ID code: '1QN3' 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' --------------------------------------------------------------------------------- 6 C1' G C 201 beta 2 7 5 28 C1' C C 202 beta 24 29 27 47 C1' T C 203 beta 43 48 46 67 C1' A C 204 beta 63 68 66 88 C1' T C 205 beta 84 89 87 108 C1' A C 206 beta 104 109 107 129 C1' A C 207 beta 125 130 128 150 C1' A C 208 beta 146 151 149 171 C1' C C 209 beta 167 172 170 190 C1' G C 210 beta 186 191 189 212 C1' G C 211 beta 208 213 211 234 C1' G C 212 beta 230 235 233 256 C1' C C 213 beta 252 257 255 275 C1' A C 214 beta 271 276 274 294 C1' T D 215 beta 290 295 293 314 C1' G D 216 beta 310 315 313 336 C1' C D 217 beta 332 337 335 355 C1' C D 218 beta 351 356 354 374 C1' C D 219 beta 370 375 373 393 C1' G D 220 beta 389 394 392 415 C1' T D 221 beta 411 416 414 435 C1' T D 222 beta 431 436 434 455 C1' T D 223 beta 451 456 454 475 C1' A D 224 beta 471 476 474 496 C1' T D 225 beta 492 497 495 516 C1' A D 226 beta 512 517 515 537 C1' G D 227 beta 533 538 536 559 C1' C D 228 beta 555 560 558 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 5 C2' G C 201 6 3 27 C2' C C 202 28 25 46 C2' T C 203 47 44 66 C2' A C 204 67 64 87 C2' T C 205 88 85 107 C2' A C 206 108 105 128 C2' A C 207 129 126 149 C2' A C 208 150 147 170 C2' C C 209 171 168 189 C2' G C 210 190 187 211 C2' G C 211 212 209 233 C2' G C 212 234 231 255 C2' C C 213 256 253 274 C2' A C 214 275 272 293 C2' T D 215 294 291 313 C2' G D 216 314 311 335 C2' C D 217 336 333 354 C2' C D 218 355 352 373 C2' C D 219 374 371 392 C2' G D 220 393 390 414 C2' T D 221 415 412 434 C2' T D 222 435 432 454 C2' T D 223 455 452 474 C2' A D 224 475 472 495 C2' T D 225 496 493 515 C2' A D 226 516 513 536 C2' G D 227 537 534 558 C2' C D 228 559 556 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 3 C3' G C 201 OK 1 4 5 25 C3' C C 202 OK 23 26 27 44 C3' T C 203 OK 42 45 46 64 C3' A C 204 OK 62 65 66 85 C3' T C 205 OK 83 86 87 105 C3' A C 206 OK 103 106 107 126 C3' A C 207 OK 124 127 128 147 C3' A C 208 OK 145 148 149 168 C3' C C 209 OK 166 169 170 187 C3' G C 210 OK 185 188 189 209 C3' G C 211 OK 207 210 211 231 C3' G C 212 OK 229 232 233 253 C3' C C 213 OK 251 254 255 272 C3' A C 214 OK 270 273 274 291 C3' T D 215 OK 289 292 293 311 C3' G D 216 OK 309 312 313 333 C3' C D 217 OK 331 334 335 352 C3' C D 218 OK 350 353 354 371 C3' C D 219 OK 369 372 373 390 C3' G D 220 OK 388 391 392 412 C3' T D 221 OK 410 413 414 432 C3' T D 222 OK 430 433 434 452 C3' T D 223 OK 450 453 454 472 C3' A D 224 OK 470 473 474 493 C3' T D 225 OK 491 494 495 513 C3' A D 226 OK 511 514 515 534 C3' G D 227 OK 532 535 536 556 C3' C D 228 OK 554 557 558 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 1 C4' G C 201 3 2 23 C4' C C 202 OK 25 22 24 42 C4' T C 203 OK 44 41 43 62 C4' A C 204 OK 64 61 63 83 C4' T C 205 OK 85 82 84 103 C4' A C 206 OK 105 102 104 124 C4' A C 207 OK 126 123 125 145 C4' A C 208 OK 147 144 146 166 C4' C C 209 OK 168 165 167 185 C4' G C 210 OK 187 184 186 207 C4' G C 211 OK 209 206 208 229 C4' G C 212 OK 231 228 230 251 C4' C C 213 OK 253 250 252 270 C4' A C 214 OK 272 269 271 289 C4' T D 215 OK 291 288 290 309 C4' G D 216 OK 311 308 310 331 C4' C D 217 OK 333 330 332 350 C4' C D 218 OK 352 349 351 369 C4' C D 219 OK 371 368 370 388 C4' G D 220 OK 390 387 389 410 C4' T D 221 OK 412 409 411 430 C4' T D 222 OK 432 429 431 450 C4' T D 223 OK 452 449 451 470 C4' A D 224 OK 472 469 471 491 C4' T D 225 OK 493 490 492 511 C4' A D 226 OK 513 510 512 532 C4' G D 227 OK 534 531 533 554 C4' C D 228 OK 556 553 555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 22 C5' C C 202 21 23 41 C5' T C 203 40 42 61 C5' A C 204 60 62 82 C5' T C 205 81 83 102 C5' A C 206 101 103 123 C5' A C 207 122 124 144 C5' A C 208 143 145 165 C5' C C 209 164 166 184 C5' G C 210 183 185 206 C5' G C 211 205 207 228 C5' G C 212 227 229 250 C5' C C 213 249 251 269 C5' A C 214 268 270 288 C5' T D 215 287 289 308 C5' G D 216 307 309 330 C5' C D 217 329 331 349 C5' C D 218 348 350 368 C5' C D 219 367 369 387 C5' G D 220 386 388 409 C5' T D 221 408 410 429 C5' T D 222 428 430 449 C5' T D 223 448 450 469 C5' A D 224 468 470 490 C5' T D 225 489 491 510 C5' A D 226 509 511 531 C5' G D 227 530 532 553 C5' C D 228 552 554 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C C 202 OK OK 4 19 20 21 37 P T C 203 OK OK 26 38 39 40 57 P A C 204 OK OK 45 58 59 60 78 P T C 205 OK OK 65 79 80 81 98 P A C 206 OK OK 86 99 100 101 119 P A C 207 OK OK 106 120 121 122 140 P A C 208 OK OK 127 141 142 143 161 P C C 209 OK OK 148 162 163 164 180 P G C 210 OK OK 169 181 182 183 202 P G C 211 OK OK 188 203 204 205 224 P G C 212 OK OK 210 225 226 227 246 P C C 213 OK OK 232 247 248 249 265 P A C 214 OK OK 254 266 267 268 304 P G D 216 OK OK 292 305 306 307 326 P C D 217 OK OK 312 327 328 329 345 P C D 218 OK OK 334 346 347 348 364 P C D 219 OK OK 353 365 366 367 383 P G D 220 OK OK 372 384 385 386 405 P T D 221 OK OK 391 406 407 408 425 P T D 222 OK OK 413 426 427 428 445 P T D 223 OK OK 433 446 447 448 465 P A D 224 OK OK 453 466 467 468 486 P T D 225 OK OK 473 487 488 489 506 P A D 226 OK OK 494 507 508 509 527 P G D 227 OK OK 514 528 529 530 549 P C D 228 OK OK 535 550 551 552 ---------------------------------------------------------------------------------