ID code: '4PMI' 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' --------------------------------------------------------------------------------- 12 C1' G A 36 beta 7 13 10 35 C1' G A 37 beta 30 36 33 58 C1' G A 38 beta 53 59 56 81 C1' A A 39 beta 76 82 79 103 C1' G A 40 beta 98 104 101 126 C1' U A 41 beta 121 127 124 146 C1' A A 42 beta 141 147 144 168 C1' U A 43 beta 163 169 166 188 C1' A A 44 beta 183 189 186 210 C1' U A 45 beta 205 211 208 230 C1' G A 46 beta 225 231 228 253 C1' G A 47 beta 248 254 251 276 C1' G A 48 beta 271 277 274 299 C1' C A 49 beta 294 300 297 319 C1' G A 50 beta 314 320 317 342 C1' C A 51 beta 337 343 340 362 C1' A A 52 beta 357 363 360 384 C1' C A 53 beta 379 385 382 404 C1' U A 54 beta 399 405 402 424 C1' U A 55 beta 419 425 422 444 C1' C A 56 beta 439 445 442 464 C1' G A 57 beta 459 465 462 487 C1' G A 58 beta 482 488 485 510 C1' U A 66 beta 505 511 508 530 C1' G A 67 beta 525 531 528 553 C1' A A 68 548 551 565 C1' C A 69 beta 560 566 563 585 C1' G A 70 beta 580 586 583 608 C1' G A 71 beta 603 609 606 631 C1' U A 72 beta 626 632 629 651 C1' A A 73 beta 646 652 649 673 C1' C A 74 beta 668 674 671 693 C1' A A 75 beta 688 694 691 715 C1' G A 76 beta 710 716 713 738 C1' G A 77 beta 733 739 736 761 C1' C A 78 beta 756 762 759 781 C1' U A 79 beta 776 782 779 801 C1' C A 80 beta 796 802 799 821 C1' C A 81 beta 816 822 819 841 C1' U A 82 beta 836 842 839 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G A 36 OK 12 8 11 33 C2' G A 37 OK 35 31 34 56 C2' G A 38 OK 58 54 57 79 C2' A A 39 OK 81 77 80 101 C2' G A 40 OK 103 99 102 124 C2' U A 41 OK 126 122 125 144 C2' A A 42 OK 146 142 145 166 C2' U A 43 OK 168 164 167 186 C2' A A 44 OK 188 184 187 208 C2' U A 45 OK 210 206 209 228 C2' G A 46 OK 230 226 229 251 C2' G A 47 OK 253 249 252 274 C2' G A 48 OK 276 272 275 297 C2' C A 49 OK 299 295 298 317 C2' G A 50 OK 319 315 318 340 C2' C A 51 OK 342 338 341 360 C2' A A 52 OK 362 358 361 382 C2' C A 53 OK 384 380 383 402 C2' U A 54 OK 404 400 403 422 C2' U A 55 OK 424 420 423 442 C2' C A 56 OK 444 440 443 462 C2' G A 57 OK 464 460 463 485 C2' G A 58 OK 487 483 486 508 C2' U A 66 OK 510 506 509 528 C2' G A 67 OK 530 526 529 551 C2' A A 68 OK 553 549 552 563 C2' C A 69 OK 565 561 564 583 C2' G A 70 OK 585 581 584 606 C2' G A 71 OK 608 604 607 629 C2' U A 72 OK 631 627 630 649 C2' A A 73 OK 651 647 650 671 C2' C A 74 OK 673 669 672 691 C2' A A 75 OK 693 689 692 713 C2' G A 76 OK 715 711 714 736 C2' G A 77 OK 738 734 737 759 C2' C A 78 OK 761 757 760 779 C2' U A 79 OK 781 777 780 799 C2' C A 80 OK 801 797 800 819 C2' C A 81 OK 821 817 820 839 C2' U A 82 OK 841 837 840 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G A 36 OK 6 9 10 31 C3' G A 37 OK 29 32 33 54 C3' G A 38 OK 52 55 56 77 C3' A A 39 OK 75 78 79 99 C3' G A 40 OK 97 100 101 122 C3' U A 41 OK 120 123 124 142 C3' A A 42 OK 140 143 144 164 C3' U A 43 OK 162 165 166 184 C3' A A 44 OK 182 185 186 206 C3' U A 45 OK 204 207 208 226 C3' G A 46 OK 224 227 228 249 C3' G A 47 OK 247 250 251 272 C3' G A 48 OK 270 273 274 295 C3' C A 49 OK 293 296 297 315 C3' G A 50 OK 313 316 317 338 C3' C A 51 OK 336 339 340 358 C3' A A 52 OK 356 359 360 380 C3' C A 53 OK 378 381 382 400 C3' U A 54 OK 398 401 402 420 C3' U A 55 OK 418 421 422 440 C3' C A 56 OK 438 441 442 460 C3' G A 57 OK 458 461 462 483 C3' G A 58 OK 481 484 485 506 C3' U A 66 OK 504 507 508 526 C3' G A 67 OK 524 527 528 549 C3' A A 68 OK 547 550 551 561 C3' C A 69 OK 559 562 563 581 C3' G A 70 OK 579 582 583 604 C3' G A 71 OK 602 605 606 627 C3' U A 72 OK 625 628 629 647 C3' A A 73 OK 645 648 649 669 C3' C A 74 OK 667 670 671 689 C3' A A 75 OK 687 690 691 711 C3' G A 76 OK 709 712 713 734 C3' G A 77 OK 732 735 736 757 C3' C A 78 OK 755 758 759 777 C3' U A 79 OK 775 778 779 797 C3' C A 80 OK 795 798 799 817 C3' C A 81 OK 815 818 819 837 C3' U A 82 OK 835 838 839 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G A 36 OK 8 5 7 29 C4' G A 37 OK 31 28 30 52 C4' G A 38 OK 54 51 53 75 C4' A A 39 OK 77 74 76 97 C4' G A 40 OK 99 96 98 120 C4' U A 