ID code: '3OVB' 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' --------------------------------------------------------------------------------- 7314 C1' G C 1 beta 7309 7315 7312 7337 C1' G C 2 beta 7332 7338 7335 7360 C1' A C 3 beta 7355 7361 7358 7382 C1' A C 4 beta 7377 7383 7380 7404 C1' G C 5 beta 7399 7405 7402 7427 C1' U C 6 beta 7422 7428 7425 7447 C1' A C 7 beta 7442 7448 7445 7469 C1' G C 8 beta 7464 7470 7467 7492 C1' A C 9 beta 7487 7493 7490 7514 C1' U C 10 beta 7509 7515 7512 7534 C1' G C 11 beta 7529 7535 7532 7557 C1' G C 12 beta 7552 7558 7555 7580 C1' U C 13 beta 7575 7581 7578 7600 C1' U C 14 beta 7595 7601 7598 7620 C1' C C 15 beta 7615 7621 7618 7640 C1' A C 16 beta 7635 7641 7638 7662 C1' A C 17 beta 7657 7663 7660 7684 C1' G C 18 beta 7679 7685 7682 7707 C1' U C 19 beta 7702 7708 7705 7727 C1' C C 20 beta 7722 7728 7725 7747 C1' C C 21 beta 7742 7748 7745 7767 C1' A C 22 beta 7762 7768 7765 7789 C1' U C 23 beta 7784 7790 7787 7809 C1' U C 24 beta 7804 7810 7807 7829 C1' U C 25 beta 7824 7830 7827 7849 C1' A C 26 beta 7844 7850 7847 7871 C1' C C 27 beta 7866 7872 7869 7891 C1' U C 28 beta 7886 7892 7889 7911 C1' U C 29 beta 7906 7912 7909 7931 C1' C C 30 beta 7926 7932 7929 7951 C1' C C 31 beta 7946 7952 7949 7971 C1' A C 32 beta 7966 7972 7969 7993 C1' C C 33 beta 7988 7994 7991 8073 C1' G D 1 beta 8068 8074 8071 8096 C1' G D 2 beta 8091 8097 8094 8119 C1' A D 3 beta 8114 8120 8117 8141 C1' A D 4 beta 8136 8142 8139 8163 C1' G D 5 beta 8158 8164 8161 8186 C1' U D 6 beta 8181 8187 8184 8206 C1' A D 7 beta 8201 8207 8204 8228 C1' G D 8 beta 8223 8229 8226 8251 C1' A D 9 beta 8246 8252 8249 8273 C1' U D 10 beta 8268 8274 8271 8293 C1' G D 11 beta 8288 8294 8291 8316 C1' G D 12 beta 8311 8317 8314 8339 C1' U D 13 beta 8334 8340 8337 8359 C1' U D 14 beta 8354 8360 8357 8379 C1' C D 15 beta 8374 8380 8377 8399 C1' A D 16 beta 8394 8400 8397 8421 C1' A D 17 beta 8416 8422 8419 8443 C1' G D 18 beta 8438 8444 8441 8466 C1' U D 19 beta 8461 8467 8464 8486 C1' C D 20 beta 8481 8487 8484 8506 C1' C D 21 beta 8501 8507 8504 8526 C1' A D 22 beta 8521 8527 8524 8548 C1' U D 23 beta 8543 8549 8546 8568 C1' U D 24 beta 8563 8569 8566 8588 C1' U D 25 beta 8583 8589 8586 8608 C1' A D 26 beta 8603 8609 8606 8630 C1' C D 27 beta 8625 8631 8628 8650 C1' U D 28 beta 8645 8651 8648 8670 C1' U D 29 beta 8665 8671 8668 8690 C1' C D 30 beta 8685 8691 8688 8710 C1' C D 31 beta 8705 8711 8708 8730 C1' A D 32 beta 8725 8731 8728 8752 C1' C D 33 beta 8747 8753 8750 8956 C1' ATP C 851 beta 8951 8957 8954 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------------------------------------------- Seq