Figure 3

Comparison of the protein and mRNA secondary structures. Residue contact maps (RCM) were obtained from the PBD files of four protein structures (1CBI, 1EIO, 1IFC, 1OPA) using the SeqX tool (left column). Energy dot plots (EDP) for the coding sequences were obtained using the mfold tool (right column). The left diagonal portions of these two maps are compared in the central part of the figure. Blue horizontal lines in the background correspond to the main amino acid co-location sites in the RCM. Intact RNA (123) as well as subsequences containing only the 1st and 3rd codon letters (13) are compared. The black dots in the RCMs indicate amino acids that are within 6 Å of each other in the protein structure. The colored (grass-like) areas in the EDPs indicate the energetically most likely RNA interactions (color code in increasing order: yellow, green red, black). The full names and the lengths of the proteins (number of amino acid residues): 1CBI: CELLULAR RETINOIC ACID BINDING PROTEIN I (136), 1EIO: ILEAL LIPID BINDING PROTEIN (127), 1IFC: INTESTINAL FATTY ACID BINDING PROTEIN (132), 1OPA: CELLULAR RETINOL BINDING PROTEIN II (135).