Residue-by-residue listing for refined_13 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 - - - -68.7 - - - - - - - 182.4 - 32.4 - 2 GLY 2 - - - - - - - - - - - 183.8 - - - 3 HIS 3 B - 182.0 - - - - - - - - 176.9 - 35.6 - 4 HIS 4 B - - -72.4 - - - - - - - 176.2 - 32.6 - 5 HIS 5 B - - -71.9 - - - - - - - 173.2 - 35.4 - * * 6 HIS 6 B - 189.2 - - - - - - - - 189.4 - 34.2 - +* +* 7 HIS 7 B - - -62.4 - - - - - - - 173.1 -.9 33.1 - * * * 8 HIS 8 B - - -62.9 - - - - - - - 180.9 -.5 35.2 - ** ** 9 LEU 9 b - - -61.2 178.5 - - - - - - 180.1 -.7 33.2 - +* +* 10 GLU 10 S XX - - -60.9 178.8 - - - - - - 180.3 -1.2 30.6 - **** * **** 11 MET 11 B 61.2 - - 182.2 - - - - - - 180.0 -1.6 33.8 - 12 ALA 12 b - - - - - - - - - - 179.0 - 33.4 - 13 SER 13 B - - -62.0 - - - - - - - 176.7 -.7 34.0 - +* +* 14 GLU 14 B - - -63.5 - - - - - - - 185.4 - 35.6 - 15 GLU 15 B - 204.1 - - - - - - - - 180.5 -.6 35.1 - * +* +* 16 GLY 16 S - - - - - - - - - - - 186.0 -1.1 - - * * * 17 GLN 17 e B 53.0 - - 182.0 - - - - - - 177.4 - 31.3 - 18 VAL 18 E B - 181.5 - - - - - - - - 179.2 - 35.5 - Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 19 ILE 19 E B - - -58.5 178.8 - - - - - - 180.4 -3.2 33.0 - +* +* 20 ALA 20 E B - - - - - - - - - - 179.5 -.5 34.4 - ** ** 21 CYS 21 E B - - -54.1 - - - - - - - 176.8 -1.1 36.1 - * * 22 HIS 22 S A - - -66.4 - - - - - - - 180.9 - 33.2 - 23 THR 23 h B 53.7 - - - - - - - - - 178.2 - 34.6 - 24 VAL 24 H A - 178.8 - - - -68.9 -30.2 - - - 177.6 - 32.7 - 25 GLU 25 H A - - -66.1 - - -55.0 -47.6 - - - 177.5 - 34.9 - 26 THR 26 H A - - -49.4 - - -74.0 -50.9 - - - 184.3 - 35.7 - * * * 27 TRP 27 H A - 170.7 - - - -52.8 -54.3 - - - 183.1 -2.7 34.4 - * * * 28 ASN 28 H A - 184.8 - - - -64.1 -40.3 - - - 181.6 -3.3 34.7 - +* +* 29 GLU 29 H A - 181.9 - 178.9 - -64.7 -40.7 - - - 179.9 -.9 33.3 - +* +* 30 GLN 30 H A - - -61.2 - - -62.1 -43.3 - - - 179.7 -2.4 34.8 - 31 LEU 31 H A - - -64.9 178.6 - -67.6 -45.9 - - - 178.0 -1.8 35.4 - 32 GLN 32 H A - 183.3 - 181.7 - -60.2 -40.7 - - - 177.8 -2.7 34.2 - 33 LYS 33 H A - 179.7 - 173.1 - -65.1 -40.8 - - - 179.6 -2.8 32.9 - * * 34 ALA 34 H A - - - - - -68.3 -41.5 - - - 180.8 -2.4 34.0 - 35 ASN 35 H A - 188.5 - - - -65.8 -52.5 - - - 180.4 -3.1 35.9 - * * * 36 GLU 36 H A - 179.8 - 185.8 - -58.3 -42.6 - - - 181.6 -3.2 35.2 - +* +* 37 SER 37 H A - - -55.2 - - -79.7 -8.7 - - - 179.6 -2.2 33.9 - * +** +** 38 LYS 38 h L - 193.5 - 184.9 - - - - - - 180.2 -.9 33.2 - * * 39 THR 39 t B - - -47.9 - - - - - - - 180.3 -2.7 35.2 - * * 40 LEU 40 E B - 188.9 - 172.1 - - - - - - 183.3 -.5 34.3 - ** ** 41 VAL 41 E B 58.8 - - - - - - - - - 177.6 -.6 33.5 - +* +* 42 VAL 42 E B - 179.9 - - - - - - - - 184.1 -2.0 33.6 - 43 VAL 43 E B - 184.6 - - - - - - - - 176.6 -3.0 34.6 - * * 44 ASP 44 E B - 168.9 - - - - - - - - 176.0 -3.4 35.0 - +* +* 45 PHE 45 E B - - -67.4 - - - - - - - 186.6 -3.3 34.8 - * +* +* 46 THR 46 E B - 182.6 - - - - - - - - 175.2 -2.8 36.2 - * * 47 ALA 47 t B - - - - - - - - - - 180.9 - 34.1 - 48 SER 48 T A 51.5 - - - - - - - - - 183.3 - 34.0 - 49 TRP 49 T A 48.9 - - - - - - - - - 177.6 - 