Contacts of the helix formed by residues 180 - 195 (chain B) in PDB entry 6G2T


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 180 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  GLY      3.5     6.5    -      -       -      +
    156B  ASP      3.0    16.2    -      -       -      +
    157B  GLY      2.9    32.3    -      -       -      +
    159B  THR*     4.6     1.1    -      -       -      -
    179B  LEU*     1.3    76.1    -      -       -      +
    181B  GLY*     1.3    62.7    +      -       -      +
    182B  ARG*     3.2     1.8    -      -       +      +
    183B  ASP*     3.1    20.4    +      -       -      +
    184B  LEU*     3.0    28.3    +      -       -      +
    260B  LEU*     4.4     3.6    -      -       -      +
    302B  THR*     4.9     2.2    -      -       -      -
----------------------------------------------------------
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Residues in contact with GLY 181 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    155B  GLY      3.1    12.6    +      -       -      -
    156B  ASP*     4.4     5.6    -      -       -      -
    180B  ALA*     1.3    72.7    -      -       -      +
    182B  ARG*     1.3    61.4    +      -       -      +
    184B  LEU*     3.0    14.7    +      -       -      +
    185B  THR      2.9    11.3    +      -       -      -
    212B  LYS*     2.6    32.3    +      -       -      -
    302B  THR*     4.1    16.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 182 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     13B  SER*     5.8     0.7    -      -       -      -
     68B  TYR*     4.2    16.3    -      -       +      -
     70B  ILE      5.6     1.3    -      -       -      -
     71B  GLU*     3.0    43.3    +      -       -      -
     72B  HIS*     5.2     5.6    +      -       -      +
    156B  ASP*     3.4    41.5    +      -       -      +
    180B  ALA*     3.2     1.0    -      -       +      -
    181B  GLY*     1.3    76.0    -      -       -      +
    183B  ASP*     1.3    71.2    +      -       -      +
    185B  THR*     3.1    19.1    +      -       -      -
    186B  ASP*     3.2    23.9    +      -       -      -
    205B  ARG*     3.3    46.9    -      -       -      +
    209B  ARG*     6.4     0.4    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 183 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     72B  HIS*     3.5    28.3    +      -       -      -
    178B  ASP      3.3    23.0    -      -       -      +
    179B  LEU*     3.9     1.5    -      -       -      -
    180B  ALA*     3.1    27.5    +      -       -      +
    182B  ARG*     1.3    84.6    +      -       -      +
    184B  LEU*     1.3    62.3    +      -       +      +
    186B  ASP*     3.2    15.3    +      -       -      +
    187B  TYR*     3.2    19.8    +      -       -      +
    266B  LEU*     4.4    18.9    -      -       +      +
    268B  MET*     5.5     2.6    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 184 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    179B  LEU*     6.3     0.2    -      -       +      -
    180B  ALA      3.0    18.2    +      -       -      +
    181B  GLY*     3.0    10.3    +      -       -      +
    183B  ASP*     1.3    78.5    -      -       -      +
    185B  THR*     1.3    50.8    +      -       -      +
    187B  TYR*     3.1     8.9    +      -       +      +
    188B  LEU*     2.7    35.4    +      -       -      +
    212B  LYS*     4.2    11.0    -      -       +      -
    256B  CYS*     3.1    33.0    -      -       +      +
    257B  PRO*     5.0     2.5    -      -       +      -
    259B  ALA*     4.0    15.0    -      -       +      -
    260B  LEU*     3.8    31.2    -      -       +      -
    266B  LEU*     5.3     5.6    -      -       +      -
    302B  THR*     3.7    23.1    -      -       -      +
    305B  TYR*     4.1    14.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with THR 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    181B  GLY      2.9     5.1    +      -       -      -
    182B  ARG*     3.1    14.6    +      -       -      -
    184B  LEU*     1.3    76.6    -      -       -      +
    186B  ASP*     1.3    56.3    +      -       -      +
    188B  LEU*     3.2     7.5    +      -       -      +
    189B  MET*     2.8    28.4    +      -       -      +
    205B  ARG*     3.7    31.2    -      -       +      +
    208B  VAL*     3.6    25.1    -      -       +      +
    209B  ARG*     4.1    14.8    -      -       +      +
    212B  LYS*     2.8    31.3    +      -       -      +
----------------------------------------------------------
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Residues in contact with ASP 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    182B  ARG*     3.2    17.1    +      -       -      +
    183B  ASP*     3.2    13.8    +      -       -      +
    185B  THR*     1.3    76.1    -      -       -      +
    187B  TYR*     1.3    62.6    +      -       -      +
    189B  MET*     3.1    29.7    -      -       -      +
    190B  LYS*     3.2    11.9    +      -       -      +
    205B  ARG*     2.9    38.7    +      -       -      -
    283C  LYS*     5.5     8.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with TYR 187 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183B  ASP      3.2     3.7    +      -       -      +
    184B  LEU*     3.1    11.8    +      -       -      +
    186B  ASP*     1.3    80.2    -      -       -      +
    188B  LEU*     1.3    55.8    +      -       -      +
    190B  LYS*     3.3    35.9    +      -       -      +
    191B  ILE*     2.9    41.8    +      -       +      +
    255B  ARG*     4.3    19.3    +      -       +      +
    256B  CYS*     3.4    41.3    -      -       +      -
    259B  ALA*     4.8     4.3    -      -       +      -
    265B  PHE*     3.7    49.4    -      +       +      +
    266B  LEU*     3.7    31.2    -      -       +      -
----------------------------------------------------------
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Residues in contact with LEU 188 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184B  LEU      2.7    20.4    +      -       -      +
