Entering edit mode
2.7 years ago
Mo
▴
920
Hello,
I would like to know how once could calculate positive and negative for a given sequence? The PDB of the protein is 1ak4. It has two chain A and B. I am looking to find a way that I can easily extract the interference residue and assign them a + or negative.
I have checked and I found I can get to know where two sequence are interfering using pymol ! but I still dont know how to extract only those part like the output I showed. also I still dont know how to assign the positive and negative , I guess this is something to do with PSSM
Lets say my seq is this
>seq A
MVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
>seq D
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMY
I know the answer would be like that but I dont know how to calculate it
# Get Interface Residues
# PDB file ./pdb/1AK4.pdb
# Target chain : A
# Interacting chains : D
# Cut-off for surface: 5.0 Percentage
# Cut-off for interface 1.0 Angstrom^2
#
ITF 1 - 1 A MET 1 232.39 119.70
ITF 2 - 1 A VAL 2 111.00 73.30
ITF 3 - 1 A ASN 3 31.23 21.70
ITF 4 - 1 A PRO 4 15.13 11.10
ITF 5 - 1 A THR 5 17.18 12.30
ITF 6 - 0 A VAL 6 0.00 0.00
ITF 7 - 1 A PHE 7 21.11 10.60
ITF 8 - 0 A PHE 8 0.71 0.40
ITF 9 - 1 A ASP 9 35.64 25.40
ITF 10 - 0 A ILE 10 3.62 2.10
ITF 11 - 0 A ALA 11 3.81 3.50
ITF 12 - 1 A VAL 12 9.11 6.00
ITF 13 - 1 A ASP 13 82.19 58.50
ITF 14 - 1 A GLY 14 61.40 76.70
ITF 15 - 1 A GLU 15 108.42 62.90
ITF 16 - 1 A PRO 16 125.11 91.90
ITF 17 - 1 A LEU 17 58.38 32.70
ITF 18 - 1 A GLY 18 23.67 29.50
ITF 19 - 1 A ARG 19 110.75 46.40
ITF 20 - 0 A VAL 20 0.97 0.60
ITF 21 - 1 A SER 21 7.95 6.80
ITF 22 - 0 A PHE 22 0.36 0.20
ITF 23 - 1 A GLU 23 36.17 21.00
ITF 24 - 0 A LEU 24 0.00 0.00
ITF 25 - 1 A PHE 25 29.45 14.80
ITF 26 - 1 A ALA 26 21.34 19.80
ITF 27 - 1 A ASP 27 76.78 54.70
ITF 28 - 1 A LYS 28 85.06 42.40
ITF 29 - 0 A VAL 29 0.16 0.10
ITF 30 - 1 A PRO 30 71.57 52.60
ITF 31 - 1 A LYS 31 66.66 33.20
ITF 32 - 0 A THR 32 0.26 0.20
ITF 33 - 0 A ALA 33 0.26 0.20
ITF 34 - 1 A GLU 34 64.23 37.30
ITF 35 - 0 A ASN 35 0.15 0.10
ITF 36 - 0 A PHE 36 0.14 0.10
ITF 37 - 1 A ARG 37 31.48 13.20
ITF 38 - 0 A ALA 38 0.00 0.00
ITF 39 - 0 A LEU 39 0.69 0.40
ITF 40 - 0 A SER 40 1.81 1.60
ITF 41 - 1 A THR 41 48.13 34.60
ITF 42 - 1 A GLY 42 32.18 40.20
ITF 43 - 1 A GLU 43 101.95 59.20
ITF 44 - 1 A LYS 44 94.28 47.00
ITF 45 - 1 A GLY 45 75.09 93.70
ITF 46 - 1 A PHE 46 66.16 33.20
ITF 47 - 1 A GLY 47 13.70 17.10
