Conserved Plasmodium falciparum merozoite high activity binding peptides (HABPs) involved in red blood cell (RBC) invasion which are present in merozoite surface proteins (MSPs) involved in attachment, rolling over RBC, those derived from soluble proteins loosely bound to the membrane, and those present in microneme and rhoptry organelles have an alpha-helical structure and bind with high affinity to HLA-DR52 molecules. On the contrary, conserved HABPs belonging to molecules anchored to the membrane by a GPI tail, or a transmembranal region, or those molecules presenting PEXEL motifs have a strand, turn or unordered configuration and bind with high affinity to HLA-DR53 molecules. Such functional, cellular, structural, and immunological compartmentalisation has tremendous implications in subunit-based, multi-epitope, synthetic, anti-malarial vaccine development.