Contacts of the strand formed by residues 193 - 197 (chain A) in PDB entry 1BGO


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 TYR 193 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ARG*     3.6    43.1    -      -       -      +
     13A  VAL*     3.2    26.2    -      -       -      +
     14A  THR      4.4     1.6    +      -       -      -
     16A  VAL*     3.4    20.2    -      -       +      +
    145A  TYR*     3.5     3.3    -      -       -      -
    167A  VAL*     4.3     8.5    -      -       +      -
    179A  ILE*     4.2     8.3    -      -       +      -
    180A  ILE      3.2    21.3    -      -       -      +
    181A  LYS*     3.4    27.6    -      -       +      +
    188A  TRP*     3.8     2.8    -      -       -      -
    189A  GLY      3.7     0.5    -      -       -      -
    190A  ASN*     2.7    46.5    +      -       +      +
    191A  LYS*     3.1    22.9    -      -       +      -
    192A  GLY*     1.3    81.9    -      -       -      +
    194A  ILE*     1.3    64.5    +      -       -      +
    195A  LEU*     5.7     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 194 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    142A  PHE*     3.3    40.4    -      -       +      -
    145A  TYR*     3.7    36.3    -      -       +      -
    150A  TYR*     3.8    10.3    -      -       +      -
    178A  TRP      3.4     0.3    -      -       -      +
    179A  ILE*     4.0     0.5    -      -       -      -
    180A  ILE*     3.0    53.1    +      -       +      +
    182A  ASN*     5.1     1.8    -      -       +      -
    188A  TRP*     3.6    21.8    -      -       +      -
    193A  TYR*     1.3    77.6    -      -       -      +
    195A  LEU*     1.3    76.8    +      -       -      +
    196A  MET*     3.8     6.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 195 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  ARG*     5.6     3.6    -      -       -      +
    145A  TYR*     3.6     9.2    +      -       -      +
    148A  GLY      3.7    13.4    -      -       -      +
    149A  VAL*     3.5     4.9    -      -       +      -
    150A  TYR*     2.8    34.7    +      -       -      +
    172A  GLN*     3.8    30.1    -      -       -      +
    177A  HIS*     3.6    39.3    -      -       +      +
    178A  TRP      3.1     4.9    -      -       -      -
    179A  ILE*     4.3    24.2    -      -       +      -
    190A  ASN*     6.1     4.9    -      -       +      +
    193A  TYR*     5.7     2.5    -      -       +      -
    194A  ILE*     1.3    79.1    -      -       -      +
    196A  MET*     1.3    54.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 196 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    135A  ILE*     4.1    29.6    -      -       +      -
    142A  PHE*     4.2    14.8    -      -       +      -
    149A  VAL*     3.9     2.2    -      -       -      -
    150A  TYR*     3.9    13.9    -      -       +      +
    177A  HIS*     3.3     0.9    -      -       -      -
    178A  TRP*     2.9    35.5    +      -       +      +
    180A  ILE*     3.8    26.9    -      -       +      -
    194A  ILE*     3.8    19.3    -      -       +      -
    195A  LEU*     1.3    76.1    -      -       -      +
    197A  ALA*     1.3    69.6    +      -       -      +
    203A  ALA*     4.4     6.1    -      -       +      +
    204A  CYS*     3.7    38.1    -      -       +      -
    206A  ILE*     4.6     4.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 197 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    118A  GLU*     4.4     1.2    -      -       -      +
    149A  VAL*     3.5    16.9    -      -       +      +
    150A  TYR      2.9    21.9    +      -       -      +
    151A  TYR*     3.8    28.3    -      -       +      -
    176A  LYS      3.8     0.9    -      -       -      -
    178A  TRP*     3.8     7.6    +      -       -      -
    196A  MET*     1.3    73.6    -      -       -      +
    198A  ARG*     1.3    59.7    +      -       -      +
    199A  ASN      4.3     0.3    +      -       -      -
    200A  LYS*     3.9    18.2    +      -       +      -
    203A  ALA*     4.3    19.0    +      -       +      +
    206A  ILE*     5.1     2.1    -      -       -      +
----------------------------------------------------------
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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