Residue-by-residue listing for refined_5 Page 1 ---------------------------------------- This listing highlights the residues in the structure which may need investigation. The ideal values and standard deviations against which the structure has been compared are shown in the following table: <------------------------------- I D E A L V A L U E S -------------------------------> Chi-1 dihedral Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality g(-) trans g(+) Chi-2 phi helix psi rt-hand lf-hand bond dihedral en. C-alpha ------------------------------------------------------------------------------------------ Ideal value 64.1 183.6 -66.7 177.4 -65.4 -65.3 -39.4 96.8 -85.8 2.0 180.0 -2.0 33.9 Standard deviation 15.7 16.8 15.0 18.5 11.2 11.9 11.3 14.8 10.7 .1 5.8 .8 3.5 ------------------------------------------------------------------------------------------ In the listing below, properties that deviate from these values are highlighted by asterisks and plus-signs. Each asterisk represents one standard deviation, and each plus-sign represents half a standard deviation. So, a highlight such as +***, indicates that the value of the parameter is between 3.5 and 4.0 standard deviations from the ideal value shown above. Where the deviation is greater than 4.5 standard deviations its numerical value is shown; for example, *5.5*. The final column gives the maximum deviation in each row, while the maximum column deviations are shown at the end of the listing. Also at the end are the keys to the codes used for the secondary structure and Ramachandran plot assignments. Full print-out. ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - - - -64.9 - - - - - - - 180.0 - 34.1 - 2 GLY 2 t - - - - - - - - - - - 184.4 - - - 3 HIS 3 T XX - - -66.9 - - - - - - - 174.3 - 31.4 - **** **** 4 HIS 4 T a - - -63.8 - - - - - - - 177.1 -2.5 33.1 - 5 HIS 5 t b - 184.2 - - - - - - - - 173.7 -.5 33.5 - * ** ** 6 HIS 6 B - - -76.6 - - - - - - - 179.8 - 31.8 - 7 HIS 7 B - 181.5 - - - - - - - - 177.7 - 35.3 - 8 HIS 8 b - - -70.5 - - - - - - - 175.8 - 32.1 - 9 LEU 9 b 59.2 - - - - - - - - - 187.5 - 28.7 - * * * 10 GLU 10 S a - - -65.4 - - - - - - - 182.1 - 34.2 - 11 MET 11 S a - 189.5 - 187.8 - - - - - - 185.8 - 36.2 - * * 12 ALA 12 l - - - - - - - - - - 184.4 - 31.3 - 13 SER 13 a - - -56.6 - - - - - - - 180.4 - 35.5 - 14 GLU 14 B - 185.4 - 176.7 - - - - - - 184.2 - 34.4 - 15 GLU 15 b 63.0 - - - - - - - - - 173.6 -.5 35.0 - * ** ** 16 GLY 16 S - - - - - - - - - - - 183.4 -2.7 - - 17 GLN 17 e B 56.8 - - 183.9 - - - - - - 173.4 -.6 29.8 - * +* * +* 18 VAL 18 E B 62.3 - - - - - - - - - 178.1 -.5 35.7 - ** ** 19 ILE 19 E B - - -57.0 178.9 - - - - - - 178.6 -2.6 30.9 - 20 ALA 20 E B - - - - - - - - - - 181.3 -.7 34.0 - +* +* Residue-by-residue listing for refined_5 Page 2 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 21 CYS 21 E B - - -53.8 - - - - - - - 177.2 -1.6 35.7 - 22 HIS 22 S A - - -67.4 - - - - - - - 180.6 -.6 33.2 - +* +* 23 THR 23 h B 54.2 - - - - - - - - - 179.7 - 34.7 - 24 VAL 24 H A 63.3 - - - - -74.5 -24.7 - - - 176.2 - 31.6 - * * 25 GLU 25 H A - - -55.8 - - -58.0 -50.9 - - - 179.6 - 35.6 - * * 26 THR 26 H A - - -56.7 - - -67.6 -40.7 - - - 176.9 - 34.6 - 27 TRP 27 H A - 172.2 - - - -55.0 -50.5 - - - 179.0 -1.9 34.7 - 28 ASN 28 H A - 175.9 - - - -58.7 -43.5 - - - 181.6 -3.2 34.5 - +* +* 29 GLU 29 H A - 184.5 - 175.2 - -65.4 -47.6 - - - 176.2 -1.8 32.2 - 30 GLN 30 H A - - -94.1 - - -57.7 -39.6 - - - 177.2 -2.8 33.3 - +* * +* 31 LEU 31 H A - - -67.9 178.9 - -67.8 -42.9 - - - 176.3 -2.1 34.8 - 32 GLN 32 H A - 178.2 - 178.9 - -59.3 -43.1 - - - 176.1 -2.5 34.4 - 33 LYS 33 H A - 179.1 - 181.3 - -59.9 -48.9 - - - 181.2 -2.9 34.7 - * * 34 ALA 34 H A - - - - - -65.5 -39.2 - - - 182.1 -2.7 33.5 - 35 ASN 35 H A - 183.8 - - - -66.7 -56.0 - - - 183.4 -3.2 37.5 - * +* * +* 36 GLU 36 H A - 185.2 - 181.2 - -67.0 -29.0 - - - 181.6 -2.8 33.6 - * * 37 SER 37 H A - 185.0 - - - -95.5 -2.4 - - - 181.5 -1.9 33.6 - +** *** *** 38 LYS 38 h l - - -83.5 173.6 - - - - - - 178.3 -1.0 31.6 - * * * 39 THR 39 e B - - -48.5 - - - - - - - 180.0 -1.6 35.5 - * * 40 LEU 40 E B - 182.0 - 168.1 - - - - - - 185.4 - 34.3 - 41 VAL 41 E B 60.4 - - - - - - - - - 176.0 -.7 32.9 - +* +* 42 VAL 42 E B - 183.4 - - - - - - - - 185.4 -3.0 34.3 - * * 43 VAL 43 E B - 182.5 - - - - - - - - 175.8 -3.5 34.9 - +* +* 44 ASP 44 E B - 162.5 - - - - - - - - 172.3 -3.3 35.8 - * * +* +* 45 PHE 45 E B - - -63.5 - - - - - - - 184.1 -3.0 35.4 - * * 46 THR 46 E B - - -67.9 - - - - - - - 177.3 -2.3 35.5 - 47 ALA 47 t B - - - - - - - - - - 182.8 - 34.1 - 48 SER 48 T A - - -57.5 - - - - - - - 181.4 - 33.2 - 49 TRP 49 T A 47.0 - - - - - - - - - 179.6 - 30.9 - * * 50 CYS 50 h B 48.5 - - - - - - - -121.8 2.8 186.5 -1.6 29.5 - *** *8.0* * * *8.0* 51 GLY 51 H - - - - - - -59.1 -66.6 - - - 181.6 -.6 - - ** +* ** 52 PRO 52 H - - - - - -56.4 -56.4 -30.4 - - - 180.8 - 38.6 - * * 53 CYS 53 H A - - -45.1 150.1 - -72.0 -39.4 - -121.8 2.8 178.8 - 36.5 - * * *** *8.0* *8.0* 54 ARG 54 H A - 186.6 - 183.7 - -70.9 -28.9 - - - 178.2 -1.9 34.1 - 55 PHE 55 H A - 180.5 - - - -65.8 -32.7 - - - 183.1 -1.8 35.1 - Residue-by-residue listing for refined_5 Page 3 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 56 ILE 56 H A - 192.4 - - - -90.4 -11.2 - - - 180.6 -1.1 33.4 - ** ** * ** 57 ALA 57 H A - - - - - -58.5 -52.0 - - - 178.5 -.7 31.8 - * +* +* 58 PRO 58 H - - - - - -57.7 -57.7 -33.0 - - - 180.7 - 38.8 - * * 59 PHE 59 H A - 184.7 - - - -68.2 -47.4 - - - 179.5 - 35.1 - 60 PHE 60 H A - 181.4 - - - -66.3 -37.7 - - - 178.2 -2.4 34.2 - 61 ALA 61 H A - - - - - -67.5 -30.6 - - - 179.2 -2.8 33.6 - * * 62 ASP 62 H A - 196.5 - - - -75.2 -40.5 - - - 175.6 -1.5 34.5 - 63 LEU 63 H A - - -69.4 181.2 - -52.8 -35.8 - - - 177.4 -2.3 35.2 - * * 64 ALA 64 H A - - - - - -59.0 -31.7 - - - 181.3 -1.3 33.5 - 65 LYS 65 H A - 191.1 - 179.8 - -78.0 -19.2 - - - 177.6 -1.6 33.1 - * +* +* 66 LYS 66 H A - - -74.1 - - -79.5 -34.1 - - - 184.5 -1.1 32.1 - * * * 67 LEU 67 h B - - -65.2 172.1 - - - - - - 179.3 -1.3 32.6 - 68 PRO 68 S - - - - - -73.7 - - - - - 184.6 - 38.7 - * * 69 ASN 69 S A - 187.6 - - - - - - - - 181.9 - 33.6 - 70 VAL 70 S B - 178.6 - - - - - - - - 178.9 - 33.0 - 71 LEU 71 E B - 177.8 - - - - - - - - 177.5 -2.9 34.7 - * * 72 PHE 72 E B - - -59.6 - - - - - - - 181.8 -.9 34.4 - * * 73 LEU 73 E B - - -68.1 170.6 - - - - - - 182.5 -2.6 33.9 - 74 LYS 74 E B - 189.8 - - - - - - - - 180.6 -1.9 35.7 - 75 VAL 75 E B - 179.5 - - - - - - - - 179.9 -3.6 34.8 - ** ** 76 ASP 76 E B - 189.5 - - - - - - - - 185.1 -.8 33.8 - +* +* 77 THR 77 e A 52.3 - - - - - - - - - 176.2 -.8 33.2 - +* +* 78 ASP 78 T A - 186.9 - - - - - - - - 175.3 - 33.7 - 79 GLU 79 T A - - -62.4 - - - - - - - 180.1 - 36.4 - 80 LEU 80 h b - - -64.0 176.9 - - - - - - 180.9 -3.0 34.3 - * * 81 LYS 81 H A - - -61.7 - - -68.7 -44.4 - - - 182.8 -1.0 34.9 - * * 82 SER 82 H A - - -55.8 - - -63.6 -35.9 - - - 179.8 - 34.4 - 83 VAL 83 H A - 176.7 - - - -66.1 -39.2 - - - 179.4 - 33.2 - 84 ALA 84 H A - - - - - -63.0 -39.1 - - - 179.7 -1.3 33.9 - * * 85 SER 85 H A - - -55.5 - - -75.7 -35.5 - - - 184.6 -1.6 34.5 - 86 ASP 86 H A - 180.2 - - - -74.6 -36.5 - - - 179.5 -2.4 34.7 - 87 TRP 87 h A - - -66.0 - - - - - - - 179.1 -2.6 32.8 - 88 ALA 88 T l - - - - - - - - - - 178.9 - 30.7 - 89 ILE 89 t b - - -54.0 - - - - - - - 178.1 -2.5 34.5 - 90 GLN 90 A - 180.5 - 181.8 - - - - - - 181.6 -.7 34.4 - +* +* 91 ALA 91 S B - - - - - - - - - - 184.3 - 33.0 - 92 MET 