Contacts of the helix formed by residues 59 - 71 (chain A) in PDB entry 2HAN


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 CYS 59 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     42A  ALA      5.0     1.3    -      -       -      -
     43A  CYS*     3.9    15.5    -      -       -      -
     44A  ARG      4.8     2.5    -      -       -      -
     49A  CYS*     3.8    17.9    -      -       +      -
     50A  ILE      5.8     0.4    +      -       -      +
     51A  ILE*     3.7     5.7    -      -       +      +
     55A  GLN      4.6     0.6    +      -       -      -
     56A  ARG      3.9     5.6    +      -       -      -
     57A  ASN      3.4     1.0    -      -       -      -
     58A  ARG*     1.3    80.5    -      -       +      +
     60A  GLN*     1.3    64.2    +      -       -      +
     61A  TYR*     3.8     4.7    -      -       -      -
     62A  CYS*     3.4    15.3    -      -       +      -
     63A  ARG*     2.9    28.8    +      -       -      +
    352A   ZN      2.3    37.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 60 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  PHE*     3.3    21.3    -      -       +      -
     41A  TYR*     3.6    41.5    +      -       +      -
     56A  ARG      5.5     0.4    -      -       -      -
     57A  ASN*     5.2     8.5    -      -       -      +
     58A  ARG      4.2     0.4    +      -       -      -
     59A  CYS*     1.3    72.1    -      -       -      +
     61A  TYR*     1.3    62.3    +      -       -      +
     63A  ARG*     3.3     2.5    +      -       -      +
     64A  TYR*     3.0    22.3    +      -       -      +
     11D    T      3.5    20.2    +      -       -      -
     12D    T      3.0    30.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 61 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     40A  THR*     6.0     2.2    -      -       +      -
     41A  TYR*     3.3    37.7    -      -       +      +
     42A  ALA*     3.8     6.2    +      -       -      -
     43A  CYS*     3.5    38.1    -      -       +      +
     47A  ARG*     3.8    46.6    +      -       +      +
     59A  CYS*     3.3     1.4    -      -       -      -
     60A  GLN*     1.3    77.7    -      -       -      +
     62A  CYS*     1.3    65.0    +      -       -      +
     64A  TYR*     3.4     3.9    +      +       -      +
     65A  GLN*     2.9    69.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 62 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     43A  CYS*     3.8     0.7    -      -       -      -
     47A  ARG*     3.6    24.5    -      -       -      -
     48A  ASN*     4.4     0.2    -      -       -      -
     49A  CYS*     3.3    32.1    -      -       +      +
     51A  ILE*     3.8    13.8    -      -       +      +
     59A  CYS*     3.3     6.4    +      -       -      -
     61A  TYR*     1.3    85.1    -      -       -      +
     63A  ARG*     1.3    56.9    +      -       -      +
     65A  GLN*     3.4     4.9    +      -       -      +
     66A  LYS*     3.0    29.3    +      -       -      +
    352A   ZN      2.1    36.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 63 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  ILE*     4.5     2.9    -      -       +      +
     26A  GLY*     3.2    22.0    -      -       -      -
     27A  CYS*     3.2    21.6    -      -       -      +
     30A  PHE*     3.5    46.0    -      -       +      +
     51A  ILE*     3.5    25.9    -      -       +      +
     56A  ARG*     3.5    34.7    -      -       -      +
     57A  ASN*     3.2    17.8    +      -       -      +
     59A  CYS      2.9    16.8    +      -       -      +
     60A  GLN*     3.7     5.4    -      -       -      +
     62A  CYS*     1.3    77.4    -      -       -      +
     64A  TYR*     1.3    57.3    +      -       -      +
     66A  LYS*     3.2     3.9    +      -       -      +
     67A  CYS*     2.9    33.5    +      -       -      -
     12D    T      4.5     3.2    +      -       -      -
     13D    G      2.8    29.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 64 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     30A  PHE*     3.5    12.5    -      +       +      -
     31A  PHE*     3.6    32.3    -      +       -      -
     34A  THR*     3.5    31.6    -      -       +      -
     35A  VAL*     4.5     0.9    -      -       +      -
     39A  LEU      5.4     4.0    -      -       -      -
     40A  THR*     6.5     0.4    -      -       -      -
