Residue-by-residue listing for refined_4 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 - - - -56.8 - - - - - - - 177.4 - 35.0 - 2 GLY 2 - - - - - - - - - - - 183.6 - - - 3 HIS 3 B - 185.6 - - - - - - - - 183.0 - 35.2 - 4 HIS 4 B - - -60.9 - - - - - - - 175.5 -.7 35.2 - +* +* 5 HIS 5 b - - -68.1 - - - - - - - 180.1 - 33.1 - 6 HIS 6 B 55.8 - - - - - - - - - 178.8 -.9 31.9 - +* +* 7 HIS 7 A - 178.6 - - - - - - - - 181.3 - 33.9 - 8 HIS 8 XX - 186.1 - - - - - - - - 181.3 - 32.1 - **** **** 9 LEU 9 B - 183.3 - - - - - - - - 180.9 - 33.7 - 10 GLU 10 B - - -57.1 180.0 - - - - - - 173.0 -.9 36.2 - * * * 11 MET 11 B - - -66.2 - - - - - - - 184.3 -.5 33.3 - +* +* 12 ALA 12 B - - - - - - - - - - 175.5 -.6 34.3 - +* +* 13 SER 13 B 54.0 - - - - - - - - - 183.0 - 33.3 - 14 GLU 14 B - - -72.3 - - - - - - - 181.2 - 32.4 - 15 GLU 15 S B 56.0 - - 180.8 - - - - - - 178.5 - 34.1 - 16 GLY 16 S - - - - - - - - - - - 181.0 -2.3 - - 17 GLN 17 e B 53.2 - - 175.5 - - - - - - 175.4 -.5 31.8 - +* +* 18 VAL 18 E B - 180.5 - - - - - - - - 182.5 - 35.1 - 19 ILE 19 E B - - -59.8 - - - - - - - 181.5 -3.0 32.9 - * * Residue-by-residue listing for refined_4 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 ----------------------------------------------------------------------------------------------------------------------------------- 20 ALA 20 E B - - - - - - - - - - 180.8 -.8 33.5 - +* +* 21 CYS 21 E B - - -50.1 - - - - - - - 177.2 -2.3 36.2 - * * 22 HIS 22 A - - -59.3 - - - - - - - 182.4 -.7 34.9 - +* +* 23 THR 23 h B 57.2 - - - - - - - - - 178.8 - 34.9 - 24 VAL 24 H A 64.4 - - - - -69.0 -22.7 - - - 178.5 - 32.7 - * * 25 GLU 25 H A - 183.4 - 186.5 - -60.8 -51.5 - - - 179.9 - 36.2 - * * 26 THR 26 H A - - -53.8 - - -66.3 -42.9 - - - 178.4 - 34.7 - 27 TRP 27 H A - 173.4 - - - -57.0 -47.0 - - - 179.9 -1.9 34.8 - 28 ASN 28 H A - 185.6 - - - -59.8 -42.4 - - - 179.9 -3.1 35.2 - * * 29 GLU 29 H A - 183.1 - 181.4 - -64.4 -47.2 - - - 182.2 -1.9 34.0 - 30 GLN 30 H A - - -69.8 - - -59.1 -38.4 - - - 179.0 -2.6 33.6 - 31 LEU 31 H A - - -65.8 179.4 - -68.6 -47.4 - - - 176.4 -2.0 33.9 - 32 GLN 32 H A - 176.7 - - - -61.2 -42.4 - - - 178.1 -1.9 32.9 - 33 LYS 33 H A - 179.9 - 180.7 - -57.0 -43.5 - - - 180.0 -3.3 34.2 - +* +* 34 ALA 34 H A - - - - - -69.2 -48.5 - - - 182.6 -2.3 33.9 - 35 ASN 35 H A - 189.8 - - - -60.0 -54.3 - - - 183.5 -3.0 37.6 - * * * * 36 GLU 36 H A - 183.3 - 180.0 - -60.8 -43.3 - - - 183.0 -3.3 35.0 - +* +* 37 SER 37 H A - - -52.8 - - -86.1 -3.0 - - - 180.6 -1.8 35.0 - +* *** *** 38 LYS 38 h l - 187.9 - 187.2 - - - - - - 183.0 -1.0 33.2 - * * 39 THR 39 e B - - -45.3 - - - - - - - 179.1 -1.8 35.4 - * * 40 LEU 40 E B - 184.0 - 171.2 - - - - - - 183.8 -.8 35.0 - +* +* 41 VAL 41 E B 58.8 - - - - - - - - - 177.7 -1.5 33.1 - 42 VAL 42 E B - 178.8 - - - - - - - - 184.6 -3.2 33.8 - +* +* 43 VAL 43 E B - 183.8 - - - - - - - - 173.8 -2.5 35.6 - * * 44 ASP 44 E B - 175.2 - - - - - - - - 180.4 -2.2 33.0 - 45 PHE 45 E B - - -60.6 - - - - - - - 177.4 -2.8 36.8 - * * 46 THR 46 E B - 189.5 - - - - - - - - 177.9 -2.5 32.6 - 47 ALA 47 t B - - - - - - - - - - 182.7 - 34.0 - 48 SER 48 