ID code: '1NG9' 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' A E 1 beta 4 9 7 29 C1' G E 2 beta 25 30 28 51 C1' C E 3 beta 47 52 50 70 C1' T E 4 beta 66 71 69 90 C1' G E 5 beta 86 91 89 112 C1' C E 6 beta 108 113 111 131 C1' C E 7 beta 127 132 130 150 C1' A E 8 beta 146 151 149 171 C1' G E 9 beta 167 172 170 193 C1' G E 10 beta 189 194 192 215 C1' C E 11 beta 211 216 214 234 C1' A E 12 beta 230 235 233 255 C1' C E 13 beta 251 256 254 274 C1' C E 14 beta 270 275 273 293 C1' A E 15 beta 289 294 292 314 C1' G E 16 beta 310 315 313 336 C1' T E 17 beta 332 337 335 354 C1' A F 14 beta 350 355 353 375 C1' C F 15 beta 371 376 374 394 C1' T F 16 beta 390 395 393 414 C1' G F 17 beta 410 415 413 436 C1' G F 18 beta 432 437 435 458 C1' T F 19 beta 454 459 457 478 C1' G F 20 beta 474 479 477 500 C1' C F 21 beta 496 501 499 519 C1' T F 22 beta 515 520 518 539 C1' T F 23 beta 535 540 538 559 C1' G F 24 beta 555 560 558 581 C1' G F 25 beta 577 582 580 603 C1' C F 26 beta 599 604 602 622 C1' A F 27 beta 618 623 621 643 C1' G F 28 beta 639 644 642 665 C1' C F 29 beta 661 666 664 684 C1' T F 30 beta 680 685 683 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' A E 1 8 5 28 C2' G E 2 29 26 50 C2' C E 3 51 48 69 C2' T E 4 70 67 89 C2' G E 5 90 87 111 C2' C E 6 112 109 130 C2' C E 7 131 128 149 C2' A E 8 150 147 170 C2' G E 9 171 168 192 C2' G E 10 193 190 214 C2' C E 11 215 212 233 C2' A E 12 234 231 254 C2' C E 13 255 252 273 C2' C E 14 274 271 292 C2' A E 15 293 290 313 C2' G E 16 314 311 335 C2' T E 17 336 333 353 C2' A F 14 354 351 374 C2' C F 15 375 372 393 C2' T F 16 394 391 413 C2' G F 17 414 411 435 C2' G F 18 436 433 457 C2' T F 19 458 455 477 C2' G F 20 478 475 499 C2' C F 21 500 497 518 C2' T F 22 519 516 538 C2' T F 23 539 536 558 C2' G F 24 559 556 580 C2' G F 25 581 578 602 C2' C F 26 603 600 621 C2' A F 27 622 619 642 C2' G F 28 643 640 664 C2' C F 29 665 662 683 C2' T F 30 684 681 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' A E 1 OK 3 6 7 26 C3' G E 2 OK 24 27 28 48 C3' C E 3 OK 46 49 50 67 C3' T E 4 OK 65 68 69 87 C3' G E 5 OK 85 88 89 109 C3' C E 6 OK 107 110 111 128 C3' C E 7 OK 126 129 130 147 C3' A E 8 OK 145 148 149 168 C3' G E 9 OK 166 169 170 190 C3' G E 10 OK 188 191 192 212 C3' C E 11 OK 210 213 214 231 C3' A E 12 OK 229 232 233 252 C3' C E 13 OK 250 253 254 271 C3' C E 14 OK 269 272 273 290 C3' A E 15 OK 288 291 292 311 C3' G E 16 OK 309 312 313 333 C3' T E 17 OK 331 334 335 351 C3' A F 14 OK 349 352 353 372 C3' C F 15 OK 370 373 374 391 C3' T F 16 OK 389 392 393 411 C3' G F 17 OK 409 412 413 433 C3' G F 18 OK 431 434 435 455 C3' T F 19 OK 453 456 457 475 C3' G F 20 OK 473 476 477 497 C3' C F 21 OK 495 498 499 516 C3' T F 22 OK 514 517 518 536 C3' T F 23 OK 534 537 538 556 C3' G F 24 OK 554 557 558 578 C3' G F 25 OK 576 579 580 600 C3' C F 26 OK 598 601 602 619 C3' A F 27 OK 617 620 621 640 C3' G F 28 OK 638 641 642 662 C3' C F 29 OK 660 663 664 681 C3' T F 30 OK 679 682 683 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' A E 1 OK 5 2 4 24 C4' G E 2 OK 26 23 25 46 C4' C E 3 OK 48 45 47 65 C4' T E 4 OK 67 64 66 85 C4' G E 5 OK 87 84 86 107 C4' C E 6 OK 109 106 108 126 C4' C E 7 OK 128 125 127 145 C4' A E 8 OK 147 144 146 166 C4' G E 9 OK 