Contacts of the helix formed by residues 92 - 113 (chain X) in PDB entry 2OU0


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 92 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     90X  SER      4.1     0.6    +      -       -      -
     91X  LEU*     1.3    74.9    -      -       -      +
     93X  ALA*     1.3    58.9    +      -       -      +
     94X  VAL*     3.1    16.5    +      -       -      +
     95X  ARG*     3.0    60.4    +      -       -      +
     96X  ARG*     2.9    28.5    +      -       -      +
    124X  LYS*     4.9     2.8    +      -       -      +
    126X  TRP*     4.8     2.1    -      -       -      -
    156X  GLY*     4.5     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 93 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92X  ASP*     1.3    74.8    -      -       -      +
     94X  VAL*     1.3    63.7    +      -       +      +
     96X  ARG*     3.6    16.1    +      -       -      +
     97X  ALA*     3.3    19.6    +      -       -      +
    158X  TRP*     5.1     1.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 94 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     92X  ASP*     3.1    10.2    +      -       -      +
     93X  ALA*     1.3    76.8    -      -       +      +
     95X  ARG*     1.3    62.0    +      -       -      +
     97X  ALA*     3.1    19.8    +      -       -      +
     98X  ALA      3.4     4.2    +      -       -      -
    152X  THR*     3.7    15.4    -      -       +      +
    156X  GLY      3.6    33.0    -      -       -      +
    157X  THR*     3.7    18.4    -      -       -      +
    158X  TRP*     3.7    34.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ARG 95 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     91X  LEU*     4.0    14.8    -      -       +      -
     92X  ASP*     3.0    35.0    +      -       -      +
     94X  VAL*     1.3    70.9    -      -       -      +
     96X  ARG*     1.3    65.7    +      -       -      +
     98X  ALA*     3.1    10.9    +      -       -      +
     99X  ALA*     3.0    18.9    +      -       -      +
    126X  TRP*     3.4    57.1    -      -       -      +
    152X  THR      3.7    14.4    -      -       -      +
    153X  PHE*     2.7    31.0    +      -       +      +
    154X  ARG      3.3    14.1    +      -       -      -
    155X  THR      3.3    24.0    +      -       -      -
    156X  GLY*     3.6    13.8    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 96 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     88X  TYR*     3.0    60.6    +      -       +      +
     89X  ASP*     2.9    35.5    +      -       -      +
     91X  LEU*     3.0    16.6    +      -       +      +
     92X  ASP      2.9    23.3    +      -       -      +
     93X  ALA*     3.6    12.9    -      -       -      +
     95X  ARG*     1.3    74.9    -      -       -      +
     97X  ALA*     1.3    57.2    +      -       -      +
     99X  ALA*     3.3     7.3    +      -       -      +
    100X  ILE*     2.9    34.3    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 97 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3X  ILE*     3.1    33.7    -      -       +      +
      6X  MET*     4.1     2.5    -      -       -      -
     93X  ALA      3.3     8.9    +      -       -      +
     94X  VAL      3.1    12.6    +      -       -      +
     96X  ARG*     1.3    73.6    -      -       -      +
     98X  ALA*     1.3    59.9    +      -       -      +
    100X  ILE*     3.3     6.2    +      -       +      +
    101X  ASN*     2.8    26.9    +      -       -      +
    158X  TRP*     3.4    29.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 98 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6X  MET*     3.9    11.3    -      -       +      +
     94X  VAL      3.4     2.8    +      -       -      -
     95X  ARG      3.1    10.9    +      -       -      +
     97X  ALA*     1.3    77.6    -      -       -      +
     99X  ALA*     1.3    62.2    +      -       -      +
    101X  ASN*     3.4     4.1    +      -       -      +
    102X  MET*     3.1    26.9    +      -       -      +
    149X  VAL*     3.7    10.5    -      -       +      +
    152X  THR*     4.0    23.1    -      -       +      -
    153X  PHE*     3.6    28.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 99 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     78X  ILE*     4.2     2.2    -      -       -      -
     88X  TYR*     4.1    10.5    -      -       +      -
     91X  LEU*     4.2     3.6    -      -       +      -
     95X  ARG      3.0    11.4    +      -       -      +
     96X  ARG      3.3     8.9    +      -       -      +
     98X  ALA*     1.3    74.3    -      -       -      +
    100X  ILE*     1.3    64.8    +      -       -      +
