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6ZQB Internal, Hairpin and 3-way Junction Loop Motifs

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Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/D2/4:9NANA
1/D2/120:125NANA
1/D2/196:201NANA
1/D2/251:257NANA
1/D2/301:305NANA
1/D2/360:365NANA
1/D2/424:433NANA
1/D3/70:81NANA
1/D3/154:160Other HL
homologous
HL_4V88_188		NA

HL_43074.18*
1/D3/189:196NANA
1/D3/230:235UNCG
geometric
HL_3U4M_001		NA

HL_79299.11*
1/D3/275:279NANA
1/D3/330:338
homologous
HL_4V88_193		NA

HL_93727.5*
1/D3/368:377
geometric
HL_4V88_198		NA

HL_30541.1*
1/D3/393:404
homologous
HL_4V88_195		NA

HL_22443.1*
1/D3/414:419UNCG
homologous
HL_4V88_196		NA

HL_79299.11*
1/D3/450:456
homologous
HL_4V88_197		NA

HL_50374.1*
1/D3/491:496Other HL
geometric
HL_1L9A_001		NA

HL_43074.18*
1/D3/520:532
homologous
HL_4V88_199		NA

HL_17086.2*
1/D3/561:566
geometric
HL_5TBW_006		NA

HL_98557.5*
1/D3/900:909
homologous
HL_4V88_206		NA

HL_87219.4*
1/D3/937:942Other HL
homologous
HL_4V88_207		NA

HL_43074.18*
1/D3/1055:1064NANA
1/D3/1129:1139NANA
1/D3/1501:1506GNRA
homologous
HL_4V88_218		NA

HL_43074.18*
1/D3/1594:1602
geometric
HL_4OOG_001		NA

HL_68529.2*
1/D3/1629:1636
geometric
HL_2Y8W_001		NA

HL_69459.1*
1/D3/1698:1703GNRA
geometric
HL_1M5K_003		NA

HL_43074.18*
1/D3/1778:1783NANA
1/D4/201:248NANA
1/D4/266:305NANA

Problematic loops

#loop idProblemSequence
HL_6ZQB_008NA
HL_6ZQB_009NA
HL_6ZQB_023NA
HL_6ZQB_028
geometric
HL_5TBW_044
HL_6ZQB_029
geometric
HL_5NFV_001

Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/D2/17:18,
1/D2/62:64		NANA
1/D2/93:96,
1/D2/148:157		NANA
1/D2/97:99,
1/D2/145:147		NANA
1/D2/100:105,
1/D2/139:144		NANA
1/D2/107:110,
1/D2/136:137		NANA
1/D2/116:117,
1/D2/128:130		NANA
1/D2/167:172,
1/D2/224:228		NANA
1/D2/175:179,
1/D2/218:221		NANA
1/D2/187:189,
1/D2/208:210		NANA
1/D2/238:240,
1/D2/273:274		NANA
1/D2/245:248,
1/D2/264:268		NANA
1/D2/250:251,
1/D2/257:262		NANA
1/D2/337:340,
1/D2/386:387		NANA
1/D2/340:341,
1/D2/384:386		NANA
1/D2/341:343,
1/D2/381:384		NANA
1/D2/346:349,
1/D2/375:378		NANA
1/D2/352:355,
1/D2/371:372		NANA
1/D2/355:356,
1/D2/369:371		NANA
1/D2/402:408,
1/D2/448:455		NANA
1/D2/413:414,
1/D2/441:443		NANA
1/D2/414:417,
1/D2/437:441		NANA
1/D2/466:471,
1/D4/47:50		NANA
1/D3/58:63,
1/D3/87:89
homologous
IL_4V88_389		NA

IL_96451.1*
1/D3/64:70,
1/D3/81:86		NANA
1/D3/109:112,
1/D3/302:305		Tandem non-canonical cWW pairs
homologous
IL_4V88_391		NA

IL_85877.10*
1/D3/113:117,
1/D3/299:301		Multiple bulged bases, near cWW
geometric
IL_5M0H_002		NA

IL_01312.13*
1/D3/117:122,
1/D3/295:299
homologous
IL_4V88_393		NA

IL_76386.1*
1/D3/150:152,
1/D3/162:164
homologous
IL_4V88_395		NA

IL_87880.2*
1/D3/186:189,
1/D3/196:199		Double sheared
homologous
IL_4V88_396		NA

IL_09705.7*
1/D3/206:208,
1/D3/257:259
homologous
IL_4V88_398		NA

IL_01312.13*
1/D3/265:267,
1/D3/288:289		Single bulged A
homologous
IL_4V88_399		NA

IL_80007.16*
1/D3/270:273,
1/D3/283:285
homologous
IL_4V88_400		NA

IL_05922.1*
1/D3/274:275,
1/D3/279:282		Single stack bend
geometric
IL_4LFB_041		NA

IL_04038.4*
1/D3/311:316,
1/D3/348:355		Kink-turn with non-sequential stacking
homologous
IL_4V88_402		NA

IL_29549.9*
1/D3/318:323,
1/D3/345:346
geometric
IL_5Y58_001		NA

IL_98882.3*
1/D3/364:368,
1/D3/377:380		Tandem non-canonical cWW pairs
geometric
IL_3WBM_002		NA

IL_85877.10*
1/D3/389:391,
1/D3/406:408		Isolated cWH basepair
homologous
IL_4V88_405		NA

IL_42589.6*
1/D3/411:413,
1/D3/420:422		Isolated near basepair
homologous
IL_4V88_406		NA

