lecture8 - Bioinformatics 2 Lecture 8 Why are...

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Bioinformatics 2 -- Lecture 8 Why are beta-alpha-beta units right handed ? Homology Model reFnement
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R-handed βαβ L-handed βαβ 1.5% 98.5% Do proteins fold using a “right-hand rule”? βαβ supersecondary structure units are mostly right-handed
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3 Theories from the 70’s • Thornton, Sternberg, Scheraga (1976, 1989) βαβ units are right-handed because the helix draws a straight line between the upturned edges of the beta sheet. • Richardson (1975) βαβ units are right handed because L- amino acids in the extended state are already right-handed, so when they collapse to a bab unit, they stay right- handed.
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1tm9A R 0.83 6 57 74 92 106 1tx4A L 0.10 21 192 203 209 214 1tx4A R 0.86 14 64 75 90 102 1tx4A R 1.00 5 165 183 185 188 1tx9A L 0.00 11 88 97 104 109 1tx9A R 1.00 2 75 85 88 97 3 17 21 26 37 2 28 38 44 58 5 53 67 73 85 13 167 191 204 214 6 204 214 216 231 4 283 291 294 303 24 356 371 373 382 5 388 404 413 427 16 477 490 495 511 8 203 226 234 242 4 156 164 168 177 6 294 300 317 321 5 4 14 18 27 2 5 21 25 35 7 186 203 211 225 9 211 225 229 246 1 26 45 50 63 9 9 18 22 38 20 22 38 50 63 11 68 77 87 93 8 135 150 160 178 3 67 78 84 97 17 43 57 60 72 10 60 72 77 91 2 102 116 123 132 6 17 23 25 45 1w0jA L 0.00 14 381 402 412 428 1w0jA L 0.00 9 412 428 438 450 1w0jA L 0.00 5 438 450 458 475 1w0jA L 0.00 2 458 475 477 485 1w26A L 0.00 5 263 297 304 321 1w26A L 0.00 8 364 377 381 390 1x9nA R 1.00 2 289 301 305 322 1xlyA L 0.00 4 11 44 49 71 1xlyA R 1.00 1 92 128 138 161 1xn8A L 0.00 5 6 12 16 20 1xn8A L 0.00 5 23 41 55 70 PDB code/chain R/L frac R Contacts Helix 1 Helix 2 Helix residue rang 1j0tA L 0.06 16 16 31 37 40 49 56 1jj2O L 0.00 9 4 14 28 33 37 45 1jj2O L 0.00 5 90 111 116 127 134 141 1jr3A R 0.78 9 278 297 304 308 310 319 1jr3A R 1.00 11 246 258 261 273 278 297 1jswA L 0.00 6 47 65 70 83 104 121 1jswA L 0.00 1jswA L 0.00 1jswA R 1.00 1k6kA R 1.00 1k6kA R 1.00 1k8kE R 1.00 1kjsA R 0.76 1kp8A L 0.00 1kp8A R 0.82 1l8wA L 0.00 1lbuA R 1.00 1lkpA R 1.00 1llaA L 0.00 1llaA R 1.00 1llpA L 0.00 1llpA R 1.00 1lp1A L 0.00 1lriA R 0.86 1lriA R 1.00 1m1eB R 1.00 1m98A L 0.00 1m98A L 0.00 1m98A L 0.11 1m9xC R 1.00 1m9xC R 1.00 1m9xC R 1.00 1mi1A L 0.00 5 2266 2271 2275 2280 2286 2297 1miwA L 0.00 2 351 357 364 379 386 403 1miwA R 1.00 8 147 153 155 167 174 182 1miwA R 1.00 5 155 167 174 182 184 189 1miwA R 1.00 14 248 258 264 270 275 290 1miwA R 1.00 9 275 290 299 305 307 321 1miwA R 1.00 4 299 305 307 321 327 337 1mp1A R 1.00 1 82 92 96 102 105 114 1mvcA L 0.00 7 264 285 294 303 305 316 1mvcA R 1.00 8 305 316 334 339 343 359 1mvcA R 1.00 3 364 375 386 407 414 419 PDB code/chain R/L frac R Contacts Helix 1 Helix 2 Helix 3 Helix residue ranges 1a26A R 1.00 14 703 721 726 739 755 778 1a9xA R 1.00 6 420 429 433 445 449 456 1a9xA R 1.00 7 433 445 449 456 460 479 1a9xA R 1.00 8 460 479 486 494 499 506 1a9xA R 1.00 1 486 494 499 506 510 519 1aa7A R 0.89 28 109 117 121 132 140 157 1aa7A R 1.00 3 19 33 39 47 54 67 1aa7A R 1.00 1 39 47 54 67 78 83 1aa7A R 1.00 18 90 105 109 117 121 132 1abvA L 0.00 3 23 39 41 47 53 64 1adtA L 0.00 4 180 194 200 203 212 224 1aepA L 0.00 9 34 65 69 86 94 121 1aepA R 1.00 2 69 86 94 121 126 129 1aepA
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lecture8 - Bioinformatics 2 Lecture 8 Why are...

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