ID code: '1NKP' 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' --------------------------------------------------------------------------------- 11 C1' G F 102 beta 7 12 10 33 C1' A F 103 beta 29 34 32 54 C1' G F 104 beta 50 55 53 76 C1' T F 105 beta 72 77 75 96 C1' A F 106 beta 92 97 95 117 C1' G F 107 beta 113 118 116 139 C1' C F 108 beta 135 140 138 158 C1' A F 109 beta 154 159 157 179 C1' C F 110 beta 175 180 178 198 C1' G F 111 beta 194 199 197 220 C1' T F 112 beta 216 221 219 240 C1' G F 113 beta 236 241 239 262 C1' C F 114 beta 258 263 261 281 C1' T F 115 beta 277 282 280 301 C1' A F 116 beta 297 302 300 322 C1' C F 117 beta 318 323 321 341 C1' T F 118 beta 337 342 340 361 C1' C F 119 beta 357 362 360 381 C1' G G 302 beta 377 382 380 403 C1' A G 303 beta 399 404 402 424 C1' G G 304 beta 420 425 423 446 C1' T G 305 beta 442 447 445 466 C1' A G 306 beta 462 467 465 487 C1' G G 307 beta 483 488 486 509 C1' C G 308 beta 505 510 508 528 C1' A G 309 beta 524 529 527 549 C1' C G 310 beta 545 550 548 568 C1' G G 311 beta 564 569 567 590 C1' T G 312 beta 586 591 589 610 C1' G G 313 beta 606 611 609 632 C1' C G 314 beta 628 633 631 651 C1' T G 315 beta 647 652 650 671 C1' A G 316 beta 667 672 670 692 C1' C G 317 beta 688 693 691 711 C1' T G 318 beta 707 712 710 731 C1' C G 319 beta 727 732 730 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' G F 102 11 8 32 C2' A F 103 33 30 53 C2' G F 104 54 51 75 C2' T F 105 76 73 95 C2' A F 106 96 93 116 C2' G F 107 117 114 138 C2' C F 108 139 136 157 C2' A F 109 158 155 178 C2' C F 110 179 176 197 C2' G F 111 198 195 219 C2' T F 112 220 217 239 C2' G F 113 240 237 261 C2' C F 114 262 259 280 C2' T F 115 281 278 300 C2' A F 116 301 298 321 C2' C F 117 322 319 340 C2' T F 118 341 338 360 C2' C F 119 361 358 380 C2' G G 302 381 378 402 C2' A G 303 403 400 423 C2' G G 304 424 421 445 C2' T G 305 446 443 465 C2' A G 306 466 463 486 C2' G G 307 487 484 508 C2' C G 308 509 506 527 C2' A G 309 528 525 548 C2' C G 310 549 546 567 C2' G G 311 568 565 589 C2' T G 312 590 587 609 C2' G G 313 610 607 631 C2' C G 314 632 629 650 C2' T G 315 651 648 670 C2' A G 316 671 668 691 C2' C G 317 692 689 710 C2' T G 318 711 708 730 C2' C G 319 731 728 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' G F 102 OK 6 9 10 30 C3' A F 103 OK 28 31 32 51 C3' G F 104 OK 49 52 53 73 C3' T F 105 OK 71 74 75 93 C3' A F 106 OK 91 94 95 114 C3' G F 107 OK 112 115 116 136 C3' C F 108 OK 134 137 138 155 C3' A F 109 OK 153 156 157 176 C3' C F 110 OK 174 177 178 195 C3' G F 111 OK 193 196 197 217 C3' T F 112 OK 215 218 219 237 C3' G F 113 OK 235 238 239 259 C3' C F 114 OK 257 260 261 278 C3' T F 115 OK 276 279 280 298 C3' A F 116 OK 296 299 300 319 C3' C F 117 OK 317 320 321 338 C3' T F 118 OK 336 339 340 358 C3' C F 119 OK 356 359 360 378 C3' G G 302 OK 376 379 380 400 C3' A G 303 OK 398 401 402 421 C3' G G 304 OK 419 422 423 443 C3' T G 305 OK 441 444 445 463 C3' A G 306 OK 461 464 465 484 C3' G G 307 OK 482 485 486 506 C3' C G 308 OK 504 507 508 525 C3' A G 309 OK 523 526 527 546 C3' C G 310 OK 544 547 548 565 C3' G G 311 OK 563 566 567 587 C3' T G 312 OK 585 588 589 607 C3' G G 313 OK 605 608 609 629 C3' C G 314 OK 627 630 631 648 C3' T G 315 OK 646 649 650 668 C3' A G 316 OK 666 669 670 689 C3' C G 317 OK 687 690 691 708 C3' T G 318 OK 706 709 710 728 C3' C G 319 OK 726 729 730 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' G F 102 OK 8 5 7 28 C4' A F 103 OK 30 27 29 49 C4' G F 104 OK 51 48 50 71 C4' T F 105 OK 73 70 72 91 C4' A F 106 OK 93 90 92 112 C4' G F 107 OK 114 111 113 134 C4' C F 108 OK 136 133 135 153 C4' A F 109 OK 155 152 154 174 C4' C F 