Complet list of 2a3d hssp file
Complete list of 2a3d.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 2A3D
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 2014-05-14
HEADER THREE-HELIX BUNDLE 01-APR-99 2A3D
COMPND MOL_ID: 1; MOLECULE: PROTEIN (DE NOVO THREE-HELIX BUNDLE); CHAIN: A; E
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; ORGANISM_TAXID: 3
AUTHOR S.T.R.WALSH,H.CHENG,J.W.BRYSON,H.RODER,W.F.DEGRADO
DBREF 2A3D A 1 73 PDB 2A3D 2A3D 1 73
SEQLENGTH 73
NCHAIN 1 chain(s) in 2A3D data set
NALIGN 5
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 : A3K8U2_9RHOB 0.41 0.58 11 69 224 282 59 0 0 471 A3K8U2 Uncharacterized protein OS=Sagittula stellata E-37 GN=SSE37_17845 PE=4 SV=1
2 : G4YI88_PHYSP 0.38 0.51 7 69 1349 1411 63 0 0 1814 G4YI88 Putative uncharacterized protein OS=Phytophthora sojae (strain P6497) GN=PHYSODRAFT_471354 PE=4 SV=1
3 : V4ZT84_9ARCH 0.38 0.69 16 73 76 133 58 0 0 264 V4ZT84 ROS/MUCR transcriptional regulator protein OS=uncultured archaeon A07HB70 GN=A07HB70_01524 PE=4 SV=1
4 : M0PDS7_9EURY 0.37 0.57 10 72 359 421 63 0 0 669 M0PDS7 Uncharacterized protein (Fragment) OS=Halorubrum aidingense JCM 13560 GN=C461_05889 PE=4 SV=1
5 : K6PYU0_9FIRM 0.34 0.56 5 72 291 358 68 0 0 1242 K6PYU0 Chromosome partition protein Smc OS=Thermaerobacter subterraneus DSM 13965 GN=smc PE=3 SV=1
## ALIGNMENTS 1 - 5
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A M > 0 0 148 1 0
2 2 A G H > + 0 0 56 1 0
3 3 A S H >> S+ 0 0 25 1 0
4 4 A W H 3> S+ 0 0 103 1 0
5 5 A A H 3X S+ 0 0 53 2 0 A
6 6 A E H X S+ 0 0 54 5 71 AA RE
13 13 A A H 3X S+ 0 0 40 5 71 AQ RA
14 14 A I H 3X S+ 0 0 15 5 27 II LV
15 15 A K H <4 S+ 0 0 128 5 82 DA ER
16 16 A T H >X S+ 0 0 85 6 75 GQAST
17 17 A R H >X S+ 0 0 141 6 40 RRRAR
18 18 A L H 3< S+ 0 0 25 6 68 LRRLL
19 19 A Q H <4 S+ 0 0 154 6 66 TEDEA
20 20 A A H << + 0 0 67 6 59 AKAAV
21 21 A L < + 0 0 9 6 47 LLVAL
22 22 A G S S+ 0 0 64 6 41 EGGED
23 23 A G S > S+ 0 0 47 6 79 KTASE
24 24 A S G >>> + 0 0 13 6 97 RLLER
25 25 A E G 345S+ 0 0 137 6 82 PEHRA
26 26 A A G <45S+ 0 0 92 6 66 VEEEA
27 27 A E T X>5S+ 0 0 60 6 61 ESESQ
28 28 A L H 3X5S+ 0 0 3 6 43 ELMLL
29 29 A A H 3> S+ 0 0 54 6 78 VRAAS
31 31 A F H >X S+ 0 0 11 6 104 SVTER
32 32 A E H 3X S+ 0 0 104 6 73 PDHRE
33 33 A K H 3X S+ 0 0 168 6 50 EQDDQ
34 34 A E H XX S+ 0 0 81 6 43 AEAEE
35 35 A I H 3X S+ 0 0 16 6 63 IRFIL
36 36 A A H >X S+ 0 0 62 6 71 ALAEG
37 37 A A H S+ 0 0 88 6 85 ALQSA
52 52 A E T >4 S+ 0 0 108 6 81 QLAEG
53 53 A V T >4 S+ 0 0 6 6 72 KLVVA
54 54 A E T >> S+ 0 0 95 6 11 EEDEE
55 55 A A H XX S+ 0 0 69 6 59 AEATE
56 56 A L H <> S+ 0 0 8 6 84 LQKLA
57 57 A R H <4 S+ 0 0 148 6 74 EQRRA
58 58 A K H > S+ 0 0 44 6 49 AAADQ
62 62 A A H 3X S+ 0 0 55 6 65 ARARA
63 63 A I H 3< S+ 0 0 26 6 29 LIFLL
64 64 A R H X S+ 0 0 109 6 59 KDEEA
66 66 A E H 3X S+ 0 0 108 6 40 QKEEE
67 67 A L H 3> S+ 0 0 4 6 73 IQALL
68 68 A Q H << S+ 0 0 141 6 64 EETSE
