Contacts of the helix formed by residues 82 - 92 (chain H) in PDB entry 5DST


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 HIS 82 (chain H).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    257G  GLU*     3.0    41.8    +      -       -      -
    394G  ARG*     3.6    26.3    +      -       -      +
     79H  SER*     3.9    11.6    +      -       -      +
     80H  TYR      3.2     1.6    -      -       -      -
     81H  ALA*     1.3    78.1    -      -       -      +
     83H  PHE*     1.3    82.0    +      +       -      +
     84H  GLY*     2.7    26.4    +      -       -      -
     85H  ILE*     3.3    15.8    +      -       +      +
     86H  HIS*     3.6    12.7    +      -       -      -
    145H  ILE*     4.9     0.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 83 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235G  LYS*     5.9     0.4    -      -       +      -
    239G  TRP*     3.5    17.3    -      +       -      -
    250G  ILE*     3.6    29.4    -      -       +      -
    253G  VAL*     4.2    17.7    -      -       +      -
    254G  ALA*     3.7    38.8    -      -       +      -
    257G  GLU*     3.3    33.4    -      -       +      -
    259G  LEU*     6.3     2.9    -      -       +      -
     81H  ALA      3.6     4.4    +      -       -      -
     82H  HIS*     1.3    85.0    -      +       -      +
     84H  GLY*     1.3    75.8    +      -       -      +
     86H  HIS*     3.4     6.0    +      -       -      +
     87H  GLU*     3.1    41.9    +      -       -      -
    145H  ILE*     4.7    11.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLY 84 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     82H  HIS*     2.7    17.5    +      -       -      -
     83H  PHE*     1.3    96.8    -      -       -      +
     85H  ILE*     1.3    61.4    +      -       -      -
     87H  GLU*     3.3     9.8    -      -       -      +
     88H  GLU*     3.2    18.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 85 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79H  SER      4.2    15.0    -      -       -      +
     80H  TYR*     3.9    26.5    -      -       +      +
     82H  HIS*     3.3    13.5    +      -       +      +
     84H  GLY*     1.3    73.2    -      -       -      +
     86H  HIS*     1.3    85.0    +      -       +      +
     88H  GLU*     3.1    27.0    +      -       +      +
     89H  MET*     3.2    33.1    +      -       +      +
    189H  TYR*     6.2     0.2    -      -       -      +
    334H  HIS*     5.8     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 86 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    239G  TRP*     5.1     1.3    -      -       +      -
    250G  ILE*     6.0     0.2    -      -       +      -
     80H  TYR*     2.8    38.7    +      +       +      -
     82H  HIS      3.6     9.9    +      -       -      -
     83H  PHE*     3.4     8.5    +      -       -      +
     84H  GLY      3.3     0.4    -      -       -      -
     85H  ILE*     1.3    80.7    -      -       +      +
     87H  GLU*     1.3    55.9    +      -       -      +
     89H  MET*     3.2    11.6    +      -       -      +
     90H  LEU*     2.7    44.7    +      -       +      +
    121H  GLY*     3.9    10.0    -      -       -      -
    122H  THR*     3.7    39.3    -      -       +      -
    145H  ILE*     3.5    18.2    -      -       +      +
    401H  SAH      3.8    29.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 87 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    235G  LYS*     3.3    36.6    +      -       -      +
    238G  TRP*     4.0     7.9    -      -       +      -
    239G  TRP*     3.6    38.2    +      -       +      -
     83H  PHE*     3.1    26.3    +      -       -      +
     84H  GLY*     3.3    12.4    -      -       -      +
     86H  HIS*     1.3    76.4    -      -       -      +
     88H  GLU*     1.3    63.9    +      -       -      +
     90H  LEU      3.2     0.3    +      -       -      -
     91H  LYS*     2.6    68.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 88 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84H  GLY      3.2     7.8    +      -       -      +
     85H  ILE*     3.1    23.9    +      -       +      +
     87H  GLU*     1.3    81.2    -      -       -      +
     89H  MET*     1.3    61.7    +      -       +      +
     91H  LYS*     3.5     5.4    +      -       -      +
     92H  ASP*     3.3    20.4    +      -       -      +
    189H  TYR*     4.7     9.5    +      -       -      -
    332H  TYR*     4.3     9.3    +      -       -      +
    334H  HIS*     3.6    38.2    -      -       +      +
    336H  LYS*     5.0     5.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 89 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80H  TYR*     4.1    20.2    -      -       +      +
     85H  ILE*     3.2    26.1    +      -       +      +
     86H  HIS*     3.5    14.6    -      -       -      +
     88H  GLU*     1.3    77.5    -      -       -      +
     90H  LEU*     1.3    62.7    +      -       -      +
     92H  ASP*     3.2    11.3    +      -       -      +
     95H  ARG*     3.1    37.3    +      -       -      +
     96H  THR*     3.1     4.2    +      -       -      -
    185H  GLU*     3.5    24.2    -      -       -      +
    187H  MET      5.3     2.0    -      -       -      +
    334H  HIS*     4.1    25.6    -      -       +      +
    401H  SAH      3.5    39.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 90 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    238G  TRP*     3.7    27.3    -      -       +      -
    239G  TRP*     4.3     4.3    -      -       +      -
    242G  VAL*     3.9    17.5    -      -       +      -
    243G  TYR*     2.6    36.0    +      -       -      -
    247G  MET*     4.3     7.6    -      -       +      -
     86H  HIS      2.7    29.8    +      -       -      +
     89H  MET*     1.3    73.5    -      -       -      +
     91H  LYS*     1.3    55.2    +      -       -      +
     92H  ASP      3.4     0.5    +      -       -      -
     95H  ARG*     4.2     7.4    -      -       -      +
     96H  THR*     3.4     9.9    +      -       +      -
    122H  THR*     4.1    26.0    -      -       +      +
    124H  ILE*     3.7    42.6    -      -       +      -
    401H  SAH      4.6     2.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 91 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    234G  PHE*     2.9    63.6    +      -       +      -
    235G  LYS*     4.5     0.6    -      -       -      +
    238G  TRP*     3.4    42.2    -      -       +      +
    243G  TYR*     4.3     1.6    -      -       -      -
     87H  GLU*     2.6    49.6    +      -       +      +
     88H  GLU*     4.1     4.9    -      -       -      +
     90H  LEU*     1.3    74.4    -      -       -      +
     92H  ASP*     1.3    58.3    +      -       -      +
     93H  GLU*     2.9    18.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 92 (chain H). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    243G  TYR*     4.0     1.3    -      -       -      -
     88H  GLU      3.3    11.3    +      -       -      +
     89H  MET      3.2    12.7    +      -       -      +
     90H  LEU      3.2     0.6    -      -       -      -
     91H  LYS*     1.3    71.6    -      -       -      +
     93H  GLU*     1.3    62.7    +      -       -      +
     94H  VAL*     3.3    12.8    +      -       -      +
     95H  ARG*     3.2    24.9    +      -       +      +
     96H  THR*     3.0    24.6    +      -       -      -
    332H  TYR*     4.1     9.1    -      -       +      +
    333H  THR*     3.5    14.2    -      -       -      -
    334H  HIS*     2.9    46.5    +      -       +      +
    335H  TRP*     4.1     0.7    -      -       -      -
----------------------------------------------------------
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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