title: Geometry motivated alternative view on local protein backbone structures.
abstract: We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (φ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, which is not possible for an R-plot, where structural regimes connected by periodicity appear disconnected. But there are other advantages, like a clear discrimination of the handedness of a local structure, a larger spread of the different local structure domains--the latter can yield a better separation of different local secondary structure motives--and many more. Compared to the R-plot we are not aware of any major disadvantage to classify local polypeptide structures with the (d, ϑ)-plot, except that it requires some elementary computations. To facilitate usage of the new (d, ϑ)-plot for protein structures we provide a web application (http://agknapp.chemie.fu-berlin.de/secsass), which shows the (d, ϑ)-plot side-by-side with the R-plot.
authors.affiliation: Institute of Chemistry and Biochemistry, Freie Universität Berlin, D-14195, Berlin, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Zacharias
authors.forename: Ernst Walter
authors.initials: EW
authors.lastname: Knapp
mesh_terms: D000465:Algorithms; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*
chemical_list: D010455:Peptides; D011506:Proteins
keywords: (d, ϑ)-plot; alternative Ramachandran plot; backbone conformation plot; generic helix parameters; protein geometry; protein secondary structure