69 69 A A H >< S+ 0 0 40 6 39 ATATA
70 70 A Y H >< S+ 0 0 54 4 81 TAA
71 71 A R T 3< S+ 0 0 145 4 0 RRR
72 72 A H T < 0 0 138 4 50 DDQ
73 73 A N < 0 0 140 2 66 E
## 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 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
2 2 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
3 3 A 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
4 4 A 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0.000 0 1.00
5 5 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0.000 0 1.00
6 6 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 2 0 0 0.000 0 1.00
7 7 A 0 0 0 0 67 0 0 0 33 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0.637 21 0.07
8 8 A 0 0 0 0 0 0 0 0 0 0 33 0 0 0 0 33 0 33 0 0 3 0 0 1.099 36 0.15
9 9 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 33 0 67 0 0 0 3 0 0 0.637 21 0.49
10 10 A 0 0 0 25 0 0 0 0 25 0 0 0 0 0 50 0 0 0 0 0 4 0 0 1.040 34 0.13
11 11 A 0 80 0 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0.500 16 0.95
12 12 A 0 0 0 0 0 0 0 0 60 0 0 0 0 0 20 0 0 20 0 0 5 0 0 0.950 31 0.28
13 13 A 0 0 0 0 0 0 0 0 60 0 0 0 0 0 20 0 20 0 0 0 5 0 0 0.950 31 0.29
14 14 A 20 20 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0.950 31 0.73
15 15 A 0 0 0 0 0 0 0 0 20 0 0 0 0 0 20 20 0 20 0 20 5 0 0 1.609 53 0.18
16 16 A 0 0 0 0 0 0 0 17 17 0 17 33 0 0 0 0 17 0 0 0 6 0 0 1.561 52 0.24
17 17 A 0 0 0 0 0 0 0 0 17 0 0 0 0 0 83 0 0 0 0 0 6 0 0 0.451 15 0.59
18 18 A 0 67 0 0 0 0 0 0 0 0 0 0 0 0 33 0 0 0 0 0 6 0 0 0.637 21 0.32
19 19 A 0 0 0 0 0 0 0 0 17 0 0 17 0 0 0 0 17 33 0 17 6 0 0 1.561 52 0.34
20 20 A 17 0 0 0 0 0 0 0 67 0 0 0 0 0 0 17 0 0 0 0 6 0 0 0.868 28 0.41
21 21 A 17 67 0 0 0 0 0 0 17 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.868 28 0.52
22 22 A 0 0 0 0 0 0 0 50 0 0 0 0 0 0 0 0 0 33 0 17 6 0 0 1.011 33 0.58
23 23 A 0 0 0 0 0 0 0 17 17 0 17 17 0 0 0 17 0 17 0 0 6 0 0 1.792 59 0.20
24 24 A 0 33 0 0 0 0 0 0 0 0 17 0 0 0 33 0 0 17 0 0 6 0 0 1.330 44 0.02
25 25 A 0 0 0 0 0 0 0 0 17 17 0 0 0 17 17 0 0 33 0 0 6 0 0 1.561 52 0.18
26 26 A 17 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 0 50 0 0 6 0 0 1.011 33 0.34
27 27 A 0 0 0 0 0 0 0 0 0 0 33 0 0 0 0 0 17 50 0 0 6 0 0 1.011 33 0.39
28 28 A 0 67 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 6 0 0 0.868 28 0.57
29 29 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
30 30 A 17 0 0 0 0 0 0 0 50 0 17 0 0 0 17 0 0 0 0 0 6 0 0 1.242 41 0.21
31 31 A 17 0 0 0 17 0 0 0 0 0 17 17 0 0 17 0 0 17 0 0 6 0 0 1.792 59 -0.05
32 32 A 0 0 0 0 0 0 0 0 0 17 0 0 0 17 17 0 0 33 0 17 6 0 0 1.561 52 0.26
33 33 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 33 17 0 33 6 0 0 1.330 44 0.50
34 34 A 0 0 0 0 0 0 0 0 33 0 0 0 0 0 0 0 0 67 0 0 6 0 0 0.637 21 0.56
35 35 A 0 17 50 0 17 0 0 0 0 0 0 0 0 0 17 0 0 0 0 0 6 0 0 1.242 41 0.36
36 36 A 0 17 0 0 0 0 0 17 50 0 0 0 0 0 0 0 0 17 0 0 6 0 0 1.242 41 0.29
