diff --git a/propka/bonds.py b/propka/bonds.py
index 850c2ed..4d58dec 100644
--- a/propka/bonds.py
+++ b/propka/bonds.py
@@ -3,6 +3,7 @@ from __future__ import division
 from __future__ import print_function
 
 import pickle,sys,os,math,propka.calculations
+import json
 
 import pkg_resources
 from propka.lib import info, warning
@@ -28,11 +29,9 @@ class bondmaker:
         self.max_sq_distance = max(list(self.distances_squared.values())+[self.default_dist_squared])
 
         # protein bonding data
-        self.data_file_name = pkg_resources.resource_filename(__name__, 'protein_bonds.dat')
-
-        data = open(self.data_file_name,'rb')
-        self.protein_bonds = pickle.load(data)
-        data.close()
+        self.data_file_name = pkg_resources.resource_filename(__name__, 'protein_bonds.json')
+        with open(self.data_file_name,'rt') as json_file:
+            self.protein_bonds = json.load(json_file)
 
 
         self.intra_residue_backbone_bonds = {'N': ['CA'],
diff --git a/propka/protein_bonds.dat b/propka/protein_bonds.dat
deleted file mode 100644
index fc6f5d8..0000000
--- a/propka/protein_bonds.dat
+++ /dev/null
@@ -1,568 +0,0 @@
-(dp0
-S'CYS'
-p1
-(dp2
-S'CB'
-p3
-(lp4
-S'CA'
-p5
-aS'SG'
-p6
-asg5
-(lp7
-g3
-asg6
-(lp8
-g3
-aS'SG'
-p9
-assS'GLN'
-p10
-(dp11
-S'CB'
-p12
-(lp13
-S'CA'
-p14
-aS'CG'
-p15
-asg14
-(lp16
-g12
-asg15
-(lp17
-g12
-aS'CD'
-p18
-asg18
-(lp19
-g15
-aS'OE1'
-p20
-aS'NE2'
-p21
-asg21
-(lp22
-g18
-asg20
-(lp23
-g18
-assS'HIS'
-p24
-(dp25
-S'CD2'
-p26
-(lp27
-S'CG'
-p28
-aS'NE2'
-p29
-asS'CB'
-p30
-(lp31
-S'CA'
-p32
-ag28
-asg32
-(lp33
-g30
-asg28
-(lp34
-g30
-aS'ND1'
-p35
-ag26
-asS'CE1'
-p36
-(lp37
-g35
-ag29
-asg35
-(lp38
-g28
-ag36
-asg29
-(lp39
-g26
-ag36
-assS'ASN'
-p40
-(dp41
-S'CB'
-p42
-(lp43
-S'CA'
-p44
-aS'CG'
-p45
-asg44
-(lp46
-g42
-asS'ND2'
-p47
-(lp48
-g45
-asg45
-(lp49
-g42
-aS'OD1'
-p50
-ag47
-asg50
-(lp51
-g45
-assS'VAL'
-p52
-(dp53
-S'CG1'
-p54
-(lp55
-S'CB'
-p56
-asg56
-(lp57
-S'CA'
-p58
-ag54
-aS'CG2'
-p59
-asg58
-(lp60
-g56
-asg59
-(lp61
-g56
-assS'LYS'
-p62
-(dp63
-S'CB'
-p64
-(lp65
-S'CA'
-p66
-aS'CG'
-p67
-asg66
-(lp68
-g64
-asg67
-(lp69
-g64
-aS'CD'
-p70
-asS'CE'
-p71
-(lp72
-g70
-aS'NZ'
-p73
-asg70
-(lp74
-g67
-ag71
-asg73
-(lp75
-g71
-assS'ILE'
-p76
-(dp77
-S'CG1'
-p78
-(lp79
-S'CB'
-p80
-aS'CD1'
-p81
-asg80
-(lp82
-S'CA'
-p83
-ag78
-aS'CG2'
-p84
-asg83
-(lp85
-g80
-asg84
-(lp86
-g80
-asg81
-(lp87
-g78
-assS'PRO'
-p88
-(dp89
-S'CB'
-p90
-(lp91
-S'CA'
-p92
-aS'CG'
-p93
-asg92
-(lp94
-g90
-asS'CD'
-p95
-(lp96
-S'N'
-p97
-ag93
-asg93
-(lp98
-g90
-ag95
-asg97
-(lp99
