throbber
Genentech Exhibit 2001
`
`Pfizer v. Genentech
`Pfizer v. Genentech
`IPR2017-01488
`IPR2017-01488
`Genentech Exhibit 2001
`
`Page 1
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`NeeEN
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`Table of Contents
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`Page 12
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`

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`Project No.
`Book No.
`
`From Page No.__
`
`On
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`LFbY # Aden sisegnt |eget) Ponapewt
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`fiw Hat 1PAJ—AHFL AMP BFAB
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`deperpettitnns hac WM, Ca, C atonne? (1/35alone) |
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`3480-771
`
`
`
`To Page No.
`
`Page 14
`
`

`

`64 template TITLE (hvurage Corrs
`
`Project No
`Book No
`
`From Page No.__
`
`BRK ARERR ER RARER RE RH RRR KERR IR ERE RRR NI RE RIK KIRK RIK TIN INR RRR RD
`Ga:::: letters ~ Ca < 1.0A from 1FB4 HV
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`() denotes be
`
`Witnessed & Understood by me,
`
`Invented by
`
`To Page No.
`
`Page 15
`
`Page 15
`
`
`

`

`4
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`Project No._._
`Book No. TITLE
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`GAP IN SEQUENCE:
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`GAP IN SEQUENCE:
`8-
`17 in file: 1FB4.PDBASALA
`GAP IN SBQUENCE:
`23-
`33 in file:1FB4.PDBASALA
`GAP IN SEQUENCE:
`4i-
`45 in file: 1F54.PDBASALA
`GAP IN SEQUENCE:
`51i-
`58 in file:1FB4.?DBASALA
`GAP IN SEQUENCE:
`62-
`67 in file:1FB4.PDBASALA
`GAP IN SEQUENCE:
`72-
`76 in file: 1FPB4.PDBASALA
`GAP IN SEQUENCE:
`B3-
`92 in file:1FB4.PDBASALA
`GAP IN SEQUENCE:
`98- 107 in file: 1FB4.PDBASALA
`1PBJ.PDBASALA
`62 residues and
`GAP IN SEQUENCE:
`o-
`3
`in file:1FBJ.PDBASALA
`GAP IN SEQUENCE:
`17 in file:1FBJ.PDBASALA
`8-
`GAP IN SEQUENCE:
`23-
`33 in file:1FBJ.PDBASALA
`GAP IN SEQUENCE:
`4i-
`45 in file: 1FBJ.PDBASALA
`51-
`58 in file:1FBJ.PDBASALA
`GAP IN SEQUENCE:
`62-
`67 in file: 1FBJ.PDBASALA
`72-
`76 in file: 1FBJ.PDBASALA
`GAP IN SEQUENCE:
`GAP IN SEQUENCE:
`83-
`92 in file:1PBJ.PDBASALA
`GAP IN SEQUENCE:
`98- 107 in file: 1FBJ.PDBASALA
`2HFL. PDBASALA
`62 residues and
`GAP IN SEQUENCE:
`o=
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`GAP IN SEQUENCE:
`17 in file: 2HFL.PDBASALA
`8-
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`23-
`33 in file: 2HFL.PDBASALA
`GAP IN SEQUENCE:
`4l1-
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`GAP IN SEQUENCE:
`51-
`58 in file: 2HFL.PDBASALA
`GAP IN SEQUENCE:
`62~
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`GAP IN SEQUENCE:
`72-
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`(GAP IN SEQUENCE:
`83-
`92 in file: 2HPL.PDBASALA
`GAP IN SEQUENCE:
`98- 105 in file: 2HFL.PDBASALA
`2MCP. PDBASALA
`62 residues and
`(GAP IN SEQUENCE:
`o-
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`GAP IN SEQUENCE:
`17 in file: 2MCP.PDBASALA
`8-
`GAP IN SEQUENCE:
`23-
`33 in file: 2MCP,.PDBASALA
`GAP IN SEQUENCE:
`4l-
`45 in file: 2MCP.PDBASALA
`GAP IN SEQUENCE:
`51-
`60 in file: 2MCP.PDBASALA
`' GAP IN SEQUENCE:
`64-
`69 in file: 2MCP.PDBASALA
`GAP IN SEQUENCE:
`74-
`78 in file:
`2MCP.PDBASALA
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`85-
`94 in file: 2MCP.PDBASALA
`GAP IN SEQUENCE:
`100- 111 in file: 2MCP.PDBASALA
`3FAB. PDBASALA
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`GAP IN SEQUENCE:
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`23-
`33 in file: 3FAB.PDBASALA
`GAP IN SEQUENCE:
`41-
`45 in file: 3FAB.PDBASALA
`_ GAP IN SEQUENCE:
`51-
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`GAP IN SEQUENCE:
`61-
`66 in file:3PAB.PDBASALA
`GAP IN SEQUENCE:
`71-
`75 in file:3FAB.PDBASALA
`GAP IN SEQUENCE:
`82-
`91 in file: 3PAB.PDBASALA
`GAP IN SEQUENCE:
`97- 108 in file:3FAB.PDBASALA
`_ GAP IN SEQUENCE:
`108- 107 in file:3FAB.PDBASALA
`MAXAT =
`306 : MAXRES =
`62
`B-factor range is:
`2,00 ta 33.72
`~ B-factor BIN range is: Zt
`34
`B-FACTOR STATS DO NOT INCLUDE 3PAB
`Dist range
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`|ssNeCa Ca-C C=O C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca-C-N O-C-N N-Ca- m4
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`
`Page 16
`
`Page 16
`
`

