Driving Forces for Transmembrane α-Helix Oligomerization Alex J. Sodt, Teresa Head-Gordon  Biophysical Journal  Volume 99, Issue 1, Pages 227-237 (July 2010) DOI: 10.1016/j.bpj.2010.03.071 Copyright © 2010 Biophysical Society Terms and Conditions

Figure 1 The residue-residue contact free energy for each amino acid. Side-chain volumes are taken from Harpaz et al. (39). Residues are colored/shaded according to the reduced-alphabet grouping (Table 1). Biophysical Journal 2010 99, 227-237DOI: (10.1016/j.bpj.2010.03.071) Copyright © 2010 Biophysical Society Terms and Conditions

Figure 2 A helix wheel depicting the facial positions assuming 3.6 residues/turn. Biophysical Journal 2010 99, 227-237DOI: (10.1016/j.bpj.2010.03.071) Copyright © 2010 Biophysical Society Terms and Conditions

Figure 3 The found/expected odds ratio of finding small (S), medium-small (MS), medium-large (ML), and large (L) residues on TM sequences with Gly, Val, and Ile included (a) and excluded (b). See Table 3 for residue classification. Biophysical Journal 2010 99, 227-237DOI: (10.1016/j.bpj.2010.03.071) Copyright © 2010 Biophysical Society Terms and Conditions

Figure 4 The found/expected odds ratio of finding polar and apolar residues on TM sequences with Gly, Val, and Ile included (a) and excluded (b). See Table 1 for residue classification. Biophysical Journal 2010 99, 227-237DOI: (10.1016/j.bpj.2010.03.071) Copyright © 2010 Biophysical Society Terms and Conditions

Figure 5 RMSD versus energy for the TM section of three proteins. The model performs poorly for the upper system (2wit), moderately well for the middle system (3b44), and well for the lower (2yvx). The black points are members of the ensemble from which the potential is derived, whereas the gray points are structures closer to the native state. Biophysical Journal 2010 99, 227-237DOI: (10.1016/j.bpj.2010.03.071) Copyright © 2010 Biophysical Society Terms and Conditions