how to calculate positive and negative for a given protein sequence
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Entering edit mode
18 months 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

>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

proteomics • 747 views
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Entering edit mode

what do you mean with "calculate positive and negative"?

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@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

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Entering edit mode

You mean positive and negative electrostatic charge?

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Entering edit mode

@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

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Entering edit mode

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 -