The following is an example of an HSSP file that can be used as input to the I-sites Server. Only the required keyworded lines are shown in this example, for clarity. Any number of additional header lines with no keyword or the keyword "REMARK" are allowed and ignored.

Certain keywords are required to have associated values in the format shown below.
The keywords are:

HSSP             !!! Signals HSSP format
PDBID      code  !!! Optional. The label 'code' is used in the output predictions.
SEQLENGTH   238  !!! the length of the parent sequence is 238 
NALIGN        5  !!! the number of aligned sequences is 5 
## PROTEINS      !!! signals the beginning of sequence identifier lines (5 of them)
                 !!! The next line (column labels) is required, too.
## ALIGNMENTS    !!! Signals the beginning of the alignment data. (238 lines)
                 !!! The next line (column labels) is required, too.
##               !!! end of ALIGNMENTS

For more information on how to write such a file see:
Sander C., Schneider R. : Database of homology-derived protein structures. Proteins, 9:56-68 (1991).

HSSP HOMOLOGY DERIVED SECONDARY STRUCTURE OF PROTEINS , VERSION 1.0 1991 PDBID 2pcd SEQLENGTH 433 NCHAIN 18 chain(s) in 2pcd data set KCHAIN 3 chain(s) used here ; chain(s) : A,M NALIGN 16 ## PROTEINS : EMBL/SWISSPROT identifier and alignment statistics NR. ID STRID %IDE %WSIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCNUM PROTEIN 1 : pcxb_psepu 2PCD 1.00 1.00 270 435 71 236 166 0 0 238 P00437 PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAI 2 : pcxa_psepu 2PCD 1.00 1.00 1 200 1 200 200 0 0 200 P00436 PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHA 3 : pcxb_psepu 2PCD 1.00 1.00 202 268 1 67 67 0 0 238 P00437 PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAI 4 : pcxb_acica 0.62 0.73 270 429 72 231 160 0 0 237 P20372 PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAI 5 : pcxb_burce 0.55 0.66 270 435 70 234 165 1 1 235 P15110 PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAI 6 : pcxa_acica 0.54 0.63 3 199 7 208 197 1 5 209 P20371 PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHA 7 : pcxa_burce 0.47 0.51 2 199 1 196 192 6 10 197 P15109 PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHA 8 : pcxb_acica 0.47 0.70 212 268 12 68 57 0 0 237 P20372 PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAI 9 : pcxa_acica 0.37 0.43 274 434 50 206 155 4 8 209 P20371 PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHA 10 : pcxa_psepu 2PCD 0.35 0.39 274 434 46 197 150 5 13 200 P00436 PROTOCATECHUATE 3,4-DIOXYGENASE ALPHA CHA 11 : cata_acica 0.32 0.32 272 426 129 292 151 4 17 311 P07773 CATECHOL 1,2-DIOXYGENASE (EC 1.13.11.1). 12 : pcxb_psepu 2PCD 0.32 0.38 1 197 35 235 189 7 20 238 P00437 PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAI 13 : pcxb_acica 0.32 0.38 2 196 37 235 187 7 20 237 P20372 PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAI 14 : pheb_psesp 0.31 0.31 274 435 131 299 148 5 35 302 P31019 CATECHOL 1,2-DIOXYGENASE (EC 1.13.11.1). 15 : pcxb_burce 0.30 0.33 1 197 34 233 188 8 21 235 P15110 PROTOCATECHUATE 3,4-DIOXYGENASE BETA CHAI 16 : tcbc_psesp 0.30 0.28 277 432 100 250 140 5 27 251 P27098 CHLOROCATECHOL 1,2-DIOXYGENASE (EC 1.13.1 ## ALIGNMENTS 1 - 16 SeqNo PDBNo AA STRUCTURE BP1 BP2 ACC NOCC VAR ....:....1....:....2....:....3....:....4....:....5....:....6....:....7 1 1 A P 0 0 111 3 21 P A P 2 2 A I - 0 0 150 5 19 I M LL M 3 3 A E - 0 0 159 6 51 E QT VI I 4 4 A L - 0 0 59 6 55 L ET SS P 5 5 A L - 0 0 81 6 14 L LL II L 6 6 A P - 0 0 54 6 36 P KK PA K 7 7 A E - 0 0 6 6 15 E EQ QE E 8 8 A T - 0 0 0 6 29 T TT ST R 9 9 A P - 0 0 0 6 47 P PP IL L 10 10 A S - 0 0 2 6 16 S SS SS R 11 11 A Q - 0 0 3 6 22 Q QQ EE D 12 12 A T - 0 0 1 6 31 T TT TV Q 13 13 A A - 0 0 2 6 49 A GV TT Y 14 14 A G > - 0 0 3 6 16 G GG GA A 15 15 A P T 3 S+ 0 0 55 6 0 P PP PP P 16 16 A Y T >> + 0 0 33 6 44 Y YY NH V 17 17 A V H X> + 0 0 0 4 38 V VF .. Y 18 18 A H H 3> S+ 0 0 6 3 38 H HA .. . 19 19 A I H <4 S+ 0 0 0 3 33 I IY .. . 20 20 A G H << S+ 0 0 2 3 0 G GG .. . ..... etc etc etc ..... 429 530 M Q E +P 209 0H 48 7 46 Q RR EE T A 430 531 M R E -P 208 0H 89 6 47 R D NG A R 431 532 M K E -P 207 0H 73 6 31 K A EE E E 432 533 M T - 0 0 58 6 32 T T TT E H 433 534 M H - 0 0 105 5 53 H P VV E 434 535 M F 0 0 212 5 14 F M FF L 435 536 M E 0 0 139 3 21 E E Q ##