Contacts of the strand formed by residues 154 - 159 (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 154 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92A  LEU      2.9    15.4    +      -       -      +
     93A  ILE*     3.9    10.5    -      -       +      -
     94A  VAL*     3.0    31.2    +      -       -      +
    123A  VAL*     4.3     3.4    -      -       -      -
    124A  LYS*     4.2    10.3    -      -       +      -
    125A  TRP*     3.3    19.7    -      -       +      +
    142A  ALA*     3.4    33.0    -      -       +      +
    145A  MET*     3.8    16.8    -      -       +      -
    146A  ALA*     3.7    26.9    -      -       +      +
    152A  GLY      4.1     0.7    -      -       -      +
    153A  PRO*     1.3    80.0    -      -       -      +
    155A  TYR*     1.3    62.0    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 155 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75A  THR*     2.9    44.1    +      -       +      +
     82A  LEU*     5.9     1.1    -      -       +      -
     94A  VAL*     3.3    30.1    -      -       +      -
     96A  ALA*     3.4    18.2    -      -       +      +
    112A  ASN*     2.9    22.3    +      -       -      -
    115A  ALA      3.6    22.4    -      -       -      -
    116A  ALA*     4.7     1.6    -      -       -      -
    118A  LEU*     4.5     0.3    -      -       -      +
    119A  PRO*     3.5    19.7    -      -       +      -
    123A  VAL*     4.3     6.5    -      -       +      -
    125A  TRP*     2.9    17.1    +      -       -      +
    126A  SER*     3.3    26.6    -      -       -      +
    127A  TYR*     3.0    26.6    +      -       -      -
    142A  ALA*     5.8     0.2    -      -       -      -
    154A  VAL*     1.3    77.9    -      -       -      +
    156A  LEU*     1.3    63.2    +      -       -      +
    157A  SER*     4.3    13.9    -      -       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with LEU 156 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     93A  ILE*     6.0     0.4    -      -       +      -
     94A  VAL      2.9     9.9    +      -       -      +
     95A  THR*     3.2    11.2    -      -       +      -
     96A  ALA*     3.0    25.1    +      -       -      +
    125A  TRP*     4.6     4.7    -      -       +      -
    127A  TYR*     3.4    23.8    -      -       +      +
    129A  PRO*     4.0    12.8    -      -       +      -
    135A  VAL*     4.8     2.5    -      -       +      +
    138A  ALA*     3.8    24.0    -      -       +      +
    139A  MET*     3.8    52.5    -      -       +      +
    142A  ALA*     4.8     9.9    -      -       +      -
    155A  TYR*     1.3    78.6    -      -       -      +
    157A  SER*     1.3    60.6    +      -       -      +
    158A  VAL*     4.0    17.1    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with SER 157 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     96A  ALA*     3.4     7.5    +      -       -      +
     97A  GLY      5.0     0.3    -      -       -      -
     98A  GLN*     3.5    12.8    +      -       -      +
    112A  ASN*     4.6     3.6    +      -       -      +
    115A  ALA*     3.8    20.5    -      -       -      +
    127A  TYR      3.0    12.6    +      -       -      -
    128A  GLU*     2.7    32.4    +      -       -      +
    129A  PRO*     3.1    25.5    -      -       -      +
    155A  TYR*     4.3    11.6    -      -       -      -
    156A  LEU*     1.3    73.8    -      -       -      +
    158A  VAL*     1.3    60.5    +      -       -      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 158 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     95A  THR*     5.6     4.3    -      -       -      -
     96A  ALA      3.0    11.9    +      -       -      +
     97A  GLY*     3.6     5.6    -      -       -      -
     98A  GLN*     2.9    20.5    +      -       -      -
    129A  PRO*     4.8     1.3    -      -       +      -
    135A  VAL*     4.0    21.1    -      -       +      -
    139A  MET*     5.4     1.6    -      -       +      -
    156A  LEU*     4.0    27.1    -      -       +      +
    157A  SER*     1.3    80.1    +      -       -      +
    159A  PRO*     1.3    78.0    -      -       -      +
    160A  TYR*     3.3     2.1    +      -       -      -
    162A  ASP*     3.9    14.8    -      -       +      +
    163A  TRP*     3.5    40.3    +      -       +      -
----------------------------------------------------------
 Back to top of page

Residues in contact with PRO 159 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98A  GLN*     3.6    18.8    -      -       +      +
     99A  GLN      3.4    17.9    -      -       -      +
    101A  ARG*     3.7    35.0    -      -       +      +
    104A  ILE*     4.1     6.1    -      -       +      -
    128A  GLU*     4.4     9.4    -      -       +      -
    129A  PRO*     4.8     1.6    -      -       +      -
    157A  SER      4.0     5.4    -      -       -      +
    158A  VAL*     1.3    87.6    -      -       -      +
    160A  TYR*     1.3    65.5    +      -       -      +
    161A  ASP*     3.2    14.6    -      -       -      +
    162A  ASP*     3.1    35.2    +      -       -      +
    163A  TRP*     4.2     0.5    +      -       -      -
----------------------------------------------------------
 Back to top of page


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