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Amino Acids

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Ani4

Animation of some Arginine side chain positions

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

In Foldit, there are 20 different amino acids.

Each protein has a unique sequence of amino acids. This sequence is called the "primary structure" of the protein. It's common to see the sequence listed as a string of one-character lowercase amino acid codes, for example:

rkeeivkriekyykehsngdqnryehvrqrieelsksngdesvevrggkhhrirvqdgdeidlqd

The table below lists the amino acids and their one- and three-character abbreviations.

When it comes to protein folding, one important characteristic of an amino acid is how it interacts with water. In Foldit, an amino acid is either hydrophilic, meaning it likes water, or hydrophobic, meaning it tries to avoid water. The "hydropathy index" column of the table is a more refined version of this idea.

The other main characteristic of an amino acid is it's sidechain. All amino acids have the same backbone. It's the sidechain, projecting off the backbone, which makes each amino acid different. See the amino acid gallery for examples of what each amino acid looks like in Foldit.

Table of amino acids Edit

The table below shows the amino acids used in Foldit. It includes the three-letter abbreviation and one-character code for each amino acid. Two amino acids have two names. Aspartate is also called aspartic acid, and glumate is also called glutamic acid. This is because both have acid sidechains.

The table also includes polarity; the sidechains of "polar" amino acids tend to form hydrogen bonds. The table shows whether the sidechain is acidic or basic. Finally, the table shows the hydropathy index.

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 hyrdophobic. In general, negative values are hydrophilic in Foldit, and positive values are hydrophobic. There are several exceptions in the middle of the table, however. (Click on the arrows at the top of the hydropathy index column to sort the table by hydropathy.)

Amino Acid 3-Letter 1-Letter Side chain polarity Side chain acid or base Hydropathy index

[1]

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

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

The wikipedia article proteinogenic amino acid has much more information about each amino acid

ReferencesEdit

  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 PDF; 1.9 MB

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