    102X  MET*     3.4     4.9    +      -       -      +
    103X  VAL*     3.2    25.5    +      -       -      +
    153X  PHE*     3.4    10.0    -      -       +      -
    303X  MR3      3.4    42.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 100 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3X  ILE*     3.8    28.9    -      -       +      -
      7X  LEU*     4.6     5.2    -      -       +      -
     71X  VAL*     4.5     6.3    -      -       +      +
     74X  ALA*     4.1    20.6    -      -       +      -
     75X  VAL*     3.7    27.6    -      -       +      -
     78X  ILE*     3.9    11.7    -      -       +      -
     88X  TYR*     3.6    26.9    -      -       +      +
     96X  ARG*     2.9    25.6    +      -       +      +
     97X  ALA*     3.7    10.1    -      -       -      +
     99X  ALA*     1.3    70.8    -      -       -      +
    101X  ASN*     1.3    56.9    -      -       -      +
    103X  VAL*     3.2     3.1    +      -       -      +
    104X  PHE*     2.8    32.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 101 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      3X  ILE*     3.8     2.4    -      -       +      +
      6X  MET*     3.4    25.2    -      -       -      +
      7X  LEU*     3.7    22.6    -      -       +      +
     10X  ASP*     2.7    25.5    +      -       -      -
     97X  ALA      2.8    14.2    +      -       -      +
     98X  ALA*     3.4    11.0    -      -       -      +
    100X  ILE*     1.3    76.3    -      -       -      +
    102X  MET*     1.3    62.9    +      -       -      +
    104X  PHE*     3.2     2.9    +      -       -      +
    105X  GLN*     3.0    20.8    +      -       -      +
    145X  ARG*     2.8    32.4    +      -       -      -
    149X  VAL*     3.7    13.5    -      -       +      +
    161X  TYR*     3.7     2.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with MET 102 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     98X  ALA      3.1    14.1    +      -       -      +
     99X  ALA      3.6     8.1    -      -       -      +
    100X  ILE      3.3     0.2    -      -       -      -
    101X  ASN*     1.3    78.1    +      -       -      +
    103X  VAL*     1.3    56.6    +      -       -      +
    105X  GLN*     3.2     7.2    +      -       -      +
    106X  MET*     2.9    64.3    +      -       +      +
    111X  VAL*     3.7    12.6    -      -       +      -
    114X  PHE*     4.0    21.1    -      -       +      -
    133X  LEU*     4.1     9.4    -      -       +      -
    138X  TRP*     3.8    29.2    -      -       +      -
    149X  VAL*     3.8    13.5    -      -       +      -
    153X  PHE*     3.7    22.2    -      -       -      -
    303X  MR3      3.8    13.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 103 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74X  ALA*     4.0    27.6    -      -       +      +
     77X  GLY*     6.0     0.2    -      -       -      -
     78X  ILE*     3.6    24.7    -      -       +      -
     84X  LEU*     4.1    13.7    -      -       +      -
     99X  ALA      3.2    11.8    +      -       -      +
    100X  ILE      3.2     7.0    +      -       -      +
    102X  MET*     1.3    71.2    -      -       -      +
    104X  PHE*     1.3    64.1    +      -       -      +
    107X  GLY*     2.8    27.1    +      -       -      +
    108X  GLU*     4.0    23.6    -      -       +      +
    111X  VAL*     3.8    20.4    -      -       +      -
    303X  MR3      4.3     2.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with PHE 104 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7X  LEU*     3.7    25.6    -      -       +      -
     11X  GLU*     3.6    34.5    -      -       +      -
     29X  ILE      3.4    18.6    -      -       -      -
     30X  GLY      3.5    21.0    -      -       -      +
     67X  PHE*     4.1    20.0    -      +       -      -
     70X  ASP*     3.5    42.8    -      -       +      -
     71X  VAL*     4.2     3.8    -      -       +      -
     74X  ALA*     4.4     9.5    -      -       +      +
    100X  ILE      2.8    16.9    +      -       -      +
    101X  ASN      3.3     9.4    -      -       -      +
    103X  VAL*     1.3    74.3    -      -       -      +
    105X  GLN*     1.3    60.4    +      -       -      +
    107X  GLY      4.6     0.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLN 105 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11X  GLU*     4.6     2.7    -      -       -      +
     21X  THR*     5.1     3.6    +      -       -      +
    101X  ASN*     3.0    15.5    +      -       -      +
    102X  MET*     3.2     4.9    +      -       -      +
    104X  PHE*     1.3    83.6    -      -       -      +
