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Protein Distance and Contact Maps 5

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jeff101's version from 2016-04-06 01:19

Protein Distance and Contact Maps 5

Below shows for many proteins the corresponding Cα-Cα Distance and Contact Maps (made at http://nanohub.org/resources/contactmaps using each protein's *.pdb file copied from http://www.rcsb.org). 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 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 Distance and Contact Maps 5, Protein Distance Maps 5, Protein Contact Maps 5, Protein Distance and Contact Maps, Protein Distance and Contact Maps 2, Protein Distance and Contact Maps 3, Protein Distance and Contact Maps 4, Protein Distance and Contact Maps 6, or Protein Distance and Contact Maps 7.

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

Cα-Cα
Distance Map
and
SCOPe
Family Code
Cα-Cα
Contact Map
and
PDB ID

e.1.1.1
g.64.1.1

1OC0

e.3.1.1

2P74

e.5.1.1

1GWE

e.17.1.0

2EIY

e.22.1.2

1O2D

e.23.1.1

2D1S
memorize

 

Cα-Cα
Distance Map
and
SCOPe
Family Code
Cα-Cα
Contact Map
and
PDB ID

e.38.1.1

1GQE

e.41.1.1

1K8T

e.54.1.1

1SR8

e.62.1.1

4CDP

e.78.1.1

3M4I

?

1PD1
memorize

SCOPe Class f - Membrane and cell surface proteins and peptides

Cα-Cα
Distance Map
and
SCOPe
Family Code
Cα-Cα
Contact Map
and
PDB ID

f.1.4.1

3SP7

f.13.1.1

1M0K

c.37.1.12
c.92.2.2
f.22.1.1

2QI9

c.37.1.12
f.22.1.1

4R9U

f.36.1.1

1OED
memorize

 

Cα-Cα
Distance Map
and
SCOPe
Family Code
Cα-Cα
Contact Map
and
PDB ID

f.43.1.1

2BHW

f.46.1.0

2F1M

f.46.1.0

3LNN

f.46.1.1

1VF7

f.56.1.0

4AL0
memorize

SCOPe Class g - Small proteins

Cα-Cα
Distance Map
and
SCOPe
Family Code
Cα-Cα
Contact Map
and
PDB ID

g.3.7.1

1BCG

g.13.1.1

1CCM

g.13.1.1

3NIR

g.20.1.1

1RO3

g.20.1.1

2ECH
memorize

 

Cα-Cα
Distance Map
and
SCOPe
Family Code
Cα-Cα
Contact Map
and
PDB ID

g.26.1.1

1AFP

c.56.5.1
g.30.1.1

1DTD

b.34.4.3
g.36.1.1

1DJ7

b.34.4.3
c.47.1.1
g.36.1.1

2PU9

g.46.1.1

1RJU
memorize

 

Cα-Cα
Distance Map
and
SCOPe
Family Code
Cα-Cα
Contact Map
and
PDB ID

e.1.1.1
g.64.1.1

1OC0

g.80.1.1

1WFE

g.85.1.1

2JW6

g.88.2.1

2P8Q
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!

 

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

 

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

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