Contacts of the helix formed by residues 79 - 94 (chain I) in PDB entry 5AN5


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 ASP 79 (chain I).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      0I  ALA      3.2     6.8    +      -       -      -
     76I  THR*     3.3    12.6    +      -       -      +
     77I  ASN      4.4     5.4    -      -       -      +
     78I  PHE*     1.3    78.0    -      -       -      +
     80I  ILE*     1.3    65.8    +      -       -      +
     81I  LEU      3.4     2.0    +      -       -      -
     82I  LYS*     3.4    14.1    +      -       +      +
     83I  ARG*     3.1    30.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 80 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80B  ILE*     4.3     7.4    -      -       +      -
     81B  LEU*     3.5    26.9    -      -       +      -
     84B  LEU*     3.3    30.9    -      -       +      +
     80H  ILE*     3.8    37.9    -      -       +      -
     -1I  MET*     4.0    11.0    -      -       +      -
      0I  ALA*     3.1    33.7    +      -       +      +
     78I  PHE*     3.9    10.3    -      -       +      +
     79I  ASP*     1.3    77.3    -      -       -      +
     81I  LEU*     1.3    59.5    +      -       -      +
     83I  ARG*     3.3     1.4    +      -       -      +
     84I  LEU*     2.8    32.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 81 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     76H  THR      5.9     0.2    -      -       -      +
     79H  ASP*     5.2     2.7    -      -       -      +
     80H  ILE*     4.0    29.4    -      -       +      -
     83H  ARG*     3.9    23.0    +      -       -      +
      0I  ALA*     4.8     6.0    +      -       +      +
     79I  ASP      3.4     0.6    -      -       -      -
     80I  ILE*     1.3    77.5    -      -       +      +
     82I  LYS*     1.3    61.5    +      -       -      +
     84I  LEU*     3.5     4.4    +      -       +      +
     85I  SER*     2.8    31.8    +      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 82 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     79I  ASP*     3.4    18.5    +      -       +      +
     80I  ILE      3.3     0.4    -      -       -      -
     81I  LEU*     1.3    79.4    -      -       -      +
     83I  ARG*     1.3    60.2    +      -       +      +
     85I  SER*     3.4     5.7    +      -       -      -
     86I  ASN*     3.0    28.7    +      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 83 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81B  LEU*     4.5     5.7    +      -       -      +
     84B  LEU*     3.7    26.0    -      -       +      +
     85B  SER*     4.4    12.1    -      -       -      +
     88B  GLU*     2.8    45.3    +      -       -      +
     92B  PHE*     5.8     0.5    -      -       -      -
     78I  PHE*     2.9    49.6    +      -       -      +
     79I  ASP*     3.1    17.5    +      -       +      +
     80I  ILE*     3.7     4.2    -      -       -      +
     82I  LYS*     1.3    74.6    -      -       +      +
     84I  LEU*     1.3    66.3    +      -       -      +
     86I  ASN*     3.3     6.3    +      -       -      +
     87I  LEU*     3.0    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 84 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  LEU*     4.2    12.5    -      -       +      +
     80H  ILE*     3.9    39.0    -      -       +      -
     83H  ARG*     3.9    36.6    -      -       +      +
     84H  LEU*     3.9    22.2    -      -       +      -
     87H  LEU*     3.7    27.6    -      -       +      -
     80I  ILE*     2.8    21.8    +      -       +      +
     81I  LEU*     3.8     5.8    -      -       +      +
     83I  ARG*     1.3    76.0    -      -       -      +
     85I  SER*     1.3    64.2    +      -       -      +
     87I  LEU*     3.3     4.6    +      -       -      +
     88I  GLU*     3.0    28.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 85 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83H  ARG*     3.4    17.5    +      -       -      +
     81I  LEU*     2.8    22.6    +      -       -      +
     82I  LYS*     3.6     6.5    -      -       -      -
     83I  ARG      3.3     0.2    -      -       -      -
     84I  LEU*     1.3    78.1    -      -       -      +
     86I  ASN*     1.3    62.5    +      -       -      +
     88I  GLU*     3.3     8.0    +      -       -      +
     89I  LYS*     3.0    21.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 86 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92B  PHE*     3.8    21.9    -      -       +      -
