Contacts of the strand formed by residues 130 - 137 (chain C) in PDB entry 3BQM


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 130 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    307B  TYR*     4.0    29.4    -      -       +      -
      1C  BQM      4.3    14.8    -      -       -      +
    128C  GLY      4.2     1.1    -      -       -      +
    129C  ASN*     1.3    78.0    -      -       -      +
    131C  ASP*     1.3    64.4    +      -       -      +
    132C  LEU*     4.5     1.6    -      -       +      -
    165C  SER      3.2     7.0    +      -       -      +
    166C  TYR*     3.3    35.1    -      -       +      +
    167C  GLN      3.0    26.5    +      -       -      +
    227C  ARG*     3.0     5.7    +      -       -      -
    231C  THR*     3.4     9.2    -      -       -      +
    233C  VAL*     3.6    31.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 131 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130C  VAL*     1.3    70.5    -      -       -      +
    132C  LEU*     1.3    59.2    +      -       -      +
    167C  GLN*     3.3    17.5    +      -       -      +
    183C  PHE*     3.6    16.4    -      -       +      -
    220C  PHE*     3.5    14.8    -      -       +      -
    226C  ALA*     3.4     8.7    -      -       -      +
    227C  ARG*     2.7    71.6    +      -       -      +
    230C  ALA*     3.5    12.0    -      -       +      +
    231C  THR      3.0     7.8    +      -       -      +
    232C  LYS*     5.0     2.7    -      -       +      +
    233C  VAL      2.9    23.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 132 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  BQM      2.9    29.6    -      -       +      +
    130C  VAL*     3.9     5.4    +      -       +      -
    131C  ASP*     1.3    74.2    -      -       -      +
    133C  VAL*     1.3    67.0    +      -       -      +
    134C  PHE*     3.7    39.7    -      -       +      -
    166C  TYR*     4.3    16.6    -      -       +      -
    167C  GLN      2.9    12.9    +      -       -      +
    168C  PHE*     3.3    14.3    -      -       +      +
    169C  ALA      3.0    24.3    +      -       -      +
    183C  PHE*     3.5     1.7    -      -       -      -
    233C  VAL*     3.3    35.0    -      -       +      +
    235C  ILE*     3.9    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132C  LEU*     1.3    76.2    -      -       -      +
    134C  PHE*     1.3    74.4    +      -       -      +
    169C  ALA*     3.4     9.4    -      -       +      +
    171C  VAL*     4.1    19.1    -      -       +      -
    183C  PHE*     3.6    20.0    -      -       +      -
    215C  VAL*     4.0    17.7    -      -       +      -
    219C  VAL*     3.9    15.7    -      -       +      -
    220C  PHE*     3.6    26.5    -      -       +      -
    233C  VAL      2.9    10.1    +      -       -      -
    234C  LEU*     3.4    16.1    -      -       +      +
    235C  ILE      2.8    27.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 134 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1C  BQM      3.9    19.5    -      -       -      -
    132C  LEU*     3.7    16.8    -      -       +      -
    133C  VAL*     1.3    74.2    -      -       -      +
    135C  LEU*     1.3    59.2    +      -       -      +
    136C  PHE*     3.9     0.6    -      -       -      -
    153C  PHE*     5.3     1.8    -      +       -      -
    154C  MET*     3.6    48.0    -      -       +      -
    157C  VAL*     3.9    27.4    -      -       +      -
    158C  MET*     3.7    21.1    -      -       +      -
    168C  PHE*     3.6    24.9    -      +       -      -
    169C  ALA      3.0    16.5    +      -       -      +
    170C  ALA*     3.4     7.2    -      -       +      +
    171C  VAL      2.9    27.5    +      -       -      +
    235C  ILE*     3.5    20.2    -      -       +      +
    237C  ILE*     4.8     3.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133C  VAL      3.7     0.8    +      -       -      -
    134C  PHE*     1.3    71.4    -      -       -      +
    136C  PHE*     1.3    59.2    +      -       -      +
    171C  VAL*     3.4    32.8    -      -       +      +
    173C  PHE*     3.6    26.3    -      -       +      -
    208C  THR      5.1     0.2    -      -       -      +
    211C  ALA*     3.8    24.2    -      -       +      -
    212C  ILE*     3.8    29.2    -      -       +      +
    215C  VAL*     3.8    16.2    -      -       +      -
    234C  LEU*     3.8    16.6    -      -       +      -
    235C  ILE      2.7    11.7    +      -       -      +
    236C  ILE*     3.3    17.1    -      -       +      +
    237C  ILE*     2.9    26.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 136 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134C  PHE      4.3     4.0    -      -       -      -
    135C  LEU*     1.3    73.2    -      -       -      +
    137C  ASP*     1.3    64.3    +      -       -      +
    138C  GLY      3.5     0.2    +      -       -      -
    147C  PHE*     3.7    23.3    -      +       -      -
    150C  ILE*     3.7    28.3    -      -       +      -
    151C  LEU*     3.7    24.5    -      -       +      -
    154C  MET*     3.6    28.9    -      -       +      -
    170C  ALA*     4.3     4.7    -      -       +      -
    171C  VAL      2.9    43.2    +      -       -      -
    172C  GLN*     3.3    26.3    -      -       +      -
    173C  PHE*     2.9    29.9    +      -       -      -
    180C  GLU*     4.0    16.6    -      -       +      -
    196C  LEU*     4.8     0.7    -      -       +      -
    199C  VAL*     4.3     6.3    -      -       +      -
    237C  ILE*     3.6     8.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 137 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136C  PHE*     1.3    75.1    -      -       -      +
    138C  GLY*     1.3    57.4    +      -       -      +
    139C  SER*     2.7    44.9    +      -       -      -
    142C  LEU*     3.0    20.2    -      -       +      +
    147C  PHE*     3.8     9.0    -      -       -      -
    150C  ILE*     4.1     7.0    -      -       +      +
    173C  PHE*     3.5    14.4    -      -       +      +
    206C  THR*     3.7    15.1    +      -       -      +
    237C  ILE      2.9    20.3    +      -       -      +
    238C  THR*     2.9    27.7    +      -       -      +
    239C  ASP*     3.1    21.7    +      -       -      +
    240C  GLY      4.0     0.3    +      -       -      -
----------------------------------------------------------
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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