Residue-by-residue listing for refined_12 Page 1 ---------------------------------------- This listing highlights the residues in the structure which may need investigation. The ideal values and standard deviations against which the structure has been compared are shown in the following table: <------------------------------- I D E A L V A L U E S -------------------------------> Chi-1 dihedral Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality g(-) trans g(+) Chi-2 phi helix psi rt-hand lf-hand bond dihedral en. C-alpha ------------------------------------------------------------------------------------------ Ideal value 64.1 183.6 -66.7 177.4 -65.4 -65.3 -39.4 96.8 -85.8 2.0 180.0 -2.0 33.9 Standard deviation 15.7 16.8 15.0 18.5 11.2 11.9 11.3 14.8 10.7 .1 5.8 .8 3.5 ------------------------------------------------------------------------------------------ In the listing below, properties that deviate from these values are highlighted by asterisks and plus-signs. Each asterisk represents one standard deviation, and each plus-sign represents half a standard deviation. So, a highlight such as +***, indicates that the value of the parameter is between 3.5 and 4.0 standard deviations from the ideal value shown above. Where the deviation is greater than 4.5 standard deviations its numerical value is shown; for example, *5.5*. The final column gives the maximum deviation in each row, while the maximum column deviations are shown at the end of the listing. Also at the end are the keys to the codes used for the secondary structure and Ramachandran plot assignments. Full print-out. ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - 54.4 - - - - - - - - - 178.6 - 31.1 - 2 ALA 2 b - - - - - - - - - - 176.0 - 35.8 - 3 ASP 3 b - 183.3 - - - - - - - - 187.4 - 33.8 - * * 4 THR 4 A - - -52.6 - - - - - - - 183.7 -.9 35.0 - +* +* 5 GLY 5 - - - - - - - - - - - 180.4 - - - 6 GLU 6 l - 184.0 - 174.7 - - - - - - 180.4 - 30.4 - * * 7 VAL 7 E B - - -63.3 - - - - - - - 181.8 -3.3 33.1 - +* +* 8 GLN 8 E B 54.5 - - 184.4 - - - - - - 180.5 - 34.6 - 9 PHE 9 E B - 182.1 - - - - - - - - 179.4 -1.9 35.7 - 10 MET 10 E B 65.3 - - 178.7 - - - - - - 177.1 - 33.4 - 11 LYS 11 E B 63.2 - - 178.4 - - - - - - 174.2 -1.3 34.6 - * * 12 PRO 12 E - - - - - -67.7 - - - - - 177.3 - 38.7 - * * 13 PHE 13 e B - 179.2 - - - - - - - - 180.6 -1.2 36.5 - * * 14 ILE 14 t B - - -59.5 - - - - - - - 185.1 -.6 33.2 - +* +* 15 SER 15 T A 47.0 - - - - - - - - - 177.8 -.7 32.9 - * +* +* 16 GLU 16 T A - 192.5 - - - - - - - - 183.5 - 34.5 - 17 LYS 17 T a - - -63.9 176.4 - - - - - - 186.3 -1.0 35.4 - * * * Residue-by-residue listing for refined_12 Page 2 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 18 SER 18 T A - - -48.5 - - - - - - - 175.7 -2.7 34.4 - * * 19 SER 19 T A - 185.4 - - - - - - - - 181.2 - 33.7 - 20 LYS 20 T a - - -67.7 179.6 - - - - - - 182.6 -2.2 33.4 - 21 SER 21 t B - - -58.9 - - - - - - - 180.0 -2.6 35.7 - 22 LEU 22 E B - 193.0 - - - - - - - - 185.1 -2.2 32.6 - 23 GLU 23 E B 65.6 - - - - - - - - - 179.1 - 33.6 - 24 ILE 24 e B - - -58.5 - - - - - - - 172.6 -.8 35.6 - * +* +* 25 PRO 25 h - - - - - -65.5 - - - - - 184.5 - 38.8 - * * 26 LEU 26 H A - - -69.4 - - -63.2 -23.0 - - - 178.9 - 30.1 - * * * 27 GLY 27 H - - - - - - -60.7 -36.4 - - - 177.9 - - - 28 PHE 28 H A - 184.7 - - - -83.9 -32.9 - - - 179.0 -1.3 34.7 - +* * +* 29 ASN 29 H A - 170.5 - - - -60.6 -47.8 - - - 184.4 -1.7 37.3 - 30 GLU 30 h A - - -59.5 182.3 - - - - - - 180.0 -3.1 33.5 - * * 31 TYR 31 T A - 175.9 - - - - - - - - 180.0 -.5 34.0 - ** ** 32 PHE 32 t b 62.8 - - - - - - - - - 171.5 -1.4 31.1 - * * 33 PRO 33 - - - - - -83.6 - - - - - 181.9 - 38.7 - +* * +* 34 ALA 34 B - - - - - - - - - - 166.8 - 35.2 - ** ** 35 PRO 35 S - - - - - -55.4 - - - - - 186.9 - 39.7 - * +* +* 36 PHE 36 B 64.0 - - - - - - - - - 177.5 - 31.9 - 37 PRO 37 - - - - - -70.6 - - - - - 177.9 - 39.0 - * * 38 ILE 38 S A - - -58.4 - - - - - - - 179.4 - 33.7 - 39 THR 39 B - - -45.1 - - - - - - - 181.2 - 35.3 - * * 40 VAL 40 E B - 172.1 - - - - - - - - 178.4 -3.5 36.0 - +* +* 41 ASP 41 E B - - -61.7 - - - - - - - 178.4 -1.0 32.5 - * * 42 LEU 42 E B - - -54.0 178.1 - - - - - - 181.5 -2.6 36.8 - 43 LEU 43 E B - - -69.5 - - - - - - - 177.6 -1.9 32.1 - 44 ASP 44 e B - 166.1 - - - - - - - - 186.2 -1.8 35.1 - * * * 45 TYR 45 S A - - -46.8 - - - - - - - 182.6 - 35.5 - * * 46 SER 46 S a - - -57.4 - - - - - - - 182.7 - 32.9 - 47 GLY 47 S - - - - - - - - - - - 179.6 - - - 48 ARG 48 e B - - -64.9 - - - - - - - 174.6 - 34.0 - 49 SER 49 E B - - -56.0 - - - - - - - 180.6 - 35.2 - 50 TRP 50 E B - - -59.5 - - - - - - - 181.0 -2.8 32.2 - * * 51 THR 51 E B - - -58.2 - - - - - - - 182.4 -.6 35.1 - +* +* 52 VAL 52 E B 59.5 - - - - - - - - - 175.4 -3.2 34.8 - +* +* 53 ARG 53 e B - - -64.4 180.9 - - - - - - 174.6 -.8 34.2 - +* +* Residue-by-residue listing for refined_12 Page 3 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 54 MET 54 E B - 183.6 - 184.2 - - - - - - 183.5 -.7 34.6 - +* +* 55 LYS 55 E B - 190.5 - - - - - - - - 170.9 -1.6 35.1 - +* +* 56 LYS 56 E B - - -59.3 - - - - - - - 185.1 - 36.8 - 57 ARG 57 E B - 186.3 - 179.2 - - - - - - 182.7 -3.3 34.3 - +* +* 58 GLY 58 T - - - - - - - - - - - 181.9 -.7 - - +* +* 59 GLU 59 T A - - -55.5 177.1 - - - - - - 186.2 -.7 35.9 - * +* +* 60 LYS 60 E B 58.2 - - 188.1 - - - - - - 177.4 -2.1 34.1 - 61 VAL 61 E B - - -69.3 - - - - - - - 177.0 - 32.1 - 62 PHE 62 E B - 189.9 - - - - - - - - 175.3 -1.3 35.7 - 63 LEU 63 E B - - -65.8 - - - - - - - 180.7 -3.0 32.6 - * * 64 THR 64 e b 51.9 - - - - - - - - - 184.3 -1.3 34.1 - 65 VAL 65 T B 61.3 - - - - - - - - - 185.1 - 33.2 - 66 GLY 66 h - - - - - - - - - - - 