Analysis results for 1DUH.pdb
Annotating...done.
Finding helices...done.
Finding strands...done.
Residue conformations -------------------------------------------
A31 : C C3'_endo anti
A32 : U C3'_endo anti
A33 : C C3'_endo anti
A34 : U C3'_endo anti
A35 : G C3'_endo anti
A36 : U C3'_endo anti
A37 : U C3'_endo anti
A38 : U C3'_endo anti
A39 : A C3'_endo anti
A40 : C C3'_endo anti
A41 : C C2'_endo anti
A42 : A C2'_endo syn
A43 : G C3'_endo anti
A44 : G C3'_endo anti
A45 : U C3'_endo anti
A46 : C C3'_endo anti
A47 : A C3'_endo anti
A48 : G C3'_endo anti
A49 : G C3'_endo anti
A50 : U C3'_endo anti
A51 : C C3'_endo anti
A52 : C C3'_endo anti
A53 : G C3'_endo anti
A54 : G C2'_endo anti
A55 : A C3'_endo anti
A56 : A C3'_endo anti
A57 : G C3'_endo anti
A58 : G C3'_endo anti
A59 : A C3'_endo anti
A60 : A C3'_endo anti
A61 : G C3'_endo anti
A62 : C C3'_endo anti
A63 : A C3'_endo anti
A64 : G C3'_endo anti
A65 : C C3'_endo anti
A66 : C C3'_endo anti
A67 : A C3'_endo anti
A68 : A C3'_endo anti
A69 : G C3'_endo anti
A70 : G C3'_endo anti
A71 : C C3'_endo anti
A72 : A C3'_endo anti
A73 : G C3'_endo anti
A74 : A C3'_endo anti
B31 : C C3'_endo anti
B32 : U C3'_endo anti
B33 : C C3'_endo anti
B34 : U C3'_endo anti
B35 : G C3'_endo anti
B36 : U C3'_endo anti
B37 : U C3'_endo anti
B38 : U C3'_endo anti
B39 : A C3'_endo anti
B40 : C C3'_endo anti
B41 : C C2'_endo anti
B42 : A C2'_endo syn
B43 : G C3'_endo anti
B44 : G C3'_endo anti
B45 : U C3'_endo anti
B46 : C C3'_endo anti
B47 : A C3'_endo anti
B48 : G C3'_endo anti
B49 : G C3'_endo anti
B50 : U C3'_endo anti
B51 : C C3'_endo anti
B52 : C C3'_endo anti
B53 : G C3'_endo anti
B54 : G C2'_endo anti
B55 : A C3'_endo anti
B56 : A C3'_endo anti
B57 : G C3'_endo anti
B58 : G C3'_endo anti
B59 : A C3'_endo anti
B60 : A C3'_endo anti
B61 : G C3'_endo anti
B62 : C C3'_endo anti
B63 : A C3'_endo anti
B64 : G C3'_endo anti
B65 : C C3'_endo anti
B66 : C C3'_endo anti
B67 : A C3'_endo anti
B68 : A C3'_endo anti
B69 : G C3'_endo anti
B70 : G C3'_endo anti
B71 : C C3'_endo anti
B72 : A C3'_endo anti
B73 : G C3'_endo anti
B74 : A C3'_endo anti
Base-pairs ------------------------------------------------------
A32-B74 : U-A Ww/Ww pairing cis XX
A33-B73 : C-G Ww/Ww pairing cis XIX
A34-B72 : U-A Ww/Ww pairing cis XX
A35-B71 : G-C Ww/Ww pairing cis XIX
A36-B70 : U-G Ws/Ww pairing cis XXVIII
A37-B69 : U-G Ws/Ww pairing cis XXVIII
A38-B68 : U-A Ww/Ww pairing cis XX
A43-B66 : G-C Ww/Ww pairing cis XIX
A44-B65 : G-C Ww/Ww pairing cis XIX
A45-B64 : U-G Ws/Ww pairing cis XXVIII
A46-B63 : C-A Ss/Hw pairing trans one_hbond 77
A47-B62 : A-C Hw/Ww pairing trans XXV
A48-B61 : G-G Hw/Sw pairing trans one_hbond 112
