ID code: '1NLW' 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' G F 102 beta 4 9 7 30 C1' A F 103 beta 26 31 29 51 C1' G F 104 beta 47 52 50 73 C1' T F 105 beta 69 74 72 93 C1' A F 106 beta 89 94 92 114 C1' G F 107 beta 110 115 113 136 C1' C F 108 beta 132 137 135 155 C1' A F 109 beta 151 156 154 176 C1' C F 110 beta 172 177 175 195 C1' G F 111 beta 191 196 194 217 C1' T F 112 beta 213 218 216 237 C1' G F 113 beta 233 238 236 259 C1' C F 114 beta 255 260 258 278 C1' T F 115 beta 274 279 277 298 C1' A F 116 beta 294 299 297 319 C1' C F 117 beta 315 320 318 338 C1' T F 118 beta 334 339 337 358 C1' C F 119 beta 354 359 357 375 C1' G G 302 beta 371 376 374 397 C1' A G 303 beta 393 398 396 418 C1' G G 304 beta 414 419 417 440 C1' T G 305 beta 436 441 439 460 C1' A G 306 beta 456 461 459 481 C1' G G 307 beta 477 482 480 503 C1' C G 308 beta 499 504 502 522 C1' A G 309 beta 518 523 521 543 C1' C G 310 beta 539 544 542 562 C1' G G 311 beta 558 563 561 584 C1' T G 312 beta 580 585 583 604 C1' G G 313 beta 600 605 603 626 C1' C G 314 beta 622 627 625 645 C1' T G 315 beta 641 646 644 665 C1' A G 316 beta 661 666 664 686 C1' C G 317 beta 682 687 685 705 C1' T G 318 beta 701 706 704 725 C1' C G 319 beta 721 726 724 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G F 102 8 5 29 C2' A F 103 30 27 50 C2' G F 104 51 48 72 C2' T F 105 73 70 92 C2' A F 106 93 90 113 C2' G F 107 114 111 135 C2' C F 108 136 133 154 C2' A F 109 155 152 175 C2' C F 110 176 173 194 C2' G F 111 195 192 216 C2' T F 112 217 214 236 C2' G F 113 237 234 258 C2' C F 114 259 256 277 C2' T F 115 278 275 297 C2' A F 116 298 295 318 C2' C F 117 319 316 337 C2' T F 118 338 335 357 C2' C F 119 358 355 374 C2' G G 302 375 372 396 C2' A G 303 397 394 417 C2' G G 304 418 415 439 C2' T G 305 440 437 459 C2' A G 306 460 457 480 C2' G G 307 481 478 502 C2' C G 308 503 500 521 C2' A G 309 522 519 542 C2' C G 310 543 540 561 C2' G G 311 562 559 583 C2' T G 312 584 581 603 C2' G G 313 604 601 625 C2' C G 314 626 623 644 C2' T G 315 645 642 664 C2' A G 316 665 662 685 C2' C G 317 686 683 704 C2' T G 318 705 702 724 C2' C G 319 725 722 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G F 102 OK 3 6 7 27 C3' A F 103 OK 25 28 29 48 C3' G F 104 OK 46 49 50 70 C3' T F 105 OK 68 71 72 90 C3' A F 106 OK 88 91 92 111 C3' G F 107 OK 109 112 113 133 C3' C F 108 OK 131 134 135 152 C3' A F 109 OK 150 153 154 173 C3' C F 110 OK 171 174 175 192 C3' G F 111 OK 190 193 194 214 C3' T F 112 OK 212 215 216 234 C3' G F 113 OK 232 235 236 256 C3' C F 114 OK 254 257 258 275 C3' T F 115 OK 273 276 277 295 C3' A F 116 OK 293 296 297 316 C3' C F 117 OK 314 317 318 335 C3' T F 118 OK 333 336 337 355 C3' C F 119 OK 353 356 357 372 C3' G G 302 OK 370 373 374 394 C3' A G 303 OK 392 395 396 415 C3' G G 304 OK 413 416 417 437 C3' T G 305 OK 435 438 439 457 C3' A G 306 OK 455 458 459 478 C3' G G 307 OK 476 479 480 500 C3' C G 308 OK 498 501 502 519 C3' A G 309 OK 517 520 521 540 C3' C G 310 OK 538 541 542 559 C3' G G 311 OK 557 560 561 581 C3' T G 312 OK 579 582 583 601 C3' G G 313 OK 599 602 603 623 C3' C G 314 OK 621 624 625 642 C3' T G 315 OK 640 643 644 662 C3' A G 316 OK 660 663 664 683 C3' C G 317 OK 681 684 685 702 C3' T G 318 OK 700 703 704 722 C3' C G 319 OK 720 723 724 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G F 102 OK 5 2 4 25 C4' A F 103 OK 27 24 26 46 C4' G F 104 OK 48 45 47 68 C4' T F 105 OK 70 67 69 88 C4' A F 106 OK 90 87 89 109 C4' G F 107 OK 111 108 110 131 C4' C F 108 OK 133 130 132 150 C4' A F 109 OK 152 149 151 171 C4' C F 110 OK 