31.3 - 50 CYS 50 h B 50.9 - - - - - - - -123.5 2.8 186.9 -2.0 30.3 - +*** *7.8* * * *7.8* 51 GLY 51 H - - - - - - -62.4 -69.2 - - - 181.1 -.6 - - +** +* +** 52 PRO 52 H - - - - - -51.4 -51.4 -30.7 - - - 180.4 - 38.5 - * * * * Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 53 CYS 53 H A - - -47.9 153.2 - -68.0 -37.4 - -123.5 2.8 178.9 - 36.3 - * * +*** *7.8* *7.8* 54 ARG 54 H A - 184.4 - 178.5 - -75.0 -29.6 - - - 177.8 -1.3 34.1 - 55 PHE 55 H A - 180.5 - - - -66.9 -35.5 - - - 182.4 -1.7 34.4 - 56 ILE 56 H A - 190.2 - - - -87.6 -18.0 - - - 182.2 -1.7 33.9 - +* +* +* 57 ALA 57 H A - - - - - -54.9 -45.5 - - - 178.4 -1.1 31.8 - * * 58 PRO 58 H - - - - - -59.3 -59.3 -36.8 - - - 179.2 - 38.4 - * * 59 PHE 59 H A - 179.6 - - - -65.5 -37.7 - - - 178.8 - 33.4 - 60 PHE 60 H A - 184.6 - - - -62.8 -36.2 - - - 178.7 -1.5 34.3 - 61 ALA 61 H A - - - - - -74.2 -31.9 - - - 179.5 -1.6 33.7 - 62 ASP 62 H A - 188.0 - - - -73.7 -40.2 - - - 176.9 -1.8 35.8 - 63 LEU 63 H A - 169.1 - - - -57.2 -37.6 - - - 177.7 -2.9 36.7 - * * 64 ALA 64 H A - - - - - -59.3 -33.7 - - - 178.8 -1.1 33.4 - * * 65 LYS 65 H A - 186.0 - - - -79.6 -30.1 - - - 182.0 -.9 33.3 - * * * 66 LYS 66 H A - - -64.6 181.9 - -67.2 -40.7 - - - 185.2 -1.5 34.5 - 67 LEU 67 h B - - -62.5 185.1 - - - - - - 179.7 -2.0 31.4 - 68 PRO 68 S - - - - - -46.6 - - - - - 177.6 - 38.9 - +* * +* 69 ASN 69 e b - 179.8 - - - - - - - - 181.2 - 32.5 - 70 VAL 70 E B - 174.6 - - - - - - - - 179.7 - 34.1 - 71 LEU 71 E B - 193.6 - 174.1 - - - - - - 179.9 -2.3 34.6 - 72 PHE 72 E B - - -65.8 - - - - - - - 181.6 -1.1 33.4 - * * 73 LEU 73 E B - - -71.0 162.3 - - - - - - 179.6 -2.3 34.5 - 74 LYS 74 E B - 194.6 - 179.1 - - - - - - 184.0 -2.5 35.5 - 75 VAL 75 E B - 177.5 - - - - - - - - 176.9 -3.4 33.9 - +* +* 76 ASP 76 E B - 188.6 - - - - - - - - 183.4 -.8 34.4 - +* +* 77 THR 77 e A 54.2 - - - - - - - - - 175.0 -3.8 32.6 - ** ** 78 ASP 78 T A - 174.6 - - - - - - - - 173.2 - 34.7 - * * 79 GLU 79 T A - - -67.4 - - - - - - - 182.0 - 36.4 - 80 LEU 80 h b - - -66.9 178.4 - - - - - - 182.3 -3.1 33.5 - * * 81 LYS 81 H A 54.0 - - 187.9 - -68.9 -33.4 - - - 177.5 -1.5 32.0 - 82 SER 82 H A - - -56.7 - - -71.0 -35.8 - - - 177.4 - 34.2 - 83 VAL 83 H A - 178.4 - - - -67.3 -38.9 - - - 176.9 - 34.3 - 84 ALA 84 H A - - - - - -60.4 -37.5 - - - 177.8 -2.0 34.0 - 85 SER 85 H A - - -58.4 - - -73.7 -35.0 - - - 183.7 -1.5 34.3 - 86 ASP 86 H A - 188.6 - - - -70.5 -36.6 - - - 177.4 -2.1 33.8 - 87 TRP 87 h A - - -68.2 - - - - - - - 181.1 -2.4 33.5 - 88 ALA 88 T l - - - - - - - - - - 176.5 - 30.4 - * * 89 ILE 89 t B - - -53.7 - - - - - - - 182.0 -2.7 33.9 - 90 GLN 90 A - 182.9 - 182.1 - - - - - - 182.9 -1.0 35.0 - * * 91 ALA 91 S B - - - - - - - - - - 181.7 - 33.2 - 92 MET 92 S B - - -58.1 174.6 - - - - - - -2.6 - 36.0 - Residue-by-residue listing for refined_13 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 ----------------------------------------------------------------------------------------------------------------------------------- 93 PRO 93 e cis - - - - - -93.1 - - - - - 176.4 - 39.7 - ** +* ** 94 THR 94 