ITF 48 - 0 A TYR 48 0.17 0.10
ITF 49 - 1 A LYS 49 130.62 65.00
ITF 50 - 1 A GLY 50 55.26 69.00
ITF 51 - 0 A SER 51 5.39 4.60
ITF 52 - 1 A CYS 52 28.52 21.20
ITF 53 - 0 A PHE 53 1.64 0.80
ITF 54 - 1 A HIS 54 35.01 19.10
ITF 55 + 1 A ARG 55 84.15 35.20
ITF 56 - 0 A ILE 56 0.00 0.00
ITF 57 + 1 A ILE 57 16.16 9.20
ITF 58 - 1 A PRO 58 52.14 38.30
ITF 59 - 1 A GLY 59 49.66 62.00
ITF 60 + 1 A PHE 60 47.04 23.60
ITF 61 + 0 A MET 61 3.30 1.70
ITF 62 - 0 A CYS 62 0.00 0.00
ITF 63 + 1 A GLN 63 22.48 12.60
ITF 64 - 0 A GLY 64 0.05 0.10
ITF 65 - 0 A GLY 65 0.00 0.00
ITF 66 - 0 A ASP 66 2.47 1.80
ITF 67 - 1 A PHE 67 28.81 14.40
ITF 68 - 1 A THR 68 58.83 42.20
ITF 69 + 1 A ARG 69 132.04 55.30
ITF 70 - 1 A HIS 70 101.90 55.70
ITF 71 + 1 A ASN 71 87.69 60.90
ITF 72 + 1 A GLY 72 23.48 29.30
ITF 73 + 1 A THR 73 84.99 61.00
ITF 74 - 1 A GLY 74 12.74 15.90
ITF 75 - 1 A GLY 75 6.15 7.70
ITF 76 - 1 A LYS 76 59.66 29.70
ITF 77 - 0 A SER 77 0.66 0.60
ITF 78 - 1 A ILE 78 32.66 18.70
ITF 79 - 1 A TYR 79 91.45 43.00
ITF 80 - 1 A GLY 80 47.73 59.60
ITF 81 - 1 A GLU 81 102.19 59.30
ITF 82 - 1 A LYS 82 94.01 46.80
ITF 83 - 1 A PHE 83 10.82 5.40
ITF 84 - 1 A GLU 84 74.34 43.20
ITF 85 - 1 A ASP 85 23.96 17.10
ITF 86 - 1 A GLU 86 48.02 27.90
ITF 87 - 1 A ASN 87 35.75 24.80
ITF 88 - 1 A PHE 88 78.19 39.20
ITF 89 - 1 A ILE 89 113.59 64.90
ITF 90 - 1 A LEU 90 45.99 25.70
ITF 91 - 1 A LYS 91 118.58 59.10
ITF 92 - 0 A HIS 92 1.38 0.80
ITF 93 - 1 A THR 93 71.64 51.40
ITF 94 - 1 A GLY 94 9.43 11.80
ITF 95 - 1 A PRO 95 80.39 59.10
ITF 96 - 1 A GLY 96 4.06 5.10
ITF 97 - 1 A ILE 97 16.73 9.60
ITF 98 - 0 A LEU 98 0.00 0.00
ITF 99 - 0 A SER 99 0.00 0.00
ITF 100 - 0 A MET 100 0.24 0.10
ITF 101 + 1 A ALA 101 9.47 8.80
ITF 102 + 1 A ASN 102 29.96 20.80
ITF 103 + 1 A ALA 103 97.86 90.70
ITF 104 - 1 A GLY 104 24.19 30.20
ITF 105 - 1 A PRO 105 118.02 86.70
ITF 106 - 1 A ASN 106 84.87 59.00
ITF 107 - 1 A THR 107 41.23 29.60
ITF 108 - 0 A ASN 108 0.14 0.10
ITF 109 - 1 A GLY 109 4.29 5.40
ITF 110 - 0 A SER 110 0.01 0.00
ITF 111 + 1 A GLN 111 22.51 12.60
ITF 112 - 0 A PHE 112 0.00 0.00
ITF 113 + 0 A PHE 113 6.90 3.50
ITF 114 - 0 A ILE 114 1.14 0.70
ITF 115 - 0 A CYS 115 0.00 0.00
ITF 116 - 1 A THR 116 17.70 12.70
ITF 117 - 1 A ALA 117 28.62 26.50
ITF 118 - 1 A LYS 118 108.98 54.30
ITF 119 - 0 A THR 119 0.80 0.60
ITF 120 - 1 A GLU 120 86.73 50.40
ITF 121 + 1 A TRP 121 151.00 60.60
ITF 122 + 1 A LEU 122 15.56 8.70
ITF 123 - 1 A ASP 123 53.43 38.10
