Contacts of the helix formed by residues 17 - 31 (chain A) in PDB entry 1HTI


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 ARG 17 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  GLY*     1.3   103.5    +      -       -      +
     18A  LYS*     1.3    67.0    +      -       -      +
     19A  GLN*     3.3     6.3    -      -       +      +
     20A  SER*     3.0    19.4    +      -       -      +
     21A  LEU*     3.2    16.3    +      -       -      +
     47A  TYR*     3.0    17.3    -      -       -      +
     70B  THR*     2.9    35.3    +      -       -      +
     71B  ASN*     2.6    36.8    +      -       -      +
     79B  SER*     3.6     7.8    +      -       -      -
     81B  GLY*     3.7    33.4    -      -       -      -
     82B  MET*     3.5     6.5    -      -       -      +
     85B  ASP*     3.9    11.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 18 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  ARG*     1.3    73.1    -      -       -      +
     19A  GLN*     1.3    60.5    +      -       -      +
     22A  GLY*     3.4    13.1    +      -       -      -
     47A  TYR*     3.5    23.0    +      -       +      -
     50A  PHE*     3.5    42.2    -      -       +      -
     54A  LYS*     5.5     1.2    +      -       -      -
     49B  ASP*     3.0    39.6    +      -       -      -
     53B  GLN*     5.2     1.0    -      -       -      +
     85B  ASP*     3.1    36.7    +      -       -      +
     86B  CYS*     4.4     2.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 19 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     17A  ARG*     3.1     6.3    +      -       +      +
     18A  LYS*     1.3    76.8    -      -       -      +
     20A  SER*     1.3    62.4    +      -       -      +
     22A  GLY*     3.7     0.7    -      -       -      -
     23A  GLU*     2.9    39.3    +      -       +      +
     85B  ASP*     5.1     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 20 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     16A  GLY*     4.3     4.8    -      -       -      -
     17A  ARG*     3.0    30.8    +      -       -      +
     19A  GLN*     1.3    77.4    +      -       -      +
     21A  LEU*     1.3    58.0    +      -       -      +
     23A  GLU*     3.1    14.3    +      -       -      +
     24A  LEU*     2.8    28.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 21 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  TRP*     3.4    43.9    -      -       +      -
     15A  ASN      3.7    18.2    -      -       -      +
     16A  GLY*     4.1     8.7    -      -       -      -
     17A  ARG      3.2    13.1    +      -       -      +
     20A  SER*     1.3    75.6    -      -       -      +
     22A  GLY*     1.3    61.3    +      -       -      +
     24A  LEU*     3.1     8.6    +      -       +      +
     25A  ILE*     2.9    33.3    +      -       -      +
     43A  PRO*     5.0     0.2    -      -       +      -
     44A  PRO*     4.7     3.4    -      -       +      -
     47A  TYR*     3.8    38.1    -      -       +      -
     50A  PHE*     4.0    13.9    -      -       +      -
     51A  ALA*     5.5     0.7    -      -       +      -
    236A  LEU*     4.2    15.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 22 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  LYS      3.4    12.9    +      -       -      -
     19A  GLN      3.4     5.9    +      -       -      -
     20A  SER      3.3     0.2    -      -       -      -
     21A  LEU*     1.3    77.8    -      -       -      +
     23A  GLU*     1.3    60.8    +      -       -      +
     25A  ILE*     3.2     9.5    +      -       -      +
     26A  GLY*     3.0    19.9    +      -       -      -
     50A  PHE*     3.8    13.3    -      -       -      -
     54A  LYS*     4.8     9.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 23 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  GLN*     2.9    26.2    +      -       -      +
     20A  SER*     3.1    12.6    +      -       -      +
     22A  GLY*     1.3    74.2    -      -       -      +
     24A  LEU*     1.3    62.3    +      -       -      +
     26A  GLY*     3.1    11.7    +      -       -      -
     27A  THR*     3.3    12.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 24 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  TRP*     4.2    17.7    -      -       +      -
     20A  SER      2.8    16.2    +      -       -      +
     21A  LEU*     3.1     9.1    +      -       +      +
     23A  GLU*     1.3    70.4    -      -       -      +
     25A  ILE*     1.3    63.6    +      -       -      +
     26A  GLY      3.0     1.0    +      -       -      -
     27A  THR*     3.0    23.9    +      -       +      +
