ID code: '1G2D' 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 A 2 beta 4 9 7 30 C1' A A 3 beta 26 31 29 51 C1' C A 4 beta 47 52 50 70 C1' G A 5 beta 66 71 69 92 C1' C A 6 beta 88 93 91 111 C1' T A 7 beta 107 112 110 131 C1' A A 8 beta 127 132 130 152 C1' T A 9 beta 148 153 151 172 C1' A A 10 beta 168 173 171 193 C1' A A 11 beta 189 194 192 214 C1' A A 12 beta 210 215 213 235 C1' A A 13 beta 231 236 234 256 C1' G A 14 beta 252 257 255 278 C1' G A 15 beta 274 279 277 300 C1' A A 16 beta 296 301 299 319 C1' T B 18 beta 315 320 318 339 C1' C B 19 beta 335 340 338 358 C1' C B 20 beta 354 359 357 377 C1' T B 21 beta 373 378 376 397 C1' T B 22 beta 393 398 396 417 C1' T B 23 beta 413 418 416 437 C1' T B 24 beta 433 438 436 457 C1' A B 25 beta 453 458 456 478 C1' T B 26 beta 474 479 477 498 C1' A B 27 beta 494 499 497 519 C1' G B 28 beta 515 520 518 541 C1' C B 29 beta 537 542 540 560 C1' G B 30 beta 556 561 559 582 C1' T B 31 beta 578 583 581 602 C1' C B 32 beta 598 603 601 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 2 8 5 29 C2' A A 3 30 27 50 C2' C A 4 51 48 69 C2' G A 5 70 67 91 C2' C A 6 92 89 110 C2' T A 7 111 108 130 C2' A A 8 131 128 151 C2' T A 9 152 149 171 C2' A A 10 172 169 192 C2' A A 11 193 190 213 C2' A A 12 214 211 234 C2' A A 13 235 232 255 C2' G A 14 256 253 277 C2' G A 15 278 275 299 C2' A A 16 300 297 318 C2' T B 18 319 316 338 C2' C B 19 339 336 357 C2' C B 20 358 355 376 C2' T B 21 377 374 396 C2' T B 22 397 394 416 C2' T B 23 417 414 436 C2' T B 24 437 434 456 C2' A B 25 457 454 477 C2' T B 26 478 475 497 C2' A B 27 498 495 518 C2' G B 28 519 516 540 C2' C B 29 541 538 559 C2' G B 30 560 557 581 C2' T B 31 582 579 601 C2' C B 32 602 599 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 2 OK 3 6 7 27 C3' A A 3 OK 25 28 29 48 C3' C A 4 OK 46 49 50 67 C3' G A 5 OK 65 68 69 89 C3' C A 6 OK 87 90 91 108 C3' T A 7 OK 106 109 110 128 C3' A A 8 OK 126 129 130 149 C3' T A 9 OK 147 150 151 169 C3' A A 10 OK 167 170 171 190 C3' A A 11 OK 188 191 192 211 C3' A A 12 OK 209 212 213 232 C3' A A 13 OK 230 233 234 253 C3' G A 14 OK 251 254 255 275 C3' G A 15 OK 273 276 277 297 C3' A A 16 OK 295 298 299 316 C3' T B 18 OK 314 317 318 336 C3' C B 19 OK 334 337 338 355 C3' C B 20 OK 353 356 357 374 C3' T B 21 OK 372 375 376 394 C3' T B 22 OK 392 395 396 414 C3' T B 23 OK 412 415 416 434 C3' T B 24 OK 432 435 436 454 C3' A B 25 OK 452 455 456 475 C3' T B 26 OK 473 476 477 495 C3' A B 27 OK 493 496 497 516 C3' G B 28 OK 514 517 518 538 C3' C B 29 OK 536 539 540 557 C3' G B 30 OK 555 558 559 579 C3' T B 31 OK 577 580 581 599 C3' C B 32 OK 597 600 601 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 2 OK 5 2 4 25 C4' A A 3 OK 27 24 26 46 C4' C A 4 OK 48 45 47 65 C4' G A 5 OK 67 64 66 87 C4' C A 6 OK 89 86 88 106 C4' T A 7 OK 108 105 107 126 C4' A A 8 OK 128 125 127 147 C4' T A 9 OK 