ID code: '1PYI' 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' --------------------------------------------------------------------------------- 5 C1' T D 1 beta 4 6 17 28 C1' C D 2 beta 24 29 27 47 C1' G D 3 beta 43 48 46 69 C1' G D 4 beta 65 70 68 91 C1' C D 5 beta 87 92 90 110 C1' A D 6 beta 106 111 109 131 C1' A D 7 beta 127 132 130 149 C1' T D 8 beta 148 150 161 169 C1' T D 9 beta 168 170 181 192 C1' G D 10 beta 188 193 191 214 C1' C D 11 beta 210 215 213 233 C1' C D 12 beta 229 234 232 252 C1' G D 13 beta 248 253 251 274 C1' A D 14 beta 270 275 273 290 C1' T E 15 beta 289 291 302 313 C1' C E 16 beta 309 314 312 332 C1' G E 17 beta 328 333 331 354 C1' G E 18 beta 350 355 353 376 C1' C E 19 beta 372 377 375 395 C1' A E 20 beta 391 396 394 416 C1' A E 21 beta 412 417 415 434 C1' T E 22 beta 433 435 446 454 C1' T E 23 beta 453 455 466 477 C1' G E 24 beta 473 478 476 499 C1' C E 25 beta 495 500 498 518 C1' C E 26 beta 514 519 517 537 C1' G E 27 beta 533 538 536 559 C1' A E 28 beta 555 560 558 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 17 C2' T D 1 5 15 27 C2' C D 2 28 25 46 C2' G D 3 47 44 68 C2' G D 4 69 66 90 C2' C D 5 91 88 109 C2' A D 6 110 107 130 C2' A D 7 131 128 161 C2' T D 8 149 159 181 C2' T D 9 169 179 191 C2' G D 10 192 189 213 C2' C D 11 214 211 232 C2' C D 12 233 230 251 C2' G D 13 252 249 273 C2' A D 14 274 271 302 C2' T E 15 290 300 312 C2' C E 16 313 310 331 C2' G E 17 332 329 353 C2' G E 18 354 351 375 C2' C E 19 376 373 394 C2' A E 20 395 392 415 C2' A E 21 416 413 446 C2' T E 22 434 444 466 C2' T E 23 454 464 476 C2' G E 24 477 474 498 C2' C E 25 499 496 517 C2' C E 26 518 515 536 C2' G E 27 537 534 558 C2' A E 28 559 556 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 15 C3' T D 1 OK 3 16 17 25 C3' C D 2 OK 23 26 27 44 C3' G D 3 OK 42 45 46 66 C3' G D 4 OK 64 67 68 88 C3' C D 5 OK 86 89 90 107 C3' A D 6 OK 105 108 109 128 C3' A D 7 OK 126 129 130 159 C3' T D 8 OK 147 160 161 179 C3' T D 9 OK 167 180 181 189 C3' G D 10 OK 187 190 191 211 C3' C D 11 OK 209 212 213 230 C3' C D 12 OK 228 231 232 249 C3' G D 13 OK 247 250 251 271 C3' A D 14 OK 269 272 273 300 C3' T E 15 OK 288 301 302 310 C3' C E 16 OK 308 311 312 329 C3' G E 17 OK 327 330 331 351 C3' G E 18 OK 349 352 353 373 C3' C E 19 OK 371 374 375 392 C3' A E 20 OK 390 393 394 413 C3' A E 21 OK 411 414 415 444 C3' T E 22 OK 432 445 446 464 C3' T E 23 OK 452 465 466 474 C3' G E 24 OK 472 475 476 496 C3' C E 25 OK 494 497 498 515 C3' C E 26 OK 513 516 517 534 C3' G E 27 OK 532 535 536 556 C3' A E 28 OK 554 557 558 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' T D 1 OK 15 2 4 23 C4' C D 2 OK 25 22 24 42 C4' G D 3 OK 44 41 43 64 C4' G D 4 OK 66 63 65 86 C4' C D 5 OK 88 85 87 105 C4' A D 6 OK 107 104 106 126 C4' A D 7 OK 128 125 127 147 C4' T D 8 OK 159 146 148 167 C4' T D 9 OK 179 166 168 187 C4' G D 10 OK 189 186 188 209 C4' C D 11 OK 211 208 210 228 C4' C D 12 OK 230 227 229 247 C4' G D 13 OK 249 246 248 269 C4' A D 14 OK 271 268 270 288 C4' T E 15 OK 300 287 289 308 C4' C E 16 OK 310 307 309 327 C4' G E 17 OK 329 326 328 349 C4' G E 18 OK 351 348 350 371 C4' C E 19 OK 373 370 372 390 C4' A E 20 OK 392 389 391 411 C4' A E 21 OK 413 410 412 432 C4' T E 22 OK 444 431 433 452 C4' T E 23 OK 464 451 453 472 C4' G E 24 OK 474 471 473 494 C4' C E 25 OK 496 493 495 513 C4' C E 26 OK 515 512 514 532 C4' G E 27 OK 534 531 533 554 C4' A E 28 OK 556 553 555 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' T D 1 1 3 22 C5' C D 2 21 23 41 C5' G D 3 40 42 63 C5' G D 4 62 64 85 C5' C D 5 84 86 104 C5' A D 6 103 105 125 C5' A D 7 124 126 146 C5' T D 8 145 147 166 C5' T D 9 165 167 186 C5' G D 10 185 187 208 C5' C D 11 207 209 227 C5' C D 12 226 228 246 C5' G D 13 245 247 268 C5' A D 14 267 269 287 C5' T E 15 286 288 307 C5' C E 16 306 308 326 C5' G E 17 325 327 348 C5' G E 18 347 349 370 C5' C E 19 369 371 389 C5' A E 20 388 390 410 C5' A E 21 409 411 431 C5' T E 22 430 432 451 C5' T E 23 450 452 471 C5' G E 24 470 472 493 C5' C E 25 492 494 512 C5' C E 26 511 513 531 C5' G E 27 530 532 553 C5' A E 28 552 554 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C D 2 distorted distorted 16 19 20 21 37 P G D 3 distorted distorted 26 38 39 40 59 P G D 4 distorted distorted 45 60 61 62 81 P C D 5 distorted distorted 67 82 83 84 100 P A D 6 distorted distorted 89 101 102 103 121 P A D 7 distorted distorted 108 122 123 124 142 P T D 8 distorted distorted 129 143 144 145 162 P T D 9 distorted distorted 160 163 164 165 182 P G D 10 distorted distorted 180 183 184 185 204 P C D 11 distorted distorted 190 205 206 207 223 P C D 12 distorted distorted 212 224 225 226 242 P G D 13 distorted distorted 231 243 244 245 264 P A D 14 distorted distorted 250 265 266 267 303 P C E 16 distorted distorted 301 304 305 306 322 P G E 17 distorted distorted 311 323 324 325 344 P G E 18 distorted distorted 330 345 346 347 366 P C E 19 distorted distorted 352 367 368 369 385 P A E 20 distorted distorted 374 386 387 388 406 P A E 21 distorted distorted 393 407 408 409 427 P T E 22 distorted distorted 414 428 429 430 447 P T E 23 distorted distorted 445 448 449 450 467 P G E 24 distorted distorted 465 468 469 470 489 P C E 25 distorted distorted 475 490 491 492 508 P C E 26 distorted distorted 497 509 510 511 527 P G E 27 distorted distorted 516 528 529 530 549 P A E 28 distorted distorted 535 550 551 552 ---------------------------------------------------------------------------------