92 S B - - -60.3 174.1 - - - - - - -1.5 -.6 35.8 - +* +* 93 PRO 93 e cis - - - - - -83.7 - - - - - 176.7 - 39.6 - +* +* +* Residue-by-residue listing for refined_5 Page 4 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 94 THR 94 E B - - -56.0 - - - - - - - 175.1 -2.0 34.9 - 95 PHE 95 E B - - -63.8 - - - - - - - 180.7 -2.8 35.2 - * * 96 MET 96 E B - 184.8 - 180.4 - - - - - - 180.8 -3.1 33.1 - * * 97 PHE 97 E B - - -69.6 - - - - - - - 181.4 -3.5 35.9 - +* +* 98 LEU 98 E B - - -53.9 - - - - - - - 173.9 -2.9 35.5 - * * * 99 LYS 99 E B - 171.4 - 176.1 - - - - - - 180.4 -3.2 33.0 - +* +* 100 GLU 100 e l - - -59.6 169.3 - - - - - - 181.7 -.5 34.3 - ** ** 101 GLY 101 T - - - - - - - - - - - 177.2 - - - 102 LYS 102 E B - - -70.9 - - - - - - - 184.6 -2.4 32.4 - 103 ILE 103 E B - - -55.8 176.1 - - - - - - 177.0 - 35.3 - 104 LEU 104 E a - - -67.1 187.3 - - - - - - 186.0 -2.4 34.3 - * * 105 ASP 105 E B 48.6 - - - - - - - - - 181.9 -2.5 32.7 - 106 LYS 106 E B 62.0 - - 177.9 - - - - - - 173.0 - 35.2 - * * 107 VAL 107 E B - 180.7 - - - - - - - - 182.2 -2.9 35.2 - * * 108 VAL 108 E B 60.6 - - - - - - - - - 183.1 - 32.0 - 109 GLY 109 e - - - - - - - - - - - 180.4 -3.3 - - +* +* 110 ALA 110 B - - - - - - - - - - 178.4 - 33.9 - 111 LYS 111 h B - - -59.5 178.2 - - - - - - 182.5 -1.0 35.9 - * * 112 LYS 112 H A - 182.6 - 182.9 - -68.7 -50.3 - - - 185.8 - 34.7 - 113 ASP 113 H A - 183.7 - - - -71.2 -42.1 - - - 179.1 - 32.8 - 114 GLU 114 H A - 182.4 - 177.9 - -65.3 -36.0 - - - 177.5 - 32.1 - 115 LEU 115 H A - 185.0 - - - -61.7 -51.2 - - - 176.3 -1.5 35.0 - * * 116 GLN 116 H A - - -72.4 - - -55.9 -40.3 - - - 179.7 -2.5 33.7 - 117 SER 117 H A - 184.5 - - - -65.1 -40.8 - - - 177.9 -2.6 34.2 - 118 THR 118 H A - - -56.0 - - -66.8 -36.4 - - - 176.5 -2.5 35.1 - 119 ILE 119 H A - - -59.5 - - -61.3 -49.0 - - - 179.9 -2.4 33.7 - 120 ALA 120 H A - - - - - -63.9 -32.1 - - - 176.9 -2.7 32.9 - 121 LYS 121 H A - - -81.1 180.2 - -67.4 -30.7 - - - 176.9 -1.9 34.8 - 122 HIS 122 H A - - -73.1 - - -91.6 -20.9 - - - 179.0 -1.4 33.1 - ** +* ** 123 LEU 123 h B - 195.1 - - - - - - - - 180.2 -1.8 36.2 - 124 ALA 124 - - - - - - - - - - - - -.9 33.8 - +* +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * * +* * +* +** *** *** *8.0* * ** +* *8.0* ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 56.8 183.0 -63.8 177.4 -67.9 -66.9 -38.1 - -121.8 2.8 179.8 -2.0 34.1 *** *8.0* *8.0* Standard deviations: 6.0 6.2 9.1 7.0 13.2 9.2 11.3 - .0 .0 3.2 .9 1.8 Numbers of values: 13 42 47 30 4 47 47 0 2 2 122 82 119 0 Number of cis-peptides (labelled cis): 1 Residue-by-residue listing for refined_5 Page 5 ---------------------------------------- KEY TO CODES: ------------ Regions of the Ramachandran plot Secondary structure (extended Kabsch/Sander) -------------------------------- -------------------------------------------- A - Core alpha B - residue in isolated beta-bridge a - Allowed alpha E - extended strand, participates in beta-ladder ~a - Generous alpha ** Generous G - 3-helix (3/10 helix) B - Core beta H - 4-helix (alpha-helix) b - Allowed beta I - 5-helix (pi-helix) ~b - Generous beta ** Generous S - bend L - Core left-handed alpha T - hydrogen-bonded turn l - Allowed left-handed alpha ~l - Generous left-handed alpha ** Generous e - extension of beta-strand p - Allowed epsilon g - extension of 3/10 helix ~p - Generous epsilon ** Generous h - extension of alpha-helix XX - Outside major areas **** Disallowed Residue-by-residue listing for refined_5 Page 6 ---------------------------------------- M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S ..................................... Small molecule data ......................................... <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N --------------------------------------------------------------------------------------------------- Any - 1.231 - - - - - - - - - - ( .020) Pro 1.341 - - - 1.466 122.60 116.90 - - 111.80 103.00 122.00 ( .016) ( .015) ( 5.00) ( 1.50) ( 2.50) ( 1.10) ( 1.40) Except Pro 1.329 - - - - - - - - - - 123.00 ( .014) ( 1.60) Gly - - 1.516 - 1.451 120.60 116.40 120.80 - 112.50 - - ( .018) ( .016) ( 1.70) ( 2.10) ( 2.10) ( 2.90) Except Gly - - 1.525 - - - - 120.80 - - - - ( .021) ( 1.70) Ala - - - 1.521 - - - - 110.50 - 110.40 - ( .033) ( 1.50) ( 1.50) Ile,Thr,Val - - - 1.540 - - - - 109.10 - 111.50 - ( .027) ( 2.20) ( 1.70) Except Gly,Pro - - - - 1.458 121.70 116.20 - - 111.20 - - ( .019) ( 1.80) ( 2.00) ( 2.80) The rest - - - 1.530 - - - - 110.10 - 110.50 - ( .020) ( 1.90) ( 1.70) Note. The table above shows the mean values obtained from small molecule data by Engh & Huber (1991). The values shown in brackets are standard deviations ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - 1.237 1.507 1.543 1.462 - 116.51 120.42 109.46 109.49 111.92 123.07 2 GLY 2 1.316 1.223 1.506 - 1.426 120.29 116.60 119.83 - 113.05 - 123.55 +* +* 3 HIS 3 1.342 1.227 1.533 1.547 1.496 123.93 116.40 120.98 110.83 111.25 113.48 122.62 +* * +* +* 4 HIS 4 1.311 1.226 1.496 1.540 1.448 122.78 115.87 120.74 109.99 107.78 113.49 123.37 * * * +* +* 5 HIS 5 1.321 1.228 1.524 1.544 1.442 121.78 116.08 120.84 110.07 110.65 111.92 123.03 6 HIS 6 1.306 1.236 1.508 1.539 1.455 122.52 115.34 120.91 110.52 110.44 113.72 123.72 +* +* +* 7 HIS 7 1.310 1.240 1.540 1.549 1.463 123.57 116.37 120.53 110.66 110.54 108.62 123.10 * * * * 8 HIS 8 1.326 1.233 1.522 1.553 1.464 122.74 115.01 120.54 109.68 111.62 113.82 124.41 * +* +* 9 LEU 9 1.319 1.221 1.519 1.590 1.462 126.28 115.08 122.00 115.52 107.72 114.66 122.65 *** +** +** * ** *** 10 GLU 10 1.311 1.229 1.509 1.552 1.451 121.72 115.74 121.32 109.99 111.34 110.80 122.90 * * * 11 MET 11 1.307 1.220 1.533 1.543 1.454 122.57 115.18 121.22 110.12 108.11 108.46 123.51 +* * * +* 12 ALA 12 1.329 1.219 1.515 1.535 1.468 123.99 115.42 121.74 111.78 109.72 113.30 122.84 * +* +* Residue-by-residue listing for refined_5 Page 7 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 13 SER 13 1.291 1.230 1.533 1.523 1.436 122.83 115.51 121.61 111.59 109.77 107.43 122.84 +** * +* +** 14 GLU 14 1.309 1.230 1.523 1.525 1.432 122.20 115.78 121.09 111.97 108.63 109.16 123.07 * * * 15 GLU 15 1.308 1.243 1.521 1.555 1.451 122.68 115.83 120.66 109.29 111.04 110.47 123.49 * * * 16 GLY 16 1.324 1.230 1.497 - 1.438 121.37 117.89 119.83 - 114.01 - 122.28 * * 17 GLN 17 1.315 1.233 1.477 1.497 1.433 118.65 111.89 123.09 111.18 115.80 113.21 125.00 ** +* * +* ** * +* +* * ** 18 VAL 18 1.266 1.232 1.530 1.556 1.411 125.18 119.52 119.36 110.99 106.83 109.12 121.03 **** ** +* +* +* * * **** 19 ILE 19 1.313 1.236 1.513 1.555 1.448 117.06 115.60 121.38 111.54 111.01 113.88 122.99 * +** * * +** 20 ALA 20 1.308 1.235 1.502 1.520 1.434 121.90 115.98 120.84 110.72 109.44 110.84 123.17 +* * * +* 21 CYS 21 1.297 1.232 1.511 1.514 1.410 121.80 116.11 120.95 109.89 109.26 109.24 122.91 ** +** +** 22 HIS 22 1.302 1.224 1.508 1.542 1.450 121.31 115.87 120.96 110.59 109.81 112.04 123.16 +* +* 23 THR 23 1.321 1.247 1.509 1.550 1.445 122.08 116.99 120.11 109.29 109.22 111.53 122.90 24 VAL 24 1.321 1.226 1.532 1.571 1.441 120.54 116.19 120.89 111.98 109.71 113.16 122.89 * * * 25 GLU 25 1.341 1.242 1.533 1.526 1.417 123.08 115.61 120.91 108.51 110.21 110.45 123.48 ** ** 26 THR 26 1.327 1.230 1.536 1.542 1.450 122.53 115.51 120.89 110.80 110.05 109.68 123.58 * * 27 TRP 27 1.325 1.233 1.539 1.534 1.456 123.37 115.93 120.79 111.62 111.06 108.18 123.27 * * 28 ASN 28 1.323 