ID code: '1WTP' 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' DG C 101 beta 4 9 7 30 C1' DC C 102 beta 26 31 29 49 C1' DG C 103 beta 45 50 48 71 C1' DA C 104 beta 67 72 70 91 C1' BRU C 105 beta 96 82 92 112 C1' DC C 106 beta 108 113 111 131 C1' DG C 107 beta 127 132 130 153 C1' DC C 108 beta 149 154 152 170 C1' DG D 109 beta 166 171 169 192 C1' DC D 110 beta 188 193 191 211 C1' DG D 111 beta 207 212 210 233 C1' DA D 112 beta 229 234 232 253 C1' BRU D 113 beta 258 244 254 274 C1' DC D 114 beta 270 275 273 293 C1' DG D 115 beta 289 294 292 315 C1' DC D 116 beta 311 316 314 332 C1' DG E 101 beta 328 333 331 354 C1' DC E 102 beta 350 355 353 373 C1' DG E 103 beta 369 374 372 395 C1' DA E 104 beta 391 396 394 415 C1' BRU E 105 beta 420 406 416 436 C1' DC E 106 beta 432 437 435 455 C1' DG E 107 beta 451 456 454 477 C1' DC E 108 beta 473 478 476 494 C1' DG F 109 beta 490 495 493 516 C1' DC F 110 beta 512 517 515 535 C1' DG F 111 beta 531 536 534 557 C1' DA F 112 beta 553 558 556 577 C1' BRU F 113 beta 582 568 578 598 C1' DC F 114 beta 594 599 597 617 C1' DG F 115 beta 613 618 616 639 C1' DC F 116 beta 635 640 638 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DG C 101 8 5 29 C2' DC C 102 30 27 48 C2' DG C 103 49 46 70 C2' DA C 104 71 68 92 C2' BRU C 105 91 93 111 C2' DC C 106 112 109 130 C2' DG C 107 131 128 152 C2' DC C 108 153 150 169 C2' DG D 109 170 167 191 C2' DC D 110 192 189 210 C2' DG D 111 211 208 232 C2' DA D 112 233 230 254 C2' BRU D 113 253 255 273 C2' DC D 114 274 271 292 C2' DG D 115 293 290 314 C2' DC D 116 315 312 331 C2' DG E 101 332 329 353 C2' DC E 102 354 351 372 C2' DG E 103 373 370 394 C2' DA E 104 395 392 416 C2' BRU E 105 415 417 435 C2' DC E 106 436 433 454 C2' DG E 107 455 452 476 C2' DC E 108 477 474 493 C2' DG F 109 494 491 515 C2' DC F 110 516 513 534 C2' DG F 111 535 532 556 C2' DA F 112 557 554 578 C2' BRU F 113 577 579 597 C2' DC F 114 598 595 616 C2' DG F 115 617 614 638 C2' DC F 116 639 636 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DG C 101 OK 3 6 7 27 C3' DC C 102 OK 25 28 29 46 C3' DG C 103 OK 44 47 48 68 C3' DA C 104 OK 66 69 70 93 C3' BRU C 105 OK 94 95 92 109 C3' DC C 106 OK 107 110 111 128 C3' DG C 107 OK 126 129 130 150 C3' DC C 108 OK 148 151 152 167 C3' DG D 109 OK 165 168 169 189 C3' DC D 110 OK 187 190 191 208 C3' DG D 111 OK 206 209 210 230 C3' DA D 112 OK 228 231 232 255 C3' BRU D 113 OK 256 257 254 271 C3' DC D 114 OK 269 272 273 290 C3' DG D 115 OK 288 291 292 312 C3' DC D 116 OK 310 313 314 329 C3' DG E 101 OK 327 330 331 351 C3' DC E 102 OK 349 352 353 370 C3' DG E 103 OK 368 371 372 392 C3' DA E 104 OK 390 393 394 417 C3' BRU E 105 OK 418 419 416 433 C3' DC E 106 OK 431 434 435 452 C3' DG E 107 OK 450 453 454 474 C3' DC E 108 OK 472 475 476 491 C3' DG F 109 OK 489 492 493 513 C3' DC F 110 OK 511 514 515 532 C3' DG F 111 OK 530 533 534 554 C3' DA F 112 OK 552 555 556 579 C3' BRU F 113 OK 580 581 578 595 C3' DC F 114 OK 593 596 597 614 C3' DG F 115 OK 612 615 616 636 C3' DC F 116 OK 634 637 638 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DG C 101 OK 5 2 4 25 C4' DC C 102 OK 27 24 26 44 C4' DG C 103 OK 46 43 45 66 C4' DA C 104 OK 68 65 67 94 C4' BRU C 105 OK 93 97 96 107 C4' DC C 106 OK 