Contacts of the strand formed by residues 281 - 287 (chain A) in PDB entry 1BO1


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 LEU 281 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179A  LEU*     4.5     8.5    -      -       +      -
    216A  ASP*     3.6     2.2    -      -       -      -
    217A  LEU*     2.8    41.2    +      -       +      +
    260A  PHE*     4.4    17.3    -      -       +      -
    264A  LEU*     4.9     0.4    -      -       +      -
    280A  SER*     1.3    74.4    -      -       -      +
    282A  LEU*     1.3    66.1    +      -       -      +
    283A  VAL*     3.6    27.8    +      -       +      +
    365A  MET*     4.3    12.6    -      -       +      -
    366A  ALA*     3.6    26.5    -      -       -      +
    367A  ILE*     4.1     3.4    -      -       +      +
    368A  ILE*     5.4     0.2    -      -       -      -
    407A  PHE*     3.6    22.9    -      -       +      -
    411A  MET*     4.0    23.1    -      -       +      -
    414A  ILE*     4.0    10.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 282 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  VAL*     3.5    28.3    -      -       +      -
    205A  PHE*     3.4    37.5    -      -       +      -
    214A  LYS*     3.8    13.2    -      -       +      -
    215A  TYR      3.1    19.3    -      -       -      +
    216A  ASP*     4.9     7.0    -      -       -      +
    237A  THR*     5.4     2.0    -      -       +      -
    280A  SER      4.1     1.0    +      -       -      -
    281A  LEU*     1.3    71.8    -      -       -      +
    283A  VAL*     1.3    65.3    +      -       -      +
    364A  PHE      3.2     1.6    -      -       -      +
    365A  MET*     3.1    27.2    -      -       -      +
    366A  ALA      2.8    18.2    +      -       -      +
    368A  ILE*     4.3    23.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with VAL 283 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  PHE*     4.1     3.4    -      -       -      -
    213A  ARG      3.8     0.5    -      -       -      +
    214A  LYS*     3.2     6.6    -      -       -      +
    215A  TYR*     2.8    61.3    +      -       +      -
    217A  LEU*     3.5    29.2    -      -       +      -
    243A  PHE*     5.3     1.8    -      -       +      -
    250A  LEU*     4.8    13.0    -      -       +      -
    281A  LEU*     3.6    18.4    -      -       +      +
    282A  LEU*     1.3    79.8    -      -       -      +
    284A  GLY*     1.3    61.7    +      -       -      +
    285A  ILE*     4.4    12.3    -      -       +      -
    363A  TYR*     5.8     0.9    -      -       +      -
    364A  PHE      3.3     2.2    -      -       -      -
    365A  MET*     4.0    15.5    -      -       +      -
    414A  ILE*     5.0     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  PHE*     3.6    18.9    -      -       -      -
    211A  VAL*     3.8     9.2    -      -       -      -
    213A  ARG      3.6     3.8    -      -       -      -
    283A  VAL*     1.3    76.0    -      -       -      +
    285A  ILE*     1.3    63.8    +      -       -      +
    363A  TYR*     3.3     5.9    -      -       -      +
    364A  PHE*     2.7    49.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    211A  VAL*     3.6     3.2    -      -       -      +
    212A  HIS*     2.8    28.4    +      -       +      -
    213A  ARG*     2.8    29.8    +      -       +      +
    215A  TYR*     3.5    29.8    -      -       +      -
    248A  GLN*     3.8    23.1    -      -       -      +
    249A  LYS      5.2     0.7    -      -       -      +
    250A  LEU*     4.4     5.6    -      -       +      -
    283A  VAL*     4.4     7.9    -      -       +      -
    284A  GLY*     1.3    77.5    -      -       -      +
    286A  HIS*     1.3    65.3    +      -       -      +
    287A  ASP*     4.1     1.8    -      -       +      +
    361A  GLU*     3.5    32.3    -      -       +      +
    362A  VAL      3.6     3.8    -      -       -      +
    363A  TYR*     4.1    15.5    -      -       +      -
    364A  PHE*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with HIS 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    209A  LEU*     3.9    29.7    -      -       +      +
    210A  THR*     2.7    40.4    +      -       -      +
    212A  HIS*     3.9    10.8    -      -       -      -
    285A  ILE*     1.3    75.4    -      -       -      +
    287A  ASP*     1.3    57.7    +      -       -      +
    288A  VAL*     3.5    18.5    +      -       +      -
    291A  ALA*     3.6    26.3    -      -       +      +
    343A  ASP      4.9     3.1    -      -       -      -
    361A  GLU*     3.2     8.6    -      -       -      -
    362A  VAL*     2.8    56.1    +      -       +      +
    364A  PHE*     3.9    14.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212A  HIS*     3.1    25.5    +      -       +      +
    285A  ILE*     4.1     2.5    -      -       +      +
    286A  HIS*     1.3    71.3    -      -       -      +
    288A  VAL*     1.3    64.4    +      -       -      +
    289A  ASP*     3.2    13.2    +      -       -      +
    290A  ARG*     3.1    30.7    +      -       +      +
    291A  ALA*     3.0    17.5    +      -       -      +
    360A  LYS*     3.7    31.8    -      -       -      +
    361A  GLU*     3.8    12.4    -      -       -      +
----------------------------------------------------------
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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