1.241 1.520 1.535 1.464 122.86 115.61 120.89 109.93 111.46 110.04 123.49 29 GLU 29 1.318 1.229 1.534 1.536 1.456 122.07 117.07 120.13 111.68 111.40 111.60 122.79 30 GLN 30 1.329 1.230 1.526 1.506 1.432 122.67 117.13 120.35 111.54 112.87 109.56 122.51 * * * 31 LEU 31 1.319 1.214 1.513 1.484 1.417 121.96 116.12 120.57 110.34 111.15 109.11 123.31 ** ** ** 32 GLN 32 1.313 1.230 1.514 1.527 1.453 122.81 115.55 120.72 111.43 109.64 109.32 123.72 * * 33 LYS 33 1.318 1.221 1.527 1.535 1.438 122.60 116.77 120.43 110.13 110.04 110.25 122.77 * * 34 ALA 34 1.331 1.222 1.526 1.523 1.454 121.45 116.26 120.55 110.60 111.37 110.73 123.17 35 ASN 35 1.317 1.232 1.495 1.526 1.466 122.77 114.72 121.50 106.83 110.66 109.05 123.71 * +* +* 36 GLU 36 1.305 1.244 1.546 1.529 1.462 122.00 116.78 121.02 111.01 112.24 109.90 122.20 +* +* 37 SER 37 1.315 1.242 1.546 1.535 1.441 120.76 117.07 120.20 111.22 111.77 109.95 122.73 * * 38 LYS 38 1.346 1.228 1.504 1.516 1.479 122.37 116.11 121.11 111.00 113.22 112.11 122.71 * * * 39 THR 39 1.296 1.238 1.521 1.523 1.416 120.94 116.02 121.18 108.94 107.92 110.71 122.79 ** ** * ** 40 LEU 40 1.272 1.242 1.524 1.567 1.431 121.44 117.29 119.96 113.10 105.76 109.51 122.74 **** +* * +* +* **** 41 VAL 41 1.303 1.237 1.532 1.561 1.431 120.44 115.50 121.21 111.57 112.31 110.82 123.27 +* * * +* Residue-by-residue listing for refined_5 Page 8 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 42 VAL 42 1.309 1.240 1.518 1.533 1.437 122.67 116.36 120.78 109.45 108.04 112.03 122.85 * * * * 43 VAL 43 1.298 1.231 1.526 1.542 1.438 121.80 115.17 120.96 109.27 111.98 110.22 123.87 ** * ** 44 ASP 44 1.305 1.237 1.508 1.542 1.456 124.25 117.37 120.14 108.86 110.63 109.85 122.45 +* * +* 45 PHE 45 1.313 1.242 1.514 1.524 1.415 119.94 115.18 120.83 109.80 107.60 110.31 123.94 * ** * ** 46 THR 46 1.305 1.221 1.516 1.555 1.443 123.65 116.90 119.90 109.66 109.18 109.96 123.19 +* * +* 47 ALA 47 1.296 1.225 1.509 1.519 1.436 122.35 116.52 120.48 110.58 108.19 111.11 122.99 ** * * ** 48 SER 48 1.293 1.231 1.557 1.515 1.455 122.47 117.38 120.55 111.45 113.82 109.31 122.07 +** +* +** 49 TRP 49 1.324 1.229 1.543 1.546 1.456 121.24 118.58 119.91 111.82 114.84 111.74 121.51 * * * 50 CYS 50 1.322 1.241 1.531 1.547 1.461 119.24 114.89 121.44 113.85 112.39 112.63 123.66 * +* * +* 51 GLY 51 1.331 1.239 1.526 - 1.464 123.36 118.96 119.56 - 115.31 - 121.48 +* * +* 52 PRO 52 1.358 1.231 1.527 1.530 1.482 123.07 115.61 121.36 110.24 112.41 103.49 123.02 * * * 53 CYS 53 1.308 1.220 1.530 1.495 1.449 122.42 116.14 121.45 108.15 109.55 108.98 122.41 +* +* * +* 54 ARG 54 1.313 1.216 1.533 1.526 1.448 121.55 115.68 121.27 110.81 109.19 110.43 123.05 * * 55 PHE 55 1.328 1.238 1.536 1.546 1.468 122.80 116.39 121.14 109.67 110.72 109.82 122.47 56 ILE 56 1.315 1.238 1.556 1.574 1.447 120.93 115.93 121.16 111.44 110.39 110.81 122.87 * * * * 57 ALA 57 1.335 1.233 1.552 1.531 1.472 122.70 119.92 119.29 111.43 113.02 111.50 120.79 * +* * +* 58 PRO 58 1.384 1.232 1.525 1.540 1.472 122.16 115.48 121.00 109.95 111.65 103.90 123.49 +** * +** 59 PHE 59 1.321 1.225 1.531 1.543 1.448 122.79 115.76 121.09 111.15 109.21 108.83 123.11 60 PHE 60 1.321 1.235 1.530 1.535 1.462 122.74 116.07 121.11 111.22 110.73 109.47 122.82 61 ALA 61 1.314 1.232 1.528 1.525 1.448 121.60 116.30 120.85 110.87 110.69 110.61 122.85 * * 62 ASP 62 1.323 1.228 1.508 1.511 1.465 121.82 115.06 121.17 109.75 109.05 110.82 123.76 63 LEU 63 1.333 1.236 1.531 1.531 1.449 124.07 115.58 120.89 110.00 110.96 109.22 123.51 * * 64 ALA 64 1.324 1.229 1.533 1.524 1.452 123.01 116.79 120.77 110.65 111.67 110.54 122.44 65 LYS 65 1.332 1.235 1.546 1.544 1.458 121.46 117.04 120.95 111.25 110.68 110.99 122.00 * * 66 LYS 66 1.334 1.232 