The amino acid composition is different between the cytoplasmic and extracellular sides in membrane proteins.

The amino acid composition of transmembrane proteins was analyzed for their three separate portions: the transmembrane apolar, cytoplasmic and extracellular regions. The composition was different between cytoplasmic and extracellular peptides: alanine and arginine residues were preferentially sited on the cytoplasmic side, while the threonine and cysteine/cystine were preferentially sited on the extracellular side. The composition of cytoplasmic and extracellular peptides of membrane proteins corresponded to those of intracellular and extracellular types of soluble proteins, respectively. This difference in composition was independent of the peptide orientation against the membrane. Peptide chains could be correctly assigned as either cytoplasmic or extracellular, solely from an analysis of sequence composition. For single-spanning membrane proteins the predictive accuracy was 90%, whereas for multi-spanning proteins this was 85%.