Fast neurotransmission requires that docked synaptic vesicles be located near the presynaptic N-type or P/Q-type calcium channels, Specific protein-protein interactions between a synaptic protein interaction (synprint) site on N-type and P/Q-type channels and the presynaptic SNARE proteins syntaxin, SNAP-25, and synaptotagmin are required for efficient, synchronous neurotransmitter release, Interaction of the synprint site of N-type calcium channels with syntaxin and SNAP-25 has a biphasic calcium dependence with maximal binding at 10-20 mu M. We report here that the synprint sites of the BI and rbA isoforms of the alpha(1A) subunit of P/Q-type Ca2+ channels have different patterns of interactions with synaptic proteins, The BI isoform of alpha(1A) specifically interacts with syntaxin, SNAP-25, and synaptotagmin independent of Ca2+ concentration and binds with high affinity to the C2B domain of synaptotagmin but not the C2A domain. The rbA isoform of alpha(1A) interacts specifically with synaptotagmin and SNAP-25 but not with syntaxin, Binding of synaptotagmin to the rbA isoform of alpha(1A) is Ca2+-dependent, with maximum affinity at 10-20 mu M Ca2+. Although the rbA isoform of alpha(1A) binds well to both the C2A and C2B domains of synaptotagmin, only the interaction with the C2A domain is Ca2+-dependent. These differential, Ca2+- dependent interactions of Ca2+ channel synprint sites with SNARE proteins may modulate the efficiency of transmitter release triggered by Ca2+ influx through these channels.