T A 56.2 - - - - - - - - - 181.9 - 33.0 - 49 TRP 49 T A 52.8 - - - - - - - - - 178.7 - 31.5 - 50 CYS 50 h B - 176.9 - 218.6 - - - 55.2 - 2.0 182.1 -2.0 34.1 - ** +** +** 51 GLY 51 H - - - - - - -64.1 -64.9 - - - 179.4 -.6 - - ** +* ** 52 PRO 52 H - - - - - -56.7 -56.7 -30.3 - - - 179.0 - 38.3 - * * 53 CYS 53 H A - - -53.7 - - -69.0 -38.0 55.2 - 2.0 177.5 - 35.3 - +** +** 54 ARG 54 H A - 181.3 - 180.3 - -72.0 -29.9 - - - 179.0 -1.6 35.2 - 55 PHE 55 H A - 184.0 - - - -70.4 -35.6 - - - 181.8 -1.9 35.4 - 56 ILE 56 h A - 192.5 - - - - - - - - 182.1 -1.7 34.2 - Residue-by-residue listing for refined_4 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 - - - - - -60.3 -52.2 - - - 180.6 - 30.9 - * * 58 PRO 58 H - - - - - -65.9 -65.9 -25.2 - - - 179.2 - 38.2 - * * * 59 PHE 59 H A - 192.1 - - - -71.5 -43.2 - - - 177.6 - 35.5 - 60 PHE 60 H A - 184.0 - - - -69.7 -33.7 - - - 175.6 -2.2 34.1 - 61 ALA 61 H A - - - - - -68.7 -28.5 - - - 177.8 -2.3 33.7 - 62 ASP 62 H A - 188.0 - - - -71.7 -39.1 - - - 174.1 -1.2 35.4 - * * * 63 LEU 63 H A - - -65.1 182.1 - -59.6 -45.3 - - - 176.7 -1.8 34.9 - 64 ALA 64 H A - - - - - -64.4 -31.5 - - - 178.1 -2.1 33.8 - 65 LYS 65 H A - 178.0 - 194.6 - -67.4 -40.4 - - - 186.1 -1.4 37.3 - * * 66 LYS 66 H A - 188.5 - 181.3 - -89.1 -3.3 - - - 185.3 -2.1 33.6 - +* *** *** 67 LEU 67 h B 79.5 - - 180.3 - - - - - - 170.2 -.6 34.7 - +* +* +* 68 PRO 68 S - - - - - -70.1 - - - - - 173.3 - 38.9 - * * * 69 ASN 69 e b - 184.9 - - - - - - - - 183.5 - 33.3 - 70 VAL 70 E B - 177.6 - - - - - - - - 177.6 - 34.5 - 71 LEU 71 E B - - -63.3 177.8 - - - - - - 177.2 -2.4 35.8 - 72 PHE 72 E B - - -62.0 - - - - - - - 182.7 -.7 33.6 - +* +* 73 LEU 73 E B - - -74.9 - - - - - - - 177.0 -2.6 33.0 - 74 LYS 74 E B - 181.3 - - - - - - - - 181.1 -2.8 36.5 - * * 75 VAL 75 E B - 178.7 - - - - - - - - 179.4 -2.4 34.1 - 76 ASP 76 E B - 187.5 - - - - - - - - 182.7 -1.2 33.2 - * * 77 THR 77 e A - 181.7 - - - - - - - - 181.6 -1.8 33.7 - 78 ASP 78 T A - 187.0 - - - - - - - - 174.2 - 34.7 - 79 GLU 79 T a - - -70.6 179.6 - - - - - - 184.8 - 34.7 - 80 LEU 80 h b - - -65.4 177.5 - - - - - - 180.5 -2.9 33.1 - * * 81 LYS 81 H A - - -60.8 178.5 - -68.4 -37.1 - - - 179.5 -2.0 34.3 - 82 SER 82 H A - - -55.2 - - -65.7 -36.7 - - - 177.8 - 33.9 - 83 VAL 83 H A - 178.6 - - - -70.1 -44.4 - - - 177.4 - 33.6 - 84 ALA 84 H A - - - - - -56.8 -48.2 - - - 180.4 -2.3 34.3 - 85 SER 85 H A - - -57.2 - - -60.2 -40.7 - - - 182.3 -3.0 34.4 - * * 86 ASP 86 H A - 184.1 - - - -64.6 -36.3 - - - 180.4 -2.0 34.4 - 87 TRP 87 h A - - -63.0 - - - - - - - 177.5 -1.9 33.2 - 88 ALA 88 T l - - - - - - - - - - 181.5 -1.4 33.2 - 89 ILE 89 t B - - -57.1 - - - - - - - 179.9 -3.0 34.3 - * * 90 GLN 90 a - 176.9 - 179.1 - - - - - - 182.1 - 34.6 - 91 ALA 91 S B - - - - - - - - - - 184.9 - 33.5 - 92 MET 92 S B - - -60.3 167.0 - - - - - - -4.0 - 36.3 - 93 PRO 93 e cis - - - - - -93.7 - - - - - 175.6 - 39.9 - +** +* +** 94 THR 94 E B - - -57.0 - - - - - - - 180.1 -2.1 33.8 - 95 PHE 95 E B - - -61.7 - - - - - - - 179.5 -3.2 37.7 - +* * +* 96 MET 96 E B - 183.0 - 179.0 - - - - - - 179.1 -3.5 33.2 - +* +* Residue-by-residue