

PFRMAT ABF1
TARGET T0022
AUTHOR 9293-6602-8904  J. Fernando Bazan, DNAX, bazan@dnax.org
REMARK
REMARK ================================================================
REMARK Completed Saturday to Sunday, Aug. 31-Sept. 1, 1996
REMARK
REMARK This file contains an 'ab initio' prediction for target T0022,
REMARK the enzyme L-fucose isomerase from E. coli (aa 1-591, swissprot
REMARK file fuci_ecoli), due Sept. 1, 1996.  The registered predictor is 
REMARK J. Fernando Bazan from the DNAX Research Institute in Palo Alto, 
REMARK CA (email bazan@dnax.org).  (This is my second prediction;
REMARK the first was for target T0011 which has been assigned the
REMARK accession code T0011AB395.) Below is attached a 1.1 (secondary
REMARK structure string) and 2.1 (segment pairing and contact) 
REMARK prediction in the right format. Based on the paper prediction,
REMARK a 3D model of the isomerase was built and is booked
REMARK as a 3.1-type prediction.  
REMARK
REMARK      The following text describes the methods used to arrive
REMARK at these predictions.  The CASP2 target report for the isomerase
REMARK was right - only one homolog for the E. coli sequence is 
REMARK detected, swissprot fuci_haein (as assessed by BLAST searches).
REMARK Nevertheless, the duo is aligned and sent off to various
REMARK prediction engines.  PHD and PSSP runs yield a strong a/b
REMARK alternating pattern.
REMARK 
REMARK       At the same time, threading runs (on web or SGI) are
REMARK conducted with the E. coli sequence (123D, topits, PSCAN,
REMARK ProFIT) - one tends to get large enzymes with a/b folds, 
REMARK heavily represented by the popular TIM-barrel types.  I take 
REMARK another, more intuitive tack: the chemistry and substrates/
REMARK products of this enzyme (L-fucose->L-fuculose) are similar 
REMARK to those of other isomerases, notably rhamnose isomerase
REMARK (rhaa_ecoli, 419 aa, performs L-rhamnose->L-rhamnulose), 
REMARK xylose isomerase (xyla_ecoli, 440 aa, does D-xylose->D-xylulose),
REMARK and arabinose isomerase (araa_ecoli, 500 aa, does L-arabinose->
REMARK L-ribulose).  Only the xylose isomerase has homologs available;
REMARK these are easily harvested from the databases using BLAST, and 
REMARK then aligned with ClustalW into two distinct XI families,
REMARK one E.coli-like (~440 aa) and another Strep-like (~400 aa). 
REMARK These two families are profile-merged and then an aggregate
REMARK alignment/profile calculated for the XI's that is 467 aa long
REMARK - the two family seqs are quite different, and are occasionally
REMARK punctuated by conserved aa.  This is sent thru the usual 
REMARK prediction engines. 
REMARK 
REMARK      Once again, having read Farber's comprehensive, recurrent
REMARK reviews of the b/a-barrel family, I rapidly recall that XI is 
REMARK one of the most well studied TIM-barrel-like folds.  A quick
REMARK view of 6XIA, one of many available XI structures (several 
REMARK in complexes), reveals that XI has one main domain - the eight-
REMARK fold barrel - decorated by many extra helices.  This latter
REMARK fact quickly inflates the expected ~250 aa length typical of 
REMARK many economical barrels, to the bloated 400+ aa of XI.  All of
REMARK solved XI structures are quite similar, from the more frugal
REMARK 'Strep'-like group, with principal 2o str = a-b1-a-b2-a-b3-a-
REMARK b4-a-b5-a-b6-a-b7-a-b8-(8 small a's) - b8 ends at ~aa 285 of 387.
