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 - - 181.4 - 181.4 - - - - - - 180.8 - 34.3 - 2 GLY 2 - - - - - - - - - - - 182.2 - - - 3 HIS 3 B - - -67.2 - - - - - - - 180.9 - 32.9 - 4 HIS 4 A - 181.6 - - - - - - - - 184.0 - 34.8 - 5 HIS 5 S XX 56.6 - - - - - - - - - 193.8 - 22.2 - **** ** *** **** 6 HIS 6 l - - -74.6 - - - - - - - 180.0 - 31.2 - 7 HIS 7 B - 177.6 - - - - - - - - 180.1 - 35.5 - 8 HIS 8 ~l - 179.6 - - - - - - - - 175.0 - 31.5 - ** ** 9 LEU 9 b - - -64.8 - - - - - - - 180.6 - 32.2 - 10 GLU 10 A - 193.0 - 180.1 - - - - - - 173.8 -.9 34.8 - * * * 11 MET 11 ~l - - -63.2 176.9 - - - - - - 172.2 - 33.2 - ** * ** 12 ALA 12 S b - - - - - - - - - - 185.9 - 33.1 - * * 13 SER 13 B - - -58.3 - - - - - - - 179.8 -1.9 36.8 - 14 GLU 14 t B - 177.0 - 176.8 - - - - - - 179.9 -1.7 34.3 - 15 GLU 15 T B 61.9 - - - - - - - - - 178.0 - 32.5 - 16 GLY 16 T - - - - - - - - - - - 185.5 -2.5 - - 17 GLN 17 e B 47.5 - - 176.1 - - - - - - 175.4 -.8 33.9 - * +* +* 18 VAL 18 E B 65.2 - - - - - - - - - 175.2 -.6 34.1 - +* +* 19 ILE 19 E B - - -62.1 - - - - - - - 184.0 -2.2 31.5 - 20 ALA 20 E B - - - - - - - - - - 178.3 -.7 33.9 - +* +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 21 CYS 21 E B - - -49.1 - - - - - - - 175.0 -2.6 35.8 - * * 22 HIS 22 S A - - -65.4 - - - - - - - 186.5 -.7 35.3 - * +* +* 23 THR 23 h B 58.3 - - - - - - - - - 174.5 - 36.8 - 24 VAL 24 H A 62.4 - - - - -74.7 -22.7 - - - 176.7 - 32.3 - * * 25 GLU 25 H A - 181.9 - - - -55.9 -52.6 - - - 180.9 - 36.2 - * * 26 THR 26 H A - - -51.5 - - -73.8 -38.8 - - - 182.0 - 34.5 - * * 27 TRP 27 H A - 177.1 - - - -56.8 -55.2 - - - 182.4 -1.8 34.3 - * * 28 ASN 28 H A - 181.7 - - - -66.7 -40.9 - - - 182.6 -3.0 34.6 - * * 29 GLU 29 H A - 191.2 - - - -57.7 -48.4 - - - 182.3 -1.5 35.5 - 30 GLN 30 H A - - -64.5 - - -70.3 -40.0 - - - 178.3 -2.5 34.0 - 31 LEU 31 H A - - -69.8 183.2 - -64.7 -42.4 - - - 174.8 -2.0 33.5 - 32 GLN 32 H A - 175.3 - 185.1 - -57.5 -46.7 - - - 182.1 -2.8 34.4 - * * 33 LYS 33 H A - 198.0 - - - -59.0 -37.2 - - - 177.3 -2.2 34.9 - 34 ALA 34 H A - - - - - -76.9 -42.7 - - - 184.6 -2.0 34.0 - 35 ASN 35 H A - 180.2 - - - -63.0 -55.8 - - - 184.5 -3.3 37.5 - * +* * +* 36 GLU 36 H A 60.0 - - 175.0 - -62.3 -34.2 - - - 181.8 -2.9 31.9 - * * 37 SER 37 h A - - -57.0 - - - - - - - 178.4 -.7 34.4 - +* +* 38 LYS 38 T l - - -77.9 163.4 - - - - - - 177.5 -1.5 30.1 - * * 39 THR 39 e B - - -44.6 - - - - - - - 179.1 -3.2 36.9 - * +* +* 40 LEU 40 E B 48.7 - - - - - - - - - 189.0 - 28.0 - +* +* +* 41 VAL 41 E B 59.7 - - - - - - - - - 177.0 -.6 33.9 - +* +* 42 VAL 42 E B - 179.3 - - - - - - - - 183.6 -3.0 34.1 - * * 43 VAL 43 E B - 184.9 - - - - - - - - 175.2 -3.1 35.2 - * * 44 ASP 44 E B - 168.6 - - - - - - - - 176.5 -3.1 34.0 - * * 45 PHE 45 E B - - -61.0 - - - - - - - 185.3 -3.2 36.2 - +* +* 46 THR 46 E B - 188.5 - - - - - - - - 177.9 -2.3 34.7 - 47 ALA 47 t B - - - - - - - - - - 181.8 - 34.2 - 48 SER 48 T A - - -55.2 - - - - - - - 178.6 - 34.0 - 49 TRP 49 T A 57.1 - - - - - - - - - 180.7 - 31.6 - 50 CYS 50 h B - 173.8 - 221.0 - - - 52.0 - 2.0 182.6 -2.1 