Residue-by-residue listing for refined_9 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 - - 178.7 - 180.7 - - - - - - 178.0 - 33.8 - 2 ALA 2 B - - - - - - - - - - 182.4 - 33.6 - 3 ASP 3 B - 182.3 - - - - - - - - 179.6 -1.1 34.5 - * * 4 THR 4 S ~a - - -55.3 - - - - - - - 178.9 - 35.2 - ** ** 5 GLY 5 S - - - - - - - - - - - 178.4 - - - 6 GLU 6 l - 186.1 - 176.2 - - - - - - 180.9 -1.9 31.0 - 7 VAL 7 E B - - -64.3 - - - - - - - 184.1 -3.3 32.7 - +* +* 8 GLN 8 E B 61.6 - - 186.4 - - - - - - 173.6 - 36.2 - * * 9 PHE 9 E B - 180.6 - - - - - - - - 183.6 -1.3 34.5 - * * 10 MET 10 E B - 181.4 - 179.7 - - - - - - 179.3 - 34.7 - 11 LYS 11 E B - 188.9 - 187.4 - - - - - - 172.1 -2.7 35.9 - * * 12 PRO 12 E - - - - - -69.8 - - - - - 179.0 - 38.9 - * * 13 PHE 13 e B - 182.7 - - - - - - - - 175.0 -1.8 35.0 - 14 ILE 14 t B - - -74.9 - - - - - - - 188.2 -.7 32.7 - * +* +* 15 SER 15 T A 53.3 - - - - - - - - - 180.2 -.6 32.5 - +* +* 16 GLU 16 T A - 185.6 - 184.2 - - - - - - 188.6 - 35.1 - * * 17 LYS 17 T A - 190.5 - - - - - - - - 181.1 - 33.4 - Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 18 SER 18 T A - - -56.8 - - - - - - - 179.0 -3.0 35.0 - * * 19 SER 19 T A - 183.4 - - - - - - - - 185.8 - 33.9 - 20 LYS 20 T a - - -63.0 173.9 - - - - - - 184.3 -1.0 35.6 - * * 21 SER 21 t B 51.0 - - - - - - - - - 173.1 -1.0 36.6 - * * * 22 LEU 22 E B - 193.7 - 179.4 - - - - - - 182.2 -3.0 35.9 - * * 23 GLU 23 E B 61.1 - - - - - - - - - 177.5 -.7 32.6 - +* +* 24 ILE 24 E B - - -62.6 - - - - - - - 178.4 -2.0 34.5 - 25 PRO 25 h - - - - - -55.7 - - - - - 184.4 - 38.6 - * * 26 LEU 26 H A - - -58.0 177.7 - -57.6 -43.9 - - - 181.8 - 34.5 - 27 GLY 27 H - - - - - - -77.2 -16.0 - - - 176.4 - - - ** ** 28 PHE 28 H A - 181.0 - - - -88.8 -28.7 - - - 182.6 -.8 33.5 - +* +* +* 29 ASN 29 H A - 177.9 - - - -76.1 -46.9 - - - 181.4 -2.2 34.4 - 30 GLU 30 h A 60.3 - - - - - - - - - 178.0 -2.1 29.3 - * * 31 TYR 31 T A - 175.6 - - - - - - - - 179.3 - 35.8 - 32 PHE 32 t b 65.4 - - - - - - - - - 172.0 -1.7 31.7 - * * 33 PRO 33 - - - - - -80.1 - - - - - 183.7 - 38.7 - * * * 34 ALA 34 B - - - - - - - - - - 173.0 - 35.0 - * * 35 PRO 35 - - - - - -61.1 - - - - - 184.6 - 39.3 - +* +* 36 PHE 36 B 70.7 - - - - - - - - - 175.8 - 33.4 - 37 PRO 37 - - - - - -87.2 - - - - - 176.1 - 39.3 - +* +* +* 38 ILE 38 e a - - -59.8 - - - - - - - 181.3 - 34.2 - 39 THR 39 E B - - -42.9 - - - - - - - 179.6 - 36.3 - +* +* 40 VAL 40 E B - 178.8 - - - - - - - - 179.1 -2.7 35.9 - 41 ASP 41 E B - - -67.6 - - - - - - - 177.6 -1.3 32.2 - 42 LEU 42 E B - - -56.9 178.9 - - - - - - 184.0 -3.2 35.7 - +* +* 43 LEU 43 E B - - -66.7 - - - - - - - 175.0 -3.6 33.7 - ** ** 44 ASP 44 e B - 165.1 - - - - - - - - 183.9 -2.6 34.1 - * * 45 TYR 45 S A - - -65.1 - - - - - - - 181.7 - 33.7 - 46 SER 46 S A - - -53.2 - - - - - - - 177.8 - 34.1 - 47 GLY 47 S - - - - - - - - - - - 176.5 - - - 48 ARG 48 e B - - -61.6 - - - - - - - 179.6 - 32.5 - 49 SER 49 E B 56.3 - - - - - - - - - 180.7 - 34.2 - 50 TRP 50 E B - - -56.4 - - - - - - - 178.6 -3.2 34.5 - +* +* 51 THR 51 E B - - -57.7 - - - - - - - 186.6 - 35.1 - * * 52 VAL 52 E B 63.3 - - - - - - - - - 178.6 -2.9 32.7 - * * Residue-by-residue listing for refined_9 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 ARG 53 E B - - -57.5 180.1 - - - - - - 187.4 -2.9 34.4 - * * * 54 MET 54 E B - 177.6 - 179.6 - - - - - - 175.1 -.8 35.8 - +* +* 55 LYS 55 E B - - -72.7 - - - - - - - 177.2 -2.6 33.9 - 56 LYS 56 E B - 173.9 - 165.6 - - - - - - 179.4 - 30.3 - * * 57 ARG 57 E b - 183.3 - 181.6 - - - - - - 179.0 -1.6 33.3 - 58 GLY 58 T - - - - - - - - - - - 185.3 - - - 59 GLU 59 T A - - -62.7 - - - - - - - 180.8 - 33.1 - 60 LYS 60 E B - 196.7 - - - - - - - - 180.0 -1.4 35.5 - 61 VAL 61 E B - 176.2 - - - - - - - - 175.5 -.6 34.4 - +* +* 62 PHE 62 E B - - -68.5 - - - - - - - 169.8 -1.8 34.4 - +* +* 63 LEU 63 E B - - -59.5 - - - - - - - 190.5 -2.2 33.2 - +* +* 64 THR 64 e a 55.7 - - - - - - - - - 183.1 -1.9 33.4 - 65 VAL 65 T B - 180.3 - - - - - - - - 184.0 - 34.2 - 66 GLY 66 h - - - - - - - - - - - 173.9 - - - * * 67 TRP 67 H A - 171.7 - - - -66.6 -26.5 - - - 178.2 -1.0 34.4 - * * * 68 GLU 68 H A 43.2 - - - - -69.2 -24.7 - - - 170.7 -.9 24.1 - * * +* +* +** +** 69 ASN 69 H A - - -71.1 - - -69.3 -43.5 - - - 181.8 -.8 34.3 - +* +* 70 PHE 70 H A - 174.4 - - - -63.7 -51.4 - - - 183.9 -1.4 34.1 - * * 71 VAL 71 H A 71.1 - - - - -60.7 -41.4 - - - 176.5 -3.2 33.0 - +* +* 72 LYS 72 H A - - -60.3 - - -72.5 -44.8 - - - 185.2 -1.3 31.5 - 73 ASP 73 H A - 179.5 - - - -71.3 -40.2 - - - 180.4 -3.4 33.6 - +* +* 74 ASN 74 H A - 184.9 - - - -84.8 -20.8 - - - 183.0 -3.2 35.5 - +* +* +* +* 75 ASN 75 h l - 183.9 - - - - - - - - 182.1 -.6 29.9 - +* * +* 76 LEU 76 t B 60.9 - - 175.4 - - - - - - 187.0 -.9 30.1 - * * * * 77 GLU 77 t B 55.4 - - 184.8 - - - - - - 178.0 - 36.2 - 78 ASP 78 T B 61.6 - - - - - - - - - 182.5 - 33.1 - 79 GLY 79 T - - - - - - - - - - - 177.6 -1.2 - - * * 80 LYS 80 e B - - -66.3 183.0 - - - - - - 185.2 -1.8 31.8 - 81 TYR 81 E B - - -60.2 - - - - - - - 179.3 -.5 35.3 - ** ** 82 LEU 82 E B 48.7 - - - - - - - - - 177.6 -1.7 31.0 - 83 GLN 83 E B 64.3 - - 177.8 - - - - - - 177.0 -3.0 33.6 - * * 84 PHE 84 E B - - -59.4 - - - - - - - 178.6 -2.9 35.1 - * * 85 ILE 85 E B - - -57.2 177.5 - - - - - - 178.7 -3.2 35.0 - +* +* 86 TYR 86 E B 65.7 - - - - - - - - - 180.5 -3.2 