E B - - -61.2 - - - - - - - 179.9 -2.5 33.6 - 95 PHE 95 E B - - -61.1 - - - - - - - 182.3 -2.8 36.0 - * * 96 MET 96 E B - 189.1 - - - - - - - - 183.9 -3.4 35.0 - +* +* 97 PHE 97 E B - - -67.4 - - - - - - - 177.9 -3.1 36.3 - * * 98 LEU 98 E B - - -55.4 - - - - - - - 176.5 -2.4 35.0 - 99 LYS 99 E B - 178.3 - 173.8 - - - - - - 176.6 -3.2 33.2 - +* +* 100 GLU 100 T l - - -55.2 175.8 - - - - - - 181.4 - 33.8 - 101 GLY 101 T - - - - - - - - - - - 177.5 - - - 102 LYS 102 E B - 176.6 - - - - - - - - 179.2 -2.2 34.7 - 103 ILE 103 E B - - -69.1 175.5 - - - - - - 177.1 - 34.0 - 104 LEU 104 E a - - -67.8 184.3 - - - - - - 187.2 -1.8 33.7 - * * 105 ASP 105 E B 49.6 - - - - - - - - - 178.3 -1.9 32.2 - 106 LYS 106 E B 53.0 - - - - - - - - - 179.6 - 31.6 - 107 VAL 107 E B - 181.5 - - - - - - - - 179.2 -2.7 34.9 - 108 VAL 108 E B 63.9 - - - - - - - - - 179.1 - 33.5 - 109 GLY 109 e - - - - - - - - - - - 179.4 -3.1 - - * * 110 ALA 110 B - - - - - - - - - - 176.8 - 33.6 - 111 LYS 111 h B - - -69.1 - - - - - - - 184.9 -.9 36.0 - +* +* 112 LYS 112 H A - 183.4 - 180.1 - -60.6 -50.3 - - - 180.9 - 34.1 - 113 ASP 113 H A - 185.1 - - - -73.2 -48.0 - - - 185.9 - 33.8 - * * 114 GLU 114 H A - 196.0 - - - -64.7 -32.9 - - - 176.9 - 33.3 - 115 LEU 115 H A - 184.7 - - - -61.9 -50.7 - - - 178.3 -2.2 35.4 - 116 GLN 116 H A - - -64.6 177.9 - -59.5 -34.0 - - - 176.8 -1.4 32.7 - 117 SER 117 H A - 182.8 - - - -66.1 -34.6 - - - 177.9 -2.0 34.2 - 118 THR 118 H A - - -53.4 - - -75.6 -35.8 - - - 175.9 -1.7 34.4 - 119 ILE 119 H A - - -60.8 175.6 - -62.7 -44.8 - - - 178.8 -2.5 34.2 - 120 ALA 120 H A - - - - - -65.6 -31.9 - - - 176.3 -3.0 33.3 - * * 121 LYS 121 H A - 181.6 - 180.8 - -57.9 -44.2 - - - 179.6 -1.4 36.8 - 122 HIS 122 H A - - -69.6 - - -82.0 -33.8 - - - 182.5 -1.6 34.2 - * * 123 LEU 123 h B - 196.6 - 170.5 - - - - - - 178.4 -2.7 34.7 - 124 ALA 124 - - - - - - - - - - - - - 34.3 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * * * ** +* +** +*** *7.8* +* ** +* *7.8* ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 54.4 183.7 -62.2 177.7 -62.6 -66.2 -38.9 - -123.5 2.8 179.8 -2.0 34.2 +*** *7.8* *7.8* Standard deviations: 4.6 7.1 6.4 6.8 21.0 7.8 9.5 - .0 .0 3.0 .9 1.6 Numbers of values: 12 47 43 32 4 47 47 0 2 2 122 81 119 0 Number of cis-peptides (labelled cis): 1 Residue-by-residue listing for refined_13 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_13 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 - 1.231 1.514 1.544 1.467 - 116.31 120.59 110.95 110.91 112.26 123.11 * * 2 GLY 2 1.314 1.236 1.502 - 1.443 121.36 115.35 121.38 - 110.03 - 123.27 * * 3 HIS 3 1.310 1.226 1.523 1.544 1.430 122.62 116.85 120.52 110.79 109.84 108.48 122.60 * * * * 4 HIS 4 1.311 1.235 1.513 1.543 1.456 121.95 115.13 120.95 109.49 111.65 113.21 123.89 * +* +* 5 HIS 5 1.315 1.245 1.506 1.544 1.458 124.52 116.85 119.93 107.03 108.91 112.62 123.22 * +* +* * +* 6 HIS 6 1.319 1.230 1.516 1.546 1.446 120.94 115.94 120.61 111.05 105.56 111.49 123.44 ** ** 7 HIS 7 1.303 1.224 1.494 1.527 1.457 122.43 115.26 121.09 109.63 113.50 111.73 123.64 +* * +* 