173 170 172 190 C4' G F 111 OK 192 189 191 212 C4' T F 112 OK 214 211 213 232 C4' G F 113 OK 234 231 233 254 C4' C F 114 OK 256 253 255 273 C4' T F 115 OK 275 272 274 293 C4' A F 116 OK 295 292 294 314 C4' C F 117 OK 316 313 315 333 C4' T F 118 OK 335 332 334 353 C4' C F 119 OK 355 352 354 370 C4' G G 302 OK 372 369 371 392 C4' A G 303 OK 394 391 393 413 C4' G G 304 OK 415 412 414 435 C4' T G 305 OK 437 434 436 455 C4' A G 306 OK 457 454 456 476 C4' G G 307 OK 478 475 477 498 C4' C G 308 OK 500 497 499 517 C4' A G 309 OK 519 516 518 538 C4' C G 310 OK 540 537 539 557 C4' G G 311 OK 559 556 558 579 C4' T G 312 OK 581 578 580 599 C4' G G 313 OK 601 598 600 621 C4' C G 314 OK 623 620 622 640 C4' T G 315 OK 642 639 641 660 C4' A G 316 OK 662 659 661 681 C4' C G 317 OK 683 680 682 700 C4' T G 318 OK 702 699 701 720 C4' C G 319 OK 722 719 721 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G F 102 1 3 24 C5' A F 103 23 25 45 C5' G F 104 44 46 67 C5' T F 105 66 68 87 C5' A F 106 86 88 108 C5' G F 107 107 109 130 C5' C F 108 129 131 149 C5' A F 109 148 150 170 C5' C F 110 169 171 189 C5' G F 111 188 190 211 C5' T F 112 210 212 231 C5' G F 113 230 232 253 C5' C F 114 252 254 272 C5' T F 115 271 273 292 C5' A F 116 291 293 313 C5' C F 117 312 314 332 C5' T F 118 331 333 352 C5' C F 119 351 353 369 C5' G G 302 368 370 391 C5' A G 303 390 392 412 C5' G G 304 411 413 434 C5' T G 305 433 435 454 C5' A G 306 453 455 475 C5' G G 307 474 476 497 C5' C G 308 496 498 516 C5' A G 309 515 517 537 C5' C G 310 536 538 556 C5' G G 311 555 557 578 C5' T G 312 577 579 598 C5' G G 313 597 599 620 C5' C G 314 619 621 639 C5' T G 315 638 640 659 C5' A G 316 658 660 680 C5' C G 317 679 681 699 C5' T G 318 698 700 719 C5' C G 319 718 720 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P A F 103 distorted distorted 6 21 22 23 41 P G F 104 distorted distorted 28 42 43 44 63 P T F 105 distorted distorted 49 64 65 66 83 P A F 106 distorted distorted 71 84 85 86 104 P G F 107 distorted distorted 91 105 106 107 126 P C F 108 distorted distorted 112 127 128 129 145 P A F 109 distorted distorted 134 146 147 148 166 P C F 110 distorted distorted 153 167 168 169 185 P G F 111 distorted distorted 174 186 187 188 207 P T F 112 distorted distorted 193 208 209 210 227 P G F 113 distorted distorted 215 228 229 230 249 P C F 114 distorted distorted 235 250 251 252 268 P T F 115 distorted distorted 257 269 270 271 288 P A F 116 distorted distorted 276 289 290 291 309 P C F 117 distorted distorted 296 310 311 312 328 P T F 118 distorted distorted 317 329 330 331 348 P C F 119 distorted distorted 336 349 350 351 387 P A G 303 distorted distorted 373 388 389 390 408 P G G 304 distorted distorted 395 409 410 411 430 P T G 305 distorted distorted 416 431 432 433 450 P A G 306 distorted distorted 438 451 452 453 471 P G G 307 distorted distorted 458 472 473 474 493 P C G 308 distorted distorted 479 494 495 496 512 P A G 309 distorted distorted 501 513 514 515 533 P C G 310 distorted distorted 520 534 535 536 552 P G G 311 distorted distorted 541 553 554 555 574 P T G 312 distorted distorted 560 575 576 577 594 P G G 313 distorted distorted 582 595 596 597 616 P C G 314 distorted distorted 602 617 618 619 635 P T G 315 distorted distorted 624 636 637 638 655 P A G 316 distorted distorted 643 656 657 658 676 P C G 317 distorted distorted 663 677 678 679 695 P T G 318 distorted distorted 684 696 697 698 715 P C G 319 distorted distorted 703 716 717 718 ---------------------------------------------------------------------------------