Secondary structure calculation program - copyright by David Keith Smith, 1989
1pmy-.pdb
1PMY ELECTRON TRANSFER(CUPROPROTEIN) PSEUDOAZURIN (CUPREDOXIN) (METHYLOBACTERIUM EXTORQUENS, STRAIN AM1)
Sequence length - 123
A A K K hydrogen bonding Ooi's
strk chain/ l amino u & S structure bridge dihedral angles donor acceptor donor acceptor N N
num seq.no t acids t S + patterns partners phi psi omega alpha kappa tco to/energy fr/energy to/energy fr/energy 8 14
1 1 ASP D e 0 0 999.9 165.8 -174.7 999.9 999.9 999.9 0 0.0 30 -2.4 0 0.0 0 0.0 5 22
2 2 GLU E E E Aa - 30 0 -122.1 126.2 -175.5 -164.7 999.9 163.5 0 0.0 0 0.0 0 0.0 0 0.0 7 28
3 3 VAL V E E Aa - 31 0 -107.8 140.1 178.3 -135.1 16.3 147.9 30 -2.5 32 -3.1 0 0.0 0 0.0 8 34
4 4 ALA A E E Aa - 32 0 -104.6 139.5 176.6 -173.1 17.3 153.6 0 0.0 0 0.0 0 0.0 0 0.0 8 35
5 5 VAL V E E Aa - 33 0 -130.0 126.3 179.1 -139.5 16.8 167.2 32 -2.3 34 -3.2 0 0.0 0 0.0 11 51
6 6 LYS K E E AaB - 34 19 -90.1 139.7 175.1 -140.3 4.9 138.3 19 -2.2 19 -2.0 0 0.0 8 -0.7 11 48
7 7 MET M E E A B - 0 18 -101.0 108.9 -173.1 -176.4 36.4 155.2 34 -2.7 37 -2.1 0 0.0 0 0.0 16 54
8 8 LEU L E E A B - 0 17 -121.8 143.6 171.8 -154.6 43.7 152.9 17 -2.9 17 -1.8 6 -0.7 0 0.0 14 43
9 9 ASN N E E A * S+ 0 0 -69.1 -40.9 -177.8 17.1 99.4 34.0 0 0.0 16 -2.7 0 0.0 0 0.0 8 38
10 10 SER S E E A B S+ 0 15 -139.3 126.5 -178.2 112.5 86.1 174.3 0 0.0 0 0.0 0 0.0 0 0.0 8 28
11 11 GLY G E E A B> T - 0 14 -166.9 -163.9 -180.0 -14.7 68.1 150.7 14 -2.2 14 -2.5 0 0.0 0 0.0 11 28
12 12 PRO P T T 3 TS+ 0 0 -58.5 120.1 -179.2 21.9 130.9 113.7 0 0.0 0 0.0 0 0.0 0 0.0 6 26
13 13 GLY G T T 3 TS- 0 0 103.3 -9.4 178.5 -91.5 120.2 78.3 0 0.0 0 0.0 0 0.0 0 0.0 5 30
14 14 GLY G E E AB < TS+ 11 0 115.1 -146.4 -176.8 12.4 80.9 152.6 11 -2.5 11 -2.2 0 0.0 0 0.0 7 28
15 15 MET M E E AB S+ 10 0 -77.9 139.4 175.2 10.8 115.8 124.3 0 0.0 0 0.0 0 0.0 0 0.0 9 35
16 16 MET M E E A* S+ 0 0 60.0 76.4 -178.1 155.8 86.7 8.9 9 -2.7 0 0.0 0 0.0 0 0.0 13 46
17 17 VAL V E E AB - 8 0 -132.6 156.1 173.7 -133.8 45.1 151.8 8 -1.8 8 -2.9 0 0.0 0 0.0 16 52
