In this paper, we undertake a sequence analysis of the human keratin-associated proteins (KAP). This analysis has revealed two fundamental pentapeptide quasi-repeats (A and B) of the form C-C-X-P-X and C-C-X-S/T-S/T, respectively. The A repeats are also commonly found in two subforms A(1) and A(2), -C-C-Q-P-X and C-C-R-P-X, respectively-similar to those found in sheep wool 30-40 years previously. Some high-sulphur and ultra-high sulphur proteins contain predominantly A repeats or B repeats but not regular combinations of them, whereas others are characterised by a contiguous pair of pentapeptide repeats that largely (though imperfectly) alternate to generate decapeptide motifs of the form AB, A(1)B or A(2)B. The A and B repeats sometimes occur in complex runs and can generate both 19- and 20-residue repeats of the form BABB' or BA(1)AA, respectively, where the prime indicates a motif truncated by one residue. Likewise, a 42-residue repeat with BA(1)BXAAAB (40 residues) separated by a di-serine (two residues) has been observed in an ultra-high sulphur protein from cuticle. To understand the possible conformations adopted by the A and B motifs, a search was initiated of the PDB structural database for a number of overlapping pentapeptide repeats. The total number of matches was 658 and these were found in 451 different proteins. From representative and unique structures the means and standard deviations were calculated for the Phi(i) and psi(i) angles for the C-C-X P-X and the C-C-X-S/T-S/T motifs. Molecular modelling has been employed to represent the "average" structure found from crystallographic and nmr data determined for each motif in other proteins. The conformation of consecutive A repeats with proline residues in the cis state is akin to a string of disulphide bond-stabilised pentapeptide knots between which there is relative freedom of rotation about the single bonds that link them. For B pentapeptides, however, the likelihood that a similar disulphide bond is formed appears much lower. This may give additional conformational flexibility to the chain and hence allow the A pentapeptides greater opportunity to interact appropriately with the IF via disulphide bonds, ionic interactions and/or hydrogen bonding. (c) 2006 Elsevier Inc. All rights reserved.