177.1 - - - 67 TRP 67 H A - 170.4 - - - -59.6 -24.0 - - - 183.5 -1.4 35.0 - * * 68 GLU 68 H A - 186.8 - 179.4 - -63.9 -26.1 - - - 177.0 -.6 33.6 - * +* +* 69 ASN 69 H A - - -65.3 - - -64.5 -37.3 - - - 182.6 -1.8 34.5 - 70 PHE 70 H A - 176.5 - - - -73.2 -50.1 - - - 183.9 -.9 34.9 - * * 71 VAL 71 H A 67.8 - - - - -62.3 -45.1 - - - 178.6 -2.0 33.2 - 72 LYS 72 H A - - -64.3 187.3 - -72.0 -41.5 - - - 184.5 -2.4 30.7 - 73 ASP 73 H A - 178.5 - - - -62.9 -39.8 - - - 177.9 -2.3 31.7 - 74 ASN 74 H A - - -72.4 - - -90.5 -13.9 - - - 183.7 -2.1 32.4 - ** ** ** 75 ASN 75 h l - 183.3 - - - - - - - - 183.1 -.9 31.8 - +* +* 76 LEU 76 t B 48.0 - - - - - - - - - 183.2 -1.6 29.6 - * * * 77 GLU 77 t B 59.0 - - 184.2 - - - - - - 182.4 - 32.7 - 78 ASP 78 T B 67.9 - - - - - - - - - 181.6 - 34.1 - 79 GLY 79 T - - - - - - - - - - - 179.2 -.5 - - ** ** 80 LYS 80 e B - - -58.3 178.7 - - - - - - 184.8 -1.1 34.3 - * * 81 TYR 81 E B - - -65.5 - - - - - - - 179.0 -.9 33.7 - +* +* 82 LEU 82 E B 43.8 - - - - - - - - - 175.6 -1.0 30.9 - * * * 83 GLN 83 E B - - -58.9 189.0 - - - - - - 175.2 -2.1 35.3 - 84 PHE 84 E B - - -64.0 - - - - - - - 176.4 -3.4 34.7 - +* +* 85 ILE 85 E B - - -67.4 - - - - - - - 183.1 -3.0 33.0 - * * 86 TYR 86 E B - 177.3 - - - - - - - - 173.9 -3.3 34.4 - * +* +* 87 ASP 87 e B - 181.6 - - - - - - - - 182.3 -.7 34.1 - +* +* 88 ARG 88 S b - - -62.2 - - - - - - - 181.0 - 31.1 - 89 ASP 89 S b - 194.6 - - - - - - - - 179.5 -1.6 36.2 - 90 ARG 90 e a - - -62.5 179.2 - - - - - - 183.3 - 35.2 - Residue-by-residue listing for refined_12 Page 4 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 91 THR 91 E B - 191.5 - - - - - - - - 179.3 - 33.3 - 92 PHE 92 E B - - -66.5 - - - - - - - 172.8 -2.3 34.9 - * * 93 TYR 93 E B - 176.3 - - - - - - - - 186.1 -2.1 34.5 - * * 94 VAL 94 E B - 181.4 - - - - - - - - 174.3 -1.0 34.1 - * * 95 ILE 95 E B - - -62.6 178.2 - - - - - - 182.4 -2.0 33.9 - 96 ILE 96 E B - - -55.9 177.1 - - - - - - 172.9 -.6 35.5 - * +* +* 97 TYR 97 E B - - -67.5 - - - - - - - 180.8 -2.9 33.9 - * * 98 GLY 98 S - - - - - - - - - - - 178.2 -.7 - - +* +* 99 HIS 99 S A - 181.8 - - - - - - - - 182.1 - 34.5 - 100 ASN 100 ~l - - -62.3 - - - - - - - 181.7 - 30.9 - ** ** 101 MET 101 B 66.2 - - 178.0 - - - - - - 176.4 - 35.5 - 102 CYS 102 - - 184.2 - - - - - - - - - - 34.4 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: ** * * * +* ** ** ** ** +* ** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 58.9 182.2 -61.1 180.6 -68.6 -68.1 -34.8 - - - 180.0 -1.7 34.2 Standard deviations: 7.5 7.2 6.1 4.0 10.2 10.0 11.1 - - - 3.9 .9 1.9 Numbers of values: 18 29 41 22 5 12 12 0 0 0 101 63 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_12 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 - 1.234 1.508 1.556 1.458 - 114.67 121.89 111.76 111.56 113.15 123.42 * +* +* 2 ALA 2 