Residue-by-residue listing for refined_5 Page 1 ---------------------------------------- This listing highlights the residues in the structure which may need investigation. The ideal values and standard deviations against which the structure has been compared are shown in the following table: <------------------------------- I D E A L V A L U E S -------------------------------> Chi-1 dihedral Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality g(-) trans g(+) Chi-2 phi helix psi rt-hand lf-hand bond dihedral en. C-alpha ------------------------------------------------------------------------------------------ Ideal value 64.1 183.6 -66.7 177.4 -65.4 -65.3 -39.4 96.8 -85.8 2.0 180.0 -2.0 33.9 Standard deviation 15.7 16.8 15.0 18.5 11.2 11.9 11.3 14.8 10.7 .1 5.8 .8 3.5 ------------------------------------------------------------------------------------------ In the listing below, properties that deviate from these values are highlighted by asterisks and plus-signs. Each asterisk represents one standard deviation, and each plus-sign represents half a standard deviation. So, a highlight such as +***, indicates that the value of the parameter is between 3.5 and 4.0 standard deviations from the ideal value shown above. Where the deviation is greater than 4.5 standard deviations its numerical value is shown; for example, *5.5*. The final column gives the maximum deviation in each row, while the maximum column deviations are shown at the end of the listing. Also at the end are the keys to the codes used for the secondary structure and Ramachandran plot assignments. Full print-out. ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - - - -64.0 - - - - - - - 180.2 - 33.9 - 2 GLY 2 - - - - - - - - - - - 180.3 - - - 3 HIS 3 S XX - - -66.7 - - - - - - - 181.8 - 30.1 - **** * **** 4 HIS 4 S b - - -58.7 - - - - - - - 179.6 -1.7 31.9 - 5 HIS 5 S l - 189.6 - - - - - - - - 175.2 -.8 30.6 - +* +* 6 HIS 6 B - - -65.5 - - - - - - - 178.8 - 33.7 - 7 HIS 7 b - 181.3 - - - - - - - - 184.4 - 33.4 - 8 HIS 8 b - 183.1 - - - - - - - - 176.6 - 32.0 - 9 LEU 9 b 61.4 - - - - - - - - - 182.2 -1.0 32.8 - * * 10 GLU 10 S A - - -62.3 - - - - - - - 181.2 - 32.4 - 11 MET 11 S b - 181.9 - 179.0 - - - - - - 178.4 - 34.9 - 12 ALA 12 ~p - - - - - - - - - - 176.6 - 32.3 - ** ** 13 SER 13 S a - - -55.5 - - - - - - - 186.4 - 36.1 - * * 14 GLU 14 B - 179.5 - 182.3 - - - - - - 177.2 - 36.8 - 15 GLU 15 B 70.6 - - - - - - - - - 174.7 - 33.8 - 16 GLY 16 S - - - - - - - - - - - 179.7 -2.0 - - 17 GLN 17 B 61.5 - - 182.0 - - - - - - 180.6 - 33.1 - 18 VAL 18 B 68.3 - - - - - - - - - 179.5 - 34.8 - 19 ILE 19 E B - - -58.1 179.2 - - - - - - 180.3 -2.3 34.4 - 20 ALA 20 E B - - - - - - - - - - 180.7 -.8 33.7 - +* +* 21 CYS 21 E B - - -51.2 - - - - - - - 176.3 -2.2 35.7 - * * Residue-by-residue listing for refined_5 Page 2 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 22 HIS 22 S A - - -64.3 - - - - - - - 180.6 -.6 33.7 - +* +* 23 THR 23 h B 56.8 - - - - - - - - - 176.7 - 35.5 - 24 VAL 24 H A 61.5 - - - - -73.8 -23.1 - - - 176.5 - 32.3 - * * 25 GLU 25 H A - - -73.0 - - -61.3 -51.4 - - - 179.2 - 35.6 - * * 26 THR 26 H A - - -56.7 - - -62.2 -36.7 - - - 178.9 - 34.4 - 27 TRP 27 H A - 174.0 - - - -65.1 -55.0 - - - 183.6 -1.4 34.1 - * * 28 ASN 28 H A - 188.4 - - - -65.1 -43.7 - - - 183.8 -3.3 35.0 - +* +* 29 GLU 29 H A - 183.9 - 172.8 - -58.2 -46.9 - - - 176.4 -2.8 32.5 - * * 30 GLN 30 H A - - -89.6 - - -64.4 -35.1 - - - 177.0 -1.5 33.0 - +* +* 31 LEU 31 H A - - -67.6 179.8 - -67.9 -41.6 - - - 176.2 -1.5 34.9 - 32 GLN 32 H A - 182.4 - 183.3 - -59.8 -44.9 - - - 177.8 -2.9 34.5 - * * 33 LYS 33 H A - 183.3 - 175.3 - -63.1 -36.8 - - - 178.9 -2.5 33.5 - 34 ALA 34 H A - - - - - -71.2 -36.8 - - - 181.4 -2.1 33.5 - 35 ASN 35 H A - 186.3 - - - -72.0 -54.5 - - - 182.7 -2.7 37.2 - * * 36 GLU 36 H A - 181.9 - 183.8 - -66.2 -44.1 - - - 183.7 -3.4 35.0 - +* +* 37 SER 37 h A - - -57.9 - - - - - - - 178.3 -2.1 33.8 - 38 LYS 38 t l - - -79.3 - - - - - - - 179.0 -.6 30.6 - +* +* 39 THR 39 B - - -46.7 - - - - - - - 182.0 -.6 35.3 - * +* +* 40 LEU 40 E B - 185.0 - 168.5 - - - - - - 185.6 -.5 34.2 - ** ** 41 VAL 41 E B 60.5 - - - - - - - - - 176.2 - 33.4 - 42 VAL 42 E B - 179.1 - - - - - - - - 185.7 -2.8 33.5 - * * 43 VAL 43 E B - 183.8 - - - - - - - - 176.6 -3.2 34.3 - +* +* 44 ASP 44 E B - 164.9 - - - - - - - - 177.9 -2.8 35.4 - * * 45 PHE 45 E B - - -63.7 - - - - - - - 182.2 -3.2 36.1 - +* +* 46 THR 46 E B - 184.2 - - - - - - - - 171.5 -2.5 35.6 - * * 47 ALA 47 t B - - - - - - - - - - 186.4 - 33.0 - * * 48 SER 48 T A - - -57.3 - - - - - - - 179.0 - 33.0 - 49 TRP 49 T A 51.3 - - - - - - - - - 178.9 - 31.2 - 50 CYS 50 h B - 176.3 - 218.1 - - - 53.7 - 2.0 182.1 -2.4 34.0 - ** +** +** 51 GLY 51 H - - - - - - -61.0 -67.9 - - - 180.1 -.6 - - +** +* +** 52 PRO 52 H - - - - - -57.1 -57.1 -30.7 - - - 179.4 - 38.3 - * * 53 CYS 53 H A - - -53.0 - - -70.3 -35.3 53.7 - 2.0 178.8 - 35.9 - +** +** 54 ARG 54 H A - 186.5 - 170.8 - -78.4 -29.0 - - - 175.0 -1.6 32.5 - * * Residue-by-residue listing for refined_5 Page 3 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 55 PHE 55 H A - 172.1 - - - -64.5 -33.1 - - - 184.0 -2.0 35.0 - 56 ILE 56 H A - 192.1 - - - -87.0 -14.5 - - - 182.2 -1.4 33.7 - +* ** ** 57 ALA 57 H A - - - - - -60.6 -45.4 - - - 179.7 -.6 31.8 - +* +* 58 PRO 58 H - - - - - -49.0 -49.0 -35.2 - - - 179.5 - 38.5 - * * * * 59 PHE 59 H A - 178.5 - - - -72.0 -31.3 - - - 179.8 -.7 32.5 - +* +* 60 PHE 60 H A - 193.3 - - - -72.9 -33.6 - - - 174.6 -1.0 33.9 - * * 61 ALA 61 H A - - - - - -70.3 -27.7 - - - 176.6 -1.9 34.0 - * * 62 ASP 62 H A - 185.6 - - - -70.2 -45.9 - - - 175.4 -1.1 35.5 - * * 63 LEU 63 H A - - -70.0 179.6 - -54.6 -46.1 - - - 178.4 -2.5 35.5 - 64 ALA 64 H A - - - - - -60.1 -31.7 - - - 179.3 -2.0 33.8 - 65 LYS 65 H A - 184.3 - 177.1 - -79.2 -34.3 - - - 181.7 -.9 34.3 - * * * 66 LYS 66 H A - 179.8 - - - -73.6 -40.4 - - - 182.7 -2.2 34.5 - 67 LEU 67 h b - - -68.4 169.4 - - - - - - 172.8 -2.8 33.6 - * * * 68 PRO 68 S - - - - - -78.1 - - - - - 180.0 - 39.5 - * +* +* 69 ASN 69 e A - 178.9 - - - - - - - - 181.1 - 35.9 - 70 VAL 70 E B - 177.5 - - - - - - - - 179.6 - 34.0 - 71 LEU 71 E B - 181.9 - - - - - - - - 180.8 -3.1 35.3 - * * 72 PHE 72 E B - - -59.6 - - - - - - - 179.3 -.5 34.1 - ** ** 73 LEU 73 E B - - -75.7 - - - - - - - 178.8 -2.3 32.7 - 74 LYS 74 E B - 194.9 - 183.1 - - - - - - 178.5 -3.0 36.0 - * * 75 VAL 75 E B - 177.9 - - - - - - - - 177.7 -3.4 34.2 - +* +* 76 ASP 76 E B - 187.6 - - - - - - - - 185.3 -.8 33.7 - +* +* 77 THR 77 e A 59.8 - - - - - - - - - 178.4 -2.7 33.5 - 78 ASP 78 T A - 186.7 - - - - - - - - 174.3 - 33.6 - 79 GLU 79 T A - - -65.7 - - - - - - - 181.3 - 36.0 - 80 LEU 80 h b - - -64.3 178.4 - - - - - - 180.3 -3.2 34.1 - +* +* 81 LYS 81 H A - - -63.8 - - -68.6 -42.0 - - - 182.4 -1.1 34.2 - * * 82 SER 82 H A - - -57.4 - - -69.6 -38.8 - - - 179.0 - 33.3 - 83 VAL 83 H A - 178.9 - - - -67.2 -37.6 - - - 177.8 - 32.7 - 84 ALA 84 H A - - - - - -61.2 -40.7 - - - 179.5 -1.7 34.6 - 85 SER 85 H A - 182.0 - - - -75.5 -34.3 - - - 183.9 -1.7 34.2 - 86 ASP 86 H A - 185.0 - - - -69.9 -36.8 - - - 179.4 -2.4 33.9 - 87 TRP 87 h A - - -68.7 - - - - - - - 178.5 -2.4 32.0 - 88 ALA 88 T l - - - - - - - - - - 178.4 -.7 30.9 - +* +* 89 ILE 89 t B - - -54.4 - - - - - - - 181.8 -2.7 34.4 - 90 GLN 90 A - 182.4 - 181.9 - - - - - - 182.6 -.8 34.8 - +* +* 91 ALA 91 S B - - - - - - - - - - 181.4 - 33.7 - Residue-by-residue listing for refined_5 Page 4 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 92 MET 92 S B - - -59.8 169.8 - - - - - - -2.6 -.6 36.0 - +* +* 93 PRO 93 e cis - - - - - -96.7 - - - - - 176.3 - 39.8 - +** +* +** 94 THR 94 E B - - -57.8 - - - - - - - 178.0 -2.8 34.5 - * * 95 PHE 95 E B - - -63.9 - - - - - - - 181.2 -2.9 36.1 - * * 96 MET 96 E B - 186.2 - 179.1 - - - - - - 180.2 -3.4 33.6 - +* +* 97 PHE 97 E B - - -64.3 - - - - - - - 182.4 -3.5 36.4 - +* +* 98 LEU 98 E B - - -52.7 - - - - - - - 173.6 -2.3 35.3 - * * 99 LYS 99 E B - 171.8 - 177.1 - - - - - - 180.4 -3.6 32.7 - ** ** 100 GLU 100 T l - - -61.7 178.2 - - - - - - 180.4 -.6 33.6 - +* +* 101 GLY 101 T - - - - - - - - - - - 177.8 - - - 102 LYS 102 E B - - -73.2 - - - - - - - 188.5 -2.0 30.7 - * * 103 ILE 103 E B - - -54.2 174.8 - - - - - - 173.2 - 35.5 - * * 104 LEU 104 E a - - -68.4 181.6 - - - - - - 183.3 -2.6 34.6 - 105 ASP 105 E B 55.0 - - - - - - - - - 182.0 -2.4 32.1 - 106 LYS 106 E B 61.6 - - 178.8 - - - - - - 175.1 - 35.2 - 107 VAL 107 E B - 178.3 - - - - - - - - 183.3 -3.3 34.8 - +* +* 108 VAL 108 E B 61.4 - - - - - - - - - 180.8 - 32.9 - 109 GLY 109 e - - - - - - - - - - - 181.5 -2.0 - - 110 ALA 110 B - - - - - - - - - - 167.3 - 34.2 - ** ** 111 LYS 111 h B - - -66.2 191.5 - - - - - - 184.6 -.9 32.9 - +* +* 112 LYS 112 H A - - -63.7 180.7 - -52.7 -49.9 - - - 181.4 - 34.0 - * * 113 ASP 113 H A - 177.0 - - - -61.7 -44.3 - - - 181.3 - 33.8 - 114 GLU 114 H A - 182.2 - 180.3 - -64.9 -36.2 - - - 176.1 - 33.3 - 115 LEU 115 H A - 184.7 - - - -64.0 -50.5 - - - 180.4 -2.4 35.5 - 116 GLN 116 H A - - -53.8 - - -57.8 -37.9 - - - 180.5 -2.8 33.7 - * * 117 SER 117 H A - 183.4 - - - -65.5 -43.6 - - - 179.7 -2.7 33.9 - 118 THR 118 H A - - -51.8 - - -69.1 -30.7 - - - 176.8 -2.2 34.4 - 119 ILE 119 H A - - -56.3 - - -67.3 -41.9 - - - 179.8 -2.2 33.5 - 120 ALA 120 H A - - - - - -65.6 -31.2 - - - 176.1 -2.3 33.0 - 121 LYS 121 H A - - -78.6 176.8 - -68.8 -29.9 - - - 176.7 -1.6 35.0 - 122 HIS 122 H A - - -85.1 - - -91.7 -22.1 - - - 182.4 -1.1 33.2 - * ** +* * ** 123 LEU 123 h B - 192.2 - - - - - - - - 178.8 -2.0 34.8 - 124 ALA 124 - - - - - - - - - - - - - 33.9 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * +* ** +** ** +** +** ** ** +* **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_5 Page 5 ---------------------------------------- ................................................................................................................................... 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 ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 60.8 182.4 -63.4 179.8 -70.2 -66.8 -38.7 53.7 - 2.0 179.6 -2.0 34.1 +** +** Standard deviations: 5.2 5.8 9.0 8.9 21.5 8.0 9.5 .0 - .0 3.2 .9 1.6 Numbers of values: 12 45 45 29 4 46 46 2 0 2 122 81 119 0 Number of cis-peptides (labelled cis): 1 KEY TO CODES: ------------ Regions of the Ramachandran plot Secondary structure (extended Kabsch/Sander) -------------------------------- -------------------------------------------- A - Core alpha B - residue in isolated beta-bridge a - Allowed alpha E - extended strand, participates in beta-ladder ~a - Generous alpha ** Generous G - 3-helix (3/10 helix) B - Core beta H - 4-helix (alpha-helix) b - Allowed beta I - 5-helix (pi-helix) ~b - Generous beta ** Generous S - bend L - Core left-handed alpha T - hydrogen-bonded turn l - Allowed left-handed alpha ~l - Generous left-handed alpha ** Generous e - extension of beta-strand p - Allowed epsilon g - extension of 3/10 helix ~p - Generous epsilon ** Generous h - extension of alpha-helix XX - Outside major areas **** Disallowed Residue-by-residue listing for refined_5 Page 6 ---------------------------------------- M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S ..................................... Small molecule data ......................................... <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N --------------------------------------------------------------------------------------------------- Any - 1.231 - - - - - - - - - - ( .020) Pro 1.341 - - - 1.466 122.60 116.90 - - 111.80 103.00 122.00 ( .016) ( .015) ( 5.00) ( 1.50) ( 2.50) ( 1.10) ( 1.40) Except Pro 1.329 - - - - - - - - - - 123.00 ( .014) ( 1.60) Gly - - 1.516 - 1.451 120.60 116.40 120.80 - 112.50 - - ( .018) ( .016) ( 1.70) ( 2.10) ( 2.10) ( 2.90) Except Gly - - 1.525 - - - - 120.80 - - - - ( .021) ( 1.70) Ala - - - 1.521 - - - - 110.50 - 110.40 - ( .033) ( 1.50) ( 1.50) Ile,Thr,Val - - - 1.540 - - - - 109.10 - 111.50 - ( .027) ( 2.20) ( 1.70) Except Gly,Pro - - - - 1.458 121.70 116.20 - - 111.20 - - ( .019) ( 1.80) ( 2.00) ( 2.80) The rest - - - 1.530 - - - - 110.10 - 110.50 - ( .020) ( 1.90) ( 1.70) Note. The table above shows the mean values obtained from small molecule data by Engh & Huber (1991). The values shown in brackets are standard deviations ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - 1.237 1.513 1.545 1.457 - 116.43 120.42 110.42 109.33 111.39 123.13 2 GLY 2 1.312 1.232 1.505 - 1.437 121.00 115.98 120.11 - 111.16 - 123.88 * * 3 HIS 3 1.330 1.232 1.518 1.549 1.473 124.42 117.43 120.35 111.59 112.86 113.86 122.21 +* +* +* 4 HIS 4 1.314 1.228 1.503 1.538 1.445 120.42 114.24 121.15 111.52 110.90 112.61 124.50 * * * * 5 HIS 5 1.317 1.231 1.532 1.543 1.464 125.56 115.60 121.28 112.04 113.15 112.61 122.99 ** * * ** 6 HIS 6 1.311 1.236 1.494 1.543 1.457 122.96 116.19 120.43 108.38 108.89 113.90 123.38 * * +* +* 7 HIS 7 1.289 1.234 1.514 1.553 1.433 122.17 115.67 121.35 112.55 108.18 110.52 122.90 +** * * * * +** 8 HIS 8 1.308 1.236 1.503 1.541 1.436 121.13 113.79 121.46 111.90 110.99 112.12 124.68 +* * * * * +* 9 LEU 9 1.294 1.243 1.495 1.576 1.433 125.58 118.09 119.23 113.04 105.30 112.30 122.64 +** * ** * ** +* ** * +** 10 GLU 10 1.289 1.238 1.505 1.536 1.433 119.53 115.86 120.71 110.92 110.55 112.67 123.41 +** * * * +** 11 MET 11 1.308 1.241 1.512 1.531 1.440 122.17 115.49 120.12 110.21 109.67 109.89 124.37 * * Residue-by-residue listing for refined_5 Page 7 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 12 ALA 12 1.331 1.235 1.537 1.534 1.466 124.42 115.09 122.01 111.11 113.38 111.11 122.86 +* +* 13 SER 13 1.304 1.232 1.523 1.531 1.447 123.79 114.16 122.07 110.24 106.63 108.73 123.74 +* * * +* * +* 14 GLU 14 1.314 1.236 1.520 1.527 1.434 123.62 116.60 120.45 109.90 109.88 107.44 122.94 * * * +* +* 15 GLU 15 1.309 1.234 1.520 1.560 1.441 121.62 116.63 120.42 110.33 108.97 111.93 122.92 * +* +* 16 GLY 16 1.311 1.231 1.505 - 1.450 120.92 117.35 119.93 - 114.52 - 122.72 * * 17 GLN 17 1.312 1.232 1.485 1.521 1.438 120.40 114.52 121.29 109.86 111.18 112.37 124.19 * +* * * +* 18 VAL 18 1.284 1.247 1.539 1.548 1.425 123.09 117.50 120.24 111.02 109.79 109.39 122.22 *** +* * *** 19 ILE 19 1.327 1.234 1.520 1.548 1.445 120.35 116.50 120.76 109.63 109.51 111.37 122.73 20 ALA 20 1.305 1.239 1.503 1.518 1.439 121.59 116.05 120.90 110.47 109.91 111.20 123.05 +* * * +* 21 CYS 21 1.300 1.229 1.508 1.504 1.413 121.34 115.99 121.04 109.46 109.39 109.54 122.94 ** * ** ** 22 HIS 22 1.294 1.240 1.506 1.533 1.444 121.67 114.76 121.59 110.93 108.74 111.29 123.64 ** ** 23 THR 23 1.319 1.251 1.509 1.554 1.436 123.40 116.90 