Noxiustoxin (NxTX) displays an extraordinary ability to discriminate between large conductance, calcium-activated potassium (maxi-K) channels and voltage-gated potassium (Kv1.3) channels. To identify features that contribute to this specificity, we constructed several NxTX mutants and examined their effects on whole cell current through Kv1.3 channels and on current through single maxi-K channels. Recombinant NxTX and the site-specific mutants (P10S, S14W, A25R, A25Delta) all inhibited Kv1.3 channels with Kd values of 6, 30, 0.6, 112, and 166 nM, respectively. In contrast, these same NxTX mutants had no effect on maxi-K channel activity with estimated Kd values exceeding 1 mM. To examine the role of the alpha-carbon backbone in binding specificity, we constructed four NxTX chimeras, which altered the backbone length and the alpha/beta turn. For each of these chimeras, six amino acids comprising the alpha/beta turn in iberiotoxin (IbTX) replaced the corresponding seven amino acids in NxTX (NxTX-YGSSAGA21-27-FGVDRG21-26). The chimeras differed in length of N- and C-terminal residues and in critical contact residues. In contrast to NxTX and its site-directed mutants, all of these chimeras inhibited single maxi-K channels. Under low ionic strength conditions, Kd values ranged from 0.4 to 6 microM, association rate constant values from 3 x 10(7) to 3 x 10(8) M(-1) x s(-1), and time constants for block from 5 to 20 ms. The rapid blocked times suggest that key microscopic interactions at the toxin-maxi-K channel interface may be absent. Under physiologic external ionic strength conditions, these chimera inhibited Kv1.3 channels with Kd values from 30 to 10 000 nM. These results suggest that the extraordinary specificity of NxTX for Kv1.3 over maxi-K channels is controlled, in part, by the toxin alpha-carbon backbone. These differences in the alpha-carbon backbone are likely to reflect fundamental structural differences in the external vestibules of these two channels.