31.7 - +* +* Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 87 ASP 87 e a - 189.9 - - - - - - - - 170.9 -1.1 33.8 - +* * +* 88 ARG 88 S ~a - 195.9 - - - - - - - - 188.2 - 34.3 - ** * ** 89 ASP 89 S b - 186.4 - - - - - - - - 180.5 - 37.1 - 90 ARG 90 e A - 185.6 - 174.9 - - - - - - 180.2 - 34.7 - 91 THR 91 E B - - -55.8 - - - - - - - 180.1 - 36.5 - 92 PHE 92 E B - - -64.6 - - - - - - - 177.7 -1.9 34.9 - 93 TYR 93 E B - - -51.8 - - - - - - - 184.0 -3.2 35.7 - +* +* 94 VAL 94 E B - 184.0 - - - - - - - - 178.1 -2.1 34.0 - 95 ILE 95 E B - - -66.0 - - - - - - - 176.8 -2.5 34.3 - 96 ILE 96 E B - - -62.3 - - - - - - - 180.4 - 35.0 - 97 TYR 97 E B - - -67.6 - - - - - - - 181.9 -3.3 34.2 - +* +* 98 GLY 98 S - - - - - - - - - - - 180.4 -.6 - - +* +* 99 HIS 99 l - 187.3 - - - - - - - - 182.9 - 32.3 - 100 ASN 100 B - 177.6 - - - - - - - - 180.0 - 34.2 - 101 MET 101 B 62.7 - - 180.2 - - - - - - 180.8 -.5 34.2 - ** ** 102 CYS 102 - - 184.4 - - - - - - - - - - 34.3 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * * +* +* +* ** +* ** +** +** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 59.6 182.4 -61.4 179.3 -70.8 -71.5 -35.7 - - - 180.0 -1.9 34.2 Standard deviations: 7.2 6.7 6.4 4.8 13.0 9.2 11.7 - - - 4.1 1.0 2.1 Numbers of values: 19 35 34 21 5 12 12 0 0 0 101 60 95 0 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_9 Page 5 ---------------------------------------- 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 - 1.227 1.513 1.540 1.458 - 116.52 120.93 110.32 110.00 111.26 122.49 2 ALA 2 1.308 1.235 1.505 1.520 1.436 120.94 116.02 120.60 110.95 108.87 111.26 123.31 +* * +* 3 ASP 3 1.307 1.234 1.508 1.532 1.449 121.62 115.96 120.93 110.01 110.24 110.53 123.09 +* +* 4 THR 4 1.299 1.241 1.517 1.561 1.455 123.14 113.73 122.22 109.32 107.69 111.21 124.03 ** * * ** 5 GLY 5 1.289 1.241 1.496 - 1.420 122.92 116.10 119.66 - 109.45 - 124.17 +** * +* * * +** 6 GLU 6 1.314 1.238 1.520 1.541 1.454 123.99 114.48 122.31 113.73 110.81 111.56 123.12 * * +* +* 7 VAL 7 1.303 1.233 1.511 1.558 1.429 122.80 115.55 121.04 111.00 110.02 112.58 123.39 +* +* +* 8 GLN 8 1.289 1.239 1.519 1.524 1.418 123.09 115.18 121.14 109.75 111.22 108.22 123.66 +** ** * +** 9 PHE 9 1.296 1.217 1.512 1.539 1.438 123.40 117.57 119.71 111.24 107.04 110.45 122.72 ** * * ** 10 MET 10 1.296 1.235 1.514 1.533 1.450 121.17 116.52 120.58 110.35 110.65 109.76 122.89 ** ** 11 LYS 11 1.317 1.237 1.526 1.537 1.438 121.21 118.10 120.26 108.58 109.42 110.21 121.61 * * Residue-by-residue listing for refined_9 Page 6 ---------------------------------------- ................................................................................................................................... 