advertisement: compare things at compare-stuff.com!

Secondary structural class

In 1976 Levitt and Chothia observed that the protein structures then available seemed to group naturally into four classes based upon the gross secondary structural content of their tertiary structures. These classes were: mainly-$\alpha$, mainly-$\beta$, alternating $\alpha/\beta$ and $\alpha+\beta$ (separated along chain, not alternating). Whilst being a largely subjective definition, it has served well in the intervening years.

Recently, in conjunction with the construction of a classified database of domains (see Section 1.2), an automated approach to this deceptively difficult problem was developed[Michie et al., 1996]. It was found that the distributions of the two mixed-$\alpha \beta$ classes were continuous and overlapping using any of a number of structure-derived parameters. Furthermore, the database of domains had reduced the number of $\alpha+\beta$ examples through their division into separate mainly-$\alpha$ and mainly-$\beta$ domains. Thus when dealing with domains it is acceptable to use a three class definition: mainly-$\alpha$, mainly-$\beta$ and mixed-$\alpha \beta$. Some proteins contain little or no regular secondary structure, these are often termed `irregular' proteins.