No Atom Residue Deoxyribose Ribose C1' C3' H2'1 H2'2 H2' O2' H2'1 H2'2 H2' O2' --------------------------------------------------------------------------------------------------------------------- 7312 C2' G C 1 OK 7314 7310 7313 7335 C2' G C 2 OK 7337 7333 7336 7358 C2' A C 3 OK 7360 7356 7359 7380 C2' A C 4 OK 7382 7378 7381 7402 C2' G C 5 OK 7404 7400 7403 7425 C2' U C 6 OK 7427 7423 7426 7445 C2' A C 7 OK 7447 7443 7446 7467 C2' G C 8 OK 7469 7465 7468 7490 C2' A C 9 OK 7492 7488 7491 7512 C2' U C 10 OK 7514 7510 7513 7532 C2' G C 11 OK 7534 7530 7533 7555 C2' G C 12 OK 7557 7553 7556 7578 C2' U C 13 OK 7580 7576 7579 7598 C2' U C 14 OK 7600 7596 7599 7618 C2' C C 15 OK 7620 7616 7619 7638 C2' A C 16 OK 7640 7636 7639 7660 C2' A C 17 OK 7662 7658 7661 7682 C2' G C 18 OK 7684 7680 7683 7705 C2' U C 19 OK 7707 7703 7706 7725 C2' C C 20 OK 7727 7723 7726 7745 C2' C C 21 OK 7747 7743 7746 7765 C2' A C 22 OK 7767 7763 7766 7787 C2' U C 23 OK 7789 7785 7788 7807 C2' U C 24 OK 7809 7805 7808 7827 C2' U C 25 OK 7829 7825 7828 7847 C2' A C 26 OK 7849 7845 7848 7869 C2' C C 27 OK 7871 7867 7870 7889 C2' U C 28 OK 7891 7887 7890 7909 C2' U C 29 OK 7911 7907 7910 7929 C2' C C 30 OK 7931 7927 7930 7949 C2' C C 31 OK 7951 7947 7950 7969 C2' A C 32 OK 7971 7967 7970 7991 C2' C C 33 OK 7993 7989 7992 8071 C2' G D 1 OK 8073 8069 8072 8094 C2' G D 2 OK 8096 8092 8095 8117 C2' A D 3 OK 8119 8115 8118 8139 C2' A D 4 OK 8141 8137 8140 8161 C2' G D 5 OK 8163 8159 8162 8184 C2' U D 6 OK 8186 8182 8185 8204 C2' A D 7 OK 8206 8202 8205 8226 C2' G D 8 OK 8228 8224 8227 8249 C2' A D 9 OK 8251 8247 8250 8271 C2' U D 10 OK 8273 8269 8272 8291 C2' G D 11 OK 8293 8289 8292 8314 C2' G D 12 OK 8316 8312 8315 8337 C2' U D 13 OK 8339 8335 8338 8357 C2' U D 14 OK 8359 8355 8358 8377 C2' C D 15 OK 8379 8375 8378 8397 C2' A D 16 OK 8399 8395 8398 8419 C2' A D 17 OK 8421 8417 8420 8441 C2' G D 18 OK 8443 8439 8442 8464 C2' U D 19 OK 8466 8462 8465 8484 C2' C D 20 OK 8486 8482 8485 8504 C2' C D 21 OK 8506 8502 8505 8524 C2' A D 22 OK 8526 8522 8525 8546 C2' U D 23 OK 8548 8544 8547 8566 C2' U D 24 OK 8568 8564 8567 8586 C2' U D 25 OK 8588 8584 8587 8606 C2' A D 26 OK 8608 8604 8607 8628 C2' C D 27 OK 8630 8626 8629 8648 C2' U D 28 OK 8650 8646 8649 8668 C2' U D 29 OK 8670 8666 8669 8688 C2' C D 30 OK 8690 8686 8689 8708 C2' C D 31 OK 8710 8706 8709 8728 C2' A D 32 OK 8730 8726 8729 8750 C2' C D 33 OK 8752 8748 8751 8954 C2' ATP C 851 OK 8956 8952 8955 --------------------------------------------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H3' O3' C4' H3' O3' C2' --------------------------------------------------------------------------------- 