Contacts of the strand formed by residues 149 - 157 (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 ILE 149 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  VAL*     3.5    32.1    -      -       +      -
    145A  SER*     3.5    19.5    -      -       -      -
    148A  GLU*     1.3    75.7    -      -       -      +
    150A  CYS*     1.3    65.2    +      -       -      +
    151A  LEU*     3.7    25.4    -      -       +      -
    167A  PHE      3.9     0.2    -      -       -      +
    168A  CYS*     3.1     5.0    -      -       -      +
    169A  ASP*     2.9    39.8    +      -       +      +
    170A  THR*     4.9     0.6    -      -       -      +
    179A  VAL*     3.7    20.2    -      -       +      -
    201A  LYS*     3.5     7.8    -      -       -      +
    202A  GLY*     4.8     1.1    -      -       -      -
    203A  HIS      3.5    22.7    -      -       -      +
    204A  ILE*     3.8     9.4    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with CYS 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    149A  ILE*     1.3    73.7    -      -       -      +
    151A  LEU*     1.3    62.8    +      -       -      +
    167A  PHE      3.4     3.6    -      -       -      -
    168A  CYS*     2.0    45.1    -      -       -      -
    170A  THR*     4.8     0.4    -      -       -      -
    197A  LYS*     3.3     4.2    -      -       -      -
    198A  ASP*     2.9    48.4    +      -       +      +
    201A  LYS*     2.9    35.1    +      -       -      +
    202C  ILE*     4.4     3.8    -      -       -      -
    203C  GLN      4.8     4.0    -      -       -      -
    204C  GLY*     4.9     3.1    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109A  VAL*     3.9    17.3    -      -       +      -
    141A  PHE*     3.7    27.8    -      -       +      -
    143A  VAL*     3.5    41.3    -      -       +      -
    149A  ILE*     3.7    23.3    -      -       +      -
    150A  CYS*     1.3    81.3    -      -       -      +
    152A  SER*     1.3    61.7    +      -       -      +
    166A  GLY*     3.2     3.6    -      -       -      -
    167A  PHE*     2.8    36.7    +      -       -      +
    179A  VAL*     3.9     4.0    -      -       +      -
    195A  VAL*     4.1     8.3    -      -       +      -
    196A  GLU      3.4     3.1    -      -       -      +
    197A  LYS*     3.7    23.8    -      -       +      -
    204A  ILE*     4.6     2.5    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    141A  PHE*     4.8     1.1    -      -       -      -
    151A  LEU*     1.3    77.1    -      -       -      +
    153A  ILE*     1.3    69.4    +      -       -      +
    154A  VAL*     3.5     7.8    +      -       -      +
    164A  SER      3.5    13.5    +      -       -      -
    165A  LEU      2.7    22.3    +      -       -      -
    166A  GLY*     4.3     3.6    -      -       -      -
    167A  PHE*     5.5     0.4    -      -       -      -
    195A  VAL*     3.5     4.7    -      -       -      -
    196A  GLU      2.8    36.7    +      -       -      -
    102F  GLN*     4.3    17.8    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with ILE 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    139A  PHE*     3.9    33.7    -      -       +      +
    140A  THR      4.6     0.7    -      -       -      +
    141A  PHE*     3.7    36.2    -      -       +      -
    152A  SER*     1.3    72.4    +      -       -      +
    154A  VAL*     1.3    61.3    +      -       -      +
    164A  SER*     3.2    27.4    -      -       -      -
    165A  LEU      3.9     4.4    +      -       -      -
    167A  PHE*     5.4     4.6    -      -       +      -
    182A  GLY*     4.0    16.2    -      -       -      +
    183A  MET*     4.5    13.4    -      -       +      +
    185A  LEU*     4.3    16.1    -      -       +      +
    193A  VAL*     4.0    24.5    -      -       +      -
    194A  TRP      3.6     4.5    -      -       -      +
    195A  VAL*     4.8     8.3    -      -       +      -
    214A  PHE*     4.9     4.0    -      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  SER*     3.7    21.3    -      -       -      +
    153A  ILE*     1.3    77.1    -      -       -      +
    155A  SER*     1.3    64.2    +      -       -      +
    161A  VAL*     3.5    22.2    -      -       +      -
    162A  ARG      3.6    11.7    -      -       -      +
    163A  ARG*     4.4     7.2    -      -       -      +
    185A  LEU*     5.6     0.2    -      -       -      -
    193A  VAL*     3.4     4.9    -      -       -      +
    194A  TRP*     2.8    65.0    +      -       +      +
    196A  GLU*     3.7    26.5    -      -       +      +
    102F  GLN*     4.3     9.2    -      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    153A  ILE      4.4     0.2    +      -       -      -
    154A  VAL*     1.3    80.9    -      -       -      +
    156A  SER*     1.3    57.3    +      -       -      +
    161A  VAL*     3.7     1.0    -      -       -      -
    162A  ARG*     2.7    70.1    +      -       -      +
    185A  LEU*     4.2    19.8    -      -       -      +
    187A  LEU*     4.8     0.9    -      -       -      -
    192A  GLN      3.1    13.9    -      -       -      -
    193A  VAL*     4.2    12.3    -      -       -      -
    194A  TRP*     3.8     4.2    -      -       -      -
    111F  ARG*     5.6     0.3    +      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128A  ARG*     5.2     0.9    +      -       -      -
    155A  SER*     1.3    76.6    -      -       -      +
    157A  SER*     1.3    59.0    -      -       -      +
    158A  ARG      4.3     0.2    -      -       -      -
    159A  GLY*     4.4    14.3    +      -       -      -
    160A  GLN      3.2    20.6    -      -       -      -
    161A  VAL*     4.2     1.1    -      -       -      -
    162A  ARG*     4.1     5.1    +      -       -      +
    191A  ASP*     3.2    12.3    -      -       -      +
    192A  GLN*     2.9    40.6    +      -       -      +
    194A  TRP*     3.8    21.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  SER*     1.3    72.3    -      -       -      +
    158A  ARG*     1.3    87.6    +      -       -      +
    159A  GLY      3.1     0.2    -      -       -      -
    160A  GLN*     3.1    25.2    +      -       -      +
    162A  ARG*     3.4    29.6    +      -       -      +
    188A  GLN*     4.2    13.2    +      -       -      +
    191A  ASP*     3.0    20.7    +      -       -      +
    126F  SER      4.6     3.8    -      -       -      -
    127F  THR*     6.2     0.5    -      -       -      +
----------------------------------------------------------
 Back to top of page


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