Contacts of the strand formed by residues 832 - 840 (chain A) in PDB entry 3H44


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 ILE 832 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192A  LYS*     3.8    22.2    -      -       +      -
    677A  GLN*     4.8     0.2    -      -       -      +
    679A  HIS*     3.5    48.7    -      -       +      +
    831A  TYR*     1.3    92.9    -      -       +      +
    833A  VAL*     1.3    67.5    +      -       -      +
    834A  PHE*     5.1     3.8    -      -       +      +
    849A  ILE*     4.4    11.4    -      -       +      +
    850A  ILE*     3.4     2.8    -      -       -      +
    851A  GLN*     3.2    48.9    +      -       +      +
     21C  VAL      5.9     1.8    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 833 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    819A  ALA*     4.1     4.9    -      -       +      +
    820A  PHE*     4.0    38.7    -      -       +      +
    823A  LEU*     3.8    35.4    -      -       +      +
    824A  ARG*     4.1    16.4    -      -       +      +
    829A  LEU*     5.0     0.2    -      -       +      -
    830A  GLY      4.0    17.5    -      -       -      +
    831A  TYR      3.4     4.6    +      -       -      +
    832A  ILE*     1.3    79.8    -      -       -      +
    834A  PHE*     1.3    64.5    +      -       -      +
    848A  PHE*     6.4     1.8    -      -       +      -
    849A  ILE      3.5     3.8    -      -       -      -
    850A  ILE*     4.3    18.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 834 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    832A  ILE*     5.5     4.5    -      -       +      -
    833A  VAL*     1.3    79.2    -      -       -      +
    835A  SER*     1.3    84.9    +      -       -      +
    836A  GLY*     4.3     5.6    -      -       -      -
    837A  PRO*     5.1     1.6    -      -       +      -
    847A  ARG*     3.3    40.6    -      -       -      -
    848A  PHE*     3.3     6.6    -      -       -      +
    849A  ILE*     2.8    63.7    +      -       +      +
    850A  ILE*     5.5     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with SER 835 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    812A  ALA      5.3     0.3    +      -       -      -
    815A  ILE*     4.3     8.0    +      -       -      +
    816A  SER*     4.2    17.2    +      -       -      -
    819A  ALA*     3.8    19.0    -      -       -      +
    833A  VAL*     6.4     0.2    -      -       -      -
    834A  PHE*     1.3    98.3    -      -       -      +
    836A  GLY*     1.3    59.6    +      -       -      +
    846A  LEU*     5.6     0.4    -      -       -      -
    847A  ARG      3.2     8.3    -      -       -      -
    848A  PHE*     3.7    29.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 836 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    812A  ALA*     4.3     7.8    -      -       -      +
    815A  ILE*     5.9     0.4    -      -       -      +
    834A  PHE*     4.5     5.2    -      -       -      -
    835A  SER*     1.3    78.8    +      -       -      +
    837A  PRO*     1.3    75.2    -      -       -      +
    846A  LEU*     3.4    14.6    -      -       -      +
    847A  ARG*     3.1    30.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 837 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    808A  LEU*     4.0    17.5    -      -       +      -
    809A  GLU*     4.5    16.4    -      -       +      -
    812A  ALA*     3.8    20.2    -      -       +      -
    834A  PHE*     5.0     1.7    -      -       +      -
    836A  GLY*     1.3    85.9    -      -       -      +
    838A  ARG*     1.3    58.4    +      -       -      +
    839A  ARG*     3.9    28.2    +      -       -      +
    845A  GLY      3.4     7.2    -      -       -      +
    847A  ARG*     3.4    18.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 838 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    683A  MET      5.1     1.4    +      -       -      -
    686A  LEU*     3.1    34.7    -      -       -      +
    687A  ARG*     4.2    21.3    -      -       -      +
    690A  MET*     4.2    13.7    -      -       -      +
    691A  THR*     5.9     0.8    +      -       -      -
    768A  GLU*     3.6    19.2    +      -       -      -
    792A  GLU*     4.0    15.8    +      -       -      -
    794A  TYR*     3.7    41.6    +      -       +      -
    836A  GLY      3.9     0.2    +      -       -      -
    837A  PRO*     1.3    73.2    -      -       -      +
    839A  ARG*     1.3    64.1    +      -       -      +
    840A  ALA*     3.6    20.4    -      -       -      +
    841A  ASN*     5.4     0.4    -      -       -      +
    844A  GLN*     3.0    29.9    -      -       -      +
    845A  GLY      2.7    10.7    +      -       -      +
    847A  ARG*     3.8    27.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 839 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    800A  GLN*     3.6    27.6    -      -       -      +
    805A  ASN*     3.8    19.4    +      -       -      +
    808A  LEU*     4.6     1.2    -      -       -      +
    809A  GLU*     2.8    43.7    +      -       -      +
    837A  PRO*     3.9    23.2    -      -       -      +
    838A  ARG*     1.3    86.5    -      -       -      +
    840A  ALA*     1.3    61.9    +      -       -      +
    843A  ILE      3.4     3.8    -      -       -      -
    844A  GLN*     2.7    26.9    +      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 840 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    768A  GLU*     3.6    13.7    +      -       -      +
    794A  TYR*     5.6     0.8    +      -       -      -
    800A  GLN*     4.6     0.2    -      -       -      -
    838A  ARG*     3.6    29.4    -      -       -      +
    839A  ARG*     1.3    75.0    -      -       -      +
    841A  ASN*     1.3    80.6    +      -       -      +
    842A  GLY      3.2     2.7    -      -       -      -
    843A  ILE*     2.9    19.8    +      -       -      +
----------------------------------------------------------
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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