41 OK 122 119 121 140 C4' A A 42 OK 142 139 141 162 C4' U A 43 OK 164 161 163 182 C4' A A 44 OK 184 181 183 204 C4' U A 45 OK 206 203 205 224 C4' G A 46 OK 226 223 225 247 C4' G A 47 OK 249 246 248 270 C4' G A 48 OK 272 269 271 293 C4' C A 49 OK 295 292 294 313 C4' G A 50 OK 315 312 314 336 C4' C A 51 OK 338 335 337 356 C4' A A 52 OK 358 355 357 378 C4' C A 53 OK 380 377 379 398 C4' U A 54 OK 400 397 399 418 C4' U A 55 OK 420 417 419 438 C4' C A 56 OK 440 437 439 458 C4' G A 57 OK 460 457 459 481 C4' G A 58 OK 483 480 482 504 C4' U A 66 OK 506 503 505 524 C4' G A 67 OK 526 523 525 547 C4' A A 68 OK 549 546 548 559 C4' C A 69 OK 561 558 560 579 C4' G A 70 OK 581 578 580 602 C4' G A 71 OK 604 601 603 625 C4' U A 72 OK 627 624 626 645 C4' A A 73 OK 647 644 646 667 C4' C A 74 OK 669 666 668 687 C4' A A 75 OK 689 686 688 709 C4' G A 76 OK 711 708 710 732 C4' G A 77 OK 734 731 733 755 C4' C A 78 OK 757 754 756 775 C4' U A 79 OK 777 774 776 795 C4' C A 80 OK 797 794 796 815 C4' C A 81 OK 817 814 816 835 C4' U A 82 OK 837 834 836 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G A 36 4 6 28 C5' G A 37 27 29 51 C5' G A 38 50 52 74 C5' A A 39 73 75 96 C5' G A 40 95 97 119 C5' U A 41 118 120 139 C5' A A 42 138 140 161 C5' U A 43 160 162 181 C5' A A 44 180 182 203 C5' U A 45 202 204 223 C5' G A 46 222 224 246 C5' G A 47 245 247 269 C5' G A 48 268 270 292 C5' C A 49 291 293 312 C5' G A 50 311 313 335 C5' C A 51 334 336 355 C5' A A 52 354 356 377 C5' C A 53 376 378 397 C5' U A 54 396 398 417 C5' U A 55 416 418 437 C5' C A 56 436 438 457 C5' G A 57 456 458 480 C5' G A 58 479 481 503 C5' U A 66 502 504 523 C5' G A 67 522 524 546 C5' A A 68 545 547 558 C5' C A 69 557 559 578 C5' G A 70 577 579 601 C5' G A 71 600 602 624 C5' U A 72 623 625 644 C5' A A 73 643 645 666 C5' C A 74 665 667 686 C5' A A 75 685 687 708 C5' G A 76 707 709 731 C5' G A 77 730 732 754 C5' C A 78 753 755 774 C5' U A 79 773 775 794 C5' C A 80 793 795 814 C5' C A 81 813 815 834 C5' U A 82 833 835 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G A 36 OK OK 2 3 4 24 P G A 37 distorted distorted 9 25 26 27 47 P G A 38 distorted distorted 32 48 49 50 70 P A A 39 distorted distorted 55 71 72 73 92 P G A 40 distorted distorted 78 93 94 95 115 P U A 41 distorted distorted 100 116 117 118 135 P A A 42 distorted distorted 123 136 137 138 157 P U A 43 distorted distorted 143 158 159 160 177 P A A 44 distorted distorted 165 178 179 180 199 P U A 45 distorted distorted 185 200 201 202 219 P G A 46 distorted distorted 207 220 221 222 242 P G A 47 distorted distorted 227 243 244 245 265 P G A 48 distorted distorted 250 266 267 268 288 P C A 49 distorted distorted 273 289 290 291 308 P G A 50 distorted distorted 296 309 310 311 331 P C A 51 distorted distorted 316 332 333 334 351 P A A 52 distorted distorted 339 352 353 354 373 P C A 53 distorted distorted 359 374 375 376 393 P U A 54 distorted distorted 381 394 395 396 413 P U A 55 distorted distorted 401 414 415 416 433 P C A 56 distorted distorted 421 434 435 436 453 P G A 57 distorted distorted 441 454 455 456 476 P G A 58 distorted distorted 461 477 478 479 499 P U A 66 distorted distorted 484 500 501 502 519 P G A 67 distorted distorted 507 520 521 522 542 P A A 68 distorted distorted 527 543 544 545 554 P C A 69 distorted distorted 550 555 556 557 574 P G A 70 distorted distorted 562 575 576 577 597 P G A 71 distorted distorted 582 598 599 600 620 P U A 72 distorted distorted 605 621 622 623 640 P A A 73 distorted distorted 628 641 642 643 662 P C A 74 distorted distorted 648 663 664 665 682 P A A 75 distorted distorted 670 683 684 685 704 P G A 76 distorted distorted 690 705 706 707 727 P G A 77 distorted distorted 712 728 729 730 750 P C A 78 distorted distorted 735 751 752 753 770 P U A 79 distorted distorted 758 771 772 773 790 P C A 80 distorted distorted 778 791 792 793 810 P C A 81 distorted distorted 798 811 812 813 830 P U A 82 distorted distorted 818 831 832 833 1715 P PO4 A 101 ---------------------------------------------------------------------------------