==== Secondary Structure Definition by the program DSSP, updated CMBI version by ElmK / April 1,2000 ==== DATE=6-DEC-2009 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER ENDOCYTOSIS/EXOCYTOSIS 14-DEC-01 1KMD . COMPND 2 MOLECULE: VACUOLAR MORPHOGENESIS PROTEIN VAM7; . SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; . AUTHOR J.LU,J.GARCIA,I.DULUBOVA,T.C.SUDHOF,J.RIZO . 117 1 0 0 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) . 9420.0 ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) . 69 59.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES . 12 10.3 TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES . 1 0.9 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES . 15 12.8 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES . 10 8.5 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES . 31 26.5 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES . 2 1.7 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES . 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** . 0 0 0 1 0 1 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 RESIDUES PER ALPHA HELIX . 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PARALLEL BRIDGES PER LADDER . 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ANTIPARALLEL BRIDGES PER LADDER . 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 LADDERS PER SHEET . # 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 8 A K 0 0 232 0, 0.0 2,-0.1 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 170.3 6.2 -15.8 -20.1 2 9 A M - 0 0 142 1,-0.2 2,-0.0 0, 0.0 94,-0.0 -0.449 360.0 -85.7 -97.6 173.1 5.8 -12.3 -18.8 3 10 A S - 0 0 26 -2,-0.1 2,-0.5 91,-0.1 -1,-0.2 -0.273 38.3-120.9 -74.5 164.0 4.6 -11.0 -15.4 4 11 A E - 0 0 156 91,-0.3 2,-0.2 89,-0.2 91,-0.1 -0.937 19.0-136.8-113.2 123.9 0.9 -10.5 -14.5 5 12 A K - 0 0 157 -2,-0.5 2,-0.3 89,-0.1 86,-0.1 -0.525 18.0-130.8 -77.9 142.1 -0.4 -7.1 -13.5 6 13 A L - 0 0 50 -2,-0.2 2,-1.1 84,-0.1 84,-0.1 -0.742 14.9-123.2 -95.6 140.6 -2.8 -6.9 -10.6 7 14 A R + 0 0 177 -2,-0.3 2,-0.5 83,-0.0 -1,-0.0 -0.697 42.6 163.5 -85.6 98.9 -6.1 -5.0 -10.8 8 15 A I + 0 0 6 -2,-1.1 2,-0.4 18,-0.2 18,-0.2 -0.949 3.7 163.6-122.2 112.4 -6.0 -2.5 -7.9 9 16 A K E -A 25 0A 159 16,-0.9 16,-1.2 -2,-0.5 2,-0.6 -0.959 22.3-153.6-132.8 115.6 -8.4 0.4 -8.0 10 17 A V E +A 24 0A 6 -2,-0.4 14,-0.2 14,-0.2 3,-0.0 -0.781 35.7 141.8 -91.7 119.8 -9.1 2.6 -4.9 11 18 A D E + 0 0 125 12,-1.1 2,-0.4 -2,-0.6 -1,-0.1 0.020 49.3 82.6-144.3 27.8 -12.5 4.2 -4.9 12 19 A D E +A 23 0A 59 11,-0.6 11,-3.3 70,-0.0 2,-0.3 -0.999 43.1 169.0-139.9 136.1 -13.6 4.0 -1.3 13 20 A V E -A 22 0A 45 -2,-0.4 2,-0.6 9,-0.3 9,-0.2 -0.937 13.2-166.8-150.9 123.6 -12.8 6.1 1.7 14 21 A K E -A 21 0A 74 7,-1.0 7,-1.7 -2,-0.3 2,-0.5 -0.904 16.4-147.7-115.1 104.8 -14.4 6.2 5.2 15 22 A I E -A 20 0A 82 -2,-0.6 5,-0.2 5,-0.2 58,-0.1 -0.573 21.9-177.7 -73.6 121.0 -13.4 9.2 7.3 16 23 A N - 0 0 44 3,-1.0 -2,-0.0 -2,-0.5 3,-0.0 -0.923 38.6-122.0-122.0 146.9 -13.3 8.3 11.0 17 24 A P S S+ 0 0 104 0, 0.0 3,-0.1 0, 0.0 -1,-0.1 0.705 117.3 44.5 -56.6 -20.0 -12.5 10.5 14.1 18 25 A K S S- 0 0 161 1,-0.4 2,-0.3 0, 0.0 -3,-0.0 0.820 131.5 -30.6 -93.2 -38.5 -9.6 8.2 14.8 19 26 A Y - 0 0 107 -5,-0.1 -3,-1.0 54,-0.0 2,-0.7 -0.968 58.3-101.3-173.6 161.6 -8.2 7.9 11.3 20 27 A V E -A 15 0A 5 -2,-0.3 15,-0.5 -5,-0.2 -5,-0.2 -0.857 36.5-160.8-100.2 115.4 -9.0 7.9 7.6 21 28 A L E -A 14 0A 32 -7,-1.7 -7,-1.0 -2,-0.7 2,-0.4 -0.536 5.7-142.6 -92.0 159.7 -9.2 4.4 6.0 22 29 A Y E -AB 13 33A 5 11,-2.3 11,-1.7 -9,-0.2 2,-1.3 -0.984 8.3-138.7-127.9 126.9 -9.0 3.6 2.3 23 30 A G E -AB 12 32A 0 -11,-3.3 -12,-1.1 -2,-0.4 2,-0.7 -0.668 23.4-169.0 -85.6 92.9 -11.0 0.9 0.5 24 31 A V E -AB 10 31A 5 7,-3.1 7,-3.2 -2,-1.3 2,-0.2 -0.739 10.5-147.3 -87.1 113.3 -8.4 -0.6 -1.9 25 32 A S E +A 9 0A 49 -16,-1.2 -16,-0.9 -2,-0.7 5,-0.2 -0.561 27.6 159.3 -81.0 141.8 -10.1 -2.9 -4.4 26 33 A T - 0 0 14 -2,-0.2 -18,-0.2 -18,-0.2 -20,-0.0 -0.969 58.4 -84.5-155.0 165.8 -8.3 -6.0 -5.6 27 34 A P S S+ 0 0 52 0, 0.0 3,-0.1 0, 0.0 -19,-0.1 0.769 131.6 44.0 -44.9 -28.5 -8.9 -9.4 -7.3 28 35 A N S S- 0 0 111 1,-0.3 2,-0.3 3,-0.0 -3,-0.1 0.933 125.5 -82.4 -82.8 -52.6 -9.5 -10.7 -3.7 29 36 A K - 0 0 136 -5,-0.1 2,-0.6 2,-0.0 -1,-0.3 -0.964 57.6 -45.6 167.7-176.6 -11.7 -7.8 -2.5 30 37 A R - 0 0 125 -2,-0.3 2,-0.4 -5,-0.2 -5,-0.3 -0.690 52.5-162.7 -82.6 119.1 -11.7 -4.3 -1.0 31 38 A L E -B 24 0A 24 -7,-3.2 -7,-3.1 -2,-0.6 2,-0.6 -0.874 11.4-138.9-106.5 133.5 -9.2 -3.9 1.8 32 39 A Y E +B 23 0A 95 -2,-0.4 2,-0.3 -9,-0.2 -9,-0.2 -0.805 38.5 149.6 -93.9 118.0 -9.3 -1.1 4.3 33 40 A K E -B 22 0A 33 -11,-1.7 -11,-2.3 -2,-0.6 2,-0.3 -0.843 37.8-117.8-138.3 174.6 -5.9 0.4 5.1 34 41 A R >> - 0 0 74 -2,-0.3 3,-1.7 -13,-0.2 4,-1.0 -0.905 19.7-126.2-120.0 147.6 -4.3 3.6 6.2 35 42 A Y H >> S+ 0 0 33 -15,-0.5 4,-1.9 -2,-0.3 3,-0.9 0.895 112.8 60.3 -54.9 -42.3 -1.7 5.8 4.4 36 43 A S H 3> S+ 0 0 72 1,-0.3 4,-1.5 2,-0.2 -1,-0.3 0.739 102.1 55.3 -58.4 -21.9 0.5 5.7 7.6 37 44 A E H <> S+ 0 0 59 -3,-1.7 4,-0.8 2,-0.2 -1,-0.3 0.795 103.3 53.2 -81.2 -30.2 0.5 1.9 7.1 38 45 A F H > S+ 0 0 134 -4,-0.5 4,-3.2 -5,-0.4 3,-1.4 0.979 97.8 52.7 -61.7 -58.0 10.5 -1.6 6.3 45 52 A L H 3X>S+ 0 0 0 -4,-1.9 4,-3.3 -3,-0.5 5,-0.8 0.812 105.2 59.5 -47.3 -32.7 11.1 -3.6 3.2 46 53 A E H 3X5S+ 0 0 66 -4,-1.3 4,-0.7 1,-0.2 -1,-0.3 0.893 116.2 30.7 -64.8 -40.7 14.3 -1.5 2.9 47 54 A R H <<5S+ 0 0 215 -3,-1.4 -2,-0.2 -4,-1.2 -1,-0.2 0.669 125.9 46.3 -90.6 -20.5 15.5 -2.7 6.2 48 55 A D H <5S+ 0 0 56 -4,-3.2 -3,-0.2 -5,-0.2 -2,-0.2 0.859 124.9 29.4 -87.9 -41.5 13.8 -6.1 5.9 49 56 A V H <5S- 0 0 33 -4,-3.3 -3,-0.2 -5,-0.3 -2,-0.2 0.790 96.4-136.7 -87.5 -32.5 14.9 -6.9 2.4 50 57 A G << + 0 0 67 -5,-0.8 2,-0.3 -4,-0.7 -4,-0.2 0.691 66.3 107.1 82.3 19.6 18.1 -4.9 2.5 51 58 A S S S- 0 0 33 -6,-0.6 2,-0.3 49,-0.0 -1,-0.3 -0.861 75.6 -98.0-127.7 162.5 17.6 -3.4 -0.9 52 59 A T - 0 0 126 -2,-0.3 -7,-0.0 -3,-0.1 -6,-0.0 -0.636 33.4-136.2 -82.5 133.5 16.6 0.1 -2.3 53 60 A I - 0 0 18 -2,-0.3 2,-0.1 2,-0.1 -7,-0.0 -0.787 4.4-154.8 -93.3 125.8 13.0 0.6 -3.2 54 61 A P + 0 0 94 0, 0.0 2,-0.5 0, 0.0 -1,-0.1 -0.061 56.4 119.4 -88.5 34.0 12.3 2.4 -6.5 55 62 A Y - 0 0 31 -2,-0.1 2,-0.4 2,-0.0 -2,-0.1 -0.886 65.8-125.4-105.6 126.2 8.9 3.6 -5.4 56 63 A D + 0 0 164 -2,-0.5 32,-0.1 2,-0.0 0, 0.0 -0.523 37.6 164.8 -70.5 124.1 8.2 7.3 -5.2 57 64 A F - 0 0 27 -2,-0.4 2,-0.7 2,-0.0 -2,-0.0 -0.775 20.4-160.5-145.8 96.2 6.9 8.3 -1.7 58 65 A P - 0 0 83 0, 0.0 2,-0.3 0, 0.0 -2,-0.0 -0.680 15.5-171.1 -82.0 111.0 6.9 12.0 -0.7 59 66 A E - 0 0 85 -2,-0.7 -2,-0.0 -20,-0.0 0, 0.0 -0.772 12.9-140.2-103.7 147.9 6.8 12.4 3.1 60 67 A K - 0 0 129 -2,-0.3 2,-0.1 2,-0.0 0, 0.0 -0.884 23.9-111.0-109.3 137.1 6.3 15.6 5.0 61 68 A P - 0 0 117 0, 0.0 2,-0.2 0, 0.0 -1,-0.0 -0.348 29.4-173.3 -64.7 140.6 8.1 16.4 8.3 