Contacts of the strand formed by residues 156 - 160 (chain A) in PDB entry 2R8J


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 GLU 156 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     28A  HIS*     3.2    28.5    +      -       +      +
     29A  ILE      3.3     5.2    -      -       -      -
     30A  ASP*     2.9    13.5    -      -       -      +
    151A  ARG*     3.7     0.5    -      -       -      -
    152A  ALA*     3.1    30.5    +      -       +      +
    153A  SER*     3.0    32.6    +      -       -      +
    154A  ILE      3.7     0.2    -      -       -      -
    155A  ASP*     1.3    90.8    -      -       -      +
    157A  VAL*     1.3    73.3    +      -       -      +
    272A  LYS*     3.6    12.6    +      -       -      -
   1501A   CA      2.6    27.9    -      -       -      -
   2001A  DCP      4.3     0.7    +      -       -      -
     13Q    G      3.6    14.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  ALA      3.6     0.5    -      -       -      +
     28A  HIS*     3.3     4.7    -      -       -      -
     29A  ILE*     2.9    39.7    +      -       +      +
    139A  LEU*     4.3     9.2    -      -       +      -
    142A  PHE*     3.7    48.9    -      -       +      -
    149A  VAL*     3.9    15.3    -      -       +      -
    150A  GLU      3.1    12.3    -      -       -      +
    151A  ARG*     4.2    10.1    -      -       +      -
    152A  ALA      4.3     0.7    -      -       -      +
    155A  ASP      5.5     0.2    -      -       -      -
    156A  GLU*     1.3    87.1    -      -       -      +
    158A  PHE*     1.3    63.9    +      -       -      +
    159A  LEU*     4.6     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  ILE*     4.2     5.4    -      -       +      -
     27A  ALA      3.0    10.5    -      -       -      -
     28A  HIS*     3.2    35.7    -      +       +      -
    148A  LEU      3.8     0.7    -      -       -      +
    149A  VAL*     3.3     7.3    -      -       -      +
    150A  GLU*     2.8    57.5    +      -       +      +
    152A  ALA*     3.7    22.9    -      -       +      -
    157A  VAL*     1.3    75.0    -      -       -      +
    159A  LEU*     1.3    64.8    +      -       -      +
    268A  LYS*     3.5    52.3    -      -       +      -
    271A  CYS*     4.8     0.2    -      -       +      -
    272A  LYS*     4.3     9.6    -      -       +      -
    386A  LEU*     3.9    17.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  ILE*     3.3     8.5    -      -       -      +
     27A  ALA*     2.7    40.6    +      -       +      +
     29A  ILE*     3.9    25.6    -      -       +      -
    142A  PHE*     4.5    12.8    -      -       +      +
    146A  CYS*     4.0    11.0    -      -       +      -
    148A  LEU      3.7     0.9    -      -       -      -
    149A  VAL*     3.3    38.1    -      -       +      -
    157A  VAL*     4.6     9.4    -      -       +      -
    158A  PHE*     1.3    79.5    -      -       -      +
    160A  ASP*     1.3    60.3    +      -       -      +
    161A  LEU*     3.5    19.7    +      -       +      +
    245A  CYS*     5.2     2.2    -      -       -      -
    248A  ILE*     4.1    25.1    -      -       +      -
    386A  LEU*     3.7     4.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 160 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  PRO      5.0     0.7    -      -       -      +
     18A  ALA*     3.9    15.6    -      -       -      +
     19A  TYR*     4.2     7.1    +      -       -      +
     25A  CYS      4.1     4.5    +      -       -      +
     26A  ILE*     4.1    16.9    -      -       -      +
    146A  CYS*     3.4    13.7    -      -       -      -
    147A  ASP*     4.4     3.3    -      -       -      +
    148A  LEU*     3.5    37.2    +      -       +      +
    159A  LEU*     1.3    71.4    -      -       -      +
    161A  LEU*     1.3    58.5    +      -       -      +
    162A  GLY*     2.9    21.8    +      -       -      -
    163A  ARG*     3.3    27.6    +      -       -      +
    164A  ILE*     5.5     0.3    -      -       -      +
    386A  LEU*     3.7    12.6    -      -       +      +
----------------------------------------------------------
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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