Contacts of the strand formed by residues 150 - 155 (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 PHE 150 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33A  THR*     4.0     9.6    -      -       +      -
    121A  LEU*     3.7    42.4    -      -       +      -
    137A  PHE*     3.9    30.5    -      +       +      -
    149A  LEU*     1.3    75.8    -      -       -      +
    151A  SER*     1.3    66.1    +      -       -      +
    152A  LEU*     4.2    10.5    -      -       +      -
    174A  MET*     4.8     4.5    -      -       +      -
    175A  ILE      3.2    13.9    -      -       -      +
    176A  ILE*     4.2     9.6    -      -       +      -
    178A  GLY      4.3     3.8    -      -       -      -
    199A  TYR*     3.3    24.9    -      +       -      -
    344A  VAL*     3.7     1.7    -      -       -      +
    345A  PHE*     2.7    69.7    +      +       +      +
    347A  ARG*     4.0     8.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with SER 151 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    150A  PHE*     1.3    77.3    -      -       -      +
    152A  LEU*     1.3    65.0    +      -       -      +
    173A  SER      3.8     0.2    -      -       -      +
    174A  MET*     3.4     7.3    -      -       -      +
    175A  ILE*     2.8    35.2    +      -       -      +
    178A  GLY      2.9    16.7    +      -       -      -
    179A  ILE*     4.7     0.2    -      -       -      -
    342A  TYR*     2.5    35.4    +      -       -      -
    343A  VAL      3.2    12.6    -      -       -      -
    344A  VAL*     4.0    12.8    -      -       -      -
    345A  PHE*     4.7     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 152 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  LEU*     4.1    12.6    -      -       +      -
     31A  VAL*     4.1    12.8    -      -       +      -
     33A  THR*     3.7    29.8    -      -       +      -
    150A  PHE*     4.2     6.5    -      -       +      -
    151A  SER*     1.3    75.3    -      -       -      +
    153A  GLN*     1.3    59.8    +      -       -      +
    154A  LEU*     3.9     8.8    +      -       +      -
    173A  SER      3.5     3.6    -      -       -      +
    174A  MET*     3.6    37.0    -      -       +      -
    229A  SER*     4.1     9.9    -      -       -      +
    338A  MET*     3.8    22.9    -      -       +      +
    341A  PHE      3.9     3.1    -      -       -      +
    342A  TYR*     3.8     4.8    -      -       -      -
    343A  VAL*     2.7    37.2    +      -       -      +
    345A  PHE*     3.7    13.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 153 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    151A  SER      4.3     0.2    -      -       -      -
    152A  LEU*     1.3    71.0    -      -       -      +
    154A  LEU*     1.3    60.5    +      -       -      +
    155A  CYS*     3.6    10.6    -      -       -      -
    172A  GLY*     3.0     8.0    -      -       -      -
    173A  SER*     2.8    48.6    +      -       -      +
    183A  LEU*     3.1    58.2    +      -       +      +
    341A  PHE      4.6     2.5    -      -       -      +
    342A  TYR*     3.9    14.7    -      -       +      -
    357A  SER*     3.6    23.5    +      -       -      +
    358A  ALA*     4.0     3.0    -      -       -      +
    359A  CYS*     3.6    26.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 154 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  LEU*     3.8    21.8    -      -       +      -
     14A  TYR*     3.8    49.8    -      -       +      +
     31A  VAL*     6.1     1.1    -      -       +      -
    152A  LEU*     3.9    14.2    +      -       +      +
    153A  GLN*     1.3    71.1    -      -       -      +
    155A  CYS*     1.3    62.6    +      -       -      +
    156A  GLY      3.9     0.2    -      -       -      -
    229A  SER*     4.4    12.8    -      -       -      +
    335A  ALA*     4.8     8.7    -      -       +      -
    338A  MET*     3.8    47.9    +      -       +      +
    339A  GLU*     3.2    34.9    -      -       +      +
    341A  PHE      4.7     1.1    +      -       -      +
    357A  SER*     5.1     0.7    +      -       -      -
    359A  CYS*     4.2     2.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     14A  TYR*     3.2     7.1    +      -       -      -
    153A  GLN*     3.6    15.9    -      -       -      -
    154A  LEU*     1.3    72.3    -      -       -      +
    156A  GLY*     1.3    63.8    +      -       -      +
    170A  VAL*     3.5     0.9    -      -       -      +
    171A  GLY*     2.9    43.5    +      -       -      +
    172A  GLY*     4.3     5.8    -      -       -      -
    339A  GLU      5.1     0.7    -      -       -      -
    359A  CYS*     2.1    54.5    -      -       +      +
    360A  HIS*     6.1     0.4    -      -       -      +
----------------------------------------------------------
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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