ID code: '1MM8' 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' G E 101 beta 4 9 7 30 C1' A E 102 beta 26 31 29 51 C1' G E 103 beta 47 52 50 73 C1' A E 104 beta 69 74 72 94 C1' T E 105 beta 90 95 93 114 C1' G E 106 beta 110 115 113 136 C1' T E 107 beta 132 137 135 156 C1' G E 108 beta 152 157 155 178 C1' T E 109 beta 174 179 177 198 C1' A E 110 beta 194 199 197 219 C1' T E 111 beta 215 220 218 239 C1' A E 112 beta 235 240 238 260 C1' A E 113 beta 256 261 259 281 C1' G E 114 beta 277 282 280 303 C1' A E 115 beta 299 304 302 324 C1' G E 116 beta 320 325 323 346 C1' A E 117 beta 342 347 345 367 C1' C E 118 beta 363 368 366 387 C1' G F 203 beta 383 388 386 409 C1' T F 204 beta 405 410 408 429 C1' C F 205 beta 425 430 428 448 C1' T F 206 beta 444 449 447 468 C1' C F 207 beta 464 469 467 487 C1' T F 208 beta 483 488 486 507 C1' T F 209 beta 503 508 506 527 C1' A F 210 beta 523 528 526 548 C1' T F 211 beta 544 549 547 568 C1' A F 212 beta 564 569 567 589 C1' C F 213 beta 585 590 588 608 C1' A F 214 beta 604 609 607 629 C1' C F 215 beta 625 630 628 648 C1' A F 216 beta 644 649 647 669 C1' T F 217 beta 665 670 668 689 C1' C F 218 beta 685 690 688 708 C1' T F 219 beta 704 709 707 728 C1' C F 220 beta 724 729 727 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G E 101 8 5 29 C2' A E 102 30 27 50 C2' G E 103 51 48 72 C2' A E 104 73 70 93 C2' T E 105 94 91 113 C2' G E 106 114 111 135 C2' T E 107 136 133 155 C2' G E 108 156 153 177 C2' T E 109 178 175 197 C2' A E 110 198 195 218 C2' T E 111 219 216 238 C2' A E 112 239 236 259 C2' A E 113 260 257 280 C2' G E 114 281 278 302 C2' A E 115 303 300 323 C2' G E 116 324 321 345 C2' A E 117 346 343 366 C2' C E 118 367 364 386 C2' G F 203 387 384 408 C2' T F 204 409 406 428 C2' C F 205 429 426 447 C2' T F 206 448 445 467 C2' C F 207 468 465 486 C2' T F 208 487 484 506 C2' T F 209 507 504 526 C2' A F 210 527 524 547 C2' T F 211 548 545 567 C2' A F 212 568 565 588 C2' C F 213 589 586 607 C2' A F 214 608 605 628 C2' C F 215 629 626 647 C2' A F 216 648 645 668 C2' T F 217 669 666 688 C2' C F 218 689 686 707 C2' T F 219 708 705 727 C2' C F 220 728 725 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G E 101 OK 3 6 7 27 C3' A E 102 OK 25 28 29 48 C3' G E 103 OK 46 49 50 70 C3' A E 104 OK 68 71 72 91 C3' T E 105 OK 89 92 93 111 C3' G E 106 OK 109 112 113 133 C3' T E 107 OK 131 134 135 153 C3' G E 108 OK 151 154 155 175 C3' T E 109 OK 173 176 177 195 C3' A E 110 OK 193 196 197 216 C3' T E 111 OK 214 217 218 236 C3' A E 112 OK 234 237 238 257 C3' A E 113 OK 255 258 259 278 C3' G E 114 OK 276 279 280 300 C3' A E 115 OK 298 301 302 321 C3' G E 116 OK 319 322 323 343 C3' A E 117 OK 341 344 345 364 C3' C E 118 OK 362 365 366 384 C3' G F 203 OK 382 385 386 406 C3' T F 204 OK 404 407 408 426 C3' C F 205 OK 424 427 428 445 C3' T F 206 OK 443 446 447 465 C3' C F 207 OK 463 466 467 484 C3' T F 208 OK 482 485 486 504 C3' T F 209 OK 502 505 506 524 C3' A F 210 OK 522 525 526 545 C3' T F 211 OK 543 546 547 565 C3' A F 212 OK 563 566 567 586 C3' C F 213 OK 584 587 588 605 C3' A F 214 OK 603 606 607 626 C3' C F 215 OK 624 627 628 645 C3' A F 216 OK 643 646 647 666 C3' T F 217 OK 664 667 668 686 C3' C F 218 OK 684 687 688 705 C3' T F 219 OK 703 706 707 725 C3' C F 220 OK 723 726 727 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G E 101 OK 5 2 4 25 C4' A E 102 OK 27 24 26 46 C4' G E 103 OK 48 45 47 68 C4' A E 104 OK 70 67 69 89 C4' T E 105 OK 91 88 90 109 C4' G E 106 OK 111 108 110 131 C4' T E 107 OK 133 130 132 151 C4' G E 108 OK 153 150 152 173 C4' T E 109 OK 175 172 174 193 C4' A