listing for refined_4 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 ----------------------------------------------------------------------------------------------------------------------------------- 97 PHE 97 E B - - -65.4 - - - - - - - 179.2 -3.1 36.5 - * * 98 LEU 98 E B 59.1 - - 169.7 - - - - - - 184.8 -2.2 31.6 - 99 LYS 99 E B - 181.9 - 176.9 - - - - - - 182.1 -3.3 34.0 - +* +* 100 GLU 100 e l - - -61.2 175.0 - - - - - - 183.6 -.6 33.7 - +* +* 101 GLY 101 T - - - - - - - - - - - 177.9 - - - 102 LYS 102 E B - - -62.8 170.9 - - - - - - 185.2 -2.1 35.9 - 103 ILE 103 E B - - -58.2 178.9 - - - - - - 176.9 - 33.4 - 104 LEU 104 E a - - -67.6 177.9 - - - - - - 184.8 -2.0 34.6 - 105 ASP 105 E B 49.7 - - - - - - - - - 181.0 -2.2 32.8 - 106 LYS 106 E B 56.1 - - 179.6 - - - - - - 178.5 - 33.8 - 107 VAL 107 E B - 180.3 - - - - - - - - 180.6 -2.8 34.8 - * * 108 VAL 108 E B 62.5 - - - - - - - - - 182.0 -.5 32.1 - ** ** 109 GLY 109 e - - - - - - - - - - - 180.4 -3.6 - - ** ** 110 ALA 110 B - - - - - - - - - - 179.3 - 34.3 - 111 LYS 111 h B - - -57.7 181.4 - - - - - - 180.9 -.9 36.7 - * * 112 LYS 112 H A - - -76.4 186.6 - -68.8 -50.5 - - - 186.1 - 34.2 - * * 113 ASP 113 H A - 177.2 - - - -68.1 -48.8 - - - 179.6 - 32.6 - 114 GLU 114 H A - 179.3 - 174.7 - -66.6 -29.9 - - - 178.8 - 31.7 - 115 LEU 115 H A - 188.8 - - - -61.7 -50.3 - - - 176.7 -1.1 35.1 - * * 116 GLN 116 H A - - -68.5 - - -58.0 -38.9 - - - 180.3 -2.1 33.6 - 117 SER 117 H A - - -56.4 - - -69.5 -33.8 - - - 176.8 -2.0 33.6 - 118 THR 118 H A - - -56.8 - - -71.0 -39.4 - - - 176.6 -2.4 34.2 - 119 ILE 119 H A - - -59.8 - - -59.9 -49.5 - - - 179.4 -2.6 34.1 - 120 ALA 120 H A - - - - - -66.1 -30.5 - - - 177.9 -2.7 32.9 - 121 LYS 121 H A - 192.1 - 177.1 - -64.4 -39.0 - - - 175.2 -1.6 35.6 - 122 HIS 122 H A - - -77.1 - - -73.8 -47.8 - - - 182.1 -2.0 33.8 - 123 LEU 123 h b - - -80.1 - - - - - - - 178.1 -3.2 34.3 - +* +* 124 ALA 124 - - - - - - - - - - - - -1.3 33.6 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * ** +** +* *** +** +* ** +* **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 58.2 183.0 -62.2 180.2 -71.6 -66.0 -39.5 55.2 - 2.0 179.8 -2.0 34.3 +** +** Standard deviations: 7.2 4.8 7.4 8.5 15.8 6.7 11.5 .0 - .0 3.0 .8 1.5 Numbers of values: 14 45 43 34 4 46 46 2 0 2 122 83 119 0 Number of cis-peptides (labelled cis): 1 Residue-by-residue listing for refined_4 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_4 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 - 1.232 1.513 1.558 1.460 - 117.39 119.91 109.27 107.48 111.57 122.69 * * * 2 GLY 2 1.313 1.235 1.506 - 1.443 120.86 115.64 121.19 - 110.76 - 123.17 * * 3 HIS 3 1.311 1.234 1.533 1.542 1.444 122.56 116.43 120.60 111.28 109.27 108.62 122.95 * * * 4 HIS 4 1.319 1.230 1.510 1.544 1.463 121.99 116.64 120.51 107.77 110.35 111.67 122.85 * * 5 HIS 5 1.307 1.239 1.505 1.537 1.448 121.50 116.17 120.90 109.71 109.62 113.06 122.91 +* +* +* 6 HIS 6 1.305 1.227 1.510 1.559 1.445 121.17 116.42 120.50 111.85 110.80 112.45 123.06 +* * * +* 7 HIS 7 1.309 1.238 1.524 1.545 1.459 121.28 115.07 120.67 110.82 109.94 110.68 124.26 * * 8 