8 HIS 8 1.298 1.238 1.510 1.543 1.436 122.08 116.95 119.94 109.72 106.43 110.97 123.02 ** * +* ** 9 LEU 9 1.315 1.235 1.509 1.537 1.448 121.04 115.05 120.64 110.72 110.38 111.66 124.25 10 GLU 10 1.322 1.232 1.534 1.538 1.455 124.49 117.03 120.28 112.70 112.37 112.23 122.65 +* * * +* 11 MET 11 1.318 1.227 1.518 1.548 1.455 122.31 117.10 120.24 110.72 109.53 111.17 122.65 12 ALA 12 1.312 1.240 1.519 1.525 1.449 121.40 116.08 120.89 110.95 110.36 110.93 122.93 * * Residue-by-residue listing for refined_13 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 1.308 1.240 1.515 1.539 1.444 122.98 115.84 120.60 110.05 110.21 111.26 123.54 +* +* 14 GLU 14 1.313 1.237 1.518 1.538 1.422 123.02 116.99 120.35 110.17 107.36 109.71 122.64 * +* * +* 15 GLU 15 1.302 1.241 1.526 1.531 1.437 120.16 117.43 119.82 111.24 109.12 108.73 122.73 +* * * +* 16 GLY 16 1.323 1.233 1.504 - 1.440 120.03 116.29 120.80 - 111.91 - 122.91 17 GLN 17 1.312 1.235 1.502 1.506 1.433 120.94 112.94 122.74 111.16 114.90 111.81 124.32 * * * * +* * * +* 18 VAL 18 1.282 1.242 1.524 1.557 1.438 124.16 118.16 119.68 109.01 107.57 110.99 122.13 *** * * * *** 19 ILE 19 1.316 1.221 1.528 1.549 1.437 119.83 116.63 120.99 111.03 110.16 111.84 122.34 * * * 20 ALA 20 1.299 1.234 1.513 1.515 1.441 121.66 116.44 120.59 110.31 110.12 110.25 122.96 ** ** 21 CYS 21 1.309 1.232 1.518 1.508 1.419 122.07 116.52 120.67 109.21 109.62 109.06 122.78 * * ** ** 22 HIS 22 1.308 1.233 1.511 1.543 1.455 121.78 115.81 120.73 110.36 110.36 112.00 123.46 * * 23 THR 23 1.330 1.250 1.522 1.556 1.457 122.57 116.93 119.80 108.70 109.88 111.88 123.28 24 VAL 24 1.332 1.222 1.526 1.558 1.450 121.90 116.57 120.50 110.68 110.18 112.68 122.90 25 GLU 25 1.339 1.231 1.520 1.505 1.424 122.96 116.46 120.48 110.33 111.34 109.16 123.05 * +* +* 26 THR 26 1.315 1.219 1.540 1.538 1.434 120.93 115.32 120.95 109.21 109.09 109.96 123.61 * * 27 TRP 27 1.329 1.238 1.536 1.533 1.468 124.49 116.58 120.42 111.27 113.80 107.98 122.99 +* * +* 28 ASN 28 1.311 1.238 1.513 1.534 1.459 122.26 115.45 120.95 110.21 110.31 109.90 123.57 * * 29 GLU 29 1.319 1.229 1.525 1.530 1.446 122.16 116.76 120.13 110.75 111.30 111.00 123.10 30 GLN 30 1.331 1.229 1.515 1.500 1.427 122.63 116.28 120.73 110.10 111.45 109.35 122.98 * +* +* 31 LEU 31 1.319 1.224 1.501 1.487 1.412 122.52 115.87 120.44 109.63 111.12 109.11 123.69 * ** ** ** 32 GLN 32 1.312 1.214 1.518 1.526 1.441 122.20 116.30 120.56 111.26 109.57 109.87 123.11 * * 33 LYS 33 1.318 1.233 1.526 1.536 1.443 121.71 117.12 120.04 111.43 110.97 111.08 122.82 34 ALA 34 1.335 1.230 1.520 1.522 1.455 120.98 115.55 121.02 110.40 110.43 110.63 123.41 35 ASN 35 1.317 1.229 1.496 1.517 1.460 122.90 114.76 121.17 108.56 109.94 109.90 124.06 * * 36 GLU 36 1.310 1.240 1.532 1.522 1.467 122.76 116.94 120.46 108.70 111.69 110.03 122.59 * * 37 SER 37 1.316 1.240 1.529 1.515 1.445 121.30 115.65 120.46 111.23 111.40 109.49 123.87 38 LYS 38 1.348 1.232 1.546 1.511 1.424 124.87 114.68 122.54 112.96 109.57 109.32 122.72 * * +* +* * +* +* 39 THR 39 1.304 1.242 1.535 1.532 1.434 122.92 115.94 