Amino acid dipepetide frequency for Staphylococcus phage phiNM3

Apart from single amino acid frequencies one can also calculate so called amino acid dipeptide frequency.

There is 400 possibilites (441 if we consider Xaa as additional 21st amino acid representing all non-standard or unknown amino acids). Thus, if the dipeptides would be present randomly in proteins each amino acid dipeptide should be present with 0.25% frequency. As it is not the case in the nature, for better visablity all more than expected dipepetides are marked by red, and those which are underrepresented are marked by blue in the table.

All values are presented as per milles (‰), therefore need to be multiplied by 10-3.

For more information see sequence space article on Wikipedia.

AlaCysAspGluPheGlyHisIleLysLeuMetAsnProGlnArgSerThrValTrpTyrXaa
Ala
1.957AlaAla: 1.957 ± 0.635
0.313AlaCys: 0.313 ± 0.136
2.662AlaAsp: 2.662 ± 0.385
3.915AlaGlu: 3.915 ± 0.578
2.818AlaPhe: 2.818 ± 0.593
3.68AlaGly: 3.68 ± 0.502
0.626AlaHis: 0.626 ± 0.196
4.619AlaIle: 4.619 ± 0.618
4.932AlaLys: 4.932 ± 0.53
5.089AlaLeu: 5.089 ± 0.665
1.644AlaMet: 1.644 ± 0.397
3.366AlaAsn: 3.366 ± 0.566
1.801AlaPro: 1.801 ± 0.377
3.132AlaGln: 3.132 ± 0.52
2.74AlaArg: 2.74 ± 0.438
3.445AlaSer: 3.445 ± 0.446
3.132AlaThr: 3.132 ± 0.696
3.132AlaVal: 3.132 ± 0.538
0.47AlaTrp: 0.47 ± 0.197
2.584AlaTyr: 2.584 ± 0.39
0.0AlaXaa: 0.0 ± 0.0
Cys
0.47CysAla: 0.47 ± 0.215
0.078CysCys: 0.078 ± 0.067
0.0CysAsp: 0.0 ± 0.0
0.157CysGlu: 0.157 ± 0.103
0.078CysPhe: 0.078 ± 0.071
0.313CysGly: 0.313 ± 0.141
0.078CysHis: 0.078 ± 0.087
0.626CysIle: 0.626 ± 0.232
0.235CysLys: 0.235 ± 0.148
0.313CysLeu: 0.313 ± 0.166
0.078CysMet: 0.078 ± 0.069
0.235CysAsn: 0.235 ± 0.125
0.157CysPro: 0.157 ± 0.121
0.157CysGln: 0.157 ± 0.127
0.235CysArg: 0.235 ± 0.165
0.391CysSer: 0.391 ± 0.195
0.391CysThr: 0.391 ± 0.139
0.313CysVal: 0.313 ± 0.141
0.078CysTrp: 0.078 ± 0.091
0.235CysTyr: 0.235 ± 0.131
0.0CysXaa: 0.0 ± 0.0
Asp
3.21AspAla: 3.21 ± 0.459
0.157AspCys: 0.157 ± 0.102
4.306AspAsp: 4.306 ± 0.786
5.48AspGlu: 5.48 ± 0.918
3.21AspPhe: 3.21 ± 0.489
5.793AspGly: 5.793 ± 0.869
0.939AspHis: 0.939 ± 0.247
5.167AspIle: 5.167 ± 0.616
