Analysis results for 1L9A.pdb
/soft/www-lbit/www/htdocs/mcannotate-simple/bin/annote /tmp/phpBeKUR4Annotating...done.
Finding helices...done.
Finding strands...done.
Residue conformations -------------------------------------------
B112 : G C3'_endo anti
B113 : A C3'_endo anti
B114 : C C3'_endo anti
B115 : A C3'_endo anti
B116 : C C3'_endo anti
B117 : U C3'_endo anti
B118 : A C3'_endo anti
B119 : A C3'_endo anti
B120 : G C3'_endo anti
B121 : U C3'_endo anti
B122 : U C3'_endo anti
B123 : C C3'_endo anti
B124 : G C3'_endo anti
B125 : G C3'_endo anti
B126 : C C3'_endo anti
B127 : A C3'_endo anti
B128 : U C3'_endo anti
B129 : C C3'_endo anti
B130 : A C3'_endo anti
B131 : A C3'_endo anti
B132 : U C3'_endo anti
B133 : A C3'_endo anti
B134 : U C3'_endo anti
B135 : G C3'_endo anti
B136 : G C3'_endo anti
B137 : U C3'_endo anti
B138 : G C3'_endo anti
B139 : A C3'_endo anti
B140 : C C3'_endo anti
B141 : C C3'_endo anti
B142 : U C3'_endo anti
B143 : C C3'_endo anti
B144 : C C3'_endo anti
B145 : C C3'_endo anti
B146 : G C3'_endo anti
B147 : G C3'_endo anti
B148 : G C4'_exo anti
B149 : A C3'_endo anti
B150 : G C3'_endo anti
B151 : C C3'_endo anti
B152 : G C3'_endo anti
B153 : G C3'_endo anti
B154 : G C3'_endo anti
B155 : G C3'_endo anti
B156 : G C3'_endo anti
B157 : A C3'_endo anti
B158 : C C3'_endo anti
B159 : C C3'_endo anti
B160 : A C3'_endo anti
B161 : C C3'_endo anti
B162 : C C3'_endo anti
B163 : A C3'_endo anti
B164 : G C3'_endo anti
B165 : G C3'_endo anti
B166 : U C3'_endo anti
B167 : U C3'_endo anti
B168 : G C3'_endo anti
B169 : C C3'_endo anti
B170 : C C3'_endo anti
B171 : U C3'_endo anti
B172 : A C3'_endo anti
B175 : G C3'_endo anti
B176 : A C3'_endo anti
B177 : G C3'_endo anti
B178 : G C3'_endo anti
B179 : G C3'_endo anti
B180 : G C3'_endo anti
B181 : U C3'_endo anti
B182 : G C3'_endo anti
B183 : A C3'_endo syn
B184 : A C3'_endo syn
B185 : C C3'_endo anti
B186 : C C3'_endo anti
B187 : G C3'_endo anti
B188 : G C3'_endo syn
B189 : C C3'_endo anti
B190 : C C3'_endo anti
B191 : C C3'_endo anti
B192 : A C3'_endo anti
B193 : G C3'_endo anti
B194 : G C3'_endo anti
B195 : U C3'_endo anti
B196 : C C3'_endo anti
B197 : G C3'_endo anti
B198 : G C3'_endo anti
B199 : A C3'_endo anti
B200 : A C3'_endo anti
B201 : A C3'_endo anti
B202 : C C3'_endo anti
B203 : G C3'_endo anti
B204 : G C3'_endo anti
B205 : A C3'_endo anti
B206 : G C3'_endo anti
B207 : C C3'_endo anti
B208 : A C3'_endo anti
B209 : G C3'_endo anti
B210 : G C3'_endo anti
B211 : U C3'_endo anti
B212 : C C3'_endo anti
B213 : A C3'_endo anti
B214 : A C3'_endo anti
B215 : A C3'_endo syn
B216 : A C3'_endo anti
B217 : C C3'_endo anti
B218 : U C3'_endo anti
B219 : C C3'_endo anti
B220 : C C3'_endo anti
B221 : C C3'_endo anti
B222 : G C3'_endo anti
B223 : U C3'_endo anti
B224 : G C3'_endo anti
B225 : C C3'_endo anti
B226 : U C3'_endo anti
B227 : G C3'_endo anti
B228 : A C3'_endo anti