1.514 1.548 1.464 120.41 117.10 120.13 109.07 112.24 114.05 122.77 ** ** 67 LEU 67 1.313 1.232 1.524 1.510 1.428 120.76 116.36 121.27 112.43 113.19 109.50 122.35 * +* * +* 68 PRO 68 1.339 1.234 1.536 1.537 1.467 123.39 117.26 120.50 110.31 113.79 103.12 122.24 69 ASN 69 1.325 1.225 1.523 1.536 1.459 120.28 116.56 121.24 110.46 111.47 110.87 122.19 70 VAL 70 1.296 1.232 1.527 1.554 1.446 121.12 116.16 120.90 111.02 110.85 111.57 122.90 ** ** 71 LEU 71 1.314 1.230 1.513 1.539 1.443 121.90 116.44 120.78 109.93 109.74 110.61 122.77 * * 72 PHE 72 1.298 1.235 1.502 1.525 1.434 121.53 116.28 120.79 109.75 108.41 111.49 122.93 ** * * ** Residue-by-residue listing for refined_5 Page 9 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 73 LEU 73 1.283 1.225 1.495 1.521 1.435 122.53 115.49 121.02 111.12 110.71 110.24 123.49 *** * * *** 74 LYS 74 1.296 1.228 1.517 1.567 1.433 122.44 115.87 121.05 113.73 106.55 106.55 123.05 ** +* * +* +* ** ** 75 VAL 75 1.306 1.241 1.493 1.549 1.442 122.51 116.06 120.86 109.09 108.63 111.88 123.03 +* +* +* 76 ASP 76 1.297 1.235 1.492 1.506 1.429 120.43 115.83 120.72 111.00 107.68 111.25 123.42 ** +* * +* * ** 77 THR 77 1.297 1.240 1.532 1.529 1.435 122.48 117.29 120.68 111.22 113.15 110.11 122.01 ** * ** 78 ASP 78 1.320 1.226 1.499 1.508 1.440 120.04 114.79 121.58 110.05 108.16 112.15 123.62 * * * * 79 GLU 79 1.311 1.232 1.526 1.513 1.425 122.88 115.59 121.40 108.97 109.53 108.81 123.01 * +* +* 80 LEU 80 1.310 1.238 1.533 1.512 1.403 122.72 115.33 121.39 111.82 111.37 108.64 123.25 * +** * +** 81 LYS 81 1.323 1.239 1.525 1.544 1.464 123.08 115.75 120.94 109.10 110.63 110.68 123.30 82 SER 82 1.321 1.231 1.526 1.510 1.447 122.72 116.41 120.53 110.51 111.71 109.36 123.04 * * 83 VAL 83 1.326 1.233 1.528 1.561 1.459 121.92 116.15 120.78 110.90 110.29 111.66 122.99 84 ALA 84 1.328 1.227 1.527 1.516 1.454 121.69 116.32 120.88 110.54 110.93 110.36 122.80 85 SER 85 1.314 1.232 1.548 1.529 1.446 121.60 115.96 121.03 110.80 111.32 109.26 122.98 * * * 86 ASP 86 1.328 1.235 1.529 1.534 1.478 123.12 116.46 120.88 110.07 112.53 109.28 122.66 * * 87 TRP 87 1.317 1.235 1.523 1.526 1.449 121.64 115.28 120.75 111.38 111.33 111.07 123.96 88 ALA 88 1.331 1.247 1.527 1.530 1.465 124.46 115.39 121.62 111.95 113.16 112.46 122.92 +* * +* 89 ILE 89 1.308 1.238 1.508 1.564 1.443 122.22 115.88 121.19 109.27 108.80 112.13 122.85 * * 90 GLN 90 1.294 1.232 1.512 1.527 1.434 121.03 115.87 121.23 110.67 108.79 110.49 122.87 ** * ** 91 ALA 91 1.307 1.222 1.508 1.519 1.443 121.28 115.81 121.17 111.65 109.60 111.06 123.01 +* +* 92 MET 92 1.290 1.229 1.513 1.521 1.439 122.20 118.55 119.87 109.90 109.86 108.80 121.58 +** * * +** 93 PRO 93 1.341 1.231 1.531 1.523 1.471 124.16 116.93 120.93 109.75 111.72 102.56 122.11 94 THR 94 1.294 1.227 1.513 1.528 1.428 120.41 116.70 120.44 108.77 109.49 111.48 122.85 ** +* ** 95 PHE 95 1.303 1.225 1.490 1.521 1.409 121.67 116.76 120.42 109.79 107.65 110.72 122.80 +* +* +** * +** 96 MET 96 1.281 1.226 1.498 1.521 1.423 120.39 115.12 121.18 111.33 109.63 111.48 123.68 *** * +* *** 97 PHE 97 1.279 1.244 1.500 1.504 1.398 123.75 115.82 121.24 110.54 109.56 108.20 122.93 +*** * * *** * * +*** 98 LEU 98 1.289 1.219 1.520 1.565 1.421 121.22 116.72 120.55 107.66 108.39 112.42 122.73 +** +* +* * * * +** 99 LYS 99 1.291 1.234 1.474 1.525 1.440 122.37 114.57 120.77 110.22 108.64 113.21 124.57 +** ** +* +** 100 GLU 100 1.321 1.220 1.551 1.531 1.447 124.00 116.38 121.19 109.90 110.10 110.67 122.43 * * * 101 GLY 101 1.321 1.229 1.533 - 1.454 121.25 117.14 120.34 - 113.25 - 122.52 102 LYS 102 1.328 1.231 1.513 1.559 1.466 121.52 116.12 120.36 110.50 109.81 113.35 123.52 * +* +* Residue-by-residue listing for refined_5 Page 10 