5.559AspLys: 5.559 ± 0.69
5.559AspLeu: 5.559 ± 0.645
1.331AspMet: 1.331 ± 0.315
4.384AspAsn: 4.384 ± 0.71
1.644AspPro: 1.644 ± 0.383
0.705AspGln: 0.705 ± 0.193
2.27AspArg: 2.27 ± 0.451
3.053AspSer: 3.053 ± 0.533
2.897AspThr: 2.897 ± 0.629
3.993AspVal: 3.993 ± 0.572
0.548AspTrp: 0.548 ± 0.177
2.818AspTyr: 2.818 ± 0.515
0.0AspXaa: 0.0 ± 0.0
Glu
4.306GluAla: 4.306 ± 0.718
0.313GluCys: 0.313 ± 0.164
3.68GluAsp: 3.68 ± 0.518
6.968GluGlu: 6.968 ± 0.979
2.662GluPhe: 2.662 ± 0.45
2.74GluGly: 2.74 ± 0.474
1.488GluHis: 1.488 ± 0.313
6.263GluIle: 6.263 ± 0.795
7.907GluLys: 7.907 ± 0.982
7.986GluLeu: 7.986 ± 1.012
2.27GluMet: 2.27 ± 0.402
6.107GluAsn: 6.107 ± 0.858
1.566GluPro: 1.566 ± 0.269
3.601GluGln: 3.601 ± 0.574
3.993GluArg: 3.993 ± 0.634
4.463GluSer: 4.463 ± 0.552
3.836GluThr: 3.836 ± 0.943
4.228GluVal: 4.228 ± 0.423
0.783GluTrp: 0.783 ± 0.222
3.758GluTyr: 3.758 ± 0.559
0.0GluXaa: 0.0 ± 0.0
Phe
2.349PheAla: 2.349 ± 0.568
0.078PheCys: 0.078 ± 0.089
2.897PheAsp: 2.897 ± 0.562
3.601PheGlu: 3.601 ± 0.451
0.939PhePhe: 0.939 ± 0.245
2.036PheGly: 2.036 ± 0.373
0.548PheHis: 0.548 ± 0.207
3.288PheIle: 3.288 ± 0.472
4.463PheLys: 4.463 ± 0.686
2.818PheLeu: 2.818 ± 0.36
1.253PheMet: 1.253 ± 0.356
3.758PheAsn: 3.758 ± 0.545
0.861PhePro: 0.861 ± 0.239
0.626PheGln: 0.626 ± 0.246
1.331PheArg: 1.331 ± 0.283
2.897PheSer: 2.897 ± 0.553
2.975PheThr: 2.975 ± 0.517
2.27PheVal: 2.27 ± 0.37
0.157PheTrp: 0.157 ± 0.12
1.331PheTyr: 1.331 ± 0.363
0.0PheXaa: 0.0 ± 0.0
Gly
2.975GlyAla: 2.975 ± 0.613
0.391GlyCys: 0.391 ± 0.166
3.68GlyAsp: 3.68 ± 0.467
3.132GlyGlu: 3.132 ± 0.651
2.74GlyPhe: 2.74 ± 0.532
3.993GlyGly: 3.993 ± 1.112
0.939GlyHis: 0.939 ± 0.213
4.463GlyIle: 4.463 ± 0.78
6.42GlyLys: 6.42 ± 0.721
5.559GlyLeu: 5.559 ± 0.747
1.018GlyMet: 1.018 ± 0.246
3.445GlyAsn: 3.445 ± 0.501
1.331GlyPro: 1.331 ± 0.331
1.644GlyGln: 1.644 ± 0.414
2.74GlyArg: 2.74 ± 0.608
2.427GlySer: 2.427 ± 0.389
2.662GlyThr: 2.662 ± 0.488
3.366GlyVal: 3.366 ± 0.548
0.861GlyTrp: 0.861 ± 0.278
2.662GlyTyr: 2.662 ± 0.604
0.0GlyXaa: 0.0 ± 0.0
His
1.096HisAla: 1.096 ± 0.333
0.157HisCys: 0.157 ± 0.101
1.331HisAsp: 1.331 ± 0.328
1.018HisGlu: 1.018 ± 0.243
1.253HisPhe: 1.253 ± 0.313
0.861HisGly: 0.861 ± 0.283
