Sandbox6 Eric Martz: Difference between revisions
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*<scene name='Sandbox6_Eric_Martz/83-341/2'>Segment 83-140</scene>. | *<scene name='Sandbox6_Eric_Martz/83-341/2'>Segment 83-140</scene>. | ||
*The <scene name='Sandbox6_Eric_Martz/83-341_charge/1'>distribution of charges</scene> seems unremarkable. Bear in mind that sidechain positions are incorrect in a homology model. | *The <scene name='Sandbox6_Eric_Martz/83-341_charge/1'>distribution of charges</scene> seems unremarkable. Bear in mind that sidechain positions are incorrect in a homology model. | ||
{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}} | <center>{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}</center> | ||
*The inner face of 95-140 is <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/1'>partially hydrophobic</scene>. Bear in mind that sidechain positions are incorrect in a homology model. <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/2'>Hide 141-341</scene>. The distribution of hydrophobic residues in 83-140 of the homology model is similar to that in the <scene name='Sandbox6_Eric_Martz/3e4c_147-205_hydrophobic/1'>corresponding residues 147-205 in the template 3e4c</scene>. | *The inner face of 95-140 is <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/1'>partially hydrophobic</scene>. Bear in mind that sidechain positions are incorrect in a homology model. <scene name='Sandbox6_Eric_Martz/83-341_hydrophobic/2'>Hide 141-341</scene>. The distribution of hydrophobic residues in 83-140 of the homology model is similar to that in the <scene name='Sandbox6_Eric_Martz/3e4c_147-205_hydrophobic/1'>corresponding residues 147-205 in the template 3e4c</scene>. | ||
* The inner face of 95-140 is <scene name='Sandbox6_Eric_Martz/83-341_conservation/1'>highly conserved</scene>, even based upon a multiple sequence alignment that includes mostly types other than 12<ref>ConSurf run using 80 sequences from the Uniref-90 sequence database. MSA average pairwise distance (APD) 0.94.</ref> <scene name='Sandbox6_Eric_Martz/83-341_conservation/2'>Hide 141-341</scene>. | * The inner face of 95-140 is <scene name='Sandbox6_Eric_Martz/83-341_conservation/1'>highly conserved</scene>, even based upon a multiple sequence alignment that includes mostly types other than 12<ref>ConSurf run using 80 sequences from the Uniref-90 sequence database. MSA average pairwise distance (APD) 0.94.</ref> <scene name='Sandbox6_Eric_Martz/83-341_conservation/2'>Hide 141-341</scene>. | ||
{{Template:ColorKey_ConSurf_NoGray}} | <center>{{Template:ColorKey_ConSurf_NoGray}}</center> | ||
* When the multiple sequence alignment is limited to the 14 type-12 sequences available from Uniprot (APD 0.30), most of the residues have insufficient data, but a <scene name='Sandbox6_Eric_Martz/83-341_conservation/3'>few on the outside face are highly conserved</scene>, namely Asn130, Val135, Val136, Glu139, Asn140. <scene name='Sandbox6_Eric_Martz/83-341_conservation/4'>Hide 141-341</scene>. | * When the multiple sequence alignment is limited to the 14 type-12 sequences available from Uniprot (APD 0.30), most of the residues have insufficient data, but a <scene name='Sandbox6_Eric_Martz/83-341_conservation/3'>few on the outside face are highly conserved</scene>, namely Asn130, Val135, Val136, Glu139, Asn140. <scene name='Sandbox6_Eric_Martz/83-341_conservation/4'>Hide 141-341</scene>. | ||
Revision as of 22:53, 7 February 2011
Please do not edit this page. Eric Martz, February 2011.
Homology Model for 83-341Homology Model for 83-341
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- Homology model of 83-341 on template chain A of 3e4c, 52% sequence identity ().
| Amino Terminus | Carboxy Terminus |
- .
- The seems unremarkable. Bear in mind that sidechain positions are incorrect in a homology model.
- The inner face of 95-140 is . Bear in mind that sidechain positions are incorrect in a homology model. . The distribution of hydrophobic residues in 83-140 of the homology model is similar to that in the .
- The inner face of 95-140 is , even based upon a multiple sequence alignment that includes mostly types other than 12[1] .
- When the multiple sequence alignment is limited to the 14 type-12 sequences available from Uniprot (APD 0.30), most of the residues have insufficient data, but a , namely Asn130, Val135, Val136, Glu139, Asn140. .
The homology model can be downloaded from homology-model-83-341.
NotesNotes
- ↑ ConSurf run using 80 sequences from the Uniref-90 sequence database. MSA average pairwise distance (APD) 0.94.