FANDOM


Below shows 3D Images of many proteins (copied from http://www.rcsb.org) along-side their corresponding Distance and Contact Maps (made at http://nanohub.org/resources/contactmaps using each protein's *.pdb file). Most proteins were chosen to represent different classes within the SCOPe database (http://scop.berkeley.edu). SCOPe classes a to j are natural proteins and peptides. Ones in class k are designed proteins.

Each 3D Image below uses a color scheme in which low-numbered residues are blue while high-numbered residues are red. Some images come from NMR ensembles and so show multiple strands of the same protein with the same coloring but slightly different conformations.

Each Distance Map below shows the Cα-Cα distance between every pair of amino acids in the protein as a two-dimensional matrix of shaded pixels. Dark pixels represent close pairs of residues. Light pixels represent distant pairs of residues. Low-numbered residues are in the lower left. High-numbered residues are in the upper right. Images labeled "Distance Map 1" show the 1st conformation from an NMR ensemble in which the same protein exists in multiple slightly-different conformations.

Each Contact Map below shows the Cα-Cα distance between every pair of amino acids in the protein as a two-dimensional matrix of shaded pixels. Black pixels represent pairs of residues less than 8 Angstroms apart. White pixels represent pairs of residues at least 8 Angstroms apart. Low-numbered residues are in the lower left. High-numbered residues are in the upper right. Images labeled "Contact Map 1" show the 1st conformation from an NMR ensemble in which the same protein exists in multiple slightly-different conformations.

If all the images below were scrambled, could you use your pattern-recognition skills to pick which ones went together? See http://memorize.com/distance-and-contact-maps to find out!

SCOPe Class a - All alpha proteinsEdit

Back to Top

SCOPe Class b - All beta proteinsEdit

Back to Top

SCOPe Class c - Alpha and beta proteins (a/b)Edit

Back to Top

SCOPe Class d - Alpha and beta proteins (a+b)Edit

Back to Top

SCOPe Class e - Multi-domain proteins (alpha and beta)Edit

Back to Top

SCOPe Class f - Membrane and cell surface proteins and peptidesEdit

Back to Top

SCOPe Class g - Small proteinsEdit

Back to Top

SCOPe Class h - Coiled coil proteinsEdit

Back to Top

SCOPe Class i - Low resolution protein structuresEdit

Back to Top

SCOPe Class j - PeptidesEdit

Back to Top

SCOPe Class k - Designed proteinsEdit

Back to Top

If all the images above were scrambled, could you use your pattern-recognition skills to pick which ones went together? See http://memorize.com/distance-and-contact-maps to find out!

ReferencesEdit

(1) To make Distance or Contact Maps like above, see:
Benjamin Rafferty; Zachary Carl Flohr; Ashlie Martini (2014), "Protein Contact Maps",
http://nanohub.org/resources/contactmaps (http://dx.doi.org/10.4231/D35M62761).

(2) For more details about any protein above, use its PDB ID (for example, 2QQ4) in the following:
http://www.rcsb.org/pdb/explore/explore.do?structureId=2QQ4
http://scop.berkeley.edu/search/?ver=2.05&key=2QQ4

(3) For more details about any SCOPe family above, use its code (for example, d.224.1.0) in the following:
http://scop.berkeley.edu/search/?ver=2.05&key=d.224.1.0

Ad blocker interference detected!


Wikia is a free-to-use site that makes money from advertising. We have a modified experience for viewers using ad blockers

Wikia is not accessible if you’ve made further modifications. Remove the custom ad blocker rule(s) and the page will load as expected.