==== Secondary Structure Definition by the program DSSP, updated CMBI version by ElmK / April 1,2000 ==== DATE=19-FEB-2012 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER HYDROLASE (ACID PROTEASE) 04-MAR-96 1UPJ . COMPND 2 MOLECULE: HIV-1 PROTEASE; . SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; . AUTHOR K.D.WATENPAUGH,A.M.MULICHAK,M.N.JANAKIRAMAN . 99 1 0 0 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) . 6909.0 ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) . 61 61.6 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES . 7 7.1 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES . 29 29.3 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 . 3 3.0 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 . 16 16.2 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES . 5 5.1 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES . 3 3.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES . 1 1.0 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 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 RESIDUES PER ALPHA HELIX . 0 1 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 PARALLEL BRIDGES PER LADDER . 1 1 0 0 0 2 0 1 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 0 0 0 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 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 1 A P 0 0 153 0, 0.0 2,-0.4 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0-171.3 13.0 39.9 12.1 2 2 A Q - 0 0 180 0, 0.0 2,-0.4 0, 0.0 0, 0.0 -0.797 360.0-163.3 -91.0 139.3 14.7 38.3 15.1 3 3 A I - 0 0 82 -2,-0.4 2,-0.1 6,-0.0 0, 0.0 -0.985 6.2-150.4-133.8 115.3 12.7 35.6 16.9 4 4 A T - 0 0 85 -2,-0.4 3,-0.4 4,-0.1 0, 0.0 -0.350 20.1-126.3 -73.1 160.2 13.3 34.2 20.4 5 5 A L S S+ 0 0 120 1,-0.2 -1,-0.1 -2,-0.1 -2,-0.0 0.197 80.1 103.9-102.4 14.8 12.4 30.7 21.3 6 6 A W S S+ 0 0 222 2,-0.1 2,-0.3 3,-0.0 -1,-0.2 0.673 90.9 29.0 -66.9 -27.9 10.3 31.3 24.4 7 7 A Q S S- 0 0 163 -3,-0.4 0, 0.0 3,-0.0 0, 0.0 -0.904 109.7 -76.1-130.5 155.3 7.1 30.6 22.3 8 8 A R - 0 0 180 -2,-0.3 2,-2.0 1,-0.1 -2,-0.1 -0.319 50.0-115.8 -48.5 127.1 6.6 28.3 19.3 9 9 A P + 0 0 26 0, 0.0 15,-2.7 0, 0.0 2,-0.3 -0.520 49.8 176.0 -74.1 77.9 8.1 30.1 16.2 