0.391HisHis: 0.391 ± 0.227
1.957HisIle: 1.957 ± 0.378
1.331HisLys: 1.331 ± 0.299
1.488HisLeu: 1.488 ± 0.256
0.391HisMet: 0.391 ± 0.207
1.096HisAsn: 1.096 ± 0.274
0.626HisPro: 0.626 ± 0.181
0.47HisGln: 0.47 ± 0.165
0.47HisArg: 0.47 ± 0.196
1.096HisSer: 1.096 ± 0.198
0.861HisThr: 0.861 ± 0.287
0.861HisVal: 0.861 ± 0.277
0.078HisTrp: 0.078 ± 0.079
1.253HisTyr: 1.253 ± 0.333
0.0HisXaa: 0.0 ± 0.0
Ile
5.167IleAla: 5.167 ± 0.731
0.157IleCys: 0.157 ± 0.084
5.559IleAsp: 5.559 ± 0.689
6.811IleGlu: 6.811 ± 0.69
2.897IlePhe: 2.897 ± 0.457
3.132IleGly: 3.132 ± 0.548
1.801IleHis: 1.801 ± 0.437
4.228IleIle: 4.228 ± 0.559
8.768IleLys: 8.768 ± 0.739
4.697IleLeu: 4.697 ± 0.559
1.331IleMet: 1.331 ± 0.293
6.576IleAsn: 6.576 ± 1.16
1.957IlePro: 1.957 ± 0.493
3.68IleGln: 3.68 ± 0.535
2.975IleArg: 2.975 ± 0.471
4.541IleSer: 4.541 ± 0.606
4.228IleThr: 4.228 ± 0.593
5.402IleVal: 5.402 ± 0.596
1.018IleTrp: 1.018 ± 0.377
3.288IleTyr: 3.288 ± 0.711
0.0IleXaa: 0.0 ± 0.0
Lys
5.167LysAla: 5.167 ± 0.554
0.157LysCys: 0.157 ± 0.112
6.185LysAsp: 6.185 ± 0.533
9.238LysGlu: 9.238 ± 0.99
3.366LysPhe: 3.366 ± 0.457
5.95LysGly: 5.95 ± 0.794
1.488LysHis: 1.488 ± 0.376
6.968LysIle: 6.968 ± 0.932
8.768LysLys: 8.768 ± 0.85
7.203LysLeu: 7.203 ± 0.625
2.192LysMet: 2.192 ± 0.458
5.637LysAsn: 5.637 ± 0.884
2.505LysPro: 2.505 ± 0.406
4.776LysGln: 4.776 ± 0.641
4.932LysArg: 4.932 ± 0.582
5.637LysSer: 5.637 ± 0.629
6.185LysThr: 6.185 ± 0.69
5.559LysVal: 5.559 ± 0.554
1.253LysTrp: 1.253 ± 0.387
4.149LysTyr: 4.149 ± 0.648
0.0LysXaa: 0.0 ± 0.0
Leu
4.306LeuAla: 4.306 ± 0.654
0.47LeuCys: 0.47 ± 0.187
5.324LeuAsp: 5.324 ± 0.527
7.203LeuGlu: 7.203 ± 0.717
3.758LeuPhe: 3.758 ± 0.473
3.601LeuGly: 3.601 ± 0.612
1.409LeuHis: 1.409 ± 0.305
5.95LeuIle: 5.95 ± 0.931
8.142LeuLys: 8.142 ± 0.762
6.968LeuLeu: 6.968 ± 0.868
2.114LeuMet: 2.114 ± 0.445
5.324LeuAsn: 5.324 ± 0.775
2.349LeuPro: 2.349 ± 0.397
3.132LeuGln: 3.132 ± 0.501
3.68LeuArg: 3.68 ± 0.519
5.402LeuSer: 5.402 ± 0.752
4.149LeuThr: 4.149 ± 0.596
4.149LeuVal: 4.149 ± 0.569
0.705LeuTrp: 0.705 ± 0.234
2.662LeuTyr: 2.662 ± 0.51
0.0LeuXaa: 0.0 ± 0.0
Met
1.096MetAla: 1.096 ± 0.322
0.078MetCys: 0.078 ± 0.075
1.253MetAsp: 1.253 ± 0.318