121.13 109.01 109.06 110.80 122.88 +* * +* 40 LEU 40 1.295 1.239 1.545 1.564 1.446 122.53 116.71 120.45 113.10 107.69 108.71 122.82 ** +* +* * * ** 41 VAL 41 1.318 1.240 1.538 1.569 1.446 122.04 116.11 120.86 111.28 111.36 110.61 123.01 * * 42 VAL 42 1.317 1.238 1.518 1.545 1.451 122.41 116.42 120.74 109.63 108.84 112.66 122.84 43 VAL 43 1.305 1.228 1.528 1.551 1.442 121.34 115.57 120.64 109.02 111.16 111.21 123.79 +* +* Residue-by-residue listing for refined_13 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 1.306 1.235 1.513 1.539 1.456 124.04 116.64 120.62 109.94 109.99 109.94 122.66 +* * +* 45 PHE 45 1.310 1.237 1.510 1.525 1.422 121.70 115.66 120.94 110.14 108.38 110.54 123.34 * +* * +* 46 THR 46 1.290 1.219 1.523 1.562 1.431 122.30 117.20 120.19 109.82 108.58 109.12 122.55 +** * * +** 47 ALA 47 1.293 1.227 1.503 1.519 1.434 122.33 116.83 120.14 110.56 107.90 111.27 123.03 +** * * * +** 48 SER 48 1.298 1.233 1.556 1.520 1.461 123.05 116.83 120.85 111.24 113.63 108.40 122.28 ** * * ** 49 TRP 49 1.317 1.232 1.553 1.539 1.450 122.12 118.77 119.72 112.37 115.25 110.44 121.50 * * * * * 50 CYS 50 1.328 1.245 1.541 1.547 1.476 119.70 115.38 120.93 113.29 111.37 112.43 123.69 * +* * +* 51 GLY 51 1.336 1.231 1.527 - 1.472 123.65 118.86 119.37 - 115.41 - 121.76 * +* * * +* 52 PRO 52 1.364 1.230 1.530 1.543 1.485 123.64 115.58 121.43 110.13 112.81 103.75 122.97 * * * 53 CYS 53 1.307 1.217 1.534 1.504 1.452 122.78 116.18 121.41 108.89 109.96 108.59 122.40 +* * * +* 54 ARG 54 1.312 1.220 1.520 1.525 1.452 121.53 115.35 121.43 110.86 108.88 110.49 123.21 * * 55 PHE 55 1.318 1.232 1.542 1.542 1.451 122.51 116.70 120.62 110.61 110.82 109.81 122.67 56 ILE 56 1.326 1.237 1.551 1.578 1.464 121.50 115.31 121.39 110.59 110.48 110.90 123.25 * * * 57 ALA 57 1.324 1.240 1.570 1.522 1.463 123.77 120.39 119.17 111.71 114.90 110.36 120.44 ** * ** * +* ** 58 PRO 58 1.382 1.233 1.528 1.530 1.477 121.97 116.49 120.70 110.17 112.08 103.94 122.80 +** +** 59 PHE 59 1.331 1.220 1.517 1.538 1.454 121.48 115.91 120.84 110.60 110.01 111.62 123.22 60 PHE 60 1.320 1.231 1.543 1.542 1.454 122.51 115.95 121.20 111.49 109.92 109.33 122.82 61 ALA 61 1.325 1.235 1.535 1.522 1.459 121.96 116.15 121.12 110.65 111.07 110.42 122.74 62 ASP 62 1.319 1.232 1.504 1.515 1.477 122.54 114.21 121.65 108.99 109.18 109.61 124.13 * * 63 LEU 63 1.309 1.235 1.518 1.506 1.420 125.05 114.77 121.31 110.40 110.44 106.72 123.92 * * ** +* ** ** 64 ALA 64 1.303 1.223 1.522 1.520 1.447 122.82 116.44 120.79 111.04 111.44 110.47 122.77 +* +* 65 LYS 65 1.317 1.233 1.543 1.560 1.442 121.15 116.11 120.89 113.40 109.71 109.20 122.98 +* +* +* 66 LYS 66 1.329 1.249 1.522 1.531 1.463 122.29 116.99 120.32 107.91 113.00 111.54 122.69 * * 67 LEU 67 1.314 1.229 1.533 1.533 1.438 120.65 116.57 120.43 112.83 112.88 110.98 122.90 * * * * 68 PRO 68 1.372 1.227 1.530 1.531 1.478 123.85 115.99 120.28 109.67 113.08 103.55 123.73 +* * +* 69 ASN 69 1.324 1.229 1.502 1.526 1.454 123.35 115.15 121.40 110.91 110.00 112.46 123.36 * * * 70 VAL 70 1.288 1.233 1.512 1.559 1.438 123.68 116.25 