Substitutes is the third screen of the Protein Design wizard. When using certain menu commands, the wizard opens to this screen, already prepopulated with the currently-selected residues.

Each row of the table represents a single residue.

  • Chain – The chain where the residue is located.
  • Residue – The amino acid code for the residue.
  • Position – The numerical position of the residue on the sequence.
  • Accessibility – The solvent accessibility of a residue. Possible values are Surface, Core, or Boundary.
  • Substitute – A drop-down menu from which you can choose a different amino acid residue or set of residues for the position. The selection made in this menu will replace the original residue for that row. If you selected Create a specific variant on the Workflow screen, menu options will include only individual amino acid codes.

    If you selected Search for variants that improve folding stability (early release) on that screen, this menu will also include the following options:

    • All – All 20 amino acids
    • CoreAVLIFYW (those likely to be found in protein cores)
    • SurfaceANQSTHDEKR (those likely to be found on protein surfaces)
    • Boundary – Those likely to be found at the union of the Core and Surface groups
    • PolarCNQST
    • NonpolarAGILMPV
    • AromaticFWY
    • Acidic – DE
    • BasicHKR
    • ChargedDEKRH

Core, Surface, and Boundary are defined in Pierce et al. Nonpolar, Aromatic, Acidic, Basic, Charged are defined the same as in the Composition report and other locations in Protean 3D.

  • Variant – After choosing a Substitute residue, this column will display an automatically-generated name for the variant. The name consists of the original residue, its position, and the substitute residue, in that order.

Use the Variant nomenclature drop-down menu to choose from the following options. The selected option will be reflected in how residues are listed in the Residue, Substitute, and Variant columns:

  • 1-letter – To use 1-letter amino acid codes.
  • 3-letter – To use 3-letter amino acid codes.

To learn about the optional tools in the bottom left corner of the screen, see the bottom of this topic.

Continue by doing one of the following:

  • To specify additional options, press Next to continue to the Options screen.
  • To return to a previous screen, press Back.
  • To close the Protein Design wizard without starting a search, press Cancel.

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