7310 C3' G C 1 OK 7308 7311 7312 7333 C3' G C 2 OK 7331 7334 7335 7356 C3' A C 3 OK 7354 7357 7358 7378 C3' A C 4 OK 7376 7379 7380 7400 C3' G C 5 OK 7398 7401 7402 7423 C3' U C 6 OK 7421 7424 7425 7443 C3' A C 7 OK 7441 7444 7445 7465 C3' G C 8 OK 7463 7466 7467 7488 C3' A C 9 OK 7486 7489 7490 7510 C3' U C 10 OK 7508 7511 7512 7530 C3' G C 11 OK 7528 7531 7532 7553 C3' G C 12 OK 7551 7554 7555 7576 C3' U C 13 OK 7574 7577 7578 7596 C3' U C 14 OK 7594 7597 7598 7616 C3' C C 15 OK 7614 7617 7618 7636 C3' A C 16 OK 7634 7637 7638 7658 C3' A C 17 OK 7656 7659 7660 7680 C3' G C 18 OK 7678 7681 7682 7703 C3' U C 19 OK 7701 7704 7705 7723 C3' C C 20 OK 7721 7724 7725 7743 C3' C C 21 OK 7741 7744 7745 7763 C3' A C 22 OK 7761 7764 7765 7785 C3' U C 23 OK 7783 7786 7787 7805 C3' U C 24 OK 7803 7806 7807 7825 C3' U C 25 OK 7823 7826 7827 7845 C3' A C 26 OK 7843 7846 7847 7867 C3' C C 27 OK 7865 7868 7869 7887 C3' U C 28 OK 7885 7888 7889 7907 C3' U C 29 OK 7905 7908 7909 7927 C3' C C 30 OK 7925 7928 7929 7947 C3' C C 31 OK 7945 7948 7949 7967 C3' A C 32 OK 7965 7968 7969 7989 C3' C C 33 OK 7987 7990 7991 8069 C3' G D 1 OK 8067 8070 8071 8092 C3' G D 2 OK 8090 8093 8094 8115 C3' A D 3 OK 8113 8116 8117 8137 C3' A D 4 OK 8135 8138 8139 8159 C3' G D 5 OK 8157 8160 8161 8182 C3' U D 6 OK 8180 8183 8184 8202 C3' A D 7 OK 8200 8203 8204 8224 C3' G D 8 OK 8222 8225 8226 8247 C3' A D 9 OK 8245 8248 8249 8269 C3' U D 10 OK 8267 8270 8271 8289 C3' G D 11 OK 8287 8290 8291 8312 C3' G D 12 OK 8310 8313 8314 8335 C3' U D 13 OK 8333 8336 8337 8355 C3' U D 14 OK 8353 8356 8357 8375 C3' C D 15 OK 8373 8376 8377 8395 C3' A D 16 OK 8393 8396 8397 8417 C3' A D 17 OK 8415 8418 8419 8439 C3' G D 18 OK 8437 8440 8441 8462 C3' U D 19 OK 8460 8463 8464 8482 C3' C D 20 OK 8480 8483 8484 8502 C3' C D 21 OK 8500 8503 8504 8522 C3' A D 22 OK 8520 8523 8524 8544 C3' U D 23 OK 8542 8545 8546 8564 C3' U D 24 OK 8562 8565 8566 8584 C3' U D 25 OK 8582 8585 8586 8604 C3' A D 26 OK 8602 8605 8606 8626 C3' C D 27 OK 8624 8627 8628 8646 C3' U D 28 OK 8644 8647 8648 8666 C3' U D 29 OK 8664 8667 8668 8686 C3' C D 30 OK 8684 8687 8688 8706 C3' C D 31 OK 8704 8707 8708 8726 C3' A D 32 OK 8724 8727 8728 8748 C3' C D 33 OK 8746 8749 8750 8952 C3' ATP C 851 OK 8950 8953 8954 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H4' C5' C3' H4' C5' O4' --------------------------------------------------------------------------------- 7308 C4' G C 1 OK 7310 7307 7309 7331 C4' G C 2 OK 7333 7330 7332 7354 C4' A C 3 OK 7356 7353 7355 7376 C4' A C 4 OK 7378 7375 7377 7398 C4' G C 5 OK 7400 7397 7399 