Contacts of the helix formed by residues 117 - 129 (chain C) in PDB entry 4R0C


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 ALA 117 (chain C).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    113C  SER*     3.3     9.0    -      -       -      +
    114C  SER*     3.1    14.2    +      -       -      +
    116C  GLY*     1.3    75.8    -      -       -      +
    118C  LEU*     1.3    53.0    +      -       -      +
    119C  VAL      3.6     1.1    -      -       -      -
    120C  PHE*     3.2    15.3    +      -       +      +
    121C  THR*     2.6    49.7    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 118 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110C  VAL*     3.6    33.4    -      -       +      +
    113C  SER*     3.2    12.3    -      -       -      +
    114C  SER      3.1     8.4    +      -       -      +
    115C  GLY*     3.3     8.0    +      -       -      +
    116C  GLY      3.3     0.4    -      -       -      -
    117C  ALA*     1.3    73.8    -      -       -      +
    119C  VAL*     1.3    67.4    +      -       -      +
    121C  THR*     3.8     0.2    -      -       -      -
    122C  VAL*     3.0    27.5    +      -       +      +
    147C  VAL*     3.7    23.6    -      -       +      +
    148C  PHE*     3.4    33.9    -      -       +      -
    151C  ALA*     5.0     4.3    -      -       +      -
    153C  ARG*     3.3    32.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 119 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    115C  GLY      4.8     1.0    +      -       -      -
    116C  GLY      5.0     2.3    +      -       -      +
    117C  ALA      3.6     0.2    -      -       -      -
    118C  LEU*     1.3    76.0    -      -       -      +
    120C  PHE*     1.3    65.6    +      -       -      +
    122C  VAL      3.5     0.3    +      -       -      -
    123C  ALA*     3.2    16.8    +      -       -      +
    148C  PHE*     3.8    18.6    -      -       +      -
    153C  ARG*     4.3     4.5    -      -       -      +
    161C  THR*     3.7    13.1    -      -       +      +
    221C  THR*     3.7    35.9    -      -       +      +
    224C  THR*     3.6    35.0    -      -       +      -
    225C  ARG*     4.8     4.9    -      -       +      +
    229C  GLU*     3.6    17.9    -      -       -      +
----------------------------------------------------------
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Residues in contact with PHE 120 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    116C  GLY      5.4     1.7    +      -       -      +
    117C  ALA*     3.2    18.9    +      -       +      +
    119C  VAL*     1.3    79.0    -      -       -      +
    121C  THR*     1.3    72.5    +      -       -      +
    123C  ALA*     3.0     6.1    +      -       -      +
    124C  PHE*     2.9    36.1    +      +       +      +
    214C  PHE*     5.7    10.8    -      +       -      -
    217C  THR*     3.3    31.0    -      -       +      +
    218C  GLY*     5.1     4.0    -      -       -      -
    221C  THR*     3.3    24.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with THR 121 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    109C  LEU*     3.4    45.3    -      -       +      +
    110C  VAL*     3.9     4.0    -      -       -      +
    113C  SER*     3.4    18.8    +      -       -      -
    117C  ALA*     2.6    34.3    +      -       -      +
    118C  LEU      3.9     2.2    -      -       -      -
    120C  PHE*     1.3    79.9    -      -       -      +
    122C  VAL*     1.3    57.4    +      -       -      +
    124C  PHE*     3.5     5.9    +      -       +      +
    125C  ALA*     3.0    26.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 122 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    110C  VAL*     3.5    39.3    -      -       +      -
    118C  LEU*     3.0    27.1    +      -       +      +
    119C  VAL*     4.0     3.8    -      -       -      +
    121C  THR*     1.3    76.1    -      -       -      +
    123C  ALA*     1.3    53.9    +      -       -      +
    125C  ALA*     3.4     2.8    +      -       -      +
    126C  GLY*     2.8    30.7    +      -       -      -
    140C  LEU*     4.8     4.2    -      -       +      +
    144C  ALA*     3.9    25.8    -      -       +      -
    148C  PHE*     4.4     9.0    -      -       +      -
    158C  GLY      4.3     0.4    -      -       -      +
    161C  THR*     3.6    20.4    -      -       +      -
    162C  ALA*     3.9    15.4    -      -       +      +
    165C  ALA*     4.7     0.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 123 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    119C  VAL      3.2    10.7    +      -       -      +
    120C  PHE      3.0     8.1    +      -       -      +
    122C  VAL*     1.3    76.4    -      -       -      +
    124C  PHE*     1.3    65.2    +      -       -      +
    127C  VAL*     3.1    24.3    +      -       -      +
    161C  THR*     4.1     3.4    -      -       +      -
    165C  ALA*     3.1    18.4    -      -       +      +
    217C  THR*     3.9    20.6    -      -       -      +
