ID code: '4L8R' 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' C A 1 beta 4 10 7 29 C1' C A 2 beta 24 30 27 49 C1' A A 3 beta 44 50 47 71 C1' A A 4 beta 66 72 69 93 C1' A A 5 beta 88 94 91 115 C1' G A 6 beta 110 116 113 138 C1' G A 7 beta 133 139 136 161 C1' C A 8 beta 156 162 159 181 C1' U A 9 beta 176 182 179 201 C1' C A 10 beta 196 202 199 221 C1' U A 11 beta 216 222 219 241 C1' U A 12 beta 236 242 239 261 C1' U A 13 beta 256 262 259 281 C1' U A 14 beta 276 282 279 301 C1' C A 15 beta 296 302 299 321 C1' A A 16 beta 316 322 319 343 C1' G A 17 beta 338 344 341 366 C1' A A 18 beta 361 367 364 388 C1' G A 19 beta 383 389 386 411 C1' C A 20 beta 406 412 409 431 C1' C A 21 beta 426 432 429 451 C1' A A 22 beta 446 452 449 473 C1' C A 23 beta 468 474 471 493 C1' C A 24 beta 488 494 491 513 C1' C A 25 beta 508 514 511 533 C1' A A 26 beta 528 534 531 3400 C1' U D 9 beta 3395 3401 3398 3420 C1' C D 10 beta 3415 3421 3418 3440 C1' U D 11 beta 3435 3441 3438 3460 C1' U D 12 beta 3455 3461 3458 3480 C1' U D 13 beta 3475 3481 3478 3500 C1' U D 14 beta 3495 3501 3498 3520 C1' C D 15 beta 3515 3521 3518 3540 C1' A D 16 beta 3535 3541 3538 3562 C1' G D 17 beta 3557 3563 3560 3585 C1' A D 18 beta 3580 3586 3583 3607 C1' G D 19 beta 3602 3608 3605 3630 C1' C D 20 beta 3625 3631 3628 3650 C1' C D 21 beta 3645 3651 3648 3670 C1' A D 22 beta 3665 3671 3668 3692 C1' C D 23 beta 3687 3693 3690 3712 C1' C D 24 beta 3707 3713 3710 3732 C1' C D 25 beta 3727 3733 3730 3752 C1' A D 26 beta 3747 3753 3750 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7 C2' C A 1 OK 9 5 8 27 C2' C A 2 OK 29 25 28 47 C2' A A 3 OK 49 45 48 69 C2' A A 4 OK 71 67 70 91 C2' A A 5 OK 93 89 92 113 C2' G A 6 OK 115 111 114 136 C2' G A 7 OK 138 134 137 159 C2' C A 8 OK 161 157 160 179 C2' U A 9 OK 181 177 180 199 C2' C A 10 OK 201 197 200 219 C2' U A 11 OK 221 217 220 239 C2' U A 12 OK 241 237 240 259 C2' U A 13 OK 261 257 260 279 C2' U A 14 OK 281 277 280 299 C2' C A 15 OK 301 297 300 319 C2' A A 16 OK 321 317 320 341 C2' G A 17 OK 343 339 342 364 C2' A A 18 OK 366 362 365 386 C2' G A 19 OK 388 384 387 409 C2' C A 20 OK 411 407 410 429 C2' C A 21 OK 431 427 430 449 C2' A A 22 OK 451 447 450 471 C2' C A 23 OK 473 469 472 491 C2' C A 24 OK 493 489 492 511 C2' C A 25 OK 513 509 512 531 C2' A A 26 OK 533 529 532 3398 C2' U D 9 OK 3400 3396 3399 3418 C2' C D 10 OK 3420 3416 3419 3438 C2' U D 11 OK 3440 3436 3439 3458 C2' U D 12 OK 3460 3456 3459 3478 C2' U D 13 OK 3480 3476 3479 3498 C2' U D 14 OK 3500 3496 3499 3518 C2' C D 15 OK 3520 3516 3519 3538 C2' A D 16 OK 3540 3536 3539 3560 C2' G D 17 OK 3562 3558 3561 3583 C2' A D 18 OK 3585 3581 3584 3605 C2' G D 19 OK 3607 3603 3606 3628 C2' C D 20 OK 3630 3626 3629 3648 C2' C D 21 OK 3650 3646 3649 3668 C2' A D 22 OK 3670 3666 3669 3690 C2' C D 23 OK 3692 3688 3691 3710 C2' C D 24 OK 3712 3708 3711 3730 C2' C D 25 OK 3732 3728 3731 3750 C2' A D 26 OK 3752 3748 3751 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 5 C3' C A 1 OK 3 6 7 25 C3' C A 2 OK 23 26 27 45 C3' A A 3 OK 43 46 47 