1.331MetGlu: 1.331 ± 0.324
0.705MetPhe: 0.705 ± 0.194
1.174MetGly: 1.174 ± 0.534
0.235MetHis: 0.235 ± 0.157
2.27MetIle: 2.27 ± 0.389
2.192MetLys: 2.192 ± 0.4
1.644MetLeu: 1.644 ± 0.265
0.939MetMet: 0.939 ± 0.301
1.488MetAsn: 1.488 ± 0.332
1.018MetPro: 1.018 ± 0.313
1.253MetGln: 1.253 ± 0.342
0.939MetArg: 0.939 ± 0.273
1.722MetSer: 1.722 ± 0.304
1.566MetThr: 1.566 ± 0.356
1.488MetVal: 1.488 ± 0.334
0.313MetTrp: 0.313 ± 0.146
0.783MetTyr: 0.783 ± 0.282
0.0MetXaa: 0.0 ± 0.0
Asn
4.463AsnAla: 4.463 ± 0.563
0.157AsnCys: 0.157 ± 0.122
4.776AsnAsp: 4.776 ± 0.627
5.48AsnGlu: 5.48 ± 0.947
1.801AsnPhe: 1.801 ± 0.551
5.167AsnGly: 5.167 ± 0.547
0.939AsnHis: 0.939 ± 0.315
4.463AsnIle: 4.463 ± 0.586
7.203AsnLys: 7.203 ± 0.846
4.776AsnLeu: 4.776 ± 0.64
1.566AsnMet: 1.566 ± 0.367
4.384AsnAsn: 4.384 ± 0.612
2.27AsnPro: 2.27 ± 0.337
3.053AsnGln: 3.053 ± 0.488
2.818AsnArg: 2.818 ± 0.499
4.071AsnSer: 4.071 ± 0.505
3.445AsnThr: 3.445 ± 0.44
4.228AsnVal: 4.228 ± 0.568
0.861AsnTrp: 0.861 ± 0.398
2.975AsnTyr: 2.975 ± 0.438
0.0AsnXaa: 0.0 ± 0.0
Pro
1.018ProAla: 1.018 ± 0.339
0.078ProCys: 0.078 ± 0.074
1.253ProAsp: 1.253 ± 0.263
2.505ProGlu: 2.505 ± 0.383
1.488ProPhe: 1.488 ± 0.35
0.939ProGly: 0.939 ± 0.231
0.705ProHis: 0.705 ± 0.181
2.584ProIle: 2.584 ± 0.415
2.584ProLys: 2.584 ± 0.533
1.644ProLeu: 1.644 ± 0.368
0.705ProMet: 0.705 ± 0.217
1.174ProAsn: 1.174 ± 0.272
0.939ProPro: 0.939 ± 0.196
0.861ProGln: 0.861 ± 0.327
1.253ProArg: 1.253 ± 0.26
1.722ProSer: 1.722 ± 0.315
1.488ProThr: 1.488 ± 0.347
1.801ProVal: 1.801 ± 0.277
0.157ProTrp: 0.157 ± 0.11
1.018ProTyr: 1.018 ± 0.277
0.0ProXaa: 0.0 ± 0.0
Gln
3.21GlnAla: 3.21 ± 0.46
0.548GlnCys: 0.548 ± 0.241
2.192GlnAsp: 2.192 ± 0.452
2.975GlnGlu: 2.975 ± 0.599
1.018GlnPhe: 1.018 ± 0.246
1.801GlnGly: 1.801 ± 0.409
0.783GlnHis: 0.783 ± 0.211
2.662GlnIle: 2.662 ± 0.34
3.132GlnLys: 3.132 ± 0.574
3.288GlnLeu: 3.288 ± 0.479
0.783GlnMet: 0.783 ± 0.254
3.523GlnAsn: 3.523 ± 0.539
0.939GlnPro: 0.939 ± 0.263
2.662GlnGln: 2.662 ± 0.761
2.114GlnArg: 2.114 ± 0.38
2.114GlnSer: 2.114 ± 0.421
2.036GlnThr: 2.036 ± 0.441
2.27GlnVal: 2.27 ± 0.489
0.313GlnTrp: 0.313 ± 0.151
1.566GlnTyr: 1.566 ± 0.317
0.0GlnXaa: 0.0 ± 0.0
Arg
