Proteins have segments of their polypeptide chain/chains that can be repeatedly coiled or folded into helix and pleated structures, respectively. This is due to hydrogen bonds between partially charged oxygen and hydrogen atoms in the repetitive polypeptide backbone (which excludes the amino acid side chains).
My guess is that one structure (either a helix or pleated structure) is lower in potential energy compared to the other (because one structure likely maximises the number of hydrogen bonds that can form, compared to the other), which begs the question, why do both structures form, if they are largely a result of hydrogen bonds in the polypeptide backbone, rather than only one structure forming?
Is it a result of both hydrogen bonds in the polypeptide backbone, and interactions between amino acid side chains?
My own attempt at answering the question:
Intuitively, I believe the terms 'secondary' and 'tertiary' structure are misleading. My reasoning is that, it does not make sense to say that hydrogen bonds between the atoms of different amino acids in a polypeptide backbone, bring separate amino acids closer together, before interactions between amino acid side chains (R groups) occur (especially since some of these interactions between R groups are hydrogen bonds themselves).
I assume, the previous statement can be valid stated vice versa, i.e., that interactions between amino acid side chains bring separate amino acids closer together, before hydrogen bonding can occur between the atoms of different amino acids.
Ultimately, if this is the case in reality, I would expect both H bonds and AA side chain bonds to occur, effectively, simultaneously, blurring the distinctions that have been established by humans.