Fig. 3
Ribosomal protein networks at different distance thresholds (dt) between amino acid residues in contact. Highlights of the polypeptide exit tunnel yielded region are outlined in black as a measure of structural and biological accurateness of the obtained networks. The networks were built using the \({\text{COSNet}}_i\) workflow (https://github.com/MSeidelFed/COSNet_i) with default values from PDBx/mmCIF entries 6SNT, 6GZ5, and 4V7E corresponding to Saccharomyces cerevisiae (bottom panel), Oryctolagus cuniculus (middle panel) and Triticum aestivum (upper panel) ribosome structures. The networks were analyzed as undirected graphs in Cytoscape [34], a larger node size indicates larger degree, the thickness of edges is defined as a transit probability between nodes calculated based on the number of contacts between each protein pair and the network layout is edge-weighted spring-embedded to simulate a real structurally connected network with forces acting upon it. The 60S subunit nodes have been highlighted in light blue/black, and the 40S subunit nodes in light yellow, nodes that belong to the PET region of the 60S LSU (i.e., region containing eL39 rProtein family) have been highlighted in black. Note that as \(\hbox {d}_t\) gets larger outlier proteins get into the defined regions while when \(\hbox {d}_t\) is lower rProteins are not fully interconnected and many nodes are missing. Species icons were exported from BioRender (https://biorender.com/) under a paid license. The network interactions and weights have been compiled in Additional file 2