120.81 110.43 109.47 111.28 122.89 +** * * +** 71 LEU 71 1.303 1.233 1.532 1.562 1.432 120.94 116.30 120.81 112.35 106.99 109.35 122.81 +* +* * * +* +* 72 PHE 72 1.309 1.231 1.498 1.519 1.448 121.86 115.39 121.00 109.57 110.70 112.29 123.60 * * * * Residue-by-residue listing for refined_13 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 1.288 1.218 1.503 1.519 1.437 123.16 115.93 120.69 110.94 111.01 109.41 123.37 +** * * +** 74 LYS 74 1.302 1.241 1.508 1.499 1.428 122.33 116.28 120.93 109.95 108.56 109.39 122.79 +* +* +* +* 75 VAL 75 1.299 1.239 1.499 1.553 1.438 121.91 115.29 121.22 109.67 110.99 111.83 123.50 ** * * ** 76 ASP 76 1.302 1.228 1.513 1.506 1.423 121.44 115.42 121.04 110.36 108.09 110.74 123.50 +* * +* * +* 77 THR 77 1.295 1.225 1.537 1.542 1.444 123.90 116.83 120.61 111.35 113.33 110.68 122.54 ** * * ** 78 ASP 78 1.316 1.239 1.508 1.525 1.460 121.55 113.97 121.83 110.86 107.58 110.05 124.20 * * * 79 GLU 79 1.316 1.236 1.528 1.517 1.430 124.25 116.11 121.07 109.30 110.27 108.34 122.79 * * * * 80 LEU 80 1.318 1.237 1.523 1.516 1.409 122.78 114.41 122.02 112.18 110.82 109.68 123.55 +** * +** 81 LYS 81 1.305 1.232 1.527 1.525 1.452 123.66 116.87 120.59 112.79 113.06 110.00 122.53 +* * * +* 82 SER 82 1.318 1.230 1.528 1.519 1.445 121.35 115.69 121.30 110.78 109.41 110.26 122.97 83 VAL 83 1.332 1.237 1.527 1.550 1.457 122.20 115.36 121.28 109.99 109.02 111.17 123.33 84 ALA 84 1.327 1.222 1.527 1.518 1.447 122.44 116.47 121.12 110.62 110.35 110.30 122.40 85 SER 85 1.310 1.233 1.543 1.523 1.438 121.11 116.64 120.64 110.48 111.04 109.92 122.67 * * * 86 ASP 86 1.327 1.234 1.531 1.533 1.470 122.01 116.44 120.70 110.24 111.54 110.65 122.85 87 TRP 87 1.325 1.234 1.527 1.530 1.461 122.22 114.92 120.98 110.36 111.12 111.11 124.10 88 ALA 88 1.330 1.232 1.515 1.524 1.459 124.90 115.54 121.66 111.77 112.96 113.19 122.71 +* +* +* 89 ILE 89 1.297 1.238 1.500 1.556 1.429 121.51 115.09 121.40 110.56 107.37 112.18 123.37 ** * +* * ** 90 GLN 90 1.296 1.236 1.513 1.528 1.429 122.39 116.04 120.99 110.51 109.55 109.64 122.92 ** +* ** 91 ALA 91 1.307 1.229 1.512 1.521 1.444 121.12 116.17 120.86 111.20 110.74 110.90 122.96 +* +* 92 MET 92 1.301 1.229 1.519 1.520 1.447 121.98 118.66 119.79 108.90 109.67 109.33 121.54 +* * +* 93 PRO 93 1.340 1.235 1.535 1.528 1.456 124.00 116.85 120.95 110.05 111.51 102.38 122.17 94 THR 94 1.291 1.223 1.511 1.532 1.428 120.97 116.15 120.71 110.10 109.41 112.14 123.14 +** +* +** 95 PHE 95 1.296 1.235 1.500 1.521 1.409 122.20 116.21 120.43 109.59 107.44 109.68 123.35 ** * +** * +** 96 MET 96 1.295 1.236 1.501 1.517 1.436 121.57 115.46 120.92 109.94 108.78 110.21 123.62 ** * * ** 97 PHE 97 1.282 1.248 1.515 1.508 1.408 123.53 116.18 121.30 109.24 110.89 108.45 122.52 *** * +** * * *** 98 LEU 98 1.298 1.220 1.522 1.559 1.429 120.70 117.19 120.40 107.96 107.94 112.87 122.40 ** * +* * * * ** 99 LYS 99 1.296 1.222 1.483 1.532 1.436 121.23 115.17 120.46 110.86 109.57 112.05 124.26 ** +* * ** 100 GLU 100 1.330 1.236 1.538 1.517 1.457 123.87 115.27 121.57 111.66 111.33 109.18 123.11 * * 