Contacts of the helix formed by residues 122 - 133 (chain X) in PDB entry 2ZG8


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 122 (chain X).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7X  ASN*     3.3    23.1    -      -       -      +
      8X  TYR*     3.7    11.1    -      -       -      -
      9X  SER      4.8     0.7    +      -       -      -
     12X  VAL*     4.3     8.4    -      -       +      +
     72X  ARG*     2.9    34.5    +      -       -      -
    117X  GLY*     2.9    22.8    +      -       -      +
    118X  SER*     5.1     0.2    -      -       -      +
    120X  GLN*     4.3     9.6    -      -       +      +
    121X  ALA*     1.3    73.0    -      -       -      +
    123X  PRO*     1.3    61.7    -      -       -      +
    124X  HIS*     3.6     3.5    +      -       -      +
    125X  LEU*     3.3    18.8    +      -       +      +
    126X  CYS*     3.2    20.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with PRO 123 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7X  ASN*     4.0     6.1    -      -       -      +
    121X  ALA*     3.3    12.6    -      -       +      +
    122X  ASP*     1.3    83.1    -      -       -      +
    124X  HIS*     1.3    64.9    +      -       -      +
    126X  CYS*     3.7    12.9    -      -       -      -
    127X  ASP*     3.1    26.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 124 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     68X  MET*     4.5    13.1    -      -       +      +
     71X  GLN*     5.0     9.6    +      -       +      -
     72X  ARG*     3.8    38.7    +      -       +      +
    122X  ASP*     3.3     2.7    +      -       -      +
    123X  PRO*     1.3    83.4    -      -       -      +
    125X  LEU*     1.3    60.5    +      -       -      +
    127X  ASP*     3.9     5.3    -      -       -      +
    128X  PHE*     3.0    39.8    +      +       +      +
----------------------------------------------------------
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Residues in contact with LEU 125 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8X  TYR*     5.2     0.7    -      -       +      -
     12X  VAL*     3.8    23.3    -      -       +      -
     16X  VAL*     4.4     6.1    -      -       +      -
     68X  MET*     3.9    29.6    -      -       +      -
     72X  ARG*     3.9     4.0    -      -       -      +
    113X  LEU*     3.7    25.8    -      -       +      +
    114X  HIS*     4.8     0.2    -      -       -      -
    117X  GLY*     3.8    15.5    -      -       -      -
    122X  ASP*     3.3    24.3    +      -       -      +
    124X  HIS*     1.3    79.5    +      -       -      +
    126X  CYS*     1.3    68.3    +      -       -      +
    128X  PHE*     3.2     6.4    +      -       +      +
    129X  LEU*     3.0    55.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with CYS 126 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114X  HIS*     3.2    57.9    +      -       +      +
    117X  GLY      5.2     0.2    -      -       -      -
    118X  SER*     5.2     5.8    -      -       -      +
    122X  ASP      3.2    11.5    +      -       -      +
    123X  PRO*     3.7    15.7    -      -       +      -
    124X  HIS      3.4     0.2    -      -       -      -
    125X  LEU*     1.3    85.2    -      -       +      +
    127X  ASP*     1.3    64.1    +      -       -      +
    129X  LEU*     3.5     1.6    +      -       -      +
    130X  GLU*     3.3    14.6    +      -       -      +
    182X  PLL      3.7    15.7    -      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 127 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123X  PRO      3.1    14.6    +      -       -      +
    124X  HIS*     4.0     5.9    -      -       -      +
    126X  CYS*     1.3    79.8    -      -       -      +
    128X  PHE*     1.3    67.0    +      -       -      +
    129X  LEU      3.2     0.4    -      -       -      -
    130X  GLU*     3.3     2.1    +      -       -      +
    131X  SER*     3.1    28.8    +      -       -      -
    182X  PLL      3.9    21.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 128 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64X  ARG*     3.6    23.3    -      -       +      -
     65X  LEU*     3.7    18.2    -      -       +      -
     68X  MET*     3.5    47.3    -      -       +      -
     71X  GLN*     5.4     2.7    -      -       -      -
    124X  HIS*     3.0    30.4    +      +       +      +
    125X  LEU*     3.4     6.1    -      -       -      +
    127X  ASP*     1.3    78.7    +      -       -      +
    129X  LEU*     1.3    72.5    +      -       +      +
    131X  SER*     4.9     0.4    -      -       -      -
    132X  HIS*     3.2    55.3    +      +       -      +
    133X  PHE*     3.6    28.7    -      +       -      -
----------------------------------------------------------
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Residues in contact with LEU 129 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     19X  LEU*     4.3     4.9    -      -       +      -
     65X  LEU*     4.4     3.4    -      -       +      -
    110X  LEU*     4.0    24.5    -      -       +      +
    113X  LEU*     3.5    42.6    -      -       +      -
    114X  HIS*     3.8    18.6    -      -       +      +
    125X  LEU*     3.0    35.7    +      -       +      +
    126X  CYS      3.7     4.7    -      -       -      +
    128X  PHE*     1.3    92.7    -      -       +      +
    130X  GLU*     1.3    60.6    +      -       -      +
    133X  PHE*     3.0    14.4    +      -       +      +
    134X  LEU*     2.8    35.4    +      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 130 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    114X  HIS*     4.7     0.2    -      -       -      -
    126X  CYS      3.3     4.9    +      -       -      +
    127X  ASP*     3.3     6.5    +      -       -      +
    129X  LEU*     1.3    80.3    -      -       -      +
    131X  SER*     1.3    64.0    +      -       -      +
    134X  LEU*     3.1    39.7    +      -       +      +
    135X  ASP*     3.2    41.5    +      -       +      +
    182X  PLL      3.2    39.7    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 131 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    127X  ASP*     3.1    21.2    +      -       -      -
    128X  PHE*     4.1     2.5    -      -       -      -
    130X  GLU*     1.3    83.3    -      -       -      +
    132X  HIS*     1.3    80.2    +      -       -      +
    135X  ASP*     5.1     5.4    -      -       -      +
    136X  GLU*     4.7     7.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with HIS 132 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     64X  ARG*     3.2    47.8    +      -       +      +
    128X  PHE*     3.2    43.5    +      +       -      -
    131X  SER*     1.3    95.7    +      -       -      +
    133X  PHE*     1.3    76.7    +      -       +      +
    136X  GLU*     3.6    18.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 133 (chain X). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23X  TYR*     3.2    31.2    -      +       -      -
     61X  GLY*     3.4    41.1    -      -       -      -
     64X  ARG*     3.9     8.7    -      -       +      -
     65X  LEU*     3.6    16.8    -      -       +      -
    110X  LEU*     3.6    25.1    -      -       +      -
    128X  PHE*     3.6    30.7    -      +       -      -
    129X  LEU*     3.0    19.2    +      -       +      +
    131X  SER      3.5     1.2    -      -       -      -
    132X  HIS*     1.3   102.8    -      -       +      +
    134X  LEU*     1.3    60.2    +      -       -      +
    135X  ASP      3.4     1.3    -      -       -      -
    136X  GLU*     3.3     5.7    +      -       -      +
    137X  GLU*     2.9    34.1    +      -       -      +
----------------------------------------------------------
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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