ID code: '1EA4' 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' --------------------------------------------------------------------------------- 11 C1' A W 203 beta 7 12 10 32 C1' C W 204 beta 28 33 31 51 C1' C W 205 beta 47 52 50 70 C1' G W 206 beta 66 71 69 92 C1' T W 207 beta 88 93 91 112 C1' G W 208 beta 108 113 111 134 C1' C W 209 beta 130 135 133 153 C1' A W 210 beta 149 154 152 174 C1' C W 211 beta 170 175 173 193 C1' T W 212 beta 189 194 192 213 C1' C W 213 beta 209 214 212 232 C1' A W 214 beta 228 233 231 253 C1' A W 215 beta 249 254 252 274 C1' T W 216 beta 270 275 273 294 C1' G W 217 beta 290 295 293 316 C1' C W 218 beta 312 317 315 335 C1' A W 219 beta 331 336 334 356 C1' A W 220 beta 352 357 355 377 C1' T W 221 beta 373 378 376 397 C1' C W 222 beta 393 398 396 417 C1' G X 202 beta 413 418 416 439 C1' A X 203 beta 435 440 438 460 C1' T X 204 beta 456 461 459 480 C1' T X 205 beta 476 481 479 500 C1' G X 206 beta 496 501 499 522 C1' C X 207 beta 518 523 521 541 C1' A X 208 beta 537 542 540 562 C1' T X 209 beta 558 563 561 582 C1' T X 210 beta 578 583 581 602 C1' G X 211 beta 598 603 601 624 C1' A X 212 beta 620 625 623 645 C1' G X 213 beta 641 646 644 667 C1' T X 214 beta 663 668 666 687 C1' G X 215 beta 683 688 686 709 C1' C X 216 beta 705 710 708 728 C1' A X 217 beta 724 729 727 749 C1' C X 218 beta 745 750 748 768 C1' G X 219 beta 764 769 767 790 C1' G X 220 beta 786 791 789 812 C1' T X 221 beta 808 813 811 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A W 203 11 8 31 C2' C W 204 32 29 50 C2' C W 205 51 48 69 C2' G W 206 70 67 91 C2' T W 207 92 89 111 C2' G W 208 112 109 133 C2' C W 209 134 131 152 C2' A W 210 153 150 173 C2' C W 211 174 171 192 C2' T W 212 193 190 212 C2' C W 213 213 210 231 C2' A W 214 232 229 252 C2' A W 215 253 250 273 C2' T W 216 274 271 293 C2' G W 217 294 291 315 C2' C W 218 316 313 334 C2' A W 219 335 332 355 C2' A W 220 356 353 376 C2' T W 221 377 374 396 C2' C W 222 397 394 416 C2' G X 202 417 414 438 C2' A X 203 439 436 459 C2' T X 204 460 457 479 C2' T X 205 480 477 499 C2' G X 206 500 497 521 C2' C X 207 522 519 540 C2' A X 208 541 538 561 C2' T X 209 562 559 581 C2' T X 210 582 579 601 C2' G X 211 602 599 623 C2' A X 212 624 621 644 C2' G X 213 645 642 666 C2' T X 214 667 664 686 C2' G X 215 687 684 708 C2' C X 216 709 706 727 C2' A X 217 728 725 748 C2' C X 218 749 746 767 C2' G X 219 768 765 789 C2' G X 220 790 787 811 C2' T X 221 812 809 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A W 203 OK 6 9 10 29 C3' C W 204 OK 27 30 31 48 C3' C W 205 OK 46 49 50 67 C3' G W 206 OK 65 68 69 89 C3' T W 207 OK 87 90 91 109 C3' G W 208 OK 107 110 111 131 C3' C W 209 OK 129 132 133 150 C3' A W 210 OK 148 151 152 171 C3' C W 211 OK 169 172 173 190 C3' T W 212 OK 188 191 192 210 C3' C W 213 OK 208 211 212 229 C3' A W 214 OK 227 230 231 250 C3' A W 215 OK 248 251 252 271 C3' T W 216 OK 269 272 273 291 C3' G W 217 OK 289 292 293 313 C3' C W 218 OK 311 314 315 332 C3' A W 219 OK 330 333 334 353 C3' A W 220 OK 351 354 355 374 C3' T W 221 OK 372 375 376 394 C3' C W 222 OK 392 395 396 414 C3' G X 202 OK 412 415 416 436 C3' A X 203 OK 434 437 438 457 C3' T X 204 OK 455 458 459 477 C3' T X 205 OK 475 478 479 497 C3' G X 206 OK 495 498 499 519 C3' C X 207 OK 517 520 521 538 C3' A X 208 OK 536 539 540 559 C3' T X 209 OK 557 560 561 579 C3' T X 210 OK 577 580 581 599 C3' G X 211 OK 597 600 601 621 C3' A X 212 OK 619 622 623 642 C3' G X 213 OK 640 643 644 664 C3' T X 214 OK 662 665 666 684 C3' G X 215 OK 682 685 686 706 C3' C X 216 OK 704 707 708 725 C3' A X 217 OK 723 726 727 746 C3' C X 218 OK 744 747 748 765 C3' G X 219 OK 763 766 767 787 C3' G X 220 OK 785 788 789 809 C3' T X 221 OK 807 810 811 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A W 203 OK 8 5 7 27 C4' C W 204 OK 29 26 28 46 C4' C W 205 OK 48 45 47 65 C4' G W 206 OK 67 64 66 87 C4' T W 207 OK 89 86 88 107 C4' G W 208 OK 109 106 108 129 C4' C W 209 OK 131 128 130 148 C4' A W 210 OK 150 147 149 169 C4' C W 211 OK 171 168 170 188 C4' T W 212 