Complet list of 1nyp hssp file
Complete list of 1nyp.hssp file
HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 2.0 2011
PDBID 1NYP
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 2014-05-04
HEADER CELL ADHESION 13-FEB-03 1NYP
COMPND MOL_ID: 1; MOLECULE: PINCH PROTEIN; CHAIN: A; FRAGMENT: 4TH LIM DOMAIN
SOURCE MOL_ID: 1; ORGANISM_SCIENTIFIC: HOMO SAPIENS; ORGANISM_COMMON: HUMAN;
AUTHOR A.VELYVIS,J.VAYNBERG,O.VINOGRADOVA,Y.ZHANG,C.WU,J.QIN
DBREF 1NYP A 3 66 UNP P48059 PINC_HUMAN 188 251
SEQLENGTH 66
NCHAIN 1 chain(s) in 1NYP data set
NALIGN 16
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 : H2LIC2_ORYLA 0.97 0.98 1 66 122 187 66 0 0 210 H2LIC2 Uncharacterized protein OS=Oryzias latipes GN=LOC101155756 PE=4 SV=1
2 : R4GJN0_CHICK 0.95 0.98 1 62 31 92 62 0 0 108 R4GJN0 Uncharacterized protein OS=Gallus gallus PE=4 SV=1
3 : F6X2Y2_MACMU 0.94 0.98 1 66 84 149 66 0 0 234 F6X2Y2 Uncharacterized protein (Fragment) OS=Macaca mulatta GN=LIMS2 PE=4 SV=1
4 : F7GSG5_CALJA 0.94 0.98 1 66 85 150 66 0 0 235 F7GSG5 Uncharacterized protein OS=Callithrix jacchus GN=LIMS2 PE=4 SV=1
5 : Q7Z4I3_HUMAN 0.94 0.98 1 66 86 151 66 0 0 236 Q7Z4I3 LIM-like protein 2F OS=Homo sapiens PE=2 SV=1
6 : Q7Z4I4_HUMAN 0.94 0.98 1 66 99 164 66 0 0 249 Q7Z4I4 LIM-like protein 2E OS=Homo sapiens PE=2 SV=1
7 : R4GLM9_CHICK 0.87 0.93 3 62 1 60 60 0 0 129 R4GLM9 Uncharacterized protein OS=Gallus gallus PE=4 SV=1
8 : T1H0J1_MEGSC 0.86 0.95 3 66 1 64 64 0 0 140 T1H0J1 Uncharacterized protein OS=Megaselia scalaris PE=4 SV=1
9 : B4NQY9_DROWI 0.77 0.94 1 66 53 118 66 0 0 169 B4NQY9 GK22266 OS=Drosophila willistoni GN=Dwil\GK22266 PE=4 SV=1
10 : T2MBA2_HYDVU 0.76 0.91 1 66 186 252 67 1 1 324 T2MBA2 LIM and senescent cell antigen-like-containing domain protein 2 OS=Hydra vulgaris GN=LIMS2 PE=2 SV=1
11 : H0Y592_HUMAN 0.72 0.75 4 66 2 84 83 1 20 169 H0Y592 LIM and senescent cell antigen-like-containing domain protein 2 (Fragment) OS=Homo sapiens GN=LIMS2 PE=4 SV=1
12 : B3RM06_TRIAD 0.66 0.85 1 66 186 252 67 1 1 326 B3RM06 Putative uncharacterized protein OS=Trichoplax adhaerens GN=TRIADDRAFT_18460 PE=4 SV=1
13 : Q4T3X4_TETNG 0.64 0.65 1 66 282 378 97 1 31 497 Q4T3X4 Chromosome 2 SCAF9897, whole genome shotgun sequence OS=Tetraodon nigroviridis GN=GSTENG00007598001 PE=4 SV=1
14 : W4WJA5_ATTCE 0.37 0.62 2 64 2 66 65 1 2 71 W4WJA5 Uncharacterized protein OS=Atta cephalotes PE=4 SV=1
15 : B9EPY4_SALSA 0.33 0.57 1 64 8 73 67 3 4 89 B9EPY4 Cysteine-rich protein 1 OS=Salmo salar GN=CRIP1 PE=4 SV=1
16 : Q53RZ1_HUMAN 0.33 0.58 1 64 8 73 66 1 2 89 Q53RZ1 Putative uncharacterized protein LIMS2 (Fragment) OS=Homo sapiens GN=LIMS2 PE=2 SV=1
## ALIGNMENTS 1 - 16
SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7
