Background　The　maintenance　of　protein　structural　stability　requires　the　cooperativity　among　spatially　neighboring　residues.　Previous　studies　have　shown　that　conserved　residues　tend　to　occur　clustered　together　within　enzyme　active　sites　and　protein-protein/DNA　interfaces.　It　is　possible　that　conserved　residues　form　one　or　more　local　clusters　in　protein　tertiary　structures　as　it　can　facilitate　the　formation　of　functional　motifs.　In　this　work,　we　systematically　investigate　the　spatial　distributions　of　conserved　residues　as　well　as　hot　spot　ones　within　protein-RNA　interfaces.　Results　The　analysis　of　191　polypeptide　chains　from　160　complexes　shows　the　polypeptides　interacting　with　tRNAs　evolve　relatively　rapidly.　A　statistical　analysis　of　residues　in　different　regions　shows　that　the　interface　residues　are　often　more　conserved,　while　the　most　conserved　ones　are　those　occurring　at　protein　interiors　which　maintain　the　stability　of　folded　polypeptide　chains.　Additionally,　we　found　that　77.8%　of　the　interfaces　have　the　conserved　residues　clustered　within　the　entire　interface　regions.　Appling　the　clustering　characteristics　to　the　identification　of　the　real　interface,　there　are　31.1%　of　cases　where　the　real　interfaces　are　ranked　in　top　10%　of　1000　randomly　generated　surface　patches.　In　the　conserved　clusters,　the　preferred　residues　are　the　hydrophobic　(Leu,　Ile,　Met),　aromatic　(Tyr,　Phe,　Trp)　and　interestingly　only　one　positively　charged　Arg　residues.　For　the　hot　spot　residues,　51.5%　of　them　are　situated　in　the　conserved　residue　clusters,　and　they　are　largely　consistent　with　the　preferred　residue　types　in　the　conserved　clusters.　Conclusions　The　protein-RNA　interface　residues　are　often　more　conserved　than　non-interface　surface　ones.　The　conserved　interface　residues　occur　more　spatially　clustered　relative　to　the　entire　interface　residues.　The　high　consistence　of　hot　spot　residue　types　and　the　preferred　residue　types　in　the　conserved　clusters　has　important　implications　for　the　experimental　alanine　scanning　mutagenesis　study.　This　work　deepens　the　understanding　of　the　residual　organization　at　protein-RNA　interface　and　is　of　potential　applications　in　the　identification　of　binding　site　and　hot　spot　residues.