HIS 8 1.339 1.231 1.528 1.561 1.467 124.37 116.17 121.04 112.32 109.81 111.86 122.78 +* * * +* 9 LEU 9 1.311 1.234 1.516 1.534 1.441 121.58 115.31 121.23 111.12 109.70 110.79 123.39 * * 10 GLU 10 1.301 1.235 1.509 1.530 1.435 122.40 116.96 120.25 108.26 109.61 110.11 122.76 +* * +* 11 MET 11 1.300 1.233 1.506 1.543 1.442 120.77 117.02 120.21 110.76 107.33 112.59 122.73 ** * * ** Residue-by-residue listing for refined_4 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 1.302 1.241 1.512 1.520 1.437 120.57 115.36 121.13 110.21 111.89 110.03 123.50 +* * +* 13 SER 13 1.298 1.247 1.523 1.551 1.431 123.25 116.97 120.05 112.36 107.98 110.92 122.93 ** * * * * ** 14 GLU 14 1.313 1.237 1.525 1.533 1.427 121.79 115.40 121.31 112.08 112.00 110.83 123.29 * +* * +* 15 GLU 15 1.306 1.232 1.525 1.546 1.443 122.77 116.63 120.50 111.10 110.37 110.14 122.85 +* +* 16 GLY 16 1.321 1.236 1.504 - 1.449 120.42 116.62 120.63 - 112.81 - 122.75 17 GLN 17 1.311 1.232 1.482 1.509 1.438 120.77 113.30 122.23 109.86 113.42 113.13 124.46 * ** * * * +* ** 18 VAL 18 1.272 1.231 1.515 1.552 1.431 123.75 118.28 119.70 109.55 106.64 111.41 122.01 **** * * * +* **** 19 ILE 19 1.304 1.237 1.511 1.545 1.440 119.21 115.75 121.16 111.02 110.38 111.88 123.09 +* * +* 20 ALA 20 1.306 1.238 1.507 1.515 1.431 121.59 115.51 121.26 111.16 110.30 110.74 123.23 +* * +* 21 CYS 21 1.299 1.229 1.503 1.505 1.404 122.11 116.00 121.05 109.04 108.49 109.51 122.92 ** * * +** +** 22 HIS 22 1.288 1.224 1.499 1.531 1.442 121.49 114.86 121.71 109.81 107.61 111.04 123.42 +** * * +** 23 THR 23 1.317 1.252 1.505 1.556 1.429 122.28 116.62 120.15 109.12 108.68 111.66 123.23 * +* +* 24 VAL 24 1.314 1.215 1.541 1.564 1.442 120.97 115.76 121.03 111.47 109.78 111.99 123.18 * * * 25 GLU 25 1.331 1.239 1.533 1.516 1.460 123.44 116.11 120.75 108.91 110.78 108.66 123.13 * * 26 THR 26 1.327 1.230 1.525 1.545 1.451 121.75 115.14 121.00 110.12 109.49 110.35 123.83 27 TRP 27 1.323 1.237 1.540 1.533 1.451 123.27 115.64 121.00 111.59 111.18 108.13 123.34 * * 28 ASN 28 1.321 1.240 1.526 1.535 1.459 123.32 116.09 120.65 109.56 110.50 109.80 123.24 29 GLU 29 1.334 1.222 1.515 1.539 1.459 121.76 116.08 120.51 109.28 110.36 111.86 123.39 30 GLN 30 1.324 1.229 1.513 1.488 1.423 123.14 117.22 120.14 110.88 113.69 109.41 122.63 ** +* ** 31 LEU 31 1.315 1.237 1.507 1.488 1.411 121.38 116.59 120.18 111.24 111.48 109.49 123.23 ** ** ** 32 GLN 32 1.321 1.213 1.512 1.535 1.443 120.84 115.90 120.50 111.15 109.57 111.95 123.57 33 LYS 33 1.321 1.234 1.528 1.533 1.449 123.11 117.13 119.96 110.39 110.95 110.20 122.90 34 ALA 34 1.334 1.221 1.522 1.520 1.449 120.85 115.59 120.88 110.62 110.51 110.47 123.49 35 ASN 35 1.315 1.236 1.524 1.531 1.470 123.65 114.43 121.63 108.15 110.34 107.57 123.91 * * +* +* 36 GLU 36 1.308 1.236 1.525 1.523 1.460 124.16 116.55 120.56 110.16 112.05 108.84 122.87 +* * +* 37 SER 37 1.313 1.240 1.533 1.510 1.440 121.64 116.11 120.31 110.42 111.60 108.75 123.59 * * * 38 LYS 38 1.350 1.233 1.554 1.518 1.439 124.79 114.95 122.62 112.34 110.09 109.82 122.26 +* * +* * * +* 39 THR 39 1.300 1.245 1.527 1.529 1.424 122.38 