ID code: '3S9H' 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' DT T 1 beta 4 9 7 28 C1' DC T 2 beta 24 29 27 47 C1' DA T 3 beta 43 48 46 68 C1' DA T 4 beta 64 69 67 89 C1' DG T 5 beta 85 90 88 111 C1' DT T 6 beta 107 112 110 131 C1' DA T 7 beta 127 132 130 152 C1' DA T 8 beta 148 153 151 173 C1' DG T 9 beta 169 174 172 195 C1' DC T 10 beta 191 196 194 214 C1' DA T 11 beta 210 215 213 235 C1' DG T 12 beta 231 236 234 257 C1' DT T 13 beta 253 258 256 277 C1' DC T 14 beta 273 278 276 296 C1' DC T 15 beta 292 297 295 315 C1' DG T 16 beta 311 316 314 337 C1' DC T 17 beta 333 338 336 356 C1' DG T 18 beta 352 357 355 376 C1' DG P 103 beta 372 377 375 398 C1' DC P 104 beta 394 399 397 417 C1' DG P 105 beta 413 418 416 439 C1' DG P 106 beta 435 440 438 461 C1' DA P 107 beta 457 462 460 482 C1' DC P 108 beta 478 483 481 501 C1' DT P 109 beta 497 502 500 521 C1' DG P 110 beta 517 522 520 543 C1' DC P 111 beta 539 544 542 562 C1' DT P 112 beta 558 563 561 582 C1' DT P 113 beta 578 583 581 602 C1' DA P 114 beta 598 603 601 621 C1' DOC P 115 beta 625 613 622 8047 C1' DUP A 904 beta 8051 8046 8048 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DT T 1 8 5 27 C2' DC T 2 28 25 46 C2' DA T 3 47 44 67 C2' DA T 4 68 65 88 C2' DG T 5 89 86 110 C2' DT T 6 111 108 130 C2' DA T 7 131 128 151 C2' DA T 8 152 149 172 C2' DG T 9 173 170 194 C2' DC T 10 195 192 213 C2' DA T 11 214 211 234 C2' DG T 12 235 232 256 C2' DT T 13 257 254 276 C2' DC T 14 277 274 295 C2' DC T 15 296 293 314 C2' DG T 16 315 312 336 C2' DC T 17 337 334 355 C2' DG T 18 356 353 375 C2' DG P 103 376 373 397 C2' DC P 104 398 395 416 C2' DG P 105 417 414 438 C2' DG P 106 439 436 460 C2' DA P 107 461 458 481 C2' DC P 108 482 479 500 C2' DT P 109 501 498 520 C2' DG P 110 521 518 542 C2' DC P 111 543 540 561 C2' DT P 112 562 559 581 C2' DT P 113 582 579 601 C2' DA P 114 602 599 622 C2' DOC P 115 621 623 8048 C2' DUP A 904 8047 8049 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DT T 1 OK 3 6 7 25 C3' DC T 2 OK 23 26 27 44 C3' DA T 3 OK 42 45 46 65 C3' DA T 4 OK 63 66 67 86 C3' DG T 5 OK 84 87 88 108 C3' DT T 6 OK 106 109 110 128 C3' DA T 7 OK 126 129 130 149 C3' DA T 8 OK 147 150 151 170 C3' DG T 9 OK 168 171 172 192 C3' DC T 10 OK 190 193 194 211 C3' DA T 11 OK 209 212 213 232 C3' DG T 12 OK 230 233 234 254 C3' DT T 13 OK 252 255 256 274 C3' DC T 14 OK 272 275 276 293 C3' DC T 15 OK 291 294 295 312 C3' DG T 16 OK 310 313 314 334 C3' DC T 17 OK 332 335 336 353 C3' DG T 18 OK 351 354 355 373 C3' DG P 103 OK 371 374 375 395 C3' DC P 104 OK 393 396 397 414 C3' DG P 105 OK 412 415 416 436 C3' DG P 106 OK 434 437 438 458 C3' DA P 107 OK 456 459 460 479 C3' DC P 108 OK 477 480 481 498 C3' DT P 109 OK 496 499 500 518 C3' DG P 110 OK 516 519 520 540 C3' DC P 111 OK 538 541 542 559 C3' DT P 112 OK 557 560 561 579 C3' DT P 113 OK 577 580 581 599 C3' DA P 114 OK 597 600 601 623 C3' DOC P 115 624 622 8049 C3' DUP A 904 OK 8052 8050 8048 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DT T 1 OK 5 2 4 23 C4' DC T 2 OK 25 22 24 42 C4' DA T 3 OK 44 41 43 63 C4' DA T 4 OK 65 62 64 84 C4' DG T 5 OK 86 83 85 106 C4' DT T 6 OK 108 105 107 126 C4' DA T 7 OK 128 125 127 