2.27ArgAla: 2.27 ± 0.333
0.157ArgCys: 0.157 ± 0.11
2.584ArgAsp: 2.584 ± 0.457
3.601ArgGlu: 3.601 ± 0.596
2.036ArgPhe: 2.036 ± 0.406
1.801ArgGly: 1.801 ± 0.408
0.705ArgHis: 0.705 ± 0.191
3.445ArgIle: 3.445 ± 0.538
3.601ArgLys: 3.601 ± 0.671
4.071ArgLeu: 4.071 ± 0.571
0.939ArgMet: 0.939 ± 0.226
2.975ArgAsn: 2.975 ± 0.526
0.626ArgPro: 0.626 ± 0.195
1.409ArgGln: 1.409 ± 0.341
2.349ArgArg: 2.349 ± 0.451
1.957ArgSer: 1.957 ± 0.445
2.192ArgThr: 2.192 ± 0.538
2.349ArgVal: 2.349 ± 0.374
0.705ArgTrp: 0.705 ± 0.276
2.818ArgTyr: 2.818 ± 0.605
0.0ArgXaa: 0.0 ± 0.0
Ser
3.836SerAla: 3.836 ± 0.472
0.313SerCys: 0.313 ± 0.155
4.463SerAsp: 4.463 ± 0.646
5.402SerGlu: 5.402 ± 0.743
2.74SerPhe: 2.74 ± 0.52
2.975SerGly: 2.975 ± 0.663
1.801SerHis: 1.801 ± 0.314
5.324SerIle: 5.324 ± 0.688
5.324SerLys: 5.324 ± 0.697
3.758SerLeu: 3.758 ± 0.563
1.488SerMet: 1.488 ± 0.286
4.306SerAsn: 4.306 ± 0.597
1.018SerPro: 1.018 ± 0.251
1.722SerGln: 1.722 ± 0.371
1.331SerArg: 1.331 ± 0.349
3.288SerSer: 3.288 ± 0.473
3.915SerThr: 3.915 ± 0.594
2.897SerVal: 2.897 ± 0.465
0.235SerTrp: 0.235 ± 0.112
1.801SerTyr: 1.801 ± 0.417
0.0SerXaa: 0.0 ± 0.0
Thr
3.68ThrAla: 3.68 ± 0.602
0.157ThrCys: 0.157 ± 0.09
3.601ThrAsp: 3.601 ± 0.834
3.523ThrGlu: 3.523 ± 0.435
1.801ThrPhe: 1.801 ± 0.346
3.366ThrGly: 3.366 ± 0.752
1.566ThrHis: 1.566 ± 0.315
4.071ThrIle: 4.071 ± 0.517
5.245ThrLys: 5.245 ± 0.727
4.306ThrLeu: 4.306 ± 0.517
0.783ThrMet: 0.783 ± 0.215
3.601ThrAsn: 3.601 ± 0.659
2.114ThrPro: 2.114 ± 0.387
1.879ThrGln: 1.879 ± 0.423
2.192ThrArg: 2.192 ± 0.45
3.445ThrSer: 3.445 ± 0.611
3.366ThrThr: 3.366 ± 0.608
3.68ThrVal: 3.68 ± 0.48
0.861ThrTrp: 0.861 ± 0.234
2.505ThrTyr: 2.505 ± 0.516
0.0ThrXaa: 0.0 ± 0.0
Val
3.288ValAla: 3.288 ± 0.487
0.313ValCys: 0.313 ± 0.164
3.915ValAsp: 3.915 ± 0.533
3.053ValGlu: 3.053 ± 0.524
2.74ValPhe: 2.74 ± 0.506
3.915ValGly: 3.915 ± 0.575
0.783ValHis: 0.783 ± 0.265
4.619ValIle: 4.619 ± 0.573
6.107ValLys: 6.107 ± 0.664
5.245ValLeu: 5.245 ± 0.616
1.174ValMet: 1.174 ± 0.277
3.993ValAsn: 3.993 ± 0.467
1.331ValPro: 1.331 ± 0.317
2.27ValGln: 2.27 ± 0.547
2.192ValArg: 2.192 ± 0.346
3.288ValSer: 3.288 ± 0.522
3.68ValThr: 3.68 ± 0.506
3.523ValVal: 3.523 ± 0.601
0.47ValTrp: 0.47 ± 0.227
