ID code: '1ZET' 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' --------------------------------------------------------------------------------- 11 C1' DA T 5 beta 7 12 10 32 C1' DG T 6 beta 28 33 31 54 C1' DG T 7 beta 50 55 53 76 C1' DG T 8 beta 72 77 75 97 C1' BRU T 9 beta 102 88 98 118 C1' DC T 10 beta 114 119 117 137 C1' DC T 11 beta 133 138 136 155 C1' BRU T 12 beta 160 146 156 175 C1' BRU T 13 beta 180 166 176 196 C1' DC T 14 beta 192 197 195 215 C1' DC T 15 beta 211 216 214 234 C1' DC T 16 beta 230 235 233 253 C1' DC T 17 beta 249 254 252 272 C1' DC T 18 beta 268 273 271 289 C1' DG P 1 beta 285 290 288 311 C1' DG P 2 beta 307 312 310 333 C1' DG P 3 beta 329 334 332 355 C1' DG P 4 beta 351 356 354 377 C1' DG P 5 beta 373 378 376 399 C1' DA P 6 beta 395 400 398 420 C1' DA P 7 beta 416 421 419 441 C1' DG P 8 beta 437 442 440 463 C1' DG P 9 beta 459 464 462 485 C1' DA P 10 beta 481 486 484 506 C1' DC P 11 beta 502 507 505 525 C1' DC P 12 beta 521 526 524 542 C1' DOC P 13 beta 546 534 543 3642 C1' TTP A 451 beta 3638 3643 3641 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' DA T 5 11 8 31 C2' DG T 6 32 29 53 C2' DG T 7 54 51 75 C2' DG T 8 76 73 98 C2' BRU T 9 97 99 117 C2' DC T 10 118 115 136 C2' DC T 11 137 134 156 C2' BRU T 12 155 157 176 C2' BRU T 13 175 177 195 C2' DC T 14 196 193 214 C2' DC T 15 215 212 233 C2' DC T 16 234 231 252 C2' DC T 17 253 250 271 C2' DC T 18 272 269 288 C2' DG P 1 289 286 310 C2' DG P 2 311 308 332 C2' DG P 3 333 330 354 C2' DG P 4 355 352 376 C2' DG P 5 377 374 398 C2' DA P 6 399 396 419 C2' DA P 7 420 417 440 C2' DG P 8 441 438 462 C2' DG P 9 463 460 484 C2' DA P 10 485 482 505 C2' DC P 11 506 503 524 C2' DC P 12 525 522 543 C2' DOC P 13 542 544 3641 C2' TTP A 451 3642 3639 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' DA T 5 OK 6 9 10 29 C3' DG T 6 OK 27 30 31 51 C3' DG T 7 OK 49 52 53 73 C3' DG T 8 OK 71 74 75 99 C3' BRU T 9 OK 100 101 98 115 C3' DC T 10 OK 113 116 117 134 C3' DC T 11 OK 132 135 136 157 C3' BRU T 12 OK 158 159 156 177 C3' BRU T 13 OK 178 179 176 193 C3' DC T 14 OK 191 194 195 212 C3' DC T 15 OK 210 213 214 231 C3' DC T 16 OK 229 232 233 250 C3' DC T 17 OK 248 251 252 269 C3' DC T 18 OK 267 270 271 286 C3' DG P 1 OK 284 287 288 308 C3' DG P 2 OK 306 309 310 330 C3' DG P 3 OK 328 331 332 352 C3' DG P 4 OK 350 353 354 374 C3' DG P 5 OK 372 375 376 396 C3' DA P 6 OK 394 397 398 417 C3' DA P 7 OK 415 418 419 438 C3' DG P 8 OK 436 439 440 460 C3' DG P 9 OK 458 461 462 482 C3' DA P 10 OK 480 483 484 503 C3' DC P 11 OK 501 504 505 522 C3' DC P 12 OK 520 523 524 544 C3' DOC P 13 545 543 3639 C3' TTP A 451 OK 3637 3640 3641 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' DA T 5 OK 8 5 7 27 C4' DG T 6 OK 29 26 28 49 C4' DG T 7 OK 51 48 50 71 C4' DG T 8 OK 73 70 72 100 C4' BRU T 9 OK 