Contacts of the strand formed by residues 283 - 288 (chain A) in PDB entry 3BRA


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 ILE 283 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206A  VAL*     4.7     7.6    -      -       +      -
    207A  GLU      3.5     3.4    -      -       -      +
    208A  ILE*     3.8    30.5    -      -       +      -
    234A  LEU*     5.3     6.7    -      -       +      -
    248A  ILE*     4.2     7.4    -      -       +      -
    281A  PRO*     4.2     2.9    -      -       +      +
    282A  VAL*     1.3    78.8    -      -       -      +
    284A  SER*     1.3    69.9    +      -       -      +
    285A  LEU*     4.2    11.0    +      -       +      +
    298A  ILE      3.8     0.7    -      -       -      +
    299A  THR*     3.4     2.1    -      -       -      -
    300A  ILE*     2.9    49.0    +      -       +      +
    305A  TYR*     3.6    35.9    -      -       +      -
    324A  ILE*     3.9    21.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 284 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  ARG      4.0     0.3    -      -       -      +
    206A  VAL*     3.4     8.0    -      -       -      +
    207A  GLU*     2.9    52.7    +      -       -      +
    210A  GLY*     5.9     0.7    +      -       -      -
    282A  VAL*     4.9     3.8    -      -       -      +
    283A  ILE*     1.3    71.9    -      -       -      +
    285A  LEU*     1.3    63.1    +      -       -      +
    286A  TYR*     4.1     2.6    -      -       -      -
    297A  ARG*     3.8    20.3    +      -       -      -
    298A  ILE      3.2     4.5    -      -       -      -
    299A  THR*     2.6    31.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 285 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  ILE*     4.5    21.5    -      -       +      -
    205A  ARG      3.7     2.7    -      -       -      +
    206A  VAL*     3.7    33.2    -      -       +      -
    234A  LEU*     5.0     9.2    -      -       +      -
    236A  LEU*     5.3    11.9    -      -       +      -
    283A  ILE*     4.2    12.5    +      -       +      +
    284A  SER*     1.3    74.5    -      -       -      +
    286A  TYR*     1.3    63.9    +      -       -      +
    287A  LEU*     3.8     7.8    +      -       +      +
    297A  ARG*     3.2     1.0    -      -       -      -
    298A  ILE*     2.9    42.7    +      -       +      +
    300A  ILE*     6.4     0.7    -      -       +      -
    333A  MET*     3.8    20.2    -      -       +      -
    337A  ILE*     3.7    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 286 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    203A  ILE*     3.4     7.1    -      -       -      +
    204A  VAL*     2.8    38.8    +      -       +      -
    205A  ARG*     2.7    53.6    +      -       +      +
    207A  GLU*     2.8    44.0    +      -       +      -
    284A  SER*     4.4     3.8    -      -       -      -
    285A  LEU*     1.3    75.9    -      -       -      +
    287A  LEU*     1.3    58.0    +      -       -      +
    295A  SER*     4.1    14.1    -      -       -      +
    296A  PHE      3.2     9.2    -      -       -      +
    297A  ARG*     3.0    47.7    +      -       +      -
    374A  PHE*     3.9    27.8    -      +       +      -
    376A  THR*     5.1     2.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 287 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  THR*     3.6    14.1    -      -       +      +
    201A  VAL*     4.7     6.7    -      -       +      -
    202A  ILE      3.5     7.0    -      -       -      +
    203A  ILE*     3.7    29.6    -      -       +      -
    204A  VAL*     4.2     2.0    -      -       -      -
    285A  LEU*     4.2     9.6    -      -       +      +
    286A  TYR*     1.3    77.4    -      -       -      +
    288A  MET*     1.3    65.7    +      -       -      +
    295A  SER*     3.2     7.1    -      -       -      -
    296A  PHE*     2.9    60.7    +      -       +      +
    298A  ILE*     4.1    17.0    -      -       +      -
    333A  MET*     4.6    14.8    -      -       +      -
    354A  PHE*     3.8    24.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 288 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191A  THR*     2.6    37.4    +      -       -      +
    192A  PRO*     3.4    19.7    -      -       +      +
    202A  ILE*     3.1    49.1    +      -       +      +
    204A  VAL*     3.9     5.8    -      -       +      +
    287A  LEU*     1.3    71.5    -      -       -      +
    289A  GLY*     1.3    69.5    +      -       -      +
    296A  PHE*     3.7     1.4    -      -       -      -
    379A  MET*     3.3    59.9    -      -       +      +
    380A  GLU*     3.9    23.1    -      -       -      +
----------------------------------------------------------
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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