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Figure 3 | BMC Bioinformatics

Figure 3

From: RNAmap2D – calculation, visualization and analysis of contact and distance maps for RNA and protein-RNA complex structures

Figure 3

Coloring capabilities of RNAmap2D. A) The coloring panel of RNAmap2D, with a selection of several types of pairing, stacking, and other interactions. Note that all types of pairings and stacking are identified by the program before the panel is displayed, and options corresponding to interactions undetected in the input file are disabled; B) A contact map of 23S rRNA fragment (PDB ID 1HC8_A, 3D structure as shown in Figure 2), calculated for N1/N9 atoms using the threshold of 9.5 Å and colored according to the code in panel A. The top left square represents the RNA chain, while the bottom right square shows Mg2+ ions and other heteroatoms classified as either ions or ligands. The symmetrically oriented upper right and bottom left sections indicate contacts between nucleotide residues and ions. Purple and violet bars along the sequence ruler indicate RNA secondary structure.

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