`

`i)
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`p » Project No.
`
`Book No.______
`
`
`
`5
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`2MCP, 1FBJ AND 2HFL are kappa-type
`
`capital letters = Ca < 1.0A from 2HFL HV
`
`
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`KK KEKE KKK RRR EEEKRE KER RARER ERE EERE ER KEKE EERE EAREREEAKREREERERE 1.+re ee: +.=" s -
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`
`Page 17
`
`Page 17
`
`

`

`AdaPaAaSHHHADQeamooAHGDANeAEEESExEaxnacawa=Romeo©awmnx@A4awszu@de~OamMOwo
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`{) denotes beta-strand residues
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`"Sequences of Proteins of Immunological
`consensus sequence from Kabat et al.,
`‘
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`Page 18
`
`To Page No.
`
`Page 18
`
`

`

`2HFL
`1000.0
`-93.
`129.8 -164.
`—122.
`“119.
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`
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`Page 20
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`

`

`Witnessed & Understood by me,
`
`Bond Lengths & Angles for AVERAGE after 200 cycles minimization (.COR3)
`N-Ca Ca-C C0 C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca-C-N O=C-N N-Ca-Cb
`1.454 1.526 1.230 1.337 1.530 124.2
`109.7
`220.2
`116.6
`123.3
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`Bond Lengths & Angles for AVERAGE
`(.COR4)
`after 300 cycles minimization (100 Ca released)
`H-Ca Ca-C
`C*O C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca~C-N O=C-N
`1.454 1.528 1.231 1.338 1.531 124.2
`109.9
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`Bond Lengths 4 Angles for AVERAGE
`(.COR5)
`after 600 cycles minimization (400 Ca released)
`N-Ca Ca-C
`CeO C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca-C-N O=C-N
`1,454 1.528 1.230 1.338 1.531 124.1
`110.0
`120.5
`116.5
`123.1
`6.002 0.002 0.001 0.001 0.001
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`Project No.
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`Bond Lengths & Angles for HVONFB4HV
`N-Ca Ca-C
`CQ C-N Ca-Cb C-N-Ca N-Ca~C Ca-C=0 Ca-C-N O=C-N N-Ca-Cb
`1.451 1.507 1.160 1.282 1.499
`125.3
`110.3
`120.9
`117.6
`122.2
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`Bond Lengths 4 Angles for AVERAGE after 50 cycles minimization (.COR)
`wa Ca-C
`C*O C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca~-C-N O=C-N N-Ca-Cb
`1.450 1.522 1.230 1.334 1.528 123.6
`109.4
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`Bond Lengths & Angles for AVERAGE after 100 cycles minimization (.COR2)
`N-Ca Ca-C
`C=0 C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca-C-N O=C-N N-Ca-Cb
`0.453 1.524 1.232 1.335 2.530 124.0
`108.5
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`Bond Lengths & Angles for AVERAGE after 200 cycles minimization with Ca
`{(.COR3¢)
`50 cycles with Ca at 10
`100 cycles with Ca at 2.5
`100 cycles with Ca at 0.5
`C=O C-N Ca-Cb C-N-Ca N-Ca-C Ca-C=0 Ca-C-N O=C-N N-Ca-Cb
`N-Ca Ca-c
`1.455 1.528 1.231 1.338 1.531 124.2
`110.0
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`himimneraheow 9 Book No.__
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`TITLE
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`Page 21
`
`