147 C4' DA T 8 OK 149 146 148 168 C4' DG T 9 OK 170 167 169 190 C4' DC T 10 OK 192 189 191 209 C4' DA T 11 OK 211 208 210 230 C4' DG T 12 OK 232 229 231 252 C4' DT T 13 OK 254 251 253 272 C4' DC T 14 OK 274 271 273 291 C4' DC T 15 OK 293 290 292 310 C4' DG T 16 OK 312 309 311 332 C4' DC T 17 OK 334 331 333 351 C4' DG T 18 OK 353 350 352 371 C4' DG P 103 OK 373 370 372 393 C4' DC P 104 OK 395 392 394 412 C4' DG P 105 OK 414 411 413 434 C4' DG P 106 OK 436 433 435 456 C4' DA P 107 OK 458 455 457 477 C4' DC P 108 OK 479 476 478 496 C4' DT P 109 OK 498 495 497 516 C4' DG P 110 OK 518 515 517 538 C4' DC P 111 OK 540 537 539 557 C4' DT P 112 OK 559 556 558 577 C4' DT P 113 OK 579 576 578 597 C4' DA P 114 OK 599 596 598 624 C4' DOC P 115 OK 623 626 625 8052 C4' DUP A 904 OK 8049 8053 8051 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DT T 1 1 3 22 C5' DC T 2 21 23 41 C5' DA T 3 40 42 62 C5' DA T 4 61 63 83 C5' DG T 5 82 84 105 C5' DT T 6 104 106 125 C5' DA T 7 124 126 146 C5' DA T 8 145 147 167 C5' DG T 9 166 168 189 C5' DC T 10 188 190 208 C5' DA T 11 207 209 229 C5' DG T 12 228 230 251 C5' DT T 13 250 252 271 C5' DC T 14 270 272 290 C5' DC T 15 289 291 309 C5' DG T 16 308 310 331 C5' DC T 17 330 332 350 C5' DG T 18 349 351 370 C5' DG P 103 369 371 392 C5' DC P 104 391 393 411 C5' DG P 105 410 412 433 C5' DG P 106 432 434 455 C5' DA P 107 454 456 476 C5' DC P 108 475 477 495 C5' DT P 109 494 496 515 C5' DG P 110 514 516 537 C5' DC P 111 536 538 556 C5' DT P 112 555 557 576 C5' DT P 113 575 577 596 C5' DA P 114 595 597 626 C5' DOC P 115 627 624 8053 C5' DUP A 904 8054 8052 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P DC T 2 distorted distorted 6 19 20 21 37 P DA T 3 distorted distorted 26 38 39 40 58 P DA T 4 distorted distorted 45 59 60 61 79 P DG T 5 distorted distorted 66 80 81 82 101 P DT T 6 distorted distorted 87 102 103 104 121 P DA T 7 distorted distorted 109 122 123 124 142 P DA T 8 distorted distorted 129 143 144 145 163 P DG T 9 distorted distorted 150 164 165 166 185 P DC T 10 distorted distorted 171 186 187 188 204 P DA T 11 distorted distorted 193 205 206 207 225 P DG T 12 distorted distorted 212 226 227 228 247 P DT T 13 distorted distorted 233 248 249 250 267 P DC T 14 distorted distorted 255 268 269 270 286 P DC T 15 distorted distorted 275 287 288 289 305 P DG T 16 distorted distorted 294 306 307 308 327 P DC T 17 distorted distorted 313 328 329 330 346 P DG T 18 distorted distorted 335 347 348 349 388 P DC P 104 distorted distorted 374 389 390 391 407 P DG P 105 distorted distorted 396 408 409 410 429 P DG P 106 distorted distorted 415 430 431 432 451 P DA P 107 distorted distorted 437 452 453 454 472 P DC P 108 distorted distorted 459 473 474 475 491 P DT P 109 distorted distorted 480 492 493 494 511 P DG P 110 distorted distorted 499 512 513 514 533 P DC P 111 distorted distorted 519 534 535 536 552 P DT P 112 distorted distorted 541 553 554 555 572 P DT P 113 distorted distorted 560 573 574 575 592 P DA P 114 distorted distorted 580 593 594 595 628 P DOC P 115 distorted distorted 600 629 630 627 ---------------------------------------------------------------------------------