1 1 A G 0 0 133 13 30 DDDDDD GD DD QD
2 2 A S - 0 0 118 14 71 KKKKKK KK KKSHA
3 3 A M + 0 0 191 16 20 MMMMMMMMMM MMLIL
4 4 A G + 0 0 73 17 41 GGGGGGGGGGGGGDTA
5 5 A V - 0 0 82 17 71 VVVVVVVVIIVVVHMN
6 6 A P - 0 0 32 17 41 PPPPPPPPPPPPPMPA
7 7 A I E -A 14 0A 67 17 47 IIIIIIVIIIIIIFKV
8 8 A C E >> -Ab 13 26A 0 17 0 CCCCCCCCCCCCCCCC
9 9 A G T 45S+ 0 0 23 17 56 GGGGGGGGGGGAGSPQ
10 10 A A T 45S+ 0 0 52 17 77 AAAAAATAAAAAARKR
11 11 A C T 45S- 0 0 40 17 0 CCCCCCCCCCCCCCCC
12 12 A R T <5 + 0 0 189 17 47 RRRRRRRRRRRKRRTQ
13 13 A R E < -A 8 0A 165 17 71 RRRRRRGRRQRRREKA
14 14 A P E -A 7 0A 76 17 57 PPPPPPPPPpPpPger
15 15 A I + 0 0 1 17 78 IIIIIIIIIeItIafp
16 16 A E + 0 0 175 17 57 EEEEEEEEEDEDEHAA
17 17 A G S S+ 0 0 64 17 53 GGGGGGGEEEGVGEEE
18 18 A R - 0 0 198 17 20 RRRRRRRRRRRHRKRR
19 19 A V E -C 28 0B 47 17 18 VVVVVVVVLVVIVIVI
20 20 A V E -C 27 0B 25 17 21 VVVVVVVVVVVVVVTV
21 21 A N + 0 0 119 17 44 NNNNNNNTTNNANNSN
22 22 A A > + 0 0 2 16 48 AAAAAAGAGAAAAS.S
23 23 A M T 3 S- 0 0 54 17 64 MMLLLLMLLILLMNLN
24 24 A G T 3 S+ 0 0 82 17 0 GGGGGGGGGGGGGGGG
25 25 A K S < S- 0 0 126 17 36 KKKKKKKKKKKKKEKE
26 26 A Q B -b 8 0A 71 17 79 QQQQQQQHHQQSQLDL
27 27 A W E -C 20 0B 44 17 6 WWWWWWWWWWWWWWWY
28 28 A H E >> -C 19 0B 38 17 0 HHHHHHHHHHhHhHHH
29 29 A V T 34 S+ 0 0 35 17 82 VVVVVVVVVVvAdPRE
30 30 A E T 34 S+ 0 0 90 17 65 EEEEEEEEEDMDMQPH
31 31 A H T <4 S+ 0 0 79 17 67 HHHHHHHHHHHHHCCC
32 32 A F < + 0 0 9 17 4 FFFFFFFFFFFFFFLF
33 33 A V B -D 40 0C 31 17 47 VVVVVVVVVCVAVVKV
34 34 A C > - 0 0 1 17 0 CCCCCCCCCCCCCCCC
35 35 A A T 4 S+ 0 0 43 17 19 AAAAAAAAAAAAAAEA
36 36 A K T 4 S+ 0 0 126 17 33 KKKKKKKKKKKKKQKQ
37 37 A C T 4 S- 0 0 51 17 0 CCCCCCCCCCCCCCCC
38 38 A E < + 0 0 151 17 80 EEEEEEEEEEEEEFNF
39 39 A K - 0 0 102 17 21 KKKKKKKKKKKKKRKR
40 40 A P B -D 33 0C 33 17 19 PPPPPPPPPPPPPPTP
41 41 A F + 0 0 15 17 4 FFFFFFFFFFFFFFLF
42 42 A L S S- 0 0 88 17 95 LLLLLLLLLYLHLPSP
43 43 A G S S+ 0 0 69 17 39 GGGGGGGGGGGGGDAE
44 44 A H S S- 0 0 106 17 81 HHHHHHHHHNHRHGGG
45 45 A R - 0 0 187 17 83 RRRRRRRRWRRPRISL
46 46 A H - 0 0 61 17 48 HHHHHHHHHHHHHFHF
47 47 A Y E -E 54 0D 30 17 32 YYYYYYCYYYYYYYAY
48 48 A E E +E 53 0D 93 17 0 EEEEEEEEEEEEEEEE
49 49 A R E > -E 52 0D 46 17 93 RRKKKKRNKRKHRFHF
50 50 A K T 3 S- 0 0 160 17 70 KKKKKKQRHNKNKEDE
51 51 A G T 3 S+ 0 0 47 17 0 GGGGGGGGGGGGGGGG
52 52 A L E < S-E 49 0D 77 17 79 LLLLLLRLLLLLLYKR
53 53 A A E +E 48 0D 4 17 59 AAAAAAAAAAAAAKPK
54 54 A Y E -E 47 0D 15 17 3 YYYYYYCYYYYYYYYY
55 55 A C > - 0 0 19 17 0 CCCCCCCCCCCCCCCC
56 56 A E H > S+ 0 0 115 17 22 EEEEEEEEQEEEEENE
57 57 A T H > S+ 0 0 90 17 71 TTTTTTTTATTTTHSH
58 58 A H H > S+ 0 0 58 17 52 HHHHHHHHHHHHHDpD
59 59 A Y H X S+ 0 0 34 17 3 YYYYYYYYYFYYYFyF
60 60 A N H < S+ 0 0 72 17 57 NNNNNNNHHNNNNHSQ
61 61 A Q H < S+ 0 0 153 17 67 QQQQQQQQQQQQQVAM
