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Beta turns are especially common at the loop ends of beta hairpins; they have a different distribution of types from the others; type I' is the most common, followed by types II', I and II. Additional turn types have been defined by clustering turn conformations within very high-resolution protein structures. [11]
A hairpin is a special case of a turn, in which the direction of the protein backbone reverses and the flanking secondary structure elements interact. For example, a beta hairpin connects two hydrogen-bonded , antiparallel β-strands (a rather confusing name, since a β-hairpin may contain many types of turns – α, β, γ, etc.).
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 secondary structure is assigned based on hydrogen bonding patterns as those initially proposed by Pauling et al. in 1951 (before any protein structure had ever been experimentally determined). There are eight types of secondary structure that DSSP defines: G = 3-turn helix (3 10 helix). Min length 3 residues. H = 4-turn helix . Minimum ...
The other type is the G1 beta bulge, of which there are two common sorts, both mainly occurring in association with antiparallel sheet; one residue has the α L conformation and is usually a glycine. In one sort, the beta bulge loop , one of the hydrogen bonds of the beta-bulge also forms a beta turn or alpha turn, such that the motif is often ...
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 ...
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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.