Residue-by-residue listing for refined_12 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 - - - -64.5 179.4 - - - - - - 177.9 - 34.9 - 2 GLY 2 - - - - - - - - - - - 182.7 - - - 3 HIS 3 B 60.3 - - - - - - - - - 180.0 -.7 33.3 - +* +* 4 HIS 4 B - - -68.1 - - - - - - - 177.6 - 33.5 - 5 HIS 5 B 58.3 - - - - - - - - - 180.4 - 32.3 - 6 HIS 6 b - 178.8 - - - - - - - - 177.1 - 32.7 - 7 HIS 7 S a - - -68.2 - - - - - - - 182.9 - 33.2 - 8 HIS 8 l - - -67.0 - - - - - - - 172.9 - 31.1 - * * 9 LEU 9 b - - -69.4 - - - - - - - 186.8 - 32.1 - * * 10 GLU 10 b - 182.1 - 181.4 - - - - - - 178.3 -1.4 36.0 - 11 MET 11 b - 184.1 - - - - - - - - 181.7 - 33.9 - 12 ALA 12 A - - - - - - - - - - 176.5 - 34.0 - 13 SER 13 B - - -55.0 - - - - - - - 182.2 - 35.7 - 14 GLU 14 a - 184.6 - 175.8 - - - - - - 175.8 - 33.0 - 15 GLU 15 p - - -68.8 - - - - - - - 180.4 - 31.6 - 16 GLY 16 S - - - - - - - - - - - 182.0 -.6 - - +* +* 17 GLN 17 S B 59.8 - - 178.6 - - - - - - 177.7 - 35.4 - 18 VAL 18 B 64.5 - - - - - - - - - 182.5 - 35.0 - 19 ILE 19 E B - - -64.1 - - - - - - - 179.6 -2.8 32.2 - 20 ALA 20 E B - - - - - - - - - - 182.8 -.8 33.9 - +* +* 21 CYS 21 E B - - -51.7 - - - - - - - 176.7 -2.1 35.6 - 22 HIS 22 A - - -64.1 - - - - - - - 185.2 -.6 34.5 - +* +* Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 23 THR 23 h B 54.7 - - - - - - - - - 177.4 - 35.3 - 24 VAL 24 H A 64.1 - - - - -74.5 -22.6 - - - 176.5 - 31.5 - * * 25 GLU 25 H A - - -66.1 - - -57.3 -51.8 - - - 180.5 - 35.4 - * * 26 THR 26 H A - - -55.2 - - -69.9 -40.1 - - - 177.5 - 34.2 - 27 TRP 27 H A - 171.4 - - - -53.9 -53.5 - - - 180.9 -1.8 34.2 - * * 28 ASN 28 H A - 185.3 - - - -65.8 -41.9 - - - 181.2 -3.1 34.5 - * * 29 GLU 29 H A - 179.8 - 180.7 - -56.8 -48.1 - - - 181.6 -2.2 34.5 - 30 GLN 30 H A - - -69.6 - - -66.0 -42.7 - - - 179.9 -2.8 33.7 - * * 31 LEU 31 H A - - -65.8 181.4 - -66.4 -43.6 - - - 177.0 -1.9 34.7 - 32 GLN 32 H A - 179.2 - 176.7 - -60.9 -41.9 - - - 178.2 -2.8 33.8 - * * 33 LYS 33 H A - 177.2 - 176.0 - -64.5 -42.8 - - - 180.4 -2.5 33.2 - 34 ALA 34 H A - - - - - -66.6 -38.5 - - - 180.2 -2.9 33.6 - * * 35 ASN 35 H A - 186.3 - - - -66.6 -54.4 - - - 182.5 -2.7 37.3 - * * 36 GLU 36 H A - 179.5 - 177.4 - -61.0 -37.3 - - - 181.9 -3.0 34.0 - * * 37 SER 37 h A - - -53.2 - - - - - - - 181.8 -2.3 34.8 - 38 LYS 38 T L - - -61.3 185.1 - - - - - - 182.1 -1.0 32.3 - * * 39 THR 39 e B - - -47.4 - - - - - - - 178.2 -2.2 36.0 - * * 40 LEU 40 E B - 175.9 - - - - - - - - 187.4 -.6 35.2 - * +* +* 41 VAL 41 E B 59.5 - - - - - - - - - 177.1 -.8 33.5 - +* +* 42 VAL 42 E B - 179.0 - - - - - - - - 183.0 -2.7 33.6 - 43 VAL 43 E B - 181.0 - - - - - - - - 177.6 -2.8 33.7 - * * 44 ASP 44 E B - 169.3 - - - - - - - - 173.2 -2.4 37.1 - * * 45 PHE 45 E B - - -62.2 - - - - - - - 186.5 -3.0 36.2 - * * * 46 THR 46 E B - - -60.3 - - - - - - - 175.9 -3.2 36.0 - +* +* 47 ALA 47 t B - - - - - - - - - - 181.7 - 34.3 - 48 SER 48 T A - - -58.5 - - - - - - - 182.4 - 33.3 - 49 TRP 49 T A 53.2 - - - - - - - - - 179.4 - 31.2 - 50 CYS 50 h B 44.1 - - - - - - - -97.8 2.0 184.9 -1.4 28.8 - * * * * 51 GLY 51 H - - - - - - -55.5 -60.1 - - - 179.6 - - - +* +* 52 PRO 52 H - - - - - -58.5 -58.5 -30.5 - - - 180.0 - 38.5 - * * 53 CYS 53 H A - - -52.4 157.7 - -67.6 -49.7 - -97.8 2.0 179.6 - 37.0 - * * * 54 ARG 54 H A - 180.0 - 176.7 - -65.2 -31.4 - - - 179.2 -2.6 34.3 - 55 PHE 55 H A - 177.9 - - - -75.2 -32.8 - - - 185.2 -2.2 34.1 - 56 ILE 56 H A - 196.5 - - - -87.0 -19.2 - - - 180.7 -1.9 33.7 - +* +* +* Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 57 ALA 57 H A - - - - - -55.4 -52.8 - - - 179.0 -1.6 30.9 - * * 58 PRO 58 H - - - - - -62.7 -62.7 -28.2 - - - 180.3 - 38.8 - * * 59 PHE 59 H A - 184.2 - - - -74.2 -41.8 - - - 178.0 - 33.1 - 60 PHE 60 H A - 185.9 - - - -65.6 -33.7 - - - 176.1 -2.6 33.3 - 61 ALA 61 H A - - - - - -63.9 -32.5 - - - 177.9 -2.1 33.6 - 62 ASP 62 H A - 183.9 - - - -70.4 -45.3 - - - 176.5 -1.1 34.6 - * * 63 LEU 63 H A - - -64.3 180.3 - -55.0 -39.6 - - - 178.1 -2.2 35.4 - 64 ALA 64 H A - - - - - -63.3 -36.6 - - - 177.9 -2.1 33.9 - 65 LYS 65 H A - 179.1 - - - -79.4 -28.4 - - - 182.1 -1.2 33.7 - * * * 66 LYS 66 H A - 187.3 - - - -66.2 -40.8 - - - 179.4 -2.2 34.2 - 67 LEU 67 h b - - -69.6 172.2 - - - - - - 183.1 -2.0 32.4 - 68 PRO 68 T - - - - - -73.6 - - - - - 182.9 - 38.9 - * * 69 ASN 69 e A - 188.4 - - - - - - - - 179.5 - 33.5 - 70 VAL 70 E B - 183.7 - - - - - - - - 181.5 -.7 34.2 - +* +* 71 LEU 71 E B - 200.6 - 178.0 - - - - - - 182.3 -2.7 34.9 - * * 72 PHE 72 E B - - -60.6 - - - - - - - 179.6 -.6 34.9 - +* +* 73 LEU 73 E B - - -62.7 - - - - - - - 173.1 -2.1 34.6 - * * 74 LYS 74 E B - - -73.9 - - - - - - - 178.9 -2.4 35.8 - 75 VAL 75 E B - 177.1 - - - - - - - - 177.9 -3.1 34.8 - * * 76 ASP 76 E B - 185.4 - - - - - - - - 186.3 -.8 32.9 - * +* +* 77 THR 77 e A 55.1 - - - - - - - - - 174.3 -2.1 32.0 - 78 ASP 78 T A - 182.8 - - - - - - - - 176.9 - 33.3 - 79 GLU 79 T A - - -66.5 - - - - - - - 177.5 - 36.1 - 80 LEU 80 h b - - -68.6 179.8 - - - - - - 181.9 -3.5 32.7 - +* +* 81 LYS 81 H A 57.7 - - 175.7 - -68.3 -32.2 - - - 180.1 -.9 33.5 - +* +* 82 SER 82 H A 51.6 - - - - -70.3 -44.6 - - - 178.6 - 34.6 - 83 VAL 83 H A - 179.0 - - - -63.3 -44.5 - - - 179.4 - 34.5 - 84 ALA 84 H A - - - - - -61.8 -37.8 - - - 179.4 -2.3 34.2 - 85 SER 85 H A - 186.7 - - - -75.6 -36.5 - - - 182.4 -1.8 33.8 - 86 ASP 86 H A - 182.9 - - - -66.6 -37.3 - - - 179.0 -2.7 34.8 - 87 TRP 87 h A - - -68.4 - - - - - - - 179.4 -2.4 32.3 - 88 ALA 88 T l - - - - - - - - - - 178.1 -.7 30.8 - +* +* 89 ILE 89 t B - - -55.7 - - - - - - - 184.2 -2.6 33.7 - 90 GLN 90 A - 183.3 - 177.6 - - - - - - 182.0 -1.1 34.8 - * * 91 ALA 91 S B - - - - - - - - - - 185.9 - 33.4 - * * 92 MET 92 S B - - -59.0 174.2 - - - - - - -2.6 - 35.6 - 93 PRO 93 e cis - - - - - -84.2 - - - - - 176.4 - 39.6 - +* +* +* 94 THR 94 E B - - -57.3 - - - - - - - 180.0 -2.8 34.9 - 95 PHE 95 E B - - -58.8 - - - - - - - 180.0 -3.3 35.8 - +* +* Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 96 MET 96 E B - 180.6 - 179.5 - - - - - - 181.4 -3.2 33.2 - +* +* 97 PHE 97 E B - - -67.8 - - - - - - - 182.2 -2.9 35.8 - * * 98 LEU 98 E B 59.8 - - 171.6 - - - - - - 185.1 -1.9 31.5 - 99 LYS 99 E B - 176.0 - 182.1 - - - - - - 180.4 -3.5 35.6 - +* +* 100 GLU 100 e l - - -55.8 179.7 - - - - - - 184.9 -.6 34.5 - +* +* 101 GLY 101 T - - - - - - - - - - - 175.3 - - - 102 LYS 102 E B - - -60.4 - - - - - - - 184.2 -2.5 34.7 - 103 ILE 103 E B - - -57.3 178.1 - - - - - - 179.3 - 33.7 - 104 LEU 104 E a - - -69.4 184.6 - - - - - - 184.7 -2.0 33.8 - 105 ASP 105 E B 57.2 - - - - - - - - - 187.5 -2.3 31.6 - * * 106 LYS 106 E B - 181.1 - - - - - - - - 184.0 - 34.8 - 107 VAL 107 E B - 178.7 - - - - - - - - 178.3 -2.7 36.0 - 108 VAL 108 E B 65.2 - - - - - - - - - 180.0 -.5 33.0 - ** ** 109 GLY 109 e - - - - - - - - - - - 179.4 -2.7 - - 110 ALA 110 B - - - - - - - - - - 180.7 - 34.1 - 111 LYS 111 h B - - -62.0 175.8 - - - - - - 185.1 -1.0 36.1 - * * 112 LYS 112 H A - 187.9 - 174.3 - -69.4 -35.9 - - - 180.3 -.5 32.8 - ** ** 113 ASP 113 H A - 176.0 - - - -72.3 -49.4 - - - 182.8 - 33.8 - 114 GLU 114 H A - 177.9 - 169.2 - -71.0 -34.0 - - - 179.4 - 31.2 - 115 LEU 115 H A - 185.3 - - - -59.8 -51.3 - - - 179.5 -2.3 35.2 - * * 116 GLN 116 H A - - -62.4 179.4 - -61.3 -36.8 - - - 178.3 -1.4 32.9 - 117 SER 117 H A - - -57.3 - - -69.6 -31.0 - - - 177.0 -1.7 33.8 - 118 THR 118 H A - - -60.3 - - -71.3 -35.7 - - - 177.5 -2.1 34.5 - 119 ILE 119 H A - - -59.2 - - -64.0 -53.1 - - - 179.6 -2.1 33.2 - * * 120 ALA 120 H A - - - - - -61.8 -30.8 - - - 176.9 -2.5 33.0 - 121 LYS 121 H A - 184.7 - 182.8 - -57.7 -44.3 - - - 180.6 -1.6 37.5 - * * 122 HIS 122 H A - - -74.6 - - -78.8 -19.2 - - - 176.5 -1.6 32.2 - * +* +* 123 LEU 123 h B - - -94.8 - - - - - - - 180.3 -1.1 34.1 - +* * +* 124 ALA 124 - - - - - - - - - - - - -.6 34.0 - +* +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: * * +* * +* +* +* * * ** +* ** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 57.7 182.1 -63.1 177.4 -69.7 -66.0 -39.5 - -97.8 2.0 180.2 -2.0 34.1 * * Standard deviations: 5.5 5.7 7.8 5.2 11.5 7.1 9.3 - .0 .0 3.0 .8 1.7 Numbers of values: 15 42 45 30 4 46 46 0 2 2 122 82 119 0 Number of cis-peptides (labelled cis): 1 Residue-by-residue listing for refined_12 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_12 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 - 1.242 1.507 1.533 1.462 - 116.11 120.46 108.90 109.76 111.18 123.43 2 GLY 2 1.325 1.235 1.509 - 1.437 121.31 116.42 120.87 - 111.15 - 122.71 3 HIS 3 1.297 1.235 1.511 1.550 1.445 121.68 116.89 120.14 111.29 110.44 111.08 122.97 ** * ** 4 HIS 4 1.312 1.230 1.504 1.538 1.450 120.85 116.19 120.60 109.48 110.06 112.65 123.20 * * * 5 HIS 5 1.293 1.235 1.507 1.553 1.438 122.14 116.11 120.76 111.75 109.77 112.30 123.09 +** * * * +** 6 HIS 6 1.299 1.220 1.529 1.559 1.438 121.40 116.09 120.77 112.52 110.95 110.54 122.96 ** * * * ** 7 HIS 7 1.327 1.226 1.521 1.557 1.482 122.79 116.13 120.23 108.46 111.21 113.57 123.65 * * +* +* 8 HIS 8 1.334 1.240 1.516 1.554 1.478 123.95 116.32 121.02 109.27 112.51 115.02 122.63 * * * +** +** 9 LEU 9 1.311 1.243 1.494 1.545 1.448 120.80 114.50 121.54 111.01 107.70 114.12 123.89 * * * ** ** 10 GLU 10 1.288 