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Apart from the type I, I’,II and II’ beta turns as identified via the hydrogen bond criterion, non-hydrogen-bonded beta-turns named type VIII often occur. Three other, fairly rare, types of beta turn have been identified in which the peptide bond between residues i+1 and i+2 is cis rather than trans; these are named types VIa1, VIa2 and VIb ...
According to one definition, a turn is a structural motif where the C α atoms of two residues separated by a few (usually 1 to 5) peptide bonds are close (less than 7 Å [0.70 nm]). [1] The proximity of the terminal C α atoms often correlates with formation of an inter main chain hydrogen bond between the corresponding residues.
If p(t) exceeds an arbitrary cutoff value (originally 7.5e–3), the mean of the p(j)'s exceeds 1, and p(t) exceeds the alpha helix and beta sheet probabilities for that window, then a turn is predicted. If the first two conditions are met but the probability of a beta sheet p(b) exceeds p(t), then a sheet is predicted instead.
These methods were based on the helix- or sheet-forming propensities of individual amino acids, sometimes coupled with rules for estimating the free energy of forming secondary structure elements. The first widely used techniques to predict protein secondary structure from the amino acid sequence were the Chou–Fasman method [ 17 ] [ 18 ] [ 19 ...
Beta bend ribbons may be formed from any of these types but type I is the commonest in proteins, as it is for single beta turns. Beta bend ribbons made from type I or I’ turns are somewhat twisted, while beta bend ribbons made from type II or II’ beta turns are flat. Beta bend ribbons with mixtures of different beta turn types also occur.
The ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide bond planar. [3] The figure in the top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius in solid outline, reduced radius in dashed, and ...
An alpha-helix with hydrogen bonds (yellow dots) The α-helix is the most abundant type of secondary structure in proteins. The α-helix has 3.6 amino acids per turn with an H-bond formed between every fourth residue; the average length is 10 amino acids (3 turns) or 10 Å but varies from 5 to 40 (1.5 to 11 turns).
The GOR method analyzes sequences to predict alpha helix, beta sheet, turn, or random coil secondary structure at each position based on 17-amino-acid sequence windows. The original description of the method included four scoring matrices of size 17×20, where the columns correspond to the log-odds score, which reflects the probability of finding a given amino acid at each position in the 17 ...