ID code: '1QN5' 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 E 201 beta 4 9 7 30 C1' C E 202 beta 26 31 29 49 C1' T E 203 beta 45 50 48 69 C1' A E 204 beta 65 70 68 90 C1' T E 205 beta 86 91 89 110 C1' A E 206 beta 106 111 109 131 C1' A E 207 beta 127 132 130 152 C1' G E 208 beta 148 153 151 174 C1' A E 209 beta 170 175 173 195 C1' G E 210 beta 191 196 194 217 C1' G E 211 beta 213 218 216 239 C1' G E 212 beta 235 240 238 261 C1' C E 213 beta 257 262 260 280 C1' A E 214 beta 276 281 279 299 C1' T F 215 beta 295 300 298 319 C1' G F 216 beta 315 320 318 341 C1' C F 217 beta 337 342 340 360 C1' C F 218 beta 356 361 359 379 C1' C F 219 beta 375 380 378 398 C1' T F 220 beta 394 399 397 418 C1' C F 221 beta 414 419 417 437 C1' T F 222 beta 433 438 436 457 C1' T F 223 beta 453 458 456 477 C1' A F 224 beta 473 478 476 498 C1' T F 225 beta 494 499 497 518 C1' A F 226 beta 514 519 517 539 C1' G F 227 beta 535 540 538 561 C1' C F 228 beta 557 562 560 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' G E 201 8 5 29 C2' C E 202 30 27 48 C2' T E 203 49 46 68 C2' A E 204 69 66 89 C2' T E 205 90 87 109 C2' A E 206 110 107 130 C2' A E 207 131 128 151 C2' G E 208 152 149 173 C2' A E 209 174 171 194 C2' G E 210 195 192 216 C2' G E 211 217 214 238 C2' G E 212 239 236 260 C2' C E 213 261 258 279 C2' A E 214 280 277 298 C2' T F 215 299 296 318 C2' G F 216 319 316 340 C2' C F 217 341 338 359 C2' C F 218 360 357 378 C2' C F 219 379 376 397 C2' T F 220 398 395 417 C2' C F 221 418 415 436 C2' T F 222 437 434 456 C2' T F 223 457 454 476 C2' A F 224 477 474 497 C2' T F 225 498 495 517 C2' A F 226 518 515 538 C2' G F 227 539 536 560 C2' C F 228 561 558 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' G E 201 OK 3 6 7 27 C3' C E 202 OK 25 28 29 46 C3' T E 203 OK 44 47 48 66 C3' A E 204 OK 64 67 68 87 C3' T E 205 OK 85 88 89 107 C3' A E 206 OK 105 108 109 128 C3' A E 207 OK 126 129 130 149 C3' G E 208 OK 147 150 151 171 C3' A E 209 OK 169 172 173 192 C3' G E 210 OK 190 193 194 214 C3' G E 211 OK 212 215 216 236 C3' G E 212 OK 234 237 238 258 C3' C E 213 OK 256 259 260 277 C3' A E 214 OK 275 278 279 296 C3' T F 215 OK 294 297 298 316 C3' G F 216 OK 314 317 318 338 C3' C F 217 OK 336 339 340 357 C3' C F 218 OK 355 358 359 376 C3' C F 219 OK 374 377 378 395 C3' T F 220 OK 393 396 397 415 C3' C F 221 OK 413 416 417 434 C3' T F 222 OK 432 435 436 454 C3' T F 223 OK 452 455 456 474 C3' A F 224 OK 472 475 476 495 C3' T F 225 OK 493 496 497 515 C3' A F 226 OK 513 516 517 536 C3' G F 227 OK 534 537 538 558 C3' C F 228 OK 556 559 560 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' G E 201 OK 5 2 4 25 C4' C E 202 OK 27 24 26 44 C4' T E 203 OK 46 43 45 64 C4' A E 204 OK 66 63 65 85 C4' T E 205 OK 87 84 86 105 C4' A E 206 OK 107 104 106 126 C4' A E 207 OK 128 125 127 147 C4' G E 208 OK 149 146 148 169 C4' A E 209 OK 171 168 170 190 C4' G E 210 OK 192 189 191 212 C4' G E 211 OK 214 211 213 234 C4' G E 212 OK 236 233 235 256 C4' C E 213 OK 258 255 257 275 C4' A E 214 OK 277 274 276 294 C4' T F 215 OK 296 293 295 314 C4' G F 216 OK 316 313 315 336 C4' C F 217 OK 338 335 337 355 C4' C F 218 OK 357 354 356 374 C4' C F 219 OK 376 373 375 393 C4' T F 220 OK 395 392 394 413 C4' C F 221 OK 415 412 414 432 C4' T F 222 OK 434 431 433 452 C4' T F 223 OK 454 451 453 472 C4' A F 224 OK 474 471 473 493 C4' T F 225 OK 495 492 494 513 C4' A F 226 OK 515 512 514 534 C4' G F 227 OK 536 533 535 556 C4' C F 228 OK 558 555 557 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' G E 201 1 3 24 C5' C E 202 23 25 43 C5' T E 203 42 44 63 C5' A E 204 62 64 84 C5' T E 205 83 85 104 C5' A E 206 103 105 125 C5' A E 207 124 126 146 C5' G E 208 145 147 168 C5' A E 209 167 169 189 C5' G E 210 188 190 211 C5' G E 211 210 212 233 C5' G E 212 232 234 255 C5' C E 213 254 256 274 C5' A E 214 273 275 293 C5' T F 215 292 294 313 C5' G F 216 312 314 335 C5' C F 217 334 336 354 C5' C F 218 353 355 373 C5' C F 219 372 374 392 C5' T F 220 391 393 412 C5' C F 221 411 413 431 C5' T F 222 430 432 451 C5' T F 223 450 452 471 C5' A F 224 470 472 492 C5' T F 225 491 493 512 C5' A F 226 511 513 533 C5' G F 227 532 534 555 C5' C F 228 554 556 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 20 P C E 202 OK OK 6 21 22 23 39 P T E 203 OK OK 28 40 41 42 59 P A E 204 OK OK 47 60 61 62 80 P T E 205 OK OK 67 81 82 83 100 P A E 206 OK OK 88 101 102 103 121 P A E 207 OK OK 108 122 123 124 142 P G E 208 OK OK 129 143 144 145 164 P A E 209 OK OK 150 165 166 167 185 P G E 210 OK OK 172 186 187 188 207 P G E 211 OK OK 193 208 209 210 229 P G E 212 OK OK 215 230 231 232 251 P C E 213 OK OK 237 252 253 254 270 P A E 214 OK OK 259 271 272 273 309 P G F 216 OK OK 297 310 311 312 331 P C F 217 OK OK 317 332 333 334 350 P C F 218 OK OK 339 351 352 353 369 P C F 219 OK OK 358 370 371 372 388 P T F 220 OK OK 377 389 390 391 408 P C F 221 OK OK 396 409 410 411 427 P T F 222 OK OK 416 428 429 430 447 P T F 223 OK OK 435 448 449 450 467 P A F 224 OK OK 455 468 469 470 488 P T F 225 OK OK 475 489 490 491 508 P A F 226 OK OK 496 509 510 511 529 P G F 227 OK OK 516 530 531 532 551 P C F 228 OK OK 537 552 553 554 ---------------------------------------------------------------------------------