B229 : U C3'_endo anti
B230 : C C3'_endo anti
B231 : A C3'_endo anti
B232 : G C3'_endo anti
B233 : U C3'_endo anti
B234 : A C3'_endo anti
B235 : G C3'_endo anti
B236 : U C3'_endo anti
B237 : G C3'_endo anti
B238 : U C3'_endo anti
Base-pairs ------------------------------------------------------
B113-B238 : A-U Ww/Ws pairing cis XX
B114-B237 : C-G Ww/Ww pairing cis XIX
B115-B236 : A-U Ww/Ww pairing cis XX
B116-B235 : C-G Ww/Ww pairing cis XIX
B117-B234 : U-A Ww/Ww pairing cis XX
B118-B233 : A-U Wh/Hw pairing trans one_hbond 48
B120-B230 : G-C Ww/Ww pairing cis XIX
B121-B229 : U-U Ww/Ws pairing cis 81
B123-B227 : C-G Ww/Ww pairing cis XIX
B124-B226 : G-U Ww/Ws pairing cis XXVIII
B125-B225 : G-C Ww/Ww pairing cis XIX
B126-B224 : C-G Ww/Ww pairing cis XIX
B127-B223 : A-U Ww/Ww pairing cis one_hbond
B128-B222 : U-G Ws/Ww pairing cis XXVIII
B129-B168 : C-G Ww/Ww pairing cis XIX
B130-B167 : A-U Ww/Ww pairing cis XX
B131-B166 : A-U Ww/Ww pairing cis XX
B132-B165 : U-G Ws/Ww pairing cis XXVIII
B133-B164 : A-G Hh/Ss pairing trans XI
B135-B162 : G-C Ww/Ww pairing cis XIX
B136-B161 : G-C Ww/Ww pairing cis XIX
B137-B160 : U-A Ww/Ww pairing cis XX
B138-B159 : G-C Ww/Ww pairing cis XIX
B139-B158 : A-C Wh/Ww pairing cis one_hbond 78
B140-B157 : C-A Wh/Ww pairing cis one_hbond 71
B141-B156 : C-G Ww/Ww pairing cis XIX
B142-B155 : U-G Ws/Ww pairing cis XXVIII
B143-B154 : C-G Ww/Ww pairing cis XIX
B144-B153 : C-G Ww/Ww pairing cis XIX
B145-B152 : C-G Ww/Ww pairing cis 124
B146-B151 : G-C Ww/Ww pairing cis XIX
B148-B200 : G-A Wh/Wh pairing trans one_hbond 66
B149-B201 : A-A Ww/Ww pairing trans I
B168-B169 : G-C Ss/Hh pairing adjacent cis DIR_5' one_hbond
B177-B220 : G-C Ww/Ww pairing cis XIX
B178-B219 : G-C Ww/Ww pairing cis 128
B179-B218 : G-U Ww/Ws pairing cis XXVIII
B180-B217 : G-C Ww/Ww pairing cis XIX
B181-B216 : U-A Ww/Ww pairing cis XX
B184-B215 : A-A Ww/C8 pairing trans one_hbond
B187-B212 : G-C Ww/Ww pairing cis XIX
B188-B211 : G-U Bh/Ww pairing cis one_hbond
B189-B210 : C-G Ww/Ww pairing cis XIX
B190-B209 : C-G Ww/Ww pairing cis 124
B191-B208 : C-A Ws/Wh pairing cis one_hbond 78
B192-B207 : A-C Hh/Ww pairing trans 69
B193-B206 : G-G Bh/Ww pairing cis 115
B194-B205 : G-A Ww/Ww pairing cis VIII
B195-B204 : U-G Ws/Ww pairing cis XXVIII
B196-B203 : C-G Ww/Ww pairing cis XIX
B197-B202 : G-C Ww/Ww pairing cis XIX
Base Triples ----------------------------------------------------
T1 B129-B168 B168-B169
Adjacent relations ----------------------------------------------
B112-B113 : stack adjacent
B113-B114 : stack adjacent
B114-B115 : adjacent
B115-B116 : stack adjacent
B116-B117 : stack adjacent
B117-B118 : adjacent
B118-B119 : stack adjacent
B119-B120 : stack adjacent
B120-B121 : stack adjacent
B121-B122 : stack adjacent
B122-B123 : adjacent
B123-B124 : adjacent
B124-B125 : stack adjacent
B125-B126 : stack adjacent
B126-B127 : adjacent
B127-B128 : stack adjacent
