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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 ...
Because of this it is sometimes also described as the residue following the helix. Certain motifs occur commonly at or around the C cap, notably the Schellman loop and the niche (protein structural motif). The N cap is the corresponding amino acid residue at the other end of the helix
The beta strands are parallel, and the helix is also almost parallel to the strands. This structure can be seen in almost all proteins with parallel strands. 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.
Because of this it is sometimes also described as the residue prior to the helix. Capping motifs are those often found at the N cap. Asx turns, ST turns, and asx motifs are often found at such situations, with the asx or serine or threonine residue at the N cap. The C cap is the corresponding amino acid residue at the other end of the helix
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The plot reveals whether hydrophobic amino acids are concentrated on one side of the helix, usually with polar or hydrophilic amino acids on the other. This arrangement is common in alpha helices within globular proteins, where one face of the helix is oriented toward the hydrophobic core and one face is oriented toward the solvent-exposed surface.
The data suggested that the unstretched fibres had a coiled molecular structure with a characteristic repeat of 5.1 Å (=0.51 nm). Astbury proposed that (1) the unstretched protein molecules formed a helix (which he called the α-form); and (2) the stretching caused the helix to uncoil, forming an extended state (which he called the β-form).
One of them, the L12 helix located just before the T-loop in the primary sequence, is transformed into a beta strand and helps to reorganize the T-loop so that it no longer blocks the active site. The other alpha helix, known as the PSTAIRE helix, is reorganized and helps to change the position of the key amino acids in the active site. [6] [14]