IL_01312.13*
1/D3/443:447,
1/D3/460:461		C-loop
geometric
IL_5J7L_018		NA

IL_08376.2*
1/D3/447:448,
1/D3/458:460		NANA
1/D3/482:483,
1/D3/504:506		Single bulged A
homologous
IL_4V88_409		NA

IL_80007.16*
1/D3/514:516,
1/D3/536:543		NANA
1/D3/517:520,
1/D3/532:535		Tandem non-canonical cWW pairs
geometric
IL_5C5W_003		NA

IL_85877.10*
1/D3/551:552,
1/D3/584:587		Multiple bulged bases
geometric
IL_3IGI_013		NA

IL_13730.12*
1/D3/552:559,
1/D3/568:584		NANA
1/D3/624:626,
1/D3/973:975
homologous
IL_4V88_417		NA

IL_01312.13*
1/D3/627:631,
1/D3/968:972		tSH-tHW-tHS
homologous
IL_4V88_418		NA

IL_39521.5*
1/D3/642:645,
1/D3/690:692		NANA
1/D3/645:646,
1/D3/688:690		Single stack bend
geometric
IL_7A0S_054		NA

IL_04038.4*
1/D3/646:648,
1/D3/686:688
homologous
IL_4V88_419		NA

IL_01312.13*
1/D3/865:866,
1/D3/962:965		Major groove platform; stack outside cWW
geometric
IL_4V88_428		NA

IL_70995.6*
1/D3/868:870,
1/D3/957:960		Isolated non-canonical cWW with bulges
geometric
IL_3TD0_005		NA

IL_01312.13*
1/D3/870:874,
1/D3/953:957
geometric
IL_5TBW_121		NA

IL_05867.1*
1/D3/874:878,
1/D3/950:953		Tandem non-canonical cWW pairs
geometric
IL_4V88_431		NA

IL_85877.10*
1/D3/884:889,
1/D3/923:928
geometric
IL_4LFB_030		NA

IL_94518.4*
1/D3/893:899,
1/D3/910:919		NANA
1/D3/1040:1045,
1/D3/1073:1078
geometric
IL_6O5F_001		NA

IL_52729.1*
1/D3/1051:1053,
1/D3/1066:1067		Single stack bend
geometric
IL_4C7O_002		NA

IL_72766.2*
1/D3/1117:1119,
1/D4/6:7		Single bulged G
geometric
IL_3IGI_004		NA

IL_59137.10*
1/D3/1155:1160,
1/D3/1617:1623		NANA
1/D3/1173:1178,
1/D3/1461:1466		tSH-tHW-tHS-cWW
geometric
IL_1L9A_008		NA

IL_76308.3*
1/D3/1211:1215,
1/D3/1448:1452		NANA
1/D3/1273:1274,
1/D3/1435:1437		NANA
1/D3/1470:1474,
1/D3/1533:1574		NANA
1/D3/1495:1498,
1/D3/1509:1512		Tandem non-canonical cWW pairs
homologous
IL_4V88_461		NA

IL_85877.10*
1/D3/1650:1652,
1/D3/1748:1750		AA cWW
homologous
IL_4V88_467		NA

IL_01312.13*
1/D3/1653:1656,
1/D3/1744:1747		Tandem non-canonical cWW pairs
geometric
IL_5LQO_002		NA

IL_85877.10*
1/D3/1656:1658,
1/D3/1743:1744		Single bulged U
homologous
IL_4V88_469		NA

IL_21340.1*
1/D3/1664:1667,
1/D3/1734:1737		Tandem non-canonical cWW pairs
geometric
IL_6JDV_002		NA

IL_85877.10*
1/D3/1669:1672,
1/D3/1729:1732		Double sheared
geometric
IL_1SAQ_002		NA

IL_09705.7*
1/D3/1672:1674,
1/D3/1727:1729
homologous
IL_4V88_472		NA

IL_01312.13*
1/D3/1675:1678,
1/D3/1723:1726		Tandem non-canonical cWW pairs
homologous
IL_4V88_473		NA

IL_85877.10*
1/D3/1678:1682,
1/D3/1719:1723		NANA
1/D3/1687:1690,
1/D3/1711:1714		NANA
1/D3/1690:1695,
1/D3/1706:1711		NANA
1/D4/78:85,
1/D4/325:329		NANA
1/D4/97:98,
1/D4/317:319		NANA
1/D4/111:115,
1/D4/252:259		NANA
1/D4/115:199,
1/D4/250:252		NANA

Problematic loops

#loop idProblemSequence
IL_6ZQB_023NA
IL_6ZQB_024NA
IL_6ZQB_025NA
IL_6ZQB_026NA
IL_6ZQB_027NA
IL_6ZQB_035NA
IL_6ZQB_037NA
IL_6ZQB_038NA

Valid loops

#loop idlocationannotation
(mapped to, source)		motif group
(similar to)
1/D3/633:635,
1/D3/861:865,
1/D3/965:966		NANA
1/D3/881:884,
1/D3/928:936,
1/D3/943:947
homologous
J3_4V88_033		NA
1/D3/1150:1151,
1/D3/1627:1629,
1/D3/1636:1640		NANA
1/D3/1168:1171,
1/D3/1468:1470,
1/D3/1574:1577
homologous
J3_4V88_036		NA
1/D4/105:111,
1/D4/259:263,
1/D4/308:310		NANA

Problematic loops

No problematic loops


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