An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ().

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom-the backbone dihedral angles and (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of and has not been completely described for both and backbones. Additionally, little intuitive understanding is available about a peptide's conformation simply from knowing the and values of a peptide (e.g., is the regular peptide defined by  =  =  - 100°  left-handed or right-handed?). This report provides a new metric for backbone handedness () based on interpreting a peptide backbone as a helix with axial displacement and angular displacement , both of which are derived from a peptide backbone's internal coordinates, especially dihedral angles , and . In particular, equals sin()∕||, with range [-1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric is used to characterize the handedness of every region of the Ramachandran plot for both ( = 0°) and trans ( = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (, ) space. These maps fill in the 'dead space' within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on and that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including and backbones. The intuitiveness arises from the fact that and provide, at a glance, numerous aspects of the backbone including compactness, handedness, and planarity.