119.89 107.93 107.83 112.09 123.21 * * * * 24 VAL 24 1.311 1.226 1.540 1.568 1.439 120.98 115.89 121.08 112.06 109.30 112.22 122.99 * * * * 25 GLU 25 1.340 1.223 1.520 1.521 1.425 123.32 116.49 120.33 109.59 110.72 109.17 123.15 +* +* 26 THR 26 1.334 1.234 1.536 1.550 1.457 121.91 115.51 121.35 110.50 110.30 110.20 123.12 27 TRP 27 1.307 1.238 1.542 1.538 1.442 122.11 115.97 120.97 111.59 111.60 109.05 123.03 +* +* 28 ASN 28 1.318 1.231 1.530 1.545 1.461 122.69 116.22 120.71 110.02 110.82 109.57 123.04 29 GLU 29 1.323 1.234 1.542 1.527 1.462 122.64 117.31 120.27 112.10 112.49 110.21 122.41 * * 30 GLN 30 1.326 1.225 1.522 1.490 1.428 121.88 117.34 120.09 111.48 113.05 109.77 122.57 +* +* +* 31 LEU 31 1.325 1.217 1.506 1.492 1.418 121.70 115.69 120.81 110.00 110.36 109.63 123.51 +* ** ** 32 GLN 32 1.310 1.216 1.518 1.521 1.444 122.80 116.34 120.47 110.60 109.86 109.86 123.18 * * 33 LYS 33 1.324 1.225 1.532 1.540 1.448 121.64 116.64 120.77 111.52 110.15 110.39 122.55 34 ALA 34 1.323 1.224 1.530 1.520 1.446 121.15 116.05 120.88 111.03 110.99 110.51 123.06 35 ASN 35 1.307 1.248 1.502 1.526 1.462 122.96 114.05 121.70 108.00 110.00 108.47 124.22 +* * * * * +* 36 GLU 36 1.309 1.221 1.534 1.532 1.454 123.22 117.45 120.54 109.81 112.27 109.27 121.99 * * 37 SER 37 1.311 1.234 1.534 1.516 1.439 120.91 116.30 120.59 111.71 112.23 108.93 123.10 * * * 38 LYS 38 1.342 1.246 1.513 1.502 1.469 123.53 115.45 121.28 111.69 114.65 111.98 123.18 * * * * 39 THR 39 1.301 1.232 1.525 1.521 1.415 121.92 116.04 121.40 109.63 108.00 110.30 122.54 +* ** * ** 40 LEU 40 1.267 1.234 1.530 1.559 1.429 121.58 117.24 120.02 113.80 106.59 108.57 122.72 **** * * +* +* * **** 41 VAL 41 1.313 1.225 1.535 1.570 1.444 120.95 116.08 121.15 111.11 112.05 110.64 122.75 * * * Residue-by-residue listing for refined_5 Page 8 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 42 VAL 42 1.305 1.240 1.515 1.542 1.443 122.45 116.71 120.64 110.44 108.10 112.35 122.64 +* * +* 43 VAL 43 1.304 1.233 1.524 1.553 1.436 121.12 114.76 121.25 109.54 111.73 111.07 123.98 +* * +* 44 ASP 44 1.299 1.233 1.525 1.537 1.451 124.71 117.07 120.30 110.79 109.63 108.64 122.55 ** +* * ** 45 PHE 45 1.321 1.244 1.523 1.525 1.434 121.85 116.19 120.78 108.61 109.16 109.82 123.02 * * 46 THR 46 1.299 1.205 1.527 1.554 1.433 122.17 117.04 120.27 109.73 109.13 109.83 122.68 ** * * ** 47 ALA 47 1.297 1.241 1.505 1.518 1.434 122.23 116.17 120.05 111.49 106.68 112.31 123.77 ** * +* * ** 48 SER 48 1.309 1.237 1.553 1.523 1.465 124.11 117.26 120.26 111.37 114.61 109.36 122.48 * * * * * 49 TRP 49 1.325 1.226 1.538 1.549 1.456 121.67 117.12 120.52 111.92 113.20 111.96 122.36 50 CYS 50 1.311 1.228 1.530 1.535 1.457 121.36 116.22 120.34 110.86 110.26 110.20 123.43 * * 51 GLY 51 1.333 1.231 1.528 - 1.462 122.59 118.88 119.77 - 114.19 - 121.36 * * * * 52 PRO 52 1.361 1.233 1.536 1.541 1.481 122.88 115.53 121.42 110.44 112.08 103.89 123.04 * * * 53 CYS 53 1.310 1.221 1.531 1.511 1.449 122.54 116.13 121.52 109.08 109.89 109.08 122.34 * * 54 ARG 54 1.305 1.227 1.535 1.532 1.441 121.77 115.56 121.17 113.42 109.60 110.04 123.27 +* +* +* 55 PHE 55 1.325 1.237 1.536 1.543 1.470 123.81 116.69 121.08 109.72 111.77 109.42 122.21 * * 56 ILE 56 1.315 1.235 1.552 1.573 1.450 120.51 115.43 121.16 111.01 109.94 111.00 123.29 * * * 57 ALA 57 1.327 1.232 1.567 1.523 1.468 123.42 120.41 118.91 111.15 114.95 110.86 120.68 ** ** * * * ** 58 PRO 58 1.388 1.233 1.539 1.525 1.484 122.58 117.25 120.42 109.97 114.05 103.40 122.32 +** * +** 59 PHE 59 1.325 1.220 1.532 1.539 1.459 120.97 116.93 120.83 111.08 111.35 111.71 122.22 60 PHE 60 1.310 1.230 1.535 1.535 1.457 121.33 115.66 