Tryptophan



Standard codons for W : TGG

Substitution preferences:
All protein types:
Favoured Tyr ( 2) Phe ( 1)
Disfavoured Met (-1) Leu (-2) Gln (-2) Cys (-2) Thr (-2) Gly (-2) His (-2) Ala (-3)
Lys (-3) Ile (-3) Glu (-3) Arg (-3) Ser (-3) Val (-3) Asp (-4) Asn (-4)
Pro (-4)

Intracellular proteins:
Favoured Tyr ( 2) Phe ( 1)
Neutral His ( 0) Met ( 0) Leu ( 0)
Disfavoured Arg (-1) Cys (-1) Val (-1) Lys (-1) Ile (-1) Gly (-2) Asn (-2) Gln (-2)
Pro (-2) Ser (-2) Thr (-2) Ala (-2) Asp (-2) Glu (-2)

Extracellular proteins:
Favoured Phe ( 1) Tyr ( 1)
Disfavoured Arg (-1) Gln (-1) Glu (-1) Met (-1) His (-1) Thr (-1) Val (-1) Ile (-1)
Ser (-1) Ala (-2) Gly (-2) Lys (-2) Leu (-2) Asn (-3) Asp (-3) Pro (-3)
Cys (-5)

Membrane proteins:
Favoured Arg ( 5) Lys ( 3) Cys ( 1)
Neutral Gln ( 0)
Disfavoured His (-1) Val (-2) Gly (-2) Leu (-2) Met (-2) Phe (-3) Asn (-3) Tyr (-3)
Ile (-3) Ala (-3) Ser (-3) Glu (-3) Asp (-4) Thr (-4) Pro (-6)


Substitutions: As Tryptophan is an aromatic, hydrophobic, amino acid, it prefers subsitution with other amino acids of the same type (see above).

Role in structure: Being hydrophobic, Tryptophan prefers to be buried in protein hydrophobic cores. The aromatic side chain can also mean that Tryptophan is involved in stacking interactions with other aromatic side-chains.

Role in function: As it contains a non-carbon atom (nitrogen) in the aromatic ring system, Tryptophan is more reactive than Phenylalanine though it is less reactive than Tyrosine. The Tryptophan nitrogens can play a role in binding to non-protein atoms, but such instances are rare.

Like other aromatic amino acids, Tryptophan can be involved in interactions with non-protein ligands that themselves contain aromatic groups via stacking interactions. Tryptophan and other aromatic amino acids can be involved in binding to poly-proline containing peptides, for example, in SH3 or WW domains.


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Please cite: M.J. Betts, R.B. Russell. Amino acid properties and consequences of subsitutions.
In Bioinformatics for Geneticists, M.R. Barnes, I.C. Gray eds, Wiley, 2003.
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