ID code: '4KYY' 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' --------------------------------------------------------------------------------- 9 C1' U A 1 beta 4 10 7 29 C1' U A 2 beta 24 30 27 49 C1' C A 3 beta 44 50 47 69 C1' G A 4 beta 64 70 67 92 C1' G A 5 beta 87 93 90 115 C1' U A 6 beta 110 116 113 135 C1' U A 7 beta 130 136 133 155 C1' U A 8 beta 150 156 153 175 C1' U A 9 beta 170 176 173 195 C1' G A 10 beta 190 196 193 218 C1' A A 11 beta 213 219 216 240 C1' U A 12 beta 235 241 238 260 C1' C A 13 beta 255 261 258 280 C1' C A 14 beta 275 281 278 300 C1' G A 15 beta 295 301 298 323 C1' G A 16 beta 318 324 321 346 C1' A A 17 beta 341 347 344 366 C1' U B 1 beta 361 367 364 386 C1' U B 2 beta 381 387 384 406 C1' C B 3 beta 401 407 404 426 C1' G B 4 beta 421 427 424 449 C1' G B 5 beta 444 450 447 472 C1' U B 6 beta 467 473 470 492 C1' U B 7 beta 487 493 490 512 C1' U B 8 beta 507 513 510 532 C1' U B 9 beta 527 533 530 552 C1' G B 10 beta 547 553 550 575 C1' A B 11 beta 570 576 573 597 C1' U B 12 beta 592 598 595 617 C1' C B 13 beta 612 618 615 637 C1' C B 14 beta 632 638 635 657 C1' G B 15 beta 652 658 655 680 C1' G B 16 beta 675 681 678 703 C1' A B 17 beta 698 704 701 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' U A 1 OK 9 5 8 27 C2' U A 2 OK 29 25 28 47 C2' C A 3 OK 49 45 48 67 C2' G A 4 OK 69 65 68 90 C2' G A 5 OK 92 88 91 113 C2' U A 6 OK 115 111 114 133 C2' U A 7 OK 135 131 134 153 C2' U A 8 OK 155 151 154 173 C2' U A 9 OK 175 171 174 193 C2' G A 10 OK 195 191 194 216 C2' A A 11 OK 218 214 217 238 C2' U A 12 OK 240 236 239 258 C2' C A 13 OK 260 256 259 278 C2' C A 14 OK 280 276 279 298 C2' G A 15 OK 300 296 299 321 C2' G A 16 OK 323 319 322 344 C2' A A 17 OK 346 342 345 364 C2' U B 1 OK 366 362 365 384 C2' U B 2 OK 386 382 385 404 C2' C B 3 OK 406 402 405 424 C2' G B 4 OK 426 422 425 447 C2' G B 5 OK 449 445 448 470 C2' U B 6 OK 472 468 471 490 C2' U B 7 OK 492 488 491 510 C2' U B 8 OK 512 508 511 530 C2' U B 9 OK 532 528 531 550 C2' G B 10 OK 552 548 551 573 C2' A B 11 OK 575 571 574 595 C2' U B 12 OK 597 593 596 615 C2' C B 13 OK 617 613 616 635 C2' C B 14 OK 637 633 636 655 C2' G B 15 OK 657 653 656 678 C2' G B 16 OK 680 676 679 701 C2' A B 17 OK 703 699 702 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' U A 1 OK 3 6 7 25 C3' U A 2 OK 23 26 27 45 C3' C A 3 OK 43 46 47 65 C3' G A 4 OK 63 66 67 88 C3' G A 5 OK 86 89 90 111 C3' U A 6 OK 109 112 113 131 C3' U A 7 OK 129 132 133 151 C3' U A 8 OK 149 152 153 171 C3' U A 9 OK 169 172 173 191 C3' G A 10 OK 189 192 193 214 C3' A A 11 OK 212 215 216 236 C3' U A 12 OK 234 237 238 256 C3' C A 13 OK 254 257 258 276 C3' C A 14 OK 274 277 278 296 C3' G A 15 OK 294 297 298 319 C3' G A 16 OK 317 320 321 342 C3' A A 17 OK 340 343 344 362 C3' U B 1 OK 360 363 364 382 C3' U B 2 OK 380 383 384 402 C3' C B 3 OK 400 403 404 422 C3' G B 4 OK 420 423 424 445 C3' G B 5 OK 443 446 447 468 C3' U B 6 OK 466 469 470 488 C3' U B 7 OK 486 489 490 508 C3' U B 8 OK 506 509 510 528 C3' U B 9 OK 526 529 530 548 C3' G B 10 OK 546 549 550 571 C3' A B 11 OK 569 572 573 593 C3' U B 12 OK 591 594 595 613 C3' C B 13 OK 611 614 615 633 C3' C B 14 OK 631 634 635 653 C3' G B 15 OK 651 654 655 676 C3' G B 16 OK 674 677 678 699 C3' A B 17 OK 697 700 701 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' U A 1 OK 5 2 4 23 C4' U A 2 OK 25 22 24 43 C4' C A 3 OK 45 