Contacts of the helix formed by residues 229 - 239 (chain M) in PDB entry 6D6Q


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 THR 229 (chain M).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188M  THR*     3.8    14.8    -      -       +      -
    190M  PRO*     4.4     9.2    -      -       -      +
    228M  THR*     1.3    76.3    -      -       -      +
    230M  GLU*     1.3    62.5    +      -       -      +
    231M  ILE      3.2     1.8    -      -       -      -
    232M  LEU*     2.9    21.7    +      -       +      +
    233M  ARG*     2.9    12.0    +      -       -      +
    251M  PHE*     4.7     6.5    -      -       +      -
    262M  ARG*     5.5     2.6    -      -       -      +
    265M  VAL*     3.5    22.2    -      -       +      -
    266M  TRP*     3.7    39.9    +      -       +      +
    269M  THR*     3.9    19.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 230 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228M  THR*     4.1     1.2    +      -       -      -
    229M  THR*     1.3    73.7    -      -       -      +
    231M  ILE*     1.3    65.0    +      -       -      +
    233M  ARG*     3.1    15.0    +      -       +      +
    234M  SER*     3.0    22.5    +      -       -      -
    262M  ARG*     3.6    18.2    +      -       -      +
    265M  VAL*     3.9    26.4    -      -       +      +
     21O    A      2.1    53.7    +      -       -      +
     22O    C      2.5    54.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 231 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212M  MET*     4.2     0.9    -      -       -      -
    213M  THR*     4.9    10.5    -      -       -      +
    227M  MET*     3.5    29.4    -      -       -      -
    228M  THR*     3.3    23.1    -      -       -      +
    229M  THR      3.2     0.2    -      -       -      -
    230M  GLU*     1.3    77.5    -      -       -      +
    232M  LEU*     1.3    55.9    +      -       -      +
    234M  SER*     2.6    23.9    +      -       -      -
    235M  MET*     3.0    18.7    +      -       +      +
     22O    C      2.9    37.5    -      -       -      +
     23O    A      2.9    49.8    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 232 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186M  ILE*     3.7    24.0    -      -       +      -
    188M  THR*     3.7    26.2    -      -       +      -
    227M  MET*     4.3    11.2    -      -       +      +
    228M  THR      4.3     1.7    +      -       -      +
    229M  THR*     2.9    17.0    +      -       +      +
    231M  ILE*     1.3    77.0    -      -       -      +
    233M  ARG*     1.3    60.5    +      -       -      +
    235M  MET*     3.3     4.1    +      -       -      +
    236M  LEU*     2.9    59.0    +      -       +      +
    243M  MET*     3.8    18.8    -      -       +      -
    249M  VAL*     4.8    11.0    -      -       +      -
    251M  PHE*     5.1     1.1    -      -       +      -
    269M  THR*     3.6    22.0    -      -       +      -
    273M  LEU*     5.1     6.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 233 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    229M  THR      2.9    11.4    +      -       -      +
    230M  GLU*     3.1    16.3    +      -       -      +
    232M  LEU*     1.3    74.0    -      -       -      +
    234M  SER*     1.3    65.8    +      -       -      +
    236M  LEU*     3.3     7.5    +      -       -      +
    237M  TYR*     3.0    60.6    +      -       +      -
    264M  VAL*     5.4     2.6    -      -       -      +
    265M  VAL*     4.3    25.1    -      -       +      +
    268M  GLU*     2.7    31.2    +      -       +      +
    269M  THR*     4.1    15.2    +      -       -      +
    272M  LEU*     5.3     1.1    -      -       +      -
    566M  THR*     4.2     5.9    +      -       -      -
    568M  ASN*     4.6    11.1    -      -       -      +
    569M  MET*     3.7    22.8    -      -       -      +
    572M  ASN*     5.3     1.2    -      -       -      +
    881M  SER*     5.4     6.9    -      -       -      -
     22O    C      5.1     8.3    +      -       -      -
----------------------------------------------------------
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Residues in contact with SER 234 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    230M  GLU      3.0    11.2    +      -       -      -
    231M  ILE*     2.6    22.0    +      -       -      -
    233M  ARG*     1.3    76.9    -      -       -      +
    235M  MET*     1.3    62.4    +      -       -      +
