Contacts of the strand formed by residues 839 - 843 (chain D) in PDB entry 2X36


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 839 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    784D  LEU*     3.0    22.6    -      -       -      +
    785D  ARG*     3.2    43.9    +      -       +      +
    797D  ASP      4.0    21.2    +      -       -      -
    799D  SER*     3.1    28.4    +      -       -      -
    837D  THR      3.8    12.0    +      -       -      -
    838D  SER*     1.3    72.6    -      -       -      +
    840D  ILE*     1.3    59.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 840 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    782D  THR*     3.9     7.4    -      -       -      -
    783D  SER      3.5    12.6    -      -       -      +
    784D  LEU*     4.5     4.0    -      -       +      -
    785D  ARG*     4.0     9.9    +      -       -      +
    799D  SER      2.8     9.7    +      -       -      +
    800D  LEU*     3.3    18.2    -      -       +      -
    801D  GLU      3.0    23.7    +      -       -      -
    818D  TYR*     5.1     8.3    -      -       +      +
    834D  TYR*     4.1    23.1    -      -       +      -
    835D  LEU*     4.9    13.5    -      -       +      +
    838D  SER*     4.0    19.7    -      -       -      +
    839D  HIS*     1.3    76.5    -      -       -      +
    841D  HIS*     1.3    70.8    +      -       -      +
    864D  LEU*     4.3    17.7    -      -       +      +
    867D  LEU*     3.9    16.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 841 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    781D  GLU      4.0     0.3    -      -       -      +
    782D  THR*     3.1     6.8    -      -       -      -
    783D  SER*     3.0    46.0    +      -       -      +
    785D  ARG*     3.7    24.4    -      -       +      +
    800D  LEU*     3.7     1.8    -      -       -      -
    801D  GLU*     3.6    21.5    -      -       +      -
    803D  THR*     2.3    42.8    +      -       +      +
    840D  ILE*     1.3    74.1    -      -       -      +
    842D  LEU*     1.3    59.0    +      -       -      +
    843D  HIS*     4.2    16.6    +      +       +      +
----------------------------------------------------------
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Residues in contact with LEU 842 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    780D  VAL*     3.3    32.5    -      -       +      -
    781D  GLU      3.6     7.9    -      -       -      +
    782D  THR*     3.7    15.9    -      -       +      -
    800D  LEU*     3.3    24.1    -      -       +      +
    801D  GLU      2.9     7.2    +      -       -      +
    802D  VAL*     3.4    11.0    -      -       +      -
    803D  THR*     3.1    27.2    +      -       -      +
    814D  ALA*     4.0    20.9    -      -       +      -
    841D  HIS*     1.3    71.0    -      -       -      +
    843D  HIS*     1.3    58.0    +      -       -      +
    844D  VAL*     3.7    22.2    -      -       +      -
    860D  ILE*     3.8    29.2    -      -       +      -
    863D  ALA*     4.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 843 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    779D  PHE      5.0     2.4    +      -       -      -
    780D  VAL*     3.8     5.2    -      -       -      +
    781D  GLU*     2.9    45.3    +      -       +      +
    803D  THR*     3.6    20.6    -      -       -      +
    804D  GLY*     4.0    21.0    -      -       -      -
    841D  HIS*     4.0    12.4    -      +       +      +
    842D  LEU*     1.3    73.4    -      -       -      +
    844D  VAL*     1.3    59.9    +      -       -      +
    845D  PRO*     4.0    29.2    -      -       +      +
----------------------------------------------------------
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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