ID code: '2EC0' 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' --------------------------------------------------------------------------------- 12 C1' A B 903 beta 7 13 10 34 C1' U B 904 beta 29 35 32 54 C1' G B 905 beta 49 55 52 77 C1' G B 906 beta 72 78 75 100 C1' G B 907 beta 95 101 98 123 C1' C B 908 beta 118 124 121 143 C1' C B 909 beta 138 144 141 163 C1' C B 910 beta 158 164 161 181 C1' G C 915 beta 176 182 179 204 C1' G C 916 beta 199 205 202 227 C1' G C 917 beta 222 228 225 250 C1' C C 918 beta 245 251 248 270 C1' C C 919 beta 265 271 268 290 C1' C C 920 beta 285 291 288 310 C1' A C 921 beta 305 311 308 333 C1' A E 903 beta 328 334 331 355 C1' U E 904 beta 350 356 353 375 C1' G E 905 beta 370 376 373 398 C1' G E 906 beta 393 399 396 421 C1' G E 907 beta 416 422 419 444 C1' C E 908 beta 439 445 442 464 C1' C E 909 beta 459 465 462 484 C1' C E 910 beta 479 485 482 502 C1' G F 915 beta 497 503 500 525 C1' G F 916 beta 520 526 523 548 C1' G F 917 beta 543 549 546 571 C1' C F 918 beta 566 572 569 591 C1' C F 919 beta 586 592 589 611 C1' C F 920 beta 606 612 609 631 C1' A F 921 beta 626 632 629 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 10 C2' A B 903 OK 12 8 11 32 C2' U B 904 OK 34 30 33 52 C2' G B 905 OK 54 50 53 75 C2' G B 906 OK 77 73 76 98 C2' G B 907 OK 100 96 99 121 C2' C B 908 OK 123 119 122 141 C2' C B 909 OK 143 139 142 161 C2' C B 910 OK 163 159 162 179 C2' G C 915 OK 181 177 180 202 C2' G C 916 OK 204 200 203 225 C2' G C 917 OK 227 223 226 248 C2' C C 918 OK 250 246 249 268 C2' C C 919 OK 270 266 269 288 C2' C C 920 OK 290 286 289 308 C2' A C 921 OK 310 306 309 331 C2' A E 903 OK 333 329 332 353 C2' U E 904 OK 355 351 354 373 C2' G E 905 OK 375 371 374 396 C2' G E 906 OK 398 394 397 419 C2' G E 907 OK 421 417 420 442 C2' C E 908 OK 444 440 443 462 C2' C E 909 OK 464 460 463 482 C2' C E 910 OK 484 480 483 500 C2' G F 915 OK 502 498 501 523 C2' G F 916 OK 525 521 524 546 C2' G F 917 OK 548 544 547 569 C2' C F 918 OK 571 567 570 589 C2' C F 919 OK 591 587 590 609 C2' C F 920 OK 611 607 610 629 C2' A F 921 OK 631 627 630 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 8 C3' A B 903 OK 6 9 10 30 C3' U B 904 OK 28 31 32 50 C3' G B 905 OK 48 51 52 73 C3' G B 906 OK 71 74 75 96 C3' G B 907 OK 94 97 98 119 C3' C B 908 OK 117 120 121 139 C3' C B 909 OK 137 140 141 159 C3' C B 910 OK 157 160 161 177 C3' G C 915 OK 175 178 179 200 C3' G C 916 OK 198 201 202 223 C3' G C 917 OK 221 224 225 246 C3' C C 918 OK 244 247 248 266 C3' C C 919 OK 264 267 268 286 C3' C C 920 OK 284 287 288 306 C3' A C 921 OK 304 307 308 329 C3' A E 903 OK 327 330 331 351 C3' U E 904 OK 349 352 353 371 C3' G E 905 OK 369 372 373 394 C3' G E 906 OK 392 395 396 417 C3' G E 907 OK 415 418 419 440 C3' C E 908 OK 438 441 442 460 C3' C E 909 OK 458 461 462 480 C3' C E 910 OK 478 481 482 498 C3' G F 915 OK 496 499 500 521 C3' G F 916 OK 519 522 523 544 C3' G F 917 OK 542 545 546 567 C3' C F 918 OK 565 568 569 587 C3' C F 919 OK 585 588 589 607 C3' C F 920 OK 605 608 609 627 C3' A F 921 OK 625 628 629 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 6 C4' A B 903 OK 8 5 7 28 