pdb2sse secondary structure is quite different to the DSSP4 result
Issue #901
new
The secondary structure calculated by pdb2sse is similar to that from dssp(pdb)$sse according to the pdb2sse() documentation. However I run pdb2sse() and separately DSSP (from the web server https://www3.cmbi.umcn.nl/xssp/) and the results are very different at the C-ter. The DSSP is the standard, and it seems I cannot directly compare the bio3d calculation with the dssp one, so how can I interpret those differences?
pdb2sse "CEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCEEEEEEEEECCCCCCCCCCCHHHHHHHCEEEEEEEECCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCC"
DSSP ".EEEEEEEEESTTSSHHHHHHHHHHS...SS..TT..EEEEEEEEETTEEEEEEEEE...SSS..HHHHHHHHH.SEEEEEEETT.HHHHHTHHHHHHHHHHHHT.S...EEEEEE.TT.S...S.HHHHHHHHHHHT..EEEE.TTT.TTHHHHHHHHHHHHHHHH."
Example details below
R version 4.2.0 (2022-04-22 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621) bio3d_2.4-3
library(bio3d)
example:
# read example
pdb <- read.pdb('4q21')
# get aminoacid sequence and secondary structure from pdb file
paste0(pdbseq(pdb), collapse='')
# "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKL"
paste0(pdb2sse(pdb), collapse='') %>% gsub(' ', 'C', .)
# "CEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCEEEEEEEEECCCCCCCCCCCHHHHHHHCEEEEEEEECCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCC"
# secondary structure calculated with DSSP from https://www3.cmbi.umcn.nl/xssp/
# sequence
# MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKL
# sse
# ".EEEEEEEEESTTSSHHHHHHHHHHS...SS..TT..EEEEEEEEETTEEEEEEEEE...SSS..HHHHHHHHH.SEEEEEEETT.HHHHHTHHHHHHHHHHHHT.S...EEEEEE.TT.S...S.HHHHHHHHHHHT..EEEE.TTT.TTHHHHHHHHHHHHHHHH."
## detailed DSSP output:
# # RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA
# 1 1 A M 0 0 149 0, 0.0 2,-0.4 0, 0.0 50,-0.2 0.000 360.0 360.0 360.0 126.8 64.0 51.6 33.4
# 2 2 A T E -a 51 0A 41 48,-4.6 50,-4.2 2,-0.0 2,-0.4 -0.781 360.0-152.1-100.0 142.9 62.4 54.8 32.4
# 3 3 A E E -a 52 0A 74 -2,-0.4 2,-0.4 48,-0.2 50,-0.2 -0.917 9.7-172.2-110.5 136.6 64.0 58.2 32.8
# 4 4 A Y E -a 53 0A 3 48,-2.4 50,-2.2 -2,-0.4 2,-0.7 -0.996 15.6-145.4-130.9 122.4 61.8 61.3 33.2
# 5 5 A K E -a 54 0A 55 -2,-0.4 71,-4.7 69,-0.2 72,-1.2 -0.865 25.1-177.4 -93.3 106.4 63.3 64.8 33.2
# 6 6 A L E -ab 55 77A 1 48,-1.8 50,-2.6 -2,-0.7 2,-0.4 -0.860 15.0-154.3-101.8 150.9 61.3 67.1 35.6
# 7 7 A V E -ab 56 78A 0 