  SER*     2.9    22.0    +      -       -      +
     18J  ILE*     4.2    15.5    -      -       +      -
     29J  LEU      4.1     0.2    -      -       -      -
     30J  LYS*     1.3    76.6    -      -       -      +
     32J  ILE*     1.3    62.1    +      -       -      +
     33J  SER      4.0    16.4    -      -       -      +
     34J  VAL*     5.0     1.8    -      -       +      -
     47J  ALA*     4.9     7.6    -      -       +      -
     53J  ILE*     4.0    31.0    -      -       +      -
     54J  THR      4.0     4.0    -      -       -      +
     55J  VAL*     4.4     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 32 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   19930    C      3.4    66.2    -      -       +      +
   25960    A      3.3    24.5    -      -       -      +
     14J  LYS*     2.6    42.8    +      -       -      +
     30J  LYS*     3.7    10.3    -      -       +      +
     31J  VAL*     1.3    79.9    -      -       -      +
     33J  SER*     1.3    60.5    +      -       -      +
     54J  THR*     3.0    11.2    +      -       +      +
     55J  VAL*     4.0     5.6    -      -       -      +
     56J  SER*     3.6    25.4    -      -       -      +
     68J  VAL*     4.5    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 33 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   25960    A      2.5    32.9    +      -       -      +
   25970    U      3.2    29.1    +      -       -      -
   85120   CL      3.2    14.5    -      -       -      +
     14J  LYS*     5.4     1.6    -      -       -      -
     31J  VAL*     4.0     2.8    -      -       -      +
     32J  ILE*     1.3    85.8    +      -       -      +
     34J  VAL*     1.3    65.4    +      -       -      +
     45J  PRO*     5.8     0.9    -      -       -      -
     53J  ILE*     3.1     8.3    -      -       -      +
     54J  THR*     2.7    33.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 34 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
   25970    U      2.8    22.9    +      -       -      -
     13J  GLU      6.3     0.2    -      -       -      -
     14J  LYS*     6.0     0.7    -      -       -      +
     31J  VAL*     5.0     4.5    -      -       +      -
     33J  SER*     1.3    79.7    -      -       -      +
     35J  HIS*     1.3    69.9    +      -       -      +
     37J  TYR*     3.2    29.5    +      -       +      +
     45J  PRO*     4.7     9.7    -      -       +      +
     46J  LYS      3.3    33.9    -      -       -      +
     47J  ALA*     3.3    24.0    -      -       +      -
     51J  ASP*     4.2    23.6    -      -       +      +
     52J  LYS      4.0     2.5    -      -       -      +
     53J  ILE*     4.3     1.6    -      -       +      +
----------------------------------------------------------
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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