Summary
Protein structures determined by X-ray crystallography can have unphysiological salt bridges. (1) found that this was the case with lysines in the model protein GB1 using NMR:
“the six surface-exposed lysines in protein G are not involved in significant salt bridge interactions, even though such interactions are found consistently in crystal structures”
1.
Tomlinson JH, Ullah S, Hansen PE, Williamson MP. Characterization of Salt Bridges to Lysines in the Protein G B1 Domain. Journal of the American Chemical Society. 2009;131(13):4674–84. Available from: https://doi.org/10.1021/ja808223p