Contacts of the strand formed by residues 194 - 202 (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 VAL 194 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189A  LEU      3.6     0.9    -      -       -      +
    190A  THR*     3.2     4.6    -      -       -      -
    191A  VAL      3.0    30.4    +      -       -      +
    192A  ASP*     2.7    27.4    +      -       +      +
    193A  GLY*     1.3    72.9    -      -       -      +
    195A  GLU*     1.3    72.1    +      -       -      +
    196A  THR*     3.9     7.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     94A  LYS*     5.7     2.3    -      -       -      +
    188A  ARG*     3.1    52.1    +      -       +      -
    189A  LEU      3.5     4.9    -      -       -      -
    190A  THR*     3.3    16.5    -      -       +      +
    193A  GLY      3.7     7.8    +      -       -      +
    194A  VAL*     1.3    82.7    -      -       -      +
    196A  THR*     1.3    62.1    +      -       -      +
    197A  TYR*     3.5    20.1    +      -       +      -
----------------------------------------------------------
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Residues in contact with THR 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ILE*     4.4    15.6    -      -       +      +
    151A  THR*     3.6    24.2    -      -       +      -
    188A  ARG*     3.0     5.0    -      -       -      -
    189A  LEU*     2.7    46.9    +      -       +      +
    191A  VAL*     6.1     0.7    -      -       -      +
    194A  VAL*     3.9    10.0    +      -       -      +
    195A  GLU*     1.3    77.5    +      -       -      +
    197A  TYR*     1.3    67.7    +      -       -      +
    198A  MET*     4.1    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  TYR*     3.0    28.5    -      +       -      -
    151A  THR*     2.9    31.8    -      -       -      +
    152A  VAL*     3.2    16.8    +      -       +      +
    153A  SER*     4.5     0.9    -      -       -      -
    154A  SER*     3.9    34.1    +      -       -      -
    157A  VAL*     3.1    38.1    -      -       +      -
    187A  TYR      3.4     3.4    -      -       -      -
    188A  ARG*     3.6    23.4    +      -       +      -
    195A  GLU*     3.5    26.5    +      -       +      -
    196A  THR*     1.3    78.0    -      -       -      +
    198A  MET*     1.3    64.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 198 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ILE*     4.4    12.8    -      -       +      -
     43A  LEU*     5.0    10.8    -      -       +      -
     46A  LEU*     3.9    19.5    -      -       +      -
    138A  ARG*     6.2     1.8    -      -       -      +
    140A  LEU*     5.1     5.2    -      -       +      -
    149A  ILE*     3.7    25.6    -      -       +      -
    150A  LYS      3.2    11.2    -      -       -      +
    151A  THR*     4.3    11.4    -      -       -      +
    152A  VAL*     4.2     0.6    -      -       -      +
    186A  MET*     3.3     5.0    -      -       -      +
    187A  TYR*     2.8    47.8    +      -       +      +
    189A  LEU*     3.6    26.9    -      -       +      -
    196A  THR*     4.1    18.4    -      -       +      -
    197A  TYR*     1.3    81.0    -      -       -      +
    199A  VAL*     1.3    65.3    +      -       -      +
    200A  VAL      4.1     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 199 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    148A  VAL      3.8     0.7    -      -       -      +
    149A  ILE*     4.8     0.2    -      -       -      -
    150A  LYS*     2.9    34.0    +      -       +      +
    152A  VAL*     3.4    31.0    -      -       +      -
    160A  MET*     5.0     4.5    -      -       +      -
    183A  PHE*     3.6    36.1    -      -       +      -
    185A  GLY      3.5     7.6    -      -       -      +
    186A  MET*     3.4    34.8    -      -       +      -
    198A  MET*     1.3    74.5    -      -       -      +
    200A  VAL*     1.3    62.8    +      -       -      +
    201A  THR*     3.6    10.3    +      -       +      -
    371A  LEU*     5.2     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 200 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     46A  LEU*     5.4     1.1    -      -       +      -
     50A  VAL*     5.3     3.6    -      -       +      -
    117A  TYR*     3.1    43.1    -      -       +      +
    121A  VAL*     5.2     4.5    -      -       +      -
    147A  PHE*     4.2    14.6    -      -       +      -
    148A  VAL      3.5    11.2    -      -       -      +
    149A  ILE*     4.2    27.4    -      -       +      +
    183A  PHE*     3.9     0.7    -      -       -      -
    184A  LEU*     3.0    19.9    +      -       +      -
    185A  GLY      2.8    15.2    +      -       -      +
    187A  TYR*     3.4    24.2    -      -       +      -
    199A  VAL*     1.3    73.5    -      -       -      +
    201A  THR*     1.3    70.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 201 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147A  PHE*     4.5     0.9    -      -       -      -
    148A  VAL*     2.8    44.4    +      -       -      +
    150A  LYS*     4.2    18.5    -      -       -      -
    181A  PRO*     4.8     4.9    -      -       +      -
    182A  GLN      3.5    11.9    -      -       -      +
    183A  PHE*     3.3    44.2    -      -       +      +
    184A  LEU*     4.1     6.3    -      -       -      -
    199A  VAL*     3.9     7.9    +      -       +      -
    200A  VAL*     1.3    86.6    -      -       -      +
    202A  ARG*     1.3    66.4    +      -       -      +
    203A  ASN      3.4     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 202 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110A  PHE*     2.8    37.9    +      -       -      +
    111A  GLY      4.8     2.4    +      -       -      -
    112A  ILE*     3.9    18.0    -      -       +      +
    146A  ARG*     3.7    15.0    -      -       -      +
    147A  PHE*     3.8    14.1    -      -       +      -
    181A  PRO*     6.0     0.7    -      -       -      +
    182A  GLN*     2.7    43.5    +      -       +      +
    184A  LEU*     3.6    13.3    -      -       +      +
    201A  THR*     1.3    78.6    +      -       -      +
    203A  ASN*     1.3    75.0    +      -       -      +
    204A  VAL*     3.9     1.2    +      -       -      +
    348A  VAL      4.0     8.3    +      -       -      -
    349A  TYR*     3.8    22.7    +      -       -      +
    351A  MET*     3.0    33.4    -      -       -      +
    352A  LYS*     4.9     7.4    -      -       -      -
----------------------------------------------------------
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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