Contacts of the strand formed by residues 344 - 353 (chain A) in PDB entry 2BU6


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 PHE 344 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  ASP      4.9     2.7    -      -       -      -
    283A  ARG*     3.1    57.7    -      -       +      +
    285A  GLY*     3.0    19.7    +      -       -      -
    341A  MET*     2.9    32.2    +      -       +      +
    342A  GLU      5.0     0.7    -      -       -      +
    343A  GLY*     1.3    81.8    -      -       -      +
    345A  GLY*     1.3    72.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 345 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    282A  ASP*     3.1    17.3    -      -       -      -
    283A  ARG*     3.9     1.1    -      -       -      -
    286A  GLY*     3.8    10.2    -      -       -      +
    340A  SER*     3.0     2.6    -      -       -      -
    341A  MET*     2.8    31.8    +      -       -      +
    344A  PHE*     1.3    92.1    -      -       -      +
    346A  THR*     1.3    63.6    +      -       -      -
    347A  ASP*     5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with THR 346 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    280A  MET      3.5     1.4    -      -       -      +
    281A  SER*     3.4     1.7    -      -       -      -
    282A  ASP*     3.0    51.3    +      -       -      +
    286A  GLY*     3.7    10.2    +      -       -      -
    287A  VAL*     4.3     4.7    +      -       -      +
    292A  ILE*     5.3     4.0    -      -       +      -
    338A  LEU*     4.4    18.2    -      -       +      -
    339A  PHE      3.9     4.5    -      -       -      +
    340A  SER*     2.8    29.0    -      -       -      +
    345A  GLY*     1.3    72.6    -      -       -      -
    347A  ASP*     1.3    80.7    +      -       -      +
    348A  ALA*     5.3     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 347 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    279A  LYS*     3.3    30.1    +      -       +      +
    280A  MET      3.4     3.4    -      -       -      -
    281A  SER*     3.0    26.8    +      -       -      -
    282A  ASP      5.1     0.9    -      -       -      +
    338A  LEU*     3.6     2.6    -      -       -      -
    339A  PHE*     2.9    60.8    +      -       +      +
    345A  GLY      5.4     0.2    -      -       -      -
    346A  THR*     1.3    82.2    +      -       -      +
    348A  ALA*     1.3    59.7    +      -       -      +
    349A  VAL      4.2     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 348 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    244A  LEU*     3.9    30.2    -      -       +      +
    278A  ILE      3.6     1.6    -      -       -      +
    279A  LYS*     3.4     1.2    -      -       -      -
    280A  MET*     2.8    44.7    +      -       +      +
    336A  LEU*     5.3     0.2    -      -       +      -
    337A  GLN      3.4     6.3    -      -       -      +
    338A  LEU*     3.2    23.3    -      -       +      -
    346A  THR*     5.3     1.3    -      -       +      -
    347A  ASP*     1.3    72.7    -      -       -      +
    349A  VAL*     1.3    60.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 349 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    277A  SER*     4.5     5.8    -      -       -      -
    278A  ILE      3.3    10.3    -      -       -      +
    279A  LYS*     3.6    25.4    -      -       +      +
    336A  LEU*     3.2     6.2    -      -       -      +
    337A  GLN      2.8    38.4    +      -       -      +
    339A  PHE*     3.3    35.7    -      -       +      -
    348A  ALA*     1.3    77.4    -      -       -      +
    350A  ILE*     1.3    67.6    +      -       -      +
    351A  TYR*     3.3    42.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 350 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    237A  LEU*     4.6     6.5    -      -       +      -
    240A  MET*     3.8    34.5    -      -       +      -
    241A  LEU*     4.0    24.9    -      -       +      -
    244A  LEU*     3.8    31.2    -      -       +      -
    276A  LEU      3.8     1.7    -      -       -      +
    277A  SER*     3.5     3.8    -      -       -      -
    278A  ILE*     2.8    45.6    +      -       +      +
    329A  ALA*     4.7     0.4    -      -       +      -
    335A  ASP      3.5     9.0    -      -       -      +
    336A  LEU*     4.1     9.2    -      -       +      -
    349A  VAL*     1.3    74.5    -      -       -      +
    351A  TYR*     1.3    61.5    +      -       -      +
    352A  LEU*     3.8    30.0    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 351 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    275A  ASP*     4.4    16.8    -      -       -      +
    276A  LEU      4.0     2.0    -      -       -      -
    277A  SER*     3.4    23.6    -      -       -      -
    334A  GLY*     2.8     8.0    -      -       -      -
    335A  ASP*     2.7    57.5    +      -       +      +
    337A  GLN*     3.7    29.0    +      -       +      -
    339A  PHE*     4.6     5.9    -      -       -      -
    349A  VAL*     3.3    39.3    -      -       +      +
    350A  ILE*     1.3    71.2    -      -       -      +
    352A  LEU*     1.3    65.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 352 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  MET*     3.6    39.3    -      -       +      -
    232A  TYR*     3.5    34.1    -      -       +      +
    237A  LEU*     4.2    21.3    -      -       +      -
    240A  MET*     4.1     6.1    -      -       +      -
    275A  ASP*     3.6     8.5    -      -       -      +
    276A  LEU*     3.0    43.9    +      -       +      +
    278A  ILE*     4.5     4.3    -      -       +      -
    329A  ALA*     4.9     7.0    -      -       -      +
    332A  PHE      5.7     0.2    -      -       -      -
    334A  GLY*     4.3     4.5    -      -       -      -
    350A  ILE*     3.8    24.2    -      -       +      +
    351A  TYR*     1.3    77.5    -      -       -      +
    353A  LYS*     1.3    62.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 353 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230A  MET*     3.5    18.4    -      -       -      +
    232A  TYR*     5.6     1.5    -      -       -      -
    274A  GLU*     3.6    25.1    +      -       +      +
    275A  ASP*     4.9     6.7    +      -       -      +
    276A  LEU      4.6     0.2    -      -       -      -
    332A  PHE      3.7    20.2    +      -       -      +
    333A  GLN*     3.6    28.9    +      -       +      +
    334A  GLY*     5.0     0.4    -      -       -      -
    352A  LEU*     1.3    75.9    -      -       -      +
    354A  ALA*     1.3    64.3    +      -       -      +
    355A  LEU      3.6     1.0    +      -       -      +
    358A  ASP*     3.8    34.5    -      -       +      +
    359A  SER*     3.7    21.9    +      -       -      +
----------------------------------------------------------
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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