ID code: '2I9G' 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' --------------------------------------------------------------------------------- 12 C1' DG D 1 beta 8 13 11 34 C1' DT D 2 beta 30 35 33 54 C1' DC D 3 beta 50 55 53 73 C1' DG D 4 beta 69 74 72 95 C1' DG D 5 beta 91 96 94 115 C1' DG P 1 beta 111 116 114 137 C1' DC P 2 beta 133 138 136 156 C1' DT P 3 beta 152 157 155 176 C1' DG P 4 beta 172 177 175 198 C1' DA P 5 beta 194 199 197 219 C1' DT P 6 beta 215 220 218 239 C1' DG P 7 beta 235 240 238 261 C1' DC P 8 beta 257 262 260 280 C1' DG P 9 beta 276 281 279 300 C1' DOC P 10 beta 304 292 301 318 C1' DC T 1 beta 314 319 317 337 C1' DC T 2 beta 333 338 336 356 C1' DG T 3 beta 352 357 355 378 C1' DA T 4 beta 374 379 377 399 C1' DC T 5 beta 395 400 398 418 C1' DG T 6 beta 414 419 417 440 C1' DG T 7 beta 436 441 439 462 C1' DC T 8 beta 458 463 461 481 C1' DG T 9 beta 477 482 480 503 C1' DC T 10 beta 499 504 502 522 C1' DA T 11 beta 518 523 521 543 C1' DT T 12 beta 539 544 542 563 C1' DC T 13 beta 559 564 562 582 C1' DA T 14 beta 578 583 581 603 C1' DG T 15 beta 599 604 602 625 C1' DC T 16 beta 621 626 624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 11 C2' DG D 1 12 9 33 C2' DT D 2 34 31 53 C2' DC D 3 54 51 72 C2' DG D 4 73 70 94 C2' DG D 5 95 92 114 C2' DG P 1 115 112 136 C2' DC P 2 137 134 155 C2' DT P 3 156 153 175 C2' DG P 4 176 173 197 C2' DA P 5 198 195 218 C2' DT P 6 219 216 238 C2' DG P 7 239 236 260 C2' DC P 8 261 258 279 C2' DG P 9 280 277 301 C2' DOC P 10 300 302 317 C2' DC T 1 318 315 336 C2' DC T 2 337 334 355 C2' DG T 3 356 353 377 C2' DA T 4 378 375 398 C2' DC T 5 399 396 417 C2' DG T 6 418 415 439 C2' DG T 7 440 437 461 C2' DC T 8 462 459 480 C2' DG T 9 481 478 502 C2' DC T 10 503 500 521 C2' DA T 11 522 519 542 C2' DT T 12 543 540 562 C2' DC T 13 563 560 581 C2' DA T 14 582 579 602 C2' DG T 15 603 600 624 C2' DC T 16 625 622 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 9 C3' DG D 1 OK 7 10 11 31 C3' DT D 2 OK 29 32 33 51 C3' DC D 3 OK 49 52 53 70 C3' DG D 4 OK 68 71 72 92 C3' DG D 5 OK 90 93 94 112 C3' DG P 1 OK 110 113 114 134 C3' DC P 2 OK 132 135 136 153 C3' DT P 3 OK 151 154 155 173 C3' DG P 4 OK 171 174 175 195 C3' DA P 5 OK 193 196 197 216 C3' DT P 6 OK 214 217 218 236 C3' DG P 7 OK 234 237 238 258 C3' DC P 8 OK 256 259 260 277 C3' DG P 9 OK 275 278 279 302 C3' DOC P 10 303 301 315 C3' DC T 1 OK 313 316 317 334 C3' DC T 2 OK 332 335 336 353 C3' DG T 3 OK 351 354 355 375 C3' DA T 4 OK 373 376 377 396 C3' DC T 5 OK 394 397 398 415 C3' DG T 6 OK 413 416 417 437 C3' DG T 7 OK 435 438 439 459 C3' DC T 8 OK 457 460 461 478 C3' DG T 9 OK 476 479 480 500 C3' DC T 10 OK 498 501 502 519 C3' DA T 11 OK 517 520 521 540 C3' DT T 12 OK 538 541 542 560 C3' DC T 13 OK 558 561 562 579 C3' DA T 14 OK 577 580 581 600 C3' DG T 15 OK 598 601 602 622 C3' DC T 16 OK 620 623 624 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7 C4' DG D 1 OK 9 6 8 29 C4' DT D 2 OK 31 28 30 49 C4' DC D 3 OK 51 48 50 68 C4' DG D 4 OK 70 67 69 90 C4' DG D 5 OK 92 89 91 110 C4' DG P 1 