Assemblies of chiral cysteine (CYS) and Au nanorods (GNRs) are constructed in two typical patterns, end-to-end and side-by-side. Impressively, side-by-side assembled GNRs with CYS show obviously stronger plasmonic circular dichrosim (CD) response compared with the end-to-end assemblies. The corresponding theoretical calculation elucidates the intrinsic relationship among geometric structure, electromagnetic interaction, and induced plasmonic CD of the assemblies. This work will significantly benefit the design and application of plasmonic nanodevices with controllable chiroptical responses.