A49-B60 : G-A Ww/Ww pairing cis VIII
A50-B59 : U-A Ww/Ww pairing cis XX
A51-B58 : C-G Ww/Ww pairing cis XIX
A52-B57 : C-G Ww/Ww pairing cis XIX
A53-B56 : G-A Ss/Hh pairing trans XI
A54-B55 : G-A Ss/Hh pairing trans XI
A55-B54 : A-G Hh/Ss pairing trans XI
A56-B53 : A-G Hh/Ss pairing trans XI
A57-B52 : G-C Ww/Ww pairing cis XIX
A58-B51 : G-C Ww/Ww pairing cis XIX
A59-B50 : A-U Ww/Ww pairing cis XX
A60-B49 : A-G Ww/Ww pairing cis VIII
A61-B48 : G-G Sw/Hw pairing trans one_hbond 112
A62-B47 : C-A Ww/Hw pairing trans XXV
A63-B46 : A-C Hw/Ss pairing trans one_hbond 77
A64-B45 : G-U Ww/Ws pairing cis XXVIII
A65-B44 : C-G Ww/Ww pairing cis XIX
A66-B43 : C-G Ww/Ww pairing cis XIX
A68-B38 : A-U Ww/Ww pairing cis XX
A69-B37 : G-U Ww/Ws pairing cis XXVIII
A70-B36 : G-U Ww/Ws pairing cis XXVIII
A71-B35 : C-G Ww/Ww pairing cis XIX
A72-B34 : A-U Ww/Ww pairing cis XX
A73-B33 : G-C Ww/Ww pairing cis XIX
A74-B32 : A-U Ww/Ww pairing cis XX
Base Triples ----------------------------------------------------
Adjacent relations ----------------------------------------------
A31-A32 : stack adjacent
A32-A33 : adjacent
A33-A34 : adjacent
A34-A35 : stack adjacent
A35-A36 : stack adjacent
A36-A37 : adjacent
A37-A38 : adjacent
A38-A39 : adjacent
A39-A40 : stack adjacent
A40-A41 : adjacent
A41-A42 : adjacent
A42-A43 : adjacent
A43-A44 : stack adjacent
A44-A45 : stack adjacent
A45-A46 : stack adjacent
A46-A47 : adjacent
A47-A48 : stack adjacent
A48-A49 : stack adjacent
A49-A50 : stack adjacent
A50-A51 : stack adjacent
A51-A52 : stack adjacent
A52-A53 : stack adjacent
A53-A54 : stack adjacent
A54-A55 : adjacent
A55-A56 : stack adjacent
A56-A57 : stack adjacent
A57-A58 : stack adjacent
A58-A59 : stack adjacent
A59-A60 : stack adjacent
A60-A61 : stack adjacent
A61-A62 : adjacent
A62-A63 : stack adjacent
A63-A64 : stack adjacent
A64-A65 : stack adjacent
A65-A66 : adjacent
A66-A67 : stack adjacent
A67-A68 : stack adjacent
A68-A69 : stack adjacent
A69-A70 : stack adjacent
A70-A71 : stack adjacent
A71-A72 : adjacent
A72-A73 : stack adjacent
A73-A74 : stack adjacent
B31-B32 : stack adjacent
B32-B33 : adjacent
B33-B34 : adjacent
B34-B35 : stack adjacent
B35-B36 : stack adjacent
B36-B37 : adjacent
B37-B38 : adjacent
B38-B39 : adjacent
B39-B40 : stack adjacent
B40-B41 : adjacent
B41-B42 : adjacent
B42-B43 : adjacent
B43-B44 : stack adjacent
B44-B45 : stack adjacent
B45-B46 : stack adjacent
B46-B47 : adjacent
B47-B48 : stack adjacent
B48-B49 : stack adjacent
B49-B50 : stack adjacent
B50-B51 : stack adjacent
B51-B52 : stack adjacent
B52-B53 : stack adjacent
B53-B54 : stack adjacent
B54-B55 : adjacent
B55-B56 : stack adjacent
B56-B57 : stack adjacent
