We inspect the geometry of proteins by identifying their backbones as framed polygons. We find that the left-handed helix region of the Ramachandran map for non-glycyl residues corresponds to an isolated and highly localized sector in the orientation of the Cβ carbons, when viewed in a Frenet frame that is centered at the corresponding Cα carbons. We show that this localization in the orientati...

The main-chain conformations of 237 384 amino acids in 1042 protein subunits from the PDB were analyzed with Ramachandran plots. The populated areas of the empirical Ramachandran plot differed markedly from the classical plot in all regions. All amino acids in alpha-helices are found within a very narrow range of phi, psi angles. As many as 40% of all amino acids are found in this most populate...

We present a combined quantum mechanics and molecular mechanics study of the deep ultraviolet ππ* resonance Raman spectra of β-sheet amyloid fibrils Aβ(34-42) and Aβ(1-40). Effects of conformational fluctuations are described using a Ramachandran angle map, thus avoiding repeated ab initio calculations. Experimentally observed effects of hydrogen-deuterium exchange are reproduced. We propose th...

On the occasion of their fiftieth birthday, it is opportune to review the first half century of Ramachandran plots. In the present review, some of the most relevant aspects of this fifty-year history are summarized, from the original ideas of Gopalasamudram Narayana Ramachandran to subsequent revisions and to applications in structural biology. This will not be a guided walk through five decade...

© Rzepa This article is distributed under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution, and redistribution in any medium, provided that the original author and source are credited. This is really just a postscript to the previous post. There I showed how a search of the (small molecule) crystal database revealed the s-cis ...

In our previous paper, we proposed that when attention is used to track salient features of a moving object, other weaker motion signals can be captured and appear to move in synehrony with the tracked features (Culham & Cavanagh, 1994b). In one experiment, when observers used attention to track the bars of an ambiguous counterphase grating in either direction, superimposed dynamic luminance do...