==== Secondary Structure Definition by the program DSSP, updated CMBI version by ElmK / April 1,2000 ==== DATE=12-JUN-2011 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER HYDROLASE 02-SEP-10 3OQD . COMPND 2 MOLECULE: HIV-1 PROTEASE; . SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; . AUTHOR R.S.YEDIDI,G.PROTEASA,J.L.MARTINEZ-CAJAS,J.F.VICKREY,P.D.MAR . 99 1 0 0 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) . 6992.0 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 . 6 6.1 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES . 31 31.3 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 . 13 13.1 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES . 6 6.1 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES . 5 5.1 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 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 RESIDUES PER ALPHA HELIX . 0 2 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 . 1 0 1 0 0 1 1 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 0 128 0, 0.0 2,-0.5 0, 0.0 0, 0.0 0.000 360.0 360.0 360.0 166.5 -11.8 -3.9 6.9 2 2 A Q - 0 0 181 2,-0.0 2,-0.6 0, 0.0 0, 0.0 -0.994 360.0-163.6-112.1 122.8 -11.5 -3.5 3.1 3 3 A I - 0 0 74 -2,-0.5 2,-0.1 6,-0.0 0, 0.0 -0.937 4.6-152.3-115.6 115.0 -10.0 -0.2 2.3 4 4 A T - 0 0 92 -2,-0.6 3,-0.3 1,-0.1 -2,-0.0 -0.376 16.0-130.5 -79.3 168.0 -10.3 1.3 -1.2 5 5 A L S S+ 0 0 119 1,-0.2 -1,-0.1 -2,-0.1 -2,-0.0 0.101 74.5 107.5-117.3 24.1 -7.6 3.6 -2.5 6 6 A W S S+ 0 0 234 2,-0.1 2,-0.3 3,-0.0 -1,-0.2 0.806 91.9 30.9 -69.9 -28.6 -9.5 6.6 -3.9 7 7 A Q S S- 0 0 162 -3,-0.3 0, 0.0 1,-0.0 0, 0.0 -0.805 111.1 -76.7-119.7 165.9 -8.3 8.6 -0.9 8 8 A R - 0 0 203 -2,-0.3 2,-2.4 1,-0.1 -2,-0.1 -0.445 49.0-119.2 -59.7 129.5 -5.1 8.2 1.2 9 9 A P + 0 0 25 0, 0.0 15,-2.8 0, 0.0 2,-0.4 -0.412 48.4 167.2 -78.8 74.6 -5.5 5.2 3.5 10 10 A I E +A 23 0A 69 -2,-2.4 2,-0.3 13,-0.2 13,-0.2 -0.716 8.6 179.2 -91.3 129.3 -5.2 7.0 6.8 11 11 A V E -A 22 0A 14 11,-3.0 11,-2.5 -2,-0.4 2,-0.4 -0.862 30.6-105.1-128.3 162.4 -6.2 5.0 9.8 12 12 A T E -A 21 0A 66 -2,-0.3 55,-1.5 9,-0.2 2,-0.3 -0.767 36.0-172.9 -90.9 132.6 -6.4 5.4 