    220C  VAL*     3.8    28.7    -      -       +      -
    221C  THR*     4.4     1.8    -      -       -      +
----------------------------------------------------------
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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
----------------------------------------------------------
    109C  LEU*     4.2    11.9    -      -       +      -
    120C  PHE*     2.9    27.6    +      +       +      +
    121C  THR*     3.8     8.7    -      -       +      +
    123C  ALA*     1.3    73.8    -      -       -      +
    125C  ALA*     1.3    64.2    +      -       -      +
    126C  GLY      2.9     5.1    +      -       -      -
    127C  VAL*     3.0    13.3    +      -       -      +
    128C  LEU*     3.0    45.0    +      -       +      +
    174C  LEU*     3.8    27.1    -      -       +      -
    213C  THR*     4.1    15.7    -      -       +      -
    214C  PHE*     5.0    11.7    -      +       -      -
    217C  THR*     3.6    24.3    +      -       +      +
    802C  BOG      4.1    24.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 125 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106C  LEU*     3.8    19.6    -      -       +      +
    109C  LEU*     4.0    22.9    -      -       +      -
    110C  VAL*     4.3     9.0    -      -       +      -
    121C  THR      3.0    15.9    +      -       -      +
    122C  VAL      3.7     4.0    -      -       -      +
    124C  PHE*     1.3    79.2    -      -       -      +
    126C  GLY*     1.3    60.3    +      -       -      +
    128C  LEU*     3.4     7.8    +      -       -      +
    129C  SER*     3.2    16.5    +      -       -      -
    140C  LEU*     3.2    23.9    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLY 126 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    122C  VAL      2.8    17.4    +      -       -      -
    123C  ALA      3.6     2.9    -      -       -      -
    124C  PHE      2.9     0.8    -      -       -      -
    125C  ALA*     1.3    75.3    -      -       -      +
    127C  VAL*     1.3    61.4    +      -       -      +
    129C  SER*     2.7    21.7    +      -       -      -
    130C  SER*     4.5     0.7    +      -       -      -
    140C  LEU*     3.7     2.9    -      -       -      +
    162C  ALA*     4.9     1.3    -      -       -      -
    165C  ALA*     3.1    18.7    -      -       -      +
    166C  VAL*     3.3    24.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with VAL 127 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    123C  ALA      3.1    14.1    +      -       -      +
    124C  PHE      3.0    10.7    +      -       -      +
    126C  GLY*     1.3    74.2    -      -       -      +
    128C  LEU*     1.3    68.8    +      -       +      +
    129C  SER      3.2     0.2    +      -       -      -
    130C  SER*     2.8    27.0    +      -       -      -
    165C  ALA*     3.4    12.3    -      -       +      +
    169C  GLY      4.1    10.1    -      -       -      +
    172C  ALA*     3.4    10.2    -      -       +      +
    173C  ASN*     3.2     5.1    +      -       -      -
    213C  THR*     3.5    35.7    -      -       +      +
    216C  VAL*     3.5    34.3    -      -       +      -
    217C  THR*     3.9     9.0    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 128 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106C  LEU*     4.2     8.1    -      -       +      -
    109C  LEU*     4.6     7.4    -      -       +      -
    124C  PHE*     3.0    52.3    +      -       +      +
    125C  ALA*     3.8     8.7    -      -       -      +
    126C  GLY      3.2     0.2    -      -       -      -
    127C  VAL*     1.3    86.0    -      -       +      +
    129C  SER*     1.3    58.4    +      -       -      +
    130C  SER      3.0     6.2    +      -       -      -
    131C  LEU*     3.3    16.8    +      -       +      +
    173C  ASN*     3.2    26.6    +      -       -      +
    174C  LEU*     4.2    28.9    -      -       +      +
    213C  THR*     5.0     0.7    -      -       +      -
    802C  BOG      4.2    19.1    -      -       +      -
    803C  LMT      4.3    16.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with SER 129 (chain C). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    106C  LEU*     3.5    30.1    -      -       -      -
    125C  ALA      3.2     8.8    +      -       -      -
    126C  GLY      2.7    20.1    +      -       -      -
    127C  VAL      3.1     0.4    -      -       -      -
    128C  LEU*     1.3    73.5    -      -       -      +
    130C  SER*     1.3    55.9    +      -       -      +
    131C  LEU      3.1     6.3    -      -       -      -
    132C  THR*     2.8    35.9    +      -       -      +
    136C  GLY*     3.6    19.3    +      -       -      -
    140C  LEU*     4.0     1.6    -      -       -      -
    166C  VAL*     3.4    18.9    -      -       -      +
----------------------------------------------------------
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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