    106X  MET*     1.3    61.4    +      -       +      +
    107X  GLY      3.7     0.2    -      -       -      -
    138X  TRP*     2.9    30.6    +      -       -      -
    142X  THR*     3.2    35.2    +      -       -      +
    145X  ARG*     3.2    42.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 106 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    102X  MET*     2.9    49.1    +      -       +      +
    105X  GLN*     1.3    77.8    -      -       +      +
    107X  GLY*     1.3    64.9    +      -       -      +
    110X  GLY*     4.1    12.8    +      -       -      -
    111X  VAL*     3.3    26.2    -      -       +      +
    114X  PHE*     3.6    25.1    -      -       -      -
    138X  TRP*     3.6    38.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 107 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    103X  VAL*     2.8    21.2    +      -       -      -
    104X  PHE      4.6     0.8    +      -       -      -
    105X  GLN      3.7     0.6    -      -       -      -
    106X  MET*     1.3    84.1    -      -       -      +
    108X  GLU*     1.3    65.9    +      -       -      -
    109X  THR      3.3     3.1    -      -       -      -
    110X  GLY      3.3     0.7    +      -       -      -
    111X  VAL*     3.2    19.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 108 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     77X  GLY*     3.0    35.7    -      -       -      +
     80X  ARG*     5.2     1.2    -      -       -      +
     81X  ASN*     2.7    31.7    +      -       -      +
     84X  LEU*     3.8    19.4    -      -       +      +
    103X  VAL*     4.0    19.7    -      -       +      +
    107X  GLY*     1.3    69.7    -      -       -      -
    109X  THR*     1.3    68.1    +      -       -      +
    111X  VAL      4.5     0.2    -      -       -      +
    112X  ALA*     3.0    30.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 109 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81X  ASN*     5.6     1.3    -      -       -      +
    107X  GLY      3.3     0.8    -      -       -      -
    108X  GLU*     1.3    80.6    -      -       -      +
    110X  GLY*     1.3    66.7    +      -       -      +
    112X  ALA*     3.3    14.0    +      -       +      +
    113X  GLY*     3.3     9.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 110 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106X  MET*     4.1    21.6    +      -       -      -
    107X  GLY      3.3     8.8    +      -       -      -
    109X  THR*     1.3    80.7    -      -       -      +
    111X  VAL*     1.3    60.0    +      -       -      +
    113X  GLY*     3.4     9.0    +      -       -      -
    114X  PHE*     3.4    15.1    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 111 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     84X  LEU*     4.0     5.8    -      -       +      -
    102X  MET*     3.7     9.6    -      -       +      -
    103X  VAL*     3.7    28.3    -      -       +      +
    106X  MET*     3.3    27.8    -      -       +      -
    107X  GLY      3.2    10.7    +      -       -      +
    108X  GLU      4.0     3.6    -      -       -      +
    110X  GLY*     1.3    71.2    -      -       -      +
    112X  ALA*     1.3    59.4    +      -       -      +
    113X  GLY      3.1     4.7    -      -       -      -
    114X  PHE*     2.9    33.8    +      -       +      +
    118X  LEU*     3.9     5.8    -      -       +      +
    303X  MR3      3.6    42.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 112 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     81X  ASN*     4.3    17.0    -      -       -      +
     83X  LYS*     4.0    23.4    -      -       +      +
     84X  LEU*     3.8    19.0    -      -       +      +
    108X  GLU      3.0    19.5    +      -       -      +
    109X  THR*     3.3     7.1    +      -       +      +
    111X  VAL*     1.3    75.9    -      -       -      +
    113X  GLY*     1.3    56.0    +      -       -      +
    114X  PHE      3.2     2.8    +      -       -      -
    115X  THR*     3.6    11.6    +      -       -      -
    118X  LEU*     3.9    10.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 113 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109X  THR      3.3    10.8    +      -       -      -
    110X  GLY      3.4     5.1    +      -       -      -
    111X  VAL      3.1     1.6    -      -       -      -
    112X  ALA*     1.3    73.3    -      -       -      +
    114X  PHE*     1.3    59.8    +      -       -      +
    115X  THR*     3.1    16.4    +      -       -      -
----------------------------------------------------------
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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