Contacts of the helix formed by residues 85 - 93 (chain R) in PDB entry 2X86


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 85 (chain R).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     83R  GLU*     2.9    22.5    +      -       -      +
     84R  TRP*     1.3    74.2    -      -       -      +
     86R  GLY*     1.3    57.2    +      -       -      +
     87R  LYS*     2.9    12.1    +      -       -      +
     88R  TYR*     2.7    32.7    +      -       +      +
     89R  MET*     2.9    28.7    +      -       -      +
     34S  LYS*     3.2    37.2    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 86 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84R  TRP      3.0     8.5    +      -       -      -
     85R  ASP*     1.3    70.9    +      -       -      +
     87R  LYS*     1.3    60.8    +      -       -      +
     89R  MET*     4.1     1.6    -      -       -      -
     90R  MET*     2.8    36.0    +      -       -      +
    139R  VAL*     4.1    24.5    -      -       -      -
     33S  LEU*     2.9    25.1    +      -       -      -
     34S  LYS      3.3     1.0    +      -       -      -
     36S  GLY*     4.1     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with LYS 87 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     85R  ASP*     2.9     8.4    +      -       -      +
     86R  GLY*     1.3    77.3    -      -       -      +
     88R  TYR*     1.3    63.3    +      -       -      +
     90R  MET*     4.0     2.7    -      -       -      +
     91R  ASP*     3.0    45.3    +      -       -      +
     32S  ASN*     4.2    10.3    -      -       -      +
     33S  LEU*     3.3    11.1    +      -       -      +
     34S  LYS*     3.9    22.7    -      -       +      +
     50S  TYR*     6.5     0.4    -      -       -      -
     52S  ASP*     3.6    37.4    +      -       +      +
     54S  GLU*     5.4     5.3    -      -       -      +
     55S  ASP*     5.6     0.8    +      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 88 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53R  LYS*     3.0    25.9    +      -       -      -
     78R  CYS*     3.6    30.3    -      -       +      -
     83R  GLU*     4.6    14.4    -      -       +      -
     85R  ASP*     2.7    30.1    +      -       +      +
     87R  LYS*     1.3    73.9    -      -       -      +
     89R  MET*     1.3    67.4    +      -       -      +
     91R  ASP*     3.1     6.5    +      -       +      +
     92R  ASN*     2.8    52.3    +      -       +      +
    400R  NAP      3.3    17.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 89 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78R  CYS*     3.9    16.2    -      -       -      +
     80R  SER      3.9    10.1    -      -       -      +
     83R  GLU*     3.4    48.7    -      -       +      +
     85R  ASP      2.9    15.1    +      -       -      +
     86R  GLY*     3.3     8.7    +      -       -      +
     88R  TYR*     1.3    80.4    -      -       -      +
     90R  MET*     1.3    58.4    +      -       -      +
     92R  ASN*     5.0     0.4    -      -       -      -
     93R  ASN*     2.9    60.5    +      -       -      +
    139R  VAL*     3.8    13.9    -      -       +      +
    140R  PHE*     3.9    15.9    -      -       -      +
    143R  SER*     3.6    20.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with MET 90 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     86R  GLY*     2.8    24.7    +      -       -      +
     87R  LYS*     4.1     2.9    -      -       -      +
     89R  MET*     1.3    73.4    -      -       +      +
     91R  ASP*     1.3    58.4    +      -       -      +
     94R  TYR*     3.2    28.0    +      -       +      +
     95R  GLN*     2.8    29.2    +      -       -      +
    139R  VAL*     5.0     4.3    -      -       -      -
    142R  TYR*     4.1    20.9    -      -       +      -
    143R  SER*     3.9    23.1    -      -       -      -
    146R  LEU*     3.6    32.5    -      -       +      -
     33S  LEU*     3.7    19.7    -      -       +      -
     50S  TYR*     4.1    28.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 91 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     57R  LEU*     6.2     0.2    -      -       -      +
     87R  LYS*     3.0    42.1    +      -       -      +
     88R  TYR*     3.7     6.6    -      -       +      +
     90R  MET*     1.3    77.0    -      -       -      +
     92R  ASN*     1.3    60.3    +      -       +      +
     95R  GLN*     3.3    18.7    -      -       -      +
     96R  TYR*     2.9    31.4    +      -       -      +
     52S  ASP*     5.2     4.3    -      -       -      +
     55S  ASP*     4.1    16.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 92 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     53R  LYS*     2.8    30.0    +      -       -      +
     74R  HIS*     5.7     0.3    +      -       -      -
     76R  GLY      5.1     0.7    -      -       -      +
     77R  ALA*     4.9     0.9    -      -       -      -
     78R  CYS*     3.2     7.9    -      -       -      +
     88R  TYR*     2.8    46.6    +      -       +      +
     89R  MET      4.4     0.2    -      -       -      +
     91R  ASP*     1.3    75.6    -      -       +      +
     93R  ASN*     1.3    72.8    +      -       -      +
     96R  TYR*     3.0    23.4    -      -       -      +
    400R  NAP      2.9    35.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASN 93 (chain R). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77R  ALA*     3.4    13.2    -      -       +      +
     78R  CYS*     2.8    46.8    +      -       -      -
     89R  MET*     2.9    29.6    +      -       -      +
     92R  ASN*     1.3    84.6    +      -       -      +
     94R  TYR*     1.3    63.9    +      -       -      +
     97R  SER*     2.8    33.5    +      -       -      -
    140R  PHE*     4.0     7.9    -      -       -      -
    143R  SER*     3.2    29.0    +      -       -      +
    144R  LYS*     4.6     7.0    -      -       +      +
    147R  PHE*     6.0     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