Calculate structure: Difference between revisions

Line 90:

'''Detection of Known γ-turns'''

Out of the eleven classic γ-turns identified by Miner-White et. al.<ref name="Miner" /> ''Calculate structure'' only identifies and displays the hbond of thermolysin. Miner-White et. al. indicate that two hbonds are present in the classic γ-turn in thermolysin (They also state that the turn in thermolysin is the only one of the eleven that has two hbonds.), but ''Calculate structure'' only displays one and the T segment of the turn is '''not''' listed in the summary displayed in the console. (select protein; calculate structure; cartoon; color structure; calculate hbonds structure)

Out of the eleven classic γ-turns identified by Miner-White et. al.<ref name="Miner" /> ''Calculate structure'' only identifies and displays the hbond of thermolysin. Miner-White et. al. indicate that two hbonds are present in the classic γ-turn in thermolysin (They also state that the turn in thermolysin is the only one of the eleven that has two hbonds.), but ''Calculate structure'' only displays one and the T segment of the turn is '''not''' listed in the summary displayed in the console. <center>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</center>

* <scene name='Calculate_structure/Thermolysin2/1'>Thermolysin</scene> (8TLN, which now supersedes 3TLN which was actually used by Miner-White et. al.); <scene name='Calculate_structure/Thermolysin/2'>Isolated view</scene> - run 'calculate hbonds structure' to confirm presence of hbond; reported torsional angles are 75,-54.

The hbonds were not identified by ''Calculate structure'' in the other ten classic turns and the T segments were not included in the summary displayed in the console. Several illustrations are given.

* <scene name='Calculate_structure/Alpha_lytic/2'>α-lytic protease</scene>; <scene name='Calculate_structure/Alpha_lytic2/1'>Isolated turn</scene> - run 'calculate hbonds structure' to confirm absence of intra-turn hbond; reported torsional angles are 93, -70.

* <scene name='Calculate_structure/Proteinase_a/1'>Proteinase A</scene> (2SGA); <scene name='Calculate_structure/Proteinase_a2/1'>Isolated turn</scene> - reported torsional angles are 80, -75.

* <scene name='Calculate_structure/Ldh/1'>Lactate dehydrogenase</scene> (6LDH, supersedes 4LDH) - three classic γ-turns high lighted; <scene name='Calculate_structure/Ldh2/1'>Isolate turns</scene>.

* <scene name='Calculate_structure/Ldh/1'>Lactate dehydrogenase</scene> (6LDH, supersedes 4LDH) - three classic γ-turns high lighted; <scene name='Calculate_structure/Ldh2/1'>Isolate turns</scene> - none have the appearance of a γ-turn and none have torsional angles that a classic or even a reverse γ-turn would have. Substantial differences between 4LDH and 6LDH could account for the lack of γ-turns in these three sequences.

* 101-~~106~~

* 103-106 - T: 102_103 is on the summary, but as indicated by the hbond 101-104 forms a β-turn.

* 208-210

* 208-210 - T: 207_208 is on the summary, but as indicated by the hbond 206-209 forms a β-turn.

* 278-280

* 278-280 - T: 275_276 is the clo9seste segment on the summary.

</blockquote>

~~However, with some of these turns a residue making up the turn is included along with contiguous residues in a T segment of the summary.~~

</StructureSection>

Calculate structure: Difference between revisions

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@@ Line 90: / Line 90: @@
 '''Detection of Known γ-turns'''
-Out of the eleven classic γ-turns identified by Miner-White et. al.<ref name="Miner" /> ''Calculate structure'' only identifies and displays the hbond of thermolysin. Miner-White et. al. indicate that two hbonds are present in the classic γ-turn in thermolysin (They also state that the turn in thermolysin is the only one of the eleven that has two hbonds.), but ''Calculate structure'' only displays one and the T segment of the turn is '''not''' listed in the summary displayed in the console. (select protein; calculate structure; cartoon; color structure; calculate hbonds structure)
+Out of the eleven classic γ-turns identified by Miner-White et. al.<ref name="Miner" /> ''Calculate structure'' only identifies and displays the hbond of thermolysin. Miner-White et. al. indicate that two hbonds are present in the classic γ-turn in thermolysin (They also state that the turn in thermolysin is the only one of the eleven that has two hbonds.), but ''Calculate structure'' only displays one and the T segment of the turn is '''not''' listed in the summary displayed in the console. <center>select protein; calculate structure; cartoon; color structure; calculate hbonds structure</center>
 * <scene name='Calculate_structure/Thermolysin2/1'>Thermolysin</scene> (8TLN, which now supersedes 3TLN which was actually used by Miner-White et. al.);  <scene name='Calculate_structure/Thermolysin/2'>Isolated view</scene> - run 'calculate hbonds structure' to confirm presence of hbond; reported torsional angles are 75,-54.
 The hbonds were not identified by ''Calculate structure'' in the other ten classic turns  and the T segments were not included in the summary displayed in the console. Several illustrations are given.
 * <scene name='Calculate_structure/Alpha_lytic/2'>α-lytic protease</scene>; <scene name='Calculate_structure/Alpha_lytic2/1'>Isolated turn</scene> - run 'calculate hbonds structure' to confirm absence of intra-turn hbond; reported torsional angles are 93, -70.
 * <scene name='Calculate_structure/Proteinase_a/1'>Proteinase A</scene> (2SGA); <scene name='Calculate_structure/Proteinase_a2/1'>Isolated turn</scene> - reported torsional angles are 80, -75.
-* <scene name='Calculate_structure/Ldh/1'>Lactate dehydrogenase</scene> (6LDH, supersedes 4LDH) - three classic γ-turns high lighted; <scene name='Calculate_structure/Ldh2/1'>Isolate turns</scene>.
+* <scene name='Calculate_structure/Ldh/1'>Lactate dehydrogenase</scene> (6LDH, supersedes 4LDH) - three classic γ-turns high lighted; <scene name='Calculate_structure/Ldh2/1'>Isolate turns</scene> - none have the appearance of a γ-turn and none have torsional angles that a classic or even a reverse γ-turn would have. Substantial differences between 4LDH and 6LDH could account for the lack of γ-turns in these three sequences.
 <blockquote>
-* 101-106
+* 103-106 - T: 102_103 is on the summary, but as indicated by the hbond 101-104 forms a β-turn.
-* 208-210
+* 208-210 - T: 207_208 is on the summary, but as indicated by the hbond 206-209 forms a β-turn.
-* 278-280
+* 278-280 - T: 275_276 is the clo9seste segment on the summary.
 </blockquote>
-However, with some of these turns a residue making up the turn is included along with contiguous residues in a T segment of the summary.
 </StructureSection>