REMARK Could FI, RI and AI be quite divergent members of the same
REMARK structural family?   To cut short this story, the answer
REMARK is likely yes for FI and RI, and unsure for AI. The enlarged-XI
REMARK profile aligns FI and RI pretty well to XI, or effectively
REMARK to each other (in succession); AI does not join the fold as 
REMARK easily so it is dropped from the analysis.  Interestingly,
REMARK Eloffson's PSCAN combined seq/str profile threading program
REMARK significantly places 6XIA as the highest scoring match to both 
REMARK FI and RI; AI does not ring the same bell.  The combined XI-RI-FI
REMARK alignment/profile is 598 aa in length.  
REMARK 
REMARK     Part of this alignment follows, with Fi_ec being the target
REMARK sequence - the first amino acid below is residue A70, so we're
REMARK missing an N-terminal bit that is missing in Xi_st (PDB 6XIA).
REMARK Landmark residues in alignment have a *; 2o str labeled for
REMARK barrel.  Key residues in active site for XI are marked by +'s.
REMARK For details of XI, see Whitlow et al., Proteins 9, 153, 1991; 
REMARK Lavie et al., Biochem. 33, 5469, 1994; Whitaker et al., JBC 270,
REMARK 22895, 1995. The key point about XI mechanism concerns the use
REMARK of 2 divalent cations (like Mg2+) that mediate a hydride shift
REMARK during the interconversion.  The sidechain ligands to these
REMARK cations are conserved in FI, so I presume that it also
REMARK functions by a similar catalytic mechanism.
REMARK
REMARK        51                                 +               100
REMARK Xi_Ec  PDELVLGKRM EEHLRFAACY WHTFCWNGAD .MFGVGAF.. NRPWQQPGEA 
REMARK Xi_St  .....NYQPT PED.RFTFGL W.TVGWEGRD .PFGDAT... .......... 
REMARK Ri_Ec  IDVEEALRQL DRL.PVSMHC WQGDDVSGFE NPEGSLTGGI QATGNYPGKA 
REMARK Fi_Ec  ACEEKFSSQN VGLTITVTPC W.CYGSETID .MDPTRP... KAIWGFNG.. 
REMARK Fi_Ha  ACADKFKREN VGLTITVTPC W.CYGSETID .MDPHMP... KAIWGFNG.. 
REMARK                       ------ *            
REMARK                         b1
REMARK        101                            +                   150
REMARK Xi_Ec  LALAKRKADV AFEFFHKLHV ....PFYCFH DVDVSPEGAS LKEYINNFAQ 
REMARK Xi_St  .RTALDPVES VRRLAELGA. ....HGVTFH DDDLIPFGS. ...SDSERYE 
REMARK Ri_Ec  RNASELRADL EQAMRLIPGP ....KRLNLH AIYLESDTPV ..SRDQIKPE 
REMARK Fi_Ec  .TERPGAVYL AAALAAHSQK GIPAFSIYGH DVQDADDTS. ..IPADVEEK 
REMARK Fi_Ha  .TERPGAVYL AAALAGHSQL GLPAFSIYGT EVQEADDTN. ..IPEDVKEK 
REMARK              ==== =======        ---- * *              ======
REMARK                   a1               b2
REMARK        151                        +                        200
REMARK Xi_Ec  MVDVLAGKQE ESGV..KLLW GTANCFTNPRY GAG....AAT N.PDPEVFSW 
REMARK Xi_St  HVKRFRQALD DTGM..KVPM ATTNLFTHPVF KDG....GFT A.NDRDVRRY 
REMARK Ri_Ec  HFKNWVEWAK ANQ...LGLD FNPSCFSHPLS ADG....FTL SHADDSIRQF 
REMARK Fi_Ec  LLRFARAGLA VASMKGKSYL SLG.GVSMGIA GSIVDHNFFE SWLGMKVQAV 
REMARK Fi_Ha  LLRFARAGLA VASIRGKSYL SIG.SVSMGIA GSIVNQAFFQ EYLGMRNEYV 