62 69 A G + 0 0 65 1,-0.1 -2,-0.0 2,-0.1 7,-0.0 -0.602 27.3 138.0-139.4 77.9 6.0 16.5 11.4 63 70 A V S S- 0 0 138 -2,-0.2 -1,-0.1 0, 0.0 0, 0.0 0.954 84.6 -49.5 -81.4 -78.8 7.9 17.8 14.5 64 71 A L S S+ 0 0 131 5,-0.0 2,-0.7 0, 0.0 5,-0.1 -0.054 71.7 162.0-156.3 39.4 5.6 20.0 16.5 65 72 A D + 0 0 60 1,-0.2 0, 0.0 3,-0.1 0, 0.0 -0.558 4.7 168.9 -71.1 110.7 4.1 22.5 14.0 66 73 A R S > S+ 0 0 209 -2,-0.7 3,-0.6 2,-0.1 -1,-0.2 0.768 79.6 43.7 -91.9 -31.2 1.0 24.0 15.6 67 74 A R T 3 S+ 0 0 234 1,-0.2 -1,-0.1 3,-0.0 -2,-0.1 0.821 116.0 47.4 -81.9 -34.1 0.5 26.8 13.0 68 75 A W T 3 S+ 0 0 213 2,-0.0 -1,-0.2 -4,-0.0 -3,-0.1 0.012 85.6 148.5 -95.6 27.1 1.2 24.5 10.1 69 76 A Q < - 0 0 150 -3,-0.6 2,-0.3 -5,-0.1 -3,-0.1 -0.129 32.0-150.8 -58.8 158.6 -1.2 21.8 11.4 70 77 A R - 0 0 160 7,-0.0 2,-0.7 4,-0.0 -1,-0.1 -0.960 13.7-122.1-135.5 152.7 -3.1 19.6 9.0 71 78 A R > - 0 0 172 -2,-0.3 3,-1.8 1,-0.1 6,-0.2 -0.846 10.0-158.3 -99.1 112.1 -6.4 17.8 9.1 72 79 A Y T 3 S+ 0 0 74 -2,-0.7 -1,-0.1 1,-0.3 -52,-0.1 0.744 96.7 55.9 -57.7 -23.2 -6.1 14.1 8.5 73 80 A D T 3 S+ 0 0 62 -58,-0.1 -1,-0.3 -56,-0.1 -58,-0.1 -0.061 79.4 127.4-100.4 31.7 -9.7 14.1 7.4 74 81 A D X> - 0 0 57 -3,-1.8 4,-2.9 1,-0.1 3,-0.7 -0.806 55.2-148.4 -94.0 119.8 -9.1 16.8 4.7 75 82 A P H 3> S+ 0 0 92 0, 0.0 4,-3.4 0, 0.0 5,-0.2 0.843 98.2 61.6 -52.1 -36.5 -10.4 15.9 1.2 76 83 A E H 3> S+ 0 0 151 1,-0.2 4,-0.9 2,-0.2 5,-0.1 0.915 113.8 33.2 -57.5 -45.3 -7.6 17.9 -0.3 77 84 A M H <> S+ 0 0 39 -3,-0.7 4,-2.2 -6,-0.2 -1,-0.2 0.818 118.5 54.4 -80.3 -33.0 -5.0 15.6 1.4 78 85 A I H X S+ 0 0 15 -4,-2.9 4,-1.4 2,-0.2 -2,-0.2 0.883 99.6 62.2 -67.7 -39.9 -7.2 12.5 1.1 79 86 A D H X S+ 0 0 100 -4,-3.4 4,-0.8 -5,-0.2 3,-0.3 0.929 113.3 33.9 -51.4 -52.3 -7.7 13.0 -2.7 80 87 A E H < S+ 0 0 110 -4,-0.9 3,-0.3 1,-0.2 -1,-0.2 0.898 109.8 64.0 -72.4 -41.6 -3.9 12.6 -3.3 81 88 A R H < S+ 0 0 41 -4,-2.2 -1,-0.2 1,-0.2 -2,-0.2 0.763 96.4 64.5 -53.4 -24.3 -3.4 10.1 -0.6 82 89 A R H >< S+ 0 0 58 -4,-1.4 3,-0.8 -3,-0.3 4,-0.4 0.980 98.1 54.3 -63.9 -59.6 -5.8 7.9 -2.6 83 90 A I T 3< S+ 0 0 86 -4,-0.8 -74,-0.0 -3,-0.3 0, 0.0 -0.207 91.1 49.8 -72.6 167.2 -3.5 7.5 -5.7 84 91 A G T 3> S+ 0 0 38 1,-0.0 4,-1.1 -27,-0.0 -1,-0.2 0.056 95.4 78.1 92.4 -26.2 0.0 6.2 -5.5 85 92 A L H <> S+ 0 