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 PRO 12 1.334 1.240 1.528 1.542 1.455 122.10 117.42 120.25 110.09 109.11 104.19 122.26 * * * 13 PHE 13 1.300 1.239 1.528 1.544 1.439 120.39 116.82 120.18 110.50 109.65 109.52 122.99 ** ** 14 ILE 14 1.329 1.237 1.511 1.588 1.433 121.69 116.29 120.33 112.34 106.84 112.60 123.38 +* * * +* +* 15 SER 15 1.323 1.215 1.510 1.533 1.451 123.03 116.65 120.65 111.33 112.90 111.01 122.68 16 GLU 16 1.304 1.235 1.525 1.508 1.426 120.56 116.92 120.97 108.87 111.16 110.30 122.05 +* * +* +* 17 LYS 17 1.317 1.239 1.520 1.536 1.448 119.52 115.71 120.98 111.64 110.32 110.48 123.18 * * 18 SER 18 1.313 1.211 1.539 1.522 1.438 122.07 117.70 120.38 109.29 111.53 110.00 121.91 * * * 19 SER 19 1.319 1.229 1.525 1.539 1.452 120.54 116.78 120.68 109.84 111.27 111.24 122.55 20 LYS 20 1.316 1.234 1.511 1.519 1.457 120.69 116.51 120.44 108.82 112.68 109.28 123.04 21 SER 21 1.295 1.225 1.501 1.524 1.428 121.33 115.76 120.53 109.11 110.70 108.35 123.71 ** * +* * ** 22 LEU 22 1.289 1.249 1.515 1.549 1.429 122.34 116.44 120.22 110.41 104.67 109.79 123.31 +** +* ** +** 23 GLU 23 1.294 1.234 1.523 1.560 1.428 121.86 115.77 121.61 111.18 110.69 112.26 122.58 +** * +* * +** 24 ILE 24 1.302 1.238 1.531 1.550 1.436 121.42 117.57 120.07 110.08 109.05 110.96 122.30 +* * +* 25 PRO 25 1.346 1.236 1.533 1.526 1.472 123.17 115.64 120.95 110.66 112.18 103.12 123.40 * * 26 LEU 26 1.319 1.242 1.531 1.528 1.462 123.74 116.46 120.76 109.71 112.50 109.82 122.78 * * 27 GLY 27 1.322 1.234 1.509 - 1.455 120.97 116.23 121.05 - 112.44 - 122.70 28 PHE 28 1.304 1.208 1.524 1.540 1.436 121.20 116.12 121.03 111.44 109.76 110.86 122.83 +* * * +* 29 ASN 29 1.313 1.230 1.531 1.517 1.457 121.92 117.67 120.38 109.35 113.00 110.13 121.94 * * 30 GLU 30 1.334 1.240 1.525 1.556 1.471 120.39 113.78 122.06 114.34 111.32 112.98 124.16 * * ** * ** 31 TYR 31 1.303 1.237 1.540 1.534 1.429 125.20 117.46 120.35 111.67 110.61 106.93 122.18 +* +* +* ** ** 32 PHE 32 1.335 1.235 1.546 1.565 1.453 120.16 117.73 121.31 111.48 112.65 112.16 120.90 +* * +* 33 PRO 33 1.336 1.247 1.510 1.523 1.440 121.92 115.82 121.05 109.52 109.40 104.95 123.13 +* +* +* 34 ALA 34 1.278 1.241 1.509 1.531 1.446 121.68 118.45 119.21 110.22 109.64 109.79 122.32 +*** * +*** 35 PRO 35 1.347 1.250 1.518 1.533 1.461 121.89 117.43 119.75 109.76 108.21 103.91 122.81 * * 36 PHE 36 1.314 1.246 1.534 1.537 1.403 121.03 117.11 121.11 111.95 110.85 110.19 121.68 * +** +** 37 PRO 37 1.322 1.236 1.517 1.527 1.435 122.11 116.71 120.76 110.39 110.22 103.05 122.50 * ** ** 38 ILE 38 1.292 1.232 1.508 1.559 1.438 120.63 115.34 