Contacts of the strand formed by residues 89 - 93 (chain B) in PDB entry 6DBU


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 CYS 89 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79B  HIS*     3.7     2.4    +      -       -      -
     80B  PHE*     2.9    57.2    +      -       +      +
     86B  LYS*     3.2    29.6    -      -       -      -
     88B  GLU*     1.3    73.2    -      -       -      +
     90B  TYR*     1.3    72.8    +      -       -      +
     91B  LEU*     5.3     0.7    -      -       +      -
    108B  MET*     3.9    29.6    -      -       +      -
    109B  LEU      3.2     7.0    -      -       -      +
    110B  SER*     3.7    23.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 90 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21B  LEU      4.4     4.3    +      -       -      -
     22B  LEU*     3.5    34.0    -      -       +      -
     23B  ASP*     3.1    42.1    +      -       -      +
     24B  LEU*     3.5    23.8    -      -       +      -
     77B  ILE*     3.5    32.8    -      -       +      -
     78B  ALA      3.5     4.3    -      -       -      -
     79B  HIS*     3.9    32.1    -      +       +      +
     89B  CYS*     1.3    81.7    -      -       -      +
     91B  LEU*     1.3    63.2    +      -       -      +
     92B  ILE*     3.9     7.2    +      -       +      +
    107B  TYR      3.6     1.6    -      -       -      +
    108B  MET*     3.6     3.6    -      -       -      -
    109B  LEU*     2.9    45.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 91 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76B  ALA      3.6     4.2    -      -       -      +
     77B  ILE*     3.6     1.9    -      -       -      +
     78B  ALA*     2.9    38.9    +      -       +      +
     80B  PHE*     4.2    16.2    -      -       +      -
     89B  CYS*     5.3     0.2    -      -       +      -
     90B  TYR*     1.3    78.0    -      -       -      +
     92B  ILE*     1.3    61.1    +      -       -      +
    106B  LEU*     3.9    24.2    -      -       +      -
    107B  TYR      3.5     1.1    -      -       -      +
    108B  MET*     4.0    18.6    -      -       +      -
    142B  LEU*     3.7    23.7    -      -       +      +
    144B  VAL*     5.1     1.3    -      -       +      -
    153B  CYS*     3.5    31.2    -      -       -      -
    187B  LEU*     3.9    32.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 92 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22B  LEU*     4.5    13.5    -      -       +      -
     31B  PHE*     3.5    37.9    -      -       +      -
     69B  LEU*     5.3     2.5    -      -       +      -
     72B  LEU*     3.8    24.9    -      -       +      -
     75B  PRO*     4.2    13.2    -      -       +      -
     76B  ALA      3.7     3.1    -      -       -      +
     77B  ILE*     4.3    12.3    -      -       +      -
     90B  TYR*     4.6    11.0    -      -       +      +
     91B  LEU*     1.3    78.7    -      -       -      +
     93B  HIS*     1.3    65.0    +      -       -      +
    106B  LEU*     3.4     1.8    -      -       -      +
    107B  TYR*     2.9    46.5    +      -       +      +
    109B  LEU*     4.5    20.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 93 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76B  ALA*     3.2    23.6    +      -       -      +
     91B  LEU      4.2     0.6    -      -       -      -
     92B  ILE*     1.3    79.3    -      -       -      +
     94B  GLY*     1.3    65.3    +      -       -      +
     95B  GLY      3.8     0.4    -      -       -      -
    104B  SER*     4.6     8.5    -      -       -      -
    105B  SER      4.1    19.5    -      -       -      -
    106B  LEU*     3.5    31.4    -      -       +      +
    129B  LEU*     4.8     3.1    -      -       +      -
    134B  PRO*     3.9    27.7    -      -       +      +
    135B  SER      4.5    10.7    +      -       -      -
    136B  ALA*     5.3     1.2    -      -       -      -
    137B  ARG*     5.3     2.0    +      -       +      -
    140B  HIS*     2.8    48.0    +      +       -      -
    142B  LEU*     5.5     3.3    -      -       +      +
    155B  LEU*     3.4    22.3    -      -       +      +
    185B  ILE*     5.5     0.7    -      -       +      -
----------------------------------------------------------
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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