Identify secondary structure and topologyΒΆ

Sketch a topology diagram on paper (use the open structure 4AKE for analysis):

  • number helices H1 - H8 (ignore short helices < 4 residues, count all helices as helix (\(\alpha\)-helix, \(\pi\)-helix , \(3_{10}\)-helix))

  • label the \(\beta\)-sheets A, B, C, number individual strands A1-A5, B1-B2, C1-C3

  • start with the central \(\beta\)-sheet as A

  • locate N-terminus (resid 1 and name CA, color blue, VDW) and C terminus

    Note

    You can do ranges: resid 1 to 5 or multiple ranges: resid 1 to 5 20 to 50.

    You can use boolean operators and, or, not. See Selections Tab and Selection Methods in the user manual for details.

  • draw connections between secondary elements in your topology diagram and label secondary structure elements.

../_images/adk-topology-incomplete.svg

Left: Structure of AdK in its open conformation, colored by secondary structure elements. Right: Incomplete topology diagram of AdK.