`

`CeeeT
`Project No.
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`Book No.—s—<iéir*TLE
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`From Page No.
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`Dihedral Angles for AVERAGE after 200 cycles minimization
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`To Page No. IG
`
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`Page 22
`
`Page 22
`
`

`

`
`Project No._____
`Book No.
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`
`
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`ee
`
`6201808887a56064i
`
`L2a341085980i
`
`L046i995646B05a8208001350299i378
`
`1000.
`
`wOrtnAuNewne
`
`Peeo
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`
`15.
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`
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`61.
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`aErx
`EEE
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`Tan
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`-1AL.rPuUwwo
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`168.
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`179.0
`176.5
`1000.0
`
`Witnessed & Understood by me,
`
`Date
`
`Dihedral Angles for AVERAGE
`after 200 cycles minimization wit
`50 cycles with Ca at 10.0
`100 cycles with Ca at 2.8
`»COR3C
`100 cycles with Ca at o. 5
`OMEGA
`PSI
`PHI
`179.8
`161.
`1000.0
`=L77.6
`103.
`=126.9
`174.4
`102.
`-96.6
`AVERAGE. PDBS
`AVERAGE . PDB3
`=L7e.5
`146.
`—12.2
`A-D-DD A-D<
`D-A-AA
`D-A< Dist D-A-AA A-D-DD A-D<=D-A<
`174.5
`170.
`=155.%
`Res# Res# Dist
`2.98
`98.0 132.8
`32.3-148.2
`4
`1000.
`1000.0
`69.6
`.00
`156.
`118.7
`6.4
`23
`40.7
`2.86
`149.3 108.9 -18.2
`33.3
`176.3
`168.
`1000.0
`179.5 =h.0
`142.
`98
`3.0% 227.3 117,59 -10.6 THe
`73.3
`rd
`17722
`164.
`-118.7
`90
`147.
`128.1
`20.0
`21
`=68.1
`2.69
`139.9 115.6
`17.3 -<So.8
`~1 78.7
`157.
`=150.6
`7
`-90
`154.
`192,8
`<=23.2
`“61.4
`2.94
`131.0 11)...
`&.9 =F
`175.4
`91.
`-133.6
`L32.3
`-5.8
`ak
`143.
`-41.4
`3.01
`152.5.123.8
`2.5
`28.3
`83
`178.6
`142.
`=74.5
`160.
`18
`-90
`13..
`-2.5
`-80.2
`2.84
`149.1 107.5 -28.5 -95.4
`=LTS.9
`156.
`116.6
`142.
`133.1 ~11.6
`61.3
`3.98
`199.9 113.2 -21.9 Fie
`81
`=1739.6
`97.
`-146.0
`89
`T33..
`123.5
`8.2
`20
`-49.3
`2.98
`134.2124.7
`3.9 “TH.2
`1000.
`1000.0
`=—2.2
`112.4
`29.5
`78
`166.
`.76
`30.3
`2-89
`136.9 119.6
`18.7 80,2
`177.2
`130.
`1000.0
`143.
`iz2.9 8.9
`22
`.00
`50.0
`2.91
`429.3 126.2 -22.6 Te
`144.
`178.5
`—99.5
`164.
`123.2 3.5
`52
`97
`42.9
`2.84
`152.8 110.6 -31.1 “BLS
`148.
`176.9
`=Laz.a
`126.7
`ce
`166.
`95
`34
`=32;0
`2.95
`2145.0 128.7
`0.0 -57.8
`178.8
`131.
`~1270..6
`147.
`120.6
`2.4
`97
`89
`72.0
`2.82
`134.7 [09.6
`L.7 “ae
`179.6
`138.
`=iLs.4
`143.
`ig6.7 “3.2
`35
`=63,6
`2.92
`136.0 116.7
`17.7 =.8
`» 95
`176.4
`144.
`=~107..7
`Laz.
`123.7
`1.5
`=15:.¢
`2.93
`158.2 2108.3
`25.4-102.4
`49
`«OL
`179.8
`105.
`~197..4
`3-
`-89
`156.
`162.0
