Prediction of Secondary Structure : Using the Chou Fasman Method

The fasta protocol for assigning amino acid residues to a series of letters is as follows:

A alanine P proline
B aspartate/asparagine Q glutamine
C cystine R arginine
D aspartate S serine
E glutamate T threonine
F phenylalanine U selenocysteine
G glycine V valine
H histidine W tryptophan
I isoleucine Y tyrosine
K lysine Z glutamate/glutamine
L leucine X any
M methionine * translation stop
N asparagine - gap of indeterminate length

Say we have a protein that is the product of the Chick Gene X (Ovalbumin related). Its sequence in Fasta format
is:

>gi|129295|sp|P01013|OVAX_CHICK GENE X PROTEIN (OVALBUMIN-RELATED)

QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAEKMKILELPFAS
GDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTSVLMALGMTDLFIPSANLTGISS
AESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHPFLFLIKHNPTNTIVYFGRYWSP

The Chou Fasman method yields a predicted secondary structure as follows:

Target Sequence:
10 20 30 40 50 60 70
QIKDLLVSSS TDLDTTLVLV NAIYFKGMWK TAFNAEDTRE MPFHVTKQES KPVQMMCMNN SFNVATLPAE

80 90 100 110 120 130 140

KMKILELPFA SGDLSMLVLL PDEVSDLERI EKTINFEKLT EWTNPNTMEK RRVKVYLPQM KIEEKYNLTS

150 160 170 180 190 200 210

VLMALGMTDL FIPSANLTGI SSAESLKISQ AVHGAFMELS EDGIEMAGST GVIEDIKHSP ESEQFRADHP

220 230
FLFLIKHNPT NTIVYFGRYW SP
Secondary Structure:
* * * * * *
Query 1 QIKDLLVSSSTDLDTTLVLVNAIYFKGMWKTAFNAEDTREMPFHVTKQESKPVQMMCMNNSFNVATLPAE 70
Helix 1 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHH 70
Sheet 1 EEEEEE EEEEEEEEEEEEEEEEEEEEEEEEE EEEEE EEEEEEEEEEEEE 70
Turns 1 T T T T T T 70
Struc 1 HHHEEEHETHHHEEEEEEEEEEEEHHHHHHEHHHHHHHHHHEEEEHHHHHTHHHHHEEETEEEEHHHHHH 70

* * * * * *
Query 71 KMKILELPFASGDLSMLVLLPDEVSDLERIEKTINFEKLTEWTNPNTMEKRRVKVYLPQMKIEEKYNLTS 140
Helix 71 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHHH 140
Sheet 71 EEEEEE EEEEEE EEEEEEE EEEEEEE EEEEE 140
Turns 71 TT T T TT TT T 140
Struc 71 HHHHHHHHHHTTHHEEEEHHHHHHHHHHHHHTHHHHHHHHHECTTCCHHHHHEEEEHHHHHHHTHEEEEE 140

* * * * * *
Query 141 VLMALGMTDLFIPSANLTGISSAESLKISQAVHGAFMELSEDGIEMAGSTGVIEDIKHSPESEQFRADHP 210
Helix 141 HHHHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHHHHHHH HHHHHHHHHHHHHHHHHHH 210
Sheet 141 EEEEEEEEEEE 210
Turns 141 T TT T T T T 210
Struc 141 HHHHEHHEEEEHHHHCCCCCCCHHHHHHHHHHHHHHHHHHTTHHHHCCCCCHHHHHHHHTHHHHHHTHHH 210

* *
Query 211 FLFLIKHNPTNTIVYFGRYWSP 232
Helix 211 HHHHHH 232
Sheet 211 EEEEEEEEEEEEEEEEEEE 232
Turns 211 232
Struc 211 EEEEEHEEEEEEEEEEEEECCC 232

Total Residues: H: 194 E: 110 T: 22

Percent: H: 83.6 E: 47.4 T: 9.5