Contacts of the strand formed by residues 94 - 98 (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 94 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18J  ILE*     4.5     4.9    -      -       -      +
     19J  THR*     3.2    11.4    -      -       -      +
     21J  ALA*     4.0     6.5    -      -       +      -
     73J  VAL*     3.6     4.4    -      -       -      +
     74J  VAL*     2.7    31.4    +      -       +      -
     75J  ARG*     2.8    61.7    +      -       +      +
     92J  ASP*     4.0     2.5    -      -       -      +
     93J  ASN*     1.3    76.5    -      -       -      +
     95J  ALA*     1.3    57.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 95 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18J  ILE*     3.5    24.2    -      -       +      +
     19J  THR      2.9     5.7    +      -       -      -
     20J  CYS*     3.3     8.7    -      -       -      -
     21J  ALA      2.9    21.7    +      -       -      -
     29J  LEU*     4.0    13.2    -      -       +      +
     53J  ILE*     4.6     3.6    -      -       +      -
     71J  ALA*     4.2     8.7    -      -       +      -
     72J  VAL      3.1    20.0    -      -       -      +
     73J  VAL*     4.1     2.7    -      -       -      -
     74J  VAL      4.1     0.9    -      -       -      +
     94J  ALA*     1.3    75.5    -      -       -      +
     96J  VAL*     1.3    65.0    +      -       -      +
     97J  ILE      4.3     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 96 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21J  ALA*     3.5    25.6    -      -       +      +
     22J  ASP*     3.7    11.7    -      -       +      +
     71J  ALA*     3.3     3.1    -      -       -      -
     72J  VAL*     2.9    30.3    +      -       +      +
     74J  VAL*     3.7    23.1    -      -       +      -
     95J  ALA*     1.3    77.7    -      -       -      +
     97J  ILE*     1.3    73.2    -      -       -      +
     98J  VAL*     3.4     3.3    +      -       +      +
    104J  PRO*     4.2    11.4    -      -       +      -
    106J  GLY      6.0     0.2    -      -       -      +
    109J  LEU*     3.4    35.2    -      -       +      -
    113J  ILE*     4.8     1.3    -      -       +      -
    124J  VAL*     4.9    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 97 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     20J  CYS*     3.7    13.0    -      -       -      -
     22J  ASP*     3.1    12.2    +      -       -      +
     24J  THR*     3.4    22.7    -      -       -      +
     26J  ALA*     3.8    13.5    -      -       +      -
     29J  LEU*     4.3    14.1    -      -       +      -
     64J  MET*     3.7    18.6    -      -       +      -
     69J  LEU*     3.9    23.6    -      -       +      -
     70J  GLU      3.5    14.4    -      -       -      +
     71J  ALA*     3.9     2.2    -      -       +      -
     95J  ALA      4.3     0.2    +      -       -      -
     96J  VAL*     1.3    73.3    -      -       -      +
     98J  VAL*     1.3    67.3    +      -       -      +
    104J  PRO*     3.5     6.9    -      -       -      +
    105J  ARG*     2.9    45.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 98 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     52J  LYS*     4.5    16.8    -      -       +      -
     69J  LEU*     5.3     0.5    -      -       -      +
     70J  GLU*     2.9    41.1    +      -       +      +
     71J  ALA*     4.4     4.7    -      -       -      +
     72J  VAL*     4.7     9.4    -      -       +      -
     96J  VAL*     3.4     6.4    +      -       +      +
     97J  ILE*     1.3    80.8    -      -       -      +
     99J  ASP*     1.3    70.7    +      -       -      +
    102J  GLU*     3.1    41.3    -      -       +      +
    103J  ASP      3.6     9.6    -      -       -      +
    104J  PRO*     4.0     2.2    -      -       +      -
    105J  ARG*     4.3     3.1    -      -       -      +
    124J  VAL*     4.1    13.7    -      -       +      -
----------------------------------------------------------
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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