ID code: '1OH6' 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' A E 9 beta 167 172 170 192 C1' G E 10 beta 188 193 191 214 C1' C E 11 beta 210 215 213 233 C1' A E 12 beta 229 234 232 254 C1' C E 13 beta 250 255 253 273 C1' C E 14 beta 269 274 272 292 C1' A E 15 beta 288 293 291 313 C1' G E 16 beta 309 314 312 336 C1' C F 15 beta 332 337 335 355 C1' T F 16 beta 351 356 354 375 C1' G F 17 beta 371 376 374 397 C1' G F 18 beta 393 398 396 419 C1' T F 19 beta 415 420 418 439 C1' G F 20 beta 435 440 438 461 C1' C F 21 beta 457 462 460 480 C1' A F 22 beta 476 481 479 501 C1' T F 23 beta 497 502 500 521 C1' G F 24 beta 517 522 520 543 C1' G F 25 beta 539 544 542 565 C1' C F 26 beta 561 566 564 584 C1' A F 27 beta 580 585 583 605 C1' G F 28 beta 601 606 604 627 C1' C F 29 beta 623 628 626 646 C1' T F 30 beta 642 647 645 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- 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' A E 9 171 168 191 C2' G E 10 192 189 213 C2' C E 11 214 211 232 C2' A E 12 233 230 253 C2' C E 13 254 251 272 C2' C E 14 273 270 291 C2' A E 15 292 289 312 C2' G E 16 313 310 335 C2' C F 15 336 333 354 C2' T F 16 355 352 374 C2' G F 17 375 372 396 C2' G F 18 397 394 418 C2' T F 19 419 416 438 C2' G F 20 439 436 460 C2' C F 21 461 458 479 C2' A F 22 480 477 500 C2' T F 23 501 498 520 C2' G F 24 521 518 542 C2' G F 25 543 540 564 C2' C F 26 565 562 583 C2' A F 27 584 581 604 C2' G F 28 605 602 626 C2' C F 29 627 624 645 C2' T F 30 646 643 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A E 9 OK 166 169 170 189 C3' G E 10 OK 187 190 191 211 C3' C E 11 OK 209 212 213 230 C3' A E 12 OK 228 231 232 251 C3' C E 13 OK 249 252 253 270 C3' C E 14 OK 268 271 272 289 C3' A E 15 OK 287 290 291 310 C3' G E 16 OK 308 311 312 333 C3' C F 15 OK 331 334 335 352 C3' T F 16 OK 350 353 354 372 C3' G F 17 OK 370 373 374 394 C3' G F 18 OK 392 395 396 416 C3' T F 19 OK 414 417 418 436 C3' G F 20 OK 434 437 438 458 C3' C F 21 OK 456 459 460 477 C3' A F 22 OK 475 478 479 498 C3' T F 23 OK 496 499 500 518 C3' G F 24 OK 516 519 520 540 C3' G F 25 OK 538 541 542 562 C3' C F 26 OK 560 563 564 581 C3' A F 27 OK 579 582 583 602 C3' G F 28 OK 600 603 604 624 C3' C F 29 OK 622 625 626 643 C3' T F 30 OK 641 644 645 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A E 9 OK 168 165 167 187 C4' G E 10 OK 189 186 188 209 C4' C E 11 OK 211 208 210 228 C4' A E 12 OK 230 227 229 249 C4' C E 13 OK 251 248 250 268 C4' C E 14 OK 270 267 269 287 C4' A E 15 OK 289 286 288 308 C4' G E 16 OK 310 307 309 331 C4' C F 15 OK 333 330 332 350 C4' T F 16 OK 352 349 351 370 C4' G F 17 OK 372 369 371 392 C4' G F 18 OK 394 391 393 414 C4' T F 19 OK 416 413 415 434 C4' G F 20 OK 436 433 435 456 C4' C F 21 OK 458 455 457 475 C4' A F 22 OK 477 474 476 496 C4' T F 23 OK 498 495 497 516 C4' G F 24 OK 518 515 517 538 C4' G F 25 OK 540 537 539 560 C4' C F 26 OK 562 559 561 579 C4' A F 27 OK 581 578 580 600 C4' G F 28 OK 602 599 601 622 C4' C F 29 OK 624 621 623 641 C4' T F 30 OK 643 640 642 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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' A E 9 164 166 186 C5' G E 10 185 187 208 C5' C E 11 207 209 227 C5' A E 12 226 228 248 C5' C E 13 247 249 267 C5' C E 14 266 268 286 C5' A E 15 285 287 307 C5' G E 16 306 308 330 C5' C F 15 329 331 349 C5' T F 16 348 350 369 C5' G F 17 368 370 391 C5' G F 18 390 392 413 C5' T F 19 412 414 433 C5' G F 20 432 434 455 C5' C F 21 454 456 474 C5' A F 22 473 475 495 C5' T F 23 494 496 515 C5' G F 24 514 516 537 C5' G F 25 536 538 559 C5' C F 26 558 560 578 C5' A F 27 577 579 599 C5' G F 28 598 600 621 C5' C F 29 620 622 640 C5' T F 30 639 641 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- 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 A E 9 distorted distorted 148 162 163 164 182 P G E 10 distorted distorted 169 183 184 185 204 P C E 11 distorted distorted 190 205 206 207 223 P A E 12 distorted distorted 212 224 225 226 244 P C E 13 distorted distorted 231 245 246 247 263 P C E 14 distorted distorted 252 264 265 266 282 P A E 15 distorted distorted 271 283 284 285 303 P G E 16 distorted distorted 290 304 305 306 326 P C F 15 distorted distorted 327 328 329 345 P T F 16 distorted distorted 334 346 347 348 365 P G F 17 distorted distorted 353 366 367 368 387 P G F 18 distorted distorted 373 388 389 390 409 P T F 19 distorted distorted 395 410 411 412 429 P G F 20 distorted distorted 417 430 431 432 451 P C F 21 distorted distorted 437 452 453 454 470 P A F 22 distorted distorted 459 471 472 473 491 P T F 23 distorted distorted 478 492 493 494 511 P G F 24 distorted distorted 499 512 513 514 533 P G F 25 distorted distorted 519 534 535 536 555 P C F 26 distorted distorted 541 556 557 558 574 P A F 27 distorted distorted 563 575 576 577 595 P G F 28 distorted distorted 582 596 597 598 617 P C F 29 distorted distorted 603 618 619 620 636 P T F 30 distorted distorted 625 637 638 639 ---------------------------------------------------------------------------------