18 18 PHE F E E AB - 7 0 -99.0 142.9 177.4 -124.2 36.8 152.9 0 0.0 0 0.0 0 0.0 0 0.0 13 56
19 19 ASP D E E AB S+ 6 0 -138.2 114.4 -1.5 26.1 101.4 159.0 6 -2.0 6 -2.2 0 0.0 0 0.0 11 43
20 20 PRO P S S S- 0 0 -75.4 155.9 -178.9 -173.7 77.6 52.4 0 0.0 0 0.0 0 0.0 0 0.0 8 47
21 21 ALA A S e S+ 0 0 -90.6 -15.2 177.7 52.6 75.7 57.5 0 0.0 89 -3.3 0 0.0 0 0.0 10 55
22 22 LEU L E E Bc - 89 0 -126.2 118.3 -178.1 -176.8 69.5 172.5 0 0.0 0 0.0 0 0.0 0 0.0 10 46
23 23 VAL V E E Bc - 90 0 -120.2 127.3 175.9 -159.1 13.5 171.6 89 -2.2 91 -2.9 0 0.0 25 -0.5 9 49
24 24 ARG R E E Bc + 91 0 -103.7 121.2 -176.0 168.5 26.5 154.9 0 0.0 0 0.0 0 0.0 0 0.0 8 44
25 25 LEU L E E Bc - 92 0 -130.6 166.6 174.3 -128.3 31.1 151.3 91 -2.9 93 -2.7 23 -0.5 0 0.0 10 38
26 26 LYS K t > T - 0 0 -109.1 155.8 178.2 -81.5 49.6 136.2 0 0.0 29 -2.3 0 0.0 0 0.0 8 28
27 27 PRO P T T 3 TS+ 0 0 -58.7 137.7 -178.1 32.6 122.4 111.0 0 0.0 0 0.0 0 0.0 0 0.0 10 30
28 28 GLY G T T 3 TS+ 0 0 98.3 -21.2 179.7 125.1 92.6 86.9 68 -3.3 0 0.0 0 0.0 0 0.0 8 26
29 29 ASP D e < T - 0 0 -65.5 158.2 173.6 -156.2 44.8 104.0 26 -2.3 68 -2.6 0 0.0 0 0.0 12 32
30 30 SER S E E AaD - 2 67 -127.8 159.0 169.8 -141.7 7.7 150.0 1 -2.4 3 -2.5 0 0.0 0 0.0 12 37
31 31 ILE I E E AaD - 3 66 -116.3 139.2 168.2 -154.0 6.1 173.6 66 -2.3 66 -2.3 0 0.0 33 -0.6 11 47
32 32 LYS K E E AaD - 4 65 -107.8 119.8 179.6 -152.5 13.2 161.4 3 -3.1 5 -2.3 0 0.0 34 -0.5 12 43
33 33 PHE F E E AaD - 5 64 -93.0 123.3 -175.9 -147.9 13.6 147.6 64 -2.8 64 -1.7 31 -0.6 0 0.0 11 53
34 34 LEU L E E Aa - 6 0 -103.0 128.6 178.5 -136.2 13.8 155.5 5 -3.2 7 -2.7 32 -0.5 36 -2.3 11 38
35 35 PRO P + 0 0 -76.7 62.6 177.4 156.3 42.4 109.8 0 0.0 0 0.0 0 0.0 0 0.0 13 35
36 36 THR T S S S+ 0 0 -49.4 -52.4 174.0 24.0 78.6 24.7 34 -2.3 0 0.0 0 0.0 0 0.0 7 31
37 37 ASP D S S S- 0 0 -113.2 147.6 178.6 -118.4 97.9 155.0 7 -2.1 0 0.0 0 0.0 0 0.0 9 31
38 38 LYS K S S S+ 0 0 -77.2 167.0 173.0 52.9 85.8 114.8 0 0.0 0 0.0 0 0.0 0 0.0 9 31
39 39 GLY G S S S+ 0 0 84.2 14.7 177.8 113.0 81.1 49.6 0 0.0 0 0.0 0 0.0 0 0.0 8 35
