Figure : Complete pK a thermodynamic cycle. The horizontal arrows mark the transfer of a titratable residue between different environments: vacuum (left), water (middle), protein (right). The vertical arrows denote the free energy difference between the deprotonated and protonated form in a corresponding environment. For cysteine, the free energy associated with proton transfer from vacuum to water is known. By using this reference pK • a we need only consider the rightmost cycle: the free energy difference of a deprotonation event in water and in protein.