FIGURE 3.

Characterization of the continuity between transmembrane and EC2 helices. (A) Principle of the method (58). A transmembrane bundle is depicted in which a transmembrane helix in continuity with a soluble helix is highlighted. The helix is in contact with the protein interior and the external medium in both environments. When the helix emerges from the bilayer, conserved (nonhatched) and variable (hatched) residues, respectively, remain on the interior and exterior side of the helix whereas the more hydrophobic residues (dark gray) and the more hydrophilic (light gray) switch to opposite sides. This yields a continuous conservation periodicity profile and a drop of hydrophobicity periodicity profile. (B) Variation in the index of the helical (3.6 residue-per-turn) periodicity for sequence conservation (solid line) and sequence hydrophobicity (dotted line). (Top) Region connecting TM3 to EC2 helix A. (Bottom) Region connecting EC2 helix E to TM4. The periodicity analysis was done with the Perscan software with alignments of, respectively, 47 and 39 sequences with >35% homology with CD81 in the corresponding regions. The horizontal dotted line corresponds to the limit of significant periodicity. Identical results were obtained when a pitch of 3.5 residue-per-turn was used.