Contacts of the strand formed by residues 130 - 137 (chain B) 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 B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  BQM      4.4    15.5    -      -       -      +
    128B  GLY      3.8     1.3    +      -       -      +
    129B  ASN*     1.3    77.0    -      -       -      +
    131B  ASP*     1.3    69.1    +      -       -      +
    132B  LEU*     4.2     4.3    -      -       +      -
    165B  SER      3.1     7.2    +      -       -      +
    166B  TYR*     3.3    40.2    -      -       +      -
    167B  GLN      3.0    25.1    +      -       -      +
    227B  ARG*     3.1     2.6    +      -       -      -
    231B  THR*     3.3     9.9    -      -       -      +
    233B  VAL*     3.8    27.4    -      -       +      -
    307C  TYR*     4.1    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 131 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    130B  VAL*     1.3    72.7    -      -       -      +
    132B  LEU*     1.3    57.9    +      -       -      +
    167B  GLN*     3.5     8.4    -      -       -      +
    183B  PHE*     3.8    18.6    -      -       +      -
    220B  PHE*     3.7    16.2    -      -       +      -
    225B  GLY      5.3     0.4    -      -       -      +
    226B  ALA*     3.4    10.3    -      -       -      +
    227B  ARG*     2.8    66.0    +      -       -      +
    230B  ALA*     3.8    10.6    -      -       +      +
    231B  THR      2.9    10.6    +      -       -      +
    232B  LYS*     3.5     3.8    -      -       +      +
    233B  VAL      2.9    24.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 132 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  BQM      3.2    28.3    -      -       +      +
    130B  VAL*     3.9     8.0    +      -       +      -
    131B  ASP*     1.3    73.7    -      -       -      +
    133B  VAL*     1.3    68.0    +      -       -      +
    134B  PHE*     3.8    29.6    -      -       +      -
    166B  TYR*     4.3    19.3    -      -       +      -
    167B  GLN      2.9     9.4    +      -       -      +
    168B  PHE*     3.3    20.1    -      -       +      +
    169B  ALA      3.1    22.5    +      -       -      +
    183B  PHE*     3.8     1.2    -      -       -      -
    233B  VAL*     3.2    29.2    -      -       +      +
    235B  ILE*     3.8    20.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 133 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    132B  LEU*     1.3    74.3    -      -       -      +
    134B  PHE*     1.3    73.1    +      -       -      +
    169B  ALA*     3.4     6.7    -      -       +      +
    171B  VAL*     3.8    22.2    -      -       +      -
    183B  PHE*     3.6    28.7    -      -       +      -
    215B  VAL*     3.9    17.3    -      -       +      -
    219B  VAL*     3.8    14.8    -      -       +      -
    220B  PHE*     3.6    17.7    -      -       +      -
    233B  VAL      2.9     9.9    +      -       -      +
    234B  LEU*     3.5    16.4    -      -       +      +
    235B  ILE*     2.8    28.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 134 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1B  BQM      4.0    17.9    -      -       -      -
    132B  LEU*     3.8    16.2    -      -       +      -
    133B  VAL*     1.3    73.1    -      -       -      +
    135B  LEU*     1.3    59.4    +      -       -      +
    136B  PHE*     3.9     1.7    +      -       -      -
    153B  PHE*     5.1     2.7    -      +       -      -
    154B  MET*     3.5    52.3    -      -       +      -
    157B  VAL*     3.8    24.9    -      -       +      -
    158B  MET*     3.6    31.4    -      -       +      -
    168B  PHE*     3.8    13.0    -      +       -      -
    169B  ALA      2.9    18.0    +      -       -      +
    170B  ALA*     4.4     4.7    -      -       +      -
    171B  VAL      2.8    28.8    +      -       -      +
    235B  ILE*     3.5    20.6    -      -       +      +
    237B  ILE*     4.6     4.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 135 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    133B  VAL      3.7     1.2    +      -       -      -
    134B  PHE*     1.3    73.0    -      -       -      +
    136B  PHE*     1.3    57.5    +      -       -      +
    171B  VAL*     3.4    29.8    -      -       +      +
    173B  PHE*     3.4    30.4    -      -       +      -
    208B  THR*     5.4     0.2    -      -       +      -
    211B  ALA*     3.9    16.6    -      -       +      +
    212B  ILE*     3.8    42.2    -      -       +      +
    215B  VAL*     4.0    11.0    -      -       +      -
    234B  LEU*     3.5    19.3    -      -       +      -
    235B  ILE      2.9    10.9    +      -       -      +
    236B  ILE*     3.2    16.4    -      -       +      -
    237B  ILE      2.9    23.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 136 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    134B  PHE      4.1     4.5    -      -       -      -
    135B  LEU*     1.3    73.2    -      -       -      +
    137B  ASP*     1.3    61.5    +      -       -      +
    147B  PHE*     3.6    29.8    -      +       -      -
    150B  ILE*     3.8    24.2    -      -       +      -
    151B  LEU*     3.8    17.3    -      -       +      -
    154B  MET*     3.7    30.7    -      -       +      -
    170B  ALA*     4.2     6.1    -      -       +      -
    171B  VAL      2.9    40.5    +      -       -      -
    172B  GLN*     3.4    34.4    -      -       +      -
    173B  PHE*     2.9    33.2    +      -       -      -
    180B  GLU*     4.0    14.6    -      -       +      -
    196B  LEU*     4.9     0.7    -      -       +      -
    199B  VAL*     4.2     6.7    -      -       +      -
    237B  ILE*     3.6     8.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 137 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    136B  PHE*     1.3    72.3    -      -       -      +
    138B  GLY*     1.3    58.2    +      -       -      +
    139B  SER*     2.8    43.8    +      -       -      -
    142B  LEU*     3.1    20.3    -      -       +      +
    147B  PHE*     3.6    11.7    -      -       -      -
    150B  ILE*     4.0     8.7    -      -       +      +
    173B  PHE*     3.4    14.0    -      -       +      +
    205B  LEU      4.6     0.3    -      -       -      +
    206B  THR*     3.6    15.5    +      -       -      +
    237B  ILE      2.9    20.0    +      -       -      +
    238B  THR*     2.8    28.0    +      -       -      +
    239B  ASP*     3.1    19.8    +      -       -      +
    240B  GLY      3.9     0.5    +      -       -      -
----------------------------------------------------------
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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