62 62 A L H < S- 0 0 33 17 3 LVLLLLLLLLLLLLLL
63 63 A F < - 0 0 98 15 0 F FFFF FFFFFFFFF
64 64 A G S S- 0 0 13 15 26 G GGGG GGGGGGAGA
65 65 A D 0 0 135 12 20 D DDDD NDDDED
66 66 A V 0 0 172 12 32 V VVVV LLLVIV
## 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 15 0 0 0 0 0 0 0 0 8 0 0 77 13 0 0 0.687 22 0.69
2 2 A 0 0 0 0 0 0 0 0 7 0 14 0 0 7 0 71 0 0 0 0 14 0 0 0.895 29 0.28
3 3 A 0 13 6 81 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0.602 20 0.80
4 4 A 0 0 0 0 0 0 0 82 6 0 0 6 0 0 0 0 0 0 0 6 17 0 0 0.660 22 0.58
5 5 A 71 0 12 6 0 0 0 0 0 0 0 0 0 6 0 0 0 0 6 0 17 0 0 0.998 33 0.28
6 6 A 0 0 0 6 0 0 0 0 6 88 0 0 0 0 0 0 0 0 0 0 17 0 0 0.444 14 0.58
7 7 A 12 0 76 0 6 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 17 0 0 0.790 26 0.52
8 8 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 17 0 0 0.000 0 1.00
9 9 A 0 0 0 0 0 0 0 76 6 6 6 0 0 0 0 0 6 0 0 0 17 0 0 0.872 29 0.43
10 10 A 0 0 0 0 0 0 0 0 76 0 0 6 0 0 12 6 0 0 0 0 17 0 0 0.790 26 0.22
11 11 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 17 0 0 0.000 0 1.00
12 12 A 0 0 0 0 0 0 0 0 0 0 0 6 0 0 82 6 6 0 0 0 17 0 0 0.660 22 0.52
13 13 A 0 0 0 0 0 0 0 6 6 0 0 0 0 0 71 6 6 6 0 0 17 0 0 1.079 36 0.29
14 14 A 0 0 0 0 0 0 0 6 0 82 0 0 0 0 6 0 0 6 0 0 17 0 5 0.660 22 0.42
15 15 A 0 0 71 0 6 0 0 0 6 6 0 6 0 0 0 0 0 6 0 0 17 0 0 1.079 36 0.21
16 16 A 0 0 0 0 0 0 0 0 12 0 0 0 0 6 0 0 0 71 0 12 17 0 0 0.916 30 0.43
17 17 A 6 0 0 0 0 0 0 59 0 0 0 0 0 0 0 0 0 35 0 0 17 0 0 0.846 28 0.46
18 18 A 0 0 0 0 0 0 0 0 0 0 0 0 0 6 88 6 0 0 0 0 17 0 0 0.444 14 0.80
19 19 A 76 6 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0.678 22 0.81
20 20 A 94 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 0 0 0 0 17 0 0 0.224 7 0.79
21 21 A 0 0 0 0 0 0 0 0 6 0 6 12 0 0 0 0 0 0 76 0 17 1 0 0.790 26 0.55
22 22 A 0 0 0 0 0 0 0 13 75 0 13 0 0 0 0 0 0 0 0 0 16 0 0 0.736 24 0.51
23 23 A 0 53 6 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 17 0 0 1.115 37 0.36
24 24 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0.000 0 1.00
25 25 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 88 0 12 0 0 17 0 0 0.362 12 0.63
26 26 A 0 12 0 0 0 0 0 0 0 0 6 0 0 12 0 0 65 0 0 6 17 0 0 1.119 37 0.21
27 27 A 0 0 0 0 0 94 6 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0.224 7 0.94
28 28 A 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 17 0 2 0.000 0 1.00
29 29 A 71 0 0 0 0 0 0 0 6 6 0 0 0 0 6 0 0 6 0 6 17 0 0 1.079 36 0.17
30 30 A 0 0 0 12 0 0 0 0 0 6 0 0 0 6 0 0 6 59 0 12 17 0 0 1.316 43 0.35
31 31 A 0 0 0 0 0 0 0 0 0 0 0 0 18 82 0 0 0 0 0 0 17 0 0 0.466 15 0.32
32 32 A 0 6 0 0 94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0.224 7 0.95
33 33 A 82 0 0 0 0 0 0 0 6 0 0 0 6 0 0 6 0 0 0 0 17 0 0 0.660 22 0.52
