ConSurfDB vs. ConSurf: Difference between revisions
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===Case #2: UV Resistance Protein=== | ===Case #2: UV Resistance Protein=== | ||
<scene name='39/399854/4dnw_consurf_apd-point48/1'>''Arabidopsis'' UVB-Resistance Protein UVR8</scene> [[4dnw]] is a homodimer with an unusual number of between-chain salt bridges. '''Are the between-chain salt bridges more conserved than the within-chain salt bridges?''' | <scene name='39/399854/4dnw_consurf_apd-point48/1'>''Arabidopsis'' UVB-Resistance Protein UVR8</scene> [[4dnw]] is a homodimer with an <scene name='39/399854/4dnw_consurf_apd-point48/2'>unusual number of between-chain salt bridges</scene>. '''Are the between-chain salt bridges more conserved than the within-chain salt bridges?''' | ||
[[FirstGlance in Jmol]] displays all salt bridges 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 (APD 1.42), salt bridged residues are less conserved than average. With a custom ConSurf Server result APD 0.91, the salt-bridged residues rise to average conservation. With a custom result APD 0.48, the between-chain salt bridges have above-average conservation (7.6 vs. 6.2), while the within-chain salt bridges have average conservation (6.3). 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.''' | With the default ConSurf Server result (APD 1.42), salt bridged residues are less conserved than average. With a custom ConSurf Server result APD 0.91, the salt-bridged residues rise to average conservation. With a custom result APD 0.48, the between-chain salt bridges have above-average conservation (7.6 vs. 6.2), while the within-chain salt bridges have average conservation (6.3). 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.''' | ||
