User:Fadel A. Samatey/FlgE II/Complete Flagellar Hook Structure: Difference between revisions
Eric Martz (talk | contribs) No edit summary |
Eric Martz (talk | contribs) No edit summary |
||
| Line 95: | Line 95: | ||
===Contacts Between Monomers=== | ===Contacts Between Monomers=== | ||
The <scene name='47/478824/Hkcj_monomer_e10_v2/3'>monomer domain colors are now lighter</scene>, for contrast in this scene: Here, the monomer is <scene name='47/478824/Hkcj_monomer_e10_v2/4'>decorated with all contacting atoms</scene> from neighboring monomers in the hook assembly. The contacting atoms<ref name="contacting">"Contacting" is defined as likely hydrogen bonds, plus likely apolar interactions. Likely hydrogen bonds: oxygens or nitrogens within 3.5 Å of oxygens or nitrogens in a neighboring monomer. Apolar interactions: carbons or sulfurs within 4.0 Å of carbons or sulfurs in a neighboring monomer.</ref> are enlarged<ref>Contacting atoms are rendered at radius 3.1 Å. For comparison, the van der Waals radius of carbon is 1.7 Å.: A. Bondi, ''J. Phys. Chem.'' '''68''':441 (1964).</ref>, and colored by domain. We can now see the following: | The <scene name='47/478824/Hkcj_monomer_e10_v2/3'>monomer domain colors are now lighter</scene>, for contrast in this scene: Here, the monomer is <scene name='47/478824/Hkcj_monomer_e10_v2/4'>decorated with all contacting atoms</scene> from neighboring monomers in the hook assembly<ref name="max">The monomer chain in the above scenes is chain "e". It is one of 21 chains in the 55-chain model that has the maximum number of contacting atoms (216) from other chains. It is also one of 28 chains that have the maximum number of atoms (51) from neighboring chains contacting the L-stretch.</ref> The contacting atoms<ref name="contacting">"Contacting" is defined as likely hydrogen bonds, plus likely apolar interactions. Likely hydrogen bonds: oxygens or nitrogens within 3.5 Å of oxygens or nitrogens in a neighboring monomer. Apolar interactions: carbons or sulfurs within 4.0 Å of carbons or sulfurs in a neighboring monomer.</ref> are enlarged<ref>Contacting atoms are rendered at radius 3.1 Å. For comparison, the van der Waals radius of carbon is 1.7 Å.: A. Bondi, ''J. Phys. Chem.'' '''68''':441 (1964).</ref>, and colored by domain. We can now see the following: | ||
*<font color="#e000e0">'''Domain 0 Helices'''</font>: Most neighbor contacts are from D0 helices. A few are from neighboring D0 L-stretches. | *<font color="#e000e0">'''Domain 0 Helices'''</font>: Most neighbor contacts are from D0 helices. A few are from neighboring D0 L-stretches. | ||
| Line 105: | Line 105: | ||
*<font color="#00b0b0">'''Domain 4'''</font>: Most neighbor contacts are from D3, with a single carbon atom contacting from D2. | *<font color="#00b0b0">'''Domain 4'''</font>: Most neighbor contacts are from D3, with a single carbon atom contacting from D2. | ||
Here the <scene name='47/478824/Hkcj_monomer_e10_v2/5'>216 contacting atoms are colored by element</scene>. | Here the <scene name='47/478824/Hkcj_monomer_e10_v2/5'>216 contacting atoms are colored by element</scene><ref name="max" />. | ||
<center><big>{{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_O}} {{Template:ColorKey_Element_N}} {{Template:ColorKey_Element_S}}</big></center> | <center><big>{{Template:ColorKey_Element_C}} {{Template:ColorKey_Element_O}} {{Template:ColorKey_Element_N}} {{Template:ColorKey_Element_S}}</big></center> | ||
83 contacting atoms<ref name="contacting" /> (38%) are polar (oxygen, nitrogen), while 133 (62%) are apolar (132 carbon, 1 sulfur). The polar interactions include 20 neighbor atoms engaged in [[salt bridges]] (D0 helices:4, D0 L-stretch:3, D1:8, D2:2, D3:0, D4:3), and two [[cation-pi interactions]] (R58 in the tip of the L-stretch:F133 in D1). Thus 75% of the salt bridges and both cation-pi interactions contact D0 or D1, while only 25% of the salt bridges contact D2, D3 or D4. 109 (82%) of the apolar contacting atoms contact D0 or D1, while only 24 (11%) contact D2, D3 or D4. | 83 contacting atoms<ref name="contacting" /> (38%) are polar (oxygen, nitrogen), while 133 (62%) are apolar (132 carbon, 1 sulfur). The polar interactions include 20 neighbor atoms engaged in [[salt bridges]] (D0 helices:4, D0 L-stretch:3, D1:8, D2:2, D3:0, D4:3), and two [[cation-pi interactions]] (R58 in the tip of the L-stretch:F133 in D1). Thus 75% of the salt bridges and both cation-pi interactions contact D0 or D1, while only 25% of the salt bridges contact D2, D3 or D4. 109 (82%) of the apolar contacting atoms contact D0 or D1, while only 24 (11%) contact D2, D3 or D4. | ||