REMARK        ========== ==    ---- -                  ^^      ======
REMARK             a2             b3
REMARK        201                          +                     250
REMARK Xi_Ec  AATQVVTAME ATHKLGG... ..ENYVLWGG ...REGY... ETLLNTDLRQ 
REMARK Xi_St  ALRKTIRNID LAVELGA... ..ETYVAWGG ...REGA... ESGGAKDVRD 
REMARK Ri_Ec  WIDHCKASRR VSAYFGEQLG TPSVMNIWIP ....DGM... IPDGMKDITV 
REMARK Fi_Ec  DMTELRRRID QKIYDEAEL. ..EMALAWAD KNFRYGEDEN NKQYQRNAEQ 
REMARK Fi_Ha  DMMEIKRRLD RKIYDQEEV. ..DLALSWVK QYCKEGVDVN SLENQRNAEE 
REMARK        ========== =====         ----*                     ===
REMARK              a3                   b4
REMARK        251                                              + 300
REMARK Xi_ec  EREQLGRFMQ MVVEHKHKI. .......... .....GFQGT LLIEPKPQEP 
REMARK Xi_st  ALDRMKEAFD LLGEYVTSQ. .......... .....GYDIR FAIEPKPNEP 
REMARK Ri_ha  DRLAPRQRLL AALDEVISE. .......... .....KLNPA HHIDAVESKL 
REMARK Fi_ec  SRAVLRESLL MAMCIRDMMQ GNSKLADIGR VEESLGYNAI AAGFQ.GQRH 
REMARK Fi_ha  RAELWENVVK MTIITRDLMV GNPKLATLNY AEEALGHNAI AAGFQ.GQRH 
REMARK        ========== =========                      - ----    ^^
REMARK                 a4                                 b5
REMARK        301                                              + 350
REMARK Xi_ec  TKHQYD.YDA ATVYGFLKQ. ...FGLEKEI KLNIE..... ...ANHATLA 
REMARK Xi_st  RGDILL.PTV GHALAFIER. ...LERPELY GVNPE..... ...VGHEQMA 
REMARK Ri_ha  FGIGAESYTV GSNEFYMGY. ....ATSRQT ALCLD..... ...AGHFHPT 
REMARK Fi_ec  WTDQYPNGDT AEAILNSSFD WNGVREPFVV ATENDSLNGV AMLMGHQLTG 
REMARK Fi_ha  WTDHLPNGDF MEAMLNSTYD WNGVRPPYIL ATENDSLNAI GMLFGHQLTG 
REMARK                 = =======           --- --             **
REMARK                     a5                b6
REMARK        351                                                400
REMARK Xi_ec  G.HSFHHEIA TAIALG.... .......... .LFGSVDANR GD........ 
REMARK Xi_st  G.LNFPHGIA QALWAG.... .......... .KLFHIDLN. GQ........ 
REMARK Ri_ha  ..EVISDKIS AAMLYV.... .......... .PQLLLHVS. .......... 
REMARK Fi_ec  TAQVFADVRT YWSPEAIERV TGHKLDGLAE HGIIHLINS. GSAALDGSCK 
REMARK Fi_ha  KAQIFADVRT YWSQDSVERV TGWRP....E SGFIHLINS. GSAALDGTGE 
REMARK            ====== =====                    -----
REMARK                 a6                           b7
REMARK        401                                                450
REMARK Xi_ec  .........A QLGWDTD.QF PNSVEENALV MYEILKAGGF T........T 
REMARK Xi_st  .........N GIKYDQDLRF GAGDLRAAFW LVDLLESAGY .........S 
REMARK Ri_ha  .........R PVRWDSD.HV VLLDDETQAI ASEIVRHDLF D.....RVHI 
REMARK Fi_ec  QRDSEGNPTM KPHWEISQQE ADACLAATEW CPAIHEYFRG GGYSSRFLTE 
REMARK Fi_ha  HQDAQGNPTL KPAWDVTEEE AKRCLENTRW CPAVHEYFRG GGLSSQFLTK
REMARK                      *           ====== ======== 
REMARK                                         a7
REMARK        451    +                                           500
REMARK Xi_ec  G..GLNFDAK VRRQST.... DKYDLFYGHI GAMDTMALAL KIAARMIED. 
