Contacts of the strand formed by residues 113 - 118 (chain A) in PDB entry 2JG8


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 THR 113 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     97A  ALA*     3.4     2.0    -      -       -      -
     98A  ILE*     2.8    60.7    +      -       +      +
    100A  ARG*     3.9    19.4    -      -       -      +
    112A  ASP*     1.3    92.6    +      -       -      +
    114A  VAL*     1.3    69.9    +      -       -      +
    115A  ILE*     3.7     3.8    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 114 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  SER      4.0     3.6    -      -       -      +
     97A  ALA*     4.5     1.1    -      -       +      +
    112A  ASP      3.8     1.2    +      -       -      -
    113A  THR*     1.3    77.9    -      -       -      +
    115A  ILE*     1.3    67.1    +      -       -      +
    116A  THR      3.7    12.1    -      -       -      +
    117A  ASN*     3.6    34.8    -      -       +      +
    122A  TYR*     4.2    16.4    -      -       +      -
    124A  ASN*     3.2    41.5    -      -       +      +
   1223A  NAG      4.8     6.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 115 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  SER*     3.0    11.8    +      -       -      +
     98A  ILE*     3.8    44.2    -      -       +      -
    113A  THR*     4.2     5.8    -      -       +      +
    114A  VAL*     1.3    81.2    -      -       -      +
    116A  THR*     1.3    65.9    +      -       -      +
    159B  ARG*     4.4    11.8    +      -       -      +
    167B  VAL*     3.9    22.2    -      -       +      +
    168B  VAL*     4.9     0.2    -      -       +      -
    185B  MET*     3.9    17.0    -      -       -      -
    187B  LEU*     3.8    28.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 116 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ALA      4.1     6.7    -      -       -      +
     95A  PHE*     3.1     5.0    -      -       -      +
     96A  SER      2.9    32.6    +      -       -      +
    114A  VAL*     3.7     3.9    -      -       -      +
    115A  ILE*     1.3    84.9    +      -       -      +
    117A  ASN*     1.3    66.1    +      -       -      +
    118A  GLN*     4.3     3.4    -      -       +      +
    122A  TYR*     5.9     0.2    -      -       -      -
    140B  LEU*     3.6    31.0    -      -       +      -
    159B  ARG*     5.1     1.0    +      -       -      -
    186B  VAL*     2.7    32.6    +      -       +      -
    187B  LEU*     3.6     6.8    -      -       -      +
    188B  LYS*     4.0    12.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 117 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  ALA      3.5     3.1    -      -       -      -
     95A  PHE*     3.7     1.3    -      -       -      +
    114A  VAL*     3.6    23.8    -      -       +      +
    116A  THR*     1.3    76.8    -      -       -      +
    118A  GLN*     1.3    59.6    +      -       -      +
    119A  GLU      3.4     0.5    +      -       -      -
    120A  GLU*     2.9    37.4    +      -       +      +
    121A  PRO*     2.9    24.4    -      -       -      +
    122A  TYR*     2.8    41.1    +      -       -      +
    124A  ASN*     5.7     0.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLN 118 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  ARG*     3.3    49.6    -      -       +      +
     93A  PRO*     3.3     0.7    -      -       -      +
     94A  ALA      2.7    26.8    +      -       -      +
    116A  THR*     4.3     1.4    -      -       +      +
    117A  ASN*     1.3    69.1    -      -       -      +
    119A  GLU*     1.3    75.5    +      -       +      +
    120A  GLU      3.1     3.1    -      -       -      -
    121A  PRO*     3.1    11.1    -      -       -      +
    140B  LEU*     3.5    25.6    -      -       +      -
    188B  LYS*     3.4    32.3    +      -       -      +
----------------------------------------------------------
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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