`~-0.
`36
`154.2
`2.90
`133,8 108.1 -14.3-i37.7
`179.0
`164.
`-70.0
`143.
`133,7 -10.9
`31
`“$3.
`3.25
`136.8 175.6
`-3.2 ~Ee.T
`36
`1000.0
`65.7
`1000.
`121.0 -15.8
`159.
`96
`95
`=49.0
`2,94
`149.5 113.5
`13.8
`80.9
`~ifs.3
`isi.
`1000,0
`-83
`166.
`37
`113,0 -15.6
`-88.0
`2.82
`166.3 103.6 -17.8 101.3
`177.8
`iid.
`-140.5
`150.
`{LT .6
`6.1
`46
`68.3
`2.87
`155,1 120.9 -16.1 65.5
`87
`=173..6
`123.
`“62.7
`111.0
`12.8
`170.
`38
`- 84
`15.9
`2.97
`245,9 112.2 L7.9 Ba
`~31.
`—L79.9
`~86..7
`123.8
`25.2
`153.
`94
`a¢.2
`3.02
`134.0 118.3
`2.6 2.8
`93
`~173..4
`=L?d.
`=17T7.4
`123.4 —5.4
`128.
`34%
`~12
`77.8
`2.93
`130.3 117.5 -11.0 72.8
`=L7¥.4
`162.
`—156.7
`3.34
`102.1 123.9
`68.6~-159.8
`46
`1000.0
`—157.5
`1k. 7° Ts.3
`170.
`ta
`48
`-§5.9
`2.99
`141.7 121.4
`1.6-103.9
`i78.3
`1000.0
`8
`164.
`128.4
`8.6
`59
`Ne
`~178:.6
`-23.5 oe 134.2 127.3
`0.9 =ORLT
`—142.9
`127.2
`6.3
`148.
`50
`3,13
`60.3
`2.91¢@ 148.5 118.8
`12.0 -69.7
`177.9
`~146.6
`3.05
`88.1 140.3
`11.6-139.0
`67
`~178.4
`=76.5
`3,09
`200.0 135.2
`37.7-ERG.@
`68
`1000.0
`-66.1
`82
`2.92
`145.9 108.3 -27.0 79,8 ~
`178.2
`1000.0
`69
`2.92
`143.0 109.6 -22.6 ahd
`179.4
`-78..9
`80
`9.92
`136.1 111.6
`13.8 =9a.8
`176.8
`-126.0
`2.68
`131.0 109.7
`16.3-I08.2
`71
`179.4
`=74.6
`76
`-179..3
`=152.2
`3.23
`94.0 134.9 38.0-b49,8
`81
`1000.0
`-140.7
`114
`2.95
`128.1 130.3
`36..2-200.0
`=-i76.3
`1000.0
`92
`2.92
`150.6 105.9
`7.9
`94.0
`=—175.1
`54.3
`3,27
`94.1 135.2 40.0-143.1
`92
`169.5
`=134.6
`112
`2.85
`141.6 109.1 -18.5 77.5
`=178.4
`~82.3
`94
`3.03
`126.5 128.5
`4.1
`70.6
`-178.8
`~144.1
`3,01
`97.7 127.5 40.6-Len?
`93
`i7a.3
`=138.2
`96
`4.87
`[$0.2 103.3
`0. 7k.
`Li?.¢
`-80.8
`2.93
`172.0 120.4
`5.9 -54.4
`107
`1000.0
`=85.8
`3.29
`101.1 123.8 64.0-154.9
`112
`175..3
`1000.0
`178.8
`-85.2
`helix res
`a possible al
`179.8
`23.1
`169.6
`possible 3-10 helix res
`-107.4
`179.5
`—
`-84.2
`178.6
`~151.5
`1000.0
`83.8
`178.1
`1000.0
`179.9
`=-119.5
`177.8
`-81.2
`177.9
`-64.6
`
`bl
`
`‘
`
`anni
`snmp
`
`1.1 Ta.
`M4.) =?.8
`125.6
`1.6
`122.2 6.4
`1ia.2 90.2
`131.7
`38.6
`La.
`12.0
`120.5. ~2.€
`1239.9
`10.1
`167, 8.
`25.8
`126.0
`14.3
`
`20.6
`63.7
`-65.8
`-B5.4
`130.4
`
`-30.9
`B8.7
`66.2
`65.1
`94.3
`38.4
`
`53P
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`IOOUFEOPNHIWeRNDERHOOW
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`154.
`148.
`137.
`134.
`74.
`153.
`161.
`146.
`134.
`159.
`162.
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`denotes
`denotes
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`whWon
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`+ 20
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`- 06
`94
`~42
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`2.94
`3.14
`- 80
`~ 92
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`ve
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`To Page
`
`
`
`No.
`
`Date
`
`n-28-47
`
`+ t
`
`o
`
`ot
`
`Pest
`
`Page
`
`23
`
`Page 23
`
`

