ID code: '1J5O' 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' T T 802 beta 7 12 10 31 C1' G T 803 beta 27 32 30 53 C1' G T 804 beta 49 54 52 75 C1' C T 805 beta 71 76 74 94 C1' G T 806 beta 90 95 93 116 C1' C T 807 beta 112 117 115 135 C1' C T 808 beta 131 136 134 154 C1' C T 809 beta 150 155 153 173 C1' G T 810 beta 169 174 172 195 C1' A T 811 beta 191 196 194 216 C1' A T 812 beta 212 217 215 237 C1' C T 813 beta 233 238 236 256 C1' A T 814 beta 252 257 255 277 C1' G T 815 beta 273 278 276 299 C1' G T 816 beta 295 300 298 321 C1' G T 817 beta 317 322 320 343 C1' A T 818 beta 339 344 342 364 C1' C T 819 beta 360 365 363 381 C1' G P 821 beta 377 382 380 403 C1' T P 822 beta 399 404 402 423 C1' C P 823 beta 419 424 422 442 C1' C P 824 beta 438 443 441 461 C1' C P 825 beta 457 462 460 480 C1' T P 826 beta 476 481 479 500 C1' G P 827 beta 496 501 499 522 C1' T P 828 beta 518 523 521 542 C1' T P 829 beta 538 543 541 562 C1' C P 830 beta 558 563 561 581 C1' G P 831 beta 577 582 580 603 C1' G P 832 beta 599 604 602 625 C1' G P 833 beta 621 626 624 647 C1' C P 834 beta 643 648 646 666 C1' G P 835 beta 662 667 665 688 C1' C P 836 beta 684 689 687 707 C1' C P 837 beta 703 708 706 726 C1' A P 838 beta 722 727 725 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' T T 802 11 8 30 C2' G T 803 31 28 52 C2' G T 804 53 50 74 C2' C T 805 75 72 93 C2' G T 806 94 91 115 C2' C T 807 116 113 134 C2' C T 808 135 132 153 C2' C T 809 154 151 172 C2' G T 810 173 170 194 C2' A T 811 195 192 215 C2' A T 812 216 213 236 C2' C T 813 237 234 255 C2' A T 814 256 253 276 C2' G T 815 277 274 298 C2' G T 816 299 296 320 C2' G T 817 321 318 342 C2' A T 818 343 340 363 C2' C T 819 364 361 380 C2' G P 821 381 378 402 C2' T P 822 403 400 422 C2' C P 823 423 420 441 C2' C P 824 442 439 460 C2' C P 825 461 458 479 C2' T P 826 480 477 499 C2' G P 827 500 497 521 C2' T P 828 522 519 541 C2' T P 829 542 539 561 C2' C P 830 562 559 580 C2' G P 831 581 578 602 C2' G P 832 603 600 624 C2' G P 833 625 622 646 C2' C P 834 647 644 665 C2' G P 835 666 663 687 C2' C P 836 688 685 706 C2' C P 837 707 704 725 C2' A P 838 726 723 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' T T 802 OK 6 9 10 28 C3' G T 803 OK 26 29 30 50 C3' G T 804 OK 48 51 52 72 C3' C T 805 OK 70 73 74 91 C3' G T 806 OK 89 92 93 113 C3' C T 807 OK 111 114 115 132 C3' C T 808 OK 130 133 134 151 C3' C T 809 OK 149 152 153 170 C3' G T 810 OK 168 171 172 192 C3' A T 811 OK 190 193 194 213 C3' A T 812 OK 211 214 215 234 C3' C T 813 OK 232 235 236 253 C3' A T 814 OK 251 254 255 274 C3' G T 815 OK 272 275 276 296 C3' G T 816 OK 294 297 298 318 C3' G T 817 OK 316 319 320 340 C3' A T 818 OK 338 341 342 361 C3' C T 819 OK 359 362 363 378 C3' G P 821 OK 376 379 380 400 C3' T P 822 OK 398 401 402 420 C3' C P 823 OK 418 421 422 439 C3' C P 824 OK 437 440 441 458 C3' C P 825 OK 456 459 460 477 C3' T P 826 OK 475 478 479 497 C3' G P 827 OK 495 498 499 519 C3' T P 828 OK 517 520 521 539 C3' T P 829 OK 537 540 541 559 C3' C P 830 OK 557 560 561 578 C3' G P 831 OK 576 579 580 600 C3' G P 832 OK 598 601 602 622 C3' G P 833 OK 620 623 624 644 C3' C P 834 OK 642 645 646 663 C3' G P 835 OK 661 664 665 685 C3' C P 836 OK 683 686 687 704 C3' C P 837 OK 702 705 706 723 C3' A P 838 OK 721 724 725 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' T T 802 OK 8 5 7 26 C4' G T 803 OK 28 25 27 48 C4' G T 804 OK 50 47 49 70 C4' C T 805 OK 72 69 71 89 C4' G T 806 OK 91 88 90 111 C4' C T 807 OK 113 110 112 130 C4' C T 808 OK 132 129 131 149 C4' C T 809 OK 151 148 150 168 C4' G T 810 OK 170 167 169 190 