ID code: '1ZME' 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' --------------------------------------------------------------------------------- 29 C1' C A 2 beta 25 30 28 48 C1' G A 3 beta 44 49 47 70 C1' G A 4 beta 66 71 69 92 C1' G A 5 beta 88 93 91 114 C1' A A 6 beta 110 115 113 135 C1' A A 7 beta 131 136 134 156 C1' G A 8 beta 152 157 155 178 C1' C A 9 beta 174 179 177 197 C1' C A 10 beta 193 198 196 216 C1' A A 11 beta 212 217 215 237 C1' A A 12 beta 233 238 236 258 C1' C A 13 beta 254 259 257 277 C1' T A 14 beta 273 278 276 297 C1' C A 15 beta 293 298 296 316 C1' C A 16 beta 312 317 315 335 C1' G A 17 beta 331 336 334 376 C1' C B 2 beta 372 377 375 395 C1' G B 3 beta 391 396 394 417 C1' G B 4 beta 413 418 416 439 C1' A B 5 beta 435 440 438 460 C1' G B 6 beta 456 461 459 481 C1' 5IU B 7 beta 486 472 482 502 C1' T B 8 beta 498 503 501 522 C1' G B 9 beta 518 523 521 544 C1' G B 10 beta 540 545 543 566 C1' C B 11 beta 562 567 565 585 C1' T B 12 beta 581 586 584 604 C1' 5IU B 13 beta 609 595 605 625 C1' C B 14 beta 621 626 624 644 C1' C B 15 beta 640 645 643 663 C1' C B 16 beta 659 664 662 682 C1' G B 17 beta 678 683 681 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 28 C2' C A 2 29 26 47 C2' G A 3 48 45 69 C2' G A 4 70 67 91 C2' G A 5 92 89 113 C2' A A 6 114 111 134 C2' A A 7 135 132 155 C2' G A 8 156 153 177 C2' C A 9 178 175 196 C2' C A 10 197 194 215 C2' A A 11 216 213 236 C2' A A 12 237 234 257 C2' C A 13 258 255 276 C2' T A 14 277 274 296 C2' C A 15 297 294 315 C2' C A 16 316 313 334 C2' G A 17 335 332 375 C2' C B 2 376 373 394 C2' G B 3 395 392 416 C2' G B 4 417 414 438 C2' A B 5 439 436 459 C2' G B 6 460 457 482 C2' 5IU B 7 481 483 501 C2' T B 8 502 499 521 C2' G B 9 522 519 543 C2' G B 10 544 541 565 C2' C B 11 566 563 584 C2' T B 12 585 582 605 C2' 5IU B 13 604 606 624 C2' C B 14 625 622 643 C2' C B 15 644 641 662 C2' C B 16 663 660 681 C2' G B 17 682 679 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 26 C3' C A 2 OK 24 27 28 45 C3' G A 3 OK 43 46 47 67 C3' G A 4 OK 65 68 69 89 C3' G A 5 OK 87 90 91 111 C3' A A 6 OK 109 112 113 132 C3' A A 7 OK 130 133 134 153 C3' G A 8 OK 151 154 155 175 C3' C A 9 OK 173 176 177 194 C3' C A 10 OK 192 195 196 213 C3' A A 11 OK 211 214 215 234 C3' A A 12 OK 232 235 236 255 C3' C A 13 OK 253 256 257 274 C3' T A 14 OK 272 275 276 294 C3' C A 15 OK 292 295 296 313 C3' C A 16 OK 311 314 315 332 C3' G A 17 OK 330 333 334 373 C3' C B 2 OK 371 374 375 392 C3' G B 3 OK 390 393 394 414 C3' G B 4 OK 412 415 416 436 C3' A B 5 OK 434 437 438 457 C3' G B 6 OK 455 458 459 483 C3' 5IU B 7 OK 484 485 482 499 C3' T B 8 OK 497 500 501 519 C3' G B 9 OK 517 520 521 541 C3' G B 10 OK 539 542 543 563 C3' C B 11 OK 561 564 565 582 C3' T B 12 OK 580 583 584 606 C3' 5IU B 13 OK 607 608 605 622 C3' C B 14 OK 620 623 624 641 C3' C B 15 OK 639 642 643 660 C3' C B 16 OK 658 661 662 679 C3' G B 17 OK 677 680 681 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 24 C4' C A 2 OK 26 23 25 43 C4' G A 3 OK 45 42 44 65 C4' G A 4 OK 67 64 66 87 C4' G A 5 OK 89 86 88 109 C4' A A 6 OK 111 108 110 130 C4' A A 7 OK 132 129 131 151 