Contacts of the strand formed by residues 831 - 837 (chain A) in PDB entry 2HVH


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 GLU 831 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    637A  ARG*     5.0     8.2    +      -       -      -
    651A  ALA*     5.8     4.0    -      -       +      +
    652A  ALA      3.2    16.8    -      -       -      +
    653A  ASP*     3.8    21.0    -      -       -      +
    804A  ILE*     3.5     2.5    -      -       -      +
    827A  GLN*     3.5     4.5    -      -       -      -
    828A  VAL*     3.0    66.3    +      -       +      +
    830A  ASP*     1.3    84.9    -      -       -      +
    832A  LEU*     1.3    65.4    +      -       -      +
    833A  ILE*     4.7    10.6    -      -       +      +
    852A  MET*     4.8     1.6    -      -       -      -
    872A  TRP*     5.0     5.9    -      -       -      -
     29B  DDG      4.4    12.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 832 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    651A  ALA*     3.4     0.9    -      -       -      -
    652A  ALA*     2.9    34.1    +      -       +      +
    804A  ILE*     3.8     8.3    -      -       +      -
    807A  ALA*     4.9     1.1    -      -       +      +
    808A  MET*     3.8    36.8    -      -       +      +
    811A  LEU*     4.0    15.9    -      -       +      -
    824A  LEU*     4.0    22.4    -      -       +      -
    826A  LEU      3.6     2.9    -      -       -      +
    827A  GLN*     3.8    20.9    -      -       +      -
    831A  GLU*     1.3    81.3    -      -       -      +
    833A  ILE*     1.3    70.5    +      -       -      +
    834A  LEU*     4.3     8.3    -      -       +      -
    848A  VAL*     5.5     0.4    -      -       +      -
    852A  MET*     3.9    34.3    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 833 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    649A  ILE*     3.9    20.4    -      -       +      -
    650A  PHE      3.3     8.1    -      -       -      +
    651A  ALA*     4.3     8.3    -      -       +      -
    824A  LEU*     3.6     2.5    -      -       -      +
    825A  LEU*     2.6    43.8    +      -       +      -
    826A  LEU*     2.9    40.8    +      -       +      +
    828A  VAL*     3.8    15.7    -      -       +      -
    831A  GLU*     4.7     9.4    -      -       +      +
    832A  LEU*     1.3    81.0    -      -       -      +
    834A  LEU*     1.3    58.6    +      -       -      +
    872A  TRP*     3.5    44.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 834 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    649A  ILE*     3.4     8.1    -      -       -      +
    650A  PHE*     2.6    65.4    +      -       +      +
    652A  ALA      5.7     0.2    -      -       -      +
    811A  LEU*     4.1    24.7    -      -       +      -
    815A  LEU*     4.2    15.0    -      -       +      -
    822A  ALA*     4.7     7.4    -      -       +      -
    823A  HIS      3.3    28.9    -      -       -      +
    824A  LEU*     3.9    19.1    -      -       +      +
    825A  LEU*     4.1     5.4    -      -       -      +
    832A  LEU*     4.5     6.7    -      -       +      -
    833A  ILE*     1.3    82.0    -      -       -      +
    835A  GLU*     1.3    60.6    +      -       -      +
    844A  LEU*     4.9     5.4    -      -       +      -
    848A  VAL*     4.5    13.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 835 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    494A  LYS      5.9     0.2    +      -       -      -
    641A  VAL      4.5     0.3    -      -       -      +
    642A  PRO*     3.4     7.6    -      -       +      +
    643A  SER*     2.8    49.1    +      -       -      -
    647A  TRP*     4.0     9.5    -      -       +      -
    648A  LEU      3.1    11.0    -      -       -      +
    649A  ILE*     3.9     5.4    -      -       +      -
    822A  ALA*     3.5     1.6    -      -       -      +
    823A  HIS*     2.9    59.1    +      -       +      +
    825A  LEU*     3.7    30.1    -      -       +      +
    834A  LEU*     1.3    75.8    -      -       -      +
    836A  ALA*     1.3    65.0    +      -       -      +
    841A  MET*     5.5     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 836 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    647A  TRP*     3.0     9.0    -      -       -      -
    648A  LEU*     2.6    37.3    +      -       -      +
    822A  ALA*     3.6    22.2    -      -       +      +
    835A  GLU*     1.3    79.0    -      -       -      +
    837A  PRO*     1.3    76.1    -      -       +      +
    840A  GLU*     4.0     4.9    -      -       +      +
    841A  MET*     3.6    22.4    -      -       +      +
    844A  LEU*     4.1     5.8    -      -       +      -
----------------------------------------------------------
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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
----------------------------------------------------------
    646A  ASP*     4.8     0.4    -      -       +      +
    647A  TRP*     3.4    42.3    -      -       +      +
    821A  GLN*     3.6    28.3    -      -       +      +
    836A  ALA*     1.3    91.4    -      -       +      +
    838A  LYS*     1.3    67.5    +      -       -      +
    839A  GLU*     3.0    18.4    +      -       +      +
    840A  GLU*     3.1    41.4    +      -       +      +
    841A  MET*     4.1     2.6    -      -       -      +
----------------------------------------------------------
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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