34.4 - ** *** *** 51 GLY 51 H - - - - - - -58.1 -68.4 - - - 180.4 -.6 - - +** +* +** 52 PRO 52 H - - - - - -56.6 -56.6 -30.3 - - - 180.5 - 38.5 - * * 53 CYS 53 H A - - -52.9 - - -71.7 -37.1 52.0 - 2.0 177.9 - 35.9 - *** *** 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 ----------------------------------------------------------------------------------------------------------------------------------- 54 ARG 54 H A - 182.5 - 175.5 - -78.7 -29.4 - - - 179.2 -1.9 33.5 - * * 55 PHE 55 H A - 183.7 - - - -61.3 -27.5 - - - 183.6 -2.4 34.4 - * * 56 ILE 56 h A - 197.2 - - - - - - - - 183.8 -.8 34.5 - +* +* 57 ALA 57 H A - - - - - -59.2 -49.6 - - - 179.0 -1.0 31.5 - * * 58 PRO 58 H - - - - - -56.6 -56.6 -32.4 - - - 180.3 - 38.3 - * * 59 PHE 59 H A - 183.2 - - - -75.5 -38.9 - - - 177.1 - 32.5 - 60 PHE 60 H A - 181.6 - - - -64.4 -34.1 - - - 176.5 -1.9 33.7 - 61 ALA 61 H A - - - - - -69.8 -33.0 - - - 178.1 -2.3 33.9 - 62 ASP 62 H A - 185.4 - - - -67.4 -43.1 - - - 175.2 -1.4 35.0 - 63 LEU 63 H A - - -67.8 182.7 - -57.0 -48.2 - - - 177.7 -2.6 35.1 - 64 ALA 64 H A - - - - - -59.6 -32.7 - - - 179.5 -2.3 34.3 - 65 LYS 65 H A - 184.4 - - - -77.0 -35.4 - - - 183.1 -1.4 33.4 - 66 LYS 66 H A - 185.2 - 182.2 - -76.7 -38.0 - - - 178.1 -2.3 33.1 - 67 LEU 67 h b - - -65.1 - - - - - - - 184.8 -2.8 33.2 - * * 68 PRO 68 T - - - - - -77.8 - - - - - 183.4 - 39.0 - * * * 69 ASN 69 T A - 183.8 - - - - - - - - 181.0 - 33.6 - 70 VAL 70 t B - 182.1 - - - - - - - - 178.8 -.6 34.1 - +* +* 71 LEU 71 E B - - -62.6 178.2 - - - - - - 177.9 -1.7 35.6 - 72 PHE 72 E B - - -62.7 - - - - - - - 181.4 -.7 33.8 - +* +* 73 LEU 73 E B - - -77.1 - - - - - - - 178.7 -2.6 32.7 - 74 LYS 74 E B - 175.4 - - - - - - - - 178.0 -2.7 36.1 - 75 VAL 75 E B - 180.1 - - - - - - - - 177.5 -3.3 33.7 - +* +* 76 ASP 76 E B - 186.7 - - - - - - - - 186.0 -.6 33.8 - * +* +* 77 THR 77 e A - 181.5 - - - - - - - - 178.8 -2.7 33.1 - 78 ASP 78 T A - 183.3 - - - - - - - - 179.3 - 35.7 - 79 GLU 79 T a - - -67.0 - - - - - - - 183.6 - 36.6 - 80 LEU 80 h b - 185.1 - - - - - - - - 186.0 -3.0 33.8 - * * * 81 LYS 81 H A - 189.4 - - - -68.6 -38.0 - - - 182.2 -1.1 34.0 - * * 82 SER 82 H A - - -54.9 - - -60.4 -43.0 - - - 179.5 - 33.3 - 83 VAL 83 H A - 177.7 - - - -71.3 -37.5 - - - 177.3 - 32.9 - 84 ALA 84 H A - - - - - -61.7 -30.8 - - - 178.4 -1.6 34.0 - 85 SER 85 H A - 183.3 - - - -73.1 -35.6 - - - 183.1 -1.8 34.2 - 86 ASP 86 H A - 186.9 - - - -76.2 -35.2 - - - 179.1 -1.4 34.1 - 87 TRP 87 h A - - -70.8 - - - - - - - 180.0 -2.5 32.4 - 88 ALA 88 T l - - - - - - - - - - 182.5 -.6 31.6 - +* +* 89 ILE 89 t B - - -55.0 178.3 - - - - - - 178.9 -1.3 35.1 - 90 GLN 90 a - 182.4 - - - - - - - - 180.3 - 33.8 - 91 ALA 91 S B - - - - - - - - - - 182.4 - 33.4 - 92 MET 92 S B - - -55.0 174.2 - - - - - - -2.1 -.6 36.4 - +* +* 93 PRO 93 e cis - - - - - -91.5 - - - - - 175.4 - 39.4 - ** +* ** 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 ----------------------------------------------------------------------------------------------------------------------------------- 94 THR 94 E B - - -61.4 - - - - - - - 178.5 -2.8 34.3 - * * 95 PHE 95 E B - - -68.6 - - - - - - - 182.3 -3.2 35.3 - * * 96 MET 96 E B - 186.5 - - - - - - - - 180.8 -3.6 35.4 - ** ** 97 PHE 97 E B - - -66.5 - - - - - - - 183.7 -2.7 35.9 - 98 LEU 98 E B - - -51.0 176.7 - - - - - - 172.3 -2.8 37.6 - * * * * * 99 LYS 99 E B - 174.8 - 172.7 - - - - - - 178.9 -3.0 31.4 - * * 100 GLU 100 e l - - -60.0 164.7 - - - - - - 181.7 -.7 33.6 - +* +* 101 GLY 101 T - - - - - - - - - - - 178.3 - - - 102 LYS 102 E B - 183.0 - 180.0 - - - - - - 184.2 -2.1 34.6 - 103 ILE 103 E B - - -57.0 177.3 - - - - - - 175.2 - 33.1 - 104 LEU 104 E a - - -65.8 183.8 - - - - - - 186.0 -1.9 34.5 - * * 105 ASP 105 E B 54.8 - - - - - - - - - 184.5 -1.8 31.3 - 106 LYS 106 E B 56.8 - - 183.7 - - - - - - 176.8 - 34.5 - 107 VAL 107 E B - 180.6 - - - - - - - - 181.4 -2.9 34.5 - * * 108 VAL 108 E B 59.7 - - - - - - - - - 179.7 -.5 32.7 - ** ** 109 GLY 109 e - - - - - - - - - - - 179.7 -2.3 - - 110 ALA 110 B - - - - - - - - - - 178.7 - 34.2 - 111 LYS 111 h B - - -63.3 - - - - - - - 179.1 -.9 37.1 - * * 112 LYS 112 H A - 184.3 - 183.4 - -71.2 -51.3 - - - 184.6 - 34.4 - * * 113 ASP 113 H A - 176.8 - - - -73.0 -47.9 - - - 182.0 - 33.3 - 114 GLU 114 H A - 184.4 - 179.2 - -63.6 -29.7 - - - 177.0 - 32.8 - 115 LEU 115 H A - 184.8 - - - -63.6 -48.3 - - - 180.1 -.7 35.6 - +* +* 116 GLN 116 H A - - -50.5 - - -58.2 -39.3 - - - 179.9 -1.4 34.7 - * * 117 SER 117 H A - - -55.4 - - -68.6 -34.2 - - - 176.3 -1.9 34.0 - 118 THR 118 H A - - -61.4 - - -70.8 -34.9 - - - 176.1 -1.9 34.1 - 119 ILE 119 H A - - -58.2 176.1 - -64.0 -39.5 - - - 177.7 -2.3 34.0 - 120 ALA 120 H A - - - - - -67.2 -34.8 - - - 176.3 -2.0 33.5 - 121 LYS 121 H A - 183.8 - 178.7 - -58.2 -44.0 - - - 179.5 -1.7 35.7 - 122 HIS 122 h A - - -71.4 - - - - - - - 179.3 -1.9 33.5 - 123 LEU 123 t b - 200.7 - 174.9 - - - - - - 178.6 -.5 34.6 - * ** ** 124 ALA 124 - - - - - - - - - - - - -1.2 34.4 - * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * * * ** ** * +** *** ** ** *** **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 57.6 183.1 -61.7 179.3 -70.6 -65.9 -40.0 52.0 - 2.0 180.1 -1.9 34.1 *** *** Standard deviations: 5.0 6.0 7.7 9.6 17.1 7.0 8.7 .0 - .0 3.5 .9 2.1 Numbers of values: 13 49 40 28 4 44 44 2 0 2 122 84 119 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 - 1.237 1.527 1.538 1.465 - 116.61 120.88 110.16 110.54 110.42 122.51 2 GLY 2 1.317 1.226 1.501 - 1.434 120.34 116.81 120.39 - 111.02 - 122.80 * * 3 HIS 3 1.297 1.229 1.507 1.528 1.446 121.42 115.69 121.15 111.27 111.38 111.12 123.15 ** ** 4 HIS 4 1.301 1.231 1.525 1.548 1.450 122.36 115.32 120.59 110.93 109.76 109.39 124.05 +* +* 5 HIS 5 1.336 1.237 1.533 1.571 1.478 125.49 116.43 120.24 116.15 115.04 117.11 123.31 ** * ** *** * +*** +*** 6 HIS 6 1.341 1.226 1.508 1.554 1.480 122.99 113.98 122.06 111.10 107.34 115.19 123.95 * * * * +** +** 7 HIS 7 1.313 1.229 1.524 1.546 1.442 124.05 116.01 120.10 110.41 108.79 109.14 123.89 * * * 8 HIS 8 1.319 1.232 1.527 1.564 1.463 124.20 116.04 121.22 111.88 111.50 112.49 122.66 +* * * +* 9 LEU 9 1.309 1.236 