13.6 13 13 A I E -AB 20 66A 2 7,-2.9 7,-2.8 -2,-0.4 2,-0.5 -0.874 16.3-144.9-120.2 154.4 -3.8 3.8 15.7 14 14 A K E +AB 19 65A 101 51,-2.6 51,-2.6 -2,-0.3 2,-0.3 -0.990 28.3 161.8-122.8 122.1 -3.4 3.4 19.4 15 15 A I E > -AB 18 64A 1 3,-2.5 3,-0.8 -2,-0.5 49,-0.1 -0.994 67.1 -5.8-145.3 130.6 0.1 3.6 20.8 16 16 A G T 3 S- 0 0 60 47,-0.5 21,-0.1 -2,-0.3 -1,-0.1 0.874 127.0 -59.4 48.2 47.8 1.2 4.2 24.4 17 17 A G T 3 S+ 0 0 79 1,-0.2 2,-0.4 -3,-0.0 -1,-0.2 0.872 116.1 116.1 47.5 42.9 -2.4 5.0 25.4 18 18 A Q E < -A 15 0A 80 -3,-0.8 -3,-2.5 2,-0.0 2,-0.4 -0.995 62.4-134.8-135.7 134.3 -2.5 7.8 22.8 19 19 A L E +A 14 0A 123 -2,-0.4 2,-0.3 -5,-0.2 -5,-0.2 -0.803 33.3 170.0 -90.4 133.8 -4.7 7.9 19.7 20 20 A K E -A 13 0A 17 -7,-2.8 -7,-2.9 -2,-0.4 2,-0.4 -0.915 31.3-124.3-138.2 162.0 -3.0 8.9 16.4 21 21 A E E +A 12 0A 93 -2,-0.3 2,-0.3 -9,-0.2 62,-0.3 -0.891 34.2 171.3-104.4 142.3 -3.6 9.0 12.7 22 22 A A E -A 11 0A 0 -11,-2.5 -11,-3.0 -2,-0.4 2,-0.4 -0.994 32.0-113.8-153.1 156.6 -1.2 7.2 10.3 23 23 A L E -Ac 10 84A 37 60,-2.5 62,-2.9 -2,-0.3 2,-0.9 -0.716 22.5-132.6 -94.6 125.6 -0.9 6.3 6.6 24 24 A L E - c 0 85A 22 -15,-2.8 2,-0.7 -2,-0.4 62,-0.2 -0.710 36.6-175.2 -76.3 109.7 -1.0 2.6 5.6 25 25 A N > - 0 0 51 60,-2.9 3,-1.8 -2,-0.9 62,-0.3 -0.842 27.6-179.3-124.8 97.3 2.0 2.8 3.3 26 26 A T T 3 S+ 0 0 72 -2,-0.7 -1,-0.1 1,-0.3 60,-0.1 0.609 86.1 63.8 -68.8 -13.1 3.0 -0.3 1.3 27 27 A G T 3 S+ 0 0 67 59,-0.0 2,-0.5 60,-0.0 -1,-0.3 0.444 91.2 81.4 -84.7 -2.9 5.9 1.6 -0.2 28 28 A A < - 0 0 19 -3,-1.8 59,-2.9 57,-0.2 60,-0.2 -0.911 59.5-164.0-110.9 127.8 7.4 1.9 3.3 29 29 A D S S+ 0 0 94 -2,-0.5 59,-1.6 57,-0.2 2,-0.2 0.881 76.2 40.7 -70.2 -39.3 9.5 -0.9 4.9 30 30 A D S S- 0 0 56 57,-0.2 2,-0.5 56,-0.2 57,-0.1 -0.675 79.1-116.7-116.4 162.0 9.2 0.5 8.4 31 31 A T - 0 0 0 43,-0.4 45,-2.7 -2,-0.2 2,-0.5 -0.843 32.1-175.4 -98.0 123.9 6.7 2.3 10.7 32 32 A V E -dE 76 84A 13 52,-1.8 52,-2.7 -2,-0.5 2,-0.4 -0.985 2.0-178.6-127.0 124.9 7.8 5.8 11.7 33 33 A L E -d 77 0A 0 43,-2.9 45,-1.9 -2,-0.5 2,-0.3 -0.962 15.2-143.2-126.3 142.4 5.8 7.9 14.1 34 34 A E S S+ 0 0 52 -2,-0.4 49,-0.1 1,-0.2 43,-0.0 -0.708 74.3 8.9 -96.0 