10 10 A L E +A 23 0A 90 -2,-2.0 2,-0.3 13,-0.2 13,-0.2 -0.637 6.6 179.7 -91.9 144.0 4.8 30.6 14.3 11 11 A V E -A 22 0A 15 11,-1.7 11,-2.2 -2,-0.3 2,-0.9 -0.999 30.0-114.0-150.2 141.0 4.4 32.4 11.0 12 12 A T E -A 21 0A 81 -2,-0.3 55,-0.4 9,-0.2 56,-0.3 -0.603 34.4-174.5 -79.1 104.4 1.7 33.3 8.5 13 13 A I E -A 20 0A 1 7,-1.6 7,-1.7 -2,-0.9 2,-0.6 -0.610 17.0-145.0 -93.0 145.8 2.1 31.7 5.1 14 14 A K E +AB 19 65A 90 51,-3.2 51,-2.3 -2,-0.3 2,-0.4 -0.906 29.2 167.2-114.7 125.6 0.1 32.3 2.0 15 15 A I E > -AB 18 64A 0 3,-2.9 3,-1.0 -2,-0.6 49,-0.1 -0.956 57.3 -10.6-141.4 113.4 -0.4 29.2 -0.2 16 16 A G T 3 S- 0 0 38 47,-0.6 -1,-0.1 -2,-0.4 3,-0.1 0.909 129.3 -49.8 66.3 39.3 -2.7 28.3 -3.1 17 17 A G T 3 S+ 0 0 69 1,-0.2 2,-0.3 -3,-0.1 -1,-0.3 0.425 120.1 107.2 76.3 9.1 -4.8 31.4 -2.6 18 18 A Q E < -A 15 0A 68 -3,-1.0 -3,-2.9 2,-0.0 2,-0.4 -0.893 63.0-129.3-124.5 150.6 -5.2 30.8 1.1 19 19 A L E +A 14 0A 127 -2,-0.3 2,-0.3 -5,-0.2 -5,-0.2 -0.758 36.9 148.6 -89.5 138.6 -4.0 32.0 4.4 20 20 A K E -A 13 0A 48 -7,-1.7 -7,-1.6 -2,-0.4 2,-0.3 -0.964 38.6-118.7-159.8 160.4 -2.6 29.8 7.2 21 21 A E E -A 12 0A 117 -2,-0.3 2,-0.3 -9,-0.2 -9,-0.2 -0.852 31.9-173.6-105.9 157.6 -0.0 29.7 10.1 22 22 A A E -A 11 0A 3 -11,-2.2 -11,-1.7 -2,-0.3 2,-0.6 -0.998 25.2-109.0-157.4 150.6 3.0 27.4 10.2 23 23 A L E -Ac 10 84A 22 60,-4.1 62,-2.2 -2,-0.3 2,-0.8 -0.696 25.9-130.3 -92.3 119.0 5.8 26.3 12.4 24 24 A L E - c 0 85A 31 -15,-2.7 2,-0.6 -2,-0.6 62,-0.1 -0.519 33.1-174.8 -64.6 107.2 9.5 27.3 11.6 25 25 A D > + 0 0 54 60,-2.3 3,-0.6 -2,-0.8 62,-0.3 -0.906 26.5 173.8-121.1 97.0 11.3 24.0 11.8 26 26 A T T 3 S+ 0 0 81 -2,-0.6 -1,-0.1 1,-0.2 60,-0.1 0.410 86.2 64.0 -74.0 -5.6 15.1 23.8 11.4 27 27 A G T 3 S+ 0 0 63 -3,-0.1 2,-0.4 59,-0.0 -1,-0.2 0.753 88.4 82.0 -85.3 -21.4 14.8 20.2 12.3 28 28 A A < - 0 0 17 -3,-0.6 59,-3.0 57,-0.2 60,-0.1 -0.739 56.3-165.7 -95.1 122.8 12.8 19.4 9.2 29 29 A D S S+ 0 0 103 -2,-0.4 59,-1.2 57,-0.2 2,-0.2 0.846 79.8 38.5 -67.3 -42.7 14.6 18.8 5.7 30 30 A D S S- 0 0 48 57,-0.2 2,-0.6 58,-0.1 57,-0.2 -0.689 82.9-113.5-109.9 163.6 11.1 19.2 4.0 31 31 A T E +d 75 0A 0 43,-0.5 45,-2.4 -2,-0.2 2,-0.4 -0.868 33.1 179.6 -97.3 123.9 8.0 21.3 4.2 32 32 A V E -dE 76 84A 11 52,-0.8 