Contacts of the strand formed by residues 257 - 262 (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 HIS 257 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    254D  PRO*     6.2     0.6    -      -       -      +
    255D  ILE*     3.2    18.1    +      -       -      +
    256D  PRO*     1.3    75.2    +      -       -      +
    258D  TYR*     1.3    66.4    +      -       -      +
    271D  THR      5.6     0.2    -      -       -      -
    292D  VAL*     3.2     8.7    -      -       -      +
    293D  TYR*     2.8    69.6    +      +       +      +
    294D  ASN*     4.7     6.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 258 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    248D  CYS      3.4    22.0    -      -       -      -
    250D  ALA*     3.0    37.3    +      -       -      +
    255D  ILE*     6.1     0.2    -      -       +      -
    256D  PRO*     3.5    24.8    -      -       +      +
    257D  HIS*     1.3    79.1    -      -       -      +
    259D  GLN*     1.3    62.5    +      -       -      +
    260D  TRP*     5.0     0.2    -      -       -      +
    271D  THR*     3.1    47.7    +      -       -      +
    272D  LYS*     3.9     8.1    -      -       -      +
    273D  LYS*     3.4    34.4    -      -       +      +
    290D  CYS*     3.8    21.5    -      -       -      -
    291D  HIS      3.3     6.7    -      -       -      -
    292D  VAL*     3.9    21.5    -      -       +      -
    293D  TYR*     4.3     6.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 259 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  ASP*     3.6    42.0    -      -       +      +
    258D  TYR*     1.3    73.6    -      -       -      +
    260D  TRP*     1.3    84.2    +      -       -      +
    261D  PHE*     3.3    27.6    -      -       +      -
    266D  PRO*     3.8     7.3    -      -       +      +
    267D  LEU      2.9    28.6    +      -       -      +
    268D  THR*     5.8     0.2    -      -       -      -
    269D  HIS      4.9     2.4    +      -       -      -
    270D  GLU      3.5     6.0    +      -       -      -
    271D  THR*     3.4    20.4    -      -       -      +
    290D  CYS*     3.8     4.0    -      -       -      -
    291D  HIS      2.9    33.8    +      -       -      +
    293D  TYR*     4.8     0.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 260 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    233D  PRO*     4.1    13.7    -      -       +      -
    246D  LEU*     3.8    39.3    -      -       +      -
    247D  GLN      3.8    12.8    -      -       -      -
    248D  CYS*     3.7    19.1    -      -       +      -
    259D  GLN*     1.3    91.9    +      -       -      +
    261D  PHE*     1.3    60.7    +      -       -      +
    266D  PRO*     3.5     2.1    -      -       -      +
    267D  LEU*     2.9    30.7    +      -       +      -
    270D  GLU*     3.0    36.9    +      -       +      +
    272D  LYS      2.8    26.0    +      -       -      -
    273D  LYS      3.3    19.8    +      -       -      -
    274D  LEU      4.7     0.4    -      -       -      -
    275D  TYR*     3.9    24.6    -      -       +      +
    288D  TYR*     4.7     4.3    -      +       +      -
    289D  TRP*     3.5    28.5    -      -       -      -
    290D  CYS*     3.8    18.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 261 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    295A  ASP*     3.6    24.0    -      -       -      -
    296A  ARG*     3.8    27.6    -      -       +      -
    259D  GLN*     3.3    35.4    -      -       +      -
    260D  TRP*     1.3    72.7    -      -       -      +
    262D  LYS*     1.3    60.3    +      -       -      +
    264D  GLU*     3.8    10.5    -      -       -      -
    265D  LEU      3.2    10.8    -      -       -      +
    266D  PRO*     3.5    34.3    -      -       +      -
    267D  LEU*     4.3     3.4    -      -       -      -
    288D  TYR*     3.1    11.2    -      -       -      +
    289D  TRP*     2.8    72.2    +      +       +      +
    291D  HIS*     3.8     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 262 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    261D  PHE*     1.3    74.0    -      -       -      +
    263D  ASN*     1.3    89.7    +      -       -      +
    264D  GLU      3.1     1.3    -      -       -      -
    265D  LEU*     2.9    21.9    +      -       -      +
    267D  LEU*     4.1    21.6    -      -       +      +
    283D  GLU      2.8    29.1    +      -       -      -
    284D  HIS*     4.3     1.0    +      -       -      +
    285D  GLN      3.8    10.6    +      -       -      +
    287D  THR      3.3     9.2    -      -       -      +
    288D  TYR*     3.3    43.5    -      -       +      +
----------------------------------------------------------
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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