121.34 112.04 108.08 109.90 122.97 * * * * 61 ALA 61 1.329 1.236 1.539 1.524 1.460 122.15 115.59 121.49 110.69 109.68 110.36 122.92 62 ASP 62 1.325 1.235 1.503 1.521 1.470 122.80 114.60 121.35 108.97 108.73 110.31 124.05 * * 63 LEU 63 1.317 1.234 1.522 1.523 1.438 124.07 115.50 120.85 110.20 110.77 108.57 123.64 * * * * 64 ALA 64 1.320 1.230 1.529 1.518 1.454 123.06 116.20 121.13 110.64 111.46 110.19 122.64 65 LYS 65 1.319 1.232 1.523 1.527 1.449 121.83 115.96 120.98 110.93 110.62 109.59 123.04 66 LYS 66 1.316 1.232 1.517 1.539 1.450 122.00 116.46 120.73 109.91 110.91 110.43 122.81 67 LEU 67 1.308 1.216 1.516 1.516 1.419 121.44 117.01 120.88 110.99 113.19 109.81 122.08 * ** ** 68 PRO 68 1.340 1.231 1.533 1.533 1.474 122.76 114.06 121.95 109.91 109.44 102.94 123.98 +* * +* 69 ASN 69 1.327 1.229 1.519 1.534 1.453 124.49 115.54 121.30 109.54 110.25 108.96 123.15 +* +* 70 VAL 70 1.304 1.228 1.511 1.554 1.431 122.21 115.99 120.69 110.46 109.33 111.46 123.30 +* * +* 71 LEU 71 1.294 1.228 1.523 1.533 1.428 122.10 117.24 120.31 111.15 108.45 108.86 122.42 +** +* +** Residue-by-residue listing for refined_5 Page 9 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 72 PHE 72 1.312 1.242 1.502 1.521 1.450 120.84 115.30 121.32 108.74 110.83 112.07 123.37 * * * 73 LEU 73 1.293 1.230 1.494 1.533 1.439 122.94 114.93 121.27 108.98 111.47 113.81 123.80 +** * +* +** 74 LYS 74 1.293 1.240 1.497 1.497 1.411 122.87 116.38 120.69 108.77 108.09 109.99 122.89 +** * +* ** * +** 75 VAL 75 1.286 1.235 1.489 1.552 1.424 121.31 115.81 120.78 109.60 108.43 112.43 123.40 *** +* +* *** 76 ASP 76 1.296 1.237 1.508 1.513 1.421 120.64 116.10 120.58 111.34 107.29 111.28 123.29 ** +* * ** 77 THR 77 1.303 1.226 1.524 1.550 1.439 122.78 117.09 120.68 110.46 112.28 110.98 122.23 +* * +* 78 ASP 78 1.321 1.236 1.495 1.510 1.442 120.38 114.31 121.69 110.33 108.54 111.92 124.00 * * 79 GLU 79 1.301 1.231 1.525 1.512 1.413 123.00 116.11 121.06 109.62 109.88 108.78 122.84 +* ** * ** 80 LEU 80 1.312 1.237 1.524 1.512 1.403 122.44 115.39 121.29 111.46 111.73 109.23 123.29 * +** +** 81 LYS 81 1.320 1.242 1.525 1.541 1.458 122.89 116.44 120.89 109.75 111.24 110.87 122.66 82 SER 82 1.322 1.226 1.520 1.513 1.441 121.35 116.81 120.26 110.84 111.39 110.82 122.91 83 VAL 83 1.330 1.236 1.533 1.558 1.460 121.21 116.26 120.83 110.92 110.33 112.17 122.87 84 ALA 84 1.333 1.229 1.525 1.517 1.460 121.81 115.63 121.38 109.85 110.49 110.10 122.99 85 SER 85 1.311 1.234 1.545 1.544 1.440 122.07 116.37 121.01 111.25 110.78 109.50 122.60 * * 86 ASP 86 1.326 1.223 1.523 1.535 1.471 122.53 116.36 120.94 110.41 111.60 110.42 122.67 87 TRP 87 1.315 1.231 1.522 1.528 1.450 121.77 114.96 120.83 112.51 111.99 110.84 124.18 * * * 88 ALA 88 1.332 1.243 1.524 1.528 1.463 124.74 115.46 121.60 111.95 113.21 112.20 122.86 +* * +* 89 ILE 89 1.305 1.233 1.510 1.556 1.440 121.74 115.89 121.04 109.93 108.38 111.68 123.01 +* * +* 90 GLN 90 1.299 1.240 1.520 1.527 1.440 121.69 116.06 121.02 110.21 110.43 109.85 122.91 ** ** 91 ALA 91 1.308 1.229 1.506 1.515 1.443 121.15 116.03 121.10 110.76 110.29 110.77 122.86 * * 92 MET 92 1.293 1.227 1.520 1.510 1.435 121.70 118.48 119.96 108.45 109.73 109.75 121.56 +** * * * +** 93 PRO 93 1.326 1.240 1.547 1.527 1.448 124.08 117.11 120.91 110.10 111.55 102.08 121.94 * * * 94 THR 94 1.298 1.227 1.520 1.531 1.432 120.58 116.73 120.51 109.23 109.32 111.63 122.76 ** * ** 95 PHE 95 1.303 1.230 1.489 1.518 1.418 121.88 117.04 120.37 108.80 107.55 110.31 122.58 +* +* ** * ** 96 MET 96 1.282 1.227 1.503 1.518 1.418 120.16 115.06 121.30 111.61 110.32 110.28 123.63 *** * ** *** 97 PHE 97 1.287 1.243 1.507 1.512 1.400 124.04 