REMARK Xi_st  G..PRHFDFK PPRTE..... DFDGVWASAA GCMRNYLILK ERAAAFRAD. 
REMARK Ri_ha  G..LDFFDAS INR....... ..IAAWVIGT R.NMKKALLR ALLEP.TAD. 
REMARK Fi_ec  GGVPFTMTRV NIIKGLGPVL QIAEGWSVEL P.KDVHDILN KRTNSTWPTT 
REMARK Fi_ha  GGIPFTIHRI NLIKGLGPVL QIAEGWSIDL P.QDVHNKLN QRTNETWPTT 
REMARK           -----               ====*==== ========== ========
REMARK             b8                               a8
REMARK        501                                                550
REMARK Xi_ec  .......... .GELDKRIAQ RYSGWNSELG Q....QILKG QMSLADL... 
REMARK Xi_st  .......... .PEVQEALRA SRLDELARPT A..ADGLQAL LDDRSAF... 
REMARK Ri_ha  .......... .VRKLEAAGD .YTARLALLE E.QKSLPWQA VWEMYCQ... 
REMARK Fi_ec  WFAPRLTGKG PFTDVYSVMA NWGANHGVLT I.GHVGADFI TLASMLRIPV 
REMARK Fi_ha  WFVPRLTGKG AFTDVYSVMA NWGANHCVAT H.GHVGADLI TLASMLRIPV 
REMARK                    =========   =====          ==== ==
REMARK                        a9       a10             a11
REMARK        551                                              598
REMARK Xi_ec  ........AK YAQEHHLSPV ...HQSGRQE QLENLVNHYL FDK.....
REMARK Xi_st  ........EE FDVDAAAARG M.AFERLDQL AMDHLLGARG AAA.....
REMARK Ri_ha  .......... RHDTPAGS.. ..EWLESVRA YEKEILSRRG ........
REMARK Fi_ec  CMHNVEETKV YRPSAWAAHG M..DIEGQDY RACQNYGPLY KR......
REMARK Fi_ha  CMHNVSEKNI FRPSAWNGFG Q..DKEGQDY RACQNFGPLY K.......
REMARK                     ======      ======= ======
REMARK                       a12              a13
REMARK
REMARK      With some slight changes, the predicted, core 2o str for 
REMARK the Ecoli FI in section 1.1 below is as assigned/labeled above.
REMARK      Alternative alignments for b3 and b5 are below:
REMARK
REMARK 
REMARK        151                                    +              
REMARK Xi_Ec  MVDVLAGKQE ESGV...... ...KLLWGTANC.....FTNPRYGAGAAT NP
REMARK Xi_St  HVKRFRQALD DTGM...... ...KVPMATTNL.....FTHPVFKDGGFT.AN 
REMARK Ri_Ec  HFKNWVEWAK ANQ....... ...LGLDFNPSC.....FSHPLSADGFTLSHA 
REMARK Fi_Ec  LLRFARAGLA VASMKGKSYL SLGGVSMGIAGSIVDHNFFES.........WL 
REMARK Fi_Ha  LLRFARAGLA VASIRGKSYL SIGSVSMGIAGSIVNQAFFQE.........YL 
REMARK        ========== ==             -----                       
REMARK             a2                     b3
REMARK
REMARK        451        +                                           500
REMARK Xi_ec  G......PLNFDAKVRRQST DKYDLFYGHI GAMDTMALAL KIAARMIED. 
REMARK Xi_st  G......LRHFDFKPPRTE. DFDGVWASAA GCMRNYLILK ERAAAFRAD. 