67 C3' A A 4 OK 65 68 69 89 C3' A A 5 OK 87 90 91 111 C3' G A 6 OK 109 112 113 134 C3' G A 7 OK 132 135 136 157 C3' C A 8 OK 155 158 159 177 C3' U A 9 OK 175 178 179 197 C3' C A 10 OK 195 198 199 217 C3' U A 11 OK 215 218 219 237 C3' U A 12 OK 235 238 239 257 C3' U A 13 OK 255 258 259 277 C3' U A 14 OK 275 278 279 297 C3' C A 15 OK 295 298 299 317 C3' A A 16 OK 315 318 319 339 C3' G A 17 OK 337 340 341 362 C3' A A 18 OK 360 363 364 384 C3' G A 19 OK 382 385 386 407 C3' C A 20 OK 405 408 409 427 C3' C A 21 OK 425 428 429 447 C3' A A 22 OK 445 448 449 469 C3' C A 23 OK 467 470 471 489 C3' C A 24 OK 487 490 491 509 C3' C A 25 OK 507 510 511 529 C3' A A 26 OK 527 530 531 3396 C3' U D 9 OK 3394 3397 3398 3416 C3' C D 10 OK 3414 3417 3418 3436 C3' U D 11 OK 3434 3437 3438 3456 C3' U D 12 OK 3454 3457 3458 3476 C3' U D 13 OK 3474 3477 3478 3496 C3' U D 14 OK 3494 3497 3498 3516 C3' C D 15 OK 3514 3517 3518 3536 C3' A D 16 OK 3534 3537 3538 3558 C3' G D 17 OK 3556 3559 3560 3581 C3' A D 18 OK 3579 3582 3583 3603 C3' G D 19 OK 3601 3604 3605 3626 C3' C D 20 OK 3624 3627 3628 3646 C3' C D 21 OK 3644 3647 3648 3666 C3' A D 22 OK 3664 3667 3668 3688 C3' C D 23 OK 3686 3689 3690 3708 C3' C D 24 OK 3706 3709 3710 3728 C3' C D 25 OK 3726 3729 3730 3748 C3' A D 26 OK 3746 3749 3750 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 3 C4' C A 1 OK 5 2 4 23 C4' C A 2 OK 25 22 24 43 C4' A A 3 OK 45 42 44 65 C4' A A 4 OK 67 64 66 87 C4' A A 5 OK 89 86 88 109 C4' G A 6 OK 111 108 110 132 C4' G A 7 OK 134 131 133 155 C4' C A 8 OK 157 154 156 175 C4' U A 9 OK 177 174 176 195 C4' C A 10 OK 197 194 196 215 C4' U A 11 OK 217 214 216 235 C4' U A 12 OK 237 234 236 255 C4' U A 13 OK 257 254 256 275 C4' U A 14 OK 277 274 276 295 C4' C A 15 OK 297 294 296 315 C4' A A 16 OK 317 314 316 337 C4' G A 17 OK 339 336 338 360 C4' A A 18 OK 362 359 361 382 C4' G A 19 OK 384 381 383 405 C4' C A 20 OK 407 404 406 425 C4' C A 21 OK 427 424 426 445 C4' A A 22 OK 447 444 446 467 C4' C A 23 OK 469 466 468 487 C4' C A 24 OK 489 486 488 507 C4' C A 25 OK 509 506 508 527 C4' A A 26 OK 529 526 528 3394 C4' U D 9 OK 3396 3393 3395 3414 C4' C D 10 OK 3416 3413 3415 3434 C4' U D 11 OK 3436 3433 3435 3454 C4' U D 12 OK 3456 3453 3455 3474 C4' U D 13 OK 3476 3473 3475 3494 C4' U D 14 OK 3496 3493 3495 3514 C4' C D 15 OK 3516 3513 3515 3534 C4' A D 16 OK 3536 3533 3535 3556 C4' G D 17 OK 3558 3555 3557 3579 C4' A D 18 OK 3581 3578 3580 3601 C4' G D 19 OK 3603 3600 3602 3624 C4' C D 20 OK 3626 3623 3625 3644 C4' C D 21 OK 3646 3643 3645 3664 C4' A D 22 OK 3666 3663 3665 3686 C4' C D 23 OK 3688 3685 3687 3706 C4' C D 24 OK 3708 3705 3707 3726 C4' C D 25 OK 3728 3725 3727 3746 C4' A D 26 OK 3748 3745 3747 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 2 C5' C A 1 1 3 22 C5' C A 2 21 23 42 C5' A A 3 41 43 64 C5' A A 4 63 65 86 C5' A A 5 85 87 108 C5' G A 6 107 109 131 C5' G A 7 130 132 154 C5' C A 8 153 155 174 C5' U A 9 173 175 194 C5' C A 10 193 195 214 C5' U A 11 213 215 234 C5' U A 12 233 235 254 C5' U A 13 253 255 274 C5' U A 14 273 