101 GLY 101 1.324 1.224 1.518 - 1.444 121.76 116.78 120.52 - 112.68 - 122.70 102 LYS 102 1.316 1.231 1.531 1.547 1.447 121.87 116.45 120.38 110.72 109.57 109.81 123.17 103 ILE 103 1.324 1.234 1.522 1.564 1.463 122.73 116.27 120.61 109.91 111.06 111.20 123.10 104 LEU 104 1.315 1.237 1.512 1.530 1.425 121.47 116.30 120.78 110.03 111.20 111.46 122.87 * +* +* Residue-by-residue listing for refined_13 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 1.316 1.215 1.506 1.534 1.449 121.34 115.49 121.13 110.85 113.43 111.73 123.31 106 LYS 106 1.313 1.233 1.522 1.559 1.447 122.66 116.18 120.79 112.95 111.44 111.43 123.02 * * * * 107 VAL 107 1.307 1.232 1.515 1.564 1.457 122.46 117.13 120.08 109.23 108.67 111.45 122.76 +* +* 108 VAL 108 1.310 1.239 1.532 1.558 1.433 121.28 116.11 120.89 110.90 110.33 111.37 122.97 * * * 109 GLY 109 1.311 1.235 1.506 - 1.435 120.94 117.08 120.58 - 111.17 - 122.34 * * * 110 ALA 110 1.306 1.231 1.511 1.524 1.428 120.03 114.87 121.68 110.94 109.49 111.12 123.39 +* +* +* 111 LYS 111 1.292 1.220 1.499 1.516 1.422 123.94 117.39 119.49 110.04 107.45 109.15 123.12 +** * +* * * +** 112 LYS 112 1.308 1.233 1.539 1.523 1.439 121.96 116.71 120.74 110.92 111.90 109.49 122.55 +* * +* 113 ASP 113 1.318 1.231 1.517 1.533 1.462 121.42 116.08 120.80 109.26 111.49 111.77 123.11 114 GLU 114 1.328 1.246 1.535 1.524 1.460 121.50 116.50 120.89 110.58 111.34 110.98 122.60 115 LEU 115 1.333 1.215 1.500 1.518 1.452 121.26 115.08 121.02 108.85 108.37 110.77 123.88 * * * 116 GLN 116 1.313 1.223 1.524 1.515 1.463 122.77 116.64 120.56 111.03 112.02 111.05 122.78 * * 117 SER 117 1.313 1.238 1.538 1.536 1.454 121.53 115.78 121.56 111.02 109.46 110.10 122.65 * * 118 THR 118 1.310 1.229 1.537 1.536 1.436 122.01 115.87 121.37 110.80 109.21 110.11 122.74 * * * 119 ILE 119 1.317 1.219 1.527 1.554 1.449 122.28 116.29 120.58 110.03 109.43 111.28 123.08 120 ALA 120 1.328 1.226 1.528 1.519 1.461 122.54 115.97 120.57 111.07 111.13 110.49 123.46 121 LYS 121 1.329 1.237 1.519 1.509 1.466 123.59 114.65 121.92 108.67 109.75 108.18 123.43 * * * * 122 HIS 122 1.302 1.226 1.527 1.521 1.433 122.77 116.65 120.25 109.94 112.26 110.26 123.10 +* * +* 123 LEU 123 1.327 1.239 1.523 1.532 1.439 123.19 115.29 120.91 111.53 110.29 108.70 123.78 * * * 124 ALA 124 1.307 - 1.516 1.523 1.430 123.38 - - 110.92 108.29 110.52 - +* * * +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *** ** ** +** +* ** * +* ** ** +* *** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_13 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 1.282 1.348 1.313 .013 *** * * C-N (Pro) 1.341 .016 4 1.340 1.382 1.365 .016 +** * C-O C-O 1.231 .020 123 1.214 1.250 1.232 .007 CA-C CH1E-C (except Gly) 1.525 .021 119 1.483 1.570 1.522 .014 +* ** CH2G*-C (Gly) 1.516 .018 5 1.502 1.527 1.511 .010 CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.515 1.525 1.521 .003 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.532 1.578 1.553 .012 * CH1E-CH2E (the rest) 1.530 .020 84 1.487 1.564 1.528 .015 ** +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.408 