Contacts of the helix formed by residues 629 - 645 (chain D) in PDB entry 1HQR


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 PHE 629 (chain D).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    628D  THR*     1.3    72.5    -      -       -      +
    630D  GLN*     1.3    53.1    +      -       -      +
    632D  ILE*     3.8     9.4    -      -       +      +
    633D  ASP*     2.5    39.7    +      -       -      +
    660D  ILE*     3.6    45.1    -      -       +      -
    668D  GLU*     3.5    31.4    -      -       +      -
    670D  ILE*     3.9    18.1    -      -       +      +
    688D  TYR*     4.9     3.4    -      -       +      -
    692D  ARG*     3.0    53.2    +      -       +      +
    693D  ILE      3.4    23.8    -      -       -      -
    694D  ILE*     4.1    14.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLN 630 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572D  PHE*     3.9     6.3    -      -       +      +
    573D  GLY*     3.0    13.0    -      -       -      -
    574D  LEU*     2.6    49.5    +      -       +      +
    587D  TYR      2.8    25.8    +      -       -      +
    589D  GLY*     3.6     9.0    +      -       -      +
    628D  THR*     2.9    10.9    -      -       -      +
    629D  PHE*     1.3    80.5    -      -       -      +
    631D  GLU*     1.3    56.2    +      -       -      +
    633D  ASP*     3.4     0.9    -      -       -      +
    634D  PHE*     2.7    35.5    +      -       +      +
    688D  TYR*     3.4    52.8    +      -       +      +
    692D  ARG      4.7     0.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 631 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572D  PHE*     3.1    42.0    -      -       +      +
    591D  THR*     5.7     0.3    -      -       -      +
    622D  LEU*     4.5     8.0    -      -       +      +
    623D  GLU      5.1     2.8    +      -       -      -
    624D  LYS*     2.9    41.0    +      -       -      +
    627D  VAL*     3.1    24.8    -      -       +      +
    628D  THR*     3.0    17.2    +      -       -      +
    630D  GLN*     1.3    81.5    -      -       -      +
    632D  ILE*     1.3    63.4    +      -       -      +
    634D  PHE*     3.6     0.7    +      -       -      +
    635D  LYS*     3.4    44.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 632 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    602D  LEU*     4.8     5.8    -      -       +      -
    622D  LEU*     3.9    31.4    -      -       +      -
    627D  VAL*     4.5     5.4    -      -       +      -
    628D  THR      3.0    14.4    +      -       -      +
    629D  PHE*     3.8    10.3    -      -       +      +
    631D  GLU*     1.3    78.0    -      -       -      +
    633D  ASP*     1.3    65.9    +      -       -      +
    634D  PHE      3.3     0.3    +      -       -      -
    635D  LYS*     3.5     2.6    +      -       -      +
    636D  ILE*     3.3    35.2    +      -       +      +
    660D  ILE*     3.7    28.3    -      -       +      -
    670D  ILE*     6.1     0.4    -      -       +      -
    694D  ILE*     4.0    19.5    -      -       +      -
    696D  MET*     4.6     0.4    -      -       -      -
    699D  PHE*     3.4    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 633 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    517D  TYR*     4.2     0.3    -      -       -      -
    629D  PHE      2.5    23.4    +      -       -      +
    630D  GLN*     3.4     2.7    -      -       -      +
    632D  ILE*     1.3    75.9    -      -       -      +
    634D  PHE*     1.3    63.5    +      -       -      +
    636D  ILE*     4.1     1.4    -      -       -      +
    637D  ARG*     2.8    54.7    +      -       -      +
    658D  ILE*     3.8    15.7    -      -       -      +
    670D  ILE*     3.2    36.3    -      -       +      +
    687D  LYS*     5.0     0.2    -      -       -      -
    688D  TYR*     2.6    30.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 634 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    517D  TYR*     4.1    19.3    -      +       +      -
    519D  ILE*     3.7    29.4    -      -       +      -
    521D  PRO*     4.0    19.5    -      -       +      -
    572D  PHE*     4.3    17.5    -      +       +      -
    574D  LEU*     3.4    44.4    -      -       +      -
    630D  GLN*     2.7    19.1    +      -       +      +
    631D  GLU      3.9     4.0    -      -       -      +
    633D  ASP*     1.3    75.5    +      -       -      +
    635D  LYS*     1.3    70.9    +      -       +      +
    637D  ARG*     3.0     8.3    +      -       -      +
    638D  LYS*     2.8    59.7    +      -       +      +
    641D  MET*     5.4     0.9    -      -       +      -
    688D  TYR*     4.7     0.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 635 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    572D  PHE*     4.1    17.8    -      -       +      -
    620D  ILE*     4.3    21.8    -      -       +      +
    621D  ILE      3.7    18.4    +      -       -      +
    622D  LEU*     4.2    18.8    -      -       +      +
    623D  GLU*     5.1     3.4    -      -       -      +
    631D  GLU*     3.4    38.4    +      -       -      +
    632D  ILE*     4.1     2.2    -      -       -      +
    634D  PHE*     1.3    88.4    -      -       +      +
    636D  ILE*     1.3    58.5    +      -       -      +
    638D  LYS*     3.2     5.8    +      -       +      +
    639D  TYR*     2.8    31.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 636 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    602D  LEU*     5.2     2.5    -      -       +      -
    620D  ILE*     3.6    24.7    -      -       +      +
    632D  ILE*     3.3    35.1    +      -       +      +
    633D  ASP      4.1     0.2    -      -       -      +
    635D  LYS*     1.3    77.4    -      -       +      +
    637D  ARG*     1.3    57.5    +      -       -      +
    639D  TYR*     3.3     3.3    +      -       +      +
    640D  LEU*     2.9    29.8    +      -       +      +
    658D  ILE*     3.4    39.9    -      -       +      -
    702D  PHE*     4.0    34.5    -      -       +      -