B57-B58 : stack adjacent
B58-B59 : stack adjacent
B59-B60 : stack adjacent
B60-B61 : stack adjacent
B61-B62 : adjacent
B62-B63 : stack adjacent
B63-B64 : stack adjacent
B64-B65 : stack adjacent
B65-B66 : adjacent
B66-B67 : stack adjacent
B67-B68 : stack adjacent
B68-B69 : stack adjacent
B69-B70 : stack adjacent
B70-B71 : stack adjacent
B71-B72 : adjacent
B72-B73 : stack adjacent
B73-B74 : stack adjacent
Non-Adjacent stackings ------------------------------------------
A35-B72 : stack
A38-B69 : stack
A40-A42 : stack
A43-B67 : stack
A46-B61 : stack
A47-B63 : stack
A54-B54 : stack
A55-B55 : stack
A61-B46 : stack
A63-B47 : stack
A67-B43 : stack
A69-B38 : stack
A72-B35 : stack
B40-B42 : stack
Helices ---------------------------------------------------------
H1, length = 7, type = A :
A32-UCUGUUU-A38
B74-AGACGGA-B68
H2, length = 3, type = A :
A43-GGU-A45
B66-CCG-B64
H3, length = 3, type = A :
A50-UCC-A52
B59-AGG-B57
H4, length = 3, type = A :
A57-GGA-A59
B52-CCU-B50
H5, length = 3, type = A :
A64-GCC-A66
B45-UGG-B43
H6, length = 7, type = A :
A68-AGGCAGA-A74
B38-UUUGUCU-B32
Strands ---------------------------------------------------------
S1 single strand: A31-C-A31
S2 internal loop: A39-ACCA-A42 -- B67-A-B67
S3 internal loop: A46-CAGG-A49 -- B60-AGCA-B63
S4 internal loop: A53-GGAA-A56 -- B53-GGAA-B56
S5 internal loop: A60-AGCA-A63 -- B46-CAGG-B49
S6 internal loop: A67-A-A67 -- B39-ACCA-B42
S7 single strand: B31-C-B31
S8 internal loop: B39-ACCA-B42 -- A67-A-A67
S9 internal loop: B46-CAGG-B49 -- A60-AGCA-A63
S10 internal loop: B53-GGAA-B56 -- A53-GGAA-A56
S11 internal loop: B60-AGCA-B63 -- A46-CAGG-A49
S12 internal loop: B67-A-B67 -- A39-ACCA-A42
Tertiary base-pairs ---------------------------------------------
internal loop/internal loop: A46-B63
internal loop/internal loop: A47-B62
internal loop/internal loop: A48-B61
internal loop/internal loop: A49-B60
internal loop/internal loop: A53-B56
internal loop/internal loop: A54-B55
internal loop/internal loop: A55-B54
internal loop/internal loop: A56-B53
internal loop/internal loop: A60-B49
internal loop/internal loop: A61-B48
internal loop/internal loop: A62-B47
internal loop/internal loop: A63-B46
Sequences -------------------------------------------------------
Sequence 1 (length = 44):
A31 CUCUGUUUAC CAGGUCAGGU CCGGAAGGAA GCAGCCAAGG CAGA
-(((((((-- --(((bbbb( ((bbbb(((b bbb(((-((( ((((
ter ---------- -----XXXX- --XXXX---X XXX------- ----
Sequence 2 (length = 44):
B31 CUCUGUUUAC CAGGUCAGGU CCGGAAGGAA GCAGCCAAGG CAGA
-)))))))-- --)))bbbb) ))bbbb)))b bbb)))-))) ))))
ter ---------- -----XXXX- --XXXX---X XXX------- ----
-----------------------------------------------------------------