Contacts of the strand formed by residues 244 - 247 (chain C) 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 244 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    236C  GLN*     4.1     5.6    -      -       -      +
    238C  LEU*     4.0    11.0    -      -       +      -
    243C  THR*     1.3    72.5    -      -       -      +
    245C  VAL*     1.3    67.9    +      -       -      +
    246C  LEU*     4.0    14.4    -      -       +      -
    275C  TYR*     3.9    21.3    -      -       +      -
    276C  MET*     3.2     5.7    -      -       -      -
    277C  VAL*     2.8    45.4    +      -       +      +
    280C  VAL*     3.5    22.3    -      -       +      +
    284C  HIS*     4.6     3.4    -      -       +      -
    288C  TYR*     3.9    26.9    -      -       +      +
    306C  ILE*     3.5    38.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 245 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234C  THR*     5.2     0.5    +      -       -      -
    236C  GLN*     3.0    24.9    +      -       -      -
    243C  THR*     3.9    14.1    +      -       +      +
    244C  LEU*     1.3    80.0    -      -       -      +
    246C  LEU*     1.3    65.5    +      -       -      +
    247C  GLN*     5.0     2.5    -      -       +      +
    274C  LEU*     3.9    27.6    -      -       +      -
    275C  TYR      3.4     2.7    -      -       -      -
    276C  MET*     3.6    34.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 246 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233C  PRO*     4.1     7.9    -      -       +      -
    234C  THR      3.5    26.2    -      -       -      +
    236C  GLN*     3.8    10.5    -      -       -      +
    244C  LEU*     4.0     8.5    -      -       +      -
    245C  VAL*     1.3    75.0    -      -       -      +
    247C  GLN*     1.3    59.8    +      -       -      +
    260C  TRP*     3.8    19.7    -      -       +      -
    273C  LYS      3.7     0.3    -      -       -      +
    274C  LEU*     3.3     6.1    -      -       -      +
    275C  TYR*     2.8    48.5    +      -       +      +
    288C  TYR*     3.5    47.3    -      -       +      -
    304C  VAL*     3.9    13.7    -      -       +      -
    306C  ILE*     4.1     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 247 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    231C  VAL*     4.1    16.3    -      -       +      +
    232C  GLU      3.4     4.1    -      -       -      +
    233C  PRO*     3.1    32.2    -      -       +      +
    234C  THR      5.5     0.2    -      -       -      +
    245C  VAL*     5.2     2.4    -      -       +      +
    246C  LEU*     1.3    76.2    -      -       -      +
    248C  CYS*     1.3    64.3    +      -       -      +
    249C  VAL*     3.6    26.5    -      -       +      +
    260C  TRP*     3.9     2.9    -      -       -      -
    273C  LYS*     3.3     7.4    -      -       -      +
    274C  LEU*     3.6    26.2    -      -       +      +
----------------------------------------------------------
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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