Question about secondary protein structure

Secondary protein structure (whether the string of amino acids forms an alpha spiral or beta sheet configuration) is determined by hydrogen bonding between the oxygen atom from the carboxyl group and a hydrogen ion from the amino group. The side chains are not involved. (This is how I understand it, please correct me if I’m wrong).

So, what determines whether an alpha helix or beta sheet is formed? It seems that since the sidechains are not involved in forming the secondary structure, the order of specific amino acids shouldnt have an affect on which structure if formed. That is, the amino acids are all the same aside from their side chains, and if the side chains arent involved, what causes a polypeptide chain to become an alpha helix or beta sheet?

The side chains are involved in secondary and tertiary protein structures. While you are correct that the bonding that defines the alpha helix is based upon the backbone amino acid structures, the side chains of those amino acids are of such a type that they can “fit” into the helix - methionine, alanine, glutamate, lysine and leucine are like this. Sequences that are high in these amino acids will tend towards forming alpha helices. Proline and glycine tend to break helices, because, in the first case, it cannot form an amide hydrogen bond, and in the second, it’s a little too flexible in it’s binding and therefore is hard to force into helix shape.

In beta sheets, while again, it is the backbone structure of the amino acids that actually define them, it is the side chain structures of large, aromatic or branched amino acids that will have a propensity to force a beta sheet structure. Tyrosine, Phenylalanine, Tryptophan, Valine, Isoleucine and Threonine rich amino acid sequences will prefer a beta sheet.

Thanks, that makes it pretty clear.