121.62 110.10 108.17 111.86 123.01 +** * * +** 39 THR 39 1.303 1.239 1.529 1.523 1.419 121.86 115.15 120.50 108.88 108.88 109.29 124.34 +* ** * ** 40 VAL 40 1.303 1.230 1.536 1.584 1.458 126.07 118.76 119.45 108.82 106.03 111.21 121.78 +* +* ** * +* ** Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 41 ASP 41 1.312 1.239 1.505 1.541 1.458 120.18 115.14 121.34 110.14 111.88 113.05 123.52 * * * 42 LEU 42 1.303 1.232 1.509 1.533 1.436 123.02 116.51 120.56 109.56 107.20 110.21 122.90 +* * * +* 43 LEU 43 1.294 1.238 1.508 1.554 1.433 121.61 114.47 121.69 109.63 112.01 111.76 123.83 +** * * +** 44 ASP 44 1.294 1.242 1.514 1.524 1.434 123.90 115.98 120.51 111.07 109.16 110.36 123.51 +** * * +** 45 TYR 45 1.313 1.229 1.522 1.533 1.458 122.63 117.27 120.10 109.58 112.55 111.28 122.63 * * 46 SER 46 1.320 1.232 1.530 1.521 1.449 120.99 116.42 120.90 110.70 110.31 110.19 122.67 47 GLY 47 1.321 1.231 1.512 - 1.444 119.82 117.55 120.49 - 113.76 - 121.90 48 ARG 48 1.315 1.237 1.529 1.532 1.455 120.37 116.66 120.57 111.28 110.87 111.78 122.76 * * 49 SER 49 1.311 1.240 1.522 1.529 1.443 121.89 116.56 120.72 110.95 110.16 110.03 122.71 * * 50 TRP 50 1.304 1.227 1.515 1.537 1.436 121.45 115.99 121.04 110.32 109.98 110.48 122.96 +* * +* 51 THR 51 1.293 1.225 1.523 1.527 1.433 122.35 116.18 120.99 110.69 109.03 109.29 122.83 +** * * +** 52 VAL 52 1.297 1.226 1.529 1.564 1.435 121.82 115.20 121.58 111.82 111.86 111.04 123.15 ** * * ** 53 ARG 53 1.300 1.237 1.518 1.527 1.428 123.51 115.87 120.86 111.91 108.51 109.34 123.26 ** +* * ** 54 MET 54 1.305 1.225 1.514 1.538 1.453 122.66 116.65 120.62 110.23 111.15 108.23 122.70 +* * +* 55 LYS 55 1.318 1.232 1.505 1.535 1.438 121.75 115.52 120.89 108.96 110.05 112.56 123.58 * * * 56 LYS 56 1.303 1.238 1.479 1.526 1.442 122.69 113.81 121.89 112.60 111.58 113.35 124.30 +* ** * * +* ** 57 ARG 57 1.258 1.244 1.513 1.531 1.429 122.59 115.89 120.99 110.34 109.91 112.04 123.09 *5.0* +* *5.0* 58 GLY 58 1.298 1.249 1.508 - 1.421 120.67 115.47 121.12 - 112.24 - 123.33 ** +* ** 59 GLU 59 1.307 1.226 1.525 1.549 1.436 122.15 117.64 120.03 110.24 111.86 111.92 122.23 +* * +* 60 LYS 60 1.319 1.237 1.543 1.535 1.446 120.09 116.96 120.41 110.38 109.15 108.91 122.62 61 VAL 61 1.334 1.246 1.523 1.561 1.472 122.42 116.12 120.54 108.85 111.30 111.61 123.34 62 PHE 62 1.317 1.235 1.510 1.536 1.446 122.59 116.11 120.79 108.11 110.81 112.47 123.06 * * * 63 LEU 63 1.304 1.219 1.516 1.555 1.456 120.99 117.16 120.21 110.28 105.80 113.65 122.61 +* * +* +* +* 64 THR 64 1.299 1.238 1.549 1.550 1.445 121.03 115.31 121.56 110.81 114.34 109.88 123.12 ** * * ** 65 VAL 65 1.305 1.217 1.511 1.551 1.459 123.74 