Contacts of the strand formed by residues 147 - 152 (chain A) in PDB entry 2R32


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 147 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82A  VAL*     4.8     4.0    -      -       +      -
     86A  LYS*     3.8    28.4    +      -       -      +
     87A  LEU      3.2    13.0    -      -       -      +
     88A  GLU*     4.3    12.1    -      -       +      -
    119A  LYS*     3.4     5.9    -      -       -      +
    120A  ASN*     2.9    47.8    +      -       -      +
    145A  GLY      4.1     7.9    -      -       -      +
    146A  ASP*     1.3    77.7    -      -       -      +
    148A  ILE*     1.3    67.8    +      -       -      +
    149A  ASP*     5.6     1.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 148 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86A  LYS*     3.4     4.1    -      -       -      +
     87A  LEU*     3.0    31.8    +      -       +      +
     89A  ILE*     4.7    10.8    -      -       +      -
     97A  ILE*     4.0    21.5    -      -       +      -
    117A  LEU*     3.8    20.6    -      -       +      -
    118A  TYR      3.2     9.9    -      -       -      +
    119A  LYS*     3.9    22.0    -      -       +      -
    124A  ILE*     4.5     3.1    -      -       +      -
    142A  LEU*     4.2    24.7    -      -       +      -
    146A  ASP*     5.6     0.4    -      -       +      -
    147A  THR*     1.3    84.1    -      -       -      +
    149A  ASP*     1.3    62.4    +      -       -      +
    165A  TRP*     3.4    35.4    -      -       +      -
    167A  ILE*     4.8     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 149 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84A  ASP      4.6     1.4    -      -       -      +
     85A  TRP*     3.5    13.6    -      -       -      +
     86A  LYS*     3.5    34.2    +      -       +      +
    116A  ARG      3.6     1.6    -      -       -      +
    117A  LEU*     3.3     7.2    -      -       -      +
    118A  TYR*     2.8    49.6    +      -       +      +
    120A  ASN      5.8     0.7    -      -       -      +
    147A  THR*     4.4     1.8    -      -       -      +
    148A  ILE*     1.3    76.2    -      -       -      +
    150A  LEU*     1.3    70.1    +      -       -      +
    151A  ILE*     2.9    32.4    -      -       +      +
    165A  TRP*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 150 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  TRP*     3.3    29.9    +      -       +      +
    101A  VAL*     4.3    16.2    -      -       +      -
    115A  VAL*     3.7    20.0    -      -       +      -
    116A  ARG      3.5    17.9    -      -       -      +
    117A  LEU*     4.1    17.5    -      -       +      +
    127A  LEU*     5.7     2.0    -      -       +      -
    136A  VAL*     5.0    10.3    -      -       +      -
    149A  ASP*     1.3    83.7    +      -       -      +
    151A  ILE*     1.3    61.4    +      -       -      +
    152A  PHE*     3.8    29.2    -      -       +      -
    163A  THR*     4.8     1.8    -      -       +      -
    164A  TYR      5.0     1.6    -      -       -      +
    165A  TRP*     3.6    38.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114A  GLU      4.3     0.2    -      -       -      +
    115A  VAL*     3.6     3.3    -      -       -      +
    116A  ARG*     2.9    47.9    +      -       +      +
    118A  TYR*     3.9    26.9    -      -       +      -
    149A  ASP*     2.9    39.7    -      -       -      +
    150A  LEU*     1.3    75.8    -      -       -      +
    152A  PHE*     1.3    73.9    +      -       -      +
    153A  ASN*     4.0     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85A  TRP*     3.6    40.4    -      +       -      -
    101A  VAL*     4.6     1.1    -      -       +      -
    114A  GLU      4.1     2.7    -      -       -      -
    115A  VAL*     3.6    34.5    -      -       +      -
    116A  ARG*     5.9     0.2    -      -       -      -
    150A  LEU*     3.8    25.1    -      -       +      -
    151A  ILE*     1.3    82.9    -      -       -      +
    153A  ASN*     1.3    66.9    +      -       -      +
    154A  SER      3.8    16.4    -      -       -      +
    155A  GLU*     3.8    34.5    +      -       -      +
    158A  VAL*     4.0    25.4    -      -       +      -
    160A  LYS*     5.6     1.6    -      -       +      -
    163A  THR*     3.9    25.8    -      -       +      -
----------------------------------------------------------
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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