Contacts of the strand formed by residues 269 - 273 (chain A) in PDB entry 1BFD


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 269 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    196A  ALA*     4.5    10.5    -      -       +      +
    197A  LEU*     4.1    26.7    -      -       +      -
    200A  ALA*     3.8    27.1    -      -       +      -
    202A  ASN      4.3     0.3    -      -       -      +
    203A  PRO*     3.2     7.2    -      -       +      +
    204A  ALA      3.0    23.7    +      -       -      +
    267A  HIS*     4.5     0.3    -      -       -      +
    268A  ASP*     1.3    91.8    +      -       +      +
    270A  VAL*     1.3    69.4    +      -       -      +
    271A  LEU      4.7     0.2    -      -       -      +
    294A  ARG*     3.3    16.8    -      -       +      +
    296A  ILE*     4.2    20.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 270 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    204A  ALA*     3.4     8.3    -      -       +      +
    206A  VAL*     3.9    28.0    -      -       +      -
    264A  LEU*     4.1    26.7    -      -       +      -
    267A  HIS*     4.1    16.8    -      -       +      -
    269A  VAL*     1.3    79.8    -      -       -      +
    271A  LEU*     1.3    59.8    +      -       -      +
    272A  VAL*     3.8    11.6    +      -       +      -
    278A  PHE*     5.6     0.2    -      -       +      -
    293A  THR*     3.6    27.4    -      -       +      -
    294A  ARG      2.8    11.8    +      -       -      +
    295A  LEU*     3.4    10.1    -      -       +      +
    296A  ILE*     2.9    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 271 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193A  LEU*     4.8     5.6    -      -       +      -
    197A  LEU*     4.1    36.3    -      -       +      -
    204A  ALA      3.0    10.3    +      -       -      +
    205A  ILE*     3.4    14.3    -      -       +      +
    206A  VAL      2.9    25.6    +      -       -      +
    223A  LEU*     4.0    17.0    -      -       +      -
    227A  LEU*     5.2     2.2    -      -       +      -
    269A  VAL*     4.0     2.1    +      -       +      -
    270A  VAL*     1.3    72.5    -      -       -      +
    272A  VAL*     1.3    60.0    +      -       -      +
    273A  ILE*     3.9    25.4    -      -       +      -
    296A  ILE*     3.4    29.8    -      -       +      +
    298A  VAL*     4.4    18.8    -      -       +      -
    325A  LEU*     4.4     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 272 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    206A  VAL*     3.2    27.8    -      -       +      +
    270A  VAL*     4.1     5.2    -      -       +      -
    271A  LEU*     1.3    74.8    -      -       -      +
    273A  ILE*     1.3    64.3    +      -       -      +
    274A  GLY      4.3     0.2    -      -       -      -
    275A  ALA*     4.2    26.2    -      -       +      +
    277A  VAL*     4.2    16.2    -      -       +      -
    278A  PHE*     4.1    11.9    -      -       +      -
    295A  LEU*     3.9    34.5    -      -       +      -
    296A  ILE      2.8    12.7    +      -       -      +
    297A  SER*     3.4     6.0    -      -       -      +
    298A  VAL*     2.8    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 273 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    205A  ILE*     4.8     2.0    -      -       +      -
    206A  VAL      2.8     9.8    +      -       -      +
    207A  LEU*     3.4    23.4    -      -       +      -
    208A  GLY      2.9    25.1    +      -       -      -
    211A  VAL*     3.5    17.9    -      -       +      +
    220A  CYS*     4.5     9.0    -      -       -      -
    223A  LEU*     3.9    28.3    -      -       +      -
    271A  LEU*     3.9    23.6    -      -       +      +
    272A  VAL*     1.3    79.2    -      -       -      +
    274A  GLY*     1.3    63.6    +      -       -      +
    275A  ALA*     3.4     2.4    +      -       -      +
    298A  VAL*     3.6    15.3    -      -       +      +
    318A  ILE*     3.9    21.1    -      -       +      +
    321A  MET*     6.0     0.4    -      -       +      -
    322A  ALA*     5.3     7.9    -      -       +      +
    325A  LEU*     4.7     8.1    -      -       +      -
----------------------------------------------------------
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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