1.297 1.243 1.507 1.522 1.432 123.70 117.46 119.54 110.15 107.22 109.25 122.99 ** * * * ** 3 ASP 3 1.316 1.232 1.524 1.530 1.453 120.89 115.67 121.01 111.62 107.78 110.55 123.24 * * 4 THR 4 1.312 1.246 1.534 1.551 1.450 122.70 116.36 121.09 109.96 112.09 109.44 122.53 * * * 5 GLY 5 1.298 1.235 1.496 - 1.425 119.72 114.56 120.84 - 113.28 - 124.59 ** * +* ** 6 GLU 6 1.314 1.240 1.525 1.535 1.446 125.21 114.83 122.12 113.69 112.09 111.82 122.98 * +* +* +* 7 VAL 7 1.296 1.228 1.504 1.557 1.429 122.58 116.32 120.61 110.77 109.40 112.40 123.05 ** * +* ** 8 GLN 8 1.291 1.238 1.513 1.525 1.419 121.51 116.06 121.15 111.55 110.38 108.86 122.79 +** ** +** 9 PHE 9 1.290 1.220 1.501 1.544 1.435 121.90 117.45 119.97 110.57 108.00 109.09 122.58 +** * * * +** 10 MET 10 1.299 1.237 1.493 1.529 1.442 120.27 115.84 120.57 110.21 110.40 111.95 123.59 ** * ** 11 LYS 11 1.300 1.241 1.516 1.542 1.429 122.24 118.24 119.65 110.01 108.39 111.13 122.08 ** +* * * ** Residue-by-residue listing for refined_12 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 1.336 1.251 1.528 1.538 1.448 121.86 115.61 121.14 109.93 110.62 104.41 123.23 * * * * 13 PHE 13 1.293 1.226 1.520 1.544 1.437 122.73 118.79 119.43 110.22 107.35 108.22 121.78 +** * * * * +** 14 ILE 14 1.319 1.210 1.507 1.553 1.433 119.04 116.32 120.54 111.25 109.10 111.90 123.13 * * * * 15 SER 15 1.313 1.226 1.538 1.529 1.458 123.62 116.86 120.65 112.27 113.83 109.04 122.48 * * * * 16 GLU 16 1.314 1.223 1.542 1.552 1.437 121.34 117.46 120.62 112.23 108.58 108.96 121.78 * * * * * 17 LYS 17 1.336 1.237 1.481 1.517 1.466 119.25 115.32 120.58 107.77 111.38 111.06 123.85 ** * * ** 18 SER 18 1.314 1.212 1.535 1.525 1.434 122.98 116.79 120.91 110.88 111.31 109.39 122.29 * * * 19 SER 19 1.313 1.231 1.538 1.537 1.428 121.04 117.36 120.33 111.11 109.64 110.84 122.31 * +* +* 20 LYS 20 1.351 1.229 1.528 1.532 1.475 119.92 117.08 120.59 109.54 113.77 111.07 122.32 +* +* 21 SER 21 1.299 1.213 1.532 1.522 1.446 122.66 119.17 119.34 110.57 108.42 108.39 121.47 ** * * ** 22 LEU 22 1.307 1.243 1.521 1.560 1.449 119.15 115.98 120.75 113.77 108.36 110.37 123.26 +* +* * +* * +* 23 GLU 23 1.311 1.233 1.539 1.555 1.435 122.48 116.49 121.22 110.97 111.31 110.73 122.28 * * * * 24 ILE 24 1.312 1.235 1.531 1.559 1.449 121.43 118.21 120.11 108.09 109.43 111.24 121.61 * * * 25 PRO 25 1.341 1.250 1.536 1.536 1.465 122.34 116.69 120.81 110.44 110.08 103.54 122.49 26 LEU 26 1.319 1.223 1.526 1.546 1.456 121.81 117.29 119.95 111.38 113.76 113.76 122.73 +* +* 27 GLY 27 1.323 1.237 1.525 - 1.457 121.02 116.18 120.97 - 112.40 - 122.84 28 PHE 28 1.314 1.216 1.531 1.545 1.456 122.09 115.37 121.32 111.63 108.74 109.12 123.26 * * 29 ASN 29 1.321 1.239 1.524 1.518 1.478 123.50 115.96 120.82 107.37 112.39 108.10 123.20 * * * * * 30 GLU 30 1.322 1.233 1.513 1.528 1.457 122.18 