115.17 121.63 109.00 109.33 110.52 123.18 ** +* ** 40 LEU 40 1.277 1.243 1.551 1.568 1.436 123.02 117.22 120.36 112.71 107.02 108.38 122.41 +*** * +* * * * * +*** 41 VAL 41 1.312 1.226 1.551 1.567 1.445 121.27 116.55 120.96 111.98 111.83 110.13 122.47 * * * * 42 VAL 42 1.317 1.238 1.511 1.541 1.451 122.59 116.56 120.76 109.49 108.87 112.49 122.68 Residue-by-residue listing for refined_4 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 ----------------------------------------------------------------------------------------------------------------------------------- 43 VAL 43 1.301 1.227 1.519 1.548 1.439 121.03 116.57 120.17 108.12 110.95 110.81 123.25 ** ** 44 ASP 44 1.316 1.253 1.511 1.526 1.456 121.53 115.91 120.88 110.13 109.67 112.59 123.19 * * * 45 PHE 45 1.305 1.243 1.520 1.523 1.418 122.22 116.44 120.57 108.23 109.43 109.22 122.99 +* ** ** 46 THR 46 1.306 1.217 1.526 1.546 1.428 121.71 117.21 120.36 111.27 109.37 112.47 122.41 +* +* +* 47 ALA 47 1.292 1.237 1.508 1.515 1.435 121.93 116.52 120.01 111.01 108.19 110.84 123.47 +** * * +** 48 SER 48 1.312 1.225 1.544 1.528 1.471 122.78 117.33 120.24 110.74 114.07 110.18 122.42 * * * 49 TRP 49 1.322 1.237 1.541 1.544 1.459 121.99 116.57 121.05 112.43 113.22 111.07 122.36 * * 50 CYS 50 1.310 1.237 1.532 1.522 1.446 121.48 115.95 120.59 110.64 110.72 110.05 123.46 * * 51 GLY 51 1.334 1.228 1.532 - 1.461 122.71 119.13 119.71 - 114.08 - 121.16 * * * * 52 PRO 52 1.362 1.226 1.529 1.541 1.479 122.91 115.43 121.59 110.42 111.87 103.98 122.97 * * 53 CYS 53 1.307 1.227 1.531 1.505 1.442 122.80 116.30 121.09 110.18 110.24 108.74 122.60 +* * * +* 54 ARG 54 1.316 1.233 1.530 1.526 1.456 122.32 114.90 121.47 110.55 109.13 109.04 123.61 55 PHE 55 1.313 1.224 1.536 1.541 1.451 123.57 116.54 121.00 110.54 110.53 108.60 122.46 * * * * 56 ILE 56 1.322 1.236 1.556 1.579 1.461 121.66 115.97 121.42 110.64 110.17 110.51 122.60 * * * 57 ALA 57 1.328 1.233 1.551 1.529 1.464 122.36 120.21 119.06 111.89 113.71 111.94 120.71 * ** * * * ** 58 PRO 58 1.380 1.233 1.525 1.537 1.469 121.41 115.27 121.02 110.37 111.44 104.38 123.69 ** * * * ** 59 PHE 59 1.320 1.226 1.535 1.538 1.453 123.40 115.84 121.39 110.51 108.86 108.78 122.76 * * 60 PHE 60 1.322 1.228 1.529 1.541 1.465 122.54 115.89 121.23 111.72 109.25 109.60 122.88 61 ALA 61 1.318 1.223 1.531 1.519 1.452 121.68 116.11 121.03 110.74 110.04 110.71 122.85 62 ASP 62 1.330 1.225 1.498 1.509 1.473 122.53 114.31 122.08 108.85 108.46 110.40 123.61 * * * 63 LEU 63 1.297 1.236 1.524 1.517 1.423 123.05 115.65 120.70 111.06 110.00 108.92 123.63 ** +* ** 64 ALA 64 1.320 1.205 1.529 1.518 1.453 123.06 115.79 121.12 110.66 110.68 110.48 123.04 * * 65 LYS 65 1.308 1.238 1.535 1.526 1.467 124.38 115.30 121.67 108.90 110.99 107.06 123.03 +* * ** ** 66 LYS 66 1.306 1.227 1.548 1.536 1.453 122.64 116.02 120.70 111.66 112.05 109.42 123.28 +* * +* 67 LEU 67 1.334 1.236 1.549 1.562 1.477 124.30 117.84 120.78 108.25 113.34 111.03 121.29 * +* * * * +* 68 PRO 68 1.335 1.230 1.525 1.538 1.457 121.43 114.03 121.78 110.17 107.76 104.15 124.18 +* +* * +* +* 69 ASN 69 1.320 1.230 1.514 1.527 1.446 