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  2. Hydrophobicity scales - Wikipedia

    en.wikipedia.org/wiki/Hydrophobicity_scales

    Hydrophobicity scales. Hydrophobicity scales are values that define the relative hydrophobicity or hydrophilicity of amino acid residues. The more positive the value, the more hydrophobic are the amino acids located in that region of the protein. These scales are commonly used to predict the transmembrane alpha-helices of membrane proteins.

  3. Amino acid - Wikipedia

    en.wikipedia.org/wiki/Amino_acid

    Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. [1] Although over 500 amino acids exist in nature, by far the most important are the 22 α-amino acids incorporated into proteins. [2] Only these 22 appear in the genetic code of life. [3][4]

  4. Aromatic amino acid - Wikipedia

    en.wikipedia.org/wiki/Aromatic_amino_acid

    Aromatic amino acids, excepting histidine, absorb ultraviolet light above and beyond 250 nm and will fluoresce under these conditions. This characteristic is used in quantitative analysis, notably in determining the concentrations of these amino acids in solution. [1] [2] Most proteins absorb at 280 nm due to the presence of tyrosine and ...

  5. Helical wheel - Wikipedia

    en.wikipedia.org/wiki/Helical_wheel

    Aliphatic residues are shown as blue squares, polar or negatively charged residues as red diamonds, and positively charged residues as black octagons. 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 ...

  6. Active site - Wikipedia

    en.wikipedia.org/wiki/Active_site

    Active site. Organisation of enzyme structure and lysozyme example. Binding sites in blue, catalytic site in red and peptidoglycan substrate in black. (PDB: 9LYZ ) In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid ...

  7. 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.

  8. Non-proteinogenic amino acids - Wikipedia

    en.wikipedia.org/wiki/Non-proteinogenic_amino_acids

    Lysine. Technically, any organic compound with an amine (–NH 2) and a carboxylic acid (–COOH) functional group is an amino acid. The proteinogenic amino acids are small subset of this group that possess central carbon atom (α- or 2-) bearing an amino group, a carboxyl group, a side chain and an α-hydrogen levo conformation, with the exception of glycine, which is achiral, and proline ...

  9. Serine - Wikipedia

    en.wikipedia.org/wiki/Serine

    Serine (symbol Ser or S) [3][4] is an α- amino acid that is used in the biosynthesis of proteins. It contains an α- amino group (which is in the protonated − NH+. 3 form under biological conditions), a carboxyl group (which is in the deprotonated − COO−. form under biological conditions), and a side chain consisting of a hydroxymethyl ...