| |
Mapping φ,ψ-values into letter codes
For purposes of assigning a letter code, φ - ψ space is
tiled into 60° by 60° bins. Each bin is labeled with
a letter code, as shown in the figure below.
For example a residue with φ = -64° and ψ = -43° will be
assigned a letter code of 'O' and a residue with φ = -120° and
ψ = 135° will be assigned a letter code of 'L'
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 {'O', 'P'}, with the condition that the segment has
at least 5 successive residues with the letter code 'O'.
- β-strands are segments of 3 or more
successive residues each of which has a letter code in the set
{'L', 'G', 'F', 'A', 'R', 'M'}.
- 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: {'OO', 'OP', 'OJ', 'PO', 'PP', 'PJ', 'JO', 'JP', 'JJ',
'Mo', 'Mp', 'Mj', 'Ro', 'Rp', 'Rj',
'oo', 'op', 'oj', 'po', 'pp', 'pj', 'jo', 'jp', 'jj',
'mO', 'mP', 'mJ', 'rO', 'rP', 'rJ'}.
- Residues not classified into one of these three categories are
assigned as coil.
| |