70,-2.2 72,-2.6 -2,-0.3 2,-0.7 -0.953 8.2-147.9-124.3 127.8 61.8 70.8 36.3
# 8 8 A V E +ab 57 79A 0 48,-3.0 50,-1.6 -2,-0.4 2,-0.3 -0.904 29.7 172.1 -98.6 103.9 60.7 72.4 39.7
# 9 9 A V E + b 0 80A 4 70,-2.4 72,-3.2 -2,-0.7 2,-0.2 -0.807 13.9 106.1-109.8 163.7 59.6 76.0 39.0
# 10 10 A G E S- b 0 81A 5 -2,-0.3 72,-0.2 70,-0.2 3,-0.1 -0.754 70.3 -48.6 147.5 162.7 57.9 78.7 41.1
# 11 11 A A S > S- 0 0 8 70,-0.5 3,-0.9 78,-0.3 5,-0.3 -0.102 71.5 -94.4 -53.1 155.8 58.6 82.0 43.0
# 12 12 A G T 3 S+ 0 0 42 1,-0.2 -1,-0.1 2,-0.1 47,-0.1 -0.460 111.0 34.6 -69.5 153.7 61.6 81.8 45.2
# 13 13 A G T 3 S+ 0 0 64 -3,-0.1 -1,-0.2 21,-0.1 -2,-0.1 0.132 86.2 106.6 92.0 -17.9 60.6 80.9 48.9
# 14 14 A V S < S- 0 0 0 -3,-0.9 70,-0.2 67,-0.1 68,-0.1 0.691 98.2 -85.9 -69.5 -34.6 57.6 78.5 48.0
# 15 15 A G S > S+ 0 0 13 -4,-0.2 4,-3.6 66,-0.1 5,-0.3 0.571 80.0 134.0 136.6 9.1 59.2 75.2 48.7
# 16 16 A K H > S+ 0 0 17 -5,-0.3 4,-2.6 2,-0.2 5,-0.1 0.905 83.1 40.1 -50.8 -57.0 61.1 73.9 45.7
# 17 17 A S H > S+ 0 0 21 2,-0.2 4,-2.8 1,-0.2 5,-0.2 0.962 119.4 46.7 -63.1 -46.0 64.3 72.9 47.6
# 18 18 A A H > S+ 0 0 11 2,-0.2 4,-2.0 1,-0.2 -2,-0.2 0.901 113.5 47.5 -61.6 -49.6 62.3 71.5 50.5
# 19 19 A L H X S+ 0 0 0 -4,-3.6 4,-1.8 1,-0.2 -1,-0.2 0.945 116.3 45.2 -50.2 -55.5 59.8 69.6 48.3
# 20 20 A T H X S+ 0 0 0 -4,-2.6 4,-2.3 -5,-0.3 -2,-0.2 0.866 110.8 51.3 -61.3 -39.7 62.7 68.2 46.3
# 21 21 A I H X>S+ 0 0 6 -4,-2.8 4,-3.7 1,-0.2 5,-0.5 0.803 108.6 55.2 -66.9 -32.9 64.9 67.3 49.4
# 22 22 A Q H X5S+ 0 0 8 -4,-2.0 4,-1.2 -5,-0.2 -1,-0.2 0.881 110.8 41.0 -63.6 -49.9 61.9 65.4 50.8
# 23 23 A L H <5S+ 0 0 0 -4,-1.8 -2,-0.2 2,-0.2 -3,-0.1 0.973 122.5 43.2 -62.1 -51.5 61.4 63.2 47.8
# 24 24 A I H <5S+ 0 0 28 -4,-2.3 -2,-0.2 -5,-0.2 -3,-0.2 0.941 137.8 3.9 -59.7 -56.0 65.1 62.7 47.4
# 25 25 A Q H <5S- 0 0 92 -4,-3.7 -3,-0.2 2,-0.2 -1,-0.2 0.360 87.6-120.6-123.6 2.8 66.1 62.2 51.0
# 26 26 A N S <<S+ 0 0 98 -4,-1.2 2,-0.3 -5,-0.5 -4,-0.2 0.925 74.4 109.5 61.7 43.8 63.1 62.2 53.1
# 27 27 A H - 0 0 90 -6,-0.4 2,-0.7 -9,-0.2 -2,-0.2 -0.976 68.1-121.4-149.5 135.5 64.0 65.1 55.4
# 28 28 A F - 0 0 72 -2,-0.3 2,-0.6 119,-0.2 119,-0.1 -0.763 30.0-162.5 -79.1 116.5 62.5 68.6 55.5
# 29 29 A V + 0 0 37 -2,-0.7 2,-0.3 -11,-0.2 3,-0.2 -0.912 18.1 170.2-108.0 115.2 65.2 71.1 54.9
# 30 30 A D S S+ 0 0 88 -2,-0.6 3,-0.1 1,-0.1 -2,-0.0 -0.755 72.0 51.2 -95.3 163.7 64.8 74.7 55.9
# 31 31 A E S S+ 0 0 194 -2,-0.3 2,-0.4 1,-0.3 -1,-0.1 