Conformations of amino acids in proteins

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 α-helices are found within a very narrow range of φ, ψ angles. As many as 40% of all amino acids are found in this most populated region, covering only 2% of the Ramachandran plot. The β-sheet region is clearly subdivided into two distinct regions. These do not arise from the parallel and antiparallel β-strands, which have quite similar conformations. One β region is mainly from amino acids in random coil. The third and smallest populated area of the Ramachandran plot, often denoted left-handed α-helix, has a different position than that originally suggested by Ramachandran. Each of the 20 amino acids has its own very characteristic Ramachandran plot. Most of the glycines have conformations that were considered to be less favoured. These results may be useful for checking secondary-structure assignments in the PDB and for predicting protein folding.