The 'backbone' or 'ribbons' options from the 'Display' menu best illustrate the arrangement. If you are able to use MAGE, have a look at the Protein Science kinemages of bacteriorhodopsin modelling and refolding . In the case of a single helix, mainly hydrophobic residues would be expected, so that an apolar surface is exposed to the bilayer. If several helices are bundled, then only the side chains on the outside of the bundle need be hydrophobic. If the central channel between the helices is lined with polar residues, the resulting structure might act as a pore in the membrane through which ions may pass.
Membrane proteins are difficult to crystallize.
Because they have significant hydrophilic and hydrophobic surfaces, they are not soluble in aqueous buffer solutions yet they denature in organic solvents. Methods such as Infra-red Spectroscopy, Raman Spectroscopy and Circular Dichroism are used to deduce secondary structure. However, other approaches may identify transmembrane regions. Naturally, one would expect a relatively long, uninterrupted sequence of hydrophobic residues to represent a membrane-spanning structure. A quantitative measure of the hydrophobicity of a sequence is required.