0.581 73.3 149.8 83.8 2.6 68.0 76.6 55.5
# 32 32 A Y - 0 0 58 -3,-0.2 -1,-0.3 1,-0.1 -15,-0.1 -0.621 61.3 -96.2 -77.2 127.0 68.6 75.4 51.9
# 33 33 A D > - 0 0 73 -2,-0.4 3,-1.5 1,-0.2 -1,-0.1 -0.172 27.7-144.1 -47.0 118.4 70.5 78.0 50.0
# 34 34 A P T 3 S+ 0 0 107 0, 0.0 26,-0.3 0, 0.0 -1,-0.2 0.601 96.1 48.2 -60.5 -17.3 68.0 80.1 48.1
# 35 35 A T T 3 S+ 0 0 97 24,-0.1 2,-0.8 25,-0.1 24,-0.1 0.453 79.3 112.5-106.0 -3.8 70.4 80.4 45.2
# 36 36 A I < - 0 0 62 -3,-1.5 2,-0.6 22,-0.1 24,-0.1 -0.636 45.0-168.8 -81.5 107.6 71.5 76.9 44.7
# 37 37 A E + 0 0 45 -2,-0.8 2,-0.3 22,-0.1 21,-0.2 -0.829 25.0 151.8 -92.2 117.9 70.3 75.5 41.5
# 38 38 A D E -C 57 0A 77 19,-1.5 19,-3.6 -2,-0.6 2,-0.4 -0.990 38.3-133.1-150.6 155.5 70.8 71.8 41.4
# 39 39 A S E -C 56 0A 40 -2,-0.3 2,-0.3 17,-0.3 17,-0.2 -0.917 21.4-165.2-109.7 147.3 69.5 68.7 39.9
# 40 40 A Y E -C 55 0A 35 15,-2.0 15,-3.6 -2,-0.4 2,-0.3 -0.885 10.3-136.9-131.7 151.5 68.9 65.5 41.8
# 41 41 A R E +C 54 0A 161 -2,-0.3 2,-0.4 13,-0.2 13,-0.2 -0.839 18.6 177.5-110.3 147.6 68.2 61.8 40.9
# 42 42 A K E -C 53 0A 39 11,-1.8 11,-3.1 -2,-0.3 2,-0.6 -0.931 19.0-148.5-156.0 120.3 65.8 59.5 42.3
# 43 43 A Q E +C 52 0A 136 -2,-0.4 2,-0.3 9,-0.2 9,-0.2 -0.835 34.2 156.3 -87.4 125.4 65.0 56.0 41.4
# 44 44 A V E -C 51 0A 15 7,-3.0 7,-3.9 -2,-0.6 2,-0.5 -0.982 39.7-130.6-152.0 149.4 61.4 55.1 42.0
# 45 45 A V E -C 50 0A 85 -2,-0.3 2,-0.5 5,-0.3 5,-0.2 -0.948 27.1-178.8 -99.8 127.5 58.8 52.6 40.8
# 46 46 A I E > S-C 49 0A 3 3,-2.1 3,-1.3 -2,-0.5 -2,-0.0 -0.991 70.8 -14.3-131.0 122.3 55.5 54.2 39.8
# 47 47 A D T 3 S- 0 0 100 -2,-0.5 -1,-0.1 1,-0.3 3,-0.1 0.870 130.6 -50.8 54.7 38.0 52.6 52.1 38.6
# 48 48 A G T 3 S+ 0 0 76 1,-0.3 2,-0.4 -3,-0.0 -1,-0.3 0.603 114.3 118.8 78.5 7.9 54.9 49.1 38.1
# 49 49 A E E < - C 0 46A 46 -3,-1.3 -3,-2.1 -48,-0.0 2,-0.7 -0.909 64.1-132.5-105.0 133.9 57.4 51.1 36.1
# 50 50 A T E - C 0 45A 56 -2,-0.4 -48,-4.6 -5,-0.2 2,-0.4 -0.796 35.3-171.4 -86.8 114.8 61.0 51.7 37.2
# 51 51 A C E -aC 2 44A 0 -7,-3.9 -7,-3.0 -2,-0.7 2,-0.7 -0.905 26.7-154.7-110.4 145.9 61.7 55.3 36.8
# 52 52 A L E -aC 3 43A 18 -50,-4.2 -48,-2.4 -2,-0.4 2,-0.6 -0.951 18.9-158.8-121.4 98.9 64.7 57.5 37.0
# 53 53 A L E -aC 4 42A 0 -11,-3.1 -11,-1.8 -2,-0.7 2,-0.7 -0.797 6.4-168.9 -77.6 115.6 63.6 61.0 38.0
# 54 54 A D E -aC 5 41A 15 -50,-2.2 -48,-1.8 -2,-0.6 2,-0.5 -0.959 17.3-167.4-106.2 99.9 66.2 63.5 37.0
# 55 55 A I E -aC 6 40A 0 -15,-3.6 -15,-2.0 -2,-0.7 