Complet list of 1dmc hssp file
Complete list of 1dmc.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1DMC
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 2014-04-27
HEADER METALLOTHIONEIN 22-NOV-94 1DMC
COMPND MOL_ID: 1; MOLECULE: CD6 METALLOTHIONEIN-1; CHAIN: A; ENGINEERED: YES
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: CALLINECTES SAPIDUS; ORGANISM_COMMON:
AUTHOR S.S.NARULA,M.BROUWER,Y.HUA,I.M.ARMITAGE
DBREF 1DMC A 1 31 UNP P55949 MT1_CALSI 29 59
SEQLENGTH 31
NCHAIN 1 chain(s) in 1DMC data set
NALIGN 20
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 : MT1_CALSI 1DMC 1.00 1.00 1 31 29 59 31 0 0 59 P55949 Metallothionein-1B OS=Callinectes sapidus PE=1 SV=1
2 : Q548Y3_CALSI 1.00 1.00 1 31 29 59 31 0 0 59 Q548Y3 Cadmium-inducible metallothionein CdMT-I OS=Callinectes sapidus PE=4 SV=1
3 : T2BQT3_PORTR 0.90 0.94 1 31 29 59 31 0 0 59 T2BQT3 Metallothionein 2 OS=Portunus trituberculatus GN=MT2 PE=4 SV=1
4 : A7DY30_CANPG 0.83 0.97 1 30 29 58 30 0 0 58 A7DY30 Metallothionein OS=Cancer pagurus GN=Mt PE=4 SV=1
5 : MT1_SCYSE 0.83 0.97 1 30 28 57 30 0 0 58 P02805 Metallothionein-1 OS=Scylla serrata PE=1 SV=1
6 : A7DY28_NECPU 0.80 0.97 1 30 29 58 30 0 0 58 A7DY28 Metallothionein OS=Necora puber GN=Mt PE=4 SV=1
7 : A7DY29_CARMA 0.80 0.97 1 30 31 60 30 0 0 60 A7DY29 Metallothionein OS=Carcinus maenas GN=Mt PE=4 SV=1
8 : A7DY33_9EUCA 0.80 0.93 1 30 29 58 30 0 0 58 A7DY33 Metallothionein OS=Cyanagraea praedator GN=Mt PE=4 SV=1
9 : MT_ASTAS 0.80 0.97 1 30 29 58 30 0 0 58 P55951 Metallothionein OS=Astacus astacus PE=1 SV=1
10 : MT_CARMA 0.80 0.97 1 30 29 58 30 0 0 58 P55948 Metallothionein OS=Carcinus maenas PE=1 SV=1
11 : A7DY35_9EUCA 0.79 0.97 2 30 30 58 29 0 0 58 A7DY35 Metallothionein OS=Dromia personata GN=Mt PE=4 SV=1
12 : Q9U623_PACLE 0.79 0.97 2 30 30 58 29 0 0 58 Q9U623 Metallothionein OS=Pacifastacus leniusculus PE=4 SV=1
13 : A7DY32_BYTTH 0.77 0.93 1 30 29 58 30 0 0 58 A7DY32 Metallothionein OS=Bythograea thermydron GN=Mt PE=4 SV=1
14 : E5D8G3_PROCL 0.77 1.00 1 26 19 44 26 0 0 44 E5D8G3 Metallothionein isoform 1 (Fragment) OS=Procambarus clarkii GN=mt1 PE=2 SV=1
15 : Q86M28_CARMA 0.77 0.93 1 30 29 58 30 0 0 58 Q86M28 Metallothionein Ib OS=Carcinus maenas GN=MTIb PE=4 SV=1
16 : A7DY36_9EUCA 0.76 1.00 2 30 30 58 29 0 0 58 A7DY36 Metallothionein OS=Dromia personata GN=Mt PE=4 SV=1
17 : MT1_HOMAM 1J5L 0.76 1.00 1 29 28 56 29 0 0 58 P29499 Metallothionein-1 OS=Homarus americanus PE=1 SV=2
18 : A7DY24_BYTTH 0.73 0.93 1 30 29 58 30 0 0 58 A7DY24 Metallothionein OS=Bythograea thermydron GN=Mt PE=4 SV=1
19 : A7DY26_9EUCA 0.73 0.93 1 30 29 58 30 0 0 58 A7DY26 Metallothionein OS=Cyanagraea praedator GN=Mt PE=4 SV=1
20 : Q95P38_HOMAM 0.73 0.97 1 30 29 58 30 0 0 58 Q95P38 Metallothionein OS=Homarus americanus GN=mth PE=4 SV=1
## ALIGNMENTS 1 - 20
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A S 0 0 137 18 61 SSSSSATSST PAT APPA
2 2 A P - 0 0 38 21 0 PPPPPPPPPPPPPPPPPPPP
3 3 A C >> - 0 0 53 21 0 CCCCCCCCCCCCCCCCCCCC
4 4 A Q T 34 S+ 0 0 184 21 30 QQTDEEEEDEEDEDEEEEEE
5 5 A K T 34 S+ 0 0 151 21 0 KKKKKKKKKKKKKKKKKKKK
6 6 A C T <> S+ 0 0 1 21 0 CCCCCCCCCCCCCCCCCCCC
7 7 A T T >< S- 0 0 119 21 46 TTSTSSSSTSTTTTSTTTST
8 8 A S T 34 S+ 0 0 129 21 0 SSSSSSSSSSSSSSSSSSSS
9 9 A G T 34 + 0 0 26 21 0 GGGGGGGGGGGGGGGGGGGG