150.4 6.4 11.5 15.4 35 35 A E S S+ 0 0 153 -2,-0.3 2,-0.4 1,-0.2 -1,-0.2 0.883 82.8 131.1 48.2 53.9 5.8 12.8 18.9 36 36 A V - 0 0 9 -3,-0.3 2,-0.7 2,-0.0 -1,-0.2 -0.977 48.7-143.1-125.0 142.4 5.1 9.6 20.8 37 37 A N - 0 0 134 -2,-0.4 0, 0.0 -21,-0.1 0, 0.0 -0.950 22.3-174.4-107.3 111.4 6.9 8.9 24.1 38 38 A L - 0 0 9 -2,-0.7 2,-0.1 2,-0.1 -2,-0.0 -0.890 18.9-124.0-106.5 140.3 7.7 5.2 24.3 39 39 A P + 0 0 116 0, 0.0 2,-0.1 0, 0.0 -23,-0.0 -0.416 60.5 15.1 -79.5 155.8 9.2 3.6 27.4 40 40 A G S S- 0 0 64 -2,-0.1 -2,-0.1 19,-0.0 2,-0.0 -0.284 94.9 -11.1 92.4-167.3 12.3 1.6 27.8 41 41 A R + 0 0 230 -2,-0.1 19,-0.4 19,-0.0 2,-0.3 -0.272 54.1 167.1 -77.8 156.7 15.4 0.9 25.7 42 42 A W - 0 0 121 17,-0.1 17,-0.2 -2,-0.0 15,-0.0 -0.924 22.2-139.8-152.5 165.5 15.9 1.8 22.1 43 43 A K E -F 58 0A 115 15,-1.4 15,-3.2 -2,-0.3 13,-0.1 -0.981 31.5-100.5-131.9 149.8 18.9 1.9 19.7 44 44 A P E -F 57 0A 82 0, 0.0 2,-0.3 0, 0.0 13,-0.2 -0.324 37.3-170.9 -62.5 147.6 19.6 4.6 17.0 45 45 A K E -F 56 0A 65 11,-2.0 11,-2.6 9,-0.0 2,-0.5 -0.985 17.3-137.9-140.4 135.6 18.7 3.6 13.4 46 46 A L E +F 55 0A 104 -2,-0.3 2,-0.2 9,-0.2 9,-0.2 -0.858 30.7 175.6 -93.3 124.2 19.5 5.6 10.2 47 47 A I E +F 54 0A 32 7,-2.9 7,-2.6 -2,-0.5 2,-0.4 -0.765 45.5 22.8-122.5 171.2 16.7 5.8 7.7 48 48 A G E -F 53 0A 71 -2,-0.2 5,-0.2 5,-0.2 3,-0.1 -0.629 57.5-173.2 77.5-127.4 16.1 7.5 4.4 49 49 A G E > +F 52 0A 23 3,-1.4 3,-1.4 -2,-0.4 2,-0.7 0.040 40.6 118.3 129.9 -26.4 19.5 8.1 2.8 50 50 A I T 3 S- 0 0 181 1,-0.3 -1,-0.3 0, 0.0 0, 0.0 -0.625 101.0 -1.0 -79.8 110.8 18.8 10.2 -0.3 51 51 A G T 3 S- 0 0 93 -2,-0.7 -1,-0.3 -3,-0.1 2,-0.2 0.409 144.8 -34.7 87.9 -1.0 20.7 13.4 0.4 52 52 A G E < S-F 49 0A 41 -3,-1.4 -3,-1.4 2,-0.0 2,-0.2 -0.583 76.1 -83.6 131.7 163.1 21.7 12.1 3.8 53 53 A F E -F 48 0A 128 -2,-0.2 2,-0.4 -5,-0.2 -5,-0.2 -0.642 28.2-135.7 -98.7 158.8 20.2 9.8 6.5 54 54 A V E -F 47 0A 64 -7,-2.6 -7,-2.9 -2,-0.2 2,-0.4 -0.955 18.1-136.2-111.7 131.1 17.8 10.7 9.3 55 55 A K E +F 46 0A 151 -2,-0.4 2,-0.3 -9,-0.2 -9,-0.2 -0.747 31.5 167.6 -88.9 133.0 18.5 9.3 12.7 56 56 A V E -F 45 0A 6 -11,-2.6 -11,-2.0 -2,-0.4 2,-0.5 -0.833 38.4-102.5-134.3 