-g95
-assS'THR'
-p100
-(dp101
-S'CB'
-p102
-(lp103
-S'CA'
-p104
-aS'OG1'
-p105
-aS'CG2'
-p106
-asg104
-(lp107
-g102
-asg106
-(lp108
-g102
-asg105
-(lp109
-g102
-assS'PHE'
-p110
-(dp111
-S'CD2'
-p112
-(lp113
-S'CG'
-p114
-aS'CE2'
-p115
-asS'CB'
-p116
-(lp117
-S'CA'
-p118
-ag114
-asg118
-(lp119
-g116
-asg114
-(lp120
-g116
-aS'CD1'
-p121
-ag112
-asS'CZ'
-p122
-(lp123
-S'CE1'
-p124
-ag115
-asg121
-(lp125
-g114
-ag124
-asg124
-(lp126
-g121
-ag122
-asg115
-(lp127
-g112
-ag122
-assS'ALA'
-p128
-(dp129
-S'CB'
-p130
-(lp131
-S'CA'
-p132
-asg132
-(lp133
-g130
-assS'MET'
-p134
-(dp135
-S'CB'
-p136
-(lp137
-S'CA'
-p138
-aS'CG'
-p139
-asg138
-(lp140
-g136
-asg139
-(lp141
-g136
-aS'SD'
-p142
-asS'CE'
-p143
-(lp144
-g142
-asg142
-(lp145
-g139
-ag143
-assS'ASP'
-p146
-(dp147
-S'CB'
-p148
-(lp149
-S'CA'
-p150
-aS'CG'
-p151
-asg150
-(lp152
-g148
-asg151
-(lp153
-g148
-aS'OD1'
-p154
-aS'OD2'
-p155
-asg155
-(lp156
-g151
-asg154
-(lp157
-g151
-assS'LEU'
-p158
-(dp159
-S'CB'
-p160
-(lp161
-S'CA'
-p162
-aS'CG'
-p163
-asg162
-(lp164
-g160
-asg163
-(lp165
-g160
-aS'CD1'
-p166
-aS'CD2'
-p167
-asg166
-(lp168
-g163
-asg167
-(lp169
-g163
-assS'ARG'
-p170
-(dp171
-S'CB'
-p172
-(lp173
-S'CA'
-p174
-aS'CG'
-p175
-asg174
-(lp176
-g172
-asg175
-(lp177
-g172
-aS'CD'
-p178
-asS'NE'
-p179
-(lp180
-g178
-aS'CZ'
-p181
-asg178
-(lp182
-g175
-ag179
-asg181
-(lp183
-g179
-aS'NH1'
-p184
-aS'NH2'
-p185
-asg184
-(lp186
-g181
-asg185
-(lp187
-g181
-assS'TRP'
-p188
-(dp189
-S'CZ2'
-p190
-(lp191
-S'CE2'
-p192
-aS'CH2'
-p193
-asS'CB'
-p194
-(lp195
-S'CA'
-p196
-aS'CG'
-p197
-asg196
-(lp198
-g194
-asg197
-(lp199
-g194
-aS'CD1'
-p200
-aS'CD2'
-p201
-asg193
-(lp202
-g190
-aS'CZ3'
-p203
-asg192
-(lp204
-g201
-aS'NE1'
-p205
-ag190
-asS'CE3'
-p206
-(lp207
-g201
-ag203
-asg200
-(lp208
-g197
-ag205
-asg201
-(lp209
-g197
-ag192
-ag206
-asg203
-(lp210
-g206
-ag193
-asg205
-(lp211
-g200
-ag192
-assS'GLU'
-p212
-(dp213
-S'OE2'
-p214
-(lp215
-S'CD'
-p216
-asS'CA'
-p217
-(lp218
-S'CB'
-p219
-asS'CG'
-p220
-(lp221
-g219
-ag216
-asg216
-(lp222
-g220
-aS'OE1'
-p223
-ag214
-asg219
-(lp224
-g217
-ag220
-asg223
-(lp225
-g216
-assS'TYR'
-p226
-(dp227
-S'CD2'
-p228
-(lp229
-S'CG'
-p230
-aS'CE2'
-p231
-asS'OH'
-p232
-(lp233
-S'CZ'
-p234
-asS'CB'
-p235
-(lp236
-S'CA'
-p237
-ag230
-asg237
-(lp238
-g235
-asg230
-(lp239
-g235
-aS'CD1'
-p240
-ag228
-asg234
-(lp241
-S'CE1'
-p242
-ag231
-ag232
-asg240
-(lp243
-g230
-ag242
-asg242
-(lp244
-g240
-ag234
-asg231
-(lp245
-g228
-ag234
-assS'SER'
-p246
-(dp247
-S'OG'
-p248
-(lp249
-S'CB'
-p250
-asg250
-(lp251
-S'CA'
-p252
-ag248
-asg252
-(lp253
-g250
-ass.