115.31 121.01 110.79 111.45 110.69 123.67 31 TYR 31 1.308 1.242 1.539 1.539 1.437 123.19 117.22 120.74 111.97 111.13 109.07 122.04 * * * 32 PHE 32 1.327 1.227 1.539 1.568 1.448 119.93 118.15 121.14 111.83 113.09 112.53 120.59 +* * +* +* 33 PRO 33 1.334 1.244 1.509 1.520 1.439 122.09 115.11 121.20 109.75 109.74 104.70 123.65 +* * +* * +* 34 ALA 34 1.280 1.243 1.506 1.534 1.436 122.91 119.01 118.88 110.27 108.27 109.89 122.05 +*** * * * * +*** 35 PRO 35 1.346 1.246 1.526 1.530 1.461 121.41 118.32 119.24 109.67 106.88 103.27 122.44 +* +* 36 PHE 36 1.314 1.241 1.526 1.535 1.413 120.24 116.85 120.81 112.28 112.32 111.22 122.29 * ** * ** 37 PRO 37 1.352 1.256 1.512 1.540 1.447 122.33 116.41 120.85 109.55 110.60 104.42 122.74 * * * * 38 ILE 38 1.293 1.239 1.517 1.551 1.429 120.53 115.63 120.86 110.75 108.12 111.90 123.42 +** * * +** 39 THR 39 1.311 1.239 1.551 1.533 1.432 121.84 116.06 120.73 109.36 109.16 110.22 123.21 * * * * 40 VAL 40 1.309 1.217 1.528 1.571 1.449 125.00 118.29 120.05 109.73 107.84 109.68 121.65 * * +* * * * +* Residue-by-residue listing for refined_12 Page 7 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 41 ASP 41 1.300 1.245 1.498 1.533 1.450 119.59 114.93 121.18 110.13 111.01 113.03 123.89 ** * * * ** 42 LEU 42 1.299 1.233 1.513 1.535 1.439 123.54 117.63 119.78 108.42 107.07 109.64 122.59 ** * * * ** 43 LEU 43 1.302 1.236 1.512 1.551 1.455 120.31 113.98 121.55 109.87 112.93 113.13 124.46 +* * * +* +* 44 ASP 44 1.311 1.246 1.519 1.536 1.449 124.86 115.03 120.89 110.77 110.00 108.98 124.08 * +* +* 45 TYR 45 1.308 1.230 1.520 1.533 1.449 124.16 116.66 120.67 109.45 111.45 109.29 122.67 * * * 46 SER 46 1.310 1.242 1.535 1.523 1.430 120.75 117.94 120.17 111.90 112.33 110.04 121.87 * * * 47 GLY 47 1.321 1.229 1.515 - 1.456 118.33 118.10 119.66 - 115.52 - 122.24 * * * 48 ARG 48 1.316 1.245 1.515 1.534 1.464 120.43 115.74 121.55 109.14 110.91 111.80 122.67 49 SER 49 1.281 1.230 1.504 1.532 1.414 122.02 116.84 120.35 111.10 106.87 109.66 122.79 *** * ** +* *** 50 TRP 50 1.287 1.225 1.485 1.524 1.443 119.91 115.20 121.14 111.16 110.83 112.41 123.66 *** +* * *** 51 THR 51 1.279 1.228 1.538 1.534 1.415 122.17 115.67 121.18 111.59 109.63 108.31 123.15 +*** ** * +* +*** 52 VAL 52 1.310 1.215 1.510 1.577 1.452 123.10 117.19 120.98 109.41 109.43 111.36 121.81 * * * 53 ARG 53 1.274 1.204 1.509 1.532 1.418 119.73 116.57 120.80 111.20 108.99 110.31 122.61 +*** * ** * +*** 54 MET 54 1.300 1.235 1.475 1.534 1.442 121.32 118.45 119.49 109.45 105.47 112.60 122.03 ** ** * ** * ** 55 LYS 55 1.283 1.230 1.512 1.533 1.406 117.79 115.66 120.66 110.87 112.06 108.55 123.68 *** +** ** * *** 56 LYS 56 1.323 1.227 1.498 1.542 1.437 121.77 116.27 120.64 106.54 102.64 112.42 123.02 * * +* *** * *** 57 ARG 57 1.252 1.237 1.492 1.533 1.433 121.28 115.13 120.97 111.63 108.23 110.04 