FUNCTION. THIS PROGRAM SORTS THE PEPTIDES FROM A DISEST OF A PEPTIDE SEQUENCE BY POSITION, WEIGHT AND RETENTION ON HPLC. EACH PEPTIDES IS IDENTIFIED BY A SERIES OF PROPERTIES. A SUMMARY OF THE COMPOSITION OF THE ENTIRE PROTEIN IS SHOWN. DESCRIPTION. THIS PROGRAM CUTS A PEPTIDE SEQUENCE WITH ANY OR ALL THE ENZYMES FROM THE PUBLIC DATA FILE. THE PEPTIDES FROM EACH DIGEST ARE SORTED BY POSITION, WEIGHT AND RETENTION TIME IN A HIGH PRESSURE LIQUID CHROMATOGRAPH AT PH 2.1 .FOR EACH PEPTIDE IN EACH SORTING, THE FOLLOWING DATA ARE DISPLAYED: BEGINNING AND ENDING POSITIONS,MOLECULAR WEIGHT,HPLC RETENTION AT PH 7.4 ,HPLC RETENTION AT PH 2.1, CHARGE, NUMBER OF AROMATIC RESIDUES, NUMBER OF ACIDIC RESIDUES, NUMBER OF RESIDUES CONTAINING SULFUR, NUMBER OF HYDROPHILIC RESIDUES, AND NUMBER OF HYDROPHOBIC RESIDUES. THE CONTENT OF EACH PEPTIDE IS SHOWN WITH THE TABLE OF PEPTIDES, SORTED BY POSITION. RESTRICTIONS. A DIGEST MAY NOT PRODUCE MORE THAN 1000 PEPTIDES. IF YOU CHOOSE ALL THE ENZYMES BY TYPING A * TO THE PROMPT "ENZYME:" AND YOUR PROTEIN SEQUENCE IS OVER 500 RESIDUES LONG, THERE MAY BE A GREAT DEAL OF OUTPUT. CHOOSING THE ENZYMES. YOU ARE PRESENTED WITH THE WORD "ENZYME:" AND YOU CAN EITHER LIST THE ENZYMES YOU WANT INDIVIDUALLY WITH A CARRIAGE RETURN AFTER EACH ONE ,OR YOU CAN JUST TYPE A * AND ALL THE ENZYMES IF THE ENZYME DATA FILE WILL BE MAPPED.IF YOU LIST THE ENZYMES INDIVIDUALLY, USE A CARRIAGE RETURN BY ITSELF TO END THE LIST.ENZYMES ARE NAMED WITH OR WITHOUT SPACES. IF THE ENZYME YOU NAME IS NOT IN THE ENZYME DATA FILE THE PROGRAM WILL RESPOND WITH "ENZYME NOY FOUND". Table used by PEPTIDESORT to find the properties of the different amino acid residues. ----------------------------------------------------------------- Hydrophobicities assigned according to J. Janin Nature 277:492 (1979) AmAcid MolWt Charge Aroma Acid Base Sulfur Phil phob retn2.1 retn7.4 .. A 089.04 0.0 0 0 0 0 0 1 -0.1 0.5 R 174.10 1.0 0 0 1 0 1 0 -4.5 0.8 N 132.04 0.0 0 0 0 0 1 0 -1.6 -0.8 D 133.03 -1.0 0 1 0 0 1 0 -2.8 -8.2 B 132.51 -0.5 0 1 0 0 1 0 -2.2 -4.5 C 121.01 0.0 0 0 0 1 0 1 -2.2 -6.8 Q 146.06 0.0 0 0 0 0 1 0 -2.5 -4.8 E 147.04 -1.0 0 1 0 0 1 0 -7.5 -16.9 Z 146.55 -0.5 0 1 0 0 1 0 -5.0 -10.8 G 75.02 0.0 0 0 0 0 0 1 -0.5 0.0 H 155.06 0.0 0 0 0 0 1 0 0.8 -3.5 I 131.08 0.0 0 0 0 0 0 1 11.8 13.9 L 131.08 0.0 0 0 0 0 0 1 10.0 8.8 K 146.09 1.0 0 0 1 0 1 0 -3.2 0.1 M 149.04 0.0 0 0 0 1 0 1 7.1 4.8 F 165.07 0.0 1 0 0 0 0 1 13.9 13.2 P 115.05 0.0 0 0 0 0 1 0 8.0 6.1 S 105.03 0.0 0 0 0 0 1 0 -3.7 1.2 T 119.05 0.0 0 0 0 0 1 0 1.5 2.7 W 204.08 0.0 1 0 0 0 0 1 18.1 14.9 Y 181.06 0.0 1 0 0 0 0 1 8.2 6.1 V 117.07 0.0 0 0 0 0 0 1 3.3 2.7 Peptide cleaving enzymes and reagents used by PEPTIDESORT. --------------------------------------------------------- Refer to the enzymes by the abbreviation in the column called "name" when prompted by a program that reads this file. The right-most column is for documentary purposes. name offset site documentation .. Tryp 1 K Trypsin Tryp 1 R Trypsin Chymo 1 F Chymotrypsin Chymo 1 W Chymotrypsin Chymo 1 Y Chymotrypsin Chymo 1 L Chymotrypsin Clos 1 R Clostripain, Trypsin(Lys blocked) Myxo 1 K Myxobacter Protease,Armillaria Protease EndoK 1 K Endoproteinase Lys-C ProEn 1 P Proline Endopeptidase Staph 1 E Staphylococcal Protease TrypK 1 K Trypsin(Arg blocked) TrypR 1 R Trypsin(Lys blocked) CnBr 1 M Cyanogen Bromide IBzO 1 W IodosoBenzoate NH2OH 1 NG Hydroxylamine NTCB 0 C NTCB + Ni pH2.5 1 DP pH 2.5 NoCut 1 @ for calculations on whole peptide