Membrane proteins commonly fold into bundles of helices, and helix interactions are important for their folding, stability and function. However, the nature and distribution of the amino acids in membrane proteins is very different than in soluble proteins. The difference in the composition of the surface-exposed residues is well known and simply reflects the environment of the protein, i.e. in soluble proteins polar and charged residues are on the water-accessible surface, whereas in membrane proteins hydrophobic residues cover the lipid-exposed surface. Much less is known about the nature and distribution of amino acids in the interiors of membrane and soluble proteins.

Combining structural studies of membrane proteins with bioinformatics approaches, we have shown that both helical membrane and soluble proteins make use of a general motif for helix interactions which relies mainly on four residues (Leu, Ala, Ile, Val) to mediate helix interactions in a fashion characteristic of left-handed helical coiled-coils. However, a second motif for mediating helix interactions is revealed by the high occurrence and high average packing values of small and polar amino acids (Ala, Gly, Ser, Thr) in the helix interfaces of membrane proteins. There is a strong linear correlation between the occurrence of residues in helix-helix interfaces and their packing values. Based on this correlation, we introduced the concept of a helix packing moment to predict the orientation of helices in helical membrane proteins and membrane protein complexes. The helix packing moment is a complementary tool to the helical hydrophobic moment in the analysis of transmembrane sequences. Helix packing moments also help to identify the packing interfaces in membrane proteins with multiple transmembrane helices, where a single helix can have multiple contact surfaces.

Analyses on class A G protein-coupled receptors (GPCRs) with 7 transmembrane helices show that helix packing moments are conserved across the class A family of GPCRs and correspond to key structural contacts in rhodopsin. These contacts are distinct from the highly conserved signature motifs of GPCRs and have not previously been recognized. The specific amino acid types involved in these contacts, however, are not necessarily conserved between subfamilies of GPCRs, indicating that the same protein architecture can be supported by a diverse set of interactions. In GPCRs, as well as membrane channels and transporters, amino acids with small side chains (Gly, Ala, Ser, Cys) allow tight helix packing by mediating strong van der Waals interactions between helices. Closely packed helices, in turn, facilitate interhelical hydrogen bonding of both weakly polar (Ser, Thr, Cys) and strongly polar (Asn, Gln, Glu, Asp, His, Arg, Lys) amino acids.