     41A  TYR*     4.0    12.1    -      +       +      -
     60A  GLN      3.0    17.3    +      -       -      +
     61A  TYR*     3.8     5.2    -      +       -      +
     63A  ARG*     1.3    71.5    -      -       -      +
     65A  GLN*     1.3    79.8    +      -       -      +
     67A  CYS*     3.0    15.1    +      -       -      +
     68A  LEU*     3.1    36.7    +      -       +      +
     74A  ARG*     2.6    41.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 65 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     61A  TYR*     2.9    60.7    +      -       +      +
     62A  CYS*     3.9     5.6    -      -       -      +
     64A  TYR*     1.3    90.6    -      -       +      +
     66A  LYS*     1.3    56.9    +      -       -      +
     68A  LEU*     3.3    23.9    +      -       -      +
     69A  THR*     3.0    39.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 66 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  SER      4.7     4.0    -      -       -      -
      9A  ILE*     3.0    33.4    +      -       +      +
     51A  ILE*     2.9    43.2    +      -       +      +
     62A  CYS      3.0    17.7    +      -       -      +
     63A  ARG*     3.6     5.2    -      -       -      +
     64A  TYR      3.2     0.2    -      -       -      -
     65A  GLN*     1.3    75.2    -      -       -      +
     67A  CYS*     1.3    66.0    +      -       -      +
     69A  THR*     3.3    10.5    +      -       -      +
     70A  CYS*     3.0    32.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 67 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9A  ILE*     3.7    23.3    -      -       -      +
     27A  CYS*     4.4     9.4    -      -       -      -
     30A  PHE*     4.3    16.2    -      -       -      -
     31A  PHE*     3.7    27.4    -      -       +      -
     63A  ARG*     2.9    24.1    +      -       -      -
     64A  TYR*     3.0     7.4    +      -       -      +
     66A  LYS*     1.3    76.9    -      -       -      +
     68A  LEU*     1.3    59.5    +      -       -      +
     70A  CYS*     3.4     1.9    +      -       -      +
     71A  GLY      3.3     4.9    +      -       -      -
     72A  MET*     3.0    45.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 68 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     31A  PHE*     3.6    28.3    -      -       +      -
     64A  TYR*     3.1    42.5    +      -       +      +
     65A  GLN*     3.4    31.0    -      -       -      +
     66A  LYS      3.2     0.2    -      -       -      -
     67A  CYS*     1.3    77.5    -      -       -      +
     69A  THR*     1.3    63.1    +      -       +      +
     71A  GLY*     3.1    14.9    +      -       -      -
     72A  MET      4.0    13.8    +      -       -      +
     74A  ARG*     4.8     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 69 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     65A  GLN*     3.0    23.9    +      -       +      +
     66A  LYS*     3.3    18.8    +      -       -      +
     68A  LEU*     1.3    78.3    -      -       +      +
     70A  CYS*     1.3    65.5    +      -       -      +
     71A  GLY*     3.5     0.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with CYS 70 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8A  SER*     3.4    46.8    +      -       -      +
      9A  ILE*     3.8    13.9    -      -       +      -
     21A  VAL*     3.4    14.4    -      -       +      +
     66A  LYS*     3.0    30.6    +      -       -      +
     67A  CYS      3.8     4.9    -      -       -      +
     68A  LEU      3.2     0.4    -      -       -      -
     69A  THR*     1.3    79.1    +      -       -      +
     71A  GLY*     1.3    57.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 71 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19A  TYR      3.8     0.9    -      -       -      +
     20A  GLY*     4.5     2.6    -      -       -      -
     21A  VAL*     3.2    12.2    -      -       -      +
     68A  LEU      3.1    11.0    +      -       -      -
     69A  THR      3.3     1.5    -      -       -      -
     70A  CYS*     1.3    79.4    -      -       -      +
     72A  MET*     1.3    66.6    +      -       -      +
     73A  LYS*     3.4    25.4    -      -       -      +
----------------------------------------------------------
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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