    704D  ILE*     3.8    25.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 637 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    513D  LEU*     4.4     4.0    -      -       -      +
    517D  TYR*     3.5    48.0    +      -       +      -
    633D  ASP*     2.8    43.4    +      -       -      +
    634D  PHE*     3.0     8.6    +      -       -      +
    636D  ILE*     1.3    77.5    -      -       -      +
    638D  LYS*     1.3    55.2    +      -       -      +
    640D  LEU*     3.1     7.9    +      -       -      +
    641D  MET*     2.7    50.0    +      -       +      +
    646D  ILE*     5.1     0.4    -      -       +      -
    647D  TYR*     2.5    36.3    +      -       +      +
    658D  ILE*     4.7     0.4    -      -       +      -
    670D  ILE*     4.0     5.5    -      -       -      +
    671D  ASP      3.3    21.1    +      -       -      -
    672D  LEU*     3.2    32.0    +      -       +      -
    687D  LYS*     4.1    10.1    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 638 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    634D  PHE*     2.8    46.3    +      -       +      +
    635D  LYS*     3.2     8.9    +      -       +      +
    637D  ARG*     1.3    72.0    -      -       -      +
    639D  TYR*     1.3    60.2    +      -       -      +
    641D  MET*     3.2    15.9    +      -       +      +
    642D  ASP*     2.4    70.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 639 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    616D  LEU*     3.0    51.7    -      -       +      +
    619D  LYS*     4.6    23.0    -      -       +      +
    620D  ILE*     4.4    16.2    -      -       +      -
    635D  LYS      2.8    17.2    +      -       -      +
    636D  ILE*     3.5     7.0    -      -       +      +
    638D  LYS*     1.3    79.1    -      -       -      +
    640D  LEU*     1.3    77.6    +      -       +      +
    642D  ASP*     3.2     3.1    +      -       -      -
    643D  ASN*     2.8    59.2    +      -       -      +
    644D  TYR*     4.1    13.0    -      +       -      -
    702D  PHE*     6.5     0.2    -      +       -      -
    704D  ILE*     5.5     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 640 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    606D  LEU*     4.7     4.3    -      -       +      -
    616D  LEU*     4.7     2.9    -      -       +      -
    636D  ILE*     2.9    25.1    +      -       +      +
    637D  ARG*     3.4     4.7    -      -       -      +
    639D  TYR*     1.3    87.8    -      -       +      +
    641D  MET*     1.3    57.8    +      -       -      +
    644D  TYR*     2.7    49.7    +      -       +      +
    645D  LYS      3.1     4.7    +      -       -      -
    646D  ILE*     3.6    26.6    -      -       +      +
    672D  LEU*     3.8    30.3    -      -       +      -
    704D  ILE*     3.6    40.8    -      -       +      -
    706D  LEU*     4.7     3.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 641 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    514D  LEU*     4.8     8.7    -      -       -      +
    517D  TYR*     3.4    44.2    -      -       +      +
    518D  THR*     5.2     3.8    -      -       -      -
    634D  PHE*     5.4     1.6    -      -       +      -
    637D  ARG*     2.7    25.6    +      -       +      +
    638D  LYS*     3.4    29.6    -      -       +      +
    640D  LEU*     1.3    72.3    -      -       -      +
    642D  ASP*     1.3    63.3    +      -       -      +
    643D  ASN      2.8     3.1    +      -       -      -
    645D  LYS*     2.8    40.8    +      -       -      +
    646D  ILE*     4.1    18.2    -      -       +      +
    647D  TYR*     3.6    26.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 642 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    638D  LYS*     2.4    58.1    +      -       -      +
    639D  TYR*     3.6     6.2    -      -       -      +
    641D  MET*     1.3    74.4    -      -       -      +
    643D  ASN*     1.3    69.3    +      -       -      +
    645D  LYS*     3.7    21.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 643 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    639D  TYR*     2.8    54.7    +      -       +      +
    641D  MET      2.8     3.8    +      -       -      -
    642D  ASP*     1.3    88.4    -      -       -      +
    644D  TYR*     1.3    80.0    +      -       +      +
    645D  LYS*     3.5     7.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 644 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    606D  LEU*     3.1    25.8    -      -       +      +
    608D  ILE*     4.0    15.5    -      -       +      -
    611D  GLU*     6.1     0.2    -      -       -      -
    614D  GLN*     3.0    33.4    +      -       -      -
    616D  LEU*     4.1     3.8    -      -       -      +
    639D  TYR*     4.1    20.9    -      +       -      -
    640D  LEU*     2.7    29.6    +      -       +      +
    643D  ASN*     1.3    87.8    -      -       +      +
    645D  LYS*     1.3    72.9    +      -       -      +
    646D  ILE*     3.0    15.2    +      -       +      -
    651D  SER*     4.8     0.7    -      -       -      -
    652D  PRO*     5.8     0.2    -      -       -      +
    653D  TYR*     3.6    34.9    +      +       +      +
    706D  LEU*     4.8     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 645 (chain D). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    640D  LEU      3.1     0.2    +      -       -      -
    641D  MET*     2.8    24.7    +      -       -      +
    642D  ASP*     3.7    26.8    +      -       -      +
    643D  ASN*     4.6     5.6    -      -       -      +
    644D  TYR*     1.3    79.5    -      -       -      +
    646D  ILE*     1.3    56.2    +      -       -      +
    647D  TYR      2.9    12.5    +      -       -      -
    648D  ASP*     3.1    33.5    +      -       +      +
    651D  SER*     3.0    20.5    -      -       -      -
----------------------------------------------------------
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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