10 10 A C << + 0 0 46 21 0 CCCCCCCCCCCCCCCCCCCC
11 11 A K + 0 0 174 21 0 KKKKKKKKKKKKKKKKKKKK
12 12 A C + 0 0 14 21 0 CCCCCCCCCCCCCCCCCCCC
13 13 A A S S+ 0 0 90 21 62 AAATATTTPTSPTPTSPTSP
14 14 A T S >> S- 0 0 81 21 65 TTNNNTTNSTSSNSTSSNNS
15 15 A K H 3> S+ 0 0 144 21 0 KKKKKKKKKKKKKKKKKKKK
16 16 A E H 34 S+ 0 0 149 21 17 EEEDEEEEEEDEDEEDDDED
17 17 A E H X> S+ 0 0 110 21 13 EEEEEDDEEDEEEEDEEEEE
18 18 A C H 3X S+ 0 0 5 21 0 CCCCCCCCCCCCCCCCCCCC
19 19 A S H 3< S+ 0 0 85 21 67 SSSSSCCSACVATACAATPA
20 20 A K H <4 S+ 0 0 172 21 0 KKKKKKKKKKKKKKKKKKKK
21 21 A T H < S+ 0 0 79 21 0 TTTTTTTTTTTTTTTTTTTT
22 22 A C < - 0 0 15 21 0 CCCCCCCCCCCCCCCCCCCC
23 23 A T S S+ 0 0 133 21 57 TTTSSTTKSTSSTSTSSTKS
24 24 A K S S- 0 0 162 21 18 KKKKKKKKKKKKSKKKKSKK
25 25 A P - 0 0 73 21 6 PPPPAPPPPPPPPPPPPPPP
26 26 A C - 0 0 24 21 13 CCCCCCCCCCCCCCRCCCCC
27 27 A S S S+ 0 0 86 20 50 SSSSSSSTESSRS STSTTK
28 28 A C S S+ 0 0 51 20 0 CCCCCCCCCCCCC CCCCCC
29 29 A C S S- 0 0 17 20 0 CCCCCCCCCCCCC CCCCCC
30 30 A P 0 0 49 19 0 PPPPPPPPPPPPP PP PPP
31 31 A K 0 0 269 4 0 KKK
## SEQUENCE PROFILE AND ENTROPY
SeqNo PDBNo V L I M F W Y G A P S T C H R K Q E N D NOCC NDEL NINS ENTROPY RELENT WEIGHT
1 1 A 0 0 0 0 0 0 0 0 22 17 44 17 0 0 0 0 0 0 0 0 18 0 0 1.292 43 0.38
2 2 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 14 62 0 19 21 0 0 1.036 34 0.69
5 5 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 21 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
7 7 A 0 0 0 0 0 0 0 0 0 0 38 62 0 0 0 0 0 0 0 0 21 0 0 0.665 22 0.54
8 8 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
9 9 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
10 10 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 21 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
13 13 A 0 0 0 0 0 0 0 0 24 24 14 38 0 0 0 0 0 0 0 0 21 0 0 1.329 44 0.37
14 14 A 0 0 0 0 0 0 0 0 0 0 33 33 0 0 0 0 0 0 33 0 21 0 0 1.099 36 0.34
15 15 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 21 0 0 0.000 0 1.00
16 16 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 67 0 33 21 0 0 0.637 21 0.83
17 17 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 81 0 19 21 0 0 0.487 16 0.87
18 18 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
19 19 A 5 0 0 0 0 0 0 0 29 5 33 10 19 0 0 0 0 0 0 0 21 0 0 1.554 51 0.32
20 20 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 21 0 0 0.000 0 1.00
21 21 A 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
22 22 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 21 0 0 0.000 0 1.00
23 23 A 0 0 0 0 0 0 0 0 0 0 43 48 0 0 0 10 0 0 0 0 21 0 0 0.940 31 0.43
24 24 A 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 90 0 0 0 0 21 0 0 0.314 10 0.82
25 25 A 0 0 0 0 0 0 0 0 5 95 0 0 0 0 0 0 0 0 0 0 21 0 0 0.191 6 0.93
26 26 A 0 0 0 0 0 0 0 0 0 0 0 0 95 0 5 0 0 0 0 0 21 0 0 0.191 6 0.87
27 27 A 0 0 0 0 0 0 0 0 0 0 65 20 0 0 5 5 0 5 0 0 20 0 0 1.051 35 0.49
28 28 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
29 29 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 20 0 0 0.000 0 1.00
30 30 A 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 19 0 0 0.000 0 1.00
31 31 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 4 0 0 0.000 0 1.00
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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