Contacts of the helix formed by residues 119 - 130 (chain C) in PDB entry 4DAJ


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 ILE 119 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115C  ILE*     3.2    13.8    +      -       +      +
    118C  VAL*     1.3    97.8    -      -       +      +
    120C  SER*     1.3    73.7    +      -       -      +
    121C  MET      3.4     1.6    -      -       -      -
    122C  ASN*     2.9    13.0    +      -       -      +
    123C  LEU*     3.1    44.4    -      -       +      +
    143C  TRP*     4.2     5.4    -      -       +      -
    146C  ILE*     4.0    35.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with SER 120 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115C  ILE      4.1     0.6    +      -       -      -
    116C  ILE*     3.3    24.5    +      -       -      +
    119C  ILE*     1.3    75.6    -      -       -      +
    121C  MET*     1.3    64.5    +      -       -      +
    124C  PHE*     2.9    27.4    +      -       -      +
    143C  TRP*     3.3    15.2    +      -       -      +
    146C  ILE*     4.6     6.1    -      -       -      +
    147C  ASP*     3.2    50.0    +      -       -      +
    533C  TYR*     3.6     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 121 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     74C  THR      4.6     0.2    -      -       -      +
     77C  LEU*     4.1    13.9    -      -       +      -
     78C  ALA*     3.4    46.7    -      -       +      +
     81C  THR*     4.2    13.2    -      -       -      +
    116C  ILE*     3.2    17.2    +      -       +      +
    117C  GLY*     3.4    26.5    -      -       -      +
    119C  ILE      3.4     0.2    -      -       -      -
    120C  SER*     1.3    75.1    -      -       -      +
    122C  ASN*     1.3    56.3    +      -       -      +
    124C  PHE*     3.8     0.7    -      -       -      +
    125C  THR*     2.7    37.0    +      -       -      -
    530C  TRP*     3.6    26.3    -      -       +      -
    533C  TYR*     3.9    27.1    -      -       +      +
    537C  THR*     4.5     3.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 122 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     75C  GLY*     5.8     2.6    -      -       -      -
     78C  ALA*     4.7    11.5    -      -       -      +
    117C  GLY      4.4     4.8    +      -       -      -
    118C  VAL*     2.7    28.6    +      -       -      +
    119C  ILE      2.9     8.8    +      -       -      +
    121C  MET*     1.3    74.6    -      -       -      +
    123C  LEU*     1.3    72.5    +      -       +      +
    124C  PHE      2.9     1.6    +      -       -      -
    125C  THR*     3.0     6.7    +      -       -      -
    126C  THR*     2.9    27.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 123 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119C  ILE*     3.1    34.0    +      -       +      +
    122C  ASN*     1.3    84.2    -      -       +      +
    124C  PHE*     1.3    57.0    +      -       -      +
    126C  THR*     3.3     8.7    -      -       -      -
    127C  TYR*     2.9    28.2    +      -       -      +
    133C  TRP*     4.1    18.1    -      -       +      -
    135C  LEU*     4.6    13.7    -      -       +      -
    139C  ALA*     4.6     4.0    -      -       +      +
    143C  TRP*     3.1    49.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with PHE 124 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    120C  SER      2.9    21.1    +      -       -      +
    121C  MET*     3.8     2.7    -      -       -      +
    123C  LEU*     1.3    74.4    -      -       -      +
    125C  THR*     1.3    65.7    +      -       -      +
    126C  THR      3.1     1.5    +      -       -      -
    127C  TYR*     3.1    16.0    +      +       -      +
    128C  ILE*     2.9    28.9    +      -       +      +
    143C  TRP*     3.3    32.9    -      +       +      -
    526C  ASN*     3.5    28.0    -      -       +      -
    529C  TYR*     4.2    34.5    -      +       +      -
    530C  TRP*     3.4    45.3    -      +       -      -
    533C  TYR*     4.2    11.4    -      +       -      +
----------------------------------------------------------
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Residues in contact with THR 125 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     71C  ALA*     4.0    34.9    -      -       +      +
     74C  THR*     3.6    10.0    -      -       -      -
     75C  GLY      5.4     0.9    -      -       -      +
    121C  MET*     2.7    26.1    +      -       -      +
    122C  ASN*     3.0     5.1    +      -       -      -
    124C  PHE*     1.3    72.9    -      -       -      +
    126C  THR*     1.3    58.1    +      -       -      +
    128C  ILE*     3.3     9.8    +      -       +      +
    129C  ILE*     2.9    26.4    +      -       +      +
    530C  TRP*     3.1    25.1    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 126 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122C  ASN*     2.9    16.3    +      -       -      +
    123C  LEU*     3.3    12.8    -      -       -      +
    125C  THR*     1.3    74.1    -      -       -      +
    127C  TYR*     1.3    59.6    +      -       -      +
    128C  ILE      3.0     1.1    -      -       -      -
    129C  ILE*     2.7    26.2    +      -       +      +
    130C  MET*     2.9    37.7    +      -       +      +
    133C  TRP*     6.2     2.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 127 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123C  LEU      2.9    17.2    +      -       -      +
    124C  PHE*     3.1    19.0    +      +       -      +
    126C  THR*     1.3    76.9    -      -       -      +
    128C  ILE*     1.3    66.0    +      -       +      +
    130C  MET      4.3     0.2    -      -       -      -
    131C  ASN*     3.4    23.9    +      -       -      -
    132C  ARG      3.8    11.5    +      -       -      -
    133C  TRP*     3.4    45.5    -      +       +      -
    143C  TRP*     5.3     6.5    -      +       +      -
    218C  GLY      4.4     2.9    +      -       -      -
    219C  GLU*     3.4    27.6    -      -       -      +
    220C  CYS*     3.4    32.4    +      -       +      -
    221C  PHE*     5.9     0.2    -      -       -      -
    526C  ASN*     5.7     5.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 128 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67C  VAL*     5.3     5.6    -      -       -      +
    124C  PHE*     2.9    23.2    +      -       +      +
    125C  THR*     3.4    13.7    -      -       +      +
    127C  TYR*     1.3    81.9    -      -       +      +
    129C  ILE*     1.3    62.3    +      -       -      +
    131C  ASN*     3.6    17.5    +      -       -      +
    526C  ASN*     5.8     4.3    -      -       -      +
    530C  TRP*     5.9     2.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 129 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     67C  VAL*     5.3    10.5    -      -       +      +
     71C  ALA*     5.5    10.5    -      -       +      -
    125C  THR*     2.9    14.0    +      -       +      +
    126C  THR*     2.7    17.8    +      -       -      +
    128C  ILE*     1.3    69.5    -      -       -      +
    130C  MET*     1.3    62.8    +      -       +      +
    131C  ASN*     3.0    18.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with MET 130 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    126C  THR*     2.9    37.7    +      -       +      +
    129C  ILE*     1.3    73.6    -      -       +      +
    131C  ASN*     1.3    62.2    +      -       -      +
    132C  ARG*     2.7    38.8    +      -       +      +
    134C  ALA*     3.4    34.8    -      -       +      -
----------------------------------------------------------
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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