2,-0.7 -0.858 19.3-153.7-102.4 128.7 65.0 66.7 38.8
# 56 56 A L E -aC 7 39A 3 -50,-2.6 -48,-3.0 -2,-0.5 2,-0.8 -0.819 9.9-158.3 -91.3 112.4 66.2 70.3 38.2
# 57 57 A D E -aC 8 38A 0 -19,-3.6 -19,-1.5 -2,-0.7 -48,-0.1 -0.838 24.8-142.6 -83.1 107.7 65.5 72.3 41.5
# 58 58 A T + 0 0 13 -50,-1.6 2,-0.3 -2,-0.8 -41,-0.1 -0.443 30.1 162.0 -80.8 158.2 65.5 75.8 40.0
# 59 59 A A + 0 0 16 1,-0.2 -24,-0.1 -24,-0.1 -22,-0.1 -0.909 30.9 69.5-166.9 145.2 66.9 78.9 41.6
# 60 60 A G - 0 0 42 -26,-0.3 2,-0.5 -2,-0.3 -1,-0.2 0.490 54.4-134.1 104.4 113.6 68.0 82.4 40.4
# 61 61 A Q S S- 0 0 147 3,-0.0 2,-1.1 1,-0.0 3,-0.1 -0.869 79.7 -11.6 -98.0 124.8 65.8 85.3 39.1
# 62 62 A E S S+ 0 0 152 -2,-0.5 -1,-0.0 1,-0.1 0, 0.0 -0.810 103.9 99.6 91.8 -80.3 66.8 87.2 36.0
# 63 63 A E S S- 0 0 141 -2,-1.1 -1,-0.1 1,-0.1 2,-0.0 -0.045 72.4-130.6 -44.1 114.4 70.4 85.8 35.5
# 64 64 A Y - 0 0 175 -3,-0.1 2,-0.3 4,-0.0 -1,-0.1 -0.201 19.7-158.1 -71.6 156.7 70.3 83.0 32.8
# 65 65 A S > - 0 0 39 1,-0.1 4,-2.9 -5,-0.1 5,-0.2 -0.998 24.5-140.8-145.4 142.6 71.8 79.5 33.0
# 66 66 A A H > S+ 0 0 76 -2,-0.3 4,-3.0 1,-0.2 5,-0.1 0.926 108.3 45.9 -60.8 -50.9 72.9 76.7 30.6
# 67 67 A M H > S+ 0 0 93 2,-0.2 4,-2.6 1,-0.2 5,-0.2 0.837 113.3 48.4 -58.2 -47.9 71.5 74.0 32.7
# 68 68 A R H > S+ 0 0 29 2,-0.2 4,-2.8 3,-0.2 -2,-0.2 0.956 112.8 49.1 -63.5 -47.6 68.2 75.8 33.3
# 69 69 A D H X S+ 0 0 62 -4,-2.9 4,-2.6 1,-0.2 5,-0.3 0.956 113.5 45.9 -52.9 -55.9 67.9 76.5 29.6
# 70 70 A Q H X S+ 0 0 70 -4,-3.0 4,-3.1 1,-0.2 5,-0.3 0.918 115.3 44.7 -54.7 -51.6 68.6 72.9 28.7
# 71 71 A Y H X S+ 0 0 14 -4,-2.6 4,-2.6 1,-0.2 -1,-0.2 0.873 112.6 56.1 -62.7 -30.7 66.3 71.4 31.3
# 72 72 A M H < S+ 0 0 9 -4,-2.8 -2,-0.2 -5,-0.2 -1,-0.2 0.941 115.8 32.6 -69.4 -46.1 63.8 73.9 30.3
# 73 73 A R H < S+ 0 0 152 -4,-2.6 -2,-0.2 -5,-0.2 -1,-0.2 0.842 130.5 37.4 -80.6 -32.2 63.7 73.0 26.7
# 74 74 A T H < S+ 0 0 35 -4,-3.1 -2,-0.2 -5,-0.3 -69,-0.2 0.523 88.1 114.7 -90.3 -15.9 64.4 69.3 27.3
# 75 75 A G < - 0 0 0 -4,-2.6 -69,-0.2 -5,-0.3 3,-0.1 -0.278 54.7-150.4 -59.5 147.2 62.3 68.8 30.6
# 76 76 A E S S- 0 0 60 -71,-4.7 2,-0.3 1,-0.4 -70,-0.2 0.791 73.4 -1.0 -90.0 -29.6 59.4 66.5 30.3
# 77 77 A G E -b 6 0A 0 -72,-1.2 -70,-2.2 32,-0.1 2,-0.4 -0.985 64.7-136.9-156.1 162.2 57.2 68.0 32.8
# 78 78 A F E -bd 7 111A 0 32,-2.1 34,-1.5 -2,-0.3 2,-0.7 -0.975 7.3-143.9-128.6 133.1 57.3 70.8 35.2
# 79 79 A L E -bd 8 112A 0 -72,-2.6 -70,-2.4 -2,-0.4 2,-1.0 -0.851 