7421 C4' U C 6 OK 7423 7420 7422 7441 C4' A C 7 OK 7443 7440 7442 7463 C4' G C 8 OK 7465 7462 7464 7486 C4' A C 9 OK 7488 7485 7487 7508 C4' U C 10 OK 7510 7507 7509 7528 C4' G C 11 OK 7530 7527 7529 7551 C4' G C 12 OK 7553 7550 7552 7574 C4' U C 13 OK 7576 7573 7575 7594 C4' U C 14 OK 7596 7593 7595 7614 C4' C C 15 OK 7616 7613 7615 7634 C4' A C 16 OK 7636 7633 7635 7656 C4' A C 17 OK 7658 7655 7657 7678 C4' G C 18 OK 7680 7677 7679 7701 C4' U C 19 OK 7703 7700 7702 7721 C4' C C 20 OK 7723 7720 7722 7741 C4' C C 21 OK 7743 7740 7742 7761 C4' A C 22 OK 7763 7760 7762 7783 C4' U C 23 OK 7785 7782 7784 7803 C4' U C 24 OK 7805 7802 7804 7823 C4' U C 25 OK 7825 7822 7824 7843 C4' A C 26 OK 7845 7842 7844 7865 C4' C C 27 OK 7867 7864 7866 7885 C4' U C 28 OK 7887 7884 7886 7905 C4' U C 29 OK 7907 7904 7906 7925 C4' C C 30 OK 7927 7924 7926 7945 C4' C C 31 OK 7947 7944 7946 7965 C4' A C 32 OK 7967 7964 7966 7987 C4' C C 33 OK 7989 7986 7988 8067 C4' G D 1 OK 8069 8066 8068 8090 C4' G D 2 OK 8092 8089 8091 8113 C4' A D 3 OK 8115 8112 8114 8135 C4' A D 4 OK 8137 8134 8136 8157 C4' G D 5 OK 8159 8156 8158 8180 C4' U D 6 OK 8182 8179 8181 8200 C4' A D 7 OK 8202 8199 8201 8222 C4' G D 8 OK 8224 8221 8223 8245 C4' A D 9 OK 8247 8244 8246 8267 C4' U D 10 OK 8269 8266 8268 8287 C4' G D 11 OK 8289 8286 8288 8310 C4' G D 12 OK 8312 8309 8311 8333 C4' U D 13 OK 8335 8332 8334 8353 C4' U D 14 OK 8355 8352 8354 8373 C4' C D 15 OK 8375 8372 8374 8393 C4' A D 16 OK 8395 8392 8394 8415 C4' A D 17 OK 8417 8414 8416 8437 C4' G D 18 OK 8439 8436 8438 8460 C4' U D 19 OK 8462 8459 8461 8480 C4' C D 20 OK 8482 8479 8481 8500 C4' C D 21 OK 8502 8499 8501 8520 C4' A D 22 OK 8522 8519 8521 8542 C4' U D 23 OK 8544 8541 8543 8562 C4' U D 24 OK 8564 8561 8563 8582 C4' U D 25 OK 8584 8581 8583 8602 C4' A D 26 OK 8604 8601 8603 8624 C4' C D 27 OK 8626 8623 8625 8644 C4' U D 28 OK 8646 8643 8645 8664 C4' U D 29 OK 8666 8663 8665 8684 C4' C D 30 OK 8686 8683 8685 8704 C4' C D 31 OK 8706 8703 8705 8724 C4' A D 32 OK 8726 8723 8725 8746 C4' C D 33 OK 8748 8745 8747 8950 C4' ATP C 851 OK 8952 8949 8951 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue H5'1 H5'2 O5' H5'1 H5'2 C4' --------------------------------------------------------------------------------- 7307 C5' G C 1 7306 7308 7330 C5' G C 2 7329 7331 7353 C5' A C 3 7352 7354 7375 C5' A C 4 7374 7376 7397 C5' G C 5 7396 7398 7420 C5' U C 6 7419 7421 7440 C5' A C 7 7439 7441 7462 C5' G C 8 7461 7463 7485 C5' A C 9 7484 7486 7507 C5' U C 10 7506 7508 7527 C5' G C 11 7526 7528 7550 C5' G C 12 7549 7551 7573 C5' U C 13 7572 7574 7593 C5' U C 14 7592 7594 7613 C5' C C 15 