170.8 15.6 7.9 14.6 57 57 A R E -FG 44 77A 90 20,-2.5 20,-2.6 -2,-0.3 2,-0.6 -0.885 30.2-146.5 -98.7 124.5 15.0 5.8 17.7 58 58 A Q E -FG 43 76A 30 -15,-3.2 -15,-1.4 -2,-0.5 2,-0.5 -0.805 14.5-172.0 -94.2 119.9 14.2 2.2 17.1 59 59 A Y E - G 0 75A 8 16,-2.7 16,-2.7 -2,-0.6 3,-0.4 -0.944 12.9-147.1-109.4 128.3 11.8 0.6 19.7 60 60 A D E + 0 0 78 -2,-0.5 14,-0.2 -19,-0.4 13,-0.0 -0.633 67.0 7.4 -95.9 155.1 11.2 -3.1 19.4 61 61 A Q E S+ 0 0 158 -2,-0.2 -1,-0.2 1,-0.2 13,-0.2 0.843 78.5 175.8 50.8 43.9 8.2 -5.3 20.2 62 62 A V E - G 0 73A 12 11,-2.4 11,-1.7 -3,-0.4 2,-0.4 -0.656 31.6-125.0 -80.2 126.6 5.9 -2.2 20.8 63 63 A P E + G 0 72A 96 0, 0.0 -47,-0.5 0, 0.0 2,-0.3 -0.615 41.5 168.2 -70.3 125.3 2.3 -3.0 21.5 64 64 A I E -BG 15 71A 5 7,-2.7 7,-3.0 -2,-0.4 2,-0.5 -0.990 27.5-144.4-138.0 147.5 0.2 -1.1 19.0 65 65 A E E -BG 14 70A 45 -51,-2.6 -51,-2.6 -2,-0.3 2,-0.5 -0.962 15.1-178.4-114.4 127.0 -3.5 -1.2 18.0 66 66 A I E > S-BG 13 69A 2 3,-2.3 3,-1.2 -2,-0.5 -53,-0.2 -0.975 76.3 -23.6-127.4 113.3 -4.6 -0.6 14.3 67 67 A C T 3 S- 0 0 62 -55,-1.5 -1,-0.1 -2,-0.5 3,-0.1 0.904 128.4 -48.9 48.0 48.9 -8.3 -0.6 13.6 68 68 A G T 3 S+ 0 0 57 1,-0.2 2,-0.6 -54,-0.0 -1,-0.3 0.670 110.7 124.1 66.6 16.9 -8.9 -2.8 16.7 69 69 A H E < - G 0 66A 88 -3,-1.2 -3,-2.3 2,-0.0 2,-0.6 -0.958 51.6-151.8-105.5 111.9 -6.1 -5.3 15.8 70 70 A K E + G 0 65A 174 -2,-0.6 2,-0.3 -5,-0.2 -5,-0.2 -0.768 31.4 157.4 -82.5 117.9 -3.7 -5.5 18.8 71 71 A V E - G 0 64A 21 -7,-3.0 -7,-2.7 -2,-0.6 2,-0.4 -0.835 35.4-126.7-134.2 176.5 -0.3 -6.4 17.4 72 72 A I E + G 0 63A 97 -2,-0.3 2,-0.3 -9,-0.2 -11,-0.1 -0.983 41.6 127.0-128.7 134.0 3.4 -6.1 18.3 73 73 A G E - G 0 62A 11 -11,-1.7 -11,-2.4 -2,-0.4 2,-0.2 -0.992 56.1 -64.6-171.9 175.4 6.2 -4.7 16.2 74 74 A T E - 0 0 42 -2,-0.3 2,-0.4 -13,-0.2 -43,-0.4 -0.510 42.9-167.8 -71.8 132.4 9.1 -2.3 15.7 75 75 A V E - G 0 59A 0 -16,-2.7 -16,-2.7 -2,-0.2 2,-0.5 -0.994 10.0-150.8-123.4 127.3 8.3 1.4 15.8 76 76 A L E -dG 32 58A 1 -45,-2.7 -43,-2.9 -2,-0.4 2,-0.5 -0.825 11.6-156.2 -95.3 131.9 10.7 4.0 14.7 77 77 A V E +dG 33 57A 7 -20,-2.6 -20,-2.5 -2,-0.5 -43,-0.2 -0.960 43.5 89.8-113.5 124.0 10.2 7.3 16.6 