116.51 120.29 110.47 110.11 110.68 123.20 +* * +* 66 GLY 66 1.313 1.233 1.477 - 1.429 121.45 115.08 121.33 - 110.40 - 123.58 * ** * ** 67 TRP 67 1.320 1.235 1.511 1.536 1.437 121.72 114.63 122.01 110.66 107.62 110.89 123.30 * * * 68 GLU 68 1.309 1.223 1.538 1.558 1.421 120.87 116.25 121.25 117.74 112.85 115.10 122.50 * * +* **** +** **** 69 ASN 69 1.322 1.192 1.501 1.541 1.465 121.75 115.82 120.81 107.92 108.88 113.24 123.35 +* * * +* +* Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 70 PHE 70 1.313 1.229 1.500 1.545 1.454 123.48 116.12 120.33 109.85 111.19 111.07 123.54 * * * 71 VAL 71 1.321 1.220 1.511 1.561 1.444 121.46 115.28 121.38 111.26 110.06 111.84 123.35 72 LYS 72 1.301 1.232 1.540 1.529 1.449 121.64 117.30 120.27 111.50 112.70 112.12 122.42 ** ** 73 ASP 73 1.337 1.232 1.505 1.534 1.489 121.07 116.25 120.76 109.32 112.61 111.54 122.97 +* +* 74 ASN 74 1.297 1.236 1.509 1.539 1.445 120.93 113.89 121.12 110.48 108.04 109.24 124.88 ** * * * ** 75 ASN 75 1.339 1.240 1.511 1.541 1.462 125.40 115.37 121.67 112.98 111.72 113.28 122.86 ** +* +* ** 76 LEU 76 1.292 1.230 1.500 1.562 1.424 120.91 115.91 120.79 113.09 110.94 113.71 123.30 +** * +* +* +* +* +** 77 GLU 77 1.294 1.245 1.490 1.515 1.436 122.30 114.97 120.65 108.96 110.59 109.04 124.37 ** +* * ** 78 ASP 78 1.304 1.242 1.501 1.535 1.450 121.97 115.37 121.10 110.56 109.65 112.25 123.48 +* * * +* 79 GLY 79 1.296 1.222 1.501 - 1.430 120.78 116.35 120.73 - 110.76 - 122.92 ** * ** 80 LYS 80 1.324 1.250 1.525 1.547 1.451 121.12 116.60 120.63 112.28 110.40 112.09 122.77 * * 81 TYR 81 1.315 1.234 1.495 1.536 1.439 121.45 116.38 120.42 108.92 109.47 110.91 123.19 * * * 82 LEU 82 1.297 1.244 1.520 1.555 1.430 121.50 115.77 120.86 113.43 112.25 111.38 123.34 ** * * +* ** 83 GLN 83 1.304 1.245 1.510 1.545 1.433 122.10 115.73 120.67 109.94 109.42 112.35 123.58 +* * * +* 84 PHE 84 1.295 1.229 1.496 1.531 1.429 122.40 116.30 120.62 109.20 107.98 111.29 123.05 ** * +* * ** 85 ILE 85 1.283 1.223 1.506 1.556 1.427 121.34 117.37 120.22 109.65 107.82 111.34 122.38 *** +* * *** 86 TYR 86 1.296 1.226 1.494 1.547 1.439 119.54 116.22 120.28 111.95 110.14 112.87 123.47 ** * * * ** 87 ASP 87 1.319 1.226 1.530 1.526 1.458 121.41 115.44 121.03 110.95 109.42 110.65 123.53 88 ARG 88 1.301 1.222 1.511 1.547 1.457 124.30 112.98 122.99 110.57 104.59 112.01 123.90 +* * +* * ** ** 89 ASP 89 1.307 1.238 1.531 1.560 1.411 124.47 117.10 120.14 111.82 106.30 106.32 122.74 +* * ** +* +* ** ** 90 ARG 90 1.284 1.224 1.536 1.539 1.445 123.21 114.21 122.68 112.29 107.86 108.64 123.06 *** * * * * *** 91 THR 91 1.307 1.246 1.532 1.546 1.422 123.11 116.14 120.55 109.44 108.61 108.80 