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 103 ILE 103 1.313 1.233 1.523 1.557 1.465 123.61 116.56 120.43 108.67 111.22 110.60 123.00 * * * 104 LEU 104 1.319 1.232 1.505 1.529 1.435 121.53 115.86 121.10 109.01 110.98 111.65 123.04 * * 105 ASP 105 1.307 1.214 1.497 1.525 1.447 122.03 116.12 120.81 110.95 112.28 111.36 123.02 +* * +* 106 LYS 106 1.308 1.237 1.531 1.539 1.447 121.56 115.43 121.07 109.02 111.23 110.13 123.49 * * 107 VAL 107 1.305 1.237 1.516 1.559 1.446 123.52 117.12 120.00 108.92 106.44 111.92 122.86 +* * +* +* 108 VAL 108 1.302 1.240 1.538 1.559 1.435 121.05 115.58 121.64 112.58 111.75 111.18 122.77 +* * +* +* 109 GLY 109 1.312 1.239 1.502 - 1.441 121.84 118.46 119.64 - 109.04 - 121.89 * * * 110 ALA 110 1.322 1.240 1.508 1.524 1.443 118.56 114.96 121.43 110.85 109.19 110.87 123.57 +* +* 111 LYS 111 1.301 1.222 1.503 1.522 1.421 123.84 117.98 119.36 110.53 107.89 108.70 122.64 ** * +* * * * ** 112 LYS 112 1.310 1.238 1.531 1.516 1.431 120.56 116.20 120.88 109.33 111.22 110.40 122.88 * * * 113 ASP 113 1.327 1.228 1.508 1.531 1.461 121.48 117.00 120.26 110.57 111.47 111.87 122.72 114 GLU 114 1.331 1.230 1.520 1.534 1.459 120.06 116.55 120.61 110.95 110.36 112.86 122.83 * * 115 LEU 115 1.327 1.215 1.508 1.514 1.449 121.39 115.31 120.89 109.38 108.86 110.62 123.80 116 GLN 116 1.317 1.232 1.518 1.522 1.473 122.89 115.92 120.75 110.30 112.09 110.51 123.31 117 SER 117 1.310 1.228 1.529 1.536 1.443 122.17 115.62 121.21 111.74 109.19 109.60 123.11 * * 118 THR 118 1.311 1.236 1.541 1.540 1.441 122.90 116.22 121.06 110.50 109.67 109.29 122.70 * * * 119 ILE 119 1.329 1.221 1.523 1.563 1.449 121.65 116.40 120.34 109.45 109.07 112.81 123.20 120 ALA 120 1.329 1.226 1.529 1.519 1.464 122.14 116.54 120.80 111.19 111.60 110.80 122.65 121 LYS 121 1.317 1.233 1.526 1.487 1.409 123.27 116.53 120.87 111.45 112.22 107.75 122.60 ** +** +* +** 122 HIS 122 1.312 1.226 1.517 1.521 1.434 121.64 117.01 120.26 110.25 111.87 111.59 122.71 * * * 123 LEU 123 1.319 1.234 1.525 1.513 1.409 121.96 116.11 120.86 111.58 108.59 106.94 123.00 +** ** +** 124 ALA 124 1.304 - 1.512 1.528 1.433 121.97 - - 111.25 109.17 110.73 - +* * +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** ** *** *** +** ** * +** +* ** * **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_5 Page 11 ---------------------------------------- A N A L Y S I S O F M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S +------------------+ | BOND LENGTHS | +------------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Bond X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- C-N C-NH1 (except Pro) 1.329 .014 119 1.266 1.346 1.313 .014 **** * * C-N (Pro) 1.341 .016 4 1.339 1.384 1.356 .018 +** C-O C-O 1.231 .020 123 1.214 1.247 1.231 .007 CA-C CH1E-C (except Gly) 1.525 .021 119 1.474 1.557 1.521 .015 ** +* CH2G*-C (Gly) 1.516 .018 5 1.497 1.533 1.513 .014 * CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.516 1.535 1.524 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.523 1.574 1.551 .014 * CH1E-CH2E (the rest) 1.530 .020 84 1.484 1.590 1.530 .018 ** *** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.398 1.496 1.445 .017 *** +* NH1-CH2G* (Gly) 1.451 .016 5 1.426 1.464 1.445 .013 +* N-CH1E (Pro) 1.466 .015 4 1.467 1.482 1.473 .006 * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_5 Page 12 ---------------------------------------- +-----------------+ | BOND ANGLES | +-----------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Angle X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- CA-C-N CH1E-C-NH1 (except Gly,Pro)116.2 2.0 114 111.89 119.92 116.15 .95 ** +* CH2G*-C-NH1 (Gly) 116.4 2.1 5 116.60 118.96 117.81 .86 * CH1E-C-N (Pro) 116.9 1.5 4 115.48 117.26 