ITF 124 - 1 A GLY 124 42.01 52.40
ITF 125 - 1 A LYS 125 122.96 61.20
ITF 126 + 1 A HIS 126 32.32 17.70
ITF 127 - 0 A VAL 127 0.16 0.10
ITF 128 - 0 A VAL 128 3.64 2.40
ITF 129 - 0 A PHE 129 0.00 0.00
ITF 130 - 0 A GLY 130 0.00 0.00
ITF 131 - 1 A LYS 131 88.14 43.90
ITF 132 - 1 A VAL 132 18.18 12.00
ITF 133 - 1 A LYS 133 111.81 55.70
ITF 134 - 1 A GLU 134 122.67 71.20
ITF 135 - 1 A GLY 135 14.00 17.50
ITF 136 - 1 A MET 136 46.37 23.90
ITF 137 - 1 A ASN 137 97.69 67.90
ITF 138 - 1 A ILE 138 19.26 11.00
ITF 139 - 0 A VAL 139 0.00 0.00
ITF 140 - 1 A GLU 140 74.71 43.40
ITF 141 - 1 A ALA 141 18.56 17.20
ITF 142 - 0 A MET 142 0.47 0.20
ITF 143 - 1 A GLU 143 29.15 16.90
ITF 144 - 1 A ARG 144 185.75 77.80
ITF 145 - 1 A PHE 145 42.42 21.30
ITF 146 - 1 A GLY 146 15.07 18.80
ITF 147 - 1 A SER 147 34.94 30.00
ITF 148 + 1 A ARG 148 186.08 77.90
ITF 149 + 1 A ASN 149 111.30 77.30
ITF 150 - 0 A GLY 150 1.68 2.10
ITF 151 - 1 A LYS 151 148.82 74.10
ITF 152 - 1 A THR 152 31.11 22.30
ITF 153 - 1 A SER 153 88.96 76.40
ITF 154 - 1 A LYS 154 83.67 41.70
ITF 155 - 1 A LYS 155 135.09 67.30
ITF 156 - 0 A ILE 156 0.73 0.40
ITF 157 - 1 A THR 157 32.40 23.30
ITF 158 - 0 A ILE 158 0.04 0.00
ITF 159 - 1 A ALA 159 54.25 50.30
ITF 160 - 1 A ASP 160 51.02 36.30
ITF 161 - 1 A CYS 161 11.94 8.90
ITF 162 - 1 A GLY 162 9.33 11.70
ITF 163 - 1 A GLN 163 91.38 51.20
ITF 164 - 1 A LEU 164 53.86 30.20
ITF 165 - 1 A GLU 165 213.71 124.10
#
# Interface resdieue = 19
# Interface ALL = 7539.05
# Interface BSA = 473.49
# Interface Polar BSA = 170.53
# Interface Non-Polar BSA = 303.02
# Interface Polarity = 36.02
#
# chain A and resid 101 102 103 111 113 121 122 126 148 149 55 57 60 61 63 69 71 72 73
what do you mean with "calculate positive and negative"?
@JC simply check the output I posted, it is interface residue, some are positive and some are not. If I knew how they are calculated , I would not ask a question. But I believe the question is not complete, I am gonna modify it. thanks
You mean positive and negative electrostatic charge?
@Joe I am not sure, do you think that it is the electrostatic charges? for instance look at 1 - 1 A MET, the - means negative here
At ph7, only 2 amino acids are generally negatively charged (Asp, and Glu) so my guess is the +/- here means something else.
Unfortunately I don't understand what the output data you have given us is showing, so we have no idea how to compute which amino acids should be + and which should be -