7612 7614 7633 C5' A C 16 7632 7634 7655 C5' A C 17 7654 7656 7677 C5' G C 18 7676 7678 7700 C5' U C 19 7699 7701 7720 C5' C C 20 7719 7721 7740 C5' C C 21 7739 7741 7760 C5' A C 22 7759 7761 7782 C5' U C 23 7781 7783 7802 C5' U C 24 7801 7803 7822 C5' U C 25 7821 7823 7842 C5' A C 26 7841 7843 7864 C5' C C 27 7863 7865 7884 C5' U C 28 7883 7885 7904 C5' U C 29 7903 7905 7924 C5' C C 30 7923 7925 7944 C5' C C 31 7943 7945 7964 C5' A C 32 7963 7965 7986 C5' C C 33 7985 7987 8066 C5' G D 1 8065 8067 8089 C5' G D 2 8088 8090 8112 C5' A D 3 8111 8113 8134 C5' A D 4 8133 8135 8156 C5' G D 5 8155 8157 8179 C5' U D 6 8178 8180 8199 C5' A D 7 8198 8200 8221 C5' G D 8 8220 8222 8244 C5' A D 9 8243 8245 8266 C5' U D 10 8265 8267 8286 C5' G D 11 8285 8287 8309 C5' G D 12 8308 8310 8332 C5' U D 13 8331 8333 8352 C5' U D 14 8351 8353 8372 C5' C D 15 8371 8373 8392 C5' A D 16 8391 8393 8414 C5' A D 17 8413 8415 8436 C5' G D 18 8435 8437 8459 C5' U D 19 8458 8460 8479 C5' C D 20 8478 8480 8499 C5' C D 21 8498 8500 8519 C5' A D 22 8518 8520 8541 C5' U D 23 8540 8542 8561 C5' U D 24 8560 8562 8581 C5' U D 25 8580 8582 8601 C5' A D 26 8600 8602 8623 C5' C D 27 8622 8624 8643 C5' U D 28 8642 8644 8663 C5' U D 29 8662 8664 8683 C5' C D 30 8682 8684 8703 C5' C D 31 8702 8704 8723 C5' A D 32 8722 8724 8745 C5' C D 33 8744 8746 8949 C5' ATP C 851 8948 8950 --------------------------------------------------------------------------------- --------------------------------------------------------------------------------- Seq No Atom Residue O1P O2P O3' O1P O2P O5' --------------------------------------------------------------------------------- 7326 P G C 2 distorted distorted 7311 7327 7328 7329 7349 P A C 3 distorted distorted 7334 7350 7351 7352 7371 P A C 4 distorted distorted 7357 7372 7373 7374 7393 P G C 5 distorted distorted 7379 7394 7395 7396 7416 P U C 6 distorted distorted 7401 7417 7418 7419 7436 P A C 7 distorted distorted 7424 7437 7438 7439 7458 P G C 8 distorted distorted 7444 7459 7460 7461 7481 P A C 9 distorted distorted 7466 7482 7483 7484 7503 P U C 10 distorted distorted 7489 7504 7505 7506 7523 P G C 11 distorted distorted 7511 7524 7525 7526 7546 P G C 12 distorted distorted 7531 7547 7548 7549 7569 P U C 13 distorted distorted 7554 7570 7571 7572 7589 P U C 14 distorted distorted 7577 7590 7591 7592 7609 P C C 15 distorted distorted 7597 7610 7611 7612 7629 P A C 16 distorted distorted 7617 7630 7631 7632 7651 P A C 17 distorted distorted 7637 7652 7653 7654 7673 P G C 18 distorted distorted 7659 7674 7675 7676 7696 P U C 19 distorted distorted 7681 7697 7698 7699 7716 P C C 20 distorted