Only positions in the sequence alignment where amino acids are present for all chains are used. In both cases, the sequence alignment is displayed using Chimera’s Multalign Viewer tool. For two chains, RRDistMaps uses the Needleman–Wunsch algorithm ( Needleman and Wunsch, 1970) for more than two chains, RRDistMaps uses MUSCLE ( Edgar, 2004) via an online RBVI web service ( Huang et al., 2014). In general, however, distance map comparisons are only appropriate for proteins with the same basic architecture. This limits use of proteins with sequences similar enough to be aligned correctly, and without topological rearrangements. When only short distances are used for color-coding, the distance maps are effectively contact maps.įor multi-protein comparison, RRDistMaps identifies corresponding amino acids in the different chains using sequence alignment. A green rectangle in the legend marks the distances for which the color-coding is applied residue pairs whose RR distances fall outside of the rectangle are displayed in dark gray. Selecting residue pairs by clicking the mouse or sweeping out a rectangle automatically highlights the corresponding residues in the 3D visualization window. Moving the mouse over the distance map displays the residue pair under the cursor in the status line. If a single chain is selected, the RR distances for that chain are computed and displayed as a grayscale distance map along with a color-coding legend to its right. The user can select one or more chains and click the Calculate Map button. RRDistMaps is invoked from the Tools/ Structure Comparison menu in UCSF Chimera and displays a list of the molecular chains displayed in the 3D visualization window and an area for showing a distance map. As an extension to the molecular visualization application UCSF Chimera ( Pettersen et al., 2004), we developed RRDistMaps, a tool to interactively compute and display distance maps for individual proteins and to compare the distance maps of pairs of similar proteins.
Instead of using a single cutoff threshold for contacts, displaying a color-coded distance map can help users visualize longer-range interactions.
However, longer-range interactions may be used to identify larger-scale motions such as hinge movements. 2D contact maps provide a complementary view to 3D molecular visualization as they are unaffected by rotation or translation and can be easily compared and superimposed.Ĭontact maps are typically shown as square plots with markers denoting interactions between residues residue pairs that fall outside of the interaction threshold are completely unmarked. pairs of amino acids with α-carbons <8 Å apart ( Wu et al., 2008). RR contact maps are powerful two-dimensional (2D) representations of protein 3D structure that plot patterns of spatial interactions, e.g. Recent applications such as CMView ( Vehlow et al., 2011) examine the nature of structural differences or changes in proteins through the use of residue–residue (RR) contact maps ( Holm and Sander, 1993).
The rapid improvement of technology in recent decades has enhanced our knowledge of protein structure, as visualization software has revolutionized our understanding of molecular mechanisms.
The interface contains the unique features of identifying long-range residue motion and aligning sequences to simultaneously compare distance maps.Īvailability and implementation: RRDistMaps was developed as part of UCSF Chimera release 1.10, which is freely available at, and operates on Linux, Windows, and Mac OS. Users can target residue pairs in RRDistMaps for further navigation in Chimera. hinge motion), between unbound and bound proteins through distance patterns. An interactive utility, RRDistMaps, visualizes conformational changes, both local (e.g. We have developed a UCSF Chimera tool, RRDistMaps, to compute such generalized maps in order to analyze pairwise variations in intramolecular contacts. Binary (yes/no) contact maps with a single cutoff distance can be generalized to show continuous distance ranges. Motivation: Contact maps are a convenient method for the structural biologists to identify structural features through two-dimensional simplification.