123.29 +* +* +* +* 92 PHE 92 1.317 1.227 1.510 1.542 1.450 122.22 116.32 120.43 109.20 109.87 110.96 123.24 93 TYR 93 1.299 1.238 1.524 1.534 1.443 122.67 117.55 120.02 109.46 107.21 110.11 122.42 ** * ** 94 VAL 94 1.310 1.235 1.536 1.558 1.461 120.80 116.23 120.79 109.31 111.53 111.61 122.97 * * 95 ILE 95 1.324 1.230 1.529 1.567 1.462 122.52 116.27 120.49 109.04 110.42 111.97 123.23 * * 96 ILE 96 1.316 1.240 1.522 1.593 1.452 122.92 117.08 120.28 109.04 107.26 112.22 122.64 +* * +* 97 TYR 97 1.311 1.222 1.502 1.527 1.441 121.10 115.55 121.03 109.52 109.34 111.69 123.38 * * * 98 GLY 98 1.302 1.230 1.504 - 1.434 121.19 115.03 120.71 - 110.47 - 124.25 +* * +* Residue-by-residue listing for refined_9 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 ----------------------------------------------------------------------------------------------------------------------------------- 99 HIS 99 1.343 1.226 1.532 1.561 1.468 124.43 115.62 121.37 112.42 110.22 111.25 122.92 +* +* * +* 100 ASN 100 1.311 1.233 1.512 1.545 1.453 121.66 115.89 120.39 110.37 110.68 110.52 123.72 * * 101 MET 101 1.315 1.235 1.530 1.551 1.452 123.03 116.96 120.44 110.45 109.10 110.92 122.59 * * * 102 CYS 102 1.303 - 1.522 1.538 1.438 121.58 - - 111.31 108.76 110.11 - +* * +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *5.0* +* ** +* +** ** +* * **** ** +** * *5.0* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_9 Page 10 ---------------------------------------- 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 96 1.258 1.343 1.307 .014 *5.0* +* C-N (Pro) 1.341 .016 5 1.322 1.347 1.337 .009 * C-O C-O 1.231 .020 101 1.192 1.250 1.233 .009 +* CA-C CH1E-C (except Gly) 1.525 .021 95 1.479 1.549 1.518 .013 ** * CH2G*-C (Gly) 1.516 .018 7 1.477 1.512 1.501 .011 ** CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.520 1.531 1.526 .006 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.523 1.593 1.559 .017 +* CH1E-CH2E (the rest) 1.530 .020 75 1.508 1.565 1.538 .012 * +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.403 1.489 1.444 .014 +** +* NH1-CH2G* (Gly) 1.451 .016 7 1.420 1.455 1.433 .012 +* * N-CH1E (Pro) 1.466 .015 5 1.435 1.472 1.452 .014 ** ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_9 Page 11 ---------------------------------------- +-----------------+ | 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 89 112.98 118.76 116.15 1.07 +* * CH2G*-C-NH1 (Gly) 116.4 2.1 7 115.03 117.55 115.97 .81 CH1E-C-N (Pro) 116.9 1.5 5 115.64 117.43 116.60 .76 O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 120.90 124.88 123.03 .66 * * O-C-N (Pro) 122.0 1.4 5 122.26 123.40 122.82 .41 