116.54 120.79 110.29 108.54 108.07 122.65 +** *** * * *** 98 LEU 98 1.291 1.220 1.521 1.564 1.426 121.00 116.35 120.95 107.54 108.88 112.64 122.70 +** +* +* * * +** 99 LYS 99 1.289 1.238 1.491 1.527 1.432 122.35 115.15 120.58 111.02 108.72 112.82 124.20 +** +* * * +** 100 GLU 100 1.321 1.214 1.540 1.525 1.452 123.94 116.79 120.87 109.70 111.11 111.57 122.33 * * 101 GLY 101 1.314 1.230 1.518 - 1.448 120.53 116.83 120.55 - 112.67 - 122.62 * * Residue-by-residue listing for refined_5 Page 10 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 102 LYS 102 1.320 1.229 1.524 1.556 1.452 121.66 115.54 120.72 112.65 110.74 113.16 123.73 * * +* +* 103 ILE 103 1.308 1.231 1.529 1.555 1.465 124.58 115.69 121.16 108.19 113.19 110.11 123.16 +* +* +* 104 LEU 104 1.320 1.238 1.504 1.527 1.431 122.11 115.64 121.15 108.94 109.11 111.83 123.20 * * 105 ASP 105 1.311 1.220 1.494 1.520 1.444 122.10 115.60 121.20 110.49 112.48 112.60 123.17 * * * * 106 LYS 106 1.300 1.231 1.527 1.538 1.439 122.17 115.59 120.89 109.39 110.49 110.06 123.50 ** ** 107 VAL 107 1.307 1.235 1.516 1.561 1.449 124.04 116.86 120.19 109.30 107.09 111.93 122.93 +* * * +* 108 VAL 108 1.304 1.246 1.537 1.561 1.442 120.97 116.09 121.03 111.60 111.12 111.06 122.86 +* * +* 109 GLY 109 1.320 1.241 1.504 - 1.446 121.21 118.15 119.96 - 110.11 - 121.89 110 ALA 110 1.308 1.234 1.508 1.525 1.433 118.34 115.07 121.51 109.94 111.86 110.56 123.36 * * +* +* 111 LYS 111 1.303 1.242 1.488 1.518 1.407 123.64 116.70 119.49 111.01 106.73 113.16 123.80 +* +* +** * +* +* +** 112 LYS 112 1.310 1.227 1.526 1.502 1.417 122.90 116.56 120.06 111.16 112.31 109.19 123.31 * * ** ** 113 ASP 113 1.327 1.223 1.518 1.522 1.472 122.46 116.67 120.51 109.20 112.51 111.26 122.81 114 GLU 114 1.322 1.248 1.517 1.531 1.464 121.54 115.48 121.27 111.38 109.97 110.73 123.24 115 LEU 115 1.313 1.221 1.508 1.514 1.429 121.59 115.34 120.75 109.21 108.39 110.24 123.86 * +* * +* 116 GLN 116 1.331 1.241 1.522 1.548 1.478 122.33 116.20 120.60 108.26 110.83 113.06 123.20 * +* +* 117 SER 117 1.322 1.229 1.525 1.541 1.439 121.91 115.94 121.11 111.57 109.90 109.97 122.90 * * 118 THR 118 1.310 1.238 1.541 1.538 1.442 122.06 116.65 120.90 110.78 110.16 109.91 122.42 * * 119 ILE 119 1.334 1.214 1.524 1.553 1.447 120.52 116.52 120.61 108.86 109.51 113.41 122.83 * * 120 ALA 120 1.329 1.233 1.524 1.514 1.466 121.85 115.48 121.17 111.24 110.76 110.83 123.34 121 LYS 121 1.310 1.221 1.534 1.490 1.402 123.89 116.21 121.04 112.46 111.87 106.51 122.75 * +* +** * * ** +** 122 HIS 122 1.312 1.233 1.521 1.523 1.447 122.27 117.16 119.75 109.65 113.34 111.51 123.09 * * 123 LEU 123 1.331 1.245 1.530 1.521 1.422 122.80 115.07 121.25 112.57 110.84 107.34 123.66 +* * +* +* 124 ALA 124 1.309 - 1.516 1.528 1.431 123.69 - - 111.22 108.07 110.91 - * * * * * ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * ** ** *** ** ** * +* ** ** * **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_5 Page 11 ---------------------------------------- A N A L Y S I S O F M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S +------------------+ | BOND LENGTHS | +------------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Bond X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- C-N C-NH1 (except Pro) 1.329 .014 119 1.267 1.342 1.312 .013 **** * C-N (Pro) 1.341 .016 4 1.326 1.388 1.354 .024 +** C-O C-O 1.231 .020 123 1.205 1.251 1.232 .008 * * CA-C CH1E-C (except Gly) 1.525 .021 119 1.485 1.567 1.521 .015 +* ** CH2G*-C (Gly) 1.516 .018 5 1.504 1.528 1.512 .010 CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.514 1.534 1.522 .006 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.521 1.573 