REMARK Ri_ha  G......LDFFDASINR... ..IAAWVIGT R.NMKKALLR ALLEP.TAD. 
REMARK Fi_ec  GGVPFTMTRVNIIKGLGPVL QIAEGWSVEL P.KDVHDILN KRTNSTWPTT 
REMARK Fi_ha  GGIPFTIHRINLIKGLGPVL QIAEGWSIDL P.QDVHNKLN QRTNETWPTT 
REMARK               -----          ====*==== ========== ========
REMARK                  b8                        a8
REMARK       The reason for the above concerns the conserved Phe after b3, 
REMARK and the conserved Asp at the end of b8; the first realignment matches
REMARK the Phe with a duo of conserved FI Phe's; the second realignment 
REMARK nears the Asp position with a conserved Lys.
REMARK
REMARK       Biological implications of the model: discovery of key
REMARK conserved active site residues of the XI in the FI sequence 
REMARK -notably His140 after b1 (involved in anomeric selection and 
REMARK stabilizes transition state by h-bonding), His349 after b6 
REMARK (coordinates metal ion #2), Asp307 after b5 (instead of Glu in
REMARK XI, possibly, aiding to hold Arg303 -Lys in XI- in catalytic 
REMARK position), Trp232 after b4 (stabilizes transition state), Phe
REMARK 196 & 197 after b3 (stabilize trans state), & Glu418 after b7 
REMARK (Asp in XI, Asp in fuci_haein; hydride shift).  Several other
REMARK aromatic residues also survive the ravages of time.  In short,
REMARK the structure of FI is just an elaboration of the XI scaffold
REMARK with several longer loops, and a longer N-terminal extension.
REMARK 
REMARK        As profiles detected this relationship, HMMers should 
REMARK do quite well, as will the threaders -although the large
REMARK insertions and the abnormally large size for a 'TIM-barrel'
REMARK may obscure the relationship.
REMARK  
REMARK        That's the extent of the work. Sent in to LLNL on
REMARK Sunday, Sept. 1st at ~1:40 pm PST. 
REMARK
REMARK =====================================================================
BEGDAT 1.1 1 1.00
SS 591 1
M  C  1.00      # N-terminus
K  C  1.00
K  C  1.00
I  C  1.00
S  C  1.00
L  C  1.00
P  C  1.00
K  C  1.00
I  C  1.00
G  C  1.00
I  C  1.00
R  C  1.00
P  C  1.00
V  C  1.00
I  C  1.00
D  C  1.00
G  C  1.00
R  C  1.00
R  C  1.00
M  C  1.00
G  C  1.00
V  H  1.00       # extracore helix - segment 1
R  H  1.00
E  H  1.00
S  H  1.00
L  H  1.00
E  H  1.00
E  H  1.00
Q  H  1.00
T  H  1.00
M  H  1.00
N  H  1.00
M  H  1.00
A  H  1.00
K  H  1.00
A  H  1.00
T  H  1.00
A  H  1.00
A  H  1.00
L  H  1.00
L  H  1.00
T  H  1.00
E  H  1.00
