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The pitch of the alpha-helix (the vertical distance between consecutive turns of the helix) is 5.4 Å (0.54 nm), which is the product of 1.5 and 3.6. The most important thing is that the N-H group of one amino acid forms a hydrogen bond with the C=O group of the amino acid four residues earlier; this repeated i + 4 → i hydrogen bonding is the ...
The same operators can be used to combine named selections into a new selection; e.g. if sele alpha, name ca and sele helix, ss h are already defined, then sele alpha_not_helix, alpha not helix selects alpha carbons not in a helix. There are also a number of selection operators used for creating local selections according to defined criteria.
G = 3-turn helix (3 10 helix). Min length 3 residues. H = 4-turn helix . Minimum length 4 residues. I = 5-turn helix . Minimum length 5 residues. T = hydrogen bonded turn (3, 4 or 5 turn) E = extended strand in parallel and/or anti-parallel β-sheet conformation. Min length 2 residues.
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 alignment of the H-bonds ...
The loops connecting the beta strands and alpha helix can vary in length and often binds ligands. Beta-alpha-beta helices can be either left-handed or right-handed. When viewed from the N-terminal side of the beta strands, so that one strand is on top of the other, a left-handed beta-alpha-beta motif has the alpha helix on the left side of the ...
The Rossmann fold is a tertiary fold found in proteins that bind nucleotides, such as enzyme cofactors FAD, NAD +, and NADP +.This fold is composed of alternating beta strands and alpha helical segments where the beta strands are hydrogen bonded to each other forming an extended beta sheet and the alpha helices surround both faces of the sheet to produce a three-layered sandwich.
Such a clustering is alternatively described in the ABEGO system, where each letter stands for α (and 3 10) helix, right-handed β sheets (and extended structures), left-handed helixes, left-handed sheets, and finally unplottable cis peptide bonds sometimes seen with proline; it has been used in the classification of motifs [14] and more ...
The actin depolymerizing factor homology domain (ADF-H domain) allows for binding to actin subunits and includes the central alpha helix, the N-terminus extension, and the C terminus helix. [9] [8] The N-terminus extension consists of a tilted loop that facilitates binding to G-actin but not F-actin due to steric hindrance present in F-actin. [8]