37 37 A 0 0 0 0 0 0 0 0 67 0 0 0 0 0 33 0 0 0 0 0 6 0 0 0.637 21 0.34
38 38 A 0 0 0 0 17 0 17 0 17 0 0 0 0 0 17 17 0 17 0 0 6 0 0 1.792 59 -0.09
39 39 A 0 17 0 0 0 0 0 0 17 0 0 0 0 0 17 0 0 50 0 0 6 0 0 1.242 41 0.15
40 40 A 0 0 0 0 0 0 0 0 0 0 17 0 0 0 17 0 0 50 0 17 6 0 0 1.242 41 0.40
41 41 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 6 0 0 0.000 0 1.00
42 42 A 0 83 0 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.451 15 0.93
43 43 A 0 0 0 0 0 0 0 0 33 0 0 0 0 0 0 17 17 0 0 33 6 0 0 1.330 44 0.31
44 44 A 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0.000 0 1.00
45 45 A 0 33 0 0 0 0 33 0 0 0 17 0 0 0 0 0 17 0 0 0 6 0 0 1.330 44 0.04
46 46 A 0 17 0 0 0 0 0 0 17 0 0 0 0 0 33 17 0 17 0 0 6 0 0 1.561 52 0.06
47 47 A 0 0 0 0 0 0 0 50 0 0 0 0 0 0 17 0 17 0 0 17 6 0 0 1.242 41 0.31
48 48 A 0 0 0 0 0 0 0 0 17 0 0 0 0 0 33 33 0 17 0 0 6 0 0 1.330 44 0.27
49 49 A 17 33 0 0 17 0 0 33 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1.330 44 0.20
50 50 A 17 0 0 0 0 0 0 0 17 0 0 17 0 0 0 0 0 17 17 17 6 0 0 1.792 59 0.16
51 51 A 0 17 0 0 0 0 0 0 33 17 17 0 0 0 0 0 17 0 0 0 6 0 0 1.561 52 0.14
52 52 A 0 17 0 0 0 0 0 17 17 0 0 0 0 0 0 0 17 33 0 0 6 0 0 1.561 52 0.18
53 53 A 50 17 0 0 0 0 0 0 17 0 0 0 0 0 0 17 0 0 0 0 6 0 0 1.242 41 0.27
54 54 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 83 0 17 6 0 0 0.451 15 0.89
55 55 A 0 0 0 0 0 0 0 0 50 0 0 17 0 0 0 0 0 33 0 0 6 0 0 1.011 33 0.40
56 56 A 0 50 0 0 0 0 0 0 17 0 0 0 0 0 0 17 17 0 0 0 6 0 0 1.242 41 0.15
57 57 A 0 0 0 0 0 0 0 0 17 0 0 0 0 0 50 0 17 17 0 0 6 0 0 1.242 41 0.25
58 58 A 0 0 0 0 0 0 0 0 17 0 0 0 0 0 17 33 17 17 0 0 6 0 0 1.561 52 0.25
59 59 A 0 0 0 0 0 0 0 17 0 0 0 0 0 0 17 0 0 67 0 0 6 0 0 0.868 28 0.46
60 60 A 0 17 0 0 0 0 0 0 33 0 0 0 0 17 17 17 0 0 0 0 6 0 0 1.561 52 0.04
61 61 A 0 0 0 0 0 0 0 0 67 0 0 0 0 0 0 0 17 0 0 17 6 0 0 0.868 28 0.51
62 62 A 0 0 0 0 0 0 0 0 67 0 0 0 0 0 33 0 0 0 0 0 6 0 0 0.637 21 0.35
63 63 A 0 50 33 0 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 1.011 33 0.71
64 64 A 0 17 0 0 0 0 0 0 0 0 0 17 0 0 67 0 0 0 0 0 6 0 0 0.868 28 0.29
65 65 A 0 0 0 0 0 0 0 0 17 0 0 0 0 0 0 17 0 33 0 33 6 0 0 1.330 44 0.41
66 66 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 17 67 0 0 6 0 0 0.868 28 0.59
67 67 A 0 50 17 0 0 0 0 0 17 0 0 0 0 0 0 0 17 0 0 0 6 0 0 1.242 41 0.27
68 68 A 0 0 0 0 0 0 0 0 0 0 17 17 0 0 0 0 17 50 0 0 6 0 0 1.242 41 0.35
69 69 A 0 0 0 0 0 0 0 0 67 0 0 33 0 0 0 0 0 0 0 0 6 0 0 0.637 21 0.60
70 70 A 0 0 0 0 0 0 25 0 50 0 0 25 0 0 0 0 0 0 0 0 4 0 0 1.040 34 0.19
71 71 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 4 0 0 0.000 0 1.00
72 72 A 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 25 0 0 50 4 0 0 1.040 34 0.50
73 73 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 50 50 0 2 0 0 0.693 23 0.33
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
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