Analysis of protein-protein interface by MolSurfer

  • After opening this page, 2 windows should have appeared: the Molsurfer window showing a 2-dimensional map of the interface; and the WebMol window showing a 3-dimensional view of a protein-protein complex and its interface.

  • Open this link in a new window to see the tutorial step-by-step instructions

  • Use menu File--Open to switch between the interfaces;
  • Use menu View to switch between the properties to be displayed on the 2D map;
  • Use Mouse to move/drag/click across the map to navigate in the 3D structure;
  • To adjust the range for displaying properties on 2D map, click left/right mouse button on the color bar;
  • Use features of WebMol while viewing 3D - stereo, colouring, selecting etc;
  • Use menu File--Quit when done.

  • All images of 2D maps can be found here. Note that the parameter ranges there have fixed initial values; these can only be altered on the interactive maps.

    Details of interface mapping for the tutorial demo:
  • Each PDB file was split into 2 parts giving coordinates of the first and the second proteins forming the interface;
  • A quasi rectangular mesh with ca 1 Å spacing was generated on the analytically defined interface between these 2 proteins;
  • Points for which the sum of the distances to the closest atoms of proteins 1 and 2 exceeds 6 Å were deleted;
  • Heteroatoms that lie within 3 Å of any interface point were added;
  • The properties of each protein were projected onto every point of the interface; these are the properties assigned to the closest atom to the point;
  • Electrostatic potential of each (isolated) protein was computed with the UHBD program by solving the finite difference linearized Poisson-Boltzmann equation and the potential values were interpolated at each interface point.
  • Additionally, the changes in binding free energy upon alanine mutation were assigned to each side-chain atom of the corresponding residue.  This data can be obtained from the Alanine Scanning Energetics database for example.
  • Residue hydrophobicities were assigned according to the residue name and following the parameters in Eisenberg D., Weiss R.M., Terwilliger T.C. and Wilcox W. (1982) Farad. Symp. Chem. Soc., 17, 109-120, namely:

  •   ALA   0.25       GLN  -0.69       LEU   0.53       SER  -0.26
      ARG  -1.80       GLU  -0.62       LYS  -1.10       THR  -0.18
      ASN  -0.64       GLY   0.16       MET   0.26       TRP   0.37
      ASP  -0.72       HIS  -0.40       PHE   0.61       TYP   0.02
      CYS   0.04       ILE   0.73       PRO  -0.07       VAL   0.54
      none of the above                 0.00
  • Atomic hydrophobicities were assigned according to the atom name and follow  Eisenberg D., Wesson M., Yamashita M. (1989) Chem. Scrip., 29A, 217-221, namely:

  •   'NZ  LYS'  -38       'OE1 GLU'  -37         'C'    18
      'NH1 ARG'  -38       'OE2 GLU'  -37         'S'     5
      'NH2 ARG'  -38       'OD1 ASP'  -37         'O'    -9
                           'OD2 ASP'  -37         'N'    -9
      none of the above    0
  • Atomic radii were also assigned from the previous reference, namely:

  •   'C'    1.9 A
      'S'    1.8 A
      'O'    1.4 A
      'N'    1.7 A
      none of the above    1.9 A


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