`

`NeeeenennccececreeTT|
`
`Project No.
`te
`b.)
`
`12
`
`Book No.
`
`tom Page No.__ ee
`
`
`
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`Witnessed & Understood by me,
`
`Date
`
`Date
`
`To Page No.___.
`
`|
`
`eAfice
`
`Curt
`
`Page 24
`
`Page 24
`
`

`

`
`
`Project No.
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`Book No.
`
`13
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`_ #8
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`Page 25
`
`Page 25
`
`

`

`Project No.
`Book No.—s—<iéiTLE.
`
`Sail
`
`14
`
`! ‘Tom Page No.__
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`ZZARAZAARAAAAAAAAARQRAAAMAARAAARASASMAN™NAANARAAAAAAA!
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`PROM PDB FILE: ARCHETYPE. PDB
`Dihedral Angles for ARCHETYPE
`150.
`67
`Doing residues:
`1 to
`PHI
`PSI — 7
`Li.
`=T7.
`D-aA<
`Rest Atom
`Res# Atnm Dist D-A-AA A-D-DD A-D<
`ian
`141,
`132.
`40,
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`23
`.00
`156.5 118.7
`6.4
`a8
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`ALA 23
`5
`(98
`«9142.8 119.5
`-9.4 73,
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`111.
`=172.
`ALA 21
`21
`-90
`147.3 128.1
`10.0 -68.
`i764
`i312
`=B7.
`ALA
`82
`
`
`
`
`
`
`a .210«143.0 132.3: .90 154.0 122.8 -3.1 61.-5.1 -41,
`=150.
`ALA
`-90
`160.6 115.1
`-2.5 -80.
`“175.2
`179.
`08
`«6342.1-123,1 -11.6 6,
`461.
`171.8
`=128.
`789
`153.6 125.5
`8.2 -49,
`174.4
`164.
`—147..
`a UL So,
`174.1
`112.
`-LM.
`-00
`143.1 122.9 -0.6 50,
`176.6
`143.
`—99,
`.97
`164.4 125.2
`46.9 -42.
`179.7
`155.
`—118.
`9)
`«66,9 128.7
`7.5 -30,
`104.
`~177 a
`=140.
`8)
`347.7 120.6
`2.4 -78.
`=H.
`.95
`143.6 126.7
`-3.2 -63.
`177.6
`144.
`0 10.7 199.7
`«8315-7
`168.7
`“id.
`156.
`.89
`156.1 102.0
`-0.3-154,
`172.1
`LL.
`-120.
`.31
`143.8 133.7 -10.8 -5S.
`179.7
`150.
`“TED.
`.96
`159.4 121.0 -15.8 -49,
`=178.7
`149.
`-128.
`-83
`166.5 112.0 -15.6 ~88.