1.232 1.498 1.523 1.415 122.98 115.85 120.86 109.82 108.42 109.25 123.24 +** * ** +** 11 MET 11 1.276 1.224 1.502 1.538 1.421 121.86 115.49 121.27 111.66 107.78 110.88 123.12 +*** * +* * +*** 12 ALA 12 1.307 1.227 1.510 1.520 1.448 122.13 114.78 121.85 111.12 109.63 110.20 123.36 +* +* Residue-by-residue listing for refined_12 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 1.295 1.238 1.528 1.528 1.422 122.91 117.40 120.07 111.20 107.27 108.48 122.48 ** +* * * ** 14 GLU 14 1.303 1.246 1.520 1.536 1.441 120.72 115.77 120.17 112.79 109.86 110.05 124.02 +* * +* 15 GLU 15 1.333 1.235 1.522 1.542 1.466 124.51 115.64 121.61 111.73 113.90 111.37 122.68 +* +* 16 GLY 16 1.309 1.229 1.501 - 1.435 120.33 115.61 120.77 - 111.03 - 123.62 * * * 17 GLN 17 1.317 1.232 1.503 1.525 1.433 122.26 114.56 121.38 108.38 110.52 110.79 124.06 * * * 18 VAL 18 1.285 1.233 1.543 1.544 1.427 123.87 118.40 119.83 111.49 108.69 108.91 121.73 *** +* * * * +* *** 19 ILE 19 1.327 1.230 1.522 1.569 1.447 119.39 116.15 121.08 110.37 111.04 113.49 122.77 * * * * 20 ALA 20 1.305 1.234 1.511 1.520 1.442 121.81 116.44 120.69 110.87 109.55 110.61 122.86 +* +* 21 CYS 21 1.307 1.230 1.511 1.503 1.417 121.59 116.09 120.98 109.36 110.32 109.44 122.91 +* * ** ** 22 HIS 22 1.298 1.232 1.509 1.540 1.448 121.61 115.84 120.98 109.49 109.40 111.42 123.16 ** ** 23 THR 23 1.325 1.248 1.509 1.551 1.442 121.70 116.62 120.38 108.78 110.18 110.83 123.00 24 VAL 24 1.320 1.232 1.542 1.576 1.439 120.82 116.37 120.82 112.24 109.43 113.24 122.78 * * * * * 25 GLU 25 1.357 1.236 1.530 1.533 1.423 122.67 116.14 120.63 108.45 110.67 110.70 123.21 +* +* +* 26 THR 26 1.333 1.231 1.529 1.539 1.449 121.67 115.83 120.57 110.32 110.35 110.67 123.59 27 TRP 27 1.328 1.236 1.535 1.537 1.457 122.71 116.21 120.78 111.27 111.29 109.25 122.98 28 ASN 28 1.322 1.232 1.524 1.531 1.458 121.62 115.65 120.80 109.72 110.38 110.60 123.52 29 GLU 29 1.329 1.239 1.529 1.535 1.466 122.92 116.30 120.45 109.54 111.75 110.34 123.23 30 GLN 30 1.325 1.226 1.512 1.494 1.419 122.43 117.23 120.11 110.79 112.95 109.78 122.66 +* ** ** 31 LEU 31 1.324 1.232 1.500 1.485 1.417 121.65 115.86 120.51 109.88 111.19 109.74 123.62 * ** ** ** 32 GLN 32 1.311 1.229 1.521 1.524 1.437 121.80 115.97 120.75 111.20 109.94 110.37 123.24 * * * 33 LYS 33 1.323 1.239 1.523 1.536 1.448 121.97 116.83 120.17 111.17 110.96 110.95 122.97 34 ALA 34 1.334 1.220 1.521 1.521 1.451 121.30 115.97 120.93 110.80 110.69 110.68 123.09 35 ASN 35 1.314 1.236 1.517 1.521 1.465 122.55 114.21 121.67 107.49 109.91 108.70 124.09 * * * * 36 GLU 36 1.309 1.235 1.533 1.535 1.462 123.89 116.96 120.75 110.84 112.54 109.50 122.29 * * * 37 SER 37 1.307 1.238 1.536 1.510 1.437 120.97 116.07 120.40 110.71 111.60 108.73 123.53 +* * * +* 38 LYS 38 1.349 1.232 1.526 1.525 1.472 123.53 114.50 121.86 111.97 110.64 111.24 123.55 * * * 39 THR 39 1.308 1.240 1.529 1.531 1.430 123.64 115.01 121.65 108.29 109.80 110.17 123.33 +* * * +* 40 LEU 40 1.277 1.240 1.540 1.547 1.438 123.51 117.10 120.40 111.96 107.27 108.50 122.48 +*** * * * * +*** 