C4' A T 811 OK 192 189 191 211 C4' A T 812 OK 213 210 212 232 C4' C T 813 OK 234 231 233 251 C4' A T 814 OK 253 250 252 272 C4' G T 815 OK 274 271 273 294 C4' G T 816 OK 296 293 295 316 C4' G T 817 OK 318 315 317 338 C4' A T 818 OK 340 337 339 359 C4' C T 819 OK 361 358 360 376 C4' G P 821 OK 378 375 377 398 C4' T P 822 OK 400 397 399 418 C4' C P 823 OK 420 417 419 437 C4' C P 824 OK 439 436 438 456 C4' C P 825 OK 458 455 457 475 C4' T P 826 OK 477 474 476 495 C4' G P 827 OK 497 494 496 517 C4' T P 828 OK 519 516 518 537 C4' T P 829 OK 539 536 538 557 C4' C P 830 OK 559 556 558 576 C4' G P 831 OK 578 575 577 598 C4' G P 832 OK 600 597 599 620 C4' G P 833 OK 622 619 621 642 C4' C P 834 OK 644 641 643 661 C4' G P 835 OK 663 660 662 683 C4' C P 836 OK 685 682 684 702 C4' C P 837 OK 704 701 703 721 C4' A P 838 OK 723 720 722 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' T T 802 4 6 25 C5' G T 803 24 26 47 C5' G T 804 46 48 69 C5' C T 805 68 70 88 C5' G T 806 87 89 110 C5' C T 807 109 111 129 C5' C T 808 128 130 148 C5' C T 809 147 149 167 C5' G T 810 166 168 189 C5' A T 811 188 190 210 C5' A T 812 209 211 231 C5' C T 813 230 232 250 C5' A T 814 249 251 271 C5' G T 815 270 272 293 C5' G T 816 292 294 315 C5' G T 817 314 316 337 C5' A T 818 336 338 358 C5' C T 819 357 359 375 C5' G P 821 374 376 397 C5' T P 822 396 398 417 C5' C P 823 416 418 436 C5' C P 824 435 437 455 C5' C P 825 454 456 474 C5' T P 826 473 475 494 C5' G P 827 493 495 516 C5' T P 828 515 517 536 C5' T P 829 535 537 556 C5' C P 830 555 557 575 C5' G P 831 574 576 597 C5' G P 832 596 598 619 C5' G P 833 618 620 641 C5' C P 834 640 642 660 C5' G P 835 659 661 682 C5' C P 836 681 683 701 C5' C P 837 700 702 720 C5' A P 838 719 721 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P T T 802 distorted distorted 2 3 4 21 P G T 803 distorted distorted 9 22 23 24 43 P G T 804 distorted distorted 29 44 45 46 65 P C T 805 distorted distorted 51 66 67 68 84 P G T 806 distorted distorted 73 85 86 87 106 P C T 807 distorted distorted 92 107 108 109 125 P C T 808 distorted distorted 114 126 127 128 144 P C T 809 distorted distorted 133 145 146 147 163 P G T 810 distorted distorted 152 164 165 166 185 P A T 811 distorted distorted 171 186 187 188 206 P A T 812 distorted distorted 193 207 208 209 227 P C T 813 distorted distorted 214 228 229 230 246 P A T 814 distorted distorted 235 247 248 249 267 P G T 815 distorted distorted 254 268 269 270 289 P G T 816 distorted distorted 275 290 291 292 311 P G T 817 distorted distorted 297 312 313 314 333 P A T 818 distorted distorted 319 334 335 336 354 P C T 819 distorted distorted 341 355 356 357 393 P T P 822 distorted distorted 379 394 395 396 413 P C P 823 distorted distorted 401 414 415 416 432 P C P 824 distorted distorted 421 433 434 435 451 P C P 825 distorted distorted 440 452 453 454 470 P T P 826 distorted distorted 459 471 472 473 490 P G P 827 distorted distorted 478 491 492 493 512 P T P 828 distorted distorted 498 513 514 515 532 P T P 829 distorted distorted 520 533 534 535 552 P C P 830 distorted distorted 540 553 554 555 571 P G P 831 distorted distorted 560 572 573 574 593 P G P 832 distorted distorted 579 594 595 596 615 P G P 833 distorted distorted 601 616 617 618 637 P C P 834 distorted distorted 623 638 639 640 656 P G P 835 distorted distorted 645 657 658 659 678 P C P 836 distorted distorted 664 679 680 681 697 P C P 837 distorted distorted 686 698 699 700 716 P A P 838 distorted distorted 705 717 718 719 ---------------------------------------------------------------------------------