ID code: '2VAL' 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' --------------------------------------------------------------------------------- 9 C1' G A 1 beta 4 10 7 32 C1' C A 2 beta 27 33 30 52 C1' G A 3 beta 47 53 50 75 C1' G A 4 beta 70 76 73 98 C1' G A 5 beta 93 99 96 121 C1' A A 6 beta 116 122 119 143 C1' A A 7 beta 138 144 141 163 C1' G B 1 beta 158 164 161 186 C1' C B 2 beta 181 187 184 206 C1' G B 3 beta 201 207 204 229 C1' G B 4 beta 224 230 227 252 C1' G B 5 beta 247 253 250 275 C1' A B 6 beta 270 276 273 297 C1' A B 7 beta 292 298 295 317 C1' U C 66 beta 312 318 315 337 C1' U C 67 beta 332 338 335 357 C1' C C 68 beta 352 358 355 377 C1' C C 69 beta 372 378 375 397 C1' C C 70 beta 392 398 395 417 C1' G C 71 beta 412 418 415 440 C1' C C 72 beta 435 441 438 458 C1' U D 66 beta 453 459 456 478 C1' U D 67 beta 473 479 476 498 C1' C D 68 beta 493 499 496 518 C1' C D 69 beta 513 519 516 538 C1' C D 70 beta 533 539 536 558 C1' G D 71 beta 553 559 556 581 C1' C D 72 beta 576 582 579 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G A 1 OK 9 5 8 30 C2' C A 2 OK 32 28 31 50 C2' G A 3 OK 52 48 51 73 C2' G A 4 OK 75 71 74 96 C2' G A 5 OK 98 94 97 119 C2' A A 6 OK 121 117 120 141 C2' A A 7 OK 143 139 142 161 C2' G B 1 OK 163 159 162 184 C2' C B 2 OK 186 182 185 204 C2' G B 3 OK 206 202 205 227 C2' G B 4 OK 229 225 228 250 C2' G B 5 OK 252 248 251 273 C2' A B 6 OK 275 271 274 295 C2' A B 7 OK 297 293 296 315 C2' U C 66 OK 317 313 316 335 C2' U C 67 OK 337 333 336 355 C2' C C 68 OK 357 353 356 375 C2' C C 69 OK 377 373 376 395 C2' C C 70 OK 397 393 396 415 C2' G C 71 OK 417 413 416 438 C2' C C 72 OK 440 436 439 456 C2' U D 66 OK 458 454 457 476 C2' U D 67 OK 478 474 477 496 C2' C D 68 OK 498 494 497 516 C2' C D 69 OK 518 514 517 536 C2' C D 70 OK 538 534 537 556 C2' G D 71 OK 558 554 557 579 C2' C D 72 OK 581 577 580 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G A 1 OK 3 6 7 28 C3' C A 2 OK 26 29 30 48 C3' G A 3 OK 46 49 50 71 C3' G A 4 OK 69 72 73 94 C3' G A 5 OK 92 95 96 117 C3' A A 6 OK 115 118 119 139 C3' A A 7 OK 137 140 141 159 C3' G B 1 OK 157 160 161 182 C3' C B 2 OK 180 183 184 202 C3' G B 3 OK 200 203 204 225 C3' G B 4 OK 223 226 227 248 C3' G B 5 OK 246 249 250 271 C3' A B 6 OK 269 272 273 293 C3' A B 7 OK 291 294 295 313 C3' U C 66 OK 311 314 315 333 C3' U C 67 OK 331 334 335 353 C3' C C 68 OK 351 354 355 373 C3' C C 69 OK 371 374 375 393 C3' C C 70 OK 391 394 395 413 C3' G C 71 OK 411 414 415 436 C3' C C 72 OK 434 437 438 454 C3' U D 66 OK 452 455 456 474 C3' U D 67 OK 472 475 476 494 C3' C D 68 OK 492 495 496 514 C3' C D 69 OK 512 515 516 534 C3' C D 70 OK 532 535 536 554 C3' G D 71 OK 552 555 556 577 C3' C D 72 OK 575 578 579 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G