Contacts of the helix formed by residues 39 - 63 (chain A) in PDB entry 1R73


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 ASN 39 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     37A  LEU*     3.5    19.1    -      -       +      +
     38A  LYS*     1.3    74.3    -      -       -      +
     40A  THR*     1.3    59.5    +      -       -      +
     41A  SER*     3.1    14.5    +      -       -      -
     42A  LEU*     2.8    50.5    +      -       +      +
     43A  ILE*     3.6     2.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 40 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32A  LEU*     4.5    21.8    -      -       +      -
     37A  LEU*     5.5     2.7    -      -       +      -
     38A  LYS      3.4    10.4    +      -       -      +
     39A  ASN*     1.3    70.1    +      -       -      +
     41A  SER*     1.3    66.0    +      -       -      +
     42A  LEU      3.2     1.8    -      -       -      -
     43A  ILE*     3.3    15.1    +      -       +      +
     44A  LYS*     3.1    21.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 41 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     39A  ASN*     3.1    10.9    +      -       -      -
     40A  THR*     1.3    74.6    +      -       -      +
     42A  LEU*     1.3    66.6    +      -       -      +
     44A  LYS*     3.0     9.9    +      -       -      +
     45A  LEU*     3.0    38.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 42 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24A  GLN*     6.1     0.9    -      -       -      +
     28A  LEU*     4.8    15.7    -      -       +      -
     37A  LEU*     5.2     6.5    -      -       +      -
     39A  ASN*     2.8    32.6    +      -       +      +
     40A  THR      3.2     0.2    -      -       -      -
     41A  SER*     1.3    77.3    -      -       -      +
     43A  ILE*     1.3    55.3    +      -       -      +
     45A  LEU*     3.4     7.5    +      -       +      +
     46A  THR*     2.7    56.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 43 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LEU*     3.3    34.8    -      -       +      +
     28A  LEU*     3.5    26.0    -      -       +      -
     29A  ARG*     3.8    11.0    -      -       +      +
     37A  LEU*     3.5    27.1    -      -       +      -
     39A  ASN      3.6     3.0    +      -       -      -
     40A  THR*     3.3    21.3    +      -       +      +
     42A  LEU*     1.3    77.9    -      -       -      +
     44A  LYS*     1.3    55.7    +      -       +      +
     46A  THR*     3.0     6.8    +      -       +      -
     47A  LYS*     2.8    45.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 44 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  THR      3.1    13.3    +      -       -      +
     41A  SER*     3.0    12.5    +      -       -      +
     43A  ILE*     1.3    80.0    -      -       +      +
     45A  LEU*     1.3    71.7    +      -       +      +
     47A  LYS*     3.5    16.7    -      -       -      +
     48A  ARG*     3.2    44.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 45 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     41A  SER*     3.0    34.9    +      -       -      +
     42A  LEU*     3.5     9.6    -      -       +      +
     44A  LYS*     1.3    85.8    -      -       +      +
     46A  THR*     1.3    67.5    +      -       -      +
     48A  ARG*     3.0    36.5    +      -       -      +
     49A  ASP*     3.4    11.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 46 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  LYS*     5.0    10.0    +      -       -      +
     24A  GLN*     4.5    10.1    +      -       -      +
     25A  LEU*     4.3    11.0    -      -       +      +
     28A  LEU*     4.0    22.1    -      -       +      +
     42A  LEU*     2.7    46.4    +      -       -      +
     43A  ILE*     3.3     9.4    -      -       -      +
     45A  LEU*     1.3    74.3    -      -       -      +
     47A  LYS*     1.3    49.0    +      -       -      +
     49A  ASP*     3.2     3.9    +      -       -      +
     50A  ILE*     2.7    58.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 47 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     25A  LEU*     3.3    34.2    -      -       +      +
     43A  ILE*     2.8    28.2    +      -       +      +
     44A  LYS*     3.5    15.3    -      -       +      +
     46A  THR*     1.3    73.1    -      -       -      +