275 294 C5' C A 15 293 295 314 C5' A A 16 313 315 336 C5' G A 17 335 337 359 C5' A A 18 358 360 381 C5' G A 19 380 382 404 C5' C A 20 403 405 424 C5' C A 21 423 425 444 C5' A A 22 443 445 466 C5' C A 23 465 467 486 C5' C A 24 485 487 506 C5' C A 25 505 507 526 C5' A A 26 525 527 3393 C5' U D 9 3392 3394 3413 C5' C D 10 3412 3414 3433 C5' U D 11 3432 3434 3453 C5' U D 12 3452 3454 3473 C5' U D 13 3472 3474 3493 C5' U D 14 3492 3494 3513 C5' C D 15 3512 3514 3533 C5' A D 16 3532 3534 3555 C5' G D 17 3554 3556 3578 C5' A D 18 3577 3579 3600 C5' G D 19 3599 3601 3623 C5' C D 20 3622 3624 3643 C5' C D 21 3642 3644 3663 C5' A D 22 3662 3664 3685 C5' C D 23 3684 3686 3705 C5' C D 24 3704 3706 3725 C5' C D 25 3724 3726 3745 C5' A D 26 3744 3746 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 18 P C A 2 distorted distorted 6 19 20 21 38 P A A 3 distorted distorted 26 39 40 41 60 P A A 4 distorted distorted 46 61 62 63 82 P A A 5 distorted distorted 68 83 84 85 104 P G A 6 distorted distorted 90 105 106 107 127 P G A 7 distorted distorted 112 128 129 130 150 P C A 8 distorted distorted 135 151 152 153 170 P U A 9 distorted distorted 158 171 172 173 190 P C A 10 distorted distorted 178 191 192 193 210 P U A 11 distorted distorted 198 211 212 213 230 P U A 12 distorted distorted 218 231 232 233 250 P U A 13 distorted distorted 238 251 252 253 270 P U A 14 distorted distorted 258 271 272 273 290 P C A 15 distorted distorted 278 291 292 293 310 P A A 16 distorted distorted 298 311 312 313 332 P G A 17 distorted distorted 318 333 334 335 355 P A A 18 distorted distorted 340 356 357 358 377 P G A 19 distorted distorted 363 378 379 380 400 P C A 20 distorted distorted 385 401 402 403 420 P C A 21 distorted distorted 408 421 422 423 440 P A A 22 distorted distorted 428 441 442 443 462 P C A 23 distorted distorted 448 463 464 465 482 P C A 24 distorted distorted 470 483 484 485 502 P C A 25 distorted distorted 490 503 504 505 522 P A A 26 distorted distorted 510 523 524 525 3389 P U D 9 distorted distorted 3388 3390 3391 3392 3409 P C D 10 distorted distorted 3397 3410 3411 3412 3429 P U D 11 distorted distorted 3417 3430 3431 3432 3449 P U D 12 distorted distorted 3437 3450 3451 3452 3469 P U D 13 distorted distorted 3457 3470 3471 3472 3489 P U D 14 distorted distorted 3477 3490 3491 3492 3509 P C D 15 distorted distorted 3497 3510 3511 3512 3529 P A D 16 distorted distorted 3517 3530 3531 3532 3551 P G D 17 distorted distorted 3537 3552 3553 3554 3574 P A D 18 distorted distorted 3559 3575 3576 3577 3596 P G D 19 distorted distorted 3582 3597 3598 3599 3619 P C D 20 distorted distorted 3604 3620 3621 3622 3639 P C D 21 distorted distorted 3627 3640 3641 3642 3659 P A D 22 distorted distorted 3647 3660 3661 3662 3681 P C D 23 distorted distorted 3667 3682 3683 3684 3701 P C D 24 distorted distorted 3689 3702 3703 3704 3721 P C D 25 distorted distorted 3709 3722 3723 3724 3741 P A D 26 distorted distorted 3729 3742 3743 3744 ---------------------------------------------------------------------------------