Linear repetitions of amino acids and convergent evolution inside protein subregions of ordered secondary structures

51 polypeptides of known 3-dimensional structures have been submitted to a search for internal similarities. It is shown that the frequency of proteins displaying significant amounts of internal similarities is higher than predicted by chance. A non-negligible part of those similarities probably occurs in connection with the existence of ordered secondary structures. Indeed, similarity occurs at a much more important rate when analyses are restricted to protein subsequences corresponding to alpha helices or beta pleated sheets. Furthermore, the correlation existing between the rates at which linear and inverted repeats occur inside protein subregions of ordered secondary structures suggests that a significant part of short similarities are analogies rather than homologies. An hypothesis is put forward suggesting that the regular alternations of hydrophobicity which characterize most of alpha helices and beta strands could provoke the occurrence of significant amounts of similarities inside protein sequences.