A sequence is scanned in linearly and a moving average of hydropathy values is computed. However, a small window can be noisy and misleading. Currently it's accepted that a window of 7 to 9 detects hydrophobic helices in globular proteins, but a much larger window of 19 to 25 is appropriate for detecting transmembrane helices. Hydrophobic moment analysis Eisenberg et al . 180 o Hydrophobicity is then treated as a vector or a quantity with both magnitude and direction.
Hydrophobic moment is the vector sum of the individual hydrophobicities .
If all side chains are hydrophobic, then vectors cancel, and the hydrophobic moment is low . If one side is hydrophilic, as in an amphipathic helix , its vectors are negative in magnitude, and reinforce the positive hydrophobic vectors on the opposite side. There are still relatively few instances of high resolution structures of membrane proteins. The porins represent one major exception to the rule suggesting that transmembrane proteins are alpha-helical. There appears to be no a priori structural grounds why proteins should not be inherently stable in the polypeptide arrangements originally suggested in the Singer model, which merely require exposure of non-polar side chains on the protein surface in the regions contacting the bilayer core.