123.80 *5.5* +* * * *5.5* 58 GLY 58 1.304 1.233 1.501 - 1.421 120.92 116.10 120.90 - 111.21 - 122.97 +* +* +* 59 GLU 59 1.295 1.215 1.521 1.519 1.437 121.41 117.78 120.22 108.86 110.92 109.34 122.00 ** * ** 60 LYS 60 1.324 1.236 1.538 1.523 1.447 120.40 116.11 120.96 111.34 113.56 108.44 122.93 * * 61 VAL 61 1.336 1.233 1.487 1.543 1.463 122.54 114.23 121.70 108.00 112.21 115.26 124.06 +* ** ** 62 PHE 62 1.275 1.247 1.513 1.537 1.420 122.55 117.69 119.63 111.80 106.88 108.20 122.58 +*** +* +* * +*** 63 LEU 63 1.311 1.229 1.484 1.555 1.444 119.73 115.99 120.12 109.82 107.86 114.64 123.85 * +* * * * ** ** 64 THR 64 1.299 1.246 1.562 1.541 1.424 122.20 115.79 121.18 111.89 111.77 108.79 123.03 ** +* +* * +* ** 65 VAL 65 1.327 1.220 1.538 1.571 1.461 124.14 116.27 121.07 111.34 111.13 110.92 122.64 * * * * 66 GLY 66 1.305 1.224 1.485 - 1.431 120.96 114.87 121.55 - 109.77 - 123.54 +* +* * +* 67 TRP 67 1.326 1.240 1.525 1.542 1.459 123.10 114.41 122.00 110.30 110.24 109.49 123.51 68 GLU 68 1.300 1.227 1.559 1.529 1.441 123.18 116.32 121.13 112.52 110.30 109.00 122.53 ** +* * ** Residue-by-residue listing for refined_12 Page 8 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 69 ASN 69 1.327 1.204 1.508 1.543 1.473 122.60 115.85 120.88 108.91 110.25 111.63 123.20 * * 70 PHE 70 1.308 1.245 1.501 1.546 1.449 123.17 114.97 121.19 110.24 109.74 110.04 123.82 * * * 71 VAL 71 1.323 1.235 1.518 1.568 1.439 121.83 115.46 121.20 111.01 110.36 111.67 123.34 * * 72 LYS 72 1.311 1.230 1.507 1.521 1.437 121.54 117.76 119.50 111.17 113.48 113.23 122.72 * * +* +* 73 ASP 73 1.337 1.225 1.517 1.523 1.475 119.65 117.39 120.37 110.53 112.95 112.63 122.22 * * * 74 ASN 74 1.313 1.230 1.504 1.542 1.471 119.68 115.51 120.34 109.72 111.28 113.41 124.14 * * * +* +* 75 ASN 75 1.329 1.235 1.523 1.552 1.465 123.77 115.67 121.62 112.01 109.97 112.48 122.57 * * * * * 76 LEU 76 1.308 1.243 1.522 1.559 1.434 120.92 114.84 121.48 114.13 113.48 111.92 123.65 +* * * ** ** 77 GLU 77 1.303 1.245 1.516 1.520 1.438 124.21 115.90 119.99 111.78 110.09 111.26 124.07 +* * * +* 78 ASP 78 1.331 1.250 1.533 1.547 1.473 123.52 115.51 121.44 109.50 111.17 111.16 123.00 * * 79 GLY 79 1.307 1.225 1.499 - 1.438 121.58 115.27 121.37 - 110.38 - 123.36 +* +* 80 LYS 80 1.311 1.240 1.523 1.531 1.448 122.59 117.19 120.28 111.15 109.26 109.95 122.53 * * 81 TYR 81 1.320 1.230 1.481 1.533 1.442 120.74 115.40 120.73 109.80 110.57 111.93 123.84 ** ** 82 LEU 82 1.289 1.241 1.528 1.550 1.419 122.41 115.98 120.75 113.96 112.28 110.99 123.21 +** ** ** +** 83 GLN 83 1.313 1.233 1.497 1.531 1.443 121.94 115.95 120.38 106.53 109.04 113.16 123.67 * * +* +* +* 84 PHE 84 1.291 1.234 1.498 1.531 1.426 122.48 115.97 120.78 109.36 108.61 111.55 123.20 +** * +* +** 85 ILE 85 1.292 1.243 1.506 1.578 1.429 121.80 115.67 120.74 110.86 107.75 113.32 