40 40 HIS H + 0 0 -115.3 154.4 171.8 170.3 34.4 149.0 0 0.0 61 -2.6 0 0.0 0 0.0 14 47
41 41 ASN N - 0 0 -141.5 -171.4 176.3 -119.7 27.8 149.5 0 0.0 0 0.0 0 0.0 0 0.0 15 50
42 42 VAL V + 0 0 -136.6 132.1 179.7 168.5 31.2 171.3 0 0.0 58 -2.6 0 0.0 0 0.0 12 60
43 43 GLU E E E BEA - 77 57 -147.1 141.6 177.4 -105.4 38.0 174.1 77 -2.3 77 -2.9 0 0.0 0 0.0 12 49
44 44 THR T E E BE - 76 0 -58.2 144.6 168.3 -134.3 26.8 110.3 56 -2.7 46 -0.7 0 0.0 0 0.0 13 48
45 45 ILE I e > T - 0 0 -98.6 113.1 -178.1 -118.1 33.6 156.7 75 -2.1 48 -2.4 0 0.0 0 0.0 9 46
46 46 LYS K T T 3 TS+ 0 0 -53.4 136.6 179.7 29.4 100.1 107.6 44 -0.7 0 0.0 0 0.0 0 0.0 5 36
47 47 GLY G T T 3 TS+ 0 0 91.9 -0.1 -179.8 90.0 102.1 70.9 0 0.0 0 0.0 0 0.0 0 0.0 7 33
48 48 MET M S t < TS+ 0 0 -123.8 60.5 179.2 73.3 72.5 119.4 45 -2.4 75 -2.6 0 0.0 0 0.0 15 47
49 49 ALA A S S S- 0 0 -164.9 146.9 177.8 -98.6 82.7 158.7 0 0.0 0 0.0 0 0.0 0 0.0 14 45
50 50 PRO P t > T - 0 0 -68.4 152.3 -177.3 -93.4 55.1 102.0 0 0.0 53 -1.8 0 0.0 0 0.0 12 40
51 51 ASP D T T 3 TS+ 0 0 -67.5 137.5 -177.2 31.9 113.5 118.2 0 0.0 0 0.0 0 0.0 0 0.0 4 29
52 52 GLY G T T 3 TS+ 0 0 100.4 -21.4 177.7 128.2 84.9 82.7 0 0.0 0 0.0 0 0.0 0 0.0 5 24
53 53 ALA A t < T - 0 0 -69.8 142.0 178.3 -114.3 63.7 115.9 50 -1.8 0 0.0 0 0.0 0 0.0 8 37
54 54 ASP D - 0 0 -74.7 149.0 -179.5 -107.1 31.6 121.6 0 0.0 0 0.0 0 0.0 0 0.0 4 29
55 55 TYR Y - 0 0 -79.8 136.0 -179.9 -147.4 34.5 125.5 0 0.0 0 0.0 0 0.0 0 0.0 6 33
56 56 VAL V + 0 0 -109.5 134.5 176.7 160.8 28.0 156.2 0 0.0 44 -2.7 0 0.0 0 0.0 8 43
57 57 LYS K B B A - 43 0 -155.2 102.4 -177.0 -168.0 19.3 138.6 0 0.0 0 0.0 0 0.0 0 0.0 8 37
58 58 THR T - 0 0 -92.0 164.4 177.6 -96.4 27.6 113.6 42 -2.6 0 0.0 0 0.0 0 0.0 9 33
59 59 THR T t > T - 0 0 -86.9 130.8 -179.2 -102.9 46.6 124.2 0 0.0 62 -1.9 0 0.0 0 0.0 7 30
60 60 VAL V T T 3 TS+ 0 0 -54.1 133.3 177.6 10.7 100.6 112.1 0 0.0 0 0.0 0 0.0 0 0.0 8 33
61 61 GLY G T T 3 TS+ 0 0 77.0 5.2 179.3 113.1 102.0 65.0 40 -2.6 0 0.0 0 0.0 0 0.0 10 31
62 62 GLN Q S t < TS- 0 0 -108.2 153.4 174.8 -112.1 72.2 143.5 59 -1.9 0 0.0 0 0.0 0 0.0 10 31
