Interactions that occur between polypeptide R groups.
Important to recognize is that these interactions typically are not occurring among R groups that are physically close according to a polypeptide's amino acid sequence but instead are interactions that can possibly occur only once the polypeptide has folding upon itself in the course of protein folding.
Included among those phenomena contributing to protein tertiary structure are such things as hydrophobic interactions (resulting from van der Waals interactions as well as hydrophobic exclusion), salt bridges, hydrogen bonding, and disulfide bridges.
Not included are the interactions leading to alpha helices and beta pleated sheets. These latter structures, however, represent part of structure from which tertiary structure emerges, that is, as R groups that emerge from secondary structures interact. Thus, in addition to protein tertiary structure along with the underlying protein primary structure, there is also an underlying protein secondary structure as well as, in many cases, and overlying protein quaternary structure.
It is a combination of secondary structure and tertiary structure, both as specified by protein primary structure, that determines the shape that a polypeptide both folds into and maintains.
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