C4' G A 8 OK 153 150 152 173 C4' C A 9 OK 175 172 174 192 C4' C A 10 OK 194 191 193 211 C4' A A 11 OK 213 210 212 232 C4' A A 12 OK 234 231 233 253 C4' C A 13 OK 255 252 254 272 C4' T A 14 OK 274 271 273 292 C4' C A 15 OK 294 291 293 311 C4' C A 16 OK 313 310 312 330 C4' G A 17 OK 332 329 331 371 C4' C B 2 OK 373 370 372 390 C4' G B 3 OK 392 389 391 412 C4' G B 4 OK 414 411 413 434 C4' A B 5 OK 436 433 435 455 C4' G B 6 OK 457 454 456 484 C4' 5IU B 7 OK 483 487 486 497 C4' T B 8 OK 499 496 498 517 C4' G B 9 OK 519 516 518 539 C4' G B 10 OK 541 538 540 561 C4' C B 11 OK 563 560 562 580 C4' T B 12 OK 582 579 581 607 C4' 5IU B 13 OK 606 610 609 620 C4' C B 14 OK 622 619 621 639 C4' C B 15 OK 641 638 640 658 C4' C B 16 OK 660 657 659 677 C4' G B 17 OK 679 676 678 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 23 C5' C A 2 22 24 42 C5' G A 3 41 43 64 C5' G A 4 63 65 86 C5' G A 5 85 87 108 C5' A A 6 107 109 129 C5' A A 7 128 130 150 C5' G A 8 149 151 172 C5' C A 9 171 173 191 C5' C A 10 190 192 210 C5' A A 11 209 211 231 C5' A A 12 230 232 252 C5' C A 13 251 253 271 C5' T A 14 270 272 291 C5' C A 15 290 292 310 C5' C A 16 309 311 329 C5' G A 17 328 330 370 C5' C B 2 369 371 389 C5' G B 3 388 390 411 C5' G B 4 410 412 433 C5' A B 5 432 434 454 C5' G B 6 453 455 487 C5' 5IU B 7 488 484 496 C5' T B 8 495 497 516 C5' G B 9 515 517 538 C5' G B 10 537 539 560 C5' C B 11 559 561 579 C5' T B 12 578 580 610 C5' 5IU B 13 611 607 619 C5' C B 14 618 620 638 C5' C B 15 637 639 657 C5' C B 16 656 658 676 C5' G B 17 675 677 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 38 P G A 3 distorted distorted 27 39 40 41 60 P G A 4 distorted distorted 46 61 62 63 82 P G A 5 distorted distorted 68 83 84 85 104 P A A 6 distorted distorted 90 105 106 107 125 P A A 7 distorted distorted 112 126 127 128 146 P G A 8 distorted distorted 133 147 148 149 168 P C A 9 distorted distorted 154 169 170 171 187 P C A 10 distorted distorted 176 188 189 190 206 P A A 11 distorted distorted 195 207 208 209 227 P A A 12 distorted distorted 214 228 229 230 248 P C A 13 distorted distorted 235 249 250 251 267 P T A 14 distorted distorted 256 268 269 270 287 P C A 15 distorted distorted 275 288 289 290 306 P C A 16 distorted distorted 295 307 308 309 325 P G A 17 distorted distorted 314 326 327 328 385 P G B 3 distorted distorted 374 386 387 388 407 P G B 4 distorted distorted 393 408 409 410 429 P A B 5 distorted distorted 415 430 431 432 450 P G B 6 distorted distorted 437 451 452 453 489 P 5IU B 7 distorted distorted 458 490 491 488 492 P T B 8 distorted distorted 485 493 494 495 512 P G B 9 distorted distorted 500 513 514 515 534 P G B 10 distorted distorted 520 535 536 537 556 P C B 11 distorted distorted 542 557 558 559 575 P T B 12 distorted distorted 564 576 577 578 612 P 5IU B 13 distorted distorted 583 613 614 611 615 P C B 14 distorted distorted 608 616 617 618 634 P C B 15 distorted distorted 623 635 636 637 653 P C B 16 distorted distorted 642 654 655 656 672 P G B 17 distorted distorted 661 673 674 675 ---------------------------------------------------------------------------------