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Distance and Contact Maps 6

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jeff101's version from 2016-04-06 01:11

Distance and Contact Maps 6

Below shows 3D Images of many proteins (copied from http://www.rcsb.org) along-side their corresponding Cα-Cα 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 Cα-Cα Distance Map below shows the distance between alpha-carbons on 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.

 

Each Cα-Cα Contact Map below shows the distance between alpha-carbons on 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.

 

For larger images, see http://foldit.wikia.com/wiki/Distance_Maps or zoom in on this page.

 

For more images, see Protein Distance and Contact Maps 6, Protein Distance Maps 6, Protein Contact Maps 6, Distance and Contact Maps, Distance and Contact Maps 2, Distance and Contact Maps 3, Distance and Contact Maps 4, Distance and Contact Maps 5, or Distance and Contact Maps 7.

SCOPe Class h - Coiled coil proteins

3D Image
and
SCOPe
Family Code
Cα-Cα
Distance Map
and
PDB ID
Cα-Cα
Contact Map


h.1.10.1

1P9I

h.2.1.1

1QEY

h.3.1.1

4M44

h.4.1.1

1VSG

h.4.1.1

2VSG
memorize

 

3D Image
and
SCOPe
Family Code
Cα-Cα
Distance Map
and
PDB ID
Cα-Cα
Contact Map


h.4.4.2

2NRJ

c.23.1.1
h.4.11.1

1KMI

h.5.1.1

1AV1

h.6.1.1

2OU1

h.7.1.1

1XQ8
memorize

SCOPe Class i - Low resolution protein structures

3D Image
and
SCOPe
Family Code
Cα-Cα
Distance Map
and
PDB ID
Cα-Cα
Contact Map


i.2.1.1

2REC

i.3.1.1

1QO1

b.6.1.1
i.4.1.1

2JXM

i.5.1.1

1VCR

i.6.1.1

1M4X
memorize

 

3D Image
and
SCOPe
Family Code
Cα-Cα
Distance Map
and
PDB ID
Cα-Cα
Contact Map


i.15.1.1

1SJJ

i.17.1.1

1K4R

i.18.1.1

1MHS

i.19.1.1

1PDJ

i.19.1.1

1PDL
memorize

 

3D Image
and
SCOPe
Family Code
Cα-Cα
Distance Map
and
PDB ID
Cα-Cα
Contact Map


i.20.1.1

1Q5A

i.21.1.1

1SUV

i.25.1.1

3HQV

?

4A10
memorize

SCOPe Class j - Peptides

3D Image
and
SCOPe
Family Code
Cα-Cα
Distance Map
and
PDB ID
Cα-Cα
Contact Map


j.1.1.1

1TK2

j.9.4.1

1JFW

j.20.1.1

1TER

j.28.1.1

1EDN

j.41.1.1

1SUT

j.51.1.1

1LOI
memorize

 

3D Image
and
SCOPe
Family Code
Cα-Cα
Distance Map
and
PDB ID
Cα-Cα
Contact Map


j.60.1.1

1DPQ

j.69.1.1

1Q2F

j.77.1.1

1EI0

j.90.1.1

1OEI

j.101.1.1

1LVQ

j.101.1.1

1LVR
memorize

 

If you think you've mastered each of the tables above, try "combine tables" in the upper right corner to drill them all at once!

References

(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