41 VAL 41 1.313 1.230 1.536 1.567 1.438 121.04 116.52 120.83 111.94 111.64 109.94 122.63 * * * * * 42 VAL 42 1.312 1.239 1.513 1.539 1.444 122.09 116.31 120.75 109.76 109.26 112.48 122.93 * * 43 VAL 43 1.306 1.237 1.524 1.550 1.437 121.32 114.90 121.04 109.55 111.31 111.94 124.05 +* * +* Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 44 ASP 44 1.299 1.225 1.520 1.537 1.449 124.60 117.60 119.85 109.11 109.61 107.77 122.48 ** +* +* ** 45 PHE 45 1.317 1.233 1.517 1.525 1.430 121.07 117.12 120.05 108.58 107.36 110.17 122.76 * * * 46 THR 46 1.303 1.217 1.533 1.546 1.442 121.51 116.79 120.45 109.69 111.22 108.44 122.75 +* +* +* 47 ALA 47 1.316 1.233 1.519 1.518 1.444 122.11 116.64 120.65 110.29 108.79 110.78 122.71 48 SER 48 1.305 1.229 1.552 1.527 1.460 122.34 117.55 120.30 110.82 113.46 109.93 122.15 +* * +* 49 TRP 49 1.326 1.231 1.536 1.540 1.459 121.24 118.10 120.00 111.61 114.45 111.70 121.90 * * 50 CYS 50 1.316 1.237 1.538 1.553 1.460 120.11 115.64 120.95 114.28 113.08 112.71 123.40 * ** * ** 51 GLY 51 1.339 1.242 1.531 - 1.473 123.26 119.40 119.35 - 115.42 - 121.26 * +* * * * +* 52 PRO 52 1.371 1.219 1.524 1.543 1.478 122.50 114.88 121.59 110.38 111.16 103.94 123.51 +* * * +* 53 CYS 53 1.306 1.228 1.525 1.509 1.441 123.72 115.42 121.54 108.79 109.72 107.82 123.03 +* * * +* +* 54 ARG 54 1.314 1.217 1.531 1.532 1.444 122.73 115.92 120.99 111.63 110.31 109.07 123.06 * * 55 PHE 55 1.318 1.233 1.532 1.542 1.454 122.38 116.89 120.83 110.54 111.65 110.10 122.26 56 ILE 56 1.313 1.235 1.544 1.571 1.449 120.34 116.10 120.95 110.66 110.50 111.20 122.92 * * * 57 ALA 57 1.332 1.236 1.554 1.531 1.462 122.59 120.02 119.13 112.21 113.44 111.73 120.83 * +* * * +* 58 PRO 58 1.379 1.239 1.528 1.535 1.475 121.91 116.07 121.20 109.86 111.68 103.76 122.71 ** ** 59 PHE 59 1.324 1.228 1.527 1.539 1.445 121.25 116.55 120.64 111.37 110.08 111.27 122.79 60 PHE 60 1.325 1.230 1.531 1.538 1.459 121.64 115.98 121.13 111.55 109.42 110.89 122.88 61 ALA 61 1.326 1.237 1.535 1.517 1.457 121.76 116.27 121.03 110.86 110.45 110.57 122.67 62 ASP 62 1.333 1.225 1.487 1.513 1.466 121.37 114.52 120.90 108.61 108.99 111.88 124.58 +* +* 63 LEU 63 1.315 1.232 1.535 1.521 1.438 124.26 115.94 120.79 110.12 111.02 108.69 123.26 * * * * 64 ALA 64 1.325 1.227 1.526 1.519 1.458 122.84 115.73 121.30 110.49 111.31 110.28 122.97 65 LYS 65 1.311 1.227 1.531 1.556 1.444 122.09 115.54 121.17 113.19 109.85 108.80 123.28 * * +* +* 66 LYS 66 1.317 1.232 1.531 1.570 1.450 123.30 116.68 120.48 112.50 109.81 108.94 122.82 ** * ** 67 LEU 67 1.320 1.227 1.522 1.513 1.436 121.59 116.45 121.32 112.11 111.86 110.67 122.22 * * * 68 PRO 68 1.338 1.225 1.535 1.534 1.462 123.11 118.04 120.49 110.13 113.95 103.04 121.47 69 ASN 69 1.316 1.230 1.533 1.533 1.466 119.57 115.44 121.86 111.21 110.10 110.56 122.69 * * 70 VAL 70 1.307 1.233 1.515 1.549 1.439 122.21 116.89 120.13 110.34 108.23 111.46 122.89 +* * * +* 71 LEU 71 1.307 1.234 1.545 1.558 1.446 121.23 116.72 120.61 112.16 107.49 108.65 122.65 +* * * * * +* 72 PHE 72 1.316 1.240 1.515 1.522 1.463 