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Mapping φ,ψ-values into letter codes
For purposes of assigning a letter code, φ - ψ space is
tiled into 30° by 30° bins. Each bin is labeled with
a two letter code, as shown in the figure below.
The mesostate bins are overlayed on the experimentally observed distribution of φ,ψ reported in Hovmoller et al., Acta Cryst. D58: 768-776, 2002
For example a residue with φ = -64° and ψ = -43° (helix) will be
assigned a letter code of 'Ee' and a residue with φ = -120° and
ψ = 135° (strand) will be assigned a letter code of 'Ck'
Specific secondary structure assignments within LINUS are as follows:
- α-helices are segments of
5 or more residues, each of which has a letter code in the
set ('De','Df','Ed','Ee','Ef','Fe').
- β-strands are segments of 3 or more
successive residues each of which has a letter code in the set
('Bj','Bk','Bl','Cj','Ck','Cl','Dj','Dk','Dl').
- Assign β-turns by examining every overlapping
2-residue segment. A residue and it's succeeding residue are
assigned a turn conformation if the letter codes of the pair is
one of:
'EfDf', #5226 relative number of occurance in PDB
'EeEf', #4593
'EfEf', #4061
'EfDg', #3883
'EeDg', #2118
'EeEe', #1950
'EfCg', #1932
'EeDf', #1785
'EkJf', #1577
'EkIg', #1106
'EfEe', # 995
'EkJg', # 760
'EeCg', # 553
'DfDf', # 479
'EfCf', # 395
'DgDf', # 332
'DfDg', # 330
'IhIg', # 310
'EfDe', # 309
'EkIh', # 298
'DgCg', # 275
'DfCg', # 267
'IbDg', # 266
'DfEe', # 260
'FeEf', # 250
'IbEf', # 249
'DfEf', # 219
'IhJf', # 216
'IhJg', # 213
'IgIg', # 207
'EfCh', # 188
'DgEe', # 180
'DgEf', # 176
'EeEg', # 172
'IhIh', # 153
'EeDe', # 150
'IgJg', # 147
'EkKf', # 147
'EeCh', # 147
'IbDf', # 131
'DgDg', # 128
'EgDf', # 127
'FeDg', # 114
'ElIg', # 111
'IgIh', # 107
'DfDe', # 107
'EjIg', # 101
'EeCf', # 100
'DfCh', # 94
'DgCf', # 91
'DfCf', # 91
'DeEe', # 91
'DkIh', # 88
'FeDf', # 79
'EkIf', # 78
'EeDh', # 76
'DgCh', # 74
'IgJf', # 71
'EjJg', # 71
'FeEe', # 69
'DlIh', # 66
'EgCg', # 65
'ElIh', # 62
'EjJf', # 62
'FeCg', # 59
'DlIg', # 56
'IbCg', # 54
'EfEg', # 54
'EkJe', # 53
'FkJf', # 52
'ElJg', # 51
'DgDe', # 49
'DlJg', # 46
'EgCf', # 45
'IaEf', # 40
'FkIg', # 39
'JaEf', # 38
'EjIh', # 38
'EgEf', # 38
'DkJg', # 36
'DeEf', # 34
'EeCi', # 31
'JgIh', # 29
'IcEf', # 29
'EkKe', # 29
'DkIg', # 29
'IbEe', # 27
'EgDg', # 27
'EeFe', # 27
'EjKf', # 26
'IaDf', # 25
'HhIg', # 24
'HbDg', # 24
'ElJf', # 24
'EfDh', # 24
'IcDf', # 23
'EfBh', # 23
'IcDg', # 22
'IcCg', # 22
'FkJg', # 21
'FeCh', # 21
'IgKf', # 20
'FdDg', # 20
'EkHh', # 20
'DfDh', # 20
'DgBh', # 19
'DfBh', # 19
'DeDf', # 19
'DfFe', # 18
'EfFe', # 17
'EgEe', # 16
'EgDe', # 16
'DkJf', # 16
'JgJg', # 15
'IbEg', # 15
'IbCh', # 15
'EfBg', # 15
'DgCe', # 15
'JlEf', # 14
'CgCg', # 14
'HhJf', # 13
'EeBi', # 13
'DfBi', # 13
'IhIf', # 12
'FeEg', # 12
'FdEf', # 12
'EdEf', # 12
'DlJf', # 12
'DhCg', # 12
'JgIg', # 11
'IeBg', # 11
'FjIg', # 11
'FdCh', # 11
'EdEe', # 11
'JfIh', # 10
'JaEe', # 10
'HhJg', # 10
'HbEf', # 10
'HbCh', # 10
'FkIh', # 10
'FjJf', # 10
'ElJe', # 10
'DhDf', # 10
'CgDf' # 10
- Assign PII as residues with the following leter codes:
{'Dk', 'Dl', 'Ek', 'El'}
. Residues in these bins will be assigned as strand if they
are within the 3 residue definition above.
- Residues not classified into one of these four categories are
assigned as coil.
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