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Geometry motivated alternative view on local protein backbone structures

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.