Contacts of the helix formed by residues 184 - 200 (chain B) in PDB entry 1YCH


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 184 (chain B).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    183B  VAL*     1.3    75.6    -      -       -      +
    185B  ALA*     1.3    64.7    +      -       -      +
    186B  GLY*     2.8    29.3    +      -       -      -
    187B  LEU*     2.9    40.1    +      -       +      +
    188B  ILE*     3.2    21.5    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 185 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    180B  ASP      5.8     0.7    -      -       -      -
    183B  VAL      3.3     4.9    +      -       -      -
    184B  ASP*     1.3    73.6    +      -       -      +
    186B  GLY*     1.3    61.8    +      -       -      +
    188B  ILE*     3.3     9.4    -      -       -      +
    189B  MET*     3.2    25.6    +      -       -      +
    238B  ARG*     3.3    29.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 186 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    184B  ASP*     2.8    14.6    +      -       -      -
    185B  ALA*     1.3    75.0    -      -       -      +
    187B  LEU*     1.3    63.4    +      -       -      -
    189B  MET*     3.6     4.6    +      -       -      +
    190B  ASP*     3.2    23.2    +      -       -      +
    238B  ARG*     5.7     0.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 187 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     33B  ARG*     4.0    32.1    -      -       -      +
    183B  VAL*     5.3     3.1    -      -       +      -
    184B  ASP*     2.9    37.9    +      -       +      +
    186B  GLY*     1.3    78.0    -      -       -      +
    188B  ILE*     1.3    58.5    +      -       -      +
    190B  ASP*     3.2     8.3    +      -       -      +
    191B  GLU*     3.1    32.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with ILE 188 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    171B  GLN*     3.5    30.5    -      -       +      +
    173B  ILE*     3.9    24.9    -      -       +      -
    175B  THR*     6.3     0.2    -      -       +      -
    180B  ASP*     5.5     4.5    -      -       +      +
    183B  VAL*     3.6    24.4    -      -       +      +
    184B  ASP      3.2    12.0    +      -       -      +
    185B  ALA*     3.3    16.8    -      -       -      +
    187B  LEU*     1.3    76.8    -      -       -      +
    189B  MET*     1.3    66.7    +      -       +      +
    191B  GLU*     3.5     4.7    +      -       +      +
    192B  ALA*     3.0    26.2    +      -       -      +
    230B  ILE*     4.1    19.3    -      -       +      -
    232B  TRP*     4.2    21.4    -      -       +      -
----------------------------------------------------------
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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  ALA      3.2    16.0    +      -       -      +
    186B  GLY*     4.0     5.8    -      -       -      +
    187B  LEU      3.3     0.2    -      -       -      -
    188B  ILE*     1.3    80.9    -      -       +      +
    190B  ASP*     1.3    58.7    +      -       -      +
    192B  ALA*     3.5     4.3    +      -       -      +
    193B  ALA*     3.1    25.8    +      -       -      +
    232B  TRP*     4.0    25.6    -      -       +      -
    238B  ARG*     3.6    42.4    -      -       +      +
    239B  ILE*     4.2    15.9    -      -       +      +
    242B  ALA*     4.1    24.2    -      -       -      -
    246B  TRP*     4.3     9.9    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 190 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    186B  GLY      3.2    18.6    +      -       -      +
    187B  LEU*     3.4     9.1    -      -       -      +
    188B  ILE      3.2     0.2    -      -       -      -
    189B  MET*     1.3    77.0    -      -       -      +
    191B  GLU*     1.3    63.2    +      -       -      +
    193B  ALA*     3.2     5.0    +      -       -      +
    194B  LYS*     2.9    24.1    +      -       -      +
    299B  LYS*     3.1    40.6    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 191 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  PHE*     5.6     0.5    -      -       -      -
     33B  ARG*     3.6    33.2    +      -       -      +
    171B  GLN*     3.8    16.9    -      -       +      +
    172B  HIS      4.3    17.9    +      -       -      +
    173B  ILE*     4.0    21.7    -      -       +      +
    187B  LEU      3.1    20.0    +      -       -      +
    188B  ILE*     3.7    10.1    -      -       +      +
    190B  ASP*     1.3    80.4    -      -       -      +
    192B  ALA*     1.3    63.5    +      -       -      +
    194B  LYS*     3.2    20.6    +      -       -      +
    195B  TYR*     3.0    22.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 192 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    169B  PHE      5.6     0.2    -      -       -      +
    170B  GLY      4.2     7.1    -      -       -      +
    171B  GLN*     3.8    19.2    -      -       +      +
    188B  ILE      3.0    18.4    +      -       -      +
    189B  MET*     3.5    10.3    -      -       -      +
    190B  ASP      3.2     0.2    -      -       -      -
    191B  GLU*     1.3    76.5    -      -       -      +
    193B  ALA*     1.3    56.4    +      -       -      +
    195B  TYR*     3.4     2.9    -      -       -      +
    196B  TYR*     3.0    26.5    +      -       -      +
    232B  TRP*     4.4     3.4    -      -       +      -
    239B  ILE*     4.2    25.4    -      -       +      -
    243B  TYR*     5.1     3.1    +      -       +      -
    246B  TRP*     4.0     5.4    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 193 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    189B  MET      3.1    13.4    +      -       -      +
    190B  ASP*     3.2     8.7    +      -       -      +
    192B  ALA*     1.3    73.9    -      -       -      +
    194B  LYS*     1.3    60.6    +      -       -      +
    195B  TYR      3.1     0.2    -      -       -      -
    196B  TYR*     4.4     0.7    -      -       -      +
    197B  ALA*     2.9    32.9    +      -       -      +
    246B  TRP*     3.4    34.3    -      -       +      +