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 119.52 126.07 122.02 1.28 * ** C-NH1-CH2G* (Gly) 120.6 1.7 7 119.82 122.92 121.12 .88 * C-N-CH1E (Pro) 122.6 5.0 5 121.89 123.17 122.24 .47 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 119.21 122.99 120.80 .64 * CH2G*-C-O (Gly) 120.8 2.1 7 119.66 121.33 120.73 .51 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 110.22 110.95 110.59 .36 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 108.82 112.34 110.05 1.05 * CH2E-CH1E-C (the rest) 110.1 1.9 75 107.92 117.74 110.65 1.53 * **** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 104.59 114.34 109.95 1.90 ** * NH1-CH2G*-C (Gly) 112.5 2.9 7 109.45 113.76 111.36 1.39 * N-CH1E-C (Pro) 111.8 2.5 5 108.21 112.18 109.82 1.34 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 109.79 111.26 110.53 .74 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 108.80 112.60 111.11 1.10 +* N-CH1E-CH2E (Pro) 103.0 1.1 5 103.05 104.95 103.84 .71 +* NH1-CH1E-CH2E (the rest) 110.5 1.7 70 106.32 115.10 110.92 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_9 Page 12 ---------------------------------------- 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] 76 86.4% Residues in additional allowed regions [a,b,l,p] 10 11.4% Residues in generously allowed regions [~a,~b,~l,~p] 2 2.3% Residues in disallowed regions [XX] 0 .0% ---- ------ Number of non-glycine and non-proline residues 88 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 7 Number of proline residues 5 ---- Total number of residues 102 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 88 86.4 83.8 10.0 .3 Inside b. Omega angle st dev 101 4.1 6.0 3.0 -.6 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 95 2.1 3.1 1.6 -.6 Inside e. H-bond energy st dev 60 1.0 .8 .2 .8 Inside f. Overall G-factor 102 -.1 -.4 .3 .9 Inside 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 19 7.2 18.1 6.5 -1.7 BETTER b. Chi-1 trans st dev 35 6.7 19.0 5.3 -2.3 BETTER c. Chi-1 gauche plus st dev 34 6.4 17.5 4.9 -2.3 BETTER d. Chi-1 pooled st dev 88 7.8 18.2 4.8 -2.1 BETTER e. Chi-2 trans st dev 21 4.8 20.4 5.0 -3.1 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% 86.4 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.4 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .98 3 Residue-by-residue listing for refined_9 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.56 Chi1-chi2 distribution -.37 Chi1 only -.32 Chi3 & chi4 .14 Omega -.17 ------ -.30 ===== Main-chain covalent forces:- Main-chain bond lengths -.10 Main-chain bond angles .38 ------ .18 ===== OVERALL AVERAGE -.13 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.