Complet list of 1lmr hssp file
Complete list of 1lmr.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1LMR
THRESHOLD according to: t(L)=(290.15 * L ** -0.562) + 5
REFERENCE Sander C., Schneider R. : Database of homology-derived protein structures. Proteins, 9:56-68 (1991).
CONTACT Maintained at http://www.cmbi.ru.nl/ by Maarten L. Hekkelman
DATE file generated on 2014-05-03
HEADER TOXIN 02-MAY-02 1LMR
COMPND MOL_ID: 1; MOLECULE: TOXIN ADO1; CHAIN: A
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: AGRIOSPHODRUS DOHRNI; ORGANISM_TAXID:
AUTHOR C.BERNARD,G.CORZO,S.ADACHI-AKAHANE,G.FOURES,K.KANEMARU, Y.FURUKAWA,T.N
DBREF 1LMR A 1 35 UNP P58608 ADO1_AGRDO 1 35
SEQLENGTH 35
NCHAIN 1 chain(s) in 1LMR data set
NALIGN 2
NOTATION : ID: EMBL/SWISSPROT identifier of the aligned (homologous) protein
NOTATION : STRID: if the 3-D structure of the aligned protein is known, then STRID is the Protein Data Bank identifier as taken
NOTATION : from the database reference or DR-line of the EMBL/SWISSPROT entry
NOTATION : %IDE: percentage of residue identity of the alignment
NOTATION : %SIM (%WSIM): (weighted) similarity of the alignment
NOTATION : IFIR/ILAS: first and last residue of the alignment in the test sequence
NOTATION : JFIR/JLAS: first and last residue of the alignment in the alignend protein
NOTATION : LALI: length of the alignment excluding insertions and deletions
NOTATION : NGAP: number of insertions and deletions in the alignment
NOTATION : LGAP: total length of all insertions and deletions
NOTATION : LSEQ2: length of the entire sequence of the aligned protein
NOTATION : ACCNUM: SwissProt accession number
NOTATION : PROTEIN: one-line description of aligned protein
NOTATION : SeqNo,PDBNo,AA,STRUCTURE,BP1,BP2,ACC: sequential and PDB residue numbers, amino acid (lower case = Cys), secondary
NOTATION : structure, bridge partners, solvent exposure as in DSSP (Kabsch and Sander, Biopolymers 22, 2577-2637(1983)
NOTATION : VAR: sequence variability on a scale of 0-100 as derived from the NALIGN alignments
NOTATION : pair of lower case characters (AvaK) in the alignend sequence bracket a point of insertion in this sequence
NOTATION : dots (....) in the alignend sequence indicate points of deletion in this sequence
NOTATION : SEQUENCE PROFILE: relative frequency of an amino acid type at each position. Asx and Glx are in their
NOTATION : acid/amide form in proportion to their database frequencies
NOTATION : NOCC: number of aligned sequences spanning this position (including the test sequence)
NOTATION : NDEL: number of sequences with a deletion in the test protein at this position
NOTATION : NINS: number of sequences with an insertion in the test protein at this position
NOTATION : ENTROPY: entropy measure of sequence variability at this position
NOTATION : RELENT: relative entropy, i.e. entropy normalized to the range 0-100
NOTATION : WEIGHT: conservation weight
## PROTEINS : identifier and alignment statistics
NR. ID STRID %IDE %WSIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCNUM PROTEIN
1 : ADO1_AGRDO 1LMR 1.00 1.00 1 35 1 35 35 0 0 35 P58608 Toxin Ado1 OS=Agriosphodrus dohrni PE=1 SV=1
2 : IOB1_ISYOB 0.89 0.94 1 35 2 36 35 0 0 36 P58609 Toxin Iob1 OS=Isyndus obscurus PE=1 SV=1
## ALIGNMENTS 1 - 2
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A A 0 0 129 3 0 AA
2 2 A D - 0 0 122 3 0 DD
3 3 A D S S+ 0 0 159 3 33 DE
4 4 A D - 0 0 99 3 0 DD
5 5 A a - 0 0 36 3 0 CC
6 6 A L - 0 0 8 3 0 LL
7 7 A P > - 0 0 100 3 0 PP
8 8 A R T 3 S+ 0 0 188 3 0 RR
9 9 A G T 3 S+ 0 0 52 3 0 GG
10 10 A S < - 0 0 47 3 0 SS
11 11 A K - 0 0 146 3 0 KK
12 12 A b + 0 0 8 3 0 CC
13 13 A L S S+ 0 0 82 3 0 LL
14 14 A G S S+ 0 0 59 3 0 GG
15 15 A E - 0 0 91 3 0 EE
16 16 A N + 0 0 156 3 0 NN
17 17 A K - 0 0 39 3 0 KK
18 18 A Q - 0 0 125 3 0 QQ
19 19 A c - 0 0 19 3 0 CC
20 20 A a > - 0 0 66 3 0 CC
21 21 A K T 3 S+ 0 0 212 3 80 KE
22 22 A G T 3 S+ 0 0 40 3 106 GK
23 23 A T E < -A 34 0A 54 3 0 TT
24 24 A T E -A 33 0A 70 3 0 TT
25 25 A b E -A 32 0A 40 3 0 CC
26 26 A M E > -A 31 0A 69 3 0 MM
27 27 A F T 5S+ 0 0 148 3 0 FF
28 28 A Y T 5S+ 0 0 174 3 0 YY
29 29 A A T 5S- 0 0 20 3 0 AA
30 30 A N T 5 + 0 0 67 3 0 NN
31 31 A R E