149 146 148 167 C4' A A 10 OK 169 166 168 188 C4' A A 11 OK 190 187 189 209 C4' A A 12 OK 211 208 210 230 C4' A A 13 OK 232 229 231 251 C4' G A 14 OK 253 250 252 273 C4' G A 15 OK 275 272 274 295 C4' A A 16 OK 297 294 296 314 C4' T B 18 OK 316 313 315 334 C4' C B 19 OK 336 333 335 353 C4' C B 20 OK 355 352 354 372 C4' T B 21 OK 374 371 373 392 C4' T B 22 OK 394 391 393 412 C4' T B 23 OK 414 411 413 432 C4' T B 24 OK 434 431 433 452 C4' A B 25 OK 454 451 453 473 C4' T B 26 OK 475 472 474 493 C4' A B 27 OK 495 492 494 514 C4' G B 28 OK 516 513 515 536 C4' C B 29 OK 538 535 537 555 C4' G B 30 OK 557 554 556 577 C4' T B 31 OK 579 576 578 597 C4' C B 32 OK 599 596 598 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 2 1 3 24 C5' A A 3 23 25 45 C5' C A 4 44 46 64 C5' G A 5 63 65 86 C5' C A 6 85 87 105 C5' T A 7 104 106 125 C5' A A 8 124 126 146 C5' T A 9 145 147 166 C5' A A 10 165 167 187 C5' A A 11 186 188 208 C5' A A 12 207 209 229 C5' A A 13 228 230 250 C5' G A 14 249 251 272 C5' G A 15 271 273 294 C5' A A 16 293 295 313 C5' T B 18 312 314 333 C5' C B 19 332 334 352 C5' C B 20 351 353 371 C5' T B 21 370 372 391 C5' T B 22 390 392 411 C5' T B 23 410 412 431 C5' T B 24 430 432 451 C5' A B 25 450 452 472 C5' T B 26 471 473 492 C5' A B 27 491 493 513 C5' G B 28 512 514 535 C5' C B 29 534 536 554 C5' G B 30 553 555 576 C5' T B 31 575 577 596 C5' C B 32 595 597 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P A A 3 distorted distorted 6 21 22 23 41 P C A 4 distorted distorted 28 42 43 44 60 P G A 5 distorted distorted 49 61 62 63 82 P C A 6 distorted distorted 68 83 84 85 101 P T A 7 distorted distorted 90 102 103 104 121 P A A 8 distorted distorted 109 122 123 124 142 P T A 9 distorted distorted 129 143 144 145 162 P A A 10 distorted distorted 150 163 164 165 183 P A A 11 distorted distorted 170 184 185 186 204 P A A 12 distorted distorted 191 205 206 207 225 P A A 13 distorted distorted 212 226 227 228 246 P G A 14 distorted distorted 233 247 248 249 268 P G A 15 distorted distorted 254 269 270 271 290 P A A 16 distorted distorted 276 291 292 293 329 P C B 19 distorted distorted 317 330 331 332 348 P C B 20 distorted distorted 337 349 350 351 367 P T B 21 distorted distorted 356 368 369 370 387 P T B 22 distorted distorted 375 388 389 390 407 P T B 23 distorted distorted 395 408 409 410 427 P T B 24 distorted distorted 415 428 429 430 447 P A B 25 distorted distorted 435 448 449 450 468 P T B 26 distorted distorted 455 469 470 471 488 P A B 27 distorted distorted 476 489 490 491 509 P G B 28 distorted distorted 496 510 511 512 531 P C B 29 distorted distorted 517 532 533 534 550 P G B 30 distorted distorted 539 551 552 553 572 P T B 31 distorted distorted 558 573 574 575 592 P C B 32 distorted distorted 580 593 594 595 ---------------------------------------------------------------------------------