116.32 .78 O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.79 125.00 122.96 .61 * * O-C-N (Pro) 122.0 1.4 4 122.11 123.49 122.71 .57 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 117.06 126.28 122.05 1.31 +** +** C-NH1-CH2G* (Gly) 120.6 1.7 5 120.29 123.36 121.62 1.01 +* C-N-CH1E (Pro) 122.6 5.0 4 122.16 124.16 123.20 .72 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 119.29 123.09 120.85 .52 * CH2G*-C-O (Gly) 120.8 2.1 5 119.56 120.34 119.84 .27 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 110.54 111.95 111.08 .47 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 108.67 112.58 110.24 1.17 +* CH2E-CH1E-C (the rest) 110.1 1.9 84 106.83 115.52 110.52 1.28 +* +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 105.76 115.80 110.31 1.75 +* +* NH1-CH2G*-C (Gly) 112.5 2.9 5 109.04 115.31 112.93 2.10 * N-CH1E-C (Pro) 111.8 2.5 4 111.65 113.79 112.39 .86 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.36 113.30 111.15 .80 +* NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 109.12 113.88 111.21 1.20 * * N-CH1E-CH2E (Pro) 103.0 1.1 4 102.56 103.90 103.27 .49 NH1-CH1E-CH2E (the rest) 110.5 1.7 80 106.55 114.66 110.51 1.71 ** ** ------------------------------------------------------------------------------------------------------------- The small molecule data used in the above analysis is from Engh & Huber (1991). The atom labelling follows that used in the X-PLOR dictionary, with some additional atoms (marked with an asterisk) as defined by Engh & Huber. Residue-by-residue listing for refined_5 Page 13 ---------------------------------------- R A M A C H A N D R A N P L O T S T A T I S T I C S Residues in most favoured regions [A,B,L] 97 85.8% Residues in additional allowed regions [a,b,l,p] 15 13.3% Residues in generously allowed regions [~a,~b,~l,~p] 0 .0% Residues in disallowed regions [XX] 1 .9% ---- ------ Number of non-glycine and non-proline residues 113 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 5 Number of proline residues 4 ---- Total number of residues 124 Based on the analysis of 118 structures of resolution of at least 2.0 Angstroms and R-factor no greater than 20%, a good quality model would be expected to have over 90% in the most favoured regions [E,H,L]. S T E R E O C H E M I S T R Y O F M A I N - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. %-tage residues in A, B, L 113 85.8 83.8 10.0 .2 Inside b. Omega angle st dev 122 3.2 6.0 3.0 -.9 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 119 1.8 3.1 1.6 -.9 Inside e. H-bond energy st dev 82 .9 .8 .2 .5 Inside f. Overall G-factor 124 .0 -.4 .3 1.5 BETTER S T E R E O C H E M I S T R Y O F S I D E - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. Chi-1 gauche minus st dev 13 6.0 18.1 6.5 -1.9 BETTER b. Chi-1 trans st dev 42 6.2 19.0 5.3 -2.4 BETTER c. Chi-1 gauche plus st dev 47 9.1 17.5 4.9 -1.7 BETTER d. Chi-1 pooled st dev 102 8.2 18.2 4.8 -2.0 BETTER e. Chi-2 trans st dev 30 7.0 20.4 5.0 -2.7 BETTER M O R R I S E T A L . C L A S S I F I C A T I O N Mean St.dev Classification Parameter m s 1 2 3 4 Value Class --------- ---- --- ------------------------------------ ----- ----- Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 85.8 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.6 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .91 3 Residue-by-residue listing for refined_5 Page 14 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.24 Chi1-chi2 distribution -.15 Chi1 only .02 Chi3 & chi4 .26 Omega .04 ------ -.06 ===== Main-chain covalent forces:- Main-chain bond lengths .01 Main-chain bond angles .42 ------ .25 ===== OVERALL AVERAGE .05 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.