PHD predictions for 1shg

Different levels of data:

PHD brief
PHD normal
PHD detail

PHDsec summary overall your protein can be classified as:
mixed given the following classes:
- 'all-alpha': %H > 45% AND %E < 5%
- 'all-beta': %H < 5% AND %E > 45%
- 'alpha-beta': %H > 30% AND %E > 20%
- 'mixed': all others

Residue composition for your protein:

%A: 5.3 %C: 0.0 %D: 8.8 %E: 7.0 %F: 1.8

%G: 3.5 %H: 0.0 %I: 1.8 %K: 14.0 %L: 12.3

%M: 1.8 %N: 5.3 %P: 3.5 %Q: 3.5 %R: 3.5

%S: 3.5 %T: 5.3 %V: 10.5 %W: 3.5 %Y: 5.3

Predicted secondary structure composition for your protein:

%H: 0.0 %E: 45.6 %L: 54.4

AA : amino acid sequence

OBS_sec: observed secondary structure: H=helix, E=extended (sheet), blank=other (loop)

PHD_sec: PHD predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop)
PHD = PHD: Profile network prediction HeiDelberg

Rel_sec: reliability index for PHDsec prediction (0=low to 9=high)
Note: for the brief presentation strong predictions marked by '*'

SUB_sec: reliability index for PHDsec prediction (0=low to 9=high)
Note: for the brief presentation strong predictions marked by '*'

pH_sec: 'probability' for assigning helix (1=high, 0=low)

pE_sec: 'probability' for assigning strand (1=high, 0=low)

pL_sec: 'probability' for assigning neither helix, nor strand (1=high, 0=low)

O_3_acc: observerd relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.

P_3_acc: PHD predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.

Rel_acc: reliability index for PHDacc prediction (0=low to 9=high)
Note: for the brief presentation strong predictions marked by '*'

SUB_acc: reliability index for PHDacc prediction (0=low to 9=high)
Note: for the brief presentation strong predictions marked by '*'

OBS_acc: observerd relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between n*n % and (n+1)*(n+1) % (e.g. for n=5: 16-25%).

PHD_acc: PHD predicted relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between n*n % and (n+1)*(n+1) % (e.g. for n=5: 16-25%).

PHD results (brief)

....,....6....,....7....,....8....,....9....,....1 AA KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLD OBS_sec EEEE EEEEEE EEEEEE EEEEEEHHHEEEE PHD_sec EEEEEEEE EEE EEEEE EEEE EEE EEE Rel_sec * ****** ***** ************* *** *** * * O_3_acc eeeb b eebe e eebbebeee eb b e eeee b eeeeb b eebeeee P_3_acc eebbbbbbebeeeeeeebebeebeebebbeeeeeebbebeeeeeebbbbbebbeebe Rel_acc * * *** * * ** * *

PHD results (normal)

....,....6....,....7....,....8....,....9....,....1 AA KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLD OBS_sec EEEE EEEEEE EEEEEE EEEEEEHHHEEEE PHD_sec EEEEEEEE EEE EEEEE EEEE EEE EEE Rel_sec 918998983388886323435986999956897332687245881432121122519 SUB_sec L.EEEEEE..LLLLL.....LLLLEEEEELLLL...EEE..LLL..........E.L O_3_acc eeeb b eebe e eebbebeee eb b e eeee b eeeeb b eebeeee P_3_acc eebbbbbbebeeeeeeebebeebeebebbeeeeeebbebeeeeeebbbbbebbeebe Rel_acc 531629940110212212022200060632212211323103211314400361104 SUB_acc e..b.bbb.................b.b...................bb...b...e

PHD results (detail)