125.25 114.98 121.73 110.32 106.86 112.95 122.89 +* +* * +* 70 VAL 70 1.304 1.224 1.511 1.566 1.444 122.41 116.72 120.22 109.67 109.56 111.54 123.05 +* +* 71 LEU 71 1.303 1.226 1.522 1.526 1.421 121.83 117.00 120.36 109.64 109.23 109.37 122.60 +* +* +* Residue-by-residue listing for refined_4 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 ----------------------------------------------------------------------------------------------------------------------------------- 72 PHE 72 1.310 1.241 1.499 1.515 1.449 121.06 115.61 121.18 109.49 109.51 112.35 123.21 * * * * 73 LEU 73 1.283 1.235 1.502 1.536 1.435 122.25 113.91 121.94 108.95 112.97 112.80 124.15 *** * * * * *** 74 LYS 74 1.296 1.226 1.520 1.544 1.426 124.35 117.46 120.15 109.94 106.14 108.97 122.33 ** +* * +* ** 75 VAL 75 1.298 1.235 1.505 1.556 1.448 120.84 116.40 120.19 109.97 109.81 111.58 123.39 ** ** 76 ASP 76 1.322 1.232 1.508 1.516 1.447 120.99 115.44 121.04 110.45 109.65 112.04 123.50 77 THR 77 1.306 1.231 1.535 1.575 1.458 122.89 116.54 121.00 110.68 111.32 110.94 122.44 +* * +* 78 ASP 78 1.314 1.233 1.514 1.522 1.448 121.08 115.13 121.43 111.02 108.23 109.59 123.44 * * * 79 GLU 79 1.314 1.237 1.522 1.520 1.421 123.18 116.55 120.73 110.20 111.29 109.78 122.69 * +* +* 80 LEU 80 1.318 1.237 1.519 1.513 1.413 121.99 115.06 121.55 111.96 112.44 109.72 123.39 ** ** 81 LYS 81 1.316 1.232 1.523 1.528 1.451 122.72 116.20 121.04 110.34 110.82 110.15 122.75 82 SER 82 1.316 1.240 1.526 1.515 1.448 122.14 116.09 120.76 111.32 110.90 109.60 123.13 83 VAL 83 1.325 1.226 1.518 1.554 1.449 121.56 115.95 120.72 110.61 108.96 111.82 123.29 84 ALA 84 1.327 1.217 1.523 1.513 1.449 121.98 116.21 120.50 110.17 110.39 110.34 123.25 85 SER 85 1.326 1.238 1.538 1.527 1.455 122.49 116.54 120.64 110.17 111.77 109.74 122.77 86 ASP 86 1.332 1.237 1.522 1.534 1.470 121.94 115.61 121.38 109.54 110.75 110.73 122.99 87 TRP 87 1.312 1.226 1.533 1.528 1.433 122.11 116.20 120.40 111.47 111.48 110.41 123.40 * * * 88 ALA 88 1.350 1.234 1.539 1.527 1.487 124.18 115.96 121.20 110.97 112.24 110.32 122.76 * +* * +* 89 ILE 89 1.308 1.237 1.508 1.553 1.444 122.27 115.20 121.21 109.49 109.82 111.80 123.58 +* +* 90 GLN 90 1.294 1.238 1.512 1.525 1.430 122.43 115.94 121.03 110.69 109.67 109.93 122.98 ** * ** 91 ALA 91 1.314 1.231 1.511 1.513 1.442 121.18 116.57 120.85 111.32 109.65 110.66 122.58 * * 92 MET 92 1.300 1.234 1.520 1.517 1.434 121.13 118.18 120.24 108.86 110.48 108.86 121.58 ** * ** 93 PRO 93 1.334 1.237 1.544 1.525 1.454 123.67 118.00 120.30 109.98 110.82 102.12 121.63 94 THR 94 1.297 1.235 1.517 1.526 1.433 119.22 116.00 120.39 109.62 110.26 111.89 123.55 ** * * ** 95 PHE 95 1.317 1.228 1.497 1.532 1.420 122.70 116.92 120.52 107.24 107.41 109.49 122.56 * ** +* * ** 96 MET 96 1.286 1.238 1.498 1.521 1.426 120.48 114.99 121.21 110.89 110.17 111.68 123.79 *** * +* *** 97 PHE 97 1.288 1.246 1.504 1.511 1.395 123.41 116.18 121.35 109.29 108.78 108.77 122.47 +** *** * *** 98 LEU 98 1.275 1.218 1.513 1.567 1.408 120.73 117.42 120.61 112.86 109.24 112.77 121.96 +*** +* +** * * +*** 99 LYS 99 1.284 1.231 1.482 1.524 