`Aad
`100.
`=134.
`.87*
`150.9 117.6
`6.1
`68.
`=3a..
`-84*
`170.9 111.0
`12.6
`15.
`178.3
`138.
`M4
`153.7 123.9
`15.2
`48,
`177 4
`-130.
`115.
`13
`(198.4 137.4
`-3.4 74,
`178.8
`133.
`=70.
`ta.
`TO00 111.7
`19.9 =3m,
`=179,4
`-64.
`~102.
`175.3
`175.
`~ESa..
`- 958
`164.3 128.4
`8.6 -23.
`179.6
`i157.
`146.
`-13@ 148.6 127.1
`6.3 -60.
`.90
`154.4 126.1
`13.2
`20.
`-143.
`-93
`148.3 114.1
`-7.8 63.
`174.5
`LS4.
`.06
`137.2 125.6
`1.6 -65.
`7144.
`“LTT.
`135.
`.94
`134.3 122.2
`-6.4 ~85.
`177.4
`149,
`=T24,
`.€2
`164.1 117.8 -32.2 ag,
`178.5
`145.
`-74.
`.29°
`«79.4 116.4 -75.1-131.
`=F7,
`~180.0
`=36..
`.81@ 127.9 108.6 -17.2-101,
`.00*
`160.6 109.9
`44.4 163,
`“L?.
`167.7
`.35
`«130.5 119.5
`14.3
`69.
`174.0
`145.
`=—8.
`.46
`«72.8 125.3 ~64. 7-128,
`177.3
`=1 37.
`Li? .
`87.
`177.3
`139.
`.48@ 100.3 107.6 -10.9 -90.
`2 942407 80:
`“171.7
`171.
`=140.
`513
`A632 LF (8
`lag,
`153.2
`=Lol's
`aM
`AGL.) EbALN
`12.
`»b
`-180.0
`9.
`=$2.
`1%
`166.9 1390.5
`-2.
`=a.
`~J3.
`173.4
`44
`UBi.4 129.9 0,
`62
`is
`~180.0
`5
`
`00-258.7 loT.e 25.
`a
`-173.8
`»ako
`=i.
`92
`62.9 198,0
`14,2
`53.
`-174.2
`49.
`129.
`=-Li4.
`135.
`“112.
`ae
`» after dist denotes a possible alpha helix res
`157.
`-118.
`174.7
`@ after dist denotes a possible 3-10 helix res
`177.4
`104.
`=1394..
`117.
`-173.7
`~88.
`=109.
`170.3
`i72.
`126.
`-176.5
`99;
`177.2
`45.
`-L03.
`141.
`167.6
`=101.
`~176.1
`zd.
`“103,
`165.
`=Lia.
`-179,6
`“112.
`173.7
`Us .
`169..7
`156.
`176.8
`174.
`=178..3
`-35.
`173.9
`154.
`
`Invented by
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`EEESCECCSCECESS
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`
`Witnessed & Understood by me,
`
`To Page No.
`
`Page 26
`
`Page 26
`
`

`

` ITLE Ape
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`f ol,
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`
`7rom Page No.__
`
`15
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