1.488 1.553 1.441 121.25 115.17 121.38 110.13 108.25 114.75 123.30 * +* * * +** +** 10 GLU 10 1.296 1.226 1.510 1.519 1.425 121.23 114.09 121.18 111.80 106.78 109.24 124.69 ** +* * +* * ** 11 MET 11 1.339 1.234 1.513 1.539 1.460 124.95 116.55 121.12 109.63 114.21 111.37 122.33 +* * +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 12 ALA 12 1.309 1.236 1.512 1.525 1.437 120.24 114.68 121.57 111.61 106.67 112.12 123.38 * * +* * +* 13 SER 13 1.310 1.233 1.521 1.543 1.435 124.10 117.47 119.82 109.02 107.97 108.80 122.71 * * * * * 14 GLU 14 1.307 1.219 1.507 1.533 1.444 121.79 117.01 120.28 110.67 109.44 110.52 122.69 +* +* 15 GLU 15 1.300 1.240 1.514 1.557 1.431 120.91 116.28 120.94 111.37 109.81 112.56 122.73 ** * * * ** 16 GLY 16 1.306 1.232 1.499 - 1.432 119.88 117.39 120.24 - 112.42 - 122.37 +* * +* 17 GLN 17 1.319 1.230 1.478 1.503 1.437 119.04 111.61 123.26 109.16 113.63 111.02 125.13 ** * * * ** * * ** 18 VAL 18 1.262 1.238 1.534 1.550 1.403 125.06 118.32 120.07 112.13 109.49 109.58 121.55 *4.8* +** +* * * * *4.8* 19 ILE 19 1.300 1.230 1.516 1.564 1.441 119.28 116.38 120.89 110.72 109.42 114.67 122.73 ** * +* ** 20 ALA 20 1.305 1.225 1.506 1.513 1.444 121.41 116.32 120.86 110.24 111.26 110.67 122.81 +* +* 21 CYS 21 1.300 1.230 1.513 1.499 1.402 121.41 115.93 121.13 109.05 108.99 109.73 122.88 ** +* +** +** 22 HIS 22 1.295 1.223 1.497 1.545 1.450 121.89 114.98 121.49 108.79 107.66 111.57 123.52 ** * * ** 23 THR 23 1.310 1.245 1.510 1.553 1.431 122.35 116.77 120.22 107.76 109.41 109.96 123.02 * * * 24 VAL 24 1.325 1.233 1.540 1.571 1.448 120.47 114.79 121.28 111.71 108.37 112.81 123.89 * * * * 25 GLU 25 1.348 1.225 1.523 1.564 1.460 124.31 116.21 120.81 111.01 109.53 107.57 122.91 * +* * +* +* 26 THR 26 1.315 1.230 1.539 1.544 1.443 120.97 115.60 120.90 110.25 110.15 110.26 123.44 * * 27 TRP 27 1.325 1.235 1.539 1.536 1.459 123.17 116.58 120.66 110.91 112.54 109.03 122.73 28 ASN 28 1.320 1.239 1.515 1.530 1.464 121.57 115.20 120.91 109.65 110.87 110.42 123.87 29 GLU 29 1.320 1.241 1.536 1.531 1.458 123.13 116.10 120.88 109.28 110.88 109.33 123.00 30 GLN 30 1.324 1.232 1.513 1.485 1.421 122.57 116.90 120.39 111.03 112.68 109.11 122.71 ** +* ** 31 LEU 31 1.320 1.217 1.497 1.480 1.410 121.47 116.83 119.89 110.60 111.83 110.52 123.27 * ** +** +** 32 GLN 32 1.321 1.224 1.516 1.531 1.449 121.32 115.02 120.78 109.33 109.60 111.48 124.14 33 LYS 33 1.323 1.241 1.551 1.561 1.453 123.84 116.48 121.17 112.77 109.27 107.54 122.34 * +* * * +* +* 34 ALA 34 1.327 1.233 1.538 1.522 1.450 121.40 115.83 120.83 110.30 111.52 110.28 123.33 35 ASN 35 1.320 1.239 1.496 1.521 1.474 124.00 115.10 121.04 106.95 112.54 108.40 123.85 * * +* * +* 36 GLU 36 1.308 1.229 1.524 1.530 1.469 121.54 116.87 120.64 110.45 113.17 112.34 122.49 * * * 37 SER 37 1.302 1.236 1.531 1.500 1.424 121.00 116.67 120.15 111.10 112.05 108.71 123.18 +* +* +* * +* 38 LYS 38 1.341 1.241 1.512 1.511 1.461 122.31 114.28 122.29 113.58 113.52 111.39 123.41 +* +* 39 THR 39 1.291 1.239 1.514 1.517 1.416 123.06 116.72 120.72 107.76 106.76 109.98 122.54 +** ** +* +** 40 LEU 40 1.272 1.242 1.516 1.524 1.367 121.84 115.17 121.31 114.35 111.73 114.67 123.46 **** *4.8* ** ** *4.8* 41 VAL 41 1.285 1.237 1.538 1.565 1.436 122.06 115.97 120.96 111.40 111.90 109.78 123.06 *** * * * *** 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 ----------------------------------------------------------------------------------------------------------------------------------- 42 VAL 42 1.316 1.230 1.517 1.541 1.444 122.70 116.70 120.75 109.56 108.57 112.15 122.55 43 VAL 43 1.298 1.227 1.518 1.548 1.441 121.14 116.15 120.40 108.12 110.76 111.40 123.45 ** ** 44 ASP 44 1.302 1.245 1.504 1.527 1.452 122.75 115.92 120.76 109.92 110.15 111.36 123.27 +* +* 45 PHE 45 1.303 1.235 1.507 1.517 1.414 122.03 116.80 120.47 109.01 107.54 109.84 122.69 +* ** * ** 46 THR 46 1.289 1.229 1.523 1.570 1.429 120.52 116.68 120.33 110.70 109.41 110.24 122.97 +** * +* +** 47 ALA 47 1.302 1.238 1.501 1.517 1.435 122.20 115.98 120.30 110.36 108.53 111.14 123.72 +* * * +* 48 SER 48 1.307 1.235 1.545 1.527 1.449 123.20 116.85 120.60 111.30 112.36 109.04 122.54 +* +* 49 TRP 49 1.337 1.237 1.531 1.553 1.453 121.16 116.59 120.83 111.50 112.41 112.39 122.58 * * * 50 CYS 50 1.309 1.228 1.522 1.539 1.447 121.94 116.15 120.36 111.07 110.05 109.75 123.48 * * 51 GLY 51 1.332 1.228 1.527 - 1.461 122.54 118.83 119.60 - 114.06 - 121.57 * * * 52 PRO 52 1.358 1.235 1.531 1.541 1.477 123.02 115.27 121.33 110.30 112.19 103.77 123.40 * * * * 53 CYS 53 1.312 1.215 1.531 1.516 1.445 123.31 116.48 121.07 109.43 110.33 108.70 122.45 * * * 54 ARG 54 1.311 1.224 1.528 1.529 1.449 121.62 115.66 121.32 111.59 109.87 110.44 123.01 * * 55 PHE 55 1.322 1.228 1.538 1.545 1.461 123.10 116.78 120.79 110.38 111.42 109.84 122.40 56 ILE 56 1.322 1.242 1.557 1.573 1.457 121.01 115.72 121.43 110.28 109.95 110.52 122.80 +* * +* 57 ALA 57 1.334 1.243 1.553 1.524 1.467 122.97 120.10 119.05 111.33 114.21 111.44 120.85 * +* * * * +* 58 PRO 58 1.375 1.237 1.525 1.535 1.470 121.97 116.08 120.81 110.04 112.30 104.36 123.09 ** * ** 59 PHE 59 1.322 1.219 1.524 1.531 1.442 121.27 116.89 120.56 111.39 110.79 111.67 122.54 60 PHE 60 1.322 1.231 1.531 1.541 1.466 121.34 115.96 121.07 111.40 109.49 110.44 122.95 61 ALA 61 1.327 1.232 1.529 1.523 1.455 121.47 115.67 121.33 110.73 109.71 110.54 122.97 62 ASP 62 1.329 1.235 1.494 1.511 1.462 122.32 114.51 121.06 109.10 109.21 110.81 124.43 * * 63 LEU 63 1.312 1.232 1.521 1.521 1.432 124.24 115.80 120.59 110.52 110.64 108.97 123.58 * * * * 64 ALA 64 1.326 1.228 1.524 1.524 1.460 122.75 115.81 121.44 110.31 111.04 110.02 122.74 65 LYS 65 1.316 1.223 1.523 1.556 1.444 122.23 116.49 120.73 112.66 110.54 109.60 122.77 * * * 66 LYS 66 1.308 1.230 1.532 1.534 1.446 121.18 117.02 120.56 110.85 111.27 111.24 122.42 +* +* 67 LEU 67 1.318 1.220 1.536 1.546 1.435 121.53 117.83 120.66 110.60 109.93 111.99 121.51 * * 68 PRO 68 1.345 1.230 1.531 1.531 1.468 122.45 116.48 120.86 110.00 113.85 102.97 122.66 69 ASN 69 1.317 1.229 1.529 1.550 1.467 121.72 115.61 121.71 112.17 110.48 109.58 122.64 * * 70 VAL 70 1.310 