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AAindex is a database of amino acid indices, amino acid mutation matrices, and pair-wise contact potentials. [ 1 ] [ 2 ] The data represent various physicochemical and biochemical properties of amino acids and pairs of amino acids.
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]
The abundance of 15 N in some amino acids reflects an organism's position in a food web. This is due to the ways organisms metabolize different amino acids when they are consumed. Trophic amino acids (TrAAs) are first deaminated, meaning that the amino group is removed to produce an alpha-keto acid carbon skeleton.
The first figure shows rainbow boxes displaying the properties of amino acids. In rainbow boxes, the elements are shown in columns (e.g. the amino acids), and each set is represented by a rectangular box (e.g. the groups of amino acids sharing a given property). Each box covers the columns corresponding to the elements belonging to its set.
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The "side chain" from the α carbon connects to the nitrogen forming a pyrrolidine loop, classifying it as a aliphatic amino acid. It is non-essential in humans, meaning the body can synthesize it from the non-essential amino acid L-glutamate. It is encoded by all the codons starting with CC (CCU, CCC, CCA, and CCG).
Four of these elements (hydrogen, carbon, nitrogen, and oxygen) are essential to every living thing and collectively make up 99% of the mass of protoplasm. [1] Phosphorus and sulfur are also common essential elements, essential to the structure of nucleic acids and amino acids, respectively.