Additional File 4.

Graphical representation of the amino acid variation between H2A.Z-1 and H2A.Z-2 variants. A Protein logos representation of the overall amino acid variation at each position of the alignment of H2A.Z-1 and H2A.Z-2 variants from vertebrates. The size of the bars is proportional to the frequency for a given amino acid and the overall height is proportional to the conservation of the sites. Colors were assigned to amino acids according to their physical and chemical structural characteristics (red, acidic; blue, basic; green, polar uncharged; purple, nonpolar hydrophobic). B Tertiary structures modeled for H2A.Z-1, H2A.Z-2 and H2A.Z-e from early chordates are shown below the protein logos representation, indicating the quality of the modeling process based on amino acid energies (gromos) and the compatibility of the 3D atomic models with the corresponding protein sequences (verify3d) at each amino acid position. Residues encompassing variation in the energy environment of the atomic model, including polymorphic positions between H2A.Z-1/H2A.Z-2 and H2A.Z-e from early chordates (indicated below in red) are highlighted in the 3D figures as well as in the nearby graphs.

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Eirín-López et al. BMC Evolutionary Biology 2009 9:31   doi:10.1186/1471-2148-9-31