ID code: '3IAY' 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' DA P 1 beta 4 9 7 29 C1' DT P 2 beta 25 30 28 49 C1' DC P 3 beta 45 50 48 68 C1' DC P 4 beta 64 69 67 87 C1' DT P 5 beta 83 88 86 107 C1' DC P 6 beta 103 108 106 126 C1' DC P 7 beta 122 127 125 145 C1' DC P 8 beta 141 146 144 164 C1' DC P 9 beta 160 165 163 183 C1' DT P 10 beta 179 184 182 203 C1' DA P 11 beta 199 204 202 222 C1' DOC P 12 beta 226 214 223 240 C1' DT T 1 beta 236 241 239 260 C1' DA T 2 beta 256 261 259 281 C1' DA T 3 beta 277 282 280 302 C1' DG T 4 beta 298 303 301 324 C1' DG T 5 beta 320 325 323 346 C1' DT T 6 beta 342 347 345 366 C1' DA T 7 beta 362 367 365 387 C1' DG T 8 beta 383 388 386 409 C1' DG T 9 beta 405 410 408 431 C1' DG T 10 beta 427 432 430 453 C1' DG T 11 beta 449 454 452 475 C1' DA T 12 beta 471 476 474 496 C1' DG T 13 beta 492 497 495 518 C1' DG T 14 beta 514 519 517 540 C1' DA T 15 beta 536 541 539 561 C1' DT T 16 beta 557 562 560 7608 C1' DCP A 986 beta 7612 7600 7609 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' DA P 1 8 5 28 C2' DT P 2 29 26 48 C2' DC P 3 49 46 67 C2' DC P 4 68 65 86 C2' DT P 5 87 84 106 C2' DC P 6 107 104 125 C2' DC P 7 126 123 144 C2' DC P 8 145 142 163 C2' DC P 9 164 161 182 C2' DT P 10 183 180 202 C2' DA P 11 203 200 223 C2' DOC P 12 222 224 239 C2' DT T 1 240 237 259 C2' DA T 2 260 257 280 C2' DA T 3 281 278 301 C2' DG T 4 302 299 323 C2' DG T 5 324 321 345 C2' DT T 6 346 343 365 C2' DA T 7 366 363 386 C2' DG T 8 387 384 408 C2' DG T 9 409 406 430 C2' DG T 10 431 428 452 C2' DG T 11 453 450 474 C2' DA T 12 475 472 495 C2' DG T 13 496 493 517 C2' DG T 14 518 515 539 C2' DA T 15 540 537 560 C2' DT T 16 561 558 7609 C2' DCP A 986 7608 7610 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' DA P 1 OK 3 6 7 26 C3' DT P 2 OK 24 27 28 46 C3' DC P 3 OK 44 47 48 65 C3' DC P 4 OK 63 66 67 84 C3' DT P 5 OK 82 85 86 104 C3' DC P 6 OK 102 105 106 123 C3' DC P 7 OK 121 124 125 142 C3' DC P 8 OK 140 143 144 161 C3' DC P 9 OK 159 162 163 180 C3' DT P 10 OK 178 181 182 200 C3' DA P 11 OK 198 201 202 224 C3' DOC P 12 225 223 237 C3' DT T 1 OK 235 238 239 257 C3' DA T 2 OK 255 258 259 278 C3' DA T 3 OK 276 279 280 299 C3' DG T 4 OK 297 300 301 321 C3' DG T 5 OK 319 322 323 343 C3' DT T 6 OK 341 344 345 363 C3' DA T 7 OK 361 364 365 384 C3' DG T 8 OK 382 385 386 406 C3' DG T 9 OK 404 407 408 428 C3' DG T 10 OK 426 429 430 450 C3' DG T 11 OK 448 451 452 472 C3' DA T 12 OK 470 473 474 493 C3' DG T 13 OK 491 494 495 515 C3' DG T 14 OK 513 516 517 537 C3' DA T 15 OK 535 538 539 558 C3' DT T 16 OK 556 559 560 7610 C3' DCP A 986 OK 7611 7613 7609 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' DA P 1 OK 5 2 4 24 C4' DT P 2 OK 26 23 25 44 C4' DC P 3 OK 46 43 45 63 C4' DC P 4 OK 65 62 64 82 C4' DT P 5 OK 84 81 83 102 C4' DC P 6 OK 104 101 103 121 