K  H  1.00
L  H  1.00
R  H  1.00
H  H  1.00
A  H  1.00
C  H  1.00
G  C  1.00
A  C  1.00
A  C  1.00
V  E  1.00       # extracore strand - segment 2
E  E  1.00
C  E  1.00
V  E  1.00
I  E  1.00
S  E  1.00
D  C  1.00
T  C  1.00
C  C  1.00
I  H  1.00       # extracore helix - segment 3
A  H  1.00
G  H  1.00
M  H  1.00
A  H  1.00
E  H  1.00
A  H  1.00
A  H  1.00
A  H  1.00
C  H  1.00
E  H  1.00
E  H  1.00
K  H  1.00
F  H  1.00
S  H  1.00       # b/a barrel model in 3.1 starts here
S  C  1.00
Q  C  1.00
N  C  1.00
V  C  1.00
G  C  1.00
L  E  1.00       # strand b1 - segment 4
T  E  1.00
I  E  1.00
T  E  1.00
V  E  1.00
T  E  1.00
P  E  1.00
C  E  1.00
W  C  1.00
C  C  1.00
Y  C  1.00
G  C  1.00
S  C  1.00
E  C  1.00
T  C  1.00
I  C  1.00
D  C  1.00
M  C  1.00
D  C  1.00
P  C  1.00
T  C  1.00
R  C  1.00
P  C  1.00
K  C  1.00
A  C  1.00
I  C  1.00
W  C  1.00
G  C  1.00
F  C  1.00
N  C  1.00
G  C  1.00
T  C  1.00
E  C  1.00
R  C  1.00
P  C  1.00
G  C  1.00
A  H  1.00       # helix a1 - segment 5
V  H  1.00
Y  H  1.00
L  H  1.00
A  H  1.00
A  H  1.00
A  H  1.00
L  H  1.00
A  H  1.00
A  H  1.00
H  H  1.00
S  H  1.00
Q  H  1.00
K  C  1.00
G  C  1.00
I  C  1.00
P  C  1.00
A  C  1.00
F  E  1.00       # strand b2 - segment 6
S  E  1.00
I  E  1.00
Y  E  1.00
G  C  1.00
H  C  1.00
D  C  1.00
V  C  1.00
Q  C  1.00
D  C  1.00
A  C  1.00
D  C  1.00
D  C  1.00
T  C  1.00
S  C  1.00
I  C  1.00
P  C  1.00
A  H  1.00      # helix a2 - segment 7
D  H  1.00
V  H  1.00
E  H  1.00
E  H  1.00
K  H  1.00
L  H  1.00
L  H  1.00
R  H  1.00
F  H  1.00
A  H  1.00
R  H  1.00
A  H  1.00
G  H  1.00
L  H  1.00
A  H  1.00
V  H  1.00
A  H  1.00
S  C  1.00
M  C  1.00
K  C  1.00
G  C  1.00
K  E  1.00       # strand b3 - segment 8
S  E  1.00
Y  E  1.00
L  E  1.00
S  E  1.00
L  E  1.00
G  C  1.00
G  C  1.00
V  C  1.00
S  C  1.00
M  C  1.00
G  C  1.00
I  C  1.00
A  C  1.00
G  C  1.00
S  C  1.00
I  C  1.00
V  C  1.00
D  C  1.00
H  C  1.00
N  C  1.00
F  C  1.00
F  C  1.00
E  C  1.00
S  C  1.00
W  C  1.00
L  C  1.00
G  C  1.00
M  H  1.00        # helix a3 - segment 9
K  H  1.00
V  H  1.00
Q  H  1.00
A  H  1.00
V  H  1.00
D  H  1.00
M  H  1.00
T  H  1.00
E  H  1.00
L  H  1.00
R  H  1.00
R  H  1.00
R  H  1.00
I  H  1.00
D  H  1.00
Q  H  1.00
K  H  1.00
I  H  1.00
Y  H  1.00
D  H  1.00
E  C  1.00
A  C  1.00
E  C  1.00
L  C  1.00
E  C  1.00
M  E  1.00        # strand b4 - segment 10
A  E  1.00
L  E  1.00
A  E  1.00
W  E  1.00
A  C  1.00
D  C  1.00
