Figure 2

Comparison of 12 randomly selected protein and corresponding mRNA structures. Residue contact maps (RCM) were obtained from the PBD files of the protein structures using the SeqX tool (left triangles). Energy dot plots (EDP) for the coding sequences were obtained using the mfold tool (right triangles). The two maps were aligned along a common left diagonal axis to facilitate visual comparison between the different possible representations. 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 mostly 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): 1AM5: PEPSIN (324), 1A8D: TETANUS NEUROTOXIN (451), 1MD8: SERIN PROTEASE (329), 1ARB: ACHROMOBACTER PROTEASE I (268), 1HO9: A ALPHA-2A ADRENERGIC RECEPTOR (32), 1BIA: BIRA BIFUNCTIONAL PROTEIN (376), 1CWN: ALDEHYDE REDUCTASE (324), 1BG4: ENDO-1,4-BETA-XYLANASE (302), 1SIG: RNA POLYMERASE PRIMARY SIGMA FACTOR (339) bases, 1K40: ADHESION KINASE (126), 1EZJ: NUCLEOCAPSID PHOSPHOPROTEIN (140), 1ABN: ALDOSE REDUCTASE (315). The coordinates indicate the number of amino acid and the corresponding nucleic acid residues.