1.237 1.521 1.551 1.441 122.50 116.52 120.76 109.83 109.60 111.70 122.68 * * 71 LEU 71 1.306 1.231 1.514 1.525 1.417 121.53 116.35 120.62 110.02 109.21 109.31 122.99 +* ** ** 72 PHE 72 1.308 1.238 1.500 1.520 1.439 121.44 115.33 121.34 109.40 109.64 112.29 123.33 +* * * * +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 73 LEU 73 1.279 1.228 1.502 1.546 1.438 122.76 114.77 121.39 109.94 111.74 112.81 123.83 +*** * * * +*** 74 LYS 74 1.294 1.232 1.504 1.538 1.431 123.68 116.89 120.46 109.26 108.30 109.74 122.63 +** * * * +** 75 VAL 75 1.286 1.234 1.499 1.552 1.426 120.69 115.90 121.14 109.81 109.11 112.68 122.95 *** * +* *** 76 ASP 76 1.297 1.237 1.517 1.521 1.426 120.49 115.96 120.72 111.49 107.05 110.97 123.30 ** +* * ** 77 THR 77 1.304 1.233 1.538 1.566 1.452 122.99 117.05 120.53 111.20 112.39 110.80 122.43 +* +* 78 ASP 78 1.313 1.226 1.508 1.522 1.459 121.49 113.60 122.31 109.83 108.00 109.35 124.08 * * * * 79 GLU 79 1.295 1.235 1.526 1.513 1.422 124.76 116.29 120.89 109.16 110.92 108.05 122.81 ** +* +* * ** 80 LEU 80 1.321 1.242 1.533 1.530 1.425 122.04 113.65 122.66 112.77 108.94 109.24 123.68 +* * * * +* 81 LYS 81 1.307 1.235 1.538 1.559 1.443 124.18 116.87 120.58 113.04 111.61 107.89 122.54 +* * * +* +* +* 82 SER 82 1.319 1.242 1.540 1.512 1.461 121.59 116.88 120.41 111.17 112.44 109.87 122.67 83 VAL 83 1.328 1.230 1.526 1.555 1.460 121.06 115.90 121.09 111.05 109.89 111.92 122.95 84 ALA 84 1.325 1.223 1.527 1.519 1.462 122.17 116.37 121.07 110.76 110.69 110.09 122.55 85 SER 85 1.315 1.227 1.539 1.536 1.435 121.27 116.83 120.50 110.80 110.41 110.05 122.64 * * 86 ASP 86 1.329 1.229 1.524 1.536 1.471 121.49 115.89 121.35 110.19 110.56 110.66 122.76 87 TRP 87 1.318 1.237 1.527 1.531 1.453 122.40 115.51 120.38 111.65 112.28 110.93 124.09 88 ALA 88 1.340 1.232 1.520 1.529 1.467 124.53 115.91 121.42 111.63 111.82 112.23 122.59 +* * +* 89 ILE 89 1.306 1.237 1.515 1.554 1.441 122.08 116.14 120.81 109.23 109.72 110.88 123.00 +* +* 90 GLN 90 1.304 1.235 1.530 1.542 1.447 121.70 116.43 120.91 111.15 110.32 110.36 122.64 +* +* 91 ALA 91 1.321 1.230 1.509 1.511 1.446 121.18 115.69 121.33 110.77 110.04 111.17 122.98 92 MET 92 1.291 1.243 1.516 1.518 1.436 121.96 118.69 119.89 108.84 109.03 109.04 121.42 +** * * +** 93 PRO 93 1.330 1.229 1.544 1.527 1.458 124.17 116.68 120.98 110.14 112.14 102.42 122.26 94 THR 94 1.298 1.229 1.520 1.538 1.430 121.38 116.58 120.49 109.35 109.25 111.91 122.93 ** * ** 95 PHE 95 1.304 1.235 1.489 1.516 1.415 122.18 115.68 120.94 109.23 108.44 110.72 123.37 +* +* ** ** 96 MET 96 1.284 1.234 1.501 1.505 1.419 121.62 115.66 120.85 109.61 109.56 109.75 123.49 *** * * ** *** 97 PHE 97 1.281 1.249 1.506 1.510 1.401 122.98 116.13 121.32 110.41 108.80 108.63 122.55 *** * +** * *** 98 LEU 98 1.291 1.229 1.522 1.544 1.421 120.47 116.13 120.94 106.59 109.04 109.88 122.91 +** +* +* +** 99 LYS 99 1.296 1.238 1.481 1.523 1.431 121.66 114.71 120.77 111.66 109.54 113.65 124.41 ** ** * +* ** 100 GLU 100 1.332 1.224 1.538 1.523 1.451 123.92 115.57 121.59 111.67 110.29 109.82 122.81 * * 101 