C4' DC P 7 OK 123 120 122 140 C4' DC P 8 OK 142 139 141 159 C4' DC P 9 OK 161 158 160 178 C4' DT P 10 OK 180 177 179 198 C4' DA P 11 OK 200 197 199 225 C4' DOC P 12 OK 224 227 226 235 C4' DT T 1 OK 237 234 236 255 C4' DA T 2 OK 257 254 256 276 C4' DA T 3 OK 278 275 277 297 C4' DG T 4 OK 299 296 298 319 C4' DG T 5 OK 321 318 320 341 C4' DT T 6 OK 343 340 342 361 C4' DA T 7 OK 363 360 362 382 C4' DG T 8 OK 384 381 383 404 C4' DG T 9 OK 406 403 405 426 C4' DG T 10 OK 428 425 427 448 C4' DG T 11 OK 450 447 449 470 C4' DA T 12 OK 472 469 471 491 C4' DG T 13 OK 493 490 492 513 C4' DG T 14 OK 515 512 514 535 C4' DA T 15 OK 537 534 536 556 C4' DT T 16 OK 558 555 557 7611 C4' DCP A 986 OK 7610 7614 7612 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' DA P 1 1 3 23 C5' DT P 2 22 24 43 C5' DC P 3 42 44 62 C5' DC P 4 61 63 81 C5' DT P 5 80 82 101 C5' DC P 6 100 102 120 C5' DC P 7 119 121 139 C5' DC P 8 138 140 158 C5' DC P 9 157 159 177 C5' DT P 10 176 178 197 C5' DA P 11 196 198 227 C5' DOC P 12 228 225 234 C5' DT T 1 233 235 254 C5' DA T 2 253 255 275 C5' DA T 3 274 276 296 C5' DG T 4 295 297 318 C5' DG T 5 317 319 340 C5' DT T 6 339 341 360 C5' DA T 7 359 361 381 C5' DG T 8 380 382 403 C5' DG T 9 402 404 425 C5' DG T 10 424 426 447 C5' DG T 11 446 448 469 C5' DA T 12 468 470 490 C5' DG T 13 489 491 512 C5' DG T 14 511 513 534 C5' DA T 15 533 535 555 C5' DT T 16 554 556 7614 C5' DCP A 986 7615 7611 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 19 P DT P 2 distorted distorted 6 20 21 22 39 P DC P 3 distorted distorted 27 40 41 42 58 P DC P 4 distorted distorted 47 59 60 61 77 P DT P 5 distorted distorted 66 78 79 80 97 P DC P 6 distorted distorted 85 98 99 100 116 P DC P 7 distorted distorted 105 117 118 119 135 P DC P 8 distorted distorted 124 136 137 138 154 P DC P 9 distorted distorted 143 155 156 157 173 P DT P 10 distorted distorted 162 174 175 176 193 P DA P 11 distorted distorted 181 194 195 196 229 P DOC P 12 distorted distorted 201 230 231 228 250 P DA T 2 distorted distorted 238 251 252 253 271 P DA T 3 distorted distorted 258 272 273 274 292 P DG T 4 distorted distorted 279 293 294 295 314 P DG T 5 distorted distorted 300 315 316 317 336 P DT T 6 distorted distorted 322 337 338 339 356 P DA T 7 distorted distorted 344 357 358 359 377 P DG T 8 distorted distorted 364 378 379 380 399 P DG T 9 distorted distorted 385 400 401 402 421 P DG T 10 distorted distorted 407 422 423 424 443 P DG T 11 distorted distorted 429 444 445 446 465 P DA T 12 distorted distorted 451 466 467 468 486 P DG T 13 distorted distorted 473 487 488 489 508 P DG T 14 distorted distorted 494 509 510 511 530 P DA T 15 distorted distorted 516 531 532 533 551 P DT T 16 distorted distorted 538 552 553 554 ---------------------------------------------------------------------------------