     48A  ARG*     1.3    57.9    +      -       +      +
     50A  ILE*     3.7    10.1    -      -       +      +
     51A  ALA*     2.8    31.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 48 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     44A  LYS*     3.2    43.0    -      -       -      +
     45A  LEU*     3.0    24.0    +      -       -      +
     47A  LYS*     1.3    76.1    -      -       +      +
     49A  ASP*     1.3    58.1    +      -       -      +
     51A  ALA*     3.3     5.7    +      -       -      +
     52A  ARG*     2.9    25.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 49 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  LYS*     3.9    16.9    +      -       -      +
     45A  LEU      3.4     7.4    +      -       -      +
     46A  THR*     3.2     6.9    +      -       -      +
     47A  LYS      3.2     0.2    -      -       -      -
     48A  ARG*     1.3    77.7    -      -       +      +
     50A  ILE*     1.3    56.3    +      -       -      +
     51A  ALA      3.2     1.1    -      -       -      -
     52A  ARG*     2.8    36.9    +      -       -      +
     53A  ILE*     2.7    60.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 50 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     21A  LYS*     2.9    53.2    -      -       +      +
     22A  LYS*     3.7     6.7    -      -       +      +
     24A  GLN*     4.8     0.2    -      -       +      -
     25A  LEU*     3.5    25.4    -      -       +      -
     46A  THR*     2.7    57.6    +      -       +      +
     47A  LYS*     3.7     8.5    -      -       +      +
     49A  ASP*     1.3    69.0    -      -       -      +
     51A  ALA*     1.3    59.7    +      -       +      +
     54A  LYS*     2.7    50.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 51 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     47A  LYS      2.8    18.4    +      -       -      +
     48A  ARG*     3.5     5.6    -      -       -      +
     50A  ILE*     1.3    77.4    -      -       +      +
     52A  ARG*     1.3    56.7    +      -       -      +
     54A  LYS*     3.7    14.3    -      -       -      +
     55A  THR*     2.9    36.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 52 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET      4.6    18.9    +      -       -      +
      2A  LYS*     2.8    31.7    +      -       -      +
      3A  ALA*     4.2     5.7    +      -       -      +
      5A  GLU*     4.9     8.1    +      -       -      -
      6A  LEU*     3.3    36.1    -      -       -      +
     48A  ARG      2.9    11.7    +      -       -      +
     49A  ASP*     2.8    56.4    +      -       -      +
     51A  ALA*     1.3    74.9    -      -       -      +
     53A  ILE*     1.3    62.2    +      -       -      +
     55A  THR*     3.3     8.0    -      -       -      +
     56A  ILE*     2.8    40.5    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 53 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6A  LEU*     3.5    30.3    -      -       +      -
     18A  LEU*     3.2    50.0    -      -       +      +
     21A  LYS*     3.7    33.0    -      -       +      -
     49A  ASP*     2.7    60.7    +      -       +      +
     50A  ILE      3.9     0.9    -      -       -      +
     52A  ARG*     1.3    75.1    -      -       -      +
     54A  LYS*     1.3    57.6    +      -       -      +
     56A  ILE*     2.9    20.9    +      -       -      +
     57A  LEU      3.1    10.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 54 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     18A  LEU*     5.0     2.9    -      -       -      +
     22A  LYS*     4.4    33.2    -      -       +      -
     50A  ILE*     2.7    39.8    +      -       +      +
     51A  ALA*     3.7    14.4    -      -       -      +
     53A  ILE*     1.3    74.6    -      -       -      +
     55A  THR*     1.3    66.2    +      -       -      +
     57A  LEU*     3.5     9.9    +      -       -      +
     58A  ARG*     3.1    20.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 55 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     51A  ALA*     2.9    24.0    +      -       -      +
     52A  ARG*     3.3     8.5    -      -       -      +
     54A  LYS*     1.3    83.6    +      -       -      +
     56A  ILE*     1.3    57.4    +      -       +      +
     58A  ARG*     2.9    10.0    +      -       +      +