GLY 101 1.322 1.228 1.523 - 1.445 121.51 116.96 120.32 - 112.81 - 122.72 102 LYS 102 1.322 1.237 1.519 1.533 1.458 121.93 116.87 119.94 110.21 108.78 110.47 123.20 103 ILE 103 1.316 1.237 1.516 1.556 1.448 121.76 115.45 121.27 110.23 111.97 111.94 123.26 104 LEU 104 1.312 1.237 1.493 1.528 1.423 121.46 115.35 121.16 109.08 109.42 111.93 123.42 * * +* +* 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 ----------------------------------------------------------------------------------------------------------------------------------- 105 ASP 105 1.304 1.226 1.496 1.530 1.438 121.68 115.88 121.00 112.02 112.27 112.31 123.07 +* * * * * +* 106 LYS 106 1.302 1.235 1.527 1.542 1.442 121.55 115.78 121.19 110.85 111.75 109.34 123.02 +* +* 107 VAL 107 1.311 1.233 1.515 1.559 1.448 122.36 116.61 120.40 109.40 108.09 112.02 122.98 * * * 108 VAL 108 1.300 1.239 1.543 1.564 1.434 121.68 115.90 121.46 112.09 111.07 110.98 122.58 ** * * ** 109 GLY 109 1.310 1.237 1.504 - 1.436 120.99 117.23 120.37 - 110.67 - 122.40 * * 110 ALA 110 1.314 1.236 1.506 1.523 1.437 119.77 115.48 121.21 110.62 108.94 110.71 123.29 * * * * 111 LYS 111 1.296 1.217 1.499 1.517 1.419 123.08 118.20 119.32 108.53 108.20 108.69 122.46 ** * ** * * ** 112 LYS 112 1.310 1.226 1.524 1.525 1.431 120.12 115.16 121.25 109.86 110.30 110.78 123.56 * * * 113 ASP 113 1.319 1.236 1.524 1.529 1.464 123.22 116.53 120.56 110.80 113.14 110.30 122.90 114 GLU 114 1.327 1.242 1.525 1.535 1.469 121.87 116.03 120.98 111.65 110.79 110.93 122.98 115 LEU 115 1.321 1.219 1.503 1.510 1.444 121.64 115.14 121.01 108.70 108.90 110.36 123.84 * * * 116 GLN 116 1.319 1.234 1.524 1.536 1.473 122.64 116.00 121.14 108.44 110.28 111.56 122.86 117 SER 117 1.314 1.234 1.539 1.519 1.447 121.81 115.64 121.52 111.86 110.17 109.10 122.80 * * 118 THR 118 1.311 1.242 1.543 1.532 1.438 122.51 116.33 121.11 111.29 110.20 109.79 122.53 * * * * 119 ILE 119 1.326 1.235 1.529 1.549 1.451 121.40 115.60 120.94 109.88 108.96 111.82 123.42 120 ALA 120 1.326 1.224 1.520 1.518 1.456 122.52 116.31 120.57 110.84 110.68 110.75 123.13 121 LYS 121 1.327 1.227 1.514 1.509 1.460 122.59 114.80 121.83 108.84 109.75 109.73 123.37 * * 122 HIS 122 1.307 1.227 1.529 1.525 1.439 122.50 117.86 119.96 110.19 113.20 110.67 122.18 +* * +* 123 LEU 123 1.324 1.244 1.526 1.525 1.429 121.17 115.47 121.16 111.33 108.99 109.33 123.31 +* +* 124 ALA 124 1.297 - 1.508 1.530 1.432 122.93 - - 110.87 108.00 110.62 - ** * * ** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *4.8* ** ** *4.8* ** ** * *** +* +*** * *4.8* ----------------------------------------------------------------------------------------------------------------------------------- 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 1.262 1.348 1.312 .015 *4.8* * * C-N (Pro) 1.341 .016 4 1.330 1.375 1.352 .017 ** C-O C-O 1.231 .020 123 1.215 1.249 1.232 .006 CA-C CH1E-C (except Gly) 1.525 .021 119 1.478 1.557 1.520 .015 ** +* CH2G*-C (Gly) 1.516 .018 5 1.499 1.527 1.511 .012 CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.511 1.530 1.521 