    299B  LYS*     4.2    11.7    -      -       +      -
    302B  LEU*     3.8     8.4    -      -       +      +
    303B  ASP*     6.1     0.7    -      -       -      +
----------------------------------------------------------
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Residues in contact with LYS 194 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  PHE*     3.6    14.8    -      -       +      -
     30B  SER*     2.9    37.1    +      -       -      -
     32B  HIS*     3.6    18.8    -      -       -      +
    190B  ASP      2.9     8.9    +      -       -      +
    191B  GLU*     3.2    24.2    +      -       -      +
    193B  ALA*     1.3    76.3    -      -       -      +
    195B  TYR*     1.3    62.5    +      -       -      +
    198B  ASN*     3.0    38.9    +      -       -      +
    295B  ASN*     3.7    24.5    -      -       -      +
    296B  ASP*     3.3    24.7    +      -       -      +
    299B  LYS*     3.6    27.1    -      -       +      +
----------------------------------------------------------
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Residues in contact with TYR 195 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29B  PHE*     4.1     9.1    -      -       +      -
    167B  ASP*     2.9    55.2    +      -       +      +
    170B  GLY      3.2    28.5    -      -       -      +
    171B  GLN*     3.8     8.3    -      -       -      -
    172B  HIS*     3.8    34.5    -      +       -      +
    191B  GLU      3.0    12.1    +      -       -      +
    192B  ALA      3.4    10.1    -      -       -      +
    194B  LYS*     1.3    76.1    -      -       -      +
    196B  TYR*     1.3    70.4    +      -       -      +
    198B  ASN*     3.4     1.4    +      -       -      +
    199B  ILE*     3.0    50.7    +      -       +      +
    200B  LEU*     4.6     5.4    -      -       +      -
    228B  HIS*     3.6    12.3    -      +       -      -
    243B  TYR*     4.3    10.5    -      -       -      -
----------------------------------------------------------
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Residues in contact with TYR 196 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    192B  ALA      3.0    14.0    +      -       -      +
    193B  ALA*     3.9     3.1    -      -       -      +
    195B  TYR*     1.3    83.5    -      -       -      +
    197B  ALA*     1.3    64.3    +      -       -      +
    200B  LEU*     2.9    45.8    +      -       +      +
    201B  MET*     3.1    20.5    +      -       -      -
    204B  SER*     3.1    26.8    +      -       -      -
    207B  ILE*     4.1     8.6    -      -       +      +
    243B  TYR*     3.5    42.6    -      +       +      -
    246B  TRP*     3.7    33.4    -      +       +      -
    247B  ALA*     3.5    17.3    -      -       -      +
    302B  LEU*     3.4    32.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with ALA 197 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    193B  ALA      2.9    18.6    +      -       -      +
    194B  LYS      4.0     2.7    -      -       -      +
    196B  TYR*     1.3    82.6    -      -       -      +
    198B  ASN*     1.3    58.0    +      -       -      +
    201B  MET*     3.3    27.9    -      -       +      +
    298B  ILE*     3.4    23.0    -      -       +      +
    299B  LYS*     3.6    28.3    -      -       -      -
    302B  LEU*     4.0    14.4    -      -       +      -
    332B  LEU*     4.2     2.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with ASN 198 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  ASN*     5.0     2.3    +      -       -      -
    701A  FMN      6.2     0.2    -      -       -      +
     29B  PHE*     3.7    20.3    -      -       +      -
    194B  LYS*     3.0    29.8    +      -       -      +
    196B  TYR      3.2     0.8    -      -       -      -
    197B  ALA*     1.3    77.9    -      -       -      +
    199B  ILE*     1.3    62.8    +      -       -      +
    294B  ARG*     5.0     0.2    +      -       -      -
    295B  ASN*     3.2    51.9    +      -       -      +
    298B  ILE*     3.3    27.9    -      -       -      +
    328B  ASP*     4.4     3.6    -      -       -      +
    332B  LEU*     3.5    21.6    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 199 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    315A  ASN*     5.0     3.8    -      -       -      +
    701A  FMN      5.4     5.4    -      -       +      -
     24B  PHE*     6.1     0.2    -      -       +      -
     25B  HIS*     4.4    23.8    -      -       +      -
     29B  PHE*     4.7    11.7    -      -       +      -
    148B  HIS*     4.5    25.2    +      -       +      +
    167B  ASP*     5.8     1.3    -      -       +      -
    172B  HIS*     4.3    13.0    -      -       +      +
    195B  TYR*     3.0    51.9    +      -       +      +
    198B  ASN*     1.3    85.5    -      -       -      +
    200B  LEU*     1.3    81.6    +      -       +      +
    201B  MET      3.6     1.1    -      -       -      -
    202B  PRO*     3.7    10.8    -      -       -      +
    203B  PHE*     3.9    12.6    -      -       -      -
    332B  LEU*     5.2     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 200 (chain B). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    147B  LEU*     4.6     6.1    -      -       +      -
    148B  HIS*     4.4    15.3    -      -       +      +
    167B  ASP*     6.3     1.1    -      -       +      -
    168B  ALA*     4.5    15.0    -      -       +      +
    195B  TYR*     4.6     6.7    -      -       +      -
    196B  TYR*     2.9    34.1    +      -       +      +
    199B  ILE*     1.3    90.7    -      -       +      +
    201B  MET*     1.3    65.6    +      -       -      +
    202B  PRO*     3.3     3.6    -      -       -      -
    203B  PHE*     2.9    32.6    +      -       +      +
    204B  SER      3.7     3.6    +      -       -      -
    207B  ILE*     4.4    15.7    -      -       +      -
    243B  TYR*     3.4    40.2    -      -       +      +
----------------------------------------------------------
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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