2 protein-protein interfaces by MolSurfer
Instructions:
  • After opening this page, you should have 2 windows appeared: the Molsurfer window showing the 2 dimensional map of the interface; and the WebMol window showing the 3 dimensional view of the protein-protein complex and the interface.
  • Open this link in a new window to see tutorial 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.

    • Details of interface mapping for a 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 of ca 1 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 were deleted;
  • Heteroatoms were added which lie within 3 of any interface point;
  • 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 FD LPBE 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 property is included for interfaces for which these data are available for at least one of the proteins. See the recent compilation by A. Bogan and K. Thorn
  • Residue hydrophobicities are 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 are 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 are also 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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