Contacts of the helix formed by residues 738 - 753 (chain K) in PDB entry 1SOJ


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 ASN 738 (chain K).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    731K  TYR*     3.5    12.9    -      -       -      -
    732K  ARG      3.7    19.7    -      -       -      +
    733K  ASP*     5.4     1.1    -      -       -      +
    734K  ILE      3.1    21.9    +      -       -      +
    735K  PRO      3.8     8.5    +      -       -      -
    736K  TYR*     2.8    21.1    +      -       -      +
    737K  HIS*     1.3    74.2    -      -       -      +
    739K  ARG*     1.3    67.4    +      -       +      +
    740K  ILE*     2.8    42.5    +      -       -      +
    741K  HIS*     2.9    20.8    +      -       -      +
    742K  ALA      3.2     9.2    +      -       -      -
    951K  TRP*     5.1     3.3    -      -       -      -
----------------------------------------------------------
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Residues in contact with ARG 739 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    692K  SER      4.7     0.4    -      -       -      -
    693K  GLY*     3.5    39.8    +      -       -      -
    695K  ILE*     4.3    12.3    -      -       +      -
    696K  LEU*     4.4    13.4    -      -       +      +
    728K  GLU*     2.7    31.4    +      -       -      +
    729K  ASN*     3.1    23.0    +      -       -      +
    731K  TYR*     3.4    38.2    +      -       +      +
    732K  ARG      5.6     1.8    +      -       -      -
    733K  ASP*     5.9     2.6    +      -       -      +
    738K  ASN*     1.3    73.6    -      -       +      +
    740K  ILE*     1.3    64.0    +      -       +      +
    742K  ALA*     3.3     6.1    +      -       -      +
    743K  THR*     2.8    33.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with ILE 740 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    681K  ILE*     3.5    26.2    -      -       +      +
    682K  PHE*     4.4    16.8    -      -       +      -
    685K  VAL*     3.9    35.2    -      -       +      -
    692K  SER*     5.6     1.8    -      -       -      +
    695K  ILE*     4.8     8.1    -      -       +      -
    738K  ASN*     2.8    25.9    +      -       -      +
    739K  ARG*     1.3    77.9    -      -       +      +
    741K  HIS*     1.3    63.4    +      -       -      +
    743K  THR*     3.3     6.9    +      -       -      -
    744K  ASP*     2.9    19.6    +      -       -      +
    951K  TRP*     3.8    15.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with HIS 741 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    736K  TYR*     3.2    53.7    +      +       -      +
    737K  HIS*     4.0    11.9    -      -       -      -
    738K  ASN*     2.9    11.7    +      -       -      +
    740K  ILE*     1.3    77.1    -      -       -      +
    742K  ALA*     1.3    58.9    +      -       -      +
    744K  ASP*     3.0     8.6    +      -       -      +
    745K  VAL*     2.8    45.4    +      -       +      +
    821K  HIS*     3.3     4.8    +      +       -      -
    822K  ASP*     2.8    17.2    +      -       +      -
    937K  ASP*     3.2    15.0    -      -       -      -
    939K  ASN*     6.1     0.2    -      -       -      -
    951K  TRP*     3.7    16.0    -      -       +      -
   2143K   MG      1.8    34.0    -      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 742 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    696K  LEU*     4.2     8.5    -      -       +      -
    731K  TYR*     3.5    40.2    -      -       +      +
    738K  ASN      3.2     2.8    +      -       -      +
    739K  ARG      3.6     7.9    -      -       -      +
    741K  HIS*     1.3    78.2    -      -       -      +
    743K  THR*     1.3    64.2    +      -       -      +
    745K  VAL*     3.2     2.9    +      -       -      +
    746K  LEU*     2.8    23.6    +      -       -      +
    818K  ALA      4.0    10.9    -      -       -      +
    819K  ALA      3.9    10.1    -      -       -      +
    821K  HIS*     4.3     9.6    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 743 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    679K  PHE*     5.3     4.0    -      -       +      -
    681K  ILE*     3.9    15.5    -      -       +      -
    695K  ILE*     3.9    10.6    -      -       +      +
    696K  LEU*     3.4    31.3    +      -       -      +
    699K  VAL*     3.6    39.3    -      -       +      -
    739K  ARG      2.8    20.1    +      -       -      -
    740K  ILE*     3.5     8.7    -      -       -      -