34 34 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 17 0 0 0.000 0 1.00
35 35 A 0 0 0 0 0 0 0 0 94 0 0 0 0 0 0 0 0 6 0 0 17 0 0 0.224 7 0.80
36 36 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 88 12 0 0 0 17 0 0 0.362 12 0.66
37 37 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 17 0 0 0.000 0 1.00
38 38 A 0 0 0 0 12 0 0 0 0 0 0 0 0 0 0 0 0 82 6 0 17 0 0 0.578 19 0.19
39 39 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 88 0 0 0 0 17 0 0 0.362 12 0.79
40 40 A 0 0 0 0 0 0 0 0 0 94 0 6 0 0 0 0 0 0 0 0 17 0 0 0.224 7 0.80
41 41 A 0 6 0 0 94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0.224 7 0.95
42 42 A 0 71 0 0 0 0 6 0 0 12 6 0 0 6 0 0 0 0 0 0 17 0 0 0.998 33 0.04
43 43 A 0 0 0 0 0 0 0 82 6 0 0 0 0 0 0 0 0 6 0 6 17 0 0 0.660 22 0.60
44 44 A 0 0 0 0 0 0 0 18 0 0 0 0 0 71 6 0 0 0 6 0 17 0 0 0.885 29 0.18
45 45 A 0 6 6 0 0 6 0 0 0 6 6 0 0 0 71 0 0 0 0 0 17 0 0 1.079 36 0.16
46 46 A 0 0 0 0 12 0 0 0 0 0 0 0 0 88 0 0 0 0 0 0 17 0 0 0.362 12 0.51
47 47 A 0 0 0 0 0 0 88 0 6 0 0 0 6 0 0 0 0 0 0 0 17 0 0 0.444 14 0.68
48 48 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 17 0 0 0.000 0 1.00
49 49 A 0 0 0 0 12 0 0 0 0 0 0 0 0 12 35 35 0 0 6 0 17 0 0 1.405 46 0.06
50 50 A 0 0 0 0 0 0 0 0 0 0 0 0 0 6 6 53 6 12 12 6 17 0 0 1.507 50 0.30
51 51 A 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0.000 0 1.00
52 52 A 0 76 0 0 0 0 6 0 0 0 0 0 0 0 12 6 0 0 0 0 17 0 0 0.790 26 0.20
53 53 A 0 0 0 0 0 0 0 0 82 6 0 0 0 0 0 12 0 0 0 0 17 0 0 0.578 19 0.40
54 54 A 0 0 0 0 0 0 94 0 0 0 0 0 6 0 0 0 0 0 0 0 17 0 0 0.224 7 0.96
55 55 A 0 0 0 0 0 0 0 0 0 0 0 0 100 0 0 0 0 0 0 0 17 0 0 0.000 0 1.00
56 56 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 88 6 0 17 0 0 0.444 14 0.78
57 57 A 0 0 0 0 0 0 0 0 6 0 6 76 0 12 0 0 0 0 0 0 17 0 0 0.790 26 0.29
58 58 A 0 0 0 0 0 0 0 0 0 6 0 0 0 82 0 0 0 0 0 12 17 0 1 0.578 19 0.47
59 59 A 0 0 0 0 18 0 82 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0.466 15 0.97
60 60 A 0 0 0 0 0 0 0 0 0 0 6 0 0 18 0 0 6 0 71 0 17 0 0 0.885 29 0.43
61 61 A 6 0 0 6 0 0 0 0 6 0 0 0 0 0 0 0 82 0 0 0 17 0 0 0.660 22 0.33
62 62 A 6 94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0.224 7 0.96
63 63 A 0 0 0 0 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0.000 0 1.00
64 64 A 0 0 0 0 0 0 0 87 13 0 0 0 0 0 0 0 0 0 0 0 15 0 0 0.393 13 0.74
65 65 A 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 8 83 12 0 0 0.566 18 0.79
66 66 A 67 25 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0.824 27 0.67
## INSERTION LIST
AliNo IPOS JPOS Len Sequence
10 15 200 1 pIe
11 26 27 20 hVEVSQAGGHVASGWGVPQLRv
12 15 200 1 pIt
13 29 310 31 hVEHHVCTVCERPFQGHPFYERGGHAYCERHFd
14 14 15 2 gFVa
15 15 22 2 eVYf
15 58 67 1 pCy
16 15 22 2 rFSp
//