Contacts of the strand formed by residues 274 - 277 (chain D) in PDB entry 3BFO


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 LEU 274 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    245D  VAL*     3.8    17.9    -      -       +      -
    246D  LEU      3.3     1.3    -      -       -      -
    247D  GLN*     3.6    42.6    -      -       +      +
    260D  TRP*     4.2     0.5    +      -       -      -
    270D  GLU*     4.4     6.2    -      -       -      +
    272D  LYS*     3.7    23.8    +      -       +      +
    273D  LYS*     1.3    80.7    -      -       +      +
    275D  TYR*     1.3    59.0    -      -       -      +
    276D  MET*     4.1    36.7    +      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with TYR 275 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244D  LEU*     3.7     9.3    -      -       +      +
    245D  VAL*     3.4     1.0    -      -       -      -
    246D  LEU*     2.8    46.5    +      -       +      +
    260D  TRP*     3.9    25.5    -      +       +      +
    262D  LYS*     6.0     0.2    -      -       -      +
    267D  LEU*     3.8    24.2    -      -       +      +
    270D  GLU*     3.4    45.5    -      -       +      -
    274D  LEU*     1.3    71.9    -      -       -      +
    276D  MET*     1.3    67.0    +      -       -      +
    277D  VAL*     3.3    32.8    -      -       +      +
    284D  HIS*     4.5     5.7    +      -       -      -
    288D  TYR*     3.6    32.4    +      +       -      -
----------------------------------------------------------
 Back to top of page

Residues in contact with MET 276 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243D  THR*     5.6     2.5    -      -       +      -
    244D  LEU      3.2     5.4    -      -       -      +
    245D  VAL*     3.8    29.2    -      -       +      -
    270D  GLU*     5.0     4.0    +      -       -      +
    274D  LEU*     4.1    32.9    -      -       +      +
    275D  TYR*     1.3    88.6    -      -       -      +
    277D  VAL*     1.3    69.2    +      -       -      +
    278D  PRO*     4.2     6.1    -      -       +      +
----------------------------------------------------------
 Back to top of page

Residues in contact with VAL 277 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    242D  SER      4.2     0.5    -      -       -      +
    243D  THR*     3.5     2.4    -      -       -      +
    244D  LEU*     2.8    48.9    +      -       +      +
    275D  TYR*     3.3    37.0    -      -       +      +
    276D  MET*     1.3    79.5    -      -       -      +
    278D  PRO*     1.4    66.8    -      -       +      +
    279D  TYR      3.5     9.8    +      -       -      +
    280D  VAL*     4.0     7.2    -      -       +      -
    284D  HIS*     3.5    40.8    -      -       +      +
----------------------------------------------------------
 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