20.7-151.4 -91.9 118.6 56.1 71.0 38.8
# 80 80 A C E -bd 9 113A 3 32,-2.6 34,-1.6 -2,-0.7 2,-0.4 -0.729 16.2-160.6 -99.9 99.7 54.7 74.5 39.3
# 81 81 A V E +bd 10 114A 0 -72,-3.2 -70,-0.5 -2,-1.0 2,-0.3 -0.516 19.0 162.9 -90.0 134.7 55.1 75.5 42.9
# 82 82 A F E - d 0 115A 0 32,-2.3 34,-3.1 -2,-0.4 2,-0.5 -0.905 36.4-114.8-135.1 158.7 53.3 78.1 44.9
# 83 83 A A E > - d 0 116A 1 3,-0.5 3,-1.7 -2,-0.3 7,-0.4 -0.893 14.2-143.1 -97.5 132.1 53.0 78.8 48.5
# 84 84 A I T 3 S+ 0 0 1 32,-2.8 40,-1.2 -2,-0.5 41,-1.1 0.760 102.9 44.0 -57.9 -35.2 49.5 78.5 50.1
# 85 85 A N T 3 S+ 0 0 42 31,-0.3 -1,-0.3 38,-0.3 2,-0.2 -0.115 103.1 75.8-102.0 24.4 50.2 81.4 52.4
# 86 86 A N X> - 0 0 60 -3,-1.7 4,-1.5 1,-0.1 3,-0.5 -0.707 54.7-172.9-146.0 100.3 51.7 83.6 49.8
# 87 87 A T H 3> S+ 0 0 48 1,-0.3 4,-2.2 -2,-0.2 5,-0.2 0.815 83.7 54.8 -65.5 -43.7 49.6 85.3 47.3
# 88 88 A K H 3> S+ 0 0 109 1,-0.2 4,-1.9 2,-0.2 -1,-0.3 0.921 106.2 56.7 -56.4 -36.5 52.1 86.8 45.0
# 89 89 A S H <4 S+ 0 0 0 -3,-0.5 3,-0.4 1,-0.2 -78,-0.3 0.935 108.9 46.0 -57.1 -48.4 53.6 83.3 44.7
# 90 90 A F H >< S+ 0 0 23 -4,-1.5 3,-1.3 -7,-0.4 4,-0.3 0.842 111.3 50.9 -58.1 -47.0 50.2 82.1 43.5
# 91 91 A E H >< S+ 0 0 102 -4,-2.2 3,-0.7 1,-0.3 4,-0.3 0.767 103.0 62.0 -63.6 -28.6 49.7 85.0 41.1
# 92 92 A D T >X S+ 0 0 36 -4,-1.9 4,-1.6 -3,-0.4 3,-0.7 0.626 81.0 85.1 -73.0 -17.4 53.1 84.3 39.7
# 93 93 A I H <> S+ 0 0 1 -3,-1.3 4,-2.2 -4,-0.3 -1,-0.2 0.853 83.1 58.0 -55.4 -35.2 52.0 80.9 38.5
# 94 94 A H H <> S+ 0 0 88 -3,-0.7 4,-2.9 -4,-0.3 -1,-0.2 0.873 105.1 49.9 -63.4 -38.5 50.6 82.2 35.3
# 95 95 A Q H <> S+ 0 0 93 -3,-0.7 4,-2.3 -4,-0.3 -1,-0.2 0.896 110.4 49.0 -63.9 -48.4 54.0 83.7 34.3
# 96 96 A Y H X S+ 0 0 52 -4,-1.6 4,-2.6 2,-0.2 5,-0.2 0.914 112.7 48.8 -60.8 -38.4 55.9 80.5 35.0
# 97 97 A R H X S+ 0 0 21 -4,-2.2 4,-2.2 1,-0.2 5,-0.2 0.993 111.9 49.1 -64.0 -49.1 53.3 78.7 32.9
# 98 98 A E H X S+ 0 0 72 -4,-2.9 4,-1.1 1,-0.2 -2,-0.2 0.797 111.5 48.8 -59.0 -33.3 53.7 81.3 30.2
# 99 99 A Q H >X S+ 0 0 57 -4,-2.3 4,-2.3 2,-0.2 3,-0.6 0.965 109.1 52.5 -71.2 -45.8 57.5 81.0 30.2
# 100 100 A I H 3X S+ 0 0 0 -4,-2.6 4,-2.6 1,-0.3 5,-0.3 0.895 110.8 48.2 -54.4 -45.2 57.4 77.2 30.0
# 101 101 A K H 3X>S+ 0 0 31 -4,-2.2 5,-1.8 -5,-0.2 4,-1.2 0.792 108.1 54.4 -66.6 -35.3 55.1 77.4 27.0
# 102 102 A R H <<5S+ 0 0 170 -4,-1.1 -2,-0.2 -3,-0.6 -1,-0.2 0.954 113.5 41.0 -66.7 -47.6 57.2 79.9 25.2
# 103 103 A V H <5S+ 0 0 61 -4,-2.3 -2,-0.2 1,-0.2 -3,-0.1 0.998 121.8 40.0 -63.1 -61.6 60.3 77.8 25.5
# 104 104 A K H <5S- 0 0 61 -4,-2.6 -1,-0.2 -5,-0.2 -2,-0.2 0.824 100.9-142.2 -56.0 -24.8 58.4 74.5 24.7
# 105 105 A D T <5 + 0 0 139 -4,-1.2 2,-0.3 -5,-0.3 -3,-0.2 0.984 63.6 104.2 59.7 48.7 56.6 76.6 22.2
# 106 106 A S < - 0 0 39 -5,-1.8 -1,-0.2 1,-0.1 -2,-0.1 -0.923 67.8-145.0-165.8 145.5 53.5 74.6 23.1
# 107 107 A D S S+ 0 0 113 -2,-0.3 2,-1.3 1,-0.2 -1,-0.1 0.943 92.7 59.9 -76.0 -51.7 50.3 74.6 25.0
# 108 108 A D + 0 0 103 -7,-0.1 -1,-0.2 2,-0.0 0, 0.0 -0.645 63.0 140.0 -83.7 92.1 50.3 71.0 26.1
# 109 109 A V - 0 0 10 -2,-1.3 2,-0.3 -3,-0.1 -32,-0.1 -0.978 58.3-105.6-128.0 131.5 53.3 70.5 28.2
# 110 110 A P + 0 0 10 0, 0.0 -32,-2.1 0, 0.0 2,-0.3 -0.574 54.3 146.0 -66.8 143.1 52.8 68.4 31.2
# 111 111 A M E -d 78 0A 1 -2,-0.3 2,-0.3 -34,-0.2 -32,-0.2 -0.990 33.3-146.6-163.2 161.2 52.7 70.0 34.6
# 112 112 A V E -d 79 0A 0 -34,-1.5 -32,-2.6 -2,-0.3 2,-0.6 -0.880 22.5-125.2-133.8 150.6 51.1 69.7 37.8
# 113 113 A L E -de 80 141A 1 27,-2.4 29,-3.0 -2,-0.3 2,-0.5 -0.920 24.8-164.4-103.8 114.5 50.1 72.6 40.1
# 114 114 A V E -de 81 142A 0 -34,-1.6 -32,-2.3 -2,-0.6 2,-0.8 -0.867 9.3-166.4-100.0 119.8 51.6 72.3 43.6
# 115 115 A G E -de 82 143A 0 27,-3.6 29,-1.5 -2,-0.5 3,-0.2 -0.936 27.7-162.4-106.9 99.5 50.1 74.4 46.4
# 116 116 A N E +de 83 144A 4 -34,-3.1 -32,-2.8 -2,-0.8 -31,-0.3 -0.591 56.6 40.2 -89.2 160.3 52.8 74.0 49.1
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# 121 121 A A S S+ 0 0 98 1,-0.2 2,-4.2 2,-0.1 -1,-0.1 0.753 80.4 91.4 -92.1 -27.0 47.3 77.9 59.0
# 122 122 A A + 0 0 69 2,-0.0 -1,-0.2 1,-0.0 2,-0.1 0.090 68.4 168.6 -58.8 34.2 48.5 81.3 57.9
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# 125 125 A V S S- 0 0 2 -41,-1.1 2,-0.4 -39,-0.0 -1,-0.1 -1.000 78.4-128.5-132.2 127.6 45.0 81.2 49.0
# 126 126 A E >> - 0 0 67 -2,-0.4 4,-2.3 1,-0.1 3,-1.0 -0.630 10.4-133.6 -79.4 136.8 41.9 78.9 48.9
# 127 127 A S H 3> S+ 0 0 21 -2,-0.4 4,-3.9 1,-0.3 5,-0.2 0.910 111.8 58.4 -50.6 -36.0 42.1 75.4 47.7
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# 133 133 A L H XX S+ 0 0 30 -4,-1.2 4,-2.3 -3,-0.5 3,-0.6 0.961 110.8 50.4 -64.5 -51.6 43.1 77.6 38.2