123.56 +** * +* * * +** 86 TYR 86 1.302 1.230 1.502 1.535 1.432 121.87 115.41 121.22 109.76 111.61 110.67 123.37 +* * * +* 87 ASP 87 1.288 1.232 1.507 1.540 1.436 122.28 119.18 118.11 112.11 105.24 110.63 122.69 +** * * +* * ** +** 88 ARG 88 1.327 1.244 1.532 1.537 1.466 120.30 114.19 121.55 111.47 111.87 112.99 124.19 * * * 89 ASP 89 1.316 1.229 1.540 1.559 1.436 126.07 118.45 119.51 110.45 103.57 109.41 122.02 * * ** * +** +** 90 ARG 90 1.289 1.224 1.519 1.540 1.457 122.54 116.76 120.78 109.37 109.44 110.31 122.43 +** +** 91 THR 91 1.314 1.240 1.545 1.559 1.429 120.57 116.69 120.41 112.03 110.47 110.34 122.81 * +* * +* 92 PHE 92 1.327 1.240 1.517 1.540 1.459 121.83 115.13 121.38 107.39 111.17 112.19 123.49 * * 93 TYR 93 1.298 1.229 1.521 1.538 1.442 123.08 117.58 119.87 111.71 106.66 109.92 122.54 ** +* ** 94 VAL 94 1.314 1.230 1.529 1.563 1.454 120.69 116.07 121.01 109.64 112.17 111.02 122.92 * * 95 ILE 95 1.318 1.221 1.515 1.555 1.452 121.94 116.32 120.52 109.61 108.44 112.50 123.16 96 ILE 96 1.299 1.244 1.516 1.564 1.451 122.65 115.27 120.98 109.11 110.14 110.28 123.67 ** ** Residue-by-residue listing for refined_12 Page 9 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 97 TYR 97 1.304 1.238 1.506 1.526 1.429 122.95 115.30 120.78 110.51 108.79 111.41 123.89 +* +* +* 98 GLY 98 1.297 1.233 1.499 - 1.426 122.37 116.96 119.98 - 109.81 - 123.04 ** +* * ** 99 HIS 99 1.315 1.233 1.518 1.544 1.463 121.43 115.13 120.72 110.15 109.67 110.63 124.16 * * 100 ASN 100 1.328 1.241 1.525 1.550 1.469 124.74 115.49 121.59 111.83 111.61 113.21 122.90 * +* +* +* 101 MET 101 1.309 1.240 1.526 1.537 1.457 121.99 115.31 121.29 108.20 110.90 110.66 123.39 * * * 102 CYS 102 1.300 - 1.521 1.536 1.425 122.96 - - 110.72 107.70 110.91 - ** +* * ** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: *5.5* * ** +* +** ** * +* ** *** ** +* *5.5* ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_12 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 1.252 1.351 1.308 .016 *5.5* +* +* C-N (Pro) 1.341 .016 5 1.334 1.352 1.342 .007 C-O C-O 1.231 .020 101 1.204 1.256 1.234 .010 * * CA-C CH1E-C (except Gly) 1.525 .021 95 1.475 1.562 1.518 .017 ** +* CH2G*-C (Gly) 1.516 .018 7 1.485 1.525 1.503 .012 +* CA-CB CH1E-CH3E (Ala) 1.521 .033 2 1.522 1.534 1.528 .006 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 18 1.533 1.578 1.557 .013 * CH1E-CH2E (the rest) 1.530 .020 75 1.517 1.568 1.537 .011 +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.406 1.478 1.444 .016 +** * NH1-CH2G* (Gly) 1.451 .016 7 1.421 1.457 1.436 .014 +* N-CH1E (Pro) 1.466 .015 5 1.439 1.465 1.452 .009 +* ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_12 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 89 113.98 119.18 116.34 1.20 * * CH2G*-C-NH1 (Gly) 116.4 2.1 7 114.56 118.10 116.01 1.15 CH1E-C-N (Pro) 116.9 1.5 5 115.11 118.32 116.43 1.10 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 96 120.59 124.59 122.97 .74 +* O-C-N (Pro) 122.0 1.4 5 122.44 123.65 122.91 .46 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 117.79 126.07 121.94 1.54 ** ** C-NH1-CH2G* (Gly) 120.6 1.7 7 118.33 122.37 120.70 1.22 * * C-N-CH1E (Pro) 122.6 5.0 5 121.41 122.34 122.01 .34 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 94 118.11 122.12 120.68 .70 +* CH2G*-C-O (Gly) 120.8 2.1 7 119.66 121.55 120.75 .64 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 2 110.15 110.27 110.21 .06 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 18 108.00 112.03 110.24 1.18 * CH2E-CH1E-C (the rest) 110.1 1.9 75 106.53 114.13 110.59 1.53 +* ** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 102.64 113.83 110.01 2.21 *** NH1-CH2G*-C (Gly) 112.5 2.9 7 109.77 115.52 111.77 1.96 * N-CH1E-C (Pro) 111.8 2.5 5 106.88 110.62 109.58 1.39 +* N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 2 109.25 109.89 109.57 .32 NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 18 108.31 115.26 111.14 1.62 +* ** N-CH1E-CH2E (Pro) 103.0 1.1 5 103.27 104.70 104.07 .56 +* NH1-CH1E-CH2E (the rest) 110.5 1.7 70 108.10 114.64 110.83 1.58 * ** ------------------------------------------------------------------------------------------------------------- The small molecule data used in the above analysis is from Engh & Huber (1991). The atom labelling follows that used in the X-PLOR dictionary, with some additional atoms (marked with an asterisk) as defined by Engh & Huber. Residue-by-residue listing for refined_12 Page 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] 75 85.2% Residues in additional allowed regions [a,b,l,p] 12 13.6% Residues in generously allowed regions [~a,~b,~l,~p] 1 1.1% 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 85.2 83.8 10.0 .1 Inside b. Omega angle st dev 101 3.9 6.0 3.0 -.7 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 95 1.9 3.1 1.6 -.7 Inside e. H-bond energy st dev 63 .9 .8 .2 .5 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 18 7.5 18.1 6.5 -1.6 BETTER b. Chi-1 trans st dev 29 7.2 19.0 5.3 -2.2 BETTER c. Chi-1 gauche plus st dev 41 6.1 17.5 4.9 -2.3 BETTER d. Chi-1 pooled st dev 88 8.2 18.2 4.8 -2.1 BETTER e. Chi-2 trans st dev 22 4.0 20.4 5.0 -3.3 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% 85.2 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 .97 3 Residue-by-residue listing for refined_12 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.59 Chi1-chi2 distribution -.27 Chi1 only -.33 Chi3 & chi4 .36 Omega -.17 ------ -.26 ===== Main-chain covalent forces:- Main-chain bond lengths -.16 Main-chain bond angles .32 ------ .12 ===== OVERALL AVERAGE -.13 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.