B128-B129 : adjacent
B129-B130 : adjacent
B130-B131 : stack adjacent
B131-B132 : stack adjacent
B132-B133 : adjacent
B133-B134 : stack adjacent
B134-B135 : adjacent
B135-B136 : stack adjacent
B136-B137 : stack adjacent
B137-B138 : adjacent
B138-B139 : stack adjacent
B139-B140 : stack adjacent
B140-B141 : stack adjacent
B141-B142 : stack adjacent
B142-B143 : adjacent
B143-B144 : adjacent
B144-B145 : adjacent
B145-B146 : stack adjacent
B146-B147 : stack adjacent
B147-B148 : adjacent
B148-B149 : stack adjacent
B149-B150 : stack adjacent
B150-B151 : adjacent
B151-B152 : adjacent
B152-B153 : stack adjacent
B153-B154 : stack adjacent
B154-B155 : stack adjacent
B155-B156 : stack adjacent
B156-B157 : stack adjacent
B157-B158 : stack adjacent
B158-B159 : adjacent
B159-B160 : adjacent
B160-B161 : stack adjacent
B161-B162 : adjacent
B162-B163 : stack adjacent
B163-B164 : stack adjacent
B164-B165 : adjacent
B165-B166 : stack adjacent
B166-B167 : adjacent
B167-B168 : adjacent
B168-B169 : pairing adjacent cis one_hbond
B169-B170 : adjacent
B170-B171 : adjacent
B171-B172 : adjacent
B175-B176 : adjacent
B176-B177 : adjacent
B177-B178 : stack adjacent
B178-B179 : stack adjacent
B179-B180 : stack adjacent
B180-B181 : stack adjacent
B181-B182 : adjacent
B182-B183 : adjacent
B183-B184 : adjacent
B184-B185 : stack adjacent reverse
B185-B186 : stack adjacent
B186-B187 : adjacent
B187-B188 : stack adjacent reverse
B188-B189 : stack adjacent reverse
B189-B190 : stack adjacent
B190-B191 : stack adjacent
B191-B192 : adjacent
B192-B193 : stack adjacent
B193-B194 : stack adjacent
B194-B195 : stack adjacent
B195-B196 : adjacent
B196-B197 : adjacent
B197-B198 : stack adjacent
B198-B199 : adjacent
B199-B200 : stack adjacent
B200-B201 : stack adjacent
B201-B202 : adjacent
B202-B203 : stack adjacent
B203-B204 : stack adjacent
B204-B205 : stack adjacent
B205-B206 : stack adjacent
B206-B207 : stack adjacent
B207-B208 : stack adjacent
B208-B209 : stack adjacent
B209-B210 : stack adjacent
B210-B211 : stack adjacent
B211-B212 : adjacent
B212-B213 : stack adjacent
B213-B214 : stack adjacent
B214-B215 : stack adjacent reverse
B215-B216 : stack adjacent reverse
B216-B217 : stack adjacent
B217-B218 : stack adjacent
B218-B219 : adjacent
B219-B220 : stack adjacent
B220-B221 : adjacent
B221-B222 : stack adjacent
B222-B223 : stack adjacent
B223-B224 : stack adjacent
B224-B225 : stack adjacent
B225-B226 : stack adjacent
B226-B227 : adjacent
B227-B228 : stack adjacent
B228-B229 : stack adjacent
B229-B230 : adjacent
B230-B231 : stack adjacent
B231-B232 : stack adjacent
B232-B233 : adjacent
B233-B234 : adjacent
B234-B235 : stack adjacent
B235-B236 : stack adjacent
B236-B237 : stack adjacent
B237-B238 : stack adjacent
Non-Adjacent stackings ------------------------------------------
B115-B237 : stack
B118-B234 : stack
B120-B231 : stack
B121-B230 : stack
B124-B227 : stack