     82I  LYS*     3.0    17.1    +      -       +      +
     83I  ARG*     3.8     6.5    -      -       -      +
     84I  LEU      3.3     0.2    -      -       -      -
     85I  SER*     1.3    75.0    -      -       -      +
     87I  LEU*     1.3    64.9    +      -       -      +
     89I  LYS*     3.2    13.0    +      -       -      +
     90I  HIS*     3.1    44.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 87 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84B  LEU*     3.5    32.5    -      -       +      -
     87B  LEU*     3.9    41.7    -      -       +      +
     88B  GLU*     4.1    10.8    -      -       +      +
     91B  VAL*     4.0    21.1    -      -       +      -
     92B  PHE*     4.0    20.3    -      -       +      -
     87H  LEU*     4.2    21.8    -      -       +      -
     83I  ARG      3.0    11.5    +      -       -      +
     84I  LEU*     3.5     7.9    -      -       -      +
     86I  ASN*     1.3    75.6    -      -       -      +
     88I  GLU*     1.3    56.6    +      -       -      +
     90I  HIS*     3.2     3.5    +      -       -      +
     91I  VAL*     2.8    34.9    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 88 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83H  ARG*     2.8    61.6    +      -       -      +
     87H  LEU*     3.9    21.5    -      -       +      +
     84I  LEU*     3.0    16.7    +      -       -      +
     85I  SER*     3.6     7.1    -      -       -      +
     86I  ASN      3.2     0.2    -      -       -      -
     87I  LEU*     1.3    76.8    -      -       -      +
     89I  LYS*     1.3    57.7    +      -       -      +
     92I  PHE*     2.8    53.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 89 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85I  SER      3.0    13.5    +      -       -      +
     86I  ASN*     3.2    18.8    +      -       -      +
     88I  GLU*     1.3    77.0    -      -       -      +
     90I  HIS*     1.3    61.2    +      -       +      +
     93I  GLY*     2.9    30.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 90 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91B  VAL*     3.9    18.2    -      -       +      +
     92B  PHE*     3.3    35.9    -      +       -      -
     86I  ASN*     3.1    42.6    +      -       -      -
     87I  LEU      3.6     6.5    -      -       -      +
     89I  LYS*     1.3    80.3    -      -       +      +
     91I  VAL*     1.3    62.0    +      -       -      +
     94I  SER*     2.6    36.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 91 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     87B  LEU*     6.1     0.9    -      -       +      -
     91B  VAL*     3.9    24.5    -      -       +      -
     87H  LEU*     3.8    24.5    -      -       +      -
     90H  HIS*     3.4    37.0    +      -       +      -
     91H  VAL*     3.7    28.9    -      -       +      -
     87I  LEU*     2.8    25.5    +      -       +      +
     88I  GLU      4.2     0.4    -      -       -      +
     90I  HIS*     1.3    76.4    -      -       -      +
     92I  PHE*     1.3    64.6    +      -       +      +
     94I  SER*     3.7    12.1    +      -       -      -
----------------------------------------------------------
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Residues in contact with PHE 92 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86H  ASN*     4.2    16.8    -      -       +      -
     87H  LEU*     3.8    24.5    -      -       +      -
     90H  HIS*     3.4    51.7    +      +       +      -
     88I  GLU*     2.8    44.3    +      -       +      +
     91I  VAL*     1.3    73.6    -      -       +      +
     93I  GLY*     1.3    63.6    +      -       -      +
     94I  SER      3.5     3.5    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 93 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88I  GLU      3.9     0.2    +      -       -      -
     89I  LYS*     2.9    22.8    +      -       -      +
     92I  PHE*     1.3    77.4    -      -       -      +
     94I  SER*     1.3    64.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with SER 94 (chain I). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90I  HIS*     2.6    25.6    +      -       -      +
     91I  VAL*     3.9     9.4    -      -       -      -
     92I  PHE      3.3     5.1    -      -       -      -
     93I  GLY*     1.3    81.5    -      -       -      +
----------------------------------------------------------
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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