Analysis of a Protein Sequence Alignment (Result in Graphical Form)
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Paste your protein sequence alignment:
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Format of your Alignment
Standard Format (FASTA/GCG/PIR)
Alignment in Block Format
Select Parameters (Maximum Four,Defauly % Exposed Residues)
:
Free energy of transfer to surface (Bull & Breese, Arch. Biophys. Biochem. 161, 665 (1974) )
Average accessibility surface area (Janin et al., J. Mol. Biol. 125, 357 (1978) )
Percentage of buried residues (Janin et al., J. Mol. Biol. 125, 357 (1978) )
Percentage of exposed residues (Janin et al., J. Mol. Biol. 125, 357 (1978) )
Hydrophobic index (Ponnuswamy et al., Biochim. Biophys. Acta 623, 301 (1980) )
Hydrophobicity in folded form (Ponnuswamy et al., BBA 623, 301 (1980) )
Hydrophobicity in unfolded form (Ponnuswamy et al., BBA 623, 301 (1980) )
Hydrophobicity gain (Ponnuswamy et al., BBA 623, 301 (1980) )
Polarity (Ponnuswamy et al., Biochim. Biophys. Acta 623, 301 (1980) )
Surrounding hydrophobicity in a-helix (Ponnuswamy et al., BBA 623, 301 (1980) )
Surrounding hydrophobicity in b-sheet (Ponnuswamy et al. BBA 623, 301 (1980) )
Surrounding hydrophobicity in b-turn (Ponnuswamy et al., BBA 623, 301 (1980) )
Accessibility reduction ratio (Ponnuswamy et al., BBA 623, 301 (1980) )
Average number of surrounding residues (Ponnuswamy BBA 623, 301 (1980) )
Volume (Chothia, Nature 254, 304 (1975) )
Local flexibility (Ragone et al. 1989)
Flexibility (Bhaskaran and Ponnuswamy 1988)
Flexibility for no rigid neighbours (Karplus & Schulz, Naturwiss. 72, 212 (1985) )
Flexibility for one rigid neighbour (Karplus & Schulz, Naturwiss. 72, 212 (1985) )
Flexibility for two rigid neighbours (Karplus & Schulz, Naturwiss. 72, 212 (1985) )
Hydrophobicity (Eisenberg, Ann. Rev. Biochem. 53, 595 (1984) )
Accessible surface area in the standard state (Rose et al., Sci. 229, 834 (1985) )
Average accessible surface area in folded proteins (Rose et al., Sci. 229, 834 (1985) )
Average surrounding hydrophobicity (Manavalan et al. Nature 275, 673 (1978) )
Hydrophilicity (Hopp and Woods, PNAS 78, 3824 (1981) )
Hydropathy (Kyte and Doolittle, J. Mol. Biol. 157, 105 (1982) )
Hydrophilicity from HPLC (Parker et al. Biochemistry 25, 5425 (1986) )
Hydrophobicity (Jones, J. Theor. Biol. 125, 357 (1975) )
Refractivity (Jones, J. Theor. Biol. 125, 357 (1975) )
Normalized frequency of a-helix with weights (Levitt, Biochem. 17, 4277 (1978) )
Normalized frequency of b-sheet with weights (Levitt, Biochem. 17, 4277 (1978) )
Normalized frequency for reverse turn with weights (Levitt, Biochem. 17, 4277 (1978) )
Barrell, Bankier and Drouin (1979)
Signature for rapidly degraded proteins
Charge of amino acids (example scale)
Local concentration of aromatic amino acids
Moment Method:
Direct/No Moment
Unnormalized Moment
Normalized Moment
Smooth Moment Angle
Moment Angle
Face of Alpha Helix
Face of beta-sheet
Window Size (Default Size 7):
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Averaging Method:
Mean Over Window
Hat Over Window
Median Over Window
Data Sieve
Fourier Smoothing
Window Size (Default Size 7):
7
1
3
5
9
11
13
15
17
19
21
23
25
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Simple average
Average with standard error
Plot each sequence in alignment