109 106 108 126 C4' DG C 107 OK 128 125 127 148 C4' DC C 108 OK 150 147 149 165 C4' DG D 109 OK 167 164 166 187 C4' DC D 110 OK 189 186 188 206 C4' DG D 111 OK 208 205 207 228 C4' DA D 112 OK 230 227 229 256 C4' BRU D 113 OK 255 259 258 269 C4' DC D 114 OK 271 268 270 288 C4' DG D 115 OK 290 287 289 310 C4' DC D 116 OK 312 309 311 327 C4' DG E 101 OK 329 326 328 349 C4' DC E 102 OK 351 348 350 368 C4' DG E 103 OK 370 367 369 390 C4' DA E 104 OK 392 389 391 418 C4' BRU E 105 OK 417 421 420 431 C4' DC E 106 OK 433 430 432 450 C4' DG E 107 OK 452 449 451 472 C4' DC E 108 OK 474 471 473 489 C4' DG F 109 OK 491 488 490 511 C4' DC F 110 OK 513 510 512 530 C4' DG F 111 OK 532 529 531 552 C4' DA F 112 OK 554 551 553 580 C4' BRU F 113 OK 579 583 582 593 C4' DC F 114 OK 595 592 594 612 C4' DG F 115 OK 614 611 613 634 C4' DC F 116 OK 636 633 635 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DG C 101 1 3 24 C5' DC C 102 23 25 43 C5' DG C 103 42 44 65 C5' DA C 104 64 66 97 C5' BRU C 105 98 94 106 C5' DC C 106 105 107 125 C5' DG C 107 124 126 147 C5' DC C 108 146 148 164 C5' DG D 109 163 165 186 C5' DC D 110 185 187 205 C5' DG D 111 204 206 227 C5' DA D 112 226 228 259 C5' BRU D 113 260 256 268 C5' DC D 114 267 269 287 C5' DG D 115 286 288 309 C5' DC D 116 308 310 326 C5' DG E 101 325 327 348 C5' DC E 102 347 349 367 C5' DG E 103 366 368 389 C5' DA E 104 388 390 421 C5' BRU E 105 422 418 430 C5' DC E 106 429 431 449 C5' DG E 107 448 450 471 C5' DC E 108 470 472 488 C5' DG F 109 487 489 510 C5' DC F 110 509 511 529 C5' DG F 111 528 530 551 C5' DA F 112 550 552 583 C5' BRU F 113 584 580 592 C5' DC F 114 591 593 611 C5' DG F 115 610 612 633 C5' DC F 116 632 634 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P DC C 102 distorted distorted 6 21 22 23 39 P DG C 103 distorted distorted 28 40 41 42 61 P DA C 104 distorted distorted 47 62 63 64 99 P BRU C 105 distorted distorted 69 100 101 98 102 P DC C 106 distorted distorted 95 103 104 105 121 P DG C 107 distorted distorted 110 122 123 124 143 P DC C 108 distorted distorted 129 144 145 146 182 P DC D 110 distorted distorted 168 183 184 185 201 P DG D 111 distorted distorted 190 202 203 204 223 P DA D 112 distorted distorted 209 224 225 226 261 P BRU D 113 distorted distorted 231 262 263 260 264 P DC D 114 distorted distorted 257 265 266 267 283 P DG D 115 distorted distorted 272 284 285 286 305 P DC D 116 distorted distorted 291 306 307 308 344 P DC E 102 distorted distorted 330 345 346 347 363 P DG E 103 distorted distorted 352 364 365 366 385 P DA E 104 distorted distorted 371 386 387 388 423 P BRU E 105 distorted distorted 393 424 425 422 426 P DC E 106 distorted distorted 419 427 428 429 445 P DG E 107 distorted distorted 434 446 447 448 467 P DC E 108 distorted distorted 453 468 469 470 506 P DC F 110 distorted distorted 492 507 508 509 525 P DG F 111 distorted distorted 514 526 527 528 547 P DA F 112 distorted distorted 533 548 549 550 585 P BRU F 113 distorted distorted 555 586 587 584 588 P DC F 114 distorted distorted 581 589 590 591 607 P DG F 115 distorted distorted 596 608 609 610 629 P DC F 116 distorted distorted 615 630 631 632 ---------------------------------------------------------------------------------