1.429 120.36 114.53 120.89 111.40 109.59 110.29 124.49 *** ** +* *** 100 GLU 100 1.323 1.233 1.547 1.529 1.459 124.72 116.14 121.06 109.06 110.53 112.20 122.78 * +* * +* 101 GLY 101 1.318 1.229 1.532 - 1.454 121.39 116.29 120.76 - 112.24 - 122.96 102 LYS 102 1.325 1.231 1.531 1.534 1.466 122.94 117.12 119.94 109.55 108.66 109.09 122.92 103 ILE 103 1.322 1.237 1.533 1.562 1.476 122.39 116.11 120.72 109.64 112.47 111.71 123.17 104 LEU 104 1.329 1.236 1.513 1.527 1.442 122.36 115.67 120.83 109.26 110.65 110.98 123.48 Residue-by-residue listing for refined_4 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 1.312 1.215 1.495 1.526 1.449 123.04 116.20 120.90 110.20 111.43 112.30 122.85 * * * * 106 LYS 106 1.298 1.230 1.521 1.533 1.438 121.43 115.79 121.16 110.75 111.53 110.45 123.05 ** * ** 107 VAL 107 1.299 1.230 1.514 1.560 1.442 122.76 116.70 120.56 109.55 107.78 111.56 122.71 ** * ** 108 VAL 108 1.301 1.243 1.530 1.562 1.436 120.42 115.87 120.94 111.89 110.34 112.26 123.17 ** * * ** 109 GLY 109 1.309 1.238 1.502 - 1.431 121.49 117.44 119.97 - 110.19 - 122.58 * * * 110 ALA 110 1.316 1.232 1.504 1.521 1.435 119.65 115.25 121.29 110.69 108.78 110.54 123.41 * * * 111 LYS 111 1.298 1.210 1.500 1.519 1.414 123.03 118.91 118.86 109.54 108.17 108.43 122.23 ** * * ** * * * * ** 112 LYS 112 1.315 1.242 1.523 1.508 1.427 120.37 115.70 121.06 109.14 112.58 110.84 123.20 * * +* +* 113 ASP 113 1.315 1.237 1.517 1.521 1.454 121.87 117.34 119.96 111.05 113.04 111.01 122.68 * * 114 GLU 114 1.333 1.225 1.521 1.543 1.458 119.99 116.76 120.59 111.23 110.97 113.01 122.62 * * 115 LEU 115 1.321 1.216 1.508 1.508 1.449 121.42 115.50 120.94 109.38 108.91 110.34 123.55 * * 116 GLN 116 1.320 1.230 1.510 1.523 1.474 122.49 116.08 120.82 110.03 111.89 111.02 123.08 117 SER 117 1.303 1.230 1.527 1.520 1.447 121.27 115.65 120.87 111.70 110.12 109.96 123.45 +* +* 118 THR 118 1.318 1.229 1.534 1.546 1.438 122.82 116.54 120.61 111.02 109.65 110.27 122.82 * * 119 ILE 119 1.333 1.216 1.525 1.563 1.458 121.61 116.29 120.77 109.46 109.20 112.23 122.88 120 ALA 120 1.323 1.219 1.532 1.520 1.462 121.99 116.32 120.92 111.21 111.36 110.85 122.75 121 LYS 121 1.319 1.227 1.524 1.500 1.455 122.41 115.12 121.50 109.84 109.07 108.84 123.39 +* +* 122 HIS 122 1.319 1.230 1.529 1.531 1.445 122.56 116.74 120.60 109.56 111.53 111.38 122.66 123 LEU 123 1.316 1.226 1.511 1.516 1.412 122.84 116.21 120.85 110.41 112.41 109.71 122.90 ** ** 124 ALA 124 1.305 - 1.517 1.519 1.438 121.18 - - 111.23 109.31 110.81 - +* * +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * ** ** *** +* ** * +* +* ** +* **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_4 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 1.350 1.313 .014 **** +* * C-N (Pro) 1.341 .016 4 1.334 1.380 1.353 .019 ** C-O C-O 1.231 .020 123 1.205 1.253 1.232 .008 * * CA-C CH1E-C (except Gly) 1.525 .021 119 1.482 1.556 1.521 .015 ** * CH2G*-C (Gly) 1.516 .018 5 1.502 1.532 1.515 .014 CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.513 1.529 1.519 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.526 1.579 1.554 .013 * CH1E-CH2E (the rest) 1.530 .020 84 1.488 1.568 1.529 .016 ** +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.395 1.487 1.444 .017 *** +* NH1-CH2G* (Gly) 1.451 .016 5 1.431 1.461 1.448 .010 * N-CH1E (Pro) 1.466 .015 4 1.454 1.479 1.465 .010 ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_4 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 2.0 114 113.30 120.21 116.16 .94 * ** CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.64 119.13 117.02 1.20 * CH1E-C-N (Pro) 116.9 1.5 4 114.03 118.00 115.68 1.44 +* O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.71 124.49 122.99 .57 * O-C-N (Pro) 122.0 1.4 4 121.63 124.18 123.12 .96 +* C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 119.21 125.25 122.16 1.15 * +* C-NH1-CH2G* (Gly) 120.6 1.7 5 120.42 122.71 121.37 .77 * C-N-CH1E (Pro) 122.6 5.0 4 121.41 123.67 122.35 .97 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 118.86 122.62 120.82 .57 * * CH2G*-C-O (Gly) 120.8 2.1 5 119.71 121.19 120.45 .54 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 110.17 111.89 110.91 .45 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 108.12 111.98 110.15 .98 * CH2E-CH1E-C (the rest) 110.1 1.9 84 107.24 112.86 110.31 1.17 +* * N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 106.14 114.07 110.21 1.59 +* * NH1-CH2G*-C (Gly) 112.5 2.9 5 110.19 114.08 112.02 1.40 N-CH1E-C (Pro) 111.8 2.5 4 107.76 111.87 110.47 1.61 +* N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.03 111.94 110.67 .43 * NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 110.13 112.49 111.45 .71 N-CH1E-CH2E (Pro) 103.0 1.1 4 102.12 104.38 103.66 .90 * NH1-CH1E-CH2E (the rest) 110.5 1.7 80 107.06 113.13 110.33 1.42 ** +* ------------------------------------------------------------------------------------------------------------- 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_4 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] 102 90.3% Residues in additional allowed regions [a,b,l,p] 10 8.8% 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 90.3 83.8 10.0 .6 Inside b. Omega angle st dev 122 3.0 6.0 3.0 -1.0 BETTER c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 119 1.5 3.1 1.6 -1.0 Inside e. H-bond energy st dev 83 .8 .8 .2 .2 Inside f. Overall G-factor 124 .1 -.4 .3 1.7 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 14 7.2 18.1 6.5 -1.7 BETTER b. Chi-1 trans st dev 45 4.8 19.0 5.3 -2.7 BETTER c. Chi-1 gauche plus st dev 43 7.4 17.5 4.9 -2.1 BETTER d. Chi-1 pooled st dev 102 7.1 18.2 4.8 -2.3 BETTER e. Chi-2 trans st dev 34 8.5 20.4 5.0 -2.4 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% 90.3 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.7 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .84 2 Residue-by-residue listing for refined_4 Page 14 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.14 Chi1-chi2 distribution .00 Chi1 only .03 Chi3 & chi4 .49 Omega .09 ------ .04 ===== Main-chain covalent forces:- Main-chain bond lengths .03 Main-chain bond angles .47 ------ .28 ===== OVERALL AVERAGE .12 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.