Contacts of the strand formed by residues 449 - 454 (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 ILE 449 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    421A  GLN*     3.5    22.9    -      -       +      +
    422A  VAL      3.0    12.3    +      -       -      +
    423A  ILE*     3.4    12.3    -      -       +      -
    424A  ALA      2.9    25.8    +      -       -      -
    447A  PRO      4.4     2.2    -      -       -      +
    448A  THR*     1.3    77.8    -      -       -      +
    450A  PHE*     1.3    62.6    +      -       -      +
    451A  VAL*     4.1    19.7    +      -       +      -
    507A  LEU*     5.2     4.9    -      -       +      -
    510A  ALA*     3.8    43.3    -      -       +      +
    511A  LEU*     3.8    25.6    -      -       +      -
    517A  VAL*     3.3    13.0    -      -       +      +
    519A  ILE*     4.4     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 450 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407A  LEU*     3.7    40.4    -      -       +      -
    410A  ALA*     4.3     1.1    -      -       +      -
    411A  ILE*     4.0    16.8    -      -       +      -
    424A  ALA*     3.6    15.0    -      -       +      +
    426A  ILE*     4.4     1.8    -      -       +      -
    438A  LEU*     3.7    27.1    -      -       +      -
    441A  ALA*     4.4     4.5    -      -       +      -
    448A  THR*     3.6    41.1    -      -       +      -
    449A  ILE*     1.3    73.4    -      -       -      +
    451A  VAL*     1.3    58.0    +      -       -      +
    452A  ILE*     3.9     8.6    +      -       +      -
    492A  VAL*     5.0     2.0    -      -       +      -
    516A  PRO*     4.3    13.0    -      -       +      -
    517A  VAL      2.8    22.8    +      -       -      +
    518A  LEU*     3.3    16.1    -      -       +      +
    519A  ILE*     2.8    33.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 451 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    358A  VAL*     4.6    11.2    -      -       +      -
    362A  LEU*     4.7    11.2    -      -       +      -
    423A  ILE*     4.0    25.1    -      -       +      -
    424A  ALA      2.7    12.7    +      -       -      +
    425A  VAL*     3.5     9.6    -      -       +      +
    426A  ILE      2.9    28.1    +      -       -      +
    449A  ILE*     4.2    10.1    -      -       +      -
    450A  PHE*     1.3    75.2    -      -       -      +
    452A  ILE*     1.3    62.5    +      -       -      +
    453A  MET*     3.7    16.4    +      -       -      -
    503A  LEU*     5.7     2.2    -      -       +      -
    507A  LEU*     4.9     2.5    -      -       +      -
    519A  ILE*     3.5    13.9    -      -       +      -
    521A  VAL*     3.7    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 452 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    407A  LEU*     5.3     3.1    -      -       +      -
    426A  ILE*     3.2    21.8    -      -       +      +
    427A  GLY      4.4     0.7    -      -       -      +
    428A  ASP*     4.0    23.8    -      -       +      -
    431A  ALA*     4.2    17.7    -      -       +      -
    435A  ILE*     6.5     0.2    -      -       +      -
    450A  PHE*     4.5     9.4    -      -       +      -
    451A  VAL*     1.3    76.5    -      -       -      +
    453A  MET*     1.3    59.6    +      -       -      +
    454A  ASN*     3.3     4.4    +      -       +      +
    483A  PHE*     4.0    27.4    -      -       +      -
    518A  LEU*     3.9    39.5    -      -       +      -
    519A  ILE      2.8    13.4    +      -       -      +
    520A  GLU*     4.3     5.6    -      -       -      -
    521A  VAL*     2.8    34.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 453 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    355A  PRO*     4.2    27.8    -      -       +      -
    358A  VAL*     4.1    24.5    -      -       +      -
    359A  PHE*     4.0    26.2    -      -       +      -
    376A  SER*     3.7    23.1    -      -       -      +
    379A  THR*     4.6     1.8    -      -       +      +
    425A  VAL*     3.8    20.2    -      -       +      -
    426A  ILE      2.8    14.4    +      -       -      +
    427A  GLY*     3.7     3.4    -      -       -      -
    428A  ASP*     3.1    24.7    +      -       -      +
    451A  VAL*     4.4     9.0    -      -       -      +
    452A  ILE*     1.3    67.2    -      -       -      +
    454A  ASN*     1.3    59.6    +      -       -      +
    455A  ASN*     3.5     5.0    +      -       -      +
    521A  VAL*     3.9     5.4    -      -       -      -
    523A  THR*     3.9    21.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASN 454 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    352A  ARG*     2.8    24.3    +      -       -      -
    428A  ASP*     3.2    18.6    -      -       +      +
    452A  ILE*     3.3     1.7    +      -       +      +
    453A  MET*     1.3    72.6    -      -       -      +
    455A  ASN*     1.3    58.0    +      -       -      +
    456A  GLY*     3.0    19.4    +      -       -      -
    481A  ILE      4.1     6.9    +      -       -      -
    483A  PHE*     4.1    11.6    -      -       +      -
    520A  GLU*     2.9    36.8    +      -       +      +
    521A  VAL      2.7    18.4    +      -       -      +
    522A  SER*     3.7     1.5    -      -       -      -
    523A  THR*     3.0    13.5    +      -       -      -
----------------------------------------------------------
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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