J. Walshaw
There is a blurred distinction between "supersecondary structure" and "tertiary structure". The introduction of the term "supersecondary structure" was necessary when it became clear that certain arrangements of two or three secondary structures are present in many different protein structures, even with completely different sequences.
Note that some proteins do not consist of an assembly of these super-secondary motifs. For example, proteins of the globin family consist of eight alpha-helices in contact, but the helices do not pack against other helices which are adjacent in the sequence, with the exception of the final two, which form an antiparallel helix-turn-helix motif.
Although the term "motif" is often used to describe supersecondary structures (e.g. Branden and Tooze, 1991), it may also be used to describe a consensus sequence of amino acids identified in a number of different proteins, rather than a repeated three-dimensional conformation. Such a consensus in primary structure generally implies a similarity in tertiary structure, however (for example, the Epidermal Growth Factor-like motif described in the previous chapter). But bear in mind that there are very many protein sequences of which the three dimensional structures are not known for certain, so that the term "motif" strictly applies to primary rather than supersecondary or tertiary structure in these cases.
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J. Walshaw