0 6 -3,-0.8 4,-1.1 2,-0.2 -2,-0.1 0.939 89.6 49.5 -79.5 -52.1 -1.0 3.2 -3.4 86 93 A E H >> S+ 0 0 29 -4,-0.4 4,-2.3 1,-0.2 3,-0.5 0.881 112.9 49.5 -54.6 -41.1 -2.4 1.0 -6.2 87 94 A R H 3> S+ 0 0 172 1,-0.2 4,-1.8 2,-0.2 5,-0.3 0.899 104.5 57.3 -66.1 -41.8 0.7 1.6 -8.3 88 95 A F H 3X S+ 0 0 10 -4,-1.1 4,-0.6 1,-0.2 -1,-0.2 0.719 112.0 45.0 -62.0 -20.7 3.0 0.7 -5.4 89 96 A L H > + 0 0 26 -2,-0.4 4,-3.6 -4,-0.2 3,-0.7 0.143 44.2 117.0-111.8 16.9 10.1 -11.2 -5.2 100 107 A R H 3> S+ 0 0 97 1,-0.3 4,-1.2 2,-0.2 -1,-0.1 0.832 74.0 59.9 -52.8 -33.2 12.0 -10.3 -2.0 101 108 A W H 34 S+ 0 0 30 -3,-0.2 -1,-0.3 1,-0.2 6,-0.2 0.904 117.6 27.9 -62.8 -43.6 9.8 -7.2 -1.9 102 109 A R H <4 S+ 0 0 85 -3,-0.7 6,-0.2 -10,-0.3 -2,-0.2 0.702 110.7 69.9 -90.8 -22.8 6.6 -9.3 -1.7 103 110 A D H < S+ 0 0 121 -4,-3.6 -2,-0.2 4,-0.1 -3,-0.2 0.777 79.0 104.3 -64.7 -26.3 8.3 -12.3 -0.0 104 111 A T S X S- 0 0 12 -4,-1.2 4,-1.6 -5,-0.3 5,-0.1 -0.105 81.6-124.1 -54.3 154.3 8.7 -10.2 3.1 105 112 A K H > S+ 0 0 149 1,-0.2 4,-1.7 2,-0.2 5,-0.1 0.800 110.6 57.8 -71.6 -29.5 6.3 -10.9 6.0 106 113 A I H > S+ 0 0 35 2,-0.2 4,-1.3 1,-0.2 -1,-0.2 0.877 106.3 48.1 -68.2 -38.7 5.2 -7.3 6.0 107 114 A A H > S+ 0 0 2 2,-0.2 4,-0.8 -6,-0.2 -2,-0.2 0.919 113.6 45.9 -68.1 -44.9 4.0 -7.5 2.4 108 115 A Q H <>S+ 0 0 75 -4,-1.6 5,-3.1 -6,-0.2 -1,-0.2 0.810 119.4 42.3 -67.9 -30.2 2.1 -10.7 2.9 109 116 A D H ><5S+ 0 0 101 -4,-1.7 3,-1.3 3,-0.2 -1,-0.2 0.639 94.5 83.0 -89.5 -17.4 0.6 -9.3 6.1 110 117 A F H 3<5S+ 0 0 5 -4,-1.3 -2,-0.2 1,-0.3 -1,-0.2 0.908 109.7 21.3 -51.9 -47.7 -0.0 -5.9 4.5 111 118 A L T 3<5S- 0 0 13 -4,-0.8 -1,-0.3 -3,-0.1 -2,-0.1 0.072 118.9-101.2-109.6 21.9 -3.3 -7.2 2.9 112 119 A Q T < 5 + 0 0 150 -3,-1.3 -3,-0.2 1,-0.2 -2,-0.1 0.941 63.2 161.4 58.9 49.1 -3.8 -10.1 5.3 113 120 A L < + 0 0 55 -5,-3.1 -1,-0.2 -6,-0.2 -4,-0.1 -0.136 26.6 132.4 -92.4 38.1 -2.5 -12.6 2.8 114 121 A S - 0 0 76 -5,-0.1 -5,-0.0 1,-0.1 -3,-0.0 0.084 69.3 -86.3 -74.2-168.4 -1.8 -15.2 5.5 115 122 A K - 0 0 188 2,-0.0 -1,-0.1 0, 0.0 -2,-0.1 -0.839 43.2-154.5-109.6 96.1 -2.8 -18.8 5.4 116 123 A P 0 0 115 0, 0.0 -3,-0.0 0, 0.0 0, 0.0 -0.362 360.0 360.0 -68.9 146.1 -6.4 -19.3 6.7 117 124 A N 0 0 224 -2,-0.1 -2,-0.0 0, 0.0 0, 0.0 -0.907 360.0 360.0-137.0 360.0 -7.5 -22.6 8.2