122.37 116.21 120.89 107.86 110.84 111.59 122.89 * * 73 LEU 73 1.310 1.221 1.513 1.534 1.444 121.96 115.83 120.56 107.28 111.69 112.70 123.61 * * * * 74 LYS 74 1.319 1.238 1.510 1.527 1.421 123.62 116.21 120.74 109.02 108.09 110.31 123.03 +* * * +* Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 75 VAL 75 1.287 1.231 1.503 1.558 1.431 122.31 116.52 120.68 109.74 108.86 111.30 122.78 *** * * *** 76 ASP 76 1.303 1.229 1.501 1.504 1.434 119.81 116.12 120.68 111.02 108.55 112.20 123.18 +* * * * * +* 77 THR 77 1.292 1.239 1.540 1.537 1.438 122.63 117.88 120.03 111.74 114.37 110.65 122.02 +** * * * +** 78 ASP 78 1.316 1.242 1.506 1.513 1.456 120.19 113.90 121.76 110.49 108.48 112.00 124.34 * * 79 GLU 79 1.327 1.237 1.517 1.513 1.429 124.26 116.10 121.00 109.21 110.10 108.88 122.90 +* * +* 80 LEU 80 1.311 1.237 1.508 1.513 1.387 122.20 114.26 122.00 112.78 109.67 110.66 123.68 * +*** * +*** 81 LYS 81 1.317 1.234 1.518 1.539 1.448 123.13 115.95 121.00 111.08 111.11 110.59 123.04 82 SER 82 1.312 1.226 1.523 1.514 1.433 121.87 115.76 120.73 111.76 110.26 108.48 123.43 * * * * 83 VAL 83 1.323 1.231 1.524 1.551 1.453 122.69 115.59 121.31 109.78 109.87 110.91 123.07 84 ALA 84 1.317 1.231 1.527 1.507 1.446 122.07 116.53 120.77 110.38 111.33 109.89 122.71 85 SER 85 1.315 1.229 1.543 1.540 1.437 120.87 116.25 120.97 111.48 110.04 110.06 122.74 * * 86 ASP 86 1.327 1.233 1.532 1.537 1.473 122.83 116.47 121.03 109.96 111.45 109.52 122.47 87 TRP 87 1.316 1.237 1.522 1.523 1.453 121.75 114.95 121.01 111.66 111.88 111.16 124.02 88 ALA 88 1.329 1.239 1.525 1.531 1.458 124.55 115.55 121.51 112.11 112.88 112.33 122.87 +* * * +* 89 ILE 89 1.312 1.240 1.517 1.559 1.443 121.64 115.23 121.34 110.67 108.46 111.92 123.36 * * 90 GLN 90 1.304 1.228 1.521 1.536 1.448 122.65 116.09 121.03 110.84 110.64 109.16 122.86 +* +* 91 ALA 91 1.309 1.224 1.510 1.521 1.448 121.30 116.34 120.84 111.52 109.31 110.77 122.82 * * 92 MET 92 1.298 1.235 1.516 1.523 1.443 121.81 118.36 120.27 109.98 110.84 108.73 121.38 ** * * * ** 93 PRO 93 1.337 1.223 1.524 1.540 1.467 124.67 116.66 120.93 109.16 111.88 103.47 122.37 94 THR 94 1.291 1.229 1.522 1.520 1.423 121.21 116.54 120.56 109.32 109.00 110.90 122.90 +** +* +** 95 PHE 95 1.302 1.233 1.506 1.526 1.413 122.17 116.85 120.45 109.84 108.47 109.40 122.69 +* ** ** 96 MET 96 1.294 1.239 1.502 1.527 1.434 120.63 114.88 121.26 111.07 110.22 111.42 123.86 ** * * ** 97 PHE 97 1.290 1.243 1.502 1.510 1.401 123.85 116.17 121.35 110.50 109.48 108.53 122.48 +** * +** * * +** 98 LEU 98 1.281 1.213 1.511 1.568 1.406 120.51 117.14 120.24 113.00 109.54 112.59 122.60 *** +* +** +* * *** 99 LYS 99 1.291 1.216 1.478 1.526 1.437 122.02 114.71 120.74 109.44 109.64 109.87 124.51 +** ** * +** 100 GLU 100 1.321 1.232 1.540 1.519 1.458 124.87 116.42 120.67 107.82 110.55 112.11 122.87 +* * +* 101 GLY 101 1.314 1.224 1.537 - 1.447 121.36 117.78 120.31 - 113.20 - 121.91 * * * 102 LYS 102 1.331 1.221 1.513 1.549 1.469 120.90 117.59 119.68 107.36 107.95 113.52 122.71 * * +* +* 103 ILE 103 1.311 1.228 1.531 1.556 