Contacts of the strand formed by residues 286 - 293 (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 GLY 286 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    262D  LYS*     4.6     1.1    -      -       -      -
    263D  ASN*     3.6    13.2    -      -       -      -
    284D  HIS      3.5     1.8    +      -       -      -
    285D  GLN*     1.3    78.1    -      -       -      +
    287D  THR*     1.3    63.4    +      -       -      -
    288D  TYR*     3.5    12.0    -      -       -      -
    305D  GLU*     3.5     7.1    -      -       -      +
    306D  ILE      2.9    33.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with THR 287 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261D  PHE      3.9     0.2    -      -       -      +
    262D  LYS*     3.3     1.9    -      -       -      -
    263D  ASN*     2.7    46.1    +      -       -      -
    264D  GLU      4.7     0.2    +      -       -      -
    286D  GLY*     1.3    73.7    -      -       -      -
    288D  TYR*     1.3    64.4    +      -       -      +
    289D  TRP*     4.8     2.1    -      -       -      -
    303D  LYS*     3.6    40.8    -      -       +      +
    304D  VAL      3.3    12.7    +      -       -      +
    305D  GLU*     4.5    10.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 288 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244D  LEU*     3.9     9.3    -      -       +      +
    246D  LEU*     3.6    24.7    -      -       +      -
    260D  TRP*     4.7     6.1    -      +       +      -
    261D  PHE      3.1    13.7    -      -       -      +
    262D  LYS*     3.3    32.0    -      -       +      +
    267D  LEU*     4.0     9.6    -      -       +      -
    275D  TYR*     3.6    26.8    +      +       -      -
    284D  HIS*     2.7    40.9    +      -       -      +
    286D  GLY      3.5    16.4    -      -       -      -
    287D  THR*     1.3    75.1    -      -       -      +
    289D  TRP*     1.3    67.4    +      -       -      +
    302D  LYS      3.9     0.3    -      -       -      +
    303D  LYS*     3.3     1.6    -      -       -      -
    304D  VAL*     2.9    40.6    +      -       +      +
    306D  ILE*     3.6    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 289 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    296A  ARG*     3.7    16.2    -      -       +      -
    269C  HIS*     3.6    23.8    -      +       -      -
    233D  PRO*     5.3     0.2    -      -       -      -
    260D  TRP*     3.5    10.5    -      -       -      -
    261D  PHE*     2.8    77.5    +      +       +      +
    264D  GLU*     3.2    33.3    +      -       -      +
    287D  THR      4.8     3.1    -      -       -      -
    288D  TYR*     1.3    83.1    -      -       -      +
    290D  CYS*     1.3    74.8    +      -       -      +
    291D  HIS*     3.9     8.3    -      -       +      -
    300D  ASP*     3.0    36.8    -      -       +      -
    301D  SER*     3.4    15.7    -      -       -      +
    302D  LYS      3.7     6.7    -      -       -      +
    303D  LYS*     3.8    31.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 290 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248D  CYS*     3.9    11.9    -      -       +      -
    258D  TYR*     3.8    39.0    -      -       -      -
    259D  GLN      3.4    10.5    -      -       -      -
    260D  TRP*     3.8    37.7    -      -       +      -
    289D  TRP*     1.3    80.0    -      -       -      +
    291D  HIS*     1.3    65.2    +      -       -      +
    292D  VAL*     3.8     3.8    +      -       -      +
    300D  ASP*     3.6     1.2    -      -       -      -
    301D  SER*     2.8    40.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 291 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    294A  ASN      4.0     3.0    +      -       -      -
    295A  ASP      3.2    36.1    -      -       -      +
    296A  ARG*     2.8    25.9    +      -       -      -
    297A  ASP*     3.7     6.4    +      -       -      -
    298A  SER      5.0     0.2    -      -       -      -
    257D  HIS      3.7     0.5    -      -       -      +
    258D  TYR*     3.3     6.6    -      -       -      -
    259D  GLN      2.9    31.4    +      -       -      +
    261D  PHE*     3.8    12.1    -      -       +      -
    289D  TRP*     3.9     4.0    -      -       +      -
    290D  CYS*     1.3    72.2    -      -       -      +
    292D  VAL*     1.3    59.4    +      -       -      +
    293D  TYR*     3.6    25.1    -      +       +      +
    298D  SER*     3.5    36.1    +      -       -      -
    299D  GLN      3.8     5.6    +      -       -      -
    300D  ASP*     2.7    28.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 292 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    227D  LEU*     4.1     9.5    -      -       +      +
    229D  ILE*     3.7    16.4    -      -       +      -
    248D  CYS*     3.7    31.6    -      -       -      -
    250D  ALA*     3.5    29.2    -      -       +      -
    256D  PRO*     3.7    10.5    -      -       +      -
    257D  HIS      3.2     9.2    -      -       -      +
    258D  TYR*     3.9    11.9    -      -       +      -
    290D  CYS*     4.0     5.6    -      -       -      +
    291D  HIS*     1.3    77.6    -      -       -      +
    293D  TYR*     1.3    63.9    +      -       -      +
    298D  SER*     3.2     4.3    -      -       -      -
    299D  GLN      2.9    37.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 293 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    293A  TYR*     3.9    31.6    -      +       +      -
    294A  ASN      4.0     9.9    -      -       -      +
    295A  ASP*     3.7    29.6    -      -       +      +
    227D  LEU*     3.6     7.0    -      -       -      -
    257D  HIS*     2.8    76.0    +      +       +      +
    258D  TYR      4.1    11.8    +      -       -      -
    291D  HIS*     3.6    24.9    -      +       -      +
    292D  VAL*     1.3    79.5    -      -       -      +
    294D  ASN*     1.3    65.6    +      -       -      +
    297D  ASP      3.4     6.5    -      -       -      +
    298D  SER*     3.6    16.8    -      -       -      -
----------------------------------------------------------
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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