As Mike said, the situation is not quite as easy because there is much more than helices and sheets making up a protein's structure.
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but mutations in loops can stay because there is no structure to mess up.
I wouldn't bet my nuts on this assertion.
my biochemistry teacher said that and he seems pretty competent. i don't have a source, though.
Even unordered appearing structure (random coil) is ordered to some extend by specific sidechain interactions. It wouldn't affect the whole folding thermodynamics unless the mutation is in the hydrophobic core, but it has some effect - of course still depending on the context.
Not quite an assertion, the key word here is 'can.' But it's nice that you (mike) elaborated on how the situation can become complicated.
Can't oxygens and nitrogens hydrogen bond with each other through water molecules, too? Or am I just thinking of inhibitors being bound into the active site and using water to help pick up interactions with backbone carbonyls and nitrogens?
you can have water molecules in between. but it does not seem like you would get a defined rigid secondary structure that way.
A lot of the time, the functional binding site of a protein are in the loops, so these areas of the loops are often conserved. Plus, the structure is harder to mess up by mutation than a binding interface or catalytic cleft.
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