    185B  THR*     3.4     7.0    -      -       -      +
    187B  TYR*     1.3    70.8    -      -       -      +
    189B  MET*     1.3    64.9    +      -       -      +
    191B  ILE*     2.9    12.9    -      -       +      +
    192B  LEU*     2.8    43.2    +      -       +      +
    208B  VAL*     3.4    38.8    -      -       +      +
    209B  ARG      4.8     0.2    -      -       -      +
    211B  ILE*     5.0     7.2    -      -       +      -
    212B  LYS*     3.8    24.9    -      -       +      +
    216B  CYS*     4.7     8.5    -      -       -      -
    249B  ILE*     6.3     2.0    -      -       +      -
    252B  GLU*     4.7     4.7    -      -       +      +
    253B  ARG*     5.6     2.2    -      -       -      -
    256B  CYS*     3.3    29.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with MET 189 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    185B  THR      2.8    15.8    +      -       -      +
    186B  ASP*     3.1    42.2    -      -       -      +
    188B  LEU*     1.3    74.1    -      -       -      +
    190B  LYS*     1.3    62.3    +      -       +      +
    192B  LEU*     3.4    17.6    +      -       -      +
    193B  THR*     3.5    16.3    +      -       -      +
    199B  PHE*     3.2    41.4    +      -       +      +
    200B  THR*     4.7     8.3    -      -       -      -
    201B  THR      5.6     0.4    -      -       -      +
    205B  ARG*     4.4    25.8    -      -       +      -
    208B  VAL*     4.6    16.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with LYS 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  ASP      3.2     8.9    +      -       -      +
    187B  TYR*     3.4    46.9    +      -       -      +
    188B  LEU      3.2     0.2    -      -       -      -
    189B  MET*     1.3    84.8    -      -       +      +
    191B  ILE*     1.3    59.1    +      -       -      +
    193B  THR*     2.7    29.8    +      -       -      -
    194B  GLU*     4.2     1.6    +      -       -      +
    265B  PHE      5.4     4.3    -      -       -      -
    266B  LEU*     5.5     1.0    -      -       -      +
    109C  LEU*     4.6    24.2    -      -       +      +
    171C  PRO*     4.7    18.4    -      -       -      +
    172C  HIS*     5.1    12.8    -      -       -      +
    174C  ILE      5.5     2.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    187B  TYR*     2.9    29.7    +      -       +      +
    188B  LEU*     2.9    38.6    +      -       +      +
    190B  LYS*     1.3    75.6    -      -       -      +
    192B  LEU*     1.3    59.4    +      -       -      +
    194B  GLU*     3.0    47.2    -      -       -      +
    252B  GLU*     3.1    34.5    -      -       +      +
    255B  ARG*     3.3    35.7    -      -       -      +
    256B  CYS*     3.9     5.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 192 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    188B  LEU*     2.8    51.1    +      -       +      +
    189B  MET*     3.7     9.4    -      -       -      +
    190B  LYS      3.3     0.4    -      -       -      -
    191B  ILE*     1.3    76.6    -      -       -      +
    193B  THR*     1.3    61.9    +      -       -      +
    195B  ARG*     3.1    15.9    +      -       -      +
    197B  TYR*     3.0    35.0    +      -       +      +
    198B  SER*     5.6     0.2    -      -       -      -
    199B  PHE*     3.6    35.9    -      -       +      -
    208B  VAL*     3.9     9.0    -      -       +      -
    211B  ILE*     5.3     6.3    -      -       +      -
    247B  ILE*     5.1    11.9    -      -       +      -
    249B  ILE*     5.4     7.6    -      -       +      -
    252B  GLU*     3.0    28.4    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 193 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  MET      3.5    16.4    -      -       -      +
    190B  LYS*     2.7    20.8    +      -       -      +
    192B  LEU*     1.3    77.1    -      -       -      +
    194B  GLU*     1.3    63.8    +      -       -      +
    196B  GLY*     3.0    12.3    +      -       -      -
    197B  TYR      3.1    10.3    +      -       -      +
    198B  SER*     3.9    26.3    +      -       -      +
    199B  PHE      5.1     3.1    -      -       -      +
    109C  LEU*     3.5    38.1    +      -       +      +
    111C  PRO*     3.5    16.5    -      -       -      +
    176C  ARG*     5.1     4.5    -      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    190B  LYS      5.2     1.1    -      -       -      +
    191B  ILE*     3.0    37.1    +      -       -      +
    193B  THR*     1.3    83.8    +      -       -      +
    195B  ARG*     1.3    61.4    +      -       +      +
    196B  GLY      3.2     0.9    -      -       -      -
    251B  ASN*     5.5     0.9    -      -       -      +
    252B  GLU*     4.7     6.9    -      -       -      +
    255B  ARG*     2.7    31.9    +      -       -      -
    109C  LEU      5.0     0.4    -      -       -      -
    110C  ASN      4.2     5.8    -      -       -      +
    111C  PRO*     2.9    13.9    -      -       -      +
    112C  LYS*     2.6    61.9    +      -       +      +
    113C  ALA      4.5     0.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192B  LEU*     3.1    11.2    +      -       -      +
    194B  GLU*     1.3    84.2    +      -       +      +
    196B  GLY*     1.3    58.4    +      -       -      +
    197B  TYR*     3.7    23.7    -      -       +      -
    236B  GLU*     4.8    10.3    +      -       -      -
    248B  THR*     3.2    25.7    +      -       -      +
    249B  ILE*     4.1     2.1    -      -       -      +
    250B  GLY*     3.1    33.4    -      -       -      +
    251B  ASN*     4.0    14.8    +      -       -      -
    252B  GLU*     2.9    31.5    +      -       -      +
    111C  PRO*     4.4     1.6    -      -       -      -
    112C  LYS*     5.7     1.1    -      -       -      -
----------------------------------------------------------
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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