Are secondary structures secondary?

Crystallographically observed secondary structures in globular proteins are divided into two categories based on calculated potential values for these structures. Type I secondary structures are those which have maximum potential in observed structural state. These type I structures consist of those amino acids which intrinsically prefer that structural state. On the other hand type II secondary structures have a calculated potential value which is not maximum for the observed state. Type II structures are composed of those amino acid residues which do not intrinsically prefer the observed state and thus seem to have been formed due to tertiary interactions. All the observed secondary structures have been identified as type I or type II in 31 different globular proteins considered. It is suggested that type II structures are formed at a latter stage of protein folding mainly due to favourable tertiary interactions.