52,-2.8 -2,-0.6 2,-0.3 -0.990 2.8-174.9-127.0 129.3 4.8 19.4 5.2 33 33 A L E -d 77 0A 1 43,-2.3 45,-2.5 -2,-0.4 3,-0.2 -0.904 30.7-102.6-122.9 147.7 1.3 21.0 5.6 34 34 A E - 0 0 74 -2,-0.3 2,-0.1 43,-0.2 -1,-0.1 -0.040 67.4 -54.3 -53.0 165.7 -2.0 19.5 6.8 35 35 A E S S+ 0 0 101 43,-0.3 2,-0.3 45,-0.2 -1,-0.2 -0.263 76.6 142.8 -60.1 121.2 -4.7 18.5 4.2 36 36 A M - 0 0 13 -3,-0.2 2,-0.5 -2,-0.1 -3,-0.1 -0.983 52.0 -88.7-159.3 155.7 -5.6 21.4 1.9 37 37 A S + 0 0 92 -2,-0.3 -2,-0.0 -21,-0.1 0, 0.0 -0.640 44.1 168.3 -86.2 122.7 -6.6 22.0 -1.7 38 38 A L - 0 0 19 -2,-0.5 2,-0.1 2,-0.1 -22,-0.0 -0.974 29.7-122.4-131.1 137.1 -3.8 22.6 -4.2 39 39 A P + 0 0 102 0, 0.0 2,-0.1 0, 0.0 -23,-0.0 -0.324 67.5 31.1 -74.4 161.4 -4.0 22.7 -8.0 40 40 A G S S- 0 0 71 -2,-0.1 2,-0.2 19,-0.1 -2,-0.1 -0.325 90.8 -40.6 93.0-167.7 -1.9 20.5 -10.3 41 41 A R - 0 0 238 -2,-0.1 19,-0.4 19,-0.1 2,-0.3 -0.585 48.0-171.8 -96.3 157.0 -0.4 17.0 -10.2 42 42 A W - 0 0 119 -2,-0.2 17,-0.2 17,-0.1 15,-0.1 -0.897 18.0-129.3-145.7 168.8 1.3 15.2 -7.4 43 43 A K E -F 58 0A 109 15,-0.9 15,-2.6 -2,-0.3 2,-0.3 -0.958 30.4-112.7-123.4 136.5 3.2 12.0 -6.6 44 44 A P E +F 57 0A 92 0, 0.0 2,-0.3 0, 0.0 13,-0.2 -0.585 50.0 169.8 -67.8 128.0 2.5 9.6 -3.7 45 45 A K E -F 56 0A 59 11,-2.8 11,-3.0 -2,-0.3 2,-0.4 -0.941 25.4-139.8-142.5 161.8 5.4 9.9 -1.3 46 46 A M E -F 55 0A 102 -2,-0.3 2,-0.3 9,-0.3 9,-0.2 -0.992 16.5-178.7-131.6 134.5 6.3 8.7 2.3 47 47 A I E -F 54 0A 40 7,-1.9 7,-2.6 -2,-0.4 2,-0.3 -0.850 16.4-134.9-126.2 159.8 8.1 10.5 5.1 48 48 A G E +F 53 0A 64 -2,-0.3 5,-0.2 5,-0.3 2,-0.2 -0.871 24.4 163.0-113.6 149.5 9.2 9.6 8.6 49 49 A G - 0 0 55 3,-2.3 0, 0.0 -2,-0.3 0, 0.0 -0.755 57.7 -67.6-143.1-170.5 9.0 11.5 11.9 50 50 A I S S+ 0 0 185 1,-0.2 -1,-0.0 -2,-0.2 3,-0.0 0.942 131.1 43.2 -44.8 -64.8 9.2 10.8 15.7 51 51 A G S S- 0 0 79 -3,-0.1 2,-0.2 1,-0.0 -1,-0.2 0.742 122.7 -87.8 -58.5 -44.4 6.1 8.8 15.8 52 52 A G - 0 0 44 2,-0.0 -3,-2.3 -5,-0.0 2,-0.4 -0.818 64.7 -29.7 170.4-126.6 6.7 6.7 12.5 53 53 A F E -F 48 0A 152 -5,-0.2 2,-0.3 -2,-0.2 -5,-0.3 -0.977 43.3-170.9-129.3 144.6 5.9 7.1 8.9 54 54 A I E -F 47 0A 54 -7,-2.6 -7,-1.9 -2,-0.4 2,-0.5 -0.857 23.3-123.7-123.5 163.3 3.1 9.0 7.1 55 55 A K E -F 46 0A 