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Ani4

Animation of some Arginine sidechain positions.

Amino acids (also called segments or residues in Foldit) are the building blocks of proteins.

Each protein is identified by a unique sequence of amino acids, the primary structure of the protein.

The table below shows the 20 amino acids used in Foldit. Clicking on the arrows in the column heads changes the sort order of the table. The table is explained in detail below.

Amino Acid 3-Letter 1-Letter Hydrophobicity /

Hydropathy index[1]

polarity acidity (pH)
Alanine Ala A 1.8 nonpolar neutral
Arginine Arg R -4.5 polar basic (strongly)
Asparagine Asn N -3.5 polar neutral
Aspartate (aspartic acid) Asp D -3.5 polar acidic
Cysteine Cys C 2.5 polar neutral
Glutamate (glutamic acid) Glu E -3.5 polar acidic
Glutamine Gln Q -3.5 polar neutral
Glycine Gly G -0.4 nonpolar neutral
Histidine His H -3.2 polar basic (weakly)
Isoleucine Ile I 4.5 nonpolar neutral
Leucine Leu L 3.8 nonpolar neutral
Lysine Lys K -3.9 polar basic
Methionine Met M 1.9 nonpolar neutral
Phenylalanine Phe F 2.8 nonpolar neutral
Proline Pro P -1.6 nonpolar neutral
Serine Ser S -0.8 polar neutral
Threonine Thr T -0.7 polar neutral
Tryptophan Trp W -0.9 nonpolar neutral
Tyrosine Tyr Y -1.3 polar neutral
Valine Val V 4.2 nonpolar neutral

See the amino acid gallery for examples of what each amino acid looks like in Foldit.

See also spmm's amino acid table, which shows the odds of each amino acid being found in helix, sheet, and loop.

See proteinogenic amino acid on wikipedia for more information about each amino acid.

Detail

The table shows how amino acids are identified and lists the key characteristics of their sidechains.

Amino Acid

The first column shows each amino acid's full name, and links to its detail page.

Two amino acids have two names. Aspartate is also called aspartic acid, and glutamate is also called glutamic acid. This is because both have acid sidechains.

3-letter code

Some sources, such as the PDB, use three-letter codes to represent amino acids.

1-letter code

The primary structure of a protein is often reported one-letter codes, such as in FASTA format.

Hydrophobicity/Hydropathy index

One important characteristic of an amino acid is how it interacts with water, also known as hydrophobicity. In Foldit, an amino acid is either hydrophilic, meaning it likes water, or hydrophobic, meaning it tries to avoid water. The hydropathy index is a more refined version of this idea.

The hydropathy index values shown in blue are for amino acids classified as hydrophilic in Foldit. The values shown in orange are for amino acids considered hydrophobic. In general, negative values are hydrophilic in Foldit, and positive values are hydrophobic. There are several exceptions in the middle of the table, however.

Polarity

The amino acids listed as "polar" have sidechains with nitrogen or oxygen atoms that can form hydrogen bonds. See sidechain bonding gallery and sidechain bonding table for details on the bondable atoms

Acidity (pH)

The sidechain of each amino acid is classified as acidic, basic, or neutral.

References

  1. Kyte J & RF Doolittle: A simple method for displaying the hydropathic character of a protein in: Journal of Molecular Biology issue 157, 1982, pages 105–132 PMID 7108955