     28A  LEU*     3.0    31.9    +      -       +      +
    235A  SER      3.4    26.2    -      -       -      +
    236A  LEU*     3.4    36.6    -      -       +      +
    237A  LYS*     4.0    20.0    -      -       -      +
    238A  PRO*     4.8     1.3    -      -       +      -
    240A  PHE*     5.7     1.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with ILE 25 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  TRP*     4.2    18.2    -      -       +      -
     21A  LEU      2.9    23.7    +      -       -      +
     22A  GLY*     3.2    14.8    +      -       -      +
     24A  LEU*     1.3    70.9    -      -       -      +
     26A  GLY*     1.3    63.4    +      -       -      +
     28A  LEU*     3.2     9.9    +      -       -      +
     29A  ASN*     3.0    30.1    +      -       -      +
     50A  PHE*     3.9    19.1    -      -       +      -
     51A  ALA*     4.1    17.5    -      -       +      +
     54A  LYS*     3.4    43.7    -      -       +      +
     55A  LEU*     3.3    26.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 26 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     22A  GLY      3.0    13.7    +      -       -      -
     23A  GLU*     3.4     5.8    -      -       -      -
     24A  LEU      3.0     0.6    -      -       -      -
     25A  ILE*     1.3    75.1    -      -       -      +
     27A  THR*     1.3    63.7    +      -       -      +
     29A  ASN*     3.2    16.5    +      -       -      +
     30A  ALA*     3.3    12.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 27 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23A  GLU      3.3     8.7    +      -       -      -
     24A  LEU*     3.0    16.8    +      -       +      -
     26A  GLY*     1.3    72.1    -      -       -      +
     28A  LEU*     1.3    55.9    -      -       +      +
     30A  ALA*     2.9    27.5    +      -       -      +
     31A  ALA*     2.9    15.5    +      -       -      +
    238A  PRO*     4.0    34.9    -      -       +      +
    241A  VAL*     4.4    11.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 28 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     12A  TRP*     4.1    16.6    -      -       +      +
     24A  LEU*     3.0    23.3    +      -       +      +
     25A  ILE*     3.2    11.2    -      -       -      +
     27A  THR*     1.3    82.3    -      -       +      +
     29A  ASN*     1.3    57.7    +      -       -      +
     31A  ALA*     3.4    19.8    -      -       -      +
     41A  CYS*     3.9    24.9    -      -       -      -
     55A  LEU*     4.1    14.1    -      -       +      -
     58A  LYS*     4.4     2.4    -      -       -      -
     59A  ILE*     3.2    30.6    -      -       +      +
    235A  SER      5.7     0.2    -      -       -      +
    240A  PHE*     3.5    31.9    -      -       +      -
    241A  VAL*     4.8     8.3    -      -       +      -
    244A  ILE*     4.4     9.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 29 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  ILE*     3.0    18.3    +      -       -      +
     26A  GLY*     3.5     8.4    -      -       -      +
     27A  THR      3.1     0.2    -      -       -      -
     28A  LEU*     1.3    74.6    -      -       -      +
     30A  ALA*     1.3    56.0    +      -       -      +
     31A  ALA      3.2    10.2    -      -       -      +
     54A  LYS      3.2    23.8    +      -       -      -
     55A  LEU*     3.3    15.2    -      -       -      +
     56A  ASP*     3.0    44.4    +      -       +      +
     58A  LYS*     4.5     7.6    +      -       -      +
     59A  ILE*     4.6     0.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 30 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26A  GLY      3.3     7.3    +      -       -      +
     27A  THR*     2.9     9.6    +      -       -      +
     29A  ASN*     1.3    75.3    -      -       -      +
     31A  ALA*     1.3    66.4    +      -       -      +
     32A  LYS*     4.0     2.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 31 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27A  THR      2.9    10.9    +      -       -      +
     28A  LEU*     3.4    19.5    -      -       +      +
     29A  ASN      3.8     2.4    -      -       -      +
     30A  ALA*     1.3    83.9    -      -       -      +
     32A  LYS*     1.3    53.7    +      -       -      +
     33A  VAL*     6.4     0.4    -      -       +      -
     58A  LYS*     2.4    28.2    +      -       -      -
    241A  VAL*     3.7    35.0    -      -       +      -
    244A  ILE*     5.8     3.8    -      -       +      -
----------------------------------------------------------
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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