K  C  1.00
N  C  1.00
F  C  1.00
R  C  1.00
Y  C  1.00
G  C  1.00
E  C  1.00
D  C  1.00
E  C  1.00
N  C  1.00
N  C  1.00
K  C  1.00
Q  C  1.00
Y  C  1.00
Q  C  1.00
R  C  1.00
N  C  1.00
A  H  1.00       # helix a4 - segment 11
E  H  1.00
Q  H  1.00
S  H  1.00
R  H  1.00
A  H  1.00
V  H  1.00
L  H  1.00
R  H  1.00
E  H  1.00
S  H  1.00
L  H  1.00
L  H  1.00
M  H  1.00
A  H  1.00
M  H  1.00
C  H  1.00
I  H  1.00
R  H  1.00
D  H  1.00
M  H  1.00
M  H  1.00
Q  H  1.00
G  C  1.00
N  C  1.00
S  C  1.00
K  C  1.00
L  C  1.00
A  C  1.00
D  C  1.00
I  C  1.00
G  C  1.00
R  C  1.00
V  C  1.00
E  C  1.00
E  C  1.00
S  C  1.00
L  C  1.00
G  C  1.00
Y  C  1.00
N  C  1.00
A  C  1.00
I  E  1.00      # strand b5 - segment 12
A  E  1.00
A  E  1.00
G  E  1.00
F  E  1.00
Q  C  1.00
G  C  1.00
Q  C  1.00
R  C  1.00
H  C  1.00
W  C  1.00
T  C  1.00
D  C  1.00
Q  C  1.00
Y  C  1.00
P  C  1.00
N  C  1.00
G  C  1.00
D  C  1.00
T  H  1.00      # helix a5 - segment 13
A  H  1.00
E  H  1.00
A  H  1.00
I  H  1.00
L  H  1.00
N  H  1.00
S  H  1.00
S  C  1.00
F  C  1.00
D  C  1.00
W  C  1.00
N  C  1.00
G  C  1.00
V  C  1.00
R  C  1.00
E  C  1.00
P  C  1.00
F  E  1.00      # strand b6 - segment 14
V  E  1.00
V  E  1.00
A  E  1.00
T  E  1.00
E  C  1.00
N  C  1.00
D  C  1.00
S  C  1.00
L  C  1.00
N  C  1.00
G  C  1.00
V  C  1.00
A  C  1.00
M  C  1.00
L  C  1.00
M  C  1.00
G  C  1.00
H  C  1.00
Q  C  1.00
L  C  1.00
T  C  1.00
G  C  1.00
T  C  1.00
A  H  1.00      # kinked helix a6 - segment 15
Q  H  1.00
V  H  1.00
F  H  1.00
A  H  1.00
D  H  1.00
V  H  1.00
R  H  1.00
T  H  1.00
Y  H  1.00
W  H  1.00
S  H  1.00      # kink
P  H  1.00
E  H  1.00
A  H  1.00
I  H  1.00
E  H  1.00
R  H  1.00
V  H  1.00
T  H  1.00
G  C  1.00
H  C  1.00
K  C  1.00
L  C  1.00
D  C  1.00
G  C  1.00
L  C  1.00
A  C  1.00
E  C  1.00
H  C  1.00
G  C  1.00
I  E  1.00      # strand b7 - segment 16
I  E  1.00
H  E  1.00
L  E  1.00
I  E  1.00
N  E  1.00
S  C  1.00
G  C  1.00
S  C  1.00
A  C  1.00
A  C  1.00
L  C  1.00
D  C  1.00
G  C  1.00
S  C  1.00
C  C  1.00
K  C  1.00
Q  C  1.00
R  C  1.00
D  C  1.00
S  C  1.00
E  C  1.00
G  C  1.00
N  C  1.00
P  C  1.00
T  C  1.00
M  C  1.00
K  C  1.00
P  C  1.00
H  C  1.00
W  C  1.00
E  H  1.00       # kinked helix a7 - segment 17
I  H  1.00
S  H  1.00
Q  H  1.00
Q  H  1.00
E  H  1.00
A  H  1.00
D  H  1.00
A  H  1.00
C  H  1.00
L  H  1.00
A  H  1.00
A  H  1.00
T  H  1.00
E  H  1.00
W  H  1.00
C  H  1.00      # kinked also
