Contacts of the strand formed by residues 838 - 842 (chain B) in PDB entry 3HOU


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 SER 838 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    354A  SER*     5.0     2.2    -      -       -      -
    355A  GLY      4.9     3.8    +      -       -      -
    482A  PHE*     3.7    22.3    -      -       -      -
    833B  TYR      3.5    15.9    +      -       -      -
    834B  ASN*     2.4    29.9    -      -       -      +
    835B  GLN      2.8    21.4    +      -       -      -
    837B  ASP*     1.3    79.3    -      -       -      +
    839B  MET*     1.3    61.2    +      -       -      +
    989B  THR*     2.9    20.0    -      -       -      -
    990B  ILE      4.3     7.4    -      -       -      -
    991B  GLY*     4.5     2.6    -      -       -      -
   1011B  ILE      4.6     0.2    -      -       -      +
   1012B  ILE*     5.1     0.5    -      -       -      -
   1013B  ASN      5.0     2.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 839 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    833B  TYR      4.6     0.4    -      -       -      -
    834B  ASN*     3.8     2.2    -      -       -      -
    838B  SER*     1.3    75.9    -      -       -      +
    840B  ILE*     1.3    67.2    +      -       -      +
    841B  MET*     4.1     8.5    -      -       +      -
    980B  PHE*     3.1    50.7    -      -       +      +
    988B  GLY*     4.2    19.3    -      -       -      +
    989B  THR      2.7    19.0    +      -       -      +
    990B  ILE*     3.2    12.0    -      -       +      +
    991B  GLY*     3.0    23.6    +      -       -      -
   1010B  LEU*     3.5    29.8    -      -       +      -
   1011B  ILE      3.5    13.2    -      -       -      +
   1012B  ILE*     4.4    12.8    -      -       +      -
   1092B  TYR*     4.9     7.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 840 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    830B  TYR*     3.8    22.4    -      -       +      -
    831B  SER*     3.1    27.6    -      -       -      +
    833B  TYR*     4.2     6.7    -      -       +      -
    834B  ASN*     3.5    31.9    -      -       +      +
    839B  MET*     1.3    76.0    -      -       -      +
    841B  MET*     1.3    64.4    +      -       -      +
    992B  ILE*     3.6     9.6    -      -       +      +
    994B  TYR*     3.1    31.2    -      -       +      -
    999B  MET*     4.1    12.6    -      -       +      -
   1010B  LEU*     3.2     6.4    -      -       -      +
   1011B  ILE*     2.9    42.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with MET 841 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    839B  MET*     3.9     9.6    +      -       +      -
    840B  ILE*     1.3    77.0    -      -       -      +
    842B  ASN*     1.3    67.3    +      -       -      +
    846B  ILE*     3.8    27.1    -      -       +      -
    850B  LEU*     4.9     4.7    -      -       +      -
    851B  PHE*     3.8    29.2    -      -       +      -
    974B  PRO*     4.4     3.6    -      -       -      -
    980B  PHE*     3.9    22.9    -      -       +      -
    990B  ILE*     3.6    32.5    -      -       +      -
    992B  ILE      3.3     7.7    +      -       -      -
    993B  THR*     3.0    25.4    -      -       +      -
    994B  TYR      3.1     4.2    +      -       -      -
    999B  MET*     5.1     0.9    -      -       -      -
   1009B  ASP      3.3    12.6    -      -       -      +
   1010B  LEU*     4.0    22.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 842 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    841B  MET*     1.3    70.2    -      -       -      +
    843B  GLN*     1.3    62.4    +      -       -      +
    844B  SER*     3.4    13.8    -      -       -      -
    845B  SER*     2.4    55.0    +      -       -      +
    846B  ILE*     3.1    25.1    +      -       -      +
    848B  ARG*     4.3     4.2    -      -       -      +
    994B  TYR      3.4     3.8    -      -       -      +
    996B  ARG*     3.8    18.1    +      -       -      +
    999B  MET*     3.9    19.3    -      -       -      +
   1007B  VAL*     4.0     8.5    -      -       -      +
   1008B  PRO      3.2    25.1    +      -       -      +
   1009B  ASP*     2.8    12.1    +      -       -      +
      9J  SER      4.5     1.6    +      -       -      -
----------------------------------------------------------
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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