42 44 63 C4' G A 4 OK 65 62 64 86 C4' G A 5 OK 88 85 87 109 C4' U A 6 OK 111 108 110 129 C4' U A 7 OK 131 128 130 149 C4' U A 8 OK 151 148 150 169 C4' U A 9 OK 171 168 170 189 C4' G A 10 OK 191 188 190 212 C4' A A 11 OK 214 211 213 234 C4' U A 12 OK 236 233 235 254 C4' C A 13 OK 256 253 255 274 C4' C A 14 OK 276 273 275 294 C4' G A 15 OK 296 293 295 317 C4' G A 16 OK 319 316 318 340 C4' A A 17 OK 342 339 341 360 C4' U B 1 OK 362 359 361 380 C4' U B 2 OK 382 379 381 400 C4' C B 3 OK 402 399 401 420 C4' G B 4 OK 422 419 421 443 C4' G B 5 OK 445 442 444 466 C4' U B 6 OK 468 465 467 486 C4' U B 7 OK 488 485 487 506 C4' U B 8 OK 508 505 507 526 C4' U B 9 OK 528 525 527 546 C4' G B 10 OK 548 545 547 569 C4' A B 11 OK 571 568 570 591 C4' U B 12 OK 593 590 592 611 C4' C B 13 OK 613 610 612 631 C4' C B 14 OK 633 630 632 651 C4' G B 15 OK 653 650 652 674 C4' G B 16 OK 676 673 675 697 C4' A B 17 OK 699 696 698 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' U A 1 1 3 22 C5' U A 2 21 23 42 C5' C A 3 41 43 62 C5' G A 4 61 63 85 C5' G A 5 84 86 108 C5' U A 6 107 109 128 C5' U A 7 127 129 148 C5' U A 8 147 149 168 C5' U A 9 167 169 188 C5' G A 10 187 189 211 C5' A A 11 210 212 233 C5' U A 12 232 234 253 C5' C A 13 252 254 273 C5' C A 14 272 274 293 C5' G A 15 292 294 316 C5' G A 16 315 317 339 C5' A A 17 338 340 359 C5' U B 1 358 360 379 C5' U B 2 378 380 399 C5' C B 3 398 400 419 C5' G B 4 418 420 442 C5' G B 5 441 443 465 C5' U B 6 464 466 485 C5' U B 7 484 486 505 C5' U B 8 504 506 525 C5' U B 9 524 526 545 C5' G B 10 544 546 568 C5' A B 11 567 569 590 C5' U B 12 589 591 610 C5' C B 13 609 611 630 C5' C B 14 629 631 650 C5' G B 15 649 651 673 C5' G B 16 672 674 696 C5' A B 17 695 697 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P U A 2 distorted distorted 6 19 20 21 38 P C A 3 distorted distorted 26 39 40 41 58 P G A 4 distorted distorted 46 59 60 61 81 P G A 5 distorted distorted 66 82 83 84 104 P U A 6 distorted distorted 89 105 106 107 124 P U A 7 distorted distorted 112 125 126 127 144 P U A 8 distorted distorted 132 145 146 147 164 P U A 9 distorted distorted 152 165 166 167 184 P G A 10 distorted distorted 172 185 186 187 207 P A A 11 distorted distorted 192 208 209 210 229 P U A 12 distorted distorted 215 230 231 232 249 P C A 13 distorted distorted 237 250 251 252 269 P C A 14 distorted distorted 257 270 271 272 289 P G A 15 distorted distorted 277 290 291 292 312 P G A 16 distorted distorted 297 313 314 315 335 P A A 17 distorted distorted 320 336 337 338 375 P U B 2 distorted distorted 363 376 377 378 395 P C B 3 distorted distorted 383 396 397 398 415 P G B 4 distorted distorted 403 416 417 418 438 P G B 5 distorted distorted 423 439 440 441 461 P U B 6 distorted distorted 446 462 463 464 481 P U B 7 distorted distorted 469 482 483 484 501 P U B 8 distorted distorted 489 502 503 504 521 P U B 9 distorted distorted 509 522 523 524 541 P G B 10 distorted distorted 529 542 543 544 564 P A B 11 distorted distorted 549 565 566 567 586 P U B 12 distorted distorted 572 587 588 589 606 P C B 13 distorted distorted 594 607 608 609 626 P C B 14 distorted distorted 614 627 628 629 646 P G B 15 distorted distorted 634 647 648 649 669 P G B 16 distorted distorted 654 670 671 672 692 P A B 17 distorted distorted 677 693 694 695 ---------------------------------------------------------------------------------