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  2. Alpha helix - Wikipedia

    en.wikipedia.org/wiki/Alpha_helix

    The alpha helix is the most common structural arrangement in the secondary structure of proteins. It is also the most extreme type of local structure, and it is the local structure that is most easily predicted from a sequence of amino acids. The alpha helix has a right-handed helix conformation in which every backbone N−H group hydrogen ...

  3. Protein secondary structure - Wikipedia

    en.wikipedia.org/wiki/Protein_secondary_structure

    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 ...

  4. Transmembrane protein - Wikipedia

    en.wikipedia.org/wiki/Transmembrane_protein

    Alpha-helical proteins are present in the inner membranes of bacterial cells or the plasma membrane of eukaryotic cells, and sometimes in the bacterial outer membrane. [5] This is the major category of transmembrane proteins. In humans, 27% of all proteins have been estimated to be alpha-helical membrane proteins. [6]

  5. Transmembrane domain - Wikipedia

    en.wikipedia.org/wiki/Transmembrane_domain

    A transmembrane domain (TMD) is a membrane-spanning protein domain.TMDs may consist of one or several alpha-helices or a transmembrane beta barrel.Because the interior of the lipid bilayer is hydrophobic, the amino acid residues in TMDs are often hydrophobic, although proteins such as membrane pumps and ion channels can contain polar residues.

  6. Helical wheel - Wikipedia

    en.wikipedia.org/wiki/Helical_wheel

    A helical wheel is a type of plot or visual representation used to illustrate the properties of alpha helices in proteins. The sequence of amino acids that make up a helical region of the protein's secondary structure are plotted in a rotating manner where the angle of rotation between consecutive amino acids is 100°, so that the final ...

  7. Hydrophobicity scales - Wikipedia

    en.wikipedia.org/wiki/Hydrophobicity_scales

    Hydrophobicity scales can also be obtained by calculating the solvent accessible surface areas for amino acid residues in the expended polypeptide chain [22] or in alpha-helix and multiplying the surface areas by the empirical solvation parameters for the corresponding types of atoms. [3]

  8. Hydrophobic collapse - Wikipedia

    en.wikipedia.org/wiki/Hydrophobic_collapse

    A surface exposed alpha helix may have nonpolar residues in an N+3, N+4 position, allowing the alpha-helix to express nonpolar properties on one side when split longitudinally along the axis. Note, in the diagram, the presence of non-polar(gold) amino acids along one side of the helix when viewed through the longitudinal axis, as well as ...

  9. Protein structure prediction - Wikipedia

    en.wikipedia.org/wiki/Protein_structure_prediction

    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).