99 103 102 113 C4' DC T 10 OK 115 112 114 132 C4' DC T 11 OK 134 131 133 158 C4' BRU T 12 OK 157 161 160 178 C4' BRU T 13 OK 177 181 180 191 C4' DC T 14 OK 193 190 192 210 C4' DC T 15 OK 212 209 211 229 C4' DC T 16 OK 231 228 230 248 C4' DC T 17 OK 250 247 249 267 C4' DC T 18 OK 269 266 268 284 C4' DG P 1 OK 286 283 285 306 C4' DG P 2 OK 308 305 307 328 C4' DG P 3 OK 330 327 329 350 C4' DG P 4 OK 352 349 351 372 C4' DG P 5 OK 374 371 373 394 C4' DA P 6 OK 396 393 395 415 C4' DA P 7 OK 417 414 416 436 C4' DG P 8 OK 438 435 437 458 C4' DG P 9 OK 460 457 459 480 C4' DA P 10 OK 482 479 481 501 C4' DC P 11 OK 503 500 502 520 C4' DC P 12 OK 522 519 521 545 C4' DOC P 13 OK 544 547 546 3637 C4' TTP A 451 OK 3639 3636 3638 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' DA T 5 4 6 26 C5' DG T 6 25 27 48 C5' DG T 7 47 49 70 C5' DG T 8 69 71 103 C5' BRU T 9 104 100 112 C5' DC T 10 111 113 131 C5' DC T 11 130 132 161 C5' BRU T 12 162 158 181 C5' BRU T 13 182 178 190 C5' DC T 14 189 191 209 C5' DC T 15 208 210 228 C5' DC T 16 227 229 247 C5' DC T 17 246 248 266 C5' DC T 18 265 267 283 C5' DG P 1 282 284 305 C5' DG P 2 304 306 327 C5' DG P 3 326 328 349 C5' DG P 4 348 350 371 C5' DG P 5 370 372 393 C5' DA P 6 392 394 414 C5' DA P 7 413 415 435 C5' DG P 8 434 436 457 C5' DG P 9 456 458 479 C5' DA P 10 478 480 500 C5' DC P 11 499 501 519 C5' DC P 12 518 520 547 C5' DOC P 13 548 545 3636 C5' TTP A 451 3635 3637 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P DA T 5 distorted distorted 2 3 4 22 P DG T 6 distorted distorted 9 23 24 25 44 P DG T 7 distorted distorted 30 45 46 47 66 P DG T 8 distorted distorted 52 67 68 69 105 P BRU T 9 distorted distorted 74 106 107 104 108 P DC T 10 distorted distorted 101 109 110 111 127 P DC T 11 distorted distorted 116 128 129 130 163 P BRU T 12 distorted distorted 135 164 165 162 183 P BRU T 13 distorted distorted 159 184 185 182 186 P DC T 14 distorted distorted 179 187 188 189 205 P DC T 15 distorted distorted 194 206 207 208 224 P DC T 16 distorted distorted 213 225 226 227 243 P DC T 17 distorted distorted 232 244 245 246 262 P DC T 18 distorted distorted 251 263 264 265 301 P DG P 2 distorted distorted 287 302 303 304 323 P DG P 3 distorted distorted 309 324 325 326 345 P DG P 4 distorted distorted 331 346 347 348 367 P DG P 5 distorted distorted 353 368 369 370 389 P DA P 6 distorted distorted 375 390 391 392 410 P DA P 7 distorted distorted 397 411 412 413 431 P DG P 8 distorted distorted 418 432 433 434 453 P DG P 9 distorted distorted 439 454 455 456 475 P DA P 10 distorted distorted 461 476 477 478 496 P DC P 11 distorted distorted 483 497 498 499 515 P DC P 12 distorted distorted 504 516 517 518 549 P DOC P 13 OK OK 523 550 551 548 ---------------------------------------------------------------------------------