    742K  ALA*     1.3    76.5    -      -       -      +
    744K  ASP*     1.3    56.9    +      -       -      +
    746K  LEU*     3.0     6.0    +      -       -      +
    747K  HIS*     2.9    27.6    +      -       +      +
----------------------------------------------------------
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Residues in contact with ASP 744 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    679K  PHE*     5.7     1.6    -      -       -      -
    681K  ILE*     3.7    14.9    -      -       +      +
    740K  ILE      2.9    13.7    +      -       -      +
    741K  HIS*     3.0    11.4    +      -       -      +
    743K  THR*     1.3    76.1    -      -       -      +
    745K  VAL*     1.3    64.1    +      -       +      +
    746K  LEU      3.2     0.2    +      -       -      -
    747K  HIS*     3.2    11.5    +      -       -      +
    748K  ALA*     2.9    21.7    +      -       -      +
    939K  ASN*     3.5    20.4    +      -       -      +
    940K  GLY*     5.9     0.2    -      -       -      -
    943K  LYS*     3.2    22.3    +      -       -      -
    951K  TRP*     3.2    38.3    +      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 745 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    741K  HIS*     2.8    49.6    +      -       +      +
    742K  ALA      3.7     6.1    -      -       -      +
    744K  ASP*     1.3    72.9    -      -       +      +
    746K  LEU*     1.3    62.2    +      -       -      +
    748K  ALA*     3.3     3.2    +      -       -      +
    749K  VAL*     3.1    21.4    +      -       -      +
    818K  ALA*     4.2    13.5    -      -       +      +
    821K  HIS*     3.5    24.9    -      -       +      +
    933K  ILE*     4.6     8.1    -      -       +      -
    936K  ALA*     3.8    20.0    -      -       +      +
    937K  ASP*     3.7    24.7    -      -       +      +
    939K  ASN*     5.1     1.3    -      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 746 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    696K  LEU*     4.2    12.3    -      -       +      -
    699K  VAL*     3.7    24.0    -      -       +      -
    700K  MET*     3.1    52.5    -      -       +      +
    703K  LEU*     3.6    15.0    -      -       +      -
    742K  ALA      2.8    12.6    +      -       -      +
    743K  THR      3.0     7.8    +      -       -      +
    745K  VAL*     1.3    74.2    -      -       -      +
    747K  HIS*     1.3    67.8    +      -       -      +
    749K  VAL*     2.9    25.7    -      -       +      +
    750K  TRP*     3.0     9.9    +      -       +      +
    815K  TYR*     3.6    28.0    -      -       +      +
    818K  ALA*     3.9     7.1    -      -       +      +
    819K  ALA*     5.0     2.5    -      -       +      +
----------------------------------------------------------
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Residues in contact with HIS 747 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    674K  MET*     2.9    47.2    +      -       +      -
    676K  ASN      3.6     8.3    -      -       -      -
    677K  TRP*     3.7    19.3    -      +       -      -
    679K  PHE*     3.5    40.0    -      +       +      +
    699K  VAL*     5.4     1.3    -      -       +      -
    703K  LEU*     4.6     3.6    -      -       -      -
    743K  THR*     2.9    14.8    +      -       +      +
    744K  ASP*     3.6    17.0    +      -       -      +
    746K  LEU*     1.3    75.7    -      -       -      +
    748K  ALA*     1.3    60.0    +      -       -      +
    750K  TRP*     3.5    21.5    +      +       -      -
    751K  TYR*     2.9    35.4    +      -       +      +
    943K  LYS*     5.0     3.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 748 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    677K  TRP*     4.4    18.8    -      -       +      -
    744K  ASP*     2.9    14.1    +      -       -      +
    745K  VAL      3.5     4.9    -      -       -      +
    746K  LEU      3.1     0.2    -      -       -      -
    747K  HIS*     1.3    83.4    +      -       -      +
    749K  VAL*     1.3    53.0    +      -       -      +
    751K  TYR*     3.2     2.3    +      -       -      +
    752K  LEU*     2.7    41.7    +      -       +      +
    936K  ALA*     3.5    30.5    -      -       +      +
    939K  ASN*     4.2     9.0    -      -       -      +
    943K  LYS*     5.7     0.9    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 749 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    745K  VAL      3.1     8.0    +      -       -      +