110 OK 176 173 175 193 C4' G F 111 OK 195 192 194 215 C4' T F 112 OK 217 214 216 235 C4' G F 113 OK 237 234 236 257 C4' C F 114 OK 259 256 258 276 C4' T F 115 OK 278 275 277 296 C4' A F 116 OK 298 295 297 317 C4' C F 117 OK 319 316 318 336 C4' T F 118 OK 338 335 337 356 C4' C F 119 OK 358 355 357 376 C4' G G 302 OK 378 375 377 398 C4' A G 303 OK 400 397 399 419 C4' G G 304 OK 421 418 420 441 C4' T G 305 OK 443 440 442 461 C4' A G 306 OK 463 460 462 482 C4' G G 307 OK 484 481 483 504 C4' C G 308 OK 506 503 505 523 C4' A G 309 OK 525 522 524 544 C4' C G 310 OK 546 543 545 563 C4' G G 311 OK 565 562 564 585 C4' T G 312 OK 587 584 586 605 C4' G G 313 OK 607 604 606 627 C4' C G 314 OK 629 626 628 646 C4' T G 315 OK 648 645 647 666 C4' A G 316 OK 668 665 667 687 C4' C G 317 OK 689 686 688 706 C4' T G 318 OK 708 705 707 726 C4' C G 319 OK 728 725 727 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' G F 102 4 6 27 C5' A F 103 26 28 48 C5' G F 104 47 49 70 C5' T F 105 69 71 90 C5' A F 106 89 91 111 C5' G F 107 110 112 133 C5' C F 108 132 134 152 C5' A F 109 151 153 173 C5' C F 110 172 174 192 C5' G F 111 191 193 214 C5' T F 112 213 215 234 C5' G F 113 233 235 256 C5' C F 114 255 257 275 C5' T F 115 274 276 295 C5' A F 116 294 296 316 C5' C F 117 315 317 335 C5' T F 118 334 336 355 C5' C F 119 354 356 375 C5' G G 302 374 376 397 C5' A G 303 396 398 418 C5' G G 304 417 419 440 C5' T G 305 439 441 460 C5' A G 306 459 461 481 C5' G G 307 480 482 503 C5' C G 308 502 504 522 C5' A G 309 521 523 543 C5' C G 310 542 544 562 C5' G G 311 561 563 584 C5' T G 312 583 585 604 C5' G G 313 603 605 626 C5' C G 314 625 627 645 C5' T G 315 644 646 665 C5' A G 316 664 666 686 C5' C G 317 685 687 705 C5' T G 318 704 706 725 C5' C G 319 724 726 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P G F 102 distorted distorted 2 3 4 23 P A F 103 distorted distorted 9 24 25 26 44 P G F 104 distorted distorted 31 45 46 47 66 P T F 105 distorted distorted 52 67 68 69 86 P A F 106 distorted distorted 74 87 88 89 107 P G F 107 distorted distorted 94 108 109 110 129 P C F 108 distorted distorted 115 130 131 132 148 P A F 109 distorted distorted 137 149 150 151 169 P C F 110 distorted distorted 156 170 171 172 188 P G F 111 distorted distorted 177 189 190 191 210 P T F 112 distorted distorted 196 211 212 213 230 P G F 113 distorted distorted 218 231 232 233 252 P C F 114 distorted distorted 238 253 254 255 271 P T F 115 distorted distorted 260 272 273 274 291 P A F 116 distorted distorted 279 292 293 294 312 P C F 117 distorted distorted 299 313 314 315 331 P T F 118 distorted distorted 320 332 333 334 351 P C F 119 distorted distorted 339 352 353 354 371 P G G 302 distorted distorted 372 373 374 393 P A G 303 distorted distorted 379 394 395 396 414 P G G 304 distorted distorted 401 415 416 417 436 P T G 305 distorted distorted 422 437 438 439 456 P A G 306 distorted distorted 444 457 458 459 477 P G G 307 distorted distorted 464 478 479 480 499 P C G 308 distorted distorted 485 500 501 502 518 P A G 309 distorted distorted 507 519 520 521 539 P C G 310 distorted distorted 526 540 541 542 558 P G G 311 distorted distorted 547 559 560 561 580 P T G 312 distorted distorted 566 581 582 583 600 P G G 313 distorted distorted 588 601 602 603 622 P C G 314 distorted distorted 608 623 624 625 641 P T G 315 distorted distorted 630 642 643 644 661 P A G 316 distorted distorted 649 662 663 664 682 P C G 317 distorted distorted 669 683 684 685 701 P T G 318 distorted distorted 690 702 703 704 721 P C G 319 distorted distorted 709 722 723 724 ---------------------------------------------------------------------------------