| |
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:
('EeDe','EeDf','EeDg','EeCe','EeCf','EeCg',
'EfDe','EfDf','EfDg','EfCe','EfCf','EfCg',
'DeDe','DeDf','DeDg','DeCe','DeCf','DeCg',
'DfDe','DfDf','DfDg','DfCe','DfCf','DfCg',
'EjIg','EjJg','EjJf','EkIg','EkJg','EkJf',
'IgJg','IgJf','IhJg','IhJf',
'HbDf','HbDg',
'HcDf','HcDg',
'IbDf','IbDg','IbCf','IbCg',
'IcDf','IcDg','IcCf','IcCg',
'EeEe','EeEf','EeDf',
'EfEe','EfEf','EfDf',
'DfEe','DfEf','DfDf',
'IgIg','IgIh','IgIi','IgHh','IgHi',
'IhIg','IhIh','IhIi','IhHh','IhHi',
'IiIg','IiIh',
'HhIg','HhIh',
'HiIg','HiIh')
.
- 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 three categories are
assigned as coil.
| |