distorted 7704 7717 7718 7719 7736 P C C 21 distorted distorted 7724 7737 7738 7739 7756 P A C 22 distorted distorted 7744 7757 7758 7759 7778 P U C 23 distorted distorted 7764 7779 7780 7781 7798 P U C 24 distorted distorted 7786 7799 7800 7801 7818 P U C 25 distorted distorted 7806 7819 7820 7821 7838 P A C 26 distorted distorted 7826 7839 7840 7841 7860 P C C 27 distorted distorted 7846 7861 7862 7863 7880 P U C 28 distorted distorted 7868 7881 7882 7883 7900 P U C 29 distorted distorted 7888 7901 7902 7903 7920 P C C 30 distorted distorted 7908 7921 7922 7923 7940 P C C 31 distorted distorted 7928 7941 7942 7943 7960 P A C 32 distorted distorted 7948 7961 7962 7963 7982 P C C 33 distorted distorted 7968 7983 7984 7985 8002 P C C 34 7990 8003 P C C 34 7990 8042 P A C 35 8085 P G D 2 distorted distorted 8070 8086 8087 8088 8108 P A D 3 distorted distorted 8093 8109 8110 8111 8130 P A D 4 distorted distorted 8116 8131 8132 8133 8152 P G D 5 distorted distorted 8138 8153 8154 8155 8175 P U D 6 distorted distorted 8160 8176 8177 8178 8195 P A D 7 distorted distorted 8183 8196 8197 8198 8217 P G D 8 distorted distorted 8203 8218 8219 8220 8240 P A D 9 distorted distorted 8225 8241 8242 8243 8262 P U D 10 distorted distorted 8248 8263 8264 8265 8282 P G D 11 distorted distorted 8270 8283 8284 8285 8305 P G D 12 distorted distorted 8290 8306 8307 8308 8328 P U D 13 distorted distorted 8313 8329 8330 8331 8348 P U D 14 distorted distorted 8336 8349 8350 8351 8368 P C D 15 distorted distorted 8356 8369 8370 8371 8388 P A D 16 distorted distorted 8376 8389 8390 8391 8410 P A D 17 distorted distorted 8396 8411 8412 8413 8432 P G D 18 distorted distorted 8418 8433 8434 8435 8455 P U D 19 distorted distorted 8440 8456 8457 8458 8475 P C D 20 distorted distorted 8463 8476 8477 8478 8495 P C D 21 distorted distorted 8483 8496 8497 8498 8515 P A D 22 distorted distorted 8503 8516 8517 8518 8537 P U D 23 distorted distorted 8523 8538 8539 8540 8557 P U D 24 distorted distorted 8545 8558 8559 8560 8577 P U D 25 distorted distorted 8565 8578 8579 8580 8597 P A D 26 distorted distorted 8585 8598 8599 8600 8619 P C D 27 distorted distorted 8605 8620 8621 8622 8639 P U D 28 distorted distorted 8627 8640 8641 8642 8659 P U D 29 distorted distorted 8647 8660 8661 8662 8679 P C D 30 distorted distorted 8667 8680 8681 8682 8699 P C D 31 distorted distorted 8687 8700 8701 8702 8719 P A D 32 distorted distorted 8707 8720 8721 8722 8741 P C D 33 distorted distorted 8727 8742 8743 8744 8761 P C D 34 8749 8762 P C D 34 8749 8801 P A D 35 ---------------------------------------------------------------------------------