Contacts of the helix formed by residues 227 - 238 (chain K) in PDB entry 1J0B


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 LEU 227 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    191K  SER      5.4     1.8    -      -       -      -
    192K  GLY*     3.7    28.7    -      -       -      +
    195K  LEU*     4.2     9.2    -      -       +      -
    196K  ALA*     3.8    20.2    -      -       +      +
    223K  MET*     2.9    15.6    +      -       -      +
    224K  THR*     5.2     1.1    -      -       -      +
    226K  LYS*     1.3    80.3    -      -       -      +
    228K  ASP*     1.3    71.3    +      -       -      +
    229K  ASN      3.3     0.2    -      -       -      -
    230K  LEU*     3.1    24.1    +      -       -      +
    231K  ILE*     3.2    12.4    +      -       +      +
    245K  ARG*     4.6     7.9    -      -       -      +
    246K  PRO*     3.4    38.6    -      -       +      -
    248K  LEU*     4.5    19.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASP 228 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    224K  THR      2.5    30.4    -      -       -      +
    225K  SER*     4.0     7.1    -      -       -      +
    227K  LEU*     1.3    86.0    -      -       -      +
    229K  ASN*     1.3    60.7    +      -       -      +
    230K  LEU      3.1     1.7    +      -       -      -
    231K  ILE*     4.1     4.9    +      -       -      +
    232K  LYS*     2.9    27.6    +      -       -      +
    245K  ARG*     3.1    41.7    +      -       -      +
    246K  PRO*     4.9     1.2    -      -       -      +
    108V  LEU*     6.1     1.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 229 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    225K  SER      3.5    16.0    +      -       -      +
    226K  LYS*     4.1     5.1    -      -       -      +
    227K  LEU      3.3     0.4    -      -       -      -
    228K  ASP*     1.3    78.9    -      -       -      +
    230K  LEU*     1.3    60.0    +      -       -      +
    232K  LYS*     3.1    16.1    -      -       -      +
    233K  GLU*     3.0    44.0    +      -       -      +
    319U  ASP*     2.6    56.4    +      -       -      +
    322U  LEU*     3.3    16.8    -      -       +      +
    323U  SER*     3.5     6.0    +      -       -      -
    108V  LEU*     4.4     9.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 230 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    159K  ALA*     3.2    32.3    -      -       +      +
    161K  PRO*     4.0    16.2    -      -       +      -
    164K  THR*     3.5    26.0    -      -       -      +
    191K  SER      5.3     0.9    -      -       -      +
    192K  GLY      3.8    11.7    -      -       -      +
    193K  GLY*     3.9    11.2    -      -       -      -
    196K  ALA*     3.6    20.0    -      -       +      -
    226K  LYS      3.4    16.2    +      -       -      +
    227K  LEU*     3.1    15.1    +      -       -      +
    229K  ASN*     1.3    78.2    -      -       -      +
    231K  ILE*     1.3    65.3    +      -       -      +
    233K  GLU*     3.4     6.3    +      -       -      +
    234K  ALA*     3.3    14.6    +      -       -      +
    323U  SER*     6.1     1.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 231 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164K  THR*     5.9     0.7    -      -       -      -
    196K  ALA*     3.7    28.5    -      -       +      +
    199K  SER*     3.6    29.4    -      -       -      +
    200K  LEU*     4.5    20.9    -      -       +      -
    203K  SER*     6.5     0.4    -      -       -      -
    227K  LEU*     3.2    15.4    +      -       +      +
    228K  ASP*     4.1     5.6    +      -       -      +
    230K  LEU*     1.3    72.0    -      -       -      +
    232K  LYS*     1.3    52.6    +      -       -      +
    233K  GLU      2.7     7.6    +      -       -      -
    234K  ALA*     2.9     6.3    +      -       -      +
    235K  ALA*     2.6    34.9    +      -       +      +
    242K  VAL*     3.9    30.7    -      -       +      -
    244K  VAL      5.9     0.9    -      -       -      +
    245K  ARG*     5.6     2.2    -      -       -      -
    246K  PRO*     4.3    17.7    -      -       +      -
----------------------------------------------------------
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Residues in contact with LYS 232 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    228K  ASP      2.9    27.6    +      -       -      +
    229K  ASN*     3.1    21.3    -      -       -      +
    231K  ILE*     1.3    73.9    -      -       -      +
    233K  GLU*     1.3    62.2    +      -       -      +
    235K  ALA*     3.7    12.9    -      -       -      +
    236K  GLU*     3.3    36.0    +      -       -      +