P  H  1.00
A  H  1.00
I  H  1.00
H  H  1.00
E  H  1.00
Y  H  1.00
F  H  1.00
R  H  1.00
G  C  1.00
G  C  1.00
G  C  1.00
Y  C  1.00
S  C  1.00
S  C  1.00
R  C  1.00
F  C  1.00
L  C  1.00
T  C  1.00
E  C  1.00
G  C  1.00
G  C  1.00
V  C  1.00 
P  E  1.00      # strand b8 - segment 18
F  E  1.00
T  E  1.00
M  E  1.00
T  E  1.00
R  C  1.00
V  C  1.00
N  C  1.00
I  C  1.00
I  C  1.00
K  C  1.00
G  C  1.00
L  C  1.00
G  C  1.00
P  C  1.00
V  C  1.00
L  C  1.00
Q  C  1.00
I  H  1.00      # helix a8 - segment 19
A  H  1.00
E  H  1.00
G  H  1.00
W  H  1.00
S  H  1.00
V  H  1.00
E  H  1.00
L  H  1.00
P  H  1.00
K  H  1.00
D  H  1.00
V  H  1.00
H  H  1.00
D  H  1.00
I  H  1.00
L  H  1.00
N  H  1.00
K  H  1.00
R  H  1.00
T  H  1.00
N  H  1.00
S  H  1.00
T  H  1.00
W  H  1.00
P  C  1.00
T  C  1.00       # last residue in 3.1 model that ends core barrel
T  C  1.00
W  C  1.00
F  C  1.00
A  C  1.00
P  C  1.00
R  C  1.00
L  C  1.00
T  C  1.00
G  C  1.00
K  C  1.00
G  C  1.00
P  C  1.00
F  H  1.00      # extracore helix - segment 20
T  H  1.00
D  H  1.00
V  H  1.00
Y  H  1.00
S  H  1.00
V  H  1.00
M  H  1.00
A  H  1.00
N  C  1.00
W  C  1.00
G  H  1.00     # extracore helix - segment 21
A  H  1.00
N  H  1.00
H  H  1.00
G  H  1.00
V  C  1.00
L  C  1.00
T  C  1.00
I  C  1.00
G  C  1.00
H  C  1.00
V  C  1.00
G  C  1.00
A  H  1.00     # extracore helix - segment 22
D  H  1.00
F  H  1.00
I  H  1.00
T  H  1.00
L  H  1.00
A  H  1.00
S  H  1.00
M  C  1.00
L  C  1.00
R  C  1.00
I  C  1.00
P  C  1.00
V  C  1.00
C  C  1.00
M  C  1.00
H  C  1.00
N  C  1.00
V  C  1.00
E  C  1.00
E  C  1.00
T  C  1.00
K  C  1.00
V  C  1.00
Y  C  1.00
R  C  1.00
P  H  1.00     # extracore helix - segment 23
S  H  1.00
A  H  1.00
W  H  1.00
A  H  1.00
A  H  1.00
H  C  1.00
G  C  1.00
M  C  1.00
D  H  1.00    # extracore helix - segment 24
I  H  1.00
E  H  1.00
G  H  1.00
Q  H  1.00
D  H  1.00
Y  H  1.00
R  H  1.00
A  H  1.00
C  H  1.00
Q  H  1.00
N  H  1.00
Y  H  1.00
G  C  1.00
P  C  1.00
L  C  1.00
Y  C  1.00
K  C  1.00
R  C  1.00    # C-terminus
ENDDAT 1.1
BEGDAT 2.1 1 1.00 1
8                       
 4   6  KK  1.00   0   0  0.00       # only include strand-strand pairs,
 6   8  KK  1.00   0   0  0.00       # eight in barrel, all parallel/KK
 8  10  KK  1.00   0   0  0.00
10  12  KK  1.00   0   0  0.00
12  14  KK  1.00   0   0  0.00
14  16  KK  1.00   0   0  0.00
16  18  KK  1.00   0   0  0.00
 4  18  KK  1.00   0   0  0.00
ENDDAT 2.1
END