A 1 OK 5 2 4 26 C4' C A 2 OK 28 25 27 46 C4' G A 3 OK 48 45 47 69 C4' G A 4 OK 71 68 70 92 C4' G A 5 OK 94 91 93 115 C4' A A 6 OK 117 114 116 137 C4' A A 7 OK 139 136 138 157 C4' G B 1 OK 159 156 158 180 C4' C B 2 OK 182 179 181 200 C4' G B 3 OK 202 199 201 223 C4' G B 4 OK 225 222 224 246 C4' G B 5 OK 248 245 247 269 C4' A B 6 OK 271 268 270 291 C4' A B 7 OK 293 290 292 311 C4' U C 66 OK 313 310 312 331 C4' U C 67 OK 333 330 332 351 C4' C C 68 OK 353 350 352 371 C4' C C 69 OK 373 370 372 391 C4' C C 70 OK 393 390 392 411 C4' G C 71 OK 413 410 412 434 C4' C C 72 OK 436 433 435 452 C4' U D 66 OK 454 451 453 472 C4' U D 67 OK 474 471 473 492 C4' C D 68 OK 494 491 493 512 C4' C D 69 OK 514 511 513 532 C4' C D 70 OK 534 531 533 552 C4' G D 71 OK 554 551 553 575 C4' C D 72 OK 577 574 576 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G A 1 1 3 25 C5' C A 2 24 26 45 C5' G A 3 44 46 68 C5' G A 4 67 69 91 C5' G A 5 90 92 114 C5' A A 6 113 115 136 C5' A A 7 135 137 156 C5' G B 1 155 157 179 C5' C B 2 178 180 199 C5' G B 3 198 200 222 C5' G B 4 221 223 245 C5' G B 5 244 246 268 C5' A B 6 267 269 290 C5' A B 7 289 291 310 C5' U C 66 309 311 330 C5' U C 67 329 331 350 C5' C C 68 349 351 370 C5' C C 69 369 371 390 C5' C C 70 389 391 410 C5' G C 71 409 411 433 C5' C C 72 432 434 451 C5' U D 66 450 452 471 C5' U D 67 470 472 491 C5' C D 68 490 492 511 C5' C D 69 510 512 531 C5' C D 70 530 532 551 C5' G D 71 550 552 574 C5' C D 72 573 575 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 21 P C A 2 distorted distorted 6 22 23 24 41 P G A 3 distorted distorted 29 42 43 44 64 P G A 4 distorted distorted 49 65 66 67 87 P G A 5 distorted distorted 72 88 89 90 110 P A A 6 distorted distorted 95 111 112 113 132 P A A 7 distorted distorted 118 133 134 135 175 P C B 2 distorted distorted 160 176 177 178 195 P G B 3 distorted distorted 183 196 197 198 218 P G B 4 distorted distorted 203 219 220 221 241 P G B 5 distorted distorted 226 242 243 244 264 P A B 6 distorted distorted 249 265 266 267 286 P A B 7 distorted distorted 272 287 288 289 326 P U C 67 distorted distorted 314 327 328 329 346 P C C 68 distorted distorted 334 347 348 349 366 P C C 69 distorted distorted 354 367 368 369 386 P C C 70 distorted distorted 374 387 388 389 406 P G C 71 distorted distorted 394 407 408 409 429 P C C 72 distorted distorted 414 430 431 432 467 P U D 67 distorted distorted 455 468 469 470 487 P C D 68 distorted distorted 475 488 489 490 507 P C D 69 distorted distorted 495 508 509 510 527 P C D 70 distorted distorted 515 528 529 530 547 P G D 71 distorted distorted 535 548 549 550 570 P C D 72 distorted distorted 555 571 572 573 ---------------------------------------------------------------------------------