63 63 GLU E - 0 0 -71.6 153.0 -179.9 -172.2 43.9 118.3 0 0.0 0 0.0 0 0.0 0 0.0 8 34
64 64 ALA A E E AD - 33 0 -150.1 147.2 176.6 -148.3 18.3 170.0 33 -1.7 33 -2.8 0 0.0 0 0.0 8 39
65 65 VAL V E E AD - 32 0 -119.9 136.6 176.2 -169.7 8.5 165.3 0 0.0 0 0.0 0 0.0 0 0.0 8 38
66 66 VAL V E E AD - 31 0 -126.2 120.9 177.7 -154.9 9.3 168.7 31 -2.3 31 -2.3 0 0.0 0 0.0 8 48
67 67 LYS K E E AD - 30 0 -93.4 143.7 -176.4 -148.9 11.5 137.3 0 0.0 69 -0.5 0 0.0 0 0.0 8 43
68 68 PHE F e + 0 0 -118.7 121.5 175.7 151.0 32.8 164.9 29 -2.6 28 -3.3 0 0.0 0 0.0 10 43
69 69 ASP D + 0 0 -115.1 -37.0 -177.5 73.6 55.6 39.3 67 -0.5 0 0.0 0 0.0 0 0.0 8 33
70 70 LYS K S S S- 0 0 -79.3 133.7 175.9 -127.9 79.7 128.7 0 0.0 0 0.0 0 0.0 0 0.0 9 35
71 71 GLU E + 0 0 -76.4 155.9 -179.6 71.1 61.0 114.8 0 0.0 0 0.0 0 0.0 0 0.0 14 37
72 72 GLY G E E B F S- 0 92 135.1 -170.2 -174.0 -42.0 82.3 153.1 92 -2.4 92 -2.6 0 0.0 0 0.0 15 44
73 73 VAL V E E B F - 0 91 -104.5 126.6 -176.6 -173.0 46.0 147.4 0 0.0 0 0.0 0 0.0 0 0.0 15 55
74 74 TYR Y E E B F - 0 90 -121.9 138.1 173.8 -159.7 8.3 170.8 90 -2.6 90 -2.5 0 0.0 0 0.0 12 61
75 75 GLY G E E B F - 0 89 -117.9 137.7 179.4 -173.2 13.3 162.5 48 -2.6 45 -2.1 0 0.0 0 0.0 13 65
76 76 PHE F E E BEF - 44 88 -128.4 149.1 175.3 -164.4 4.2 164.1 88 -2.6 88 -2.3 0 0.0 0 0.0 13 69
77 77 LYS K E E BEF - 43 87 -121.3 163.8 165.5 -120.9 28.2 141.8 43 -2.9 43 -2.3 0 0.0 79 -0.6 14 62
78 78 CYS C e - 0 0 -96.1 111.9 -177.5 -142.5 33.8 164.3 86 -2.2 0 0.0 0 0.0 0 0.0 12 57
79 79 ALA A S t > TS+ 0 0 -47.9 -56.8 -179.4 42.2 94.6 19.5 77 -0.6 82 -1.4 0 0.0 0 0.0 9 38
80 80 PRO P T T 3 TS+ 0 0 -65.1 -25.1 -179.7 39.3 124.3 38.2 0 0.0 0 0.0 0 0.0 0 0.0 8 35
81 81 HIS H T T 3>TS+ 0 0 -113.5 24.9 179.4 109.2 77.1 90.5 0 0.0 86 -2.4 0 0.0 0 0.0 11 41
82 82 TYR Y T T X5TS+ 0 0 -61.8 -42.0 -179.5 52.8 80.9 16.7 79 -1.4 85 -2.5 0 0.0 0 0.0 11 44
83 83 MET M T T 35TS+ 0 0 -64.0 -25.3 174.9 56.3 106.7 41.9 0 0.0 0 0.0 0 0.0 0 0.0 9 32
84 84 MET M T T 35TS- 0 0 -88.3 7.9 175.4 -105.6 123.9 70.1 0 0.0 0 0.0 0 0.0 0 0.0 9 36
