ID code: '1EFA' 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' T D 5 beta 4 9 7 28 C1' G D 6 beta 24 29 27 50 C1' T D 7 beta 46 51 49 70 C1' G D 8 beta 66 71 69 92 C1' A D 9 beta 88 93 91 113 C1' G D 10 beta 109 114 112 135 C1' C D 11 beta 131 136 134 154 C1' G D 12 beta 150 155 153 176 C1' C D 13 beta 172 177 175 195 C1' T D 14 beta 191 196 194 215 C1' C D 15 beta 211 216 214 234 C1' A D 16 beta 230 235 233 255 C1' C D 17 beta 251 256 254 274 C1' A D 18 beta 270 275 273 295 C1' A D 19 beta 291 296 294 316 C1' T D 20 beta 312 317 315 336 C1' T D 21 beta 332 337 335 357 C1' A E 2 beta 353 358 356 378 C1' A E 3 beta 374 379 377 399 C1' T E 4 beta 395 400 398 419 C1' T E 5 beta 415 420 418 439 C1' G E 6 beta 435 440 438 461 C1' T E 7 beta 457 462 460 481 C1' G E 8 beta 477 482 480 503 C1' A E 9 beta 499 504 502 524 C1' G E 10 beta 520 525 523 546 C1' C E 11 beta 542 547 545 565 C1' G E 12 beta 561 566 564 587 C1' C E 13 beta 583 588 586 606 C1' T E 14 beta 602 607 605 626 C1' C E 15 beta 622 627 625 645 C1' A E 16 beta 641 646 644 666 C1' C E 17 beta 662 667 665 685 C1' A E 18 beta 681 686 684 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' T D 5 8 5 27 C2' G D 6 28 25 49 C2' T D 7 50 47 69 C2' G D 8 70 67 91 C2' A D 9 92 89 112 C2' G D 10 113 110 134 C2' C D 11 135 132 153 C2' G D 12 154 151 175 C2' C D 13 176 173 194 C2' T D 14 195 192 214 C2' C D 15 215 212 233 C2' A D 16 234 231 254 C2' C D 17 255 252 273 C2' A D 18 274 271 294 C2' A D 19 295 292 315 C2' T D 20 316 313 335 C2' T D 21 336 333 356 C2' A E 2 357 354 377 C2' A E 3 378 375 398 C2' T E 4 399 396 418 C2' T E 5 419 416 438 C2' G E 6 439 436 460 C2' T E 7 461 458 480 C2' G E 8 481 478 502 C2' A E 9 503 500 523 C2' G E 10 524 521 545 C2' C E 11 546 543 564 C2' G E 12 565 562 586 C2' C E 13 587 584 605 C2' T E 14 606 603 625 C2' C E 15 626 623 644 C2' A E 16 645 642 665 C2' C E 17 666 663 684 C2' A E 18 685 682 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' T D 5 OK 3 6 7 25 C3' G D 6 OK 23 26 27 47 C3' T D 7 OK 45 48 49 67 C3' G D 8 OK 65 68 69 89 C3' A D 9 OK 87 90 91 110 C3' G D 10 OK 108 111 112 132 C3' C D 11 OK 130 133 134 151 C3' G D 12 OK 149 152 153 173 C3' C D 13 OK 171 174 175 192 C3' T D 14 OK 190 193 194 212 C3' C D 15 OK 210 213 214 231 C3' A D 16 OK 229 232 233 252 C3' C D 17 OK 250 253 254 271 C3' A D 18 OK 269 272 273 292 C3' A D 19 OK 290 293 294 313 C3' T D 20 OK 311 314 315 333 C3' T D 21 OK 331 334 335 354 C3' A E 2 OK 352 355 356 375 C3' A E 3 OK 373 376 377 396 C3' T E 4 OK 394 397 398 416 C3' T E 5 OK 414 417 418 436 C3' G E 6 OK 434 437 438 458 C3' T E 7 OK 456 459 460 478 C3' G E 8 OK 476 479 480 500 C3' A E 9 OK 498 501 502 521 C3' G E 10 OK 519 522 523 543 C3' C E 11 OK 541 544 545 562 C3' G E 12 OK 560 563 564 584 C3' C E 13 OK 582 585 586 603 C3' T E 14 OK 601 604 605 623 C3' C E 15 OK 621 624 625 642 C3' A E 16 OK 640 643 644 663 C3' C E 17 OK 661 664 665 682 C3' A E 18 OK 680 683 684 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' T D 5 OK 5 2 4 23 C4' G D 6 OK 25 22 24 45 C4' T D 7 OK 47 44 46 65 C4' G D 8 OK 67 64 66 87 C4' A D 9 OK 89 86 88 108 C4' G D 10 OK 110 107 109 130 C4' C D 11 OK 132 129 131 149 C4' G D 12 OK 151 148 150 171 C4' C D 13 OK 173 170 172 190 