....,....6....,....7....,....8....,....9....,....1 AA KELVLALYDYQEKSPREVTMKKGDILTLLNSTNKDWWKVEVNDRQGFVPAAYVKKLD pH_sec 1.0 pH_sec pH_sec 0.9 pH_sec pH_sec 0.8 pH_sec pH_sec 0.7 pH_sec pH_sec 0.6 pH_sec pH_sec . 0.5 pH_sec pH_sec . ... .. 0.4 pH_sec pH_sec ... ... ... 0.3 pH_sec pH_sec ..... .. .......... ...... 0.2 pH_sec --------------------------------------------------------- pE_sec .. ... 1.0 pE_sec pE_sec ...... .... .. 0.9 pE_sec pE_sec ...... .... ... . 0.8 pE_sec pE_sec ....... . ..... ... .. . 0.7 pE_sec pE_sec ........ ... ..... ... ... ... 0.6 pE_sec pE_sec ........ ... ..... .... ..... .... 0.5 pE_sec pE_sec ......... ... ..... .... ..... ..... 0.4 pE_sec pE_sec ......... ..... ..... ...... ..... ..... 0.3 pE_sec pE_sec ......... ..... ....... ....... ............. 0.2 pE_sec --------------------------------------------------------- pL_sec . . . 1.0 pL_sec pL_sec . .... .. ... .. . 0.9 pL_sec pL_sec . ..... ... .... .. . 0.8 pL_sec pL_sec . ...... .... .... .... . 0.7 pL_sec pL_sec . ....... .... ...... ..... .. 0.6 pL_sec pL_sec .. ........ .... ...... ..... ..... .. 0.5 pL_sec pL_sec .. .......... ..... ....... ............... .. 0.4 pL_sec pL_sec .. ................ ........ ............... .. 0.3 pL_sec pL_sec ... ................. ......... .................. 0.2 pL_sec --------------------------------------------------------- P_3_acc eebbbbbbebeeeeeeebebeebeebebbeeeeeebbebeeeeeebbbbbebbeebe OBS_acc . . . . . 100% OBS_acc OBS_acc . . . .. . . .. . . 81% OBS_acc OBS_acc . .. . .. ... . ... .. . . . . 64% OBS_acc OBS_acc ... .. . . .. . ... . . .... .... .. .... 49% OBS_acc OBS_acc ... . ... ... .. . ..... ........ . . .... . .. .... 36% OBS_acc OBS_acc ... . ... ...... . ..... . .......... . .... . .. .... 25% OBS_acc OBS_acc ... . ... ...... . ..... . .......... ...... . .... .... 16% OBS_acc OBS_acc ... . ........... . ..... ............ ...... . ......... 9% OBS_acc OBS_acc ... ..................... ............ ........ ......... 4% OBS_acc --------------------------------------------------------- PHD_acc . . 100% PHD_acc PHD_acc . . 81% PHD_acc PHD_acc .. ... ... .. ...... . ..... . . 64% PHD_acc PHD_acc .. . ....... . .. .. . ...... . ...... . .. . 49% PHD_acc PHD_acc .. . ....... . .. .. . ...... . ...... . .. . 36% PHD_acc PHD_acc .. . ....... . .. .. . ...... . ...... . .. . 25% PHD_acc PHD_acc .. . ....... . .. .. . ...... . ...... . .. . 16% PHD_acc PHD_acc .. . ....... . .. .. . ...... . ...... . .. . 9% PHD_acc PHD_acc .. . ....... . .. .. . ...... . ...... . .. . 4% PHD_acc ---------------------------------------------------------

%A: 5.3	%C: 0.0	%D: 8.8	%E: 7.0	%F: 1.8
%G: 3.5	%H: 0.0	%I: 1.8	%K: 14.0	%L: 12.3
%M: 1.8	%N: 5.3	%P: 3.5	%Q: 3.5	%R: 3.5
%S: 3.5	%T: 5.3	%V: 10.5	%W: 3.5	%Y: 5.3

AA :	amino acid sequence
OBS_sec:	observed secondary structure: H=helix, E=extended (sheet), blank=other (loop)
PHD_sec:	PHD predicted secondary structure: H=helix, E=extended (sheet), blank=other (loop) PHD = PHD: Profile network prediction HeiDelberg
Rel_sec:	reliability index for PHDsec prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
SUB_sec:	reliability index for PHDsec prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'

pH_sec:	'probability' for assigning helix (1=high, 0=low)
pE_sec:	'probability' for assigning strand (1=high, 0=low)
pL_sec:	'probability' for assigning neither helix, nor strand (1=high, 0=low)
O_3_acc:	observerd relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
P_3_acc:	PHD predicted relative solvent accessibility (acc) in 3 states: b = 0-9%, i = 9-36%, e = 36-100%.
Rel_acc:	reliability index for PHDacc prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'
SUB_acc:	reliability index for PHDacc prediction (0=low to 9=high) Note: for the brief presentation strong predictions marked by '*'

OBS_acc:	observerd relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between nn % and (n+1)(n+1) % (e.g. for n=5: 16-25%).
PHD_acc:	PHD predicted relative solvent accessibility (acc) in 10 states: a value of n (=0-9) corresponds to a relative acc. of between nn % and (n+1)(n+1) % (e.g. for n=5: 16-25%).