85 85 GLY G T T <5T + 0 0 78.3 21.3 -180.0 156.7 62.3 49.7 82 -2.5 87 -1.3 0 0.0 0 0.0 12 48
86 86 MET M e T + 0 0 -130.3 26.9 179.0 125.3 36.1 85.7 0 0.0 99 -1.5 0 0.0 0 0.0 8 34
97 97 ASP D T T 3 TS+ 0 0 -51.8 -43.8 -178.5 40.9 81.2 33.8 0 0.0 0 0.0 0 0.0 0 0.0 7 27
98 98 ASN N T h > 3 TS+ 0 0 -92.7 3.7 178.3 99.8 85.4 72.3 0 0.0 102 -3.0 0 0.0 0 0.0 11 34
99 99 LEU L H H > < TS+ 0 0 -55.8 -51.2 -176.6 45.1 84.2 20.8 96 -1.5 103 -2.6 0 0.0 0 0.0 9 38
100 100 GLU E H H > TS+ 0 0 -63.6 -41.2 176.1 48.1 117.1 24.7 0 0.0 104 -1.5 0 0.0 0 0.0 7 28
101 101 ALA A H H 4 TS+ 0 0 -58.5 -48.1 -174.0 44.8 113.9 24.8 0 0.0 0 0.0 0 0.0 0 0.0 9 26
102 102 ALA A H H < > TS+ 0 0 -68.9 -39.9 -179.1 50.5 112.8 24.6 98 -3.0 105 -1.1 0 0.0 0 0.0 13 43
103 103 LYS K H H < 3 TS+ 0 0 -68.6 -27.9 178.5 62.2 104.0 34.4 99 -2.6 0 0.0 0 0.0 0 0.0 8 41
104 104 SER S T h < 3 TS+ 0 0 -74.8 -13.8 179.0 106.3 74.9 54.3 100 -1.5 0 0.0 0 0.0 0 0.0 6 31
105 105 VAL V t < T - 0 0 -68.1 138.2 -176.4 -136.1 68.5 119.0 102 -1.1 0 0.0 0 0.0 0 0.0 8 34
106 106 GLN Q + 0 0 -99.8 158.1 -178.0 174.0 26.8 134.5 0 0.0 0 0.0 0 0.0 0 0.0 5 29
107 107 HIS H - 0 0 -147.9 173.0 174.0 -69.5 40.9 153.9 0 0.0 0 0.0 0 0.0 0 0.0 6 35
108 108 ASN N h > T - 0 0 -65.4 161.1 -178.3 -99.5 57.6 105.8 0 0.0 112 -2.7 0 0.0 0 0.0 7 22
109 109 LYS K H H > TS+ 0 0 -46.4 -52.2 -179.3 50.5 120.4 33.7 0 0.0 113 -2.2 0 0.0 0 0.0 6 19
110 110 LEU L H H > TS+ 0 0 -60.8 -44.7 178.4 43.5 113.5 26.1 0 0.0 114 -0.8 0 0.0 0 0.0 9 26
111 111 THR T H H > > TS+ 0 0 -70.4 -41.4 -178.4 54.4 112.3 28.4 0 0.0 115 -1.8 0 0.0 114 -0.6 14 41
112 112 GLN Q H H X 3 TS+ 0 0 -58.2 -42.3 -175.2 53.8 105.1 27.1 108 -2.7 116 -2.3 0 0.0 0 0.0 11 35
113 113 LYS K H H < 3 TS+ 0 0 -67.5 -27.8 178.0 49.9 108.4 43.9 109 -2.2 0 0.0 0 0.0 0 0.0 8 32
114 114 ARG R H H X < TS+ 0 0 -76.3 -38.8 -178.6 47.3 111.5 36.8 110 -0.8 118 -0.6 111 -0.6 0 0.0 10 43
115 115 LEU L H H X TS+ 0 0 -72.0 -33.3 -177.0 75.9 95.7 36.3 111 -1.8 119 -3.1 0 0.0 0 0.0 11 52
