Contacts of the strand formed by residues 647 - 654 (chain A) in PDB entry 2HHQ


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 TRP 647 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    642A  PRO*     3.3    22.4    -      -       +      +
    643A  SER*     4.7     2.9    -      -       -      -
    644A  GLU*     3.3    54.5    +      -       +      +
    645A  SER      3.1    21.4    -      -       -      -
    646A  ASP*     1.3    84.0    +      -       +      +
    648A  LEU*     1.3    74.1    +      -       -      +
    821A  GLN*     3.6    36.3    -      -       +      +
    823A  HIS*     3.8    26.5    -      +       -      -
    835A  GLU*     3.8    18.6    -      -       +      -
    836A  ALA*     3.2    31.9    -      -       -      +
    837A  PRO*     3.5    31.2    -      -       +      +
    870A  SER*     5.4     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 648 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    642A  PRO*     3.7     8.3    -      -       -      -
    646A  ASP      5.5     0.7    -      -       -      -
    647A  TRP*     1.3    83.5    -      -       -      +
    649A  ILE*     1.3    62.2    +      -       -      +
    650A  PHE      3.9     0.5    +      -       -      -
    835A  GLU*     3.2     4.5    -      -       -      -
    836A  ALA      2.7    32.9    +      -       -      +
    838A  LYS*     3.8    22.2    -      -       +      -
    841A  MET*     3.7    38.1    -      -       +      +
    868A  TYR*     4.0    16.4    -      -       +      -
    869A  GLY*     3.5    22.7    -      -       -      +
    870A  SER*     3.9    15.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 649 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    493A  VAL*     5.8     2.2    -      -       +      -
    640A  PHE*     4.5     1.8    -      -       +      +
    641A  VAL*     4.0     7.2    -      -       -      +
    642A  PRO*     3.8    36.6    -      -       +      -
    648A  LEU*     1.3    72.1    -      -       -      +
    650A  PHE*     1.3    60.6    +      -       -      +
    825A  LEU*     4.2    10.5    -      -       +      -
    833A  ILE*     3.7    25.8    -      -       +      -
    834A  LEU      3.5     2.0    -      -       -      +
    835A  GLU*     4.0    14.4    -      -       +      -
    868A  TYR*     3.1     7.0    -      -       -      +
    869A  GLY      3.0    32.8    +      -       -      +
    871A  THR*     3.9    23.3    -      -       -      +
    872A  TRP*     3.9    19.7    -      -       +      +
    875A  ALA*     4.1     9.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 650 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    648A  LEU      3.9     0.6    +      -       -      +
    649A  ILE*     1.3    75.6    -      -       -      +
    651A  ALA*     1.3    62.3    +      -       -      +
    652A  ALA*     3.9    11.4    -      -       +      -
    832A  LEU      3.8     0.3    -      -       -      +
    833A  ILE*     3.4     2.4    -      -       -      +
    834A  LEU*     2.7    55.3    +      -       +      +
    841A  MET*     4.2    12.3    -      -       +      -
    844A  LEU*     3.5    42.0    -      -       +      -
    845A  CYS*     3.8    34.5    -      -       -      -
    848A  VAL*     3.7    29.8    -      -       +      -
    849A  PRO*     4.6     0.4    -      -       +      -
    866A  TYR*     3.8    23.1    -      +       +      -
    867A  HIS      3.6     3.6    -      -       -      -
    868A  TYR*     4.0    17.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with ALA 651 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    649A  ILE      4.3     0.2    -      -       -      -
    650A  PHE*     1.3    76.8    -      -       -      +
    652A  ALA*     1.3    59.8    +      -       -      +
    653A  ASP*     5.1     1.2    -      -       -      +
    831A  GLU*     4.5     6.5    -      -       -      +
    832A  LEU      3.4     3.8    -      -       -      -
    833A  ILE*     3.4    26.5    -      -       +      -
    866A  TYR*     3.1     3.8    -      -       -      +
    867A  HIS*     2.8    38.8    +      -       +      +
    872A  TRP*     5.0     2.0    -      -       -      +
    875A  ALA*     4.1    25.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 652 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    650A  PHE*     3.9     8.2    -      -       +      -
    651A  ALA*     1.3    75.4    -      -       -      +
    653A  ASP*     1.3    61.1    +      -       -      +
    831A  GLU*     3.2     2.6    -      -       -      +
    832A  LEU      2.8    34.5    +      -       -      +
    833A  ILE*     5.0     0.2    -      -       -      +
    848A  VAL*     3.7    19.3    -      -       +      -
    849A  PRO*     5.2     0.4    -      -       +      -
    852A  MET*     3.6    27.1    -      -       -      +
    864A  VAL*     3.8     6.5    -      -       +      -
    865A  ASP      3.2     9.6    -      -       -      +
    866A  TYR*     4.1     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 653 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    651A  ALA      5.1     0.9    -      -       -      +
    652A  ALA*     1.3    75.2    -      -       -      +
    654A  TYR*     1.3    63.0    +      -       -      +
    655A  SER*     4.8     0.9    -      -       -      -
    830A  ASP*     3.4     6.5    -      -       -      +
    831A  GLU*     3.5    24.2    -      -       +      +
    852A  MET*     4.6     0.7    -      -       -      -
    864A  VAL*     3.3     5.9    -      -       -      -
    865A  ASP*     2.8    58.4    +      -       -      +
    867A  HIS*     4.7     9.2    +      -       -      -
    920A   MG      2.6    26.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 654 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    653A  ASP*     1.3    71.4    -      -       -      +
    655A  SER*     1.3    60.4    +      -       -      +
    656A  GLN      3.6     1.9    +      -       -      -
    657A  ILE*     3.7    40.8    +      -       +      -
    803A  ILE*     3.6    14.0    -      -       +      +
    804A  ILE*     3.9    23.6    -      -       +      -
    807A  ALA*     3.4    18.2    -      -       -      +
    830A  ASP*     2.9    34.2    +      -       +      +
    852A  MET*     2.7    49.9    +      -       +      -
    862A  LEU*     4.2    21.5    -      -       +      -
    863A  LYS      3.4     6.7    -      -       -      +
    864A  VAL*     3.6    19.3    -      -       +      -
    920A   MG      2.8    22.2    -      -       -      -
----------------------------------------------------------
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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