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You didn't add any options to choose from but in the primary structure the aminoacid side chains are of particular interest, and their sequence too, obviously. The charge of the side chains(ionic interactions), whether they're hydrophobic or hydrophilic, how many cystines they have and where (stabilisation), etc. because without taking other molecules that assist folding into account, interaction of the side chains with the environment they're in (which is usually water and/or other parts of the protein) plays a huge part.

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