\ No newline at end of file
diff --git a/propka/protein_bonds.json b/propka/protein_bonds.json
new file mode 100644
index 0000000..b9cd50f
--- /dev/null
+++ b/propka/protein_bonds.json
@@ -0,0 +1,21 @@
+{
+    "CYS": { "CB": [ "CA", "SG" ], "CA": [ "CB" ], "SG": [ "CB", "SG" ] },
+    "GLN": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD" ], "CD": [ "CG", "OE1", "NE2" ], "NE2": [ "CD" ], "OE1": [ "CD" ] },
+    "HIS": { "CD2": [ "CG", "NE2" ], "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "ND1", "CD2" ], "CE1": [ "ND1", "NE2" ], "ND1": [ "CG", "CE1" ], "NE2": [ "CD2", "CE1" ] },
+    "ASN": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "ND2": [ "CG" ], "CG": [ "CB", "OD1", "ND2" ], "OD1": [ "CG" ] },
+    "VAL": { "CG1": [ "CB" ], "CB": [ "CA", "CG1", "CG2" ], "CA": [ "CB" ], "CG2": [ "CB" ] },
+    "LYS": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD" ], "CE": [ "CD", "NZ" ], "CD": [ "CG", "CE" ], "NZ": [ "CE" ] },
+    "ILE": { "CG1": [ "CB", "CD1" ], "CB": [ "CA", "CG1", "CG2" ], "CA": [ "CB" ], "CG2": [ "CB" ], "CD1": [ "CG1" ] },
+    "PRO": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CD": [ "N", "CG" ], "CG": [ "CB", "CD" ], "N": [ "CD" ] },
+    "THR": { "CB": [ "CA", "OG1", "CG2" ], "CA": [ "CB" ], "CG2": [ "CB" ], "OG1": [ "CB" ] },
+    "PHE": { "CD2": [ "CG", "CE2" ], "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD1", "CD2" ], "CZ": [ "CE1", "CE2" ], "CD1": [ "CG", "CE1" ], "CE1": [ "CD1", "CZ" ], "CE2": [ "CD2", "CZ" ] },
+    "ALA": { "CB": [ "CA" ], "CA": [ "CB" ] },
+    "MET": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "SD" ], "CE": [ "SD" ], "SD": [ "CG", "CE" ] },
+    "ASP": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "OD1", "OD2" ], "OD2": [ "CG" ], "OD1": [ "CG" ] },
+    "LEU": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD1", "CD2" ], "CD1": [ "CG" ], "CD2": [ "CG" ] },
+    "ARG": { "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD" ], "NE": [ "CD", "CZ" ], "CD": [ "CG", "NE" ], "CZ": [ "NE", "NH1", "NH2" ], "NH1": [ "CZ" ], "NH2": [ "CZ" ] },
+    "TRP": { "CZ2": [ "CE2", "CH2" ], "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD1", "CD2" ], "CH2": [ "CZ2", "CZ3" ], "CE2": [ "CD2", "NE1", "CZ2" ], "CE3": [ "CD2", "CZ3" ], "CD1": [ "CG", "NE1" ], "CD2": [ "CG", "CE2", "CE3" ], "CZ3": [ "CE3", "CH2" ], "NE1": [ "CD1", "CE2" ] },
+    "GLU": { "OE2": [ "CD" ], "CA": [ "CB" ], "CG": [ "CB", "CD" ], "CD": [ "CG", "OE1", "OE2" ], "CB": [ "CA", "CG" ], "OE1": [ "CD" ] },
+    "TYR": { "CD2": [ "CG", "CE2" ], "OH": [ "CZ" ], "CB": [ "CA", "CG" ], "CA": [ "CB" ], "CG": [ "CB", "CD1", "CD2" ], "CZ": [ "CE1", "CE2", "OH" ], "CD1": [ "CG", "CE1" ], "CE1": [ "CD1", "CZ" ], "CE2": [ "CD2", "CZ" ] },
+    "SER": { "OG": [ "CB" ], "CB": [ "CA", "OG" ], "CA": [ "CB" ] }
+}
\ No newline at end of file