    746K  LEU*     2.9    24.7    -      -       +      +
    748K  ALA*     1.3    73.2    -      -       -      +
    750K  TRP*     1.3    57.0    +      -       -      +
    752K  LEU*     4.4     5.2    -      -       -      -
    753K  THR*     2.6    38.3    +      -       -      +
    814K  LEU*     4.1    24.0    -      -       +      +
    815K  TYR*     3.9    16.6    -      -       +      -
    818K  ALA*     3.8    13.2    -      -       +      -
    932K  CYS*     4.0     5.4    -      -       -      +
    933K  ILE*     3.7    26.0    -      -       +      -
    936K  ALA*     3.5    21.5    -      -       +      -
----------------------------------------------------------
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Residues in contact with TRP 750 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    671K  ILE*     5.0     4.9    -      -       +      -
    674K  MET*     3.2    39.3    -      -       +      -
    675K  SER*     4.6     1.3    -      -       -      -
    703K  LEU*     3.4    39.9    -      -       +      +
    706K  ASP*     3.3    22.4    +      -       -      -
    707K  THR*     4.0    14.7    +      -       -      -
    746K  LEU*     3.0    15.6    +      -       +      +
    747K  HIS*     3.6    21.5    -      +       -      +
    749K  VAL*     1.3    80.6    -      -       -      +
    751K  TYR*     1.3    76.4    +      +       +      +
    753K  THR*     3.2     1.4    +      -       -      -
    754K  THR*     3.0    41.0    +      -       -      -
    755K  ARG*     3.0    37.5    -      -       -      -
    789K  SER*     4.1     0.8    +      -       -      -
    791K  SER*     3.7    10.3    -      -       -      -
    815K  TYR*     3.7    23.3    -      +       +      -
----------------------------------------------------------
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Residues in contact with TYR 751 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    674K  MET      4.4    10.8    -      -       -      -
    675K  SER      3.4    25.4    +      -       -      -
    677K  TRP*     3.5    56.4    +      +       +      +
    747K  HIS*     2.9    23.7    +      -       +      +
    748K  ALA      3.6     2.9    -      -       -      +
    750K  TRP*     1.3    88.2    -      +       +      +
    752K  LEU*     1.3    63.0    +      -       -      +
    754K  THR*     4.5     0.9    -      -       -      -
    755K  ARG*     3.2    53.5    +      -       +      +
   1010K  PRO*     3.9    24.0    -      -       +      +
   1060K  GLN*     4.4     5.7    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 752 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    677K  TRP*     4.0    22.7    -      -       +      -
    748K  ALA      2.7    27.0    +      -       -      +
    749K  VAL      4.1     0.7    -      -       -      +
    751K  TYR*     1.3    73.7    -      -       +      +
    753K  THR*     1.3    57.9    +      -       -      +
    754K  THR      3.5     0.2    -      -       -      -
    755K  ARG      5.0     1.1    -      -       -      +
    757K  VAL*     5.0     1.6    -      -       -      +
    802K  LEU*     3.1    19.4    -      -       -      +
    932K  CYS*     3.9    35.7    -      -       -      +
    935K  LEU*     4.3    25.6    -      -       +      -
    936K  ALA*     4.5     5.8    -      -       +      +
   1003K  TYR*     4.1     8.7    +      -       +      +
   1008K  LEU      4.4     3.6    -      -       -      +
   1009K  LEU*     4.4     4.3    -      -       +      -
   1010K  PRO*     3.7    33.8    -      -       +      +
   1061K  LEU*     4.1    12.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with THR 753 (chain K). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    749K  VAL      2.6    23.4    +      -       -      +
    750K  TRP      3.2     1.0    +      -       -      -
    751K  TYR      3.2     0.2    -      -       -      -
    752K  LEU*     1.3    79.1    -      -       -      +
    754K  THR*     1.3    59.3    +      -       -      +
    802K  LEU*     3.8    28.6    +      -       +      -
    803K  SER*     2.9    31.3    +      -       -      -
    806K  ILE*     5.3     2.2    -      -       +      -
    811K  LEU*     4.1    18.9    -      -       +      +
    814K  LEU*     4.2     7.4    -      -       +      -
    815K  TYR*     2.9    25.2    +      -       -      -
    932K  CYS*     3.8    20.4    -      -       +      -
----------------------------------------------------------
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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