# 134 134 A A H >X>S+ 0 0 0 -4,-3.0 5,-1.9 1,-0.3 4,-1.3 0.954 111.0 50.8 -47.6 -49.6 44.4 74.0 37.8
# 135 135 A R H 3<5S+ 0 0 158 -4,-3.4 -1,-0.3 1,-0.3 -2,-0.2 0.760 106.3 53.0 -61.9 -30.2 41.1 73.3 36.1
# 136 136 A S H <<5S+ 0 0 87 -4,-1.6 -1,-0.3 -3,-0.6 -2,-0.2 0.876 112.2 45.9 -72.2 -36.2 41.5 76.3 33.8
# 137 137 A Y H <<5S- 0 0 36 -4,-2.3 -2,-0.2 -3,-0.6 -1,-0.2 0.622 110.5-121.9 -72.6 -26.6 45.0 75.0 32.8
# 138 138 A G T <5S+ 0 0 63 -4,-1.3 -3,-0.2 1,-0.3 -4,-0.1 0.792 73.9 116.1 83.9 29.6 43.7 71.4 32.3
# 139 139 A I < - 0 0 17 -5,-1.9 -1,-0.3 -6,-0.2 -2,-0.2 -0.889 67.5 -97.1-134.2 161.6 46.2 70.2 34.8
# 140 140 A P - 0 0 34 0, 0.0 -27,-2.4 0, 0.0 2,-0.4 -0.212 27.0-142.8 -75.2 165.2 46.1 68.6 38.2
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# 142 142 A I E -e 114 0A 29 -29,-3.0 -27,-3.6 -2,-0.4 2,-0.5 -0.974 15.9-148.1-128.4 140.5 48.3 68.9 44.5
# 143 143 A E E +e 115 0A 44 -2,-0.3 2,-0.3 -29,-0.2 -27,-0.2 -0.953 28.1 173.7-108.6 131.8 48.7 70.2 47.9
# 144 144 A T E -e 116 0A 0 -29,-1.5 -26,-2.8 -2,-0.5 -27,-0.9 -0.814 29.0-154.2-133.5 172.3 51.9 69.4 49.7
# 145 145 A S > - 0 0 0 5,-2.1 4,-2.4 -2,-0.3 5,-0.3 -0.908 0.8-168.7-152.8 106.0 53.9 70.0 52.7
# 146 146 A A T 4 S+ 0 0 3 -2,-0.3 -1,-0.1 2,-0.2 -117,-0.0 0.765 94.5 54.8 -69.9 -23.7 57.6 69.6 52.5
# 147 147 A K T 4 S+ 0 0 111 1,-0.1 -119,-0.2 -119,-0.1 -1,-0.2 0.976 119.7 26.7 -66.7 -62.3 57.5 69.9 56.2
# 148 148 A T T 4 S- 0 0 74 2,-0.1 -2,-0.2 1,-0.0 -1,-0.1 0.687 101.5-127.6 -81.5 -10.6 55.0 67.1 56.9
# 149 149 A R >< + 0 0 57 -4,-2.4 3,-1.0 1,-0.3 4,-0.4 0.481 56.4 154.5 77.4 2.8 55.9 65.3 53.7
# 150 150 A Q T 3 - 0 0 96 -5,-0.3 -5,-2.1 1,-0.2 -1,-0.3 -0.459 65.8 -1.2 -65.0 131.4 52.3 65.3 52.9
# 151 151 A G T 3> S+ 0 0 15 -7,-0.2 4,-2.4 -2,-0.2 -1,-0.2 0.387 94.1 121.4 73.4 -6.6 51.5 65.1 49.3
# 152 152 A V H <> S+ 0 0 1 -3,-1.0 4,-1.3 -7,-0.3 5,-0.1 0.947 76.5 38.9 -61.0 -47.0 55.1 65.1 48.2
# 153 153 A E H > S+ 0 0 84 -4,-0.4 4,-3.2 1,-0.2 5,-0.3 0.850 114.0 57.1 -67.5 -35.7 55.1 61.7 46.3
# 154 154 A D H > S+ 0 0 90 1,-0.2 4,-2.8 2,-0.2 5,-0.3 0.939 104.7 52.4 -55.9 -50.5 51.7 62.4 44.9
# 155 155 A A H X S+ 0 0 0 -4,-2.4 4,-1.3 1,-0.2 -1,-0.2 0.874 116.9 35.3 -54.0 -51.1 52.9 65.6 43.4
# 156 156 A F H X S+ 0 0 0 -4,-1.3 4,-2.2 2,-0.2 -1,-0.2 0.871 118.2 50.7 -75.1 -37.5 55.8 64.1 41.6
# 157 157 A Y H X S+ 0 0 31 -4,-3.2 4,-2.3 2,-0.2 -2,-0.2 0.798 109.5 52.1 -69.0 -33.5 54.2 60.8 40.7
# 158 158 A T H X S+ 0 0 24 -4,-2.8 4,-2.3 -5,-0.3 5,-0.2 0.933 108.9 51.2 -64.1 -48.0 51.2 62.6 39.3
# 159 159 A L H X S+ 0 0 0 -4,-1.3 4,-2.0 -5,-0.3 -2,-0.2 0.916 110.3 48.9 -55.1 -43.7 53.7 64.7 37.2
# 160 160 A V H X S+ 0 0 0 -4,-2.2 4,-3.1 1,-0.2 -1,-0.2 0.953 109.4 