2.505ValTyr: 2.505 ± 0.328
0.0ValXaa: 0.0 ± 0.0
Trp
0.391TrpAla: 0.391 ± 0.162
0.078TrpCys: 0.078 ± 0.079
0.548TrpAsp: 0.548 ± 0.19
0.705TrpGlu: 0.705 ± 0.221
0.548TrpPhe: 0.548 ± 0.188
0.626TrpGly: 0.626 ± 0.238
0.078TrpHis: 0.078 ± 0.079
1.174TrpIle: 1.174 ± 0.244
0.705TrpLys: 0.705 ± 0.237
1.096TrpLeu: 1.096 ± 0.24
0.391TrpMet: 0.391 ± 0.161
0.783TrpAsn: 0.783 ± 0.3
0.078TrpPro: 0.078 ± 0.061
0.548TrpGln: 0.548 ± 0.182
0.391TrpArg: 0.391 ± 0.175
0.626TrpSer: 0.626 ± 0.224
0.47TrpThr: 0.47 ± 0.143
0.391TrpVal: 0.391 ± 0.133
0.078TrpTrp: 0.078 ± 0.072
0.626TrpTyr: 0.626 ± 0.212
0.0TrpXaa: 0.0 ± 0.0
Tyr
1.801TyrAla: 1.801 ± 0.322
0.47TyrCys: 0.47 ± 0.196
2.818TyrAsp: 2.818 ± 0.579
2.818TyrGlu: 2.818 ± 0.575
1.879TyrPhe: 1.879 ± 0.425
2.584TyrGly: 2.584 ± 0.506
0.783TyrHis: 0.783 ± 0.211
4.071TyrIle: 4.071 ± 0.606
4.776TyrLys: 4.776 ± 0.536
3.288TyrLeu: 3.288 ± 0.529
1.018TyrMet: 1.018 ± 0.25
2.74TyrAsn: 2.74 ± 0.426
0.783TyrPro: 0.783 ± 0.282
2.349TyrGln: 2.349 ± 0.418
1.644TyrArg: 1.644 ± 0.342
2.349TyrSer: 2.349 ± 0.484
2.27TyrThr: 2.27 ± 0.506
2.505TyrVal: 2.505 ± 0.497
0.391TyrTrp: 0.391 ± 0.191
1.488TyrTyr: 1.488 ± 0.512
0.0TyrXaa: 0.0 ± 0.0
Xaa
0.0XaaAla: 0.0 ± 0.0
0.0XaaCys: 0.0 ± 0.0
0.0XaaAsp: 0.0 ± 0.0
0.0XaaGlu: 0.0 ± 0.0
0.0XaaPhe: 0.0 ± 0.0
0.0XaaGly: 0.0 ± 0.0
0.0XaaHis: 0.0 ± 0.0
0.0XaaIle: 0.0 ± 0.0
0.0XaaLys: 0.0 ± 0.0
0.0XaaLeu: 0.0 ± 0.0
0.0XaaMet: 0.0 ± 0.0
0.0XaaAsn: 0.0 ± 0.0
0.0XaaPro: 0.0 ± 0.0
0.0XaaGln: 0.0 ± 0.0
0.0XaaArg: 0.0 ± 0.0
0.0XaaSer: 0.0 ± 0.0
0.0XaaThr: 0.0 ± 0.0
0.0XaaVal: 0.0 ± 0.0
0.0XaaTrp: 0.0 ± 0.0
0.0XaaTyr: 0.0 ± 0.0
0.0XaaXaa: 0.0 ± 0.0
Statistics based on 65 proteins (12774 amino acids)

Note: The error has been estimated with the bootstraping (x100) at the protein level

Above dipeptide statistics (among other stats for this proteome) you can download from this CSV file
See this proteome in: uniprot_link
Proteome-pI is available under Creative Commons Attribution-NoDerivs license, for more details see here

Reference: Kozlowski LP. Proteome-pI 2.0: Proteome Isoelectric Point Database Update. Nucleic Acids Res. 2021, doi: 10.1093/nar/gkab944 Contact: Lukasz P. Kozlowski