     59A  GLU*     2.8    57.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 56 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET      4.6    11.7    -      -       -      +
      2A  LYS      5.4     0.4    -      -       -      +
      3A  ALA*     3.6    28.7    -      -       +      -
      6A  LEU*     3.5    26.0    -      -       +      +
      7A  ARG*     4.6     5.6    -      -       +      +
     18A  LEU*     3.4    19.5    -      -       +      -
     52A  ARG*     2.8    26.9    +      -       +      +
     53A  ILE*     2.9    11.9    +      -       -      +
     55A  THR*     1.3    70.6    -      -       +      +
     57A  LEU*     1.3    63.2    +      -       -      +
     59A  GLU*     3.2    11.0    +      -       -      +
     60A  ARG*     2.9    41.5    +      -       +      +
     65A  ARG*     5.0    14.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 57 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     15A  LYS*     4.8    15.9    -      -       +      +
     18A  LEU*     3.7    23.3    -      -       +      +
     19A  GLU*     4.9     7.0    -      -       +      +
     22A  LYS*     5.9     5.2    -      -       +      +
     53A  ILE      3.1    10.6    +      -       -      +
     54A  LYS*     3.7    10.8    -      -       -      +
     55A  THR      3.2     0.2    -      -       -      -
     56A  ILE*     1.3    74.5    -      -       -      +
     58A  ARG*     1.3    63.8    +      -       -      +
     60A  ARG*     2.9    37.5    +      -       +      +
     61A  GLU*     3.0    38.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 58 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     54A  LYS*     3.1    14.9    +      -       +      +
     55A  THR*     2.9    14.2    +      -       -      +
     57A  LEU*     1.3    74.3    -      -       -      +
     59A  GLU*     1.3    57.3    +      -       +      +
     61A  GLU*     2.9    40.5    +      -       -      +
     62A  LEU*     3.1    45.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 59 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      1A  MET      5.7     1.2    -      -       -      +
     55A  THR*     2.8    42.3    +      -       +      +
     56A  ILE*     3.5    12.5    -      -       +      +
     58A  ARG*     1.3    71.4    -      -       +      +
     60A  ARG*     1.3    59.8    +      -       -      +
     62A  LEU*     3.6    10.7    +      -       -      +
     63A  GLY      3.5     2.9    +      -       -      -
     64A  ILE*     2.9    59.2    +      -       +      +
     65A  ARG*     3.9    24.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7A  ARG*     4.7    11.0    -      -       -      +
     11A  ASP*     2.8    29.7    +      -       -      -
     14A  LEU*     3.5    39.5    -      -       -      +
     15A  LYS*     4.3     7.7    -      -       -      +
     18A  LEU*     4.6     1.6    -      -       -      +
     56A  ILE*     2.9    34.5    +      -       +      +
     57A  LEU*     2.9    30.1    +      -       +      +
     59A  GLU*     1.3    73.9    -      -       -      +
     61A  GLU*     1.3    64.5    +      -       -      +
     63A  GLY*     3.9     2.9    +      -       -      -
     65A  ARG*     3.5    33.1    +      -       +      +
     66A  ARG      3.9    14.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57A  LEU*     3.0    38.7    +      -       +      +
     58A  ARG*     2.9    35.5    +      -       -      +
     60A  ARG*     1.3    76.8    -      -       -      +
     62A  LEU*     1.3    67.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     58A  ARG*     3.1    66.0    +      -       -      +
     59A  GLU*     3.8     2.2    -      -       -      -
     60A  ARG      3.5     0.2    -      -       -      -
     61A  GLU*     1.3    82.4    -      -       +      +
     63A  GLY*     1.3    55.1    +      -       -      +
     64A  ILE*     3.7    29.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     59A  GLU      3.5     1.6    +      -       -      -
     60A  ARG      3.9     4.9    +      -       -      -
     61A  GLU      3.4     4.0    +      -       -      -
     62A  LEU*     1.3    77.6    -      -       -      +
     64A  ILE*     1.3    65.5    +      -       -      +
     65A  ARG      3.2     3.9    +      -       -      -
     66A  ARG*     3.8    17.6    +      -       -      -
----------------------------------------------------------
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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