168 165 167 188 C4' G E 10 OK 190 187 189 210 C4' C E 11 OK 212 209 211 229 C4' A E 12 OK 231 228 230 250 C4' C E 13 OK 252 249 251 269 C4' C E 14 OK 271 268 270 288 C4' A E 15 OK 290 287 289 309 C4' G E 16 OK 311 308 310 331 C4' T E 17 OK 333 330 332 349 C4' A F 14 OK 351 348 350 370 C4' C F 15 OK 372 369 371 389 C4' T F 16 OK 391 388 390 409 C4' G F 17 OK 411 408 410 431 C4' G F 18 OK 433 430 432 453 C4' T F 19 OK 455 452 454 473 C4' G F 20 OK 475 472 474 495 C4' C F 21 OK 497 494 496 514 C4' T F 22 OK 516 513 515 534 C4' T F 23 OK 536 533 535 554 C4' G F 24 OK 556 553 555 576 C4' G F 25 OK 578 575 577 598 C4' C F 26 OK 600 597 599 617 C4' A F 27 OK 619 616 618 638 C4' G F 28 OK 640 637 639 660 C4' C F 29 OK 662 659 661 679 C4' T F 30 OK 681 678 680 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' A E 1 1 3 23 C5' G E 2 22 24 45 C5' C E 3 44 46 64 C5' T E 4 63 65 84 C5' G E 5 83 85 106 C5' C E 6 105 107 125 C5' C E 7 124 126 144 C5' A E 8 143 145 165 C5' G E 9 164 166 187 C5' G E 10 186 188 209 C5' C E 11 208 210 228 C5' A E 12 227 229 249 C5' C E 13 248 250 268 C5' C E 14 267 269 287 C5' A E 15 286 288 308 C5' G E 16 307 309 330 C5' T E 17 329 331 348 C5' A F 14 347 349 369 C5' C F 15 368 370 388 C5' T F 16 387 389 408 C5' G F 17 407 409 430 C5' G F 18 429 431 452 C5' T F 19 451 453 472 C5' G F 20 471 473 494 C5' C F 21 493 495 513 C5' T F 22 512 514 533 C5' T F 23 532 534 553 C5' G F 24 552 554 575 C5' G F 25 574 576 597 C5' C F 26 596 598 616 C5' A F 27 615 617 637 C5' G F 28 636 638 659 C5' C F 29 658 660 678 C5' T F 30 677 679 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P G E 2 distorted distorted 6 20 21 22 41 P C E 3 distorted distorted 27 42 43 44 60 P T E 4 distorted distorted 49 61 62 63 80 P G E 5 distorted distorted 68 81 82 83 102 P C E 6 distorted distorted 88 103 104 105 121 P C E 7 distorted distorted 110 122 123 124 140 P A E 8 distorted distorted 129 141 142 143 161 P G E 9 distorted distorted 148 162 163 164 183 P G E 10 distorted distorted 169 184 185 186 205 P C E 11 distorted distorted 191 206 207 208 224 P A E 12 distorted distorted 213 225 226 227 245 P C E 13 distorted distorted 232 246 247 248 264 P C E 14 distorted distorted 253 265 266 267 283 P A E 15 distorted distorted 272 284 285 286 304 P G E 16 distorted distorted 291 305 306 307 326 P T E 17 distorted distorted 312 327 328 329 365 P C F 15 distorted distorted 352 366 367 368 384 P T F 16 distorted distorted 373 385 386 387 404 P G F 17 distorted distorted 392 405 406 407 426 P G F 18 distorted distorted 412 427 428 429 448 P T F 19 distorted distorted 434 449 450 451 468 P G F 20 distorted distorted 456 469 470 471 490 P C F 21 distorted distorted 476 491 492 493 509 P T F 22 distorted distorted 498 510 511 512 529 P T F 23 distorted distorted 517 530 531 532 549 P G F 24 distorted distorted 537 550 551 552 571 P G F 25 distorted distorted 557 572 573 574 593 P C F 26 distorted distorted 579 594 595 596 612 P A F 27 distorted distorted 601 613 614 615 633 P G F 28 distorted distorted 620 634 635 636 655 P C F 29 distorted distorted 641 656 657 658 674 P T F 30 distorted distorted 663 675 676 677 ---------------------------------------------------------------------------------