ID code: '1L5U' CHIRALITY (03 Nov 1998) Checks the chirality and the naming of substituents of chiral and prochiral centers in nucleic acid structures. The molecular structure is read from a PDB file. Only the first model is evaluated. ---------------------------------------------------------- Center Reference for correct naming ---------------------------------------------------------- C1' alpha/beta nomenclature of anomeric sugars, base in beta position in natural nucleosids. C2' IUPAC. 1983. Eur J Biochem, 131: 9-15. C3' IUPAC. 1983. Eur J Biochem, 131: 9-15. C4' IUPAC. 1983. Eur J Biochem, 131: 9-15. C5' IUPAC. 1983. Eur J Biochem, 131: 9-15. P Brookhaven PDB entry '1BNA', O1P -> major groove, O2P -> minor groove. ---------------------------------------------------------- Author: Peter Slickers (slickers@imb-jena.de) Biocomputing, IMB Jena, Germany --------------------------------------------------------------------------------- Seq No Atom Residue H1' base O4' H1' base C2' --------------------------------------------------------------------------------- 8 C1' G B 18 beta 4 9 7 30 C1' C B 19 beta 26 31 29 49 C1' G B 20 beta 45 50 48 71 C1' A B 21 beta 67 72 70 92 C1' T B 22 beta 88 93 91 112 C1' C B 23 beta 108 113 111 131 C1' A B 24 beta 127 132 130 152 C1' C B 25 beta 148 153 151 171 C1' G B 26 beta 167 172 170 193 C1' T B 27 beta 189 194 192 213 C1' A B 28 beta 209 214 212 234 C1' C B 29 beta 230 235 233 254 C1' G C 4 beta 250 255 253 276 C1' T C 5 beta 272 277 275 296 C1' A C 6 beta 292 297 295 317 C1' C C 7 beta 313 318 316 336 C1' G C 8 beta 332 337 335 358 C1' T C 9 beta 354 359 357 378 C1' G C 10 beta 374 379 377 400 C1' A C 11 beta 396 401 399 421 C1' T C 12 beta 417 422 420 441 C1' C C 13 beta 437 442 440 460 C1' G C 14 beta 456 461 459 482 C1' C C 15 beta 478 483 481 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G B 18 8 5 29 C2' C B 19 30 27 48 C2' G B 20 49 46 70 C2' A B 21 71 68 91 C2' T B 22 92 89 111 C2' C B 23 112 109 130 C2' A B 24 131 128 151 C2' C B 25 152 149 170 C2' G B 26 171 168 192 C2' T B 27 193 190 212 C2' A B 28 213 210 233 C2' C B 29 234 231 253 C2' G C 4 254 251 275 C2' T C 5 276 273 295 C2' A C 6 296 293 316 C2' C C 7 317 314 335 C2' G C 8 336 333 357 C2' T C 9 358 355 377 C2' G C 10 378 375 399 C2' A C 11 400 397 420 C2' T C 12 421 418 440 C2' C C 13 441 438 459 C2' G C 14 460 457 481 C2' C C 15 482 479 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G B 18 OK 3 6 7 27 C3' C B 19 OK 25 28 29 46 C3' G B 20 OK 44 47 48 68 C3' A B 21 OK 66 69 70 89 C3' T B 22 OK 87 90 91 109 C3' C B 23 OK 107 110 111 128 C3' A B 24 OK 126 129 130 149 C3' C B 25 OK 147 150 151 168 C3' G B 26 OK 166 169 170 190 C3' T B 27 OK 188 191 192 210 C3' A B 28 OK 208 211 212 231 C3' C B 29 OK 229 232 233 251 C3' G C 4 OK 249 252 253 273 C3' T C 5 OK 271 274 275 293 C3' A C 6 OK 291 294 295 314 C3' C C 7 OK 312 315 316 333 C3' G C 8 OK 331 334 335 355 C3' T C 9 OK 353 356 357 375 C3' G C 10 OK 373 376 377 397 C3' A C 11 OK 395 398 399 418 C3' T C 12 OK 416 419 420 438 C3' C C 13 OK 436 439 440 457 C3' G C 14 OK 455 458 459 479 C3' C C 15 OK 477 480 481 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G B 18 OK 5 2 4 25 C4' C B 19 OK 27 24 26 44 C4' G B 20 OK 46 43 45 66 C4' A B 21 OK 68 65 67 87 C4' T B 22 OK 89 86 88 107 C4' C B 23 OK 109 106 108 126 C4' A B 24 OK 128 125 127 147 C4' C B 25 OK 149 146 148 166 C4' G B 26 OK 168 165 167 188 C4' T B 27 OK 190 187 189 208 C4' A B 28 OK 210 207 209 229 C4' C B 29 OK 231 228 230 249 C4' G C 4 OK 251 248 250 271 C4' T C 5 OK 273 270 272 291 C4' A C 6 OK 293 290 292 312 C4' C C 7 OK 314 311 313 331 C4' G C 8 OK 333 330 332 353 C4' T C 9 OK 355 352 354 373 C4' G C 10 OK 375 372 374 395 C4' A C 11 OK 397 394 396 416 C4' T C 12 OK 418 415 417 436 C4' C C 13 OK 438 435 437 455 C4' G C 14 OK 457 454 456 477 C4' C C 15 OK 479 476 478 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G B 18 1 3 24 C5' C B 19 23 25 43 C5' G B 20 42 44 65 C5' A B 21 64 66 86 C5' T B 22 85 87 106 C5' C B 23 105 107 125 C5' A B 24 124 126 146 C5' C B 25 145 147 165 C5' G B 26 164 166 187 C5' T B 27 186 188 207 C5' A B 28 206 208 228 C5' C B 29 227 229 248 C5' G C 4 247 249 270 C5' T C 5 269 271 290 C5' A C 6 289 291 311 C5' C C 7 310 312 330 C5' G C 8 329 331 352 C5' T C 9 351 353 372 C5' G C 10 371 373 394 C5' A C 11 393 395 415 C5' T C 12 414 416 435 C5' C C 13 434 436 454 C5' G C 14 453 455 476 C5' C C 15 475 477 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C B 19 distorted distorted 6 21 22 23 39 P G B 20 distorted distorted 28 40 41 42 61 P A B 21 distorted distorted 47 62 63 64 82 P T B 22 distorted distorted 69 83 84 85 102 P C B 23 distorted distorted 90 103 104 105 121 P A B 24 distorted distorted 110 122 123 124 142 P C B 25 distorted distorted 129 143 144 145 161 P G B 26 distorted distorted 150 162 163 164 183 P T B 27 distorted distorted 169 184 185 186 203 P A B 28 distorted distorted 191 204 205 206 224 P C B 29 distorted distorted 211 225 226 227 244 P G C 4 distorted distorted 245 246 247 266 P T C 5 distorted distorted 252 267 268 269 286 P A C 6 distorted distorted 274 287 288 289 307 P C C 7 distorted distorted 294 308 309 310 326 P G C 8 distorted distorted 315 327 328 329 348 P T C 9 distorted distorted 334 349 350 351 368 P G C 10 distorted distorted 356 369 370 371 390 P A C 11 distorted distorted 376 391 392 393 411 P T C 12 distorted distorted 398 412 413 414 431 P C C 13 distorted distorted 419 432 433 434 450 P G C 14 distorted distorted 439 451 452 453 472 P C C 15 distorted distorted 458 473 474 475 ---------------------------------------------------------------------------------