A Ala Alanine

1. A Ala Alanine Alanine is a small, hydrophobic residue. Its side chain, R, is just a methyl group. Alanine likes to sit in an alpha helix, it doesn’t like beta strands very much, but it hates beta-turns. If you want to mutate a residue, but you don’t have a good plan about what to replace it with, take alanine because it is a subset of all other amino acids (Gly is special).

2. C Cys Cysteine Cysteine is a small hydrophobic residue. It doesn’t like the alpha helix, but doesn’t mind strands. It can form bridges with other cysteines (Cys-Cys bridges). It can bind metals (especially Zn and Cu). The S-H group is very reactive and can easily be oxidised.

3. D Asp Aspartic acid Aspartic acid, or aspartate, is an intermediately large, hydrophilic, negatively charged residue. Its side chain normally titrates at pH 4.5. It likes to sit near the N-terminus of a helix, and in turns. It hates strands. It often occurs in active sites. It can bind ions (mainly Ca).

4. E Glu Glutamic acid Glutamic acid, or glutamate, is a large, hydrophilic, negatively charged residue. Its side chain titrates at pH 4.6. It loves the helix, doesn’t mind being in a strand, but is not so good for turns.

5. F Phe Phenylalanine Phenylalanine is a large, hydrophobic, aromatic residue. It is good for a strand, it doesn’t mind sitting in a helix, but it hates the turn.

6. G Gly Glycine Glycine is the smallest residue. It doesn’t have a side chain, so its hydrophobicity is a bit undetermined. The fact that it doesn’t have a side chain means that its backbone is very flexible so that it can make backbone turns that other residues cannot make. It is very bad for helix, bad for strand, but it is the star of the turns.

7. H His Histidine Histidine is very special. It is a large hydrophilic residue. Both its side chain nitrogens can titrate (the first one at pH 6.2). It is a little bit aromatic. It is not particularly picky about its secondary structure. It is often seen in active sites. It is neutral at physiological pH, but it can easily become positive, and occasionally even negative. It can bind metal ions (mainly Zn, Ni, Cu).

8. I Ile Isoleucine Isoleucine is an intermediately large, hydrophobic residue. It is beta branched which means that it likes to sit in a strand. It doesn’t mind sitting in a helix either, but it cries its eyes out in a turn.

9. K Lys Lysine Lysine is a large, hydrophilic, positively charged residue. It is not a good strand residue, but it doesn’t mind sitting in a helix or in a turn. Its side chain is very long and flexible.

10. L Leu Leucine Leucine is an intermediately large, hydrophobic residue. It really loves to sit in a helix. It is also good for a strand, but it hates turns.

11. M Met Methionine Methionine is a large, sulphur containing, hydrophobic residue. It loves helices, doesn’t mind sitting in a strand, but it hates turns. Methionine can bind metals with its sulphur, but this sulphur is not reactive. It is often the first residue of a molecule. The N-terminus is mostly positive and thus mostly at the surface. Therefore, the hydrophobic methionine is often at the surface. We call this a forced marriage.

12. N Asn Asparagine Asparagine is an intermediately large, polar residue. It hates the helix, is mildly un-amused in a strand, but it loves the turn. It can bind metal ions (Ca), but doesn’t do that as well as its isosteric partner aspartic acid.

13. P Pro Proline Proline is small and hydrophobic. In proline, the side chain is connected to the backbone at two places: the C and the N. Proline does not have a backbone proton*, and thus is not good for helices and strands. Due to the extra covalent bond, proline is already ‘pre-bend’, and thus good for turns. And turns tend to be at the surface. So, even though it is very hydrophobic, Pro often sits at the surface. We call this a forced marriage. *Except when at the N-terminus of the chain, of course.

14. Q Gln Glutamine Glutamine is a large, polar residue. It is not very picky about its secondary structure but has a mild preference for the helix. It is isosteric with glutamic acid.

15. R Arg Arginine Arginine is a big, hydrophilic, positively charged residue. It is not picky about its secondary structure. Its side chain contains a so-called guadinium group that is rigid.

16. S Ser Serine Serine is a small, alcoholic residue of intermediate hydrophobicity. It is not too happy in helices and strands, but it loves to sit in turns. It often forms the active site of an enzyme together with histidine and aspartic acid. It is occasionally involved in metal (Ca) binding.

17. T Thr Threonine Threonine is a small, alcoholic residue of intermediate hydrophobicity. It is beta- branched and thus good for beta strands. It doesn’t care about helices or turns. It is occasionally involved in metal (Ca) binding.

18. V Val Valine Valine is a small hydrophobic residue. It is beta-branched and thus good for beta strands. Valine doesn’t care about helices, but it hates turns. It is isosteric with threonine.

19. W Trp Tryptophan Tryptophan is the biggest residue. It is aromatic. Despite that the nitrogen in the five-ring is donor for hydrogen bonds, it is very hydrophobic. It doesn’t care about helices or turns, but it loves strands. Size matters. Its size determines that Trp is the most conserved of all residues.

20. Y Tyr Tyrosine Tyrosine is a large, aromatic, alcoholic residue of intermediate hydrophobicity. It is not so happy in a helix, indifferent about turns, and it loves a strand.