Located at the carboxyl terminal of the human papillomavirus major capsid protein L1, helix-5(h5) is crucial to L1 folding and pentamer formation. Site-directed mutagenesis of the leucine residue on site 469 into lysine, alanine, serine and glycine was performed to explore the effect of the resultant mutations on L1 pentamer formation. The soluble yields of the L1 pentamers of the L469A and L469K mutants were nearly two fold higher than that of the wild type. Molecular dynamics simulation was then performed to reveal the intrinsic mechanisms involved in the improvement of L1 pentamer yield. Accordingly, the secondary structures of h5, beta-G2, beta-B1, beta-C, beta-D, and beta-F were altered. The altered structures improved the hydrophobic interaction between h5 and beta-core "jelly" and the stability of h5. The hydrophobic surface area of residue 469 was reduced by 50% relative to that of the wild type. The C-O group of residue 469 and C-N group of L470 were both exposed to the solvent in the L469A mutant. These modifications may account for the increased solubility and stability and the promotion of pentamer formation induced by the point mutation. Therefore, the changes in the hydrophobic properties of h5 and the core structure determined the pentamer formation and solubility. This study may assist the development of a cost-effective platform for the production of prophylactic virus-like particle vaccines.