Contacts of the strand formed by residues 96 - 100 (chain S) 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 VAL 96 (chain S).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3420    C      4.9     1.6    +      -       -      -
     25S  ALA*     3.5    19.1    -      -       +      +
     26S  THR*     3.9     9.7    +      -       -      +
     42S  VAL*     4.8     1.3    -      -       +      -
     48S  VAL*     3.2    44.0    -      -       +      -
     49S  GLU      3.6     5.8    -      -       -      +
     50S  VAL*     4.1    15.5    -      -       +      -
     51S  LEU*     4.6     4.8    -      -       -      +
     72S  ILE*     4.5    14.6    -      -       +      -
     91S  LEU*     4.3    14.4    -      -       +      -
     92S  ASP      4.7     4.0    -      -       -      +
     93S  THR*     3.0    21.4    +      -       -      +
     94S  SER      3.3     3.0    -      -       -      +
     95S  ASN*     1.3    85.2    -      -       +      +
     97S  ARG*     1.3    65.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 97 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    3080    U      3.0    26.9    +      -       -      -
    3090    C      2.5    31.3    +      -       -      -
     26S  THR*     3.4    22.5    -      -       +      +
     27S  LEU      4.4     0.6    +      -       -      -
     28S  SER*     4.0    25.2    -      -       -      +
     29S  ALA      5.7     2.5    -      -       -      +
     32S  ARG*     5.2     2.0    -      -       -      +
     48S  VAL*     3.1     7.0    -      -       -      +
     49S  GLU*     2.4    80.8    +      -       +      +
     51S  LEU*     3.7    24.1    -      -       +      +
     96S  VAL*     1.3    77.7    -      -       -      +
     98S  VAL*     1.3    69.8    +      -       -      +
     99S  THR*     3.5     1.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 98 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25S  ALA*     4.1     5.8    -      -       +      -
     26S  THR      3.0     7.4    +      -       -      +
     27S  LEU*     3.7    13.0    -      -       +      -
     28S  SER*     3.1    24.1    +      -       -      -
     31S  LEU*     3.3     7.6    -      -       +      +
     40S  VAL*     3.9    19.3    -      -       +      -
     42S  VAL*     4.0    17.7    -      -       +      -
     46S  ASP*     4.1     7.0    -      -       +      +
     47S  THR      3.8     2.7    -      -       -      +
     48S  VAL*     3.5    17.9    -      -       +      -
     97S  ARG*     1.3    71.4    -      -       -      +
     99S  THR*     1.3    58.9    +      -       -      +
    100S  ASP      3.4    26.9    -      -       -      +
    101S  LEU*     3.5    24.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 99 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28S  SER*     4.1    11.0    +      -       -      -
     31S  LEU*     3.6    16.9    -      -       -      +
     47S  THR*     3.1    27.0    +      -       -      +
     49S  GLU*     3.6    42.8    -      -       +      +
     59S  GLU*     3.4    12.2    +      -       -      +
     97S  ARG*     3.9     7.2    -      -       -      +
     98S  VAL*     1.3    75.5    -      -       -      +
    100S  ASP*     1.3    64.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 100 (chain S). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31S  LEU*     4.4     2.7    -      -       -      -
     45S  GLY      5.6     1.0    -      -       -      +
     46S  ASP*     3.2     9.0    -      -       -      +
     47S  THR*     3.0    45.5    +      -       +      -
     98S  VAL*     3.4     3.9    -      -       -      +
     99S  THR*     1.3    84.6    +      -       -      +
    101S  LEU*     1.3    88.6    +      -       -      +
----------------------------------------------------------
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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