ConSurfDB vs. ConSurf: Difference between revisions
From Proteopedia
Jump to navigationJump to search
Eric Martz (talk | contribs) |
Eric Martz (talk | contribs) No edit summary |
||
| (6 intermediate revisions by the same user not shown) | |||
| Line 4: | Line 4: | ||
{{Template:ColorKey_ConSurf_NoYellow_NoGray}} | {{Template:ColorKey_ConSurf_NoYellow_NoGray}} | ||
Conservation of amino acids non-covalently interacting with a peptide in the groove of [https://www.youtube.com/watch?v=2ZakngfbHSo Major Histocompatibility Protein] Class I ([[2vaa]]). Conservation was '''not revealed''' until an [[#Average Pairwise Distance]] of 0.31 was achieved in a customized ConSurf Server job. [[#Examples|DETAILS BELOW]]. | Conservation of amino acids non-covalently interacting with a peptide ({{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_N}} {{Template:ColorKey_Element_O}}) in the groove of [https://www.youtube.com/watch?v=2ZakngfbHSo Major Histocompatibility Protein] Class I ([[2vaa]]). Conservation was '''not revealed''' until an [[#Average Pairwise Distance]] of 0.31 was achieved in a customized ConSurf Server job. [[#Examples|DETAILS BELOW]]. | ||
</td></tr></table> | </td></tr></table> | ||
Evolutionary Conservation is introduced at [[Introduction to Evolutionary Conservation]], and treated in somewhat greater depth in the article [[Conservation, Evolutionary]]. These describe how conservation patterns in 3D can help to identify functional sites in proteins. Proteopedia displays conservation patterns pre-calculated by [http://consurfdb.tau.ac.il ConSurfDB], when available. These are usually based on broad protein families that include sequences of proteins with multiple functions. Consequently, they usually '''obscure conservation''' present in a family of proteins with a single function (see [[Conservation%2C_Evolutionary#Caveats|Caveats]]). | Evolutionary Conservation is introduced at [[Introduction to Evolutionary Conservation]], and treated in somewhat greater depth in the article [[Conservation, Evolutionary]]. These describe how conservation patterns in 3D can help to identify functional sites in proteins. Proteopedia displays conservation patterns pre-calculated by [http://consurfdb.tau.ac.il ConSurfDB], when available. These are usually based on broad protein families that include sequences of proteins with multiple functions. Consequently, they usually '''obscure conservation''' present in a family of proteins with a single function (see [[Conservation%2C_Evolutionary#Caveats|Caveats]]). | ||
| Line 171: | Line 171: | ||
[[FirstGlance in Jmol]] displays <scene name='39/399854/4dnw_consurf_apd-point48/2'>all salt bridges</scene> with one click (Tools tab), colored by conservation (if pre-processed by the ConSurf Server), and can list them, '''spreadsheet-ready, including conservation level numbers, and marking those between chains'''. | [[FirstGlance in Jmol]] displays <scene name='39/399854/4dnw_consurf_apd-point48/2'>all salt bridges</scene> with one click (Tools tab), colored by conservation (if pre-processed by the ConSurf Server), and can list them, '''spreadsheet-ready, including conservation level numbers, and marking those between chains'''. | ||
With the default ConSurf Server result | With the default ConSurf Server result '''APD 1.42''', and with a custom ConSurf Server result '''APD 0.91''', the salt-bridged residues have about '''average''' conservation. With a custom result '''APD 0.48''', the between-chain salt bridges have '''above-average''' conservation (7.6 vs. 6.8), while the within-chain salt bridges have below average conservation (6.3 vs. 6.8). In conclusion, when the multiple sequence alignment is limited to sequences closely related to the query (APD 0.48), '''between-chain salt bridged residues are more conserved than are within-chain salt bridged residues.''' The difference is '''statistically significant''' (p < 0.01<ref name="stats">With APD 0.48, mean conservation of between-chain salt bridged atoms is 7.57 ± 0.13 SEM. Subtracting 3 SEM (99% confidence limit) gives 7.18. This does not overlap with either 7.16 (the all-salt-bridged atoms mean + 3 SEM) or 6.82 (the mean for within-chain salt-bridged atoms + 3 SEM).</ref>). | ||
<table class="wikitable" style="text-align:center;"> | <table class="wikitable" style="text-align:center;"> | ||
| Line 187: | Line 187: | ||
<td colspan=3> | <td colspan=3> | ||
<center> | <center> | ||
Mean Conservation Levels ± SEM | |||
</center> | </center> | ||
</td> | </td> | ||
| Line 228: | Line 228: | ||
18% | 18% | ||
</td><td> | </td><td> | ||
6.8 ± 0.12 | 6.8 ± 0.12* | ||
</td><td> | </td><td> | ||
7.6 ± 0.13 | 7.6 ± 0.13* | ||
</td><td> | </td><td> | ||
6.3 ± 0.17 | 6.3 ± 0.17* | ||
</td> | </td> | ||
</tr> | </tr> | ||
</table> | </table> | ||
*Averages are per atom for | * *Averages are per atom for 88 between-chains salt-bridged atoms, and 140 within chain salt-bridged atoms. SEM's were calculated as standard deviation divided by the square root of the atom counts. Differences for APD 0.48 are statistically significant, p < 0.01<ref name="stats" />. | ||
*Salt bridges are Lys or Arg sidechain nitrogens within 4.0 Å of Asp or Glu sidechain oxygens. | *Salt bridges are Lys or Arg sidechain nitrogens within 4.0 Å of Asp or Glu sidechain oxygens. | ||
Examples of conserved patches on other proteins, revealed by ConSurf, will be found in the articles on | Examples of conserved patches on other proteins, revealed by ConSurf, will be found in the articles on | ||
| Line 305: | Line 303: | ||
# Displays the protein, colored by conservation, in interactive 3D, using the NGL Viewer, [[FirstGlance in Jmol]], [[Chimera]], or [[PyMOL]]. | # Displays the protein, colored by conservation, in interactive 3D, using the NGL Viewer, [[FirstGlance in Jmol]], [[Chimera]], or [[PyMOL]]. | ||
==References== | ==See Also== | ||
*[[ConSurf/Index]] provides links to all pages about evolutionary conservation and ConSurf in Proteopedia. | |||
==Notes & References== | |||
{{Reflist}} | {{Reflist}} | ||