OK 112 109 111 132 C4' DC P 2 OK 134 131 133 151 C4' DT P 3 OK 153 150 152 171 C4' DG P 4 OK 173 170 172 193 C4' DA P 5 OK 195 192 194 214 C4' DT P 6 OK 216 213 215 234 C4' DG P 7 OK 236 233 235 256 C4' DC P 8 OK 258 255 257 275 C4' DG P 9 OK 277 274 276 303 C4' DOC P 10 OK 302 305 304 313 C4' DC T 1 OK 315 312 314 332 C4' DC T 2 OK 334 331 333 351 C4' DG T 3 OK 353 350 352 373 C4' DA T 4 OK 375 372 374 394 C4' DC T 5 OK 396 393 395 413 C4' DG T 6 OK 415 412 414 435 C4' DG T 7 OK 437 434 436 457 C4' DC T 8 OK 459 456 458 476 C4' DG T 9 OK 478 475 477 498 C4' DC T 10 OK 500 497 499 517 C4' DA T 11 OK 519 516 518 538 C4' DT T 12 OK 540 537 539 558 C4' DC T 13 OK 560 557 559 577 C4' DA T 14 OK 579 576 578 598 C4' DG T 15 OK 600 597 599 620 C4' DC T 16 OK 622 619 621 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 6 C5' DG D 1 5 7 28 C5' DT D 2 27 29 48 C5' DC D 3 47 49 67 C5' DG D 4 66 68 89 C5' DG D 5 88 90 109 C5' DG P 1 108 110 131 C5' DC P 2 130 132 150 C5' DT P 3 149 151 170 C5' DG P 4 169 171 192 C5' DA P 5 191 193 213 C5' DT P 6 212 214 233 C5' DG P 7 232 234 255 C5' DC P 8 254 256 274 C5' DG P 9 273 275 305 C5' DOC P 10 306 303 312 C5' DC T 1 311 313 331 C5' DC T 2 330 332 350 C5' DG T 3 349 351 372 C5' DA T 4 371 373 393 C5' DC T 5 392 394 412 C5' DG T 6 411 413 434 C5' DG T 7 433 435 456 C5' DC T 8 455 457 475 C5' DG T 9 474 476 497 C5' DC T 10 496 498 516 C5' DA T 11 515 517 537 C5' DT T 12 536 538 557 C5' DC T 13 556 558 576 C5' DA T 14 575 577 597 C5' DG T 15 596 598 619 C5' DC T 16 618 620 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 2 P DG D 1 OK OK 3 4 5 24 P DT D 2 distorted distorted 10 25 26 27 44 P DC D 3 distorted distorted 32 45 46 47 63 P DG D 4 distorted distorted 52 64 65 66 85 P DG D 5 distorted distorted 71 86 87 88 127 P DC P 2 distorted distorted 113 128 129 130 146 P DT P 3 distorted distorted 135 147 148 149 166 P DG P 4 distorted distorted 154 167 168 169 188 P DA P 5 distorted distorted 174 189 190 191 209 P DT P 6 distorted distorted 196 210 211 212 229 P DG P 7 distorted distorted 217 230 231 232 251 P DC P 8 distorted distorted 237 252 253 254 270 P DG P 9 distorted distorted 259 271 272 273 307 P DOC P 10 distorted distorted 278 308 309 306 327 P DC T 2 distorted distorted 316 328 329 330 346 P DG T 3 distorted distorted 335 347 348 349 368 P DA T 4 distorted distorted 354 369 370 371 389 P DC T 5 distorted distorted 376 390 391 392 408 P DG T 6 distorted distorted 397 409 410 411 430 P DG T 7 distorted distorted 416 431 432 433 452 P DC T 8 distorted distorted 438 453 454 455 471 P DG T 9 distorted distorted 460 472 473 474 493 P DC T 10 distorted distorted 479 494 495 496 512 P DA T 11 distorted distorted 501 513 514 515 533 P DT T 12 distorted distorted 520 534 535 536 553 P DC T 13 distorted distorted 541 554 555 556 572 P DA T 14 distorted distorted 561 573 574 575 593 P DG T 15 distorted distorted 580 594 595 596 615 P DC T 16 distorted distorted 601 616 617 618 ---------------------------------------------------------------------------------