C4' T D 14 OK 192 189 191 210 C4' C D 15 OK 212 209 211 229 C4' A D 16 OK 231 228 230 250 C4' C D 17 OK 252 249 251 269 C4' A D 18 OK 271 268 270 290 C4' A D 19 OK 292 289 291 311 C4' T D 20 OK 313 310 312 331 C4' T D 21 OK 333 330 332 352 C4' A E 2 OK 354 351 353 373 C4' A E 3 OK 375 372 374 394 C4' T E 4 OK 396 393 395 414 C4' T E 5 OK 416 413 415 434 C4' G E 6 OK 436 433 435 456 C4' T E 7 OK 458 455 457 476 C4' G E 8 OK 478 475 477 498 C4' A E 9 OK 500 497 499 519 C4' G E 10 OK 521 518 520 541 C4' C E 11 OK 543 540 542 560 C4' G E 12 OK 562 559 561 582 C4' C E 13 OK 584 581 583 601 C4' T E 14 OK 603 600 602 621 C4' C E 15 OK 623 620 622 640 C4' A E 16 OK 642 639 641 661 C4' C E 17 OK 663 660 662 680 C4' A E 18 OK 682 679 681 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' T D 5 1 3 22 C5' G D 6 21 23 44 C5' T D 7 43 45 64 C5' G D 8 63 65 86 C5' A D 9 85 87 107 C5' G D 10 106 108 129 C5' C D 11 128 130 148 C5' G D 12 147 149 170 C5' C D 13 169 171 189 C5' T D 14 188 190 209 C5' C D 15 208 210 228 C5' A D 16 227 229 249 C5' C D 17 248 250 268 C5' A D 18 267 269 289 C5' A D 19 288 290 310 C5' T D 20 309 311 330 C5' T D 21 329 331 351 C5' A E 2 350 352 372 C5' A E 3 371 373 393 C5' T E 4 392 394 413 C5' T E 5 412 414 433 C5' G E 6 432 434 455 C5' T E 7 454 456 475 C5' G E 8 474 476 497 C5' A E 9 496 498 518 C5' G E 10 517 519 540 C5' C E 11 539 541 559 C5' G E 12 558 560 581 C5' C E 13 580 582 600 C5' T E 14 599 601 620 C5' C E 15 619 621 639 C5' A E 16 638 640 660 C5' C E 17 659 661 679 C5' A E 18 678 680 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P G D 6 distorted distorted 6 19 20 21 40 P T D 7 distorted distorted 26 41 42 43 60 P G D 8 distorted distorted 48 61 62 63 82 P A D 9 distorted distorted 68 83 84 85 103 P G D 10 distorted distorted 90 104 105 106 125 P C D 11 distorted distorted 111 126 127 128 144 P G D 12 distorted distorted 133 145 146 147 166 P C D 13 distorted distorted 152 167 168 169 185 P T D 14 distorted distorted 174 186 187 188 205 P C D 15 distorted distorted 193 206 207 208 224 P A D 16 distorted distorted 213 225 226 227 245 P C D 17 distorted distorted 232 246 247 248 264 P A D 18 distorted distorted 253 265 266 267 285 P A D 19 distorted distorted 272 286 287 288 306 P T D 20 distorted distorted 293 307 308 309 326 P T D 21 distorted distorted 314 327 328 329 347 P A E 2 distorted distorted 348 349 350 368 P A E 3 distorted distorted 355 369 370 371 389 P T E 4 distorted distorted 376 390 391 392 409 P T E 5 distorted distorted 397 410 411 412 429 P G E 6 distorted distorted 417 430 431 432 451 P T E 7 distorted distorted 437 452 453 454 471 P G E 8 distorted distorted 459 472 473 474 493 P A E 9 distorted distorted 479 494 495 496 514 P G E 10 distorted distorted 501 515 516 517 536 P C E 11 distorted distorted 522 537 538 539 555 P G E 12 distorted distorted 544 556 557 558 577 P C E 13 distorted distorted 563 578 579 580 596 P T E 14 distorted distorted 585 597 598 599 616 P C E 15 distorted distorted 604 617 618 619 635 P A E 16 distorted distorted 624 636 637 638 656 P C E 17 distorted distorted 643 657 658 659 675 P A E 18 distorted distorted 664 676 677 678 ---------------------------------------------------------------------------------