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The most common secondary structures are alpha helices and beta sheets. Other helices, such as the 3 10 helix and π helix , are calculated to have energetically favorable hydrogen-bonding patterns but are rarely observed in natural proteins except at the ends of α helices due to unfavorable backbone packing in the center of the helix.
[citation needed] This state represents a combination of folded hydrophobic α-helices and partially unfolded segments covered by the detergent. For example, the "unfolded" bacteriorhodopsin in SDS micelles has four transmembrane α-helices folded, while the rest of the protein is situated at the micelle-water interface and can adopt different ...
Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation .
α-Helices Cylindrical spiral ribbons, with ribbon plane approximately following plane of peptides. β-Strands Arrows with thickness, about one-quarter as thick as they are wide, showing direction and twist of the strand from amino to carboxy end. β-sheets are seen as unified because neighboring strands twist in unison. Loops and miscellaneous
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.
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.
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).
All-β proteins are a class of structural domains in which the secondary structure is composed entirely of β-sheets, with the possible exception of a few isolated α-helices on the periphery. Common examples include the SH3 domain, the beta-propeller domain, the immunoglobulin fold and B3 DNA binding domain.