Contacts of the strand formed by residues 133 - 141 (chain H) in PDB entry 1BGX


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 133 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    128H  PRO*     3.5    11.2    -      -       -      +
    129H  VAL      4.1    10.6    +      -       -      -
    130H  SER      3.3    13.3    +      -       -      -
    131H  SER*     5.1     0.7    -      -       -      -
    132H  VAL*     1.3    76.6    +      -       -      +
    134H  LEU*     1.3    64.1    +      -       -      +
    176H  SER*     4.8     5.4    -      -       -      -
    177H  VAL      3.5     7.0    -      -       -      +
    178H  THR*     3.5    27.9    -      -       -      +
    114L  THR*     5.0     9.7    -      -       +      +
    116L  SER*     5.0     4.8    +      -       -      +
    118L  PHE*     3.3    32.9    -      -       +      -
    135L  PHE*     5.5     2.5    -      -       +      -
    137L  ASN*     4.7    16.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 134 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  LEU      5.1     0.7    -      -       -      +
    128H  PRO*     4.1    18.6    -      -       +      -
    132H  VAL*     3.8    26.5    -      -       +      -
    133H  THR*     1.3    77.0    -      -       -      +
    135H  GLY*     1.3    59.2    +      -       -      +
    150H  TRP*     4.5     4.0    -      -       +      -
    176H  SER*     3.4    24.1    -      -       -      -
    177H  VAL*     2.9    30.8    +      -       +      +
    179H  VAL*     3.9    17.0    -      -       +      -
    184H  TRP*     4.4    12.3    -      -       +      -
    189H  ILE*     4.0    27.1    -      -       +      -
    206H  ILE*     3.9    33.4    -      -       +      -
    118L  PHE*     4.7     3.6    -      -       -      -
    135L  PHE*     4.4     2.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 135 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126H  LEU*     3.7    27.8    +      -       -      +
    134H  LEU*     1.3    79.8    -      -       -      +
    136H  CYS*     1.3    61.0    +      -       -      +
    150H  TRP*     3.8     7.0    -      -       -      -
    175H  SER      3.4    11.2    -      -       -      -
    206H  ILE*     3.7    21.7    -      -       -      +
    118L  PHE*     4.9     0.2    -      -       -      -
    135L  PHE*     3.9    12.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 136 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123H  VAL*     3.7    23.8    -      -       -      -
    124H  TYR      4.2     4.0    -      -       -      -
    125H  PRO*     6.2     0.2    -      -       -      -
    126H  LEU*     4.3     2.9    -      -       -      +
    135H  GLY*     1.3    75.2    -      -       -      +
    137H  LEU*     1.3    59.4    +      -       -      +
    138H  VAL*     4.0     6.4    +      -       -      +
    148H  LEU*     4.6     6.1    -      -       +      +
    150H  TRP*     3.9    10.8    -      -       +      -
    174H  SER*     3.5     8.1    -      -       -      -
    175H  SER*     3.2    27.1    +      -       -      +
    191H  CYS*     2.0    53.2    -      -       +      -
    193H  VAL*     4.3     3.1    -      -       -      -
    204H  LYS*     5.7     0.4    -      -       -      -
    206H  ILE*     5.6     1.3    -      -       -      -
    135L  PHE*     4.9     0.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 137 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122H  SER      3.5     2.1    -      -       -      +
    123H  VAL*     3.5     4.2    -      -       -      +
    124H  TYR*     3.0    50.0    +      -       +      +
    126H  LEU*     4.5    15.2    -      -       +      +
    135H  GLY      4.4     0.4    -      -       -      -
    136H  CYS*     1.3    72.0    -      -       -      +
    138H  VAL*     1.3    63.3    +      -       -      +
    139H  LYS*     3.9    24.2    -      -       +      -
    172H  THR*     4.5    17.9    -      -       +      -
    173H  LEU      4.3     7.2    -      -       -      +
    174H  SER*     4.5    11.2    -      -       -      -
    124L  GLN*     4.1     8.1    -      -       -      +
    131L  SER*     4.1    16.8    -      -       -      +
    133L  VAL*     3.9    29.6    -      -       +      -
    135L  PHE*     6.0     0.4    -      -       +      -
    178L  THR*     4.6    10.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 138 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    121H  PRO*     4.0    26.5    -      -       +      -
    122H  SER      3.6     5.2    -      -       -      +
    123H  VAL*     4.5     5.4    -      -       +      -
    136H  CYS*     4.5     6.7    -      -       -      +
    137H  LEU*     1.3    76.2    -      -       -      +
    139H  LYS*     1.3    63.5    +      -       -      +
    141H  TYR*     4.2    15.2    -      -       +      -
    146H  VAL*     4.8     5.8    -      -       +      -
    148H  LEU*     4.2    17.5    -      -       +      -
    172H  THR*     3.7     1.8    -      -       -      +
    173H  LEU*     2.8    48.6    +      -       +      +
    193H  VAL*     3.9    37.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 139 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122H  SER*     3.2    32.4    +      -       -      -
    124H  TYR*     4.0    17.3    -      -       +      -
    137H  LEU*     3.9    20.9    -      -       +      -
    138H  VAL*     1.3    76.6    -      -       -      +
    140H  GLY*     1.3    62.7    +      -       -      +
    141H  TYR*     3.7     3.4    -      -       -      -
    170H  LEU*     6.3     0.4    -      -       -      +
    171H  TYR      3.9     5.6    -      -       -      -
    172H  THR*     3.8    25.9    +      -       +      +
    124L  GLN*     3.7    20.9    -      -       -      +
    131L  SER*     3.4    18.6    -      -       -      -
    160L  LEU*     5.6     0.8    -      -       -      +
    178L  THR*     5.9     1.0    -      -       +      +
    180L  THR*     3.9    25.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 140 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119H  THR*     3.2    16.5    -      -       -      +
    120H  ALA      2.6    23.3    -      -       -      +
    122H  SER*     5.2     0.8    +      -       -      -
    139H  LYS*     1.3    78.4    -      -       -      +
    141H  TYR*     1.3    55.7    +      -       -      +
    170H  LEU*     4.0    25.7    -      -       -      +
    171H  TYR      3.3     7.7    +      -       -      -
    172H  THR*     4.8     0.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 141 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119H  THR*     3.8    11.7    -      -       -      +
    121H  PRO*     3.9    24.0    -      -       +      -
    138H  VAL*     4.2    20.9    -      -       +      -
    139H  LYS      4.5     0.2    -      -       -      -
    140H  GLY*     1.3    81.1    -      -       -      +
    142H  PHE*     1.3    63.6    +      -       -      +
    143H  PRO      3.4    23.3    -      -       -      -
    144H  GLU*     3.2    29.1    +      -       -      -
    146H  VAL*     3.7    22.9    +      -       +      +
    164H  ALA*     3.5     3.1    -      -       -      +
    170H  LEU*     4.0     2.9    -      -       -      -
    171H  TYR*     3.1    52.4    +      -       +      +
    173H  LEU*     3.3    42.5    -      -       +      +
    195H  HIS*     4.0     9.2    -      +       +      -
----------------------------------------------------------
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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