Fig. 4: HLA-DQA1 amino-acid associations and stability prediction.
A Increased risk and predicted stability change of the two-amino-acid residue haplotypes at HLA-DQA1 positions 47 and 52. Odds ratios and P values (two-sided) are from a joint logistic regression with arginine47-serine52, the most common, set as reference, adjusting for population-specific principal components and continental populations. The reference haplotype confers the strongest protection (i.e., odds ratios indicate increase in risk compared to arginine47-serine52). Decreasing values of the predicted stability change indicate decreasing stability. B Protein structure for the reference haplotype arginine47-serine52 (left, blue) and lysine47-histidine52 (right, red). The residues in green display a potential interacting amino acid with mutated amino acids. The color scheme for interactions (dashed lines) is as follows: cyan for Van der Waals [VDW], red for hydrogen bonds, green for hydrophobic bonds, sky blue for carbonyl bonds, and orange for polar bonds. Amino acids displayed with no visible bonds indicate a prediction of weak VDW bonds.