1.477 1.444 .015 +** NH1-CH2G* (Gly) 1.451 .016 5 1.435 1.472 1.447 .013 * * N-CH1E (Pro) 1.466 .015 4 1.456 1.485 1.474 .011 * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_13 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 2.0 114 112.94 120.39 116.12 .96 +* ** CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.35 118.86 116.87 1.15 * CH1E-C-N (Pro) 116.9 1.5 4 115.58 116.85 116.23 .48 O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.44 124.32 123.04 .58 +* O-C-N (Pro) 122.0 1.4 4 122.17 123.73 122.92 .56 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 119.70 125.05 122.27 1.08 * +* C-NH1-CH2G* (Gly) 120.6 1.7 5 120.03 123.65 121.55 1.20 +* C-N-CH1E (Pro) 122.6 5.0 4 121.97 124.00 123.37 .82 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 119.17 122.74 120.79 .56 * CH2G*-C-O (Gly) 120.8 2.1 5 119.37 121.38 120.53 .65 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 110.31 111.77 110.93 .43 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 108.70 111.35 110.04 .78 * CH2E-CH1E-C (the rest) 110.1 1.9 84 107.03 113.40 110.52 1.25 +* +* N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 105.56 115.25 110.29 1.76 ** * NH1-CH2G*-C (Gly) 112.5 2.9 5 110.03 115.41 112.24 1.81 * N-CH1E-C (Pro) 111.8 2.5 4 111.51 113.08 112.37 .62 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.25 113.19 110.84 .75 +* NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 109.12 112.68 111.24 .84 * N-CH1E-CH2E (Pro) 103.0 1.1 4 102.38 103.94 103.41 .61 NH1-CH1E-CH2E (the rest) 110.5 1.7 80 106.72 113.21 110.29 1.31 ** +* ------------------------------------------------------------------------------------------------------------- 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_13 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] 105 92.9% Residues in additional allowed regions [a,b,l,p] 7 6.2% 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 92.9 83.8 10.0 .9 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 1.6 3.1 1.6 -1.0 Inside e. H-bond energy st dev 81 .9 .8 .2 .4 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 12 4.6 18.1 6.5 -2.1 BETTER b. Chi-1 trans st dev 47 7.1 19.0 5.3 -2.2 BETTER c. Chi-1 gauche plus st dev 43 6.4 17.5 4.9 -2.3 BETTER d. Chi-1 pooled st dev 102 7.9 18.2 4.8 -2.1 BETTER e. Chi-2 trans st dev 32 6.8 20.4 5.0 -2.7 BETTER M O R R I S E T A L . C L A S S I F I C A T I O N Mean St.dev Classification Parameter m s 1 2 3 4 Value Class --------- ---- --- ------------------------------------ ----- ----- Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 92.9 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 7.9 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .89 3 Residue-by-residue listing for refined_13 Page 14 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.16 Chi1-chi2 distribution -.09 Chi1 only .08 Chi3 & chi4 .33 Omega .08 ------ .00 ===== Main-chain covalent forces:- Main-chain bond lengths .09 Main-chain bond angles .47 ------ .31 ===== OVERALL AVERAGE .11 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.