51.6 -64.8 -46.4 55.2 61.5 36.0
# 161 161 A R H X S+ 0 0 102 -4,-2.3 4,-2.5 2,-0.2 -2,-0.2 0.832 108.7 51.9 -54.2 -39.1 51.8 60.0 35.2
# 162 162 A E H X S+ 0 0 39 -4,-2.3 4,-3.4 2,-0.2 5,-0.2 0.929 110.7 47.4 -63.4 -47.7 51.0 63.1 33.1
# 163 163 A I H X S+ 0 0 1 -4,-2.0 4,-1.9 2,-0.2 -2,-0.2 0.937 111.4 51.1 -56.0 -49.8 54.2 62.8 31.2
# 164 164 A R H X S+ 0 0 45 -4,-3.1 4,-1.2 1,-0.2 3,-0.3 0.946 113.7 44.9 -57.8 -43.1 53.5 59.2 30.7
# 165 165 A Q H >< S+ 0 0 124 -4,-2.5 3,-0.7 1,-0.3 -1,-0.2 0.914 107.3 56.8 -67.5 -44.2 50.1 60.1 29.4
# 166 166 A H H 3< S+ 0 0 84 -4,-3.4 -1,-0.3 1,-0.3 -2,-0.2 0.811 100.8 61.5 -60.3 -24.6 51.3 62.9 27.2
# 167 167 A K H 3< 0 0 104 -4,-1.9 -1,-0.3 -3,-0.3 -2,-0.2 0.912 360.0 360.0 -71.7 -35.6 53.5 60.4 25.6
# 168 168 A L << 0 0 188 -4,-1.2 -1,-0.3 -3,-0.7 -4,-0.0 -0.521 360.0 360.0 -80.8 71.8 50.5 58.4 24.5
Comments (4)
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Hello, actually I do not have dssp installed - the result is coming from calling pdb2sse(), not dssp().
# just to show dssp is not in my system dssp(pdb)$sse Error in .get.exepath(exefile) : could not determine path to 'dssp'
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pdb2sse()simply extracts SSE annotations in a PDB file. If no annotation, it will call ‘dssp’. So, the difference you saw is most likely because the original authors of the PDB used a different method to calculate SSE. Usually, the difference should be small (note that in PDB, there are three categories, H, E, and C; in DSSP, there are more categories, where ‘S', ‘T’, etc. can be equal to 'C’ in PDB). See PDB file format for more detail: https://www.wwpdb.org/documentation/file-format-content/format33/sect5.html -
I understand now, I appreciate the pointers.
It happens that the 4Q21 pdb entry is from '91 and had not been processed by DSSP. The data in the pdb file is missing the last helices, which explains why when read bypdb2sse()as you explain it does not match the external DSSP calculation. This DSSP calculation is what we automatically view as 3D in the pdb website.
OK for me to close report. - Log in to comment
Hi,
Bio3D does not calculate SSE itself. It calls the external DSSP executable installed in your system. Most likely, your locally installed DSSP is different from the web server. Check their versions and corresponding documentation to see if they have any description of this discrepancy.