116 116 ASP D H H X TS+ 0 0 -45.1 -52.2 -179.1 41.3 98.2 29.8 112 -2.3 120 -2.0 0 0.0 0 0.0 8 33
117 117 PRO P H H > TS+ 0 0 -71.4 -24.1 178.3 54.8 113.5 33.2 0 0.0 121 -1.3 0 0.0 0 0.0 8 27
118 118 LEU L H H < TS+ 0 0 -73.9 -44.9 179.7 45.6 109.9 22.0 114 -0.6 0 0.0 0 0.0 0 0.0 11 40
119 119 PHE F H H X > TS+ 0 0 -60.5 -42.4 -177.0 56.8 109.6 26.9 115 -3.1 122 -1.7 0 0.0 123 -1.0 9 40
120 120 ALA A H H < 3 TS+ 0 0 -55.2 -37.2 -179.9 54.6 103.0 34.2 116 -2.0 0 0.0 0 0.0 0 0.0 7 26
121 121 GLN Q T h < 3 TS+ 0 0 -78.1 -0.1 179.1 51.7 105.8 69.6 117 -1.3 0 0.0 0 0.0 0 0.0 6 23
122 122 ILE I T T 4 < T 0 0 -110.9 -18.8 176.9 999.9 999.9 61.2 119 -1.7 0 0.0 0 0.0 0 0.0 5 34
123 123 GLN Q t < T 0 0 -96.7 999.9 999.9 999.9 999.9 52.0 119 -1.0 0 0.0 0 0.0 0 0.0 4 27
1pmy-.pdb
1PMY ELECTRON TRANSFER(CUPROPROTEIN) PSEUDOAZURIN (CUPREDOXIN) (METHYLOBACTERIUM EXTORQUENS, STRAIN AM1)
author author
Kabs/Sand EEEEEEEEEETTEEEEEESSEEEE TT EEEEE SSSS EE TTSS TT B TTS EEEE S EEEEEE STTTTTT EEEEEESS TTHH Kabs/Sand
chirality -------++-+-+++--+-+--+--++------++-+++-+---+++--++---+---++------++-+-------+++++-++-------+++++++ chirality
bends SS SSSSS SSS SS SSSS SSSS SS SSS S S SSSSSS SS SSSS bends
turns TTTT TTTT TTTT TTTT TTTT TTTTTTTT TTTTT turns
5-turns >5555< 5-turns
3-turns >33< >33< >33< >33< >33< >33X33< >33< 3-turns
bridge-2 BBB*BB DDDD A FFFFFF FFFFFF bridge-2
bridge-1 aaaaa BB*BBB cccc aaaaa EE A DDDD EE cccc bridge-1
sheets AAAAAAAAAA AAAAAA BBBB AAAAA BB AAAA BBBBBB BBBBBB sheets
4-turns >>> 4-turns
summary eEEEEEEEEEETTEEEEEESeEEEEtTTeEEEEE SSSS EEeTTtStTTt B tTTt EEEEe S EEEEEEetTTTTTTeEEEEEEeS tThHH summary
sequence DEVAVKMLNSGPGGMMVFDPALVRLKPGDSIKFLPTDKGHNVETIKGMAPDGADYVKTTVGQEAVVKFDKEGVYGFKCAPHYMMGMVALVVVGDKRDNLE sequence
10 20 30 40 50 60 70 80 90 100
author author
Kabs/Sand HHHT HHHHHHHHHHHHTT Kabs/Sand
chirality ++++-+--+++++++++++++ chirality
bends SSSS SSSSSSSSSSSSS bends
turns TTTTT TTTTTTTTTTTTTTTT turns
5-turns 5-turns
3-turns >33< >33< >33< 3-turns
bridge-2 bridge-2
bridge-1 bridge-1
sheets sheets
4-turns 4<<< >>>>X