E 110 OK 195 192 194 214 C4' T E 111 OK 216 213 215 234 C4' A E 112 OK 236 233 235 255 C4' A E 113 OK 257 254 256 276 C4' G E 114 OK 278 275 277 298 C4' A E 115 OK 300 297 299 319 C4' G E 116 OK 321 318 320 341 C4' A E 117 OK 343 340 342 362 C4' C E 118 OK 364 361 363 382 C4' G F 203 OK 384 381 383 404 C4' T F 204 OK 406 403 405 424 C4' C F 205 OK 426 423 425 443 C4' T F 206 OK 445 442 444 463 C4' C F 207 OK 465 462 464 482 C4' T F 208 OK 484 481 483 502 C4' T F 209 OK 504 501 503 522 C4' A F 210 OK 524 521 523 543 C4' T F 211 OK 545 542 544 563 C4' A F 212 OK 565 562 564 584 C4' C F 213 OK 586 583 585 603 C4' A F 214 OK 605 602 604 624 C4' C F 215 OK 626 623 625 643 C4' A F 216 OK 645 642 644 664 C4' T F 217 OK 666 663 665 684 C4' C F 218 OK 686 683 685 703 C4' T F 219 OK 705 702 704 723 C4' C F 220 OK 725 722 724 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G E 101 1 3 24 C5' A E 102 23 25 45 C5' G E 103 44 46 67 C5' A E 104 66 68 88 C5' T E 105 87 89 108 C5' G E 106 107 109 130 C5' T E 107 129 131 150 C5' G E 108 149 151 172 C5' T E 109 171 173 192 C5' A E 110 191 193 213 C5' T E 111 212 214 233 C5' A E 112 232 234 254 C5' A E 113 253 255 275 C5' G E 114 274 276 297 C5' A E 115 296 298 318 C5' G E 116 317 319 340 C5' A E 117 339 341 361 C5' C E 118 360 362 381 C5' G F 203 380 382 403 C5' T F 204 402 404 423 C5' C F 205 422 424 442 C5' T F 206 441 443 462 C5' C F 207 461 463 481 C5' T F 208 480 482 501 C5' T F 209 500 502 521 C5' A F 210 520 522 542 C5' T F 211 541 543 562 C5' A F 212 561 563 583 C5' C F 213 582 584 602 C5' A F 214 601 603 623 C5' C F 215 622 624 642 C5' A F 216 641 643 663 C5' T F 217 662 664 683 C5' C F 218 682 684 702 C5' T F 219 701 703 722 C5' C F 220 721 723 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P A E 102 distorted distorted 6 21 22 23 41 P G E 103 distorted distorted 28 42 43 44 63 P A E 104 distorted distorted 49 64 65 66 84 P T E 105 distorted distorted 71 85 86 87 104 P G E 106 distorted distorted 92 105 106 107 126 P T E 107 distorted distorted 112 127 128 129 146 P G E 108 distorted distorted 134 147 148 149 168 P T E 109 distorted distorted 154 169 170 171 188 P A E 110 distorted distorted 176 189 190 191 209 P T E 111 distorted distorted 196 210 211 212 229 P A E 112 distorted distorted 217 230 231 232 250 P A E 113 distorted distorted 237 251 252 253 271 P G E 114 distorted distorted 258 272 273 274 293 P A E 115 distorted distorted 279 294 295 296 314 P G E 116 distorted distorted 301 315 316 317 336 P A E 117 distorted distorted 322 337 338 339 357 P C E 118 distorted distorted 344 358 359 360 377 P G F 203 distorted distorted 378 379 380 399 P T F 204 distorted distorted 385 400 401 402 419 P C F 205 distorted distorted 407 420 421 422 438 P T F 206 distorted distorted 427 439 440 441 458 P C F 207 distorted distorted 446 459 460 461 477 P T F 208 distorted distorted 466 478 479 480 497 P T F 209 distorted distorted 485 498 499 500 517 P A F 210 distorted distorted 505 518 519 520 538 P T F 211 distorted distorted 525 539 540 541 558 P A F 212 distorted distorted 546 559 560 561 579 P C F 213 distorted distorted 566 580 581 582 598 P A F 214 distorted distorted 587 599 600 601 619 P C F 215 distorted distorted 606 620 621 622 638 P A F 216 distorted distorted 627 639 640 641 659 P T F 217 distorted distorted 646 660 661 662 679 P C F 218 distorted distorted 667 680 681 682 698 P T F 219 distorted distorted 687 699 700 701 718 P C F 220 distorted distorted 706 719 720 721 ---------------------------------------------------------------------------------