1.464 121.74 116.67 120.64 110.14 111.24 111.33 122.68 * * 104 LEU 104 1.327 1.236 1.510 1.529 1.443 121.70 116.26 121.12 109.56 111.98 111.41 122.61 105 ASP 105 1.303 1.231 1.471 1.530 1.422 121.83 115.83 120.96 111.90 109.94 113.21 123.18 +* +** +* +* +** Residue-by-residue listing for refined_12 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 ----------------------------------------------------------------------------------------------------------------------------------- 106 LYS 106 1.272 1.230 1.517 1.551 1.410 120.71 115.57 120.68 113.77 109.68 106.98 123.67 **** * +** +* ** **** 107 VAL 107 1.310 1.232 1.516 1.564 1.444 123.21 116.29 120.81 108.60 109.28 110.39 122.88 * * 108 VAL 108 1.305 1.247 1.536 1.563 1.436 121.20 116.09 120.88 111.02 109.88 112.11 122.98 +* * +* 109 GLY 109 1.310 1.239 1.503 - 1.435 121.63 117.34 120.17 - 110.53 - 122.49 * * 110 ALA 110 1.317 1.233 1.498 1.522 1.437 119.48 115.39 120.98 110.68 108.36 111.08 123.61 * * * * * 111 LYS 111 1.295 1.218 1.497 1.518 1.413 122.74 117.35 119.86 110.66 108.20 108.25 122.79 ** * ** * * ** 112 LYS 112 1.309 1.230 1.526 1.526 1.430 121.31 116.68 120.55 111.84 111.68 110.50 122.76 * * * 113 ASP 113 1.316 1.230 1.516 1.538 1.465 121.01 116.28 120.70 109.82 111.38 111.33 122.95 114 GLU 114 1.316 1.228 1.517 1.535 1.449 120.93 117.12 120.09 112.47 112.42 111.79 122.76 * * 115 LEU 115 1.322 1.221 1.508 1.510 1.460 121.20 115.19 121.13 108.71 109.85 110.53 123.66 116 GLN 116 1.311 1.235 1.521 1.517 1.465 122.21 116.61 120.67 110.72 111.59 111.27 122.68 * * 117 SER 117 1.319 1.226 1.525 1.519 1.453 120.60 115.63 121.30 110.76 109.84 110.56 123.06 118 THR 118 1.311 1.234 1.533 1.535 1.432 122.45 116.18 121.09 110.34 109.94 110.25 122.72 * * * 119 ILE 119 1.317 1.225 1.520 1.554 1.443 121.16 116.54 120.24 110.65 109.59 112.22 123.11 120 ALA 120 1.334 1.229 1.524 1.509 1.469 121.90 115.54 120.77 111.09 111.17 110.80 123.69 121 LYS 121 1.319 1.221 1.521 1.502 1.456 123.60 115.44 121.24 108.37 109.53 107.33 123.31 * * +* +* 122 HIS 122 1.316 1.238 1.527 1.517 1.442 122.60 117.80 119.72 110.71 113.67 111.55 122.48 123 LEU 123 1.330 1.227 1.517 1.522 1.425 121.42 116.08 120.74 110.86 110.54 110.19 123.16 +* +* 124 ALA 124 1.309 - 1.513 1.525 1.440 122.34 - - 110.95 109.32 110.48 - * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** +** ** +*** +* +* ** * +** * **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_12 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 1.272 1.357 1.313 .014 **** +* * C-N (Pro) 1.341 .016 4 1.337 1.379 1.356 .019 ** C-O C-O 1.231 .020 123 1.213 1.248 1.232 .007 CA-C CH1E-C (except Gly) 1.525 .021 119 1.471 1.554 1.520 .014 +** * CH2G*-C (Gly) 1.516 .018 5 1.501 1.537 1.516 .015 * CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.507 1.531 1.520 .007 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.520 1.576 1.551 .014 * CH1E-CH2E (the rest) 1.530 .020 84 1.485 1.570 1.531 .016 ** ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.387 1.482 1.444 .017 +*** * NH1-CH2G* (Gly) 1.451 .016 5 1.435 1.473 1.445 .014 * * N-CH1E (Pro) 1.466 .015 4 1.462 1.478 1.471 .006 ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_12 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 2.0 114 113.90 120.02 116.18 .92 * +* CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.61 119.40 117.31 1.28 * CH1E-C-N (Pro) 116.9 1.5 4 114.88 118.04 116.41 1.14 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.83 124.58 122.99 .60 * O-C-N (Pro) 122.0 1.4 4 121.47 123.51 122.52 .73 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 119.39 124.87 122.03 1.13 * +* C-NH1-CH2G* (Gly) 120.6 1.7 5 120.33 123.26 121.58 .95 +* C-N-CH1E (Pro) 122.6 5.0 4 121.91 124.67 123.04 1.03 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 119.13 122.00 120.79 .51 CH2G*-C-O (Gly) 120.8 2.1 5 119.35 120.87 120.29 .54 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 110.29 112.21 111.03 .58 * CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 108.29 112.24 110.25 1.02 * CH2E-CH1E-C (the rest) 110.1 1.9 84 107.28 114.28 110.52 1.50 * ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 107.27 114.45 110.33 1.51 * * NH1-CH2G*-C (Gly) 112.5 2.9 5 110.53 115.42 112.27 1.83 * N-CH1E-C (Pro) 111.8 2.5 4 111.16 113.95 112.17 1.06 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 109.89 112.33 110.78 .62 * NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 108.44 113.49 111.12 1.20 +* * N-CH1E-CH2E (Pro) 103.0 1.1 4 103.04 103.94 103.55 .34 NH1-CH1E-CH2E (the rest) 110.5 1.7 80 106.98 115.02 110.48 1.58 ** +** ------------------------------------------------------------------------------------------------------------- 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_12 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] 100 88.5% Residues in additional allowed regions [a,b,l,p] 13 11.5% Residues in generously allowed regions [~a,~b,~l,~p] 0 .0% Residues in disallowed regions [XX] 0 .0% ---- ------ 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 88.5 83.8 10.0 .5 Inside b. Omega angle st dev 122 3.0 6.0 3.0 -1.0 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 119 1.7 3.1 1.6 -.9 Inside e. H-bond energy st dev 82 .8 .8 .2 .2 Inside f. Overall G-factor 124 .1 -.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 15 5.5 18.1 6.5 -1.9 BETTER b. Chi-1 trans st dev 42 5.7 19.0 5.3 -2.5 BETTER c. Chi-1 gauche plus st dev 45 7.8 17.5 4.9 -2.0 BETTER d. Chi-1 pooled st dev 102 7.5 18.2 4.8 -2.2 BETTER e. Chi-2 trans st dev 30 5.2 20.4 5.0 -3.0 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% 88.5 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.6 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .85 2 Residue-by-residue listing for refined_12 Page 14 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.21 Chi1-chi2 distribution -.11 Chi1 only -.01 Chi3 & chi4 .23 Omega .05 ------ -.04 ===== Main-chain covalent forces:- Main-chain bond lengths .03 Main-chain bond angles .45 ------ .27 ===== OVERALL AVERAGE .07 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.