C4' U B 904 OK 30 27 29 48 C4' G B 905 OK 50 47 49 71 C4' G B 906 OK 73 70 72 94 C4' G B 907 OK 96 93 95 117 C4' C B 908 OK 119 116 118 137 C4' C B 909 OK 139 136 138 157 C4' C B 910 OK 159 156 158 175 C4' G C 915 OK 177 174 176 198 C4' G C 916 OK 200 197 199 221 C4' G C 917 OK 223 220 222 244 C4' C C 918 OK 246 243 245 264 C4' C C 919 OK 266 263 265 284 C4' C C 920 OK 286 283 285 304 C4' A C 921 OK 306 303 305 327 C4' A E 903 OK 329 326 328 349 C4' U E 904 OK 351 348 350 369 C4' G E 905 OK 371 368 370 392 C4' G E 906 OK 394 391 393 415 C4' G E 907 OK 417 414 416 438 C4' C E 908 OK 440 437 439 458 C4' C E 909 OK 460 457 459 478 C4' C E 910 OK 480 477 479 496 C4' G F 915 OK 498 495 497 519 C4' G F 916 OK 521 518 520 542 C4' G F 917 OK 544 541 543 565 C4' C F 918 OK 567 564 566 585 C4' C F 919 OK 587 584 586 605 C4' C F 920 OK 607 604 606 625 C4' A F 921 OK 627 624 626 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 5 C5' A B 903 4 6 27 C5' U B 904 26 28 47 C5' G B 905 46 48 70 C5' G B 906 69 71 93 C5' G B 907 92 94 116 C5' C B 908 115 117 136 C5' C B 909 135 137 156 C5' C B 910 155 157 174 C5' G C 915 173 175 197 C5' G C 916 196 198 220 C5' G C 917 219 221 243 C5' C C 918 242 244 263 C5' C C 919 262 264 283 C5' C C 920 282 284 303 C5' A C 921 302 304 326 C5' A E 903 325 327 348 C5' U E 904 347 349 368 C5' G E 905 367 369 391 C5' G E 906 390 392 414 C5' G E 907 413 415 437 C5' C E 908 436 438 457 C5' C E 909 456 458 477 C5' C E 910 476 478 495 C5' G F 915 494 496 518 C5' G F 916 517 519 541 C5' G F 917 540 542 564 C5' C F 918 563 565 584 C5' C F 919 583 585 604 C5' C F 920 603 605 624 C5' A F 921 623 625 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 1 P A B 903 distorted distorted 2 3 4 23 P U B 904 distorted distorted 9 24 25 26 43 P G B 905 distorted distorted 31 44 45 46 66 P G B 906 distorted distorted 51 67 68 69 89 P G B 907 distorted distorted 74 90 91 92 112 P C B 908 distorted distorted 97 113 114 115 132 P C B 909 distorted distorted 120 133 134 135 152 P C B 910 distorted distorted 140 153 154 155 193 P G C 916 distorted distorted 178 194 195 196 216 P G C 917 distorted distorted 201 217 218 219 239 P C C 918 distorted distorted 224 240 241 242 259 P C C 919 distorted distorted 247 260 261 262 279 P C C 920 distorted distorted 267 280 281 282 299 P A C 921 distorted distorted 287 300 301 302 322 P A E 903 distorted distorted 323 324 325 344 P U E 904 distorted distorted 330 345 346 347 364 P G E 905 distorted distorted 352 365 366 367 387 P G E 906 distorted distorted 372 388 389 390 410 P G E 907 distorted distorted 395 411 412 413 433 P C E 908 distorted distorted 418 434 435 436 453 P C E 909 distorted distorted 441 454 455 456 473 P C E 910 distorted distorted 461 474 475 476 514 P G F 916 distorted distorted 499 515 516 517 537 P G F 917 distorted distorted 522 538 539 540 560 P C F 918 distorted distorted 545 561 562 563 580 P C F 919 distorted distorted 568 581 582 583 600 P C F 920 distorted distorted 588 601 602 603 620 P A F 921 distorted distorted 608 621 622 623 ---------------------------------------------------------------------------------