B127-B224 : stack
B130-B168 : stack
B133-B165 : stack
B135-B163 : stack
B138-B160 : stack
B146-B152 : stack
B187-B213 : stack
B192-B208 : stack
B196-B204 : stack
B197-B203 : stack
Helices ---------------------------------------------------------
H1, length = 5, type = A :
B113-ACACU-B117
B238-UGUGA-B234
H2, length = 4, type = A :
B123-CGGC-B126
B227-GUCG-B224
H3, length = 4, type = A :
B129-CAAU-B132
B168-GUUG-B165
H4, length = 4, type = A :
B135-GGUG-B138
B162-CCAC-B159
H5, length = 4, type = A :
B141-CUCC-B144
B156-GGGG-B153
H6, length = 3, type = A :
B179-GGU-B181
B218-UCA-B216
H7, length = 3, type = A :
B195-UCG-B197
B204-GGC-B202
Strands ---------------------------------------------------------
S1 single strand: B112-G-B112
S2 internal loop: B118-AAGUU-B122 -- B228-AUCAGU-B233
S3 single strand: B127-AU-B128
S4 internal loop: B133-AU-B134 -- B163-AG-B164
S5 internal loop: B139-AC-B140 -- B157-AC-B158
S6 loop: B145-CGGGAGCG-B152
S7 internal loop: B157-AC-B158 -- B139-AC-B140
S8 internal loop: B163-AG-B164 -- B133-AU-B134
S9 single strand: B169-CCUA-B172
S10 single strand: B175-GAGG-B178
S11 internal loop: B182-GAACCGGCCCAGG-B194 -- B205-AGCAGGUCAAA-B215
S12 loop: B198-GAAA-B201
S13 internal loop: B205-AGCAGGUCAAA-B215 -- B182-GAACCGGCCCAGG-B194
S14 single strand: B219-CCCGU-B223
S15 internal loop: B228-AUCAGU-B233 -- B118-AAGUU-B122
Tertiary base-pairs ---------------------------------------------
internal loop/internal loop: B118-B233
internal loop/internal loop: B120-B230
internal loop/internal loop: B121-B229
strand/strand: B127-B223
strand/strand: B128-B222
internal loop/internal loop: B133-B164
internal loop/internal loop: B139-B158
internal loop/internal loop: B140-B157
intraloop: B145-B152
intraloop: B146-B151
loop/loop: B148-B200
loop/loop: B149-B201
inter helix: B168-B169
strand/strand: B177-B220
strand/strand: B178-B219
internal loop/internal loop: B184-B215
internal loop/internal loop: B187-B212
internal loop/internal loop: B188-B211
internal loop/internal loop: B189-B210
internal loop/internal loop: B190-B209
internal loop/internal loop: B191-B208
internal loop/internal loop: B192-B207
internal loop/internal loop: B193-B206
internal loop/internal loop: B194-B205
Missing interactions: 51/52
Sequences -------------------------------------------------------
Sequence 1 (length = 61):
B112 GACACUAAGU UCGGCAUCAA UAUGGUGACC UCCCGGGAGC GGGGGACCA
-(((((b-bb -((((bb((( (b-((((bb( (((bb-bb-b b))))bb))
ter ------X-XX -----XX--- -X-----XX- ---XX-XX-X X----XX--
B162 CAGGUUGCCU A
)-b))))b-- -
ter --X---XX-- -
Sequence 2 (length = 64):
B175 GAGGGGUGAA CCGGCCCAGG UCGGAAACGG AGCAGGUCAA AACUCCCGU
--bb(((--b --bbbbbbbb (((--bb))) bbbbbbbb-- b)))bb-bb
ter --XX-----X --XXXXXXXX -----XX--- XXXXXXXX-- X---XX-XX
B225 CUGAUCAGUA GUGU
)))-bb--b) ))))
ter ----XX--X- ----
-----------------------------------------------------------------