1.552 .012 * CH1E-CH2E (the rest) 1.530 .020 84 1.490 1.576 1.529 .016 +* ** N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.400 1.478 1.442 .017 *** * NH1-CH2G* (Gly) 1.451 .016 5 1.437 1.462 1.449 .008 N-CH1E (Pro) 1.466 .015 4 1.448 1.484 1.472 .014 * * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_5 Page 12 ---------------------------------------- +-----------------+ | BOND ANGLES | +-----------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Angle X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- CA-C-N CH1E-C-NH1 (except Gly,Pro)116.2 2.0 114 113.79 120.41 116.11 .93 * ** CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.98 118.88 117.44 1.01 * CH1E-C-N (Pro) 116.9 1.5 4 114.06 117.25 115.99 1.30 +* O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.68 124.68 123.02 .62 * * O-C-N (Pro) 122.0 1.4 4 121.94 123.98 122.82 .78 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 118.34 125.58 122.23 1.25 +* ** C-NH1-CH2G* (Gly) 120.6 1.7 5 120.53 122.59 121.25 .71 * C-N-CH1E (Pro) 122.6 5.0 4 122.58 124.08 123.07 .59 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 118.91 122.07 120.83 .53 * CH2G*-C-O (Gly) 120.8 2.1 5 119.77 120.55 120.06 .27 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 109.85 111.95 110.89 .56 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 107.93 112.06 110.09 1.02 * CH2E-CH1E-C (the rest) 110.1 1.9 84 107.54 113.80 110.54 1.29 * +* N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 105.30 114.95 110.31 1.83 ** * NH1-CH2G*-C (Gly) 112.5 2.9 5 110.11 114.52 112.53 1.70 N-CH1E-C (Pro) 111.8 2.5 4 109.44 114.05 111.78 1.64 N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.10 112.31 110.92 .65 * NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 109.39 113.41 111.24 .99 * * N-CH1E-CH2E (Pro) 103.0 1.1 4 102.08 103.89 103.08 .67 NH1-CH1E-CH2E (the rest) 110.5 1.7 80 106.51 113.90 110.50 1.59 ** +* ------------------------------------------------------------------------------------------------------------- The small molecule data used in the above analysis is from Engh & Huber (1991). The atom labelling follows that used in the X-PLOR dictionary, with some additional atoms (marked with an asterisk) as defined by Engh & Huber. Residue-by-residue listing for refined_5 Page 13 ---------------------------------------- R A M A C H A N D R A N P L O T S T A T I S T I C S Residues in most favoured regions [A,B,L] 98 86.7% Residues in additional allowed regions [a,b,l,p] 13 11.5% Residues in generously allowed regions [~a,~b,~l,~p] 1 .9% 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 3.2 6.0 3.0 -.9 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 119 1.6 3.1 1.6 -.9 Inside e. H-bond energy st dev 81 .9 .8 .2 .5 Inside f. Overall G-factor 124 .1 -.4 .3 1.5 BETTER S T E R E O C H E M I S T R Y O F S I D E - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. Chi-1 gauche minus st dev 12 5.2 18.1 6.5 -2.0 BETTER b. Chi-1 trans st dev 45 5.8 19.0 5.3 -2.5 BETTER c. Chi-1 gauche plus st dev 45 9.0 17.5 4.9 -1.7 BETTER d. Chi-1 pooled st dev 102 7.6 18.2 4.8 -2.2 BETTER e. Chi-2 trans st dev 29 8.9 20.4 5.0 -2.3 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 9.6 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .91 3 Residue-by-residue listing for refined_5 Page 14 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.27 Chi1-chi2 distribution -.08 Chi1 only -.13 Chi3 & chi4 .29 Omega .08 ------ -.05 ===== Main-chain covalent forces:- Main-chain bond lengths -.01 Main-chain bond angles .43 ------ .25 ===== OVERALL AVERAGE .05 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.