    237M  TYR*     3.3    13.5    +      -       -      +
    238M  ARG*     2.9    29.5    +      -       -      +
     22O    C      4.7     8.7    +      -       -      -
     23O    A      3.0    27.8    +      -       -      -
     24O    C      5.2     6.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with MET 235 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    212M  MET*     3.3    39.7    -      -       +      -
    225M  LEU*     5.6     0.7    -      -       +      -
    227M  MET*     3.7    23.8    -      -       +      -
    231M  ILE*     3.0     9.7    +      -       +      +
    232M  LEU*     3.5     9.0    -      -       -      +
    234M  SER*     1.3    81.1    +      -       -      +
    236M  LEU*     1.3    56.6    +      -       -      +
    238M  ARG      2.9     3.2    +      -       -      +
    239M  GLY*     2.7    35.2    +      -       -      -
    240M  SER*     3.6     8.6    +      -       -      +
    242M  VAL*     4.5    15.3    -      -       +      -
    243M  MET*     3.8    31.6    -      -       +      -
     23O    A      3.3    40.2    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 236 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159H  ARG*     3.1    14.0    +      -       -      -
    232M  LEU*     2.9    57.6    +      -       +      +
    233M  ARG*     3.7     2.2    -      -       -      +
    235M  MET*     1.3    73.0    -      -       -      +
    237M  TYR*     1.3    65.5    +      -       -      +
    239M  GLY*     3.7     3.3    +      -       -      +
    243M  MET*     4.2    22.2    -      -       +      -
    269M  THR*     4.2     9.4    -      -       +      +
    272M  LEU*     3.4    60.9    -      -       +      +
    273M  LEU*     3.8    20.6    -      -       +      +
    274M  PRO*     4.9     2.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with TYR 237 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159H  ARG*     2.6    40.4    +      -       -      +
    233M  ARG*     3.0    42.1    +      -       +      -
    234M  SER*     3.3    13.9    -      -       -      +
    236M  LEU*     1.3    75.7    -      -       -      +
    238M  ARG*     1.3    56.4    +      -       +      +
    239M  GLY      3.2     0.2    -      -       -      -
    268M  GLU*     1.8    39.1    +      -       -      -
    272M  LEU*     3.6    25.8    -      -       +      -
    569M  MET*     3.8     2.9    -      -       -      +
    572M  ASN*     3.7    42.4    -      -       +      +
    573M  LEU*     3.8    26.0    -      -       +      +
    575M  ARG*     6.0     1.8    -      -       -      +
    576M  VAL*     5.0     5.2    -      -       +      +
    584M  MET*     5.8     0.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with ARG 238 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     80H  VAL*     3.6    18.1    -      -       +      +
    146H  GLN*     3.6    39.1    +      -       +      +
    147H  ALA*     3.6    12.1    -      -       -      +
    157H  HIS*     4.4     3.7    -      -       -      -
    159H  ARG*     4.3     5.2    -      -       -      +
    234M  SER*     2.9    19.4    +      -       -      +
    235M  MET*     2.9     7.4    +      -       -      +
    237M  TYR*     1.3    74.8    -      -       +      +
    239M  GLY*     1.3    66.8    +      -       -      +
    240M  SER*     2.9     7.5    +      -       -      +
    575M  ARG*     3.5    29.4    -      -       -      +
    879M  GLU*     4.0    14.6    +      -       -      -
     23O    A      5.2     4.0    -      -       -      +
     24O    C      3.5    31.5    +      -       -      +
     25O    C      2.8    29.2    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 239 (chain M). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    146H  GLN*     3.7     5.4    +      -       -      -
    157H  HIS*     4.2    17.0    -      -       -      -
    159H  ARG*     4.1     6.0    -      -       -      +
    235M  MET      2.7    14.3    +      -       -      -
    236M  LEU*     3.7     5.1    +      -       -      -
    237M  TYR      3.2     6.1    +      -       -      -
    238M  ARG*     1.3    71.0    -      -       -      +
    240M  SER*     1.3    68.4    +      -       -      +
    243M  MET*     5.0     7.2    -      -       -      -
    244M  ARG*     3.2    21.9    +      -       -      -
----------------------------------------------------------
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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