Preservation of protein conformation upon transfer into the gas-phase is keyfor structure determination of free single molecules, e.g. using X-ray free-electron lasers. In the gasphase, the helicity of melittin decreases strongly as the protein’s protonation state increases. We demonstrate the sensitivity of soft X-ray spectroscopy to the gas phase conformation of melittin cations ([melittin+qH]q+, q=2-4) in a cryogenic linear radiofrequency ion trap. With increasing helicity we observe a decrease of the dominating carbon 1s-* transition in the amide C=O bonds for non-dissociative single ionization and an increase for non-dissociative double ionization. As the underlying mechanism we identify inelastic electron scattering.Using an independent atom model we show that the more compact nature of the helical protein conformation substantially increases the probability for off-site intramolecular ionization by inelastic Auger electron scattering.