    242K  VAL*     4.4    16.8    -      -       +      +
    109U  LYS*     5.7     4.9    -      -       -      +
    319U  ASP*     2.4    49.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLU 233 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161K  PRO*     3.9    19.7    -      -       +      +
    229K  ASN*     3.0    38.8    +      -       -      +
    230K  LEU*     3.4     5.5    +      -       -      +
    231K  ILE      2.7     6.7    +      -       -      -
    232K  LYS*     1.3    81.4    -      -       -      +
    234K  ALA*     1.3    59.1    +      -       -      +
    235K  ALA      3.0     1.1    -      -       -      -
    236K  GLU*     3.1    10.3    +      -       -      +
    237K  LEU*     3.0    25.5    +      -       -      +
    319U  ASP      4.5     2.9    -      -       -      -
    320U  LYS*     3.7    27.9    +      -       +      +
    323U  SER*     2.6    42.9    +      -       -      -
    324U  LEU*     4.8     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ALA 234 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    161K  PRO*     3.8    12.9    -      -       +      +
    164K  THR*     3.3    24.2    -      -       +      -
    165K  LEU*     5.6     2.0    -      -       +      -
    200K  LEU*     3.2    24.9    -      -       +      -
    230K  LEU      3.3     7.8    +      -       -      +
    231K  ILE*     2.9     5.0    +      -       -      +
    233K  GLU*     1.3    78.2    -      -       -      +
    235K  ALA*     1.3    56.5    +      -       -      +
    236K  GLU      3.0     1.6    -      -       -      -
    237K  LEU*     3.3    10.5    -      -       +      +
    238K  LEU*     2.9    35.8    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 235 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    200K  LEU*     4.1     2.6    -      -       +      +
    231K  ILE*     2.6    19.7    +      -       +      +
    232K  LYS*     3.7    15.5    -      -       -      +
    234K  ALA*     1.3    78.0    -      -       -      +
    236K  GLU*     1.3    58.0    +      -       +      +
    239K  GLY      3.0     1.7    -      -       -      -
    240K  VAL*     2.4    62.7    +      -       +      +
    242K  VAL*     4.0    20.4    -      -       +      +
----------------------------------------------------------
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Residues in contact with GLU 236 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32J  ARG*     4.6     9.2    +      -       -      +
    232K  LYS*     3.3    28.3    +      -       -      +
    233K  GLU*     3.1    11.6    +      -       -      +
    234K  ALA      3.0     0.4    -      -       -      -
    235K  ALA*     1.3    79.1    -      -       +      +
    237K  LEU*     1.3    65.4    -      -       -      +
    238K  LEU      3.2     1.6    -      -       -      -
    239K  GLY*     2.9    15.9    +      -       -      +
    105U  LYS*     3.2    27.3    +      -       -      +
    107U  GLU*     5.2     3.9    -      -       -      +
    109U  LYS*     5.8     1.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 237 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     11K  LYS*     4.1    10.4    +      -       -      -
     12K  PHE*     3.3    54.1    -      -       +      -
    161K  PRO*     4.3    14.4    -      -       +      +
    162K  ILE*     3.4    32.8    -      -       +      +
    165K  LEU*     5.0     2.7    -      -       +      -
    233K  GLU      3.0    14.0    +      -       -      +
    234K  ALA*     3.3    11.0    -      -       -      +
    236K  GLU*     1.3    78.0    -      -       -      +
    238K  LEU*     1.3    61.1    +      -       +      +
----------------------------------------------------------
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Residues in contact with LEU 238 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     32J  ARG*     4.7     3.3    +      -       -      -
      8K  LEU*     2.8    66.5    -      -       +      +
      9K  LEU*     3.4    21.1    -      -       +      -
     11K  LYS*     5.5     5.4    +      -       -      +
     12K  PHE*     4.6     7.2    -      -       +      -
    165K  LEU*     3.9    16.2    -      -       +      -
    168K  VAL*     3.8    21.3    -      -       +      -
    200K  LEU*     3.7    28.5    -      -       +      -
    204K  ILE*     4.0    10.8    -      -       +      -
    234K  ALA      2.9    10.6    +      -       -      +
    237K  LEU*     1.3    79.0    -      -       +      +
    239K  GLY*     1.3    59.8    +      -       -      +
    240K  VAL*     3.3     8.5    -      -       +      -
----------------------------------------------------------
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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