78 78 A G S S- 0 0 14 -45,-1.9 -22,-0.1 -2,-0.5 2,-0.1 -0.969 76.8 -36.7 170.5 177.2 11.4 10.4 14.8 79 79 A P + 0 0 95 0, 0.0 3,-0.1 0, 0.0 -46,-0.0 -0.371 57.1 162.6 -64.8 135.4 10.6 13.3 12.5 80 80 A T - 0 0 31 1,-0.1 3,-0.1 -2,-0.1 -46,-0.1 -0.950 46.8-127.8-153.3 136.4 8.3 12.4 9.6 81 81 A P S S- 0 0 142 0, 0.0 2,-0.3 0, 0.0 -1,-0.1 0.889 101.9 -1.2 -49.7 -41.9 6.1 14.5 7.2 82 82 A F S S- 0 0 89 -3,-0.1 -50,-0.1 -50,-0.1 -60,-0.1 -0.983 91.8 -92.8-146.8 147.6 3.2 12.2 8.2 83 83 A N - 0 0 8 -2,-0.3 -60,-2.5 -62,-0.3 2,-0.4 -0.360 46.8-157.1 -58.2 137.4 3.0 9.2 10.5 84 84 A V E -cE 23 32A 21 -52,-2.7 -52,-1.8 -62,-0.2 2,-0.7 -0.983 20.6-157.0-129.9 127.4 3.5 6.0 8.5 85 85 A I E -c 24 0A 0 -62,-2.9 -60,-2.9 -2,-0.4 -57,-0.2 -0.922 31.4-164.3 -93.3 114.1 2.5 2.4 9.1 86 86 A G >> - 0 0 0 -2,-0.7 4,-1.9 -62,-0.2 3,-1.2 -0.235 37.1 -84.2 -94.1-176.1 4.9 0.4 7.0 87 87 A R H 3> S+ 0 0 118 -59,-2.9 4,-2.5 -62,-0.3 5,-0.3 0.812 119.1 71.2 -59.2 -31.8 5.0 -3.2 5.8 88 88 A N H 3> S+ 0 0 37 -59,-1.6 4,-0.6 1,-0.2 -1,-0.3 0.840 109.5 32.3 -56.9 -36.1 6.5 -4.4 9.1 89 89 A L H <> S+ 0 0 0 -3,-1.2 4,-1.9 2,-0.2 -1,-0.2 0.762 111.8 62.7 -90.6 -31.0 3.2 -3.8 10.9 90 90 A M H X>S+ 0 0 10 -4,-1.9 5,-2.9 1,-0.2 4,-0.5 0.886 101.9 52.4 -60.8 -36.1 0.9 -4.6 8.0 91 91 A T H ><5S+ 0 0 90 -4,-2.5 3,-0.7 3,-0.2 -1,-0.2 0.903 106.8 54.4 -63.5 -39.4 2.2 -8.2 8.0 92 92 A Q H 3<5S+ 0 0 106 -4,-0.6 -2,-0.2 -5,-0.3 -1,-0.2 0.869 110.7 43.7 -61.7 -41.1 1.4 -8.4 11.8 93 93 A I H 3<5S- 0 0 34 -4,-1.9 -1,-0.2 2,-0.1 -2,-0.2 0.519 115.7-117.0 -82.0 -3.8 -2.3 -7.3 11.2 94 94 A G T <<5 + 0 0 56 -3,-0.7 2,-0.3 -4,-0.5 -3,-0.2 0.775 53.4 169.5 73.0 29.8 -2.4 -9.7 8.2 95 95 A C < + 0 0 54 -5,-2.9 2,-0.3 -6,-0.2 -1,-0.2 -0.589 6.8 178.5 -76.6 129.1 -3.0 -6.8 5.8 96 96 A T - 0 0 99 -2,-0.3 2,-0.4 2,-0.0 -5,-0.0 -0.881 32.0-117.7-127.2 159.7 -2.8 -7.7 2.1 97 97 A L - 0 0 121 -2,-0.3 2,-0.4 -71,-0.0 -2,-0.0 -0.854 39.0-174.1 -91.5 134.8 -3.1 -6.0 -1.3 98 98 A N 0 0 126 -2,-0.4 -2,-0.0 0, 0.0 0, 0.0 -0.995 360.0 360.0-138.2 131.1 -6.0 -7.6 -3.4 99 99 A F 0 0 259 -2,-0.4 -2,-0.0 0, 0.0 0, 0.0 -0.957 360.0 360.0-154.4 360.0 -7.4 -7.2 -6.9