135 -2,-0.3 -9,-0.3 -9,-0.2 2,-0.2 -0.953 34.7-179.2-113.7 126.0 2.2 9.0 3.4 56 56 A V E -F 45 0A 8 -11,-3.0 -11,-2.8 -2,-0.5 2,-0.5 -0.577 28.9-119.3-118.3 170.9 2.1 12.4 1.6 57 57 A R E -FG 44 77A 80 20,-2.0 20,-2.5 -13,-0.2 2,-0.7 -0.950 30.7-137.9-103.8 132.8 1.3 13.9 -1.8 58 58 A Q E -FG 43 76A 30 -15,-2.6 -15,-0.9 -2,-0.5 2,-0.4 -0.875 20.9-178.0 -97.5 115.8 4.2 15.8 -3.4 59 59 A Y E - G 0 75A 11 16,-2.8 16,-2.9 -2,-0.7 2,-0.3 -0.876 11.0-161.4-106.6 129.4 3.6 19.1 -5.2 60 60 A D E + 0 0 73 -2,-0.4 14,-0.2 -19,-0.4 13,-0.1 -0.802 66.4 23.7-105.7 150.6 6.6 20.8 -6.8 61 61 A Q E S+ 0 0 170 -2,-0.3 2,-0.5 1,-0.2 -1,-0.2 0.804 75.8 160.6 57.6 37.6 7.0 24.4 -7.8 62 62 A I E - G 0 73A 23 11,-1.8 11,-1.6 -3,-0.2 2,-0.4 -0.810 36.7-134.6 -87.5 119.3 4.4 25.7 -5.3 63 63 A L E - G 0 72A 86 -2,-0.5 -47,-0.6 9,-0.2 2,-0.3 -0.776 27.6-178.5 -75.7 130.5 4.8 29.4 -4.6 64 64 A I E -BG 15 71A 0 7,-2.5 2,-0.8 -2,-0.4 7,-0.7 -0.981 21.9-149.0-132.3 127.5 4.5 30.3 -0.8 65 65 A E E -BG 14 70A 63 -51,-2.3 -51,-3.2 -2,-0.3 2,-0.4 -0.912 17.3-168.6-100.0 111.4 4.7 33.7 0.7 66 66 A I E > S- G 0 69A 5 3,-1.9 3,-4.9 -2,-0.8 -53,-0.2 -0.834 75.1 -26.1 -94.6 135.3 6.3 33.2 4.2 67 67 A C T 3 S- 0 0 82 -55,-0.4 -1,-0.2 -2,-0.4 -54,-0.1 0.633 129.6 -48.7 19.6 42.2 6.0 36.5 6.3 68 68 A G T 3 S+ 0 0 57 -56,-0.3 2,-0.4 1,-0.3 -1,-0.3 0.516 113.6 117.5 88.5 6.4 5.8 38.4 3.0 69 69 A H E < - G 0 66A 94 -3,-4.9 -3,-1.9 1,-0.0 -1,-0.3 -0.873 60.8-124.3-100.6 142.2 8.9 36.8 1.3 70 70 A K E + G 0 65A 145 -2,-0.4 2,-0.3 -5,-0.2 -5,-0.2 -0.533 35.9 158.7 -86.7 148.3 8.6 34.7 -1.9 71 71 A A E - G 0 64A 2 -7,-0.7 -7,-2.5 -2,-0.3 2,-0.3 -0.959 22.8-157.2-164.7 147.6 9.7 31.3 -2.3 72 72 A I E + G 0 63A 90 -2,-0.3 2,-0.2 -9,-0.2 -9,-0.2 -0.897 36.6 117.2-138.5 107.3 9.0 28.3 -4.6 73 73 A G E - G 0 62A 12 -11,-1.6 -11,-1.8 -2,-0.3 2,-0.5 -0.830 61.2 -49.3-152.3-170.0 9.6 24.7 -3.6 74 74 A T E - 0 0 33 -2,-0.2 -43,-0.5 -14,-0.2 2,-0.4 -0.678 45.2-169.3 -81.0 127.5 8.4 21.2 -3.0 75 75 A V E -dG 31 59A 0 -16,-2.9 -16,-2.8 -2,-0.5 2,-0.5 -0.984 9.3-153.1-120.4 118.9 5.5 21.1 -0.6 76 76 A L E -dG 32 58A 0 -45,-2.4 -43,-2.3 -2,-0.4 2,-0.5 -0.879 13.2-158.3 -91.3 123.3 4.4 17.6 0.9 77 77 A V E +dG 33 57A 1 -20,-2.5 -20,-2.0 -2,-0.5 -43,-0.2 -0.935 36.8 93.4-111.9 124.5 0.6 17.6 1.8 78 78 A G S S- 0 0 1 -45,-2.5 2,-1.5 -2,-0.5 -43,-0.3 -0.912 75.7 -27.1-169.8-157.6 -0.6 15.1 4.3 79 79 A P + 0 0 83 0, 0.0 -45,-0.1 0, 0.0 -2,-0.0 -0.461 69.7 145.3 -80.4 58.0 -1.6 14.0 7.8 80 80 A T - 0 0 27 -2,-1.5 -45,-0.2 1,-0.1 3,-0.1 -0.640 49.6-141.6 -96.7 153.2 0.7 16.2 9.9 81 81 A P S S+ 0 0 125 0, 0.0 2,-0.3 0, 0.0 -1,-0.1 0.762 88.4 32.4 -77.1 -29.6 -0.3 17.6 13.3 82 82 A V S S- 0 0 39 -49,-0.0 2,-0.9 -59,-0.0 -50,-0.1 -0.943 85.1-110.2-132.2 151.9 1.5 20.8 12.4 83 83 A N - 0 0 12 -2,-0.3 -60,-4.1 -62,-0.2 2,-0.5 -0.686 42.2-163.3 -83.1 111.7 2.3 22.9 9.5 84 84 A I E -cE 23 32A 19 -52,-2.8 -52,-0.8 -2,-0.9 2,-0.7 -0.776 19.2-171.9-101.3 122.6 6.1 22.5 9.0 85 85 A I E +c 24 0A 0 -62,-2.2 -60,-2.3 -2,-0.5 2,-0.2 -0.971 27.3 178.9-110.9 111.2 8.3 24.8 6.9 86 86 A G >> - 0 0 0 -2,-0.7 3,-1.8 -62,-0.1 4,-1.7 -0.472 43.3 -65.8-103.8-170.1 11.6 23.0 6.9 87 87 A R H 3> S+ 0 0 119 -59,-3.0 4,-1.1 1,-0.3 -57,-0.2 0.524 116.6 69.7 -56.3 -28.9 15.0 23.7 5.3 88 88 A N H 34 S+ 0 0 43 -59,-1.2 -1,-0.3 2,-0.1 4,-0.3 0.889 118.8 25.4 -56.7 -37.6 14.2 23.4 1.6 89 89 A L H X> S+ 0 0 0 -3,-1.8 3,-1.5 2,-0.1 4,-1.4 0.879 110.7 71.8 -95.1 -42.5 12.2 26.7 2.0 90 90 A L H 3<>S+ 0 0 8 -4,-1.7 5,-2.9 1,-0.3 -3,-0.2 0.726 97.4 52.6 -36.6 -35.6 14.1 28.2 5.1 91 91 A T T 3<5S+ 0 0 100 -4,-1.1 3,-0.4 3,-0.2 -1,-0.3 0.794 103.2 56.5 -79.6 -34.6 17.2 28.8 2.9 92 92 A Q T <45S+ 0 0 99 -3,-1.5 -2,-0.2 -4,-0.3 -1,-0.2 0.891 106.4 47.3 -61.4 -48.3 15.3 30.8 0.2 93 93 A I T <5S- 0 0 37 -4,-1.4 -1,-0.2 -24,-0.1 -2,-0.2 0.368 121.6-111.3 -85.9 5.9 13.9 33.3 2.6 94 94 A G T 5 + 0 0 59 -3,-0.4 -3,-0.2 -5,-0.2 2,-0.2 0.722 52.0 178.1 72.5 41.2 17.4 33.6 4.0 95 95 A C < + 0 0 56 -5,-2.9 2,-0.3 -8,-0.1 -1,-0.2 -0.463 3.7 175.7 -81.0 142.6 17.0 32.0 7.6 96 96 A T - 0 0 106 -2,-0.2 2,-0.5 2,-0.0 -70,-0.0 -0.909 27.9-124.6-139.5 158.9 19.8 31.4 10.2 97 97 A L - 0 0 118 -2,-0.3 2,-0.4 -71,-0.0 -2,-0.0 -0.923 26.2-174.6-105.4 130.9 20.5 30.3 13.8 98 98 A N 0 0 136 -2,-0.5 -2,-0.0 1,-0.1 0, 0.0 -0.997 360.0 360.0-130.9 128.4 22.3 32.5 16.1 99 99 A F 0 0 269 -2,-0.4 -1,-0.1 0, 0.0 0, 0.0 0.198 360.0 360.0-159.7 360.0 23.5 31.7 19.6