Contacts of the strand formed by residues 237 - 241 (chain B) in PDB entry 6HBU


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 THR 237 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     35B  ALA*     3.3    29.8    -      -       +      +
     37B  LEU*     5.4     2.7    -      -       +      +
     71B  MET      3.6     6.2    +      -       -      +
     72B  LYS      3.4     2.8    +      -       -      -
     73B  PRO*     3.7    11.4    -      -       -      -
     74B  GLY      3.9     3.1    -      -       -      -
     76B  ASN*     3.2    22.0    +      -       -      -
    205B  SER      2.9     6.3    +      -       -      +
    206B  ILE*     3.7    33.0    -      -       +      +
    207B  LEU      3.0    25.5    +      -       -      +
    235B  GLY      3.8     2.0    +      -       -      -
    236B  ARG*     1.3    71.3    -      -       -      +
    238B  ILE*     1.3    59.9    +      -       -      +
    239B  ILE*     3.7     8.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 238 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74B  GLY      3.2    11.1    +      -       -      +
     75B  LEU*     3.8    15.3    -      -       +      -
     76B  ASN*     2.7    34.5    +      -       -      +
    207B  LEU*     3.3    18.4    -      -       +      +
    209B  LEU*     3.7    28.3    -      -       +      -
    228B  LEU*     3.3    45.5    -      -       +      +
    231B  MET*     4.4     9.0    -      -       +      -
    232B  SER*     3.8    17.9    -      -       -      +
    236B  ARG*     4.4     7.4    -      -       +      +
    237B  THR*     1.3    77.7    +      -       -      +
    239B  ILE*     1.3    58.4    +      -       -      +
    240B  PHE*     3.9     6.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 239 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37B  LEU*     4.7     7.0    -      -       +      -
     71B  MET*     3.6    38.1    -      -       +      -
     76B  ASN*     3.4    13.7    -      -       -      +
     78B  ILE*     3.9    11.7    -      -       +      -
     90B  LEU*     3.7    21.3    -      -       +      +
     93B  LEU*     4.4     4.3    -      -       +      -
    206B  ILE*     3.8    18.8    -      -       +      -
    207B  LEU      3.0     6.7    +      -       -      +
    208B  PHE*     3.2    33.1    -      -       +      -
    209B  LEU      3.0    21.5    +      -       -      +
    237B  THR*     3.7    19.1    -      -       +      +
    238B  ILE*     1.3    72.8    -      -       -      +
    240B  PHE*     1.3    63.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 240 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75B  LEU*     3.6    28.0    -      -       +      -
     76B  ASN      2.9    19.5    +      -       -      +
     77B  ALA*     3.3    18.6    -      -       +      -
     78B  ILE*     2.7    38.1    +      -       -      +
     90B  LEU*     4.6     1.1    -      -       -      -
    209B  LEU*     3.2    31.0    -      -       +      +
    212B  PRO*     4.4     8.5    -      -       +      -
    225B  LEU*     3.6    19.1    -      -       +      -
    228B  LEU*     5.1     2.9    -      -       +      -
    238B  ILE*     3.9    16.8    -      -       +      -
    239B  ILE*     1.3    75.2    -      -       -      +
    241B  SER*     1.3    64.7    +      -       -      +
    242B  ILE*     3.9    18.4    -      -       +      -
    253B  PHE*     3.4    35.0    -      +       -      -
----------------------------------------------------------
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Residues in contact with SER 241 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78B  ILE*     3.3    16.2    -      -       -      -
     86B  LYS*     4.0    17.0    -      -       -      -
     90B  LEU*     3.8    12.0    -      -       -      +
    209B  LEU      3.3     3.8    +      -       -      -
    210B  ASP*     3.1    14.9    +      -       -      -
    211B  GLN*     3.2    23.5    +      -       -      +
    212B  PRO*     3.3     9.9    -      -       -      +
    240B  PHE*     1.3    74.3    -      -       -      +
    242B  ILE*     1.3    61.7    +      -       -      +
   1502B   MG      2.9    26.1    -      -       -      -
----------------------------------------------------------
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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