OK 190 187 189 208 C4' C W 213 OK 210 207 209 227 C4' A W 214 OK 229 226 228 248 C4' A W 215 OK 250 247 249 269 C4' T W 216 OK 271 268 270 289 C4' G W 217 OK 291 288 290 311 C4' C W 218 OK 313 310 312 330 C4' A W 219 OK 332 329 331 351 C4' A W 220 OK 353 350 352 372 C4' T W 221 OK 374 371 373 392 C4' C W 222 OK 394 391 393 412 C4' G X 202 OK 414 411 413 434 C4' A X 203 OK 436 433 435 455 C4' T X 204 OK 457 454 456 475 C4' T X 205 OK 477 474 476 495 C4' G X 206 OK 497 494 496 517 C4' C X 207 OK 519 516 518 536 C4' A X 208 OK 538 535 537 557 C4' T X 209 OK 559 556 558 577 C4' T X 210 OK 579 576 578 597 C4' G X 211 OK 599 596 598 619 C4' A X 212 OK 621 618 620 640 C4' G X 213 OK 642 639 641 662 C4' T X 214 OK 664 661 663 682 C4' G X 215 OK 684 681 683 704 C4' C X 216 OK 706 703 705 723 C4' A X 217 OK 725 722 724 744 C4' C X 218 OK 746 743 745 763 C4' G X 219 OK 765 762 764 785 C4' G X 220 OK 787 784 786 807 C4' T X 221 OK 809 806 808 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A W 203 4 6 26 C5' C W 204 25 27 45 C5' C W 205 44 46 64 C5' G W 206 63 65 86 C5' T W 207 85 87 106 C5' G W 208 105 107 128 C5' C W 209 127 129 147 C5' A W 210 146 148 168 C5' C W 211 167 169 187 C5' T W 212 186 188 207 C5' C W 213 206 208 226 C5' A W 214 225 227 247 C5' A W 215 246 248 268 C5' T W 216 267 269 288 C5' G W 217 287 289 310 C5' C W 218 309 311 329 C5' A W 219 328 330 350 C5' A W 220 349 351 371 C5' T W 221 370 372 391 C5' C W 222 390 392 411 C5' G X 202 410 412 433 C5' A X 203 432 434 454 C5' T X 204 453 455 474 C5' T X 205 473 475 494 C5' G X 206 493 495 516 C5' C X 207 515 517 535 C5' A X 208 534 536 556 C5' T X 209 555 557 576 C5' T X 210 575 577 596 C5' G X 211 595 597 618 C5' A X 212 617 619 639 C5' G X 213 638 640 661 C5' T X 214 660 662 681 C5' G X 215 680 682 703 C5' C X 216 702 704 722 C5' A X 217 721 723 743 C5' C X 218 742 744 762 C5' G X 219 761 763 784 C5' G X 220 783 785 806 C5' T X 221 805 807 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A W 203 distorted distorted 2 3 4 22 P C W 204 distorted distorted 9 23 24 25 41 P C W 205 distorted distorted 30 42 43 44 60 P G W 206 distorted distorted 49 61 62 63 82 P T W 207 distorted distorted 68 83 84 85 102 P G W 208 distorted distorted 90 103 104 105 124 P C W 209 distorted distorted 110 125 126 127 143 P A W 210 distorted distorted 132 144 145 146 164 P C W 211 distorted distorted 151 165 166 167 183 P T W 212 distorted distorted 172 184 185 186 203 P C W 213 distorted distorted 191 204 205 206 222 P A W 214 distorted distorted 211 223 224 225 243 P A W 215 distorted distorted 230 244 245 246 264 P T W 216 distorted distorted 251 265 266 267 284 P G W 217 distorted distorted 272 285 286 287 306 P C W 218 distorted distorted 292 307 308 309 325 P A W 219 distorted distorted 314 326 327 328 346 P A W 220 distorted distorted 333 347 348 349 367 P T W 221 distorted distorted 354 368 369 370 387 P C W 222 distorted distorted 375 388 389 390 407 P G X 202 distorted distorted 408 409 410 429 P A X 203 distorted distorted 415 430 431 432 450 P T X 204 distorted distorted 437 451 452 453 470 P T X 205 distorted distorted 458 471 472 473 490 P G X 206 distorted distorted 478 491 492 493 512 P C X 207 distorted distorted 498 513 514 515 531 P A X 208 distorted distorted 520 532 533 534 552 P T X 209 distorted distorted 539 553 554 555 572 P T X 210 distorted distorted 560 573 574 575 592 P G X 211 distorted distorted 580 593 594 595 614 P A X 212 distorted distorted 600 615 616 617 635 P G X 213 distorted distorted 622 636 637 638 657 P T X 214 distorted distorted 643 658 659 660 677 P G X 215 distorted distorted 665 678 679 680 699 P C X 216 distorted distorted 685 700 701 702 718 P A X 217 distorted distorted 707 719 720 721 739 P C X 218 distorted distorted 726 740 741 742 758 P G X 219 distorted distorted 747 759 760 761 780 P G X 220 distorted distorted 766 781 782 783 802 P T X 221 distorted distorted 788 803 804 805 ---------------------------------------------------------------------------------