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.517 1.573 1.553 .013 * CH1E-CH2E (the rest) 1.530 .020 84 1.480 1.571 1.530 .017 ** ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.367 1.480 1.443 .018 *4.8* * NH1-CH2G* (Gly) 1.451 .016 5 1.432 1.461 1.442 .011 * N-CH1E (Pro) 1.466 .015 4 1.458 1.477 1.468 .007 ------------------------------------------------------------------------------------------------------------- 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 2.0 114 111.61 120.10 116.04 1.04 ** +* CH2G*-C-NH1 (Gly) 116.4 2.1 5 116.81 118.83 117.44 .72 * CH1E-C-N (Pro) 116.9 1.5 4 115.27 116.68 116.13 .54 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.85 125.13 123.01 .64 * * O-C-N (Pro) 122.0 1.4 4 122.26 123.40 122.85 .43 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 119.04 125.49 122.12 1.19 * ** C-NH1-CH2G* (Gly) 120.6 1.7 5 119.88 122.54 121.05 .93 * C-N-CH1E (Pro) 122.6 5.0 4 121.97 124.17 122.90 .82 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 119.05 123.26 120.90 .58 * * CH2G*-C-O (Gly) 120.8 2.1 5 119.60 120.39 120.18 .30 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 110.24 111.63 110.80 .45 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 107.76 112.13 110.17 1.24 * CH2E-CH1E-C (the rest) 110.1 1.9 84 106.59 116.15 110.55 1.46 +* *** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 106.67 115.04 110.24 1.69 +* * NH1-CH2G*-C (Gly) 112.5 2.9 5 110.67 114.06 112.20 1.23 N-CH1E-C (Pro) 111.8 2.5 4 112.14 113.85 112.62 .71 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.02 112.23 110.91 .67 * NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 109.58 114.67 111.26 1.22 * +* N-CH1E-CH2E (Pro) 103.0 1.1 4 102.42 104.36 103.38 .74 * NH1-CH1E-CH2E (the rest) 110.5 1.7 80 107.54 117.11 110.49 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_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] 98 86.7% Residues in additional allowed regions [a,b,l,p] 12 10.6% Residues in generously allowed regions [~a,~b,~l,~p] 2 1.8% 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 86.7 83.8 10.0 .3 Inside b. Omega angle st dev 122 3.5 6.0 3.0 -.8 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 119 2.1 3.1 1.6 -.7 Inside e. H-bond energy st dev 84 .9 .8 .2 .3 Inside f. Overall G-factor 124 .0 -.4 .3 1.4 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 5.0 18.1 6.5 -2.0 BETTER b. Chi-1 trans st dev 49 6.0 19.0 5.3 -2.4 BETTER c. Chi-1 gauche plus st dev 40 7.7 17.5 4.9 -2.0 BETTER d. Chi-1 pooled st dev 102 7.6 18.2 4.8 -2.2 BETTER e. Chi-2 trans st dev 28 9.6 20.4 5.0 -2.2 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% 86.7 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.2 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .88 3 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 -.26 Chi1 only -.11 Chi3 & chi4 .46 Omega -.05 ------ -.08 ===== Main-chain covalent forces:- Main-chain bond lengths -.05 Main-chain bond angles .41 ------ .22 ===== OVERALL AVERAGE .02 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.