Lysine

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Standard codons for K : AAA AAG

Substitution preferences:
All protein types:
Favoured Arg ( 2) Glu ( 1) Gln ( 1)
Neutral Ser ( 0) Asn ( 0)
Disfavoured Met (-1) Ala (-1) Asp (-1) Pro (-1) Thr (-1) His (-1) Val (-2) Leu (-2)
Tyr (-2) Gly (-2) Cys (-3) Trp (-3) Ile (-3) Phe (-3)

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

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

Membrane proteins:
Favoured Arg ( 9) Gln ( 6) Asn ( 5) His ( 4) Asp ( 3) Trp ( 3) Glu ( 1) Tyr ( 1)
Disfavoured Met (-1) Ser (-1) Gly (-1) Ala (-2) Thr (-2) Cys (-3) Val (-4) Ile (-4)
Leu (-4) Pro (-4) Phe (-5)

Substitutions: Lysine is a positively charged, polar amino acid. It thus most prefers to substitute for the other positively charged amino acid Arginine, though in some circumstances it will also tolerate a change to other polar amino acids.

Role in structure: Lysine frequently plays an important role in structure. First, it can be considered to be somewhat amphipathic as the part of the side chain nearest to the backbone is long, carbon containing and hydrophobic, whereas the end of the side chain is positively charged. For this reason, one can find Lysines where part of the side-chain is buried, and only the charged portion is on the outside of the protein. However, this is by no means always the case, and generally Lysines prefer to be on the outside of proteins.

Lysines are also frequently involved in salt-bridges, where they pair with a negatively charged amino acid (such as Aspartate, shown below) to create stabilising hydrogen bonds, that can be important for protein stability.

Role in function: Lysines are quite frequent in protein active or binding sites. Lysine contains a positively charged amino on its side-chain that is sometimes involved in forming hydrogen bonds with negatively charged non-protein atoms (e.g. anions or carboxylate groups).

Lysines are also very often modified, particularly acetylated, which is one of the most common modifications in proteins known.

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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..