Residue-by-residue listing for refined_8 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 GLU 1 - - - -66.2 - - - - - - - 181.1 - 33.6 - 2 ALA 2 XX - - - - - - - - - - 181.4 - 31.3 - **** **** 3 GLU 3 b 51.0 - - 179.3 - - - - - - 182.0 - 31.9 - 4 VAL 4 S A - 184.3 - - - - - - - - 179.5 - 33.5 - 5 HIS 5 S B - 187.9 - - - - - - - - 184.6 - 35.1 - 6 ASN 6 B - 203.6 - - - - - - - - 184.0 - 32.9 - * * 7 GLN 7 B - - -57.6 173.8 - - - - - - 175.9 - 37.7 - * * 8 LEU 8 E B 59.5 - - 165.0 - - - - - - 181.2 -2.4 31.5 - 9 GLU 9 E B - - -57.2 181.4 - - - - - - 182.6 - 33.1 - 10 ILE 10 E B - - -56.2 177.0 - - - - - - 173.2 -2.5 35.7 - * * 11 LYS 11 E B 63.0 - - 180.9 - - - - - - 183.2 -3.1 32.7 - * * 12 PHE 12 E B - - -56.5 - - - - - - - 176.2 -.7 36.0 - +* +* 13 ARG 13 E B - 176.8 - 169.7 - - - - - - 184.8 -3.3 31.2 - +* +* 14 LEU 14 E B - - -52.4 185.6 - - - - - - 175.3 -3.5 36.4 - ** ** 15 THR 15 e A 45.7 - - - - - - - - - 175.8 -.9 34.6 - * * * 16 ASP 16 T A - - -64.7 - - - - - - - 179.7 - 35.3 - 17 GLY 17 t - - - - - - - - - - - 180.4 -1.4 - - 18 SER 18 e B 48.5 - - - - - - - - - 181.8 - 33.7 - 19 ASP 19 E B 55.3 - - - - - - - - - 180.2 - 32.0 - Residue-by-residue listing for refined_8 Page 2 ---------------------------------------- ................................................................................................................................... Residue Kabsch Region --------- Sander of No. Type Seq sec Ramch. Chi-1 dihedral Chi-2 Proline Phi Helix Chi-3 Chi-3 Disulph Omega H-bond Chirality Bad Max Chain no. struc plot g(-) trans g(+) trans phi helix psi rt-hand lf-hand bond dihedral en. C-alpha contacts dev ----------------------------------------------------------------------------------------------------------------------------------- 20 ILE 20 E B - - -58.3 177.9 - - - - - - 181.7 -2.8 35.7 - * * 21 GLY 21 E - - - - - - - - - - - 182.1 - - - 22 PRO 22 E - - - - - -66.8 - - - - - 177.5 - 38.5 - * * 23 LYS 23 E B - 188.7 - 182.9 - - - - - - 178.8 -2.2 34.8 - 24 ALA 24 E B - - - - - - - - - - 177.9 - 34.1 - 25 PHE 25 E B - - -57.0 - - - - - - - 171.6 -3.0 36.7 - * * * 26 PRO 26 t - - - - - -70.2 - - - - - 177.6 - 39.6 - +* +* 27 ASP 27 T A - - -57.1 - - - - - - - 184.2 - 36.1 - 28 ALA 28 T A - - - - - - - - - - 179.5 - 34.5 - 29 THR 29 t B - - -61.2 - - - - - - - 181.0 -1.8 33.2 - 30 THR 30 h B 59.0 - - - - - - - - - 175.6 - 34.7 - 31 VAL 31 H A - 179.7 - - - -67.7 -26.1 - - - 175.2 -3.5 33.9 - * +* +* 32 SER 32 H A - 186.6 - - - -62.2 -49.1 - - - 178.5 -1.4 34.5 - 33 ALA 33 H A - - - - - -69.3 -27.5 - - - 175.8 - 33.3 - * * 34 LEU 34 H A - 178.1 - - - -65.6 -42.6 - - - 174.9 -1.8 35.9 - 35 LYS 35 H A - - -71.6 175.9 - -68.9 -37.5 - - - 174.9 -2.5 32.0 - 36 GLU 36 H A - - -64.0 - - -56.8 -37.3 - - - 177.7 -2.3 35.6 - 37 THR 37 H A - - -56.1 - - -61.7 -44.8 - - - 178.4 -1.8 35.1 - 38 VAL 38 H A - 180.5 - - - -62.5 -46.6 - - - 180.6 -1.4 33.9 - 39 ILE 39 H A - - -53.5 179.1 - -58.5 -33.8 - - - 179.2 -2.8 34.9 - * * 40 SER 40 H A - - -56.4 - - -76.6 -40.5 - - - 183.2 -1.7 33.9 - 41 GLU 41 H A - - -85.2 - - -88.2 -31.3 - - - 178.4 -2.4 32.4 - * +* +* 42 TRP 42 h B - 191.8 - - - - - - - - 176.2 -3.8 36.6 - ** ** 43 PRO 43 t - - - - - -62.8 - - - - - 178.8 - 38.2 - * * 44 ARG 44 T A 55.4 - - 183.7 - - - - - - 176.5 -.8 32.2 - +* +* 45 GLU 45 T A - - -63.2 168.6 - - - - - - 178.4 - 35.2 - 46 LYS 46 t B - 181.4 - 177.1 - - - - - - 172.6 -1.8 34.9 - * * 47 GLU 47 B 60.6 - - 175.0 - - - - - - 180.3 -.6 32.3 - +* +* 48 ASN 48 S l - 184.3 - - - - - - - - 176.6 - 32.6 - 49 GLY 49 S - - - - - - - - - - - 176.5 - - - 50 PRO 50 - - - - - -59.1 - - - - - 180.0 - 39.5 - +* +* 51 LYS 51 ~a - 181.0 - 184.6 - - - - - - 183.3 - 35.2 - ** ** 52 THR 52 t B 55.9 - - - - - - - - - 181.9 - 30.6 - 53 VAL 53 T A - 177.6 - - - - - - - - 183.2 - 36.5 - 54 LYS 54 T A - - -60.9 181.0 - - - - - - 184.2 - 34.0 - 55 GLU 55 e A 54.4 - - - - - - - - - 174.7 -1.0 26.6 - * ** ** 56 VAL 56 E B 58.3 - - - - - - - - - 179.9 -1.9 32.0 - 57 LYS 57 E B - - -61.8 - - - - - - - 181.0 -1.3 33.5 - 58 LEU 58 E B - - -66.7 - - - - - - - 180.3 - 33.8 - 59 ILE 59 E B - - -66.7 - - - - - - - 175.5 -2.5 35.9 - Residue-by-residue listing for refined_8 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 ----------------------------------------------------------------------------------------------------------------------------------- 60 SER 60 E B 58.7 - - - - - - - - - 179.8 -3.0 34.5 - * * 61 ALA 61 T l - - - - - - - - - - 181.2 - 32.7 - 62 GLY 62 T - - - - - - - - - - - 182.1 - - - 63 LYS 63 E B - - -72.4 - - - - - - - 177.6 -2.0 35.4 - 64 VAL 64 E B 64.6 - - - - - - - - - 182.2 - 33.3 - 65 LEU 65 e B - - -63.5 - - - - - - - 175.4 -2.1 34.6 - 66 GLU 66 t B - - -68.4 - - - - - - - 183.9 -.6 34.3 - +* +* 67 ASN 67 T A 63.8 - - - - - - - - - 180.6 - 32.0 - 68 SER 68 T A - - -56.0 - - - - - - - 177.9 - 33.9 - 69 LYS 69 t B - - -66.5 - - - - - - - 176.1 -1.8 35.4 - 70 THR 70 B B 50.5 - - - - - - - - - 175.3 - 36.3 - 71 VAL 71 g A - 179.8 - - - - - - - - 178.1 -2.6 34.4 - 72 LYS 72 G A - 179.6 - 183.9 - - - - - - 184.3 -2.7 36.0 - 73 ASP 73 G A - 189.9 - - - - - - - - 177.8 - 33.0 - 74 TYR 74 G A - - -72.6 - - - - - - - 175.8 -.8 31.8 - +* +* 75 ARG 75 g B - - -94.9 - - - - - - - 177.9 -.7 35.0 - +* +* +* 76 SER 76 B 48.6 - - - - - - - - - 178.2 - 34.3 - 77 PRO 77 S - - - - - -56.6 - - - - - 184.5 - 38.5 - * * 78 VAL 78 S ~l 64.5 - - - - - - - - - 182.2 - 26.6 - ** ** ** 79 SER 79 B - - -57.8 - - - - - - - 182.9 - 32.5 - 80 ASN 80 B - 176.9 - - - - - - - - 181.4 - 35.5 - 81 LEU 81 B - - -62.5 176.6 - - - - - - 182.1 - 36.2 - 82 ALA 82 S b - - - - - - - - - - 172.8 -.6 31.7 - * +* +* 83 GLY 83 S - - - - - - - - - - - 173.8 -1.8 - - * * 84 ALA 84 S B - - - - - - - - - - 179.6 - 35.2 - 85 VAL 85 B - 185.8 - - - - - - - - 185.3 - 34.2 - 86 THR 86 E B - - -56.2 - - - - - - - 184.2 -2.9 34.0 - * * 87 THR 87 E B - - -52.6 - - - - - - - 175.1 -.6 35.7 - +* +* 88 MET 88 E B - - -68.8 181.7 - - - - - - 181.5 -2.6 32.6 - 89 HIS 89 E B - - -61.2 - - - - - - - 181.6 -3.2 33.0 - * * 90 VAL 90 E B - 183.7 - - - - - - - - 178.9 -2.6 34.5 - 91 ILE 91 E B - - -67.4 180.0 - - - - - - 183.0 -2.5 34.6 - 92 ILE 92 E B - - -59.7 - - - - - - - 173.7 -.6 35.0 - * +* +* 93 GLN 93 e B 57.7 - - 174.0 - - - - - - 181.0 -.9 31.9 - +* +* 94 ALA 94 B - - - - - - - - - - 172.9 - 35.6 - * * 95 PRO 95 - - - - - -67.3 - - - - - 185.4 - 38.9 - * * 96 VAL 96 b - 183.0 - - - - - - - - 173.9 - 31.1 - * * 97 THR 97 b 45.1 - - - - - - - - - 185.4 -2.1 33.5 - * * 98 GLU 98 B - 181.2 - 183.1 - - - - - - 181.1 -1.6 35.1 - Residue-by-residue listing for refined_8 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 ----------------------------------------------------------------------------------------------------------------------------------- 99 LYS 99 S ~l - 180.7 - 175.9 - - - - - - 181.4 - 30.6 - ** ** 100 GLU 100 B - - -62.3 171.0 - - - - - - 180.5 - 34.2 - 101 LYS 101 - 39.8 - - - - - - - - - - - 28.2 - +* +* +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** +* * +* +* * * ** ** **** ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 55.2 183.6 -63.0 177.9 -63.8 -67.1 -37.9 - - - 179.4 -2.0 34.1 Standard deviations: 6.9 6.1 8.5 5.3 5.3 8.9 7.7 - - - 3.4 .9 2.3 Numbers of values: 21 23 38 26 6 11 11 0 0 0 100 51 96 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_8 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 GLU 1 - 1.236 1.493 1.549 1.462 - 115.91 119.35 110.03 109.01 112.38 124.74 +* * * +* 2 ALA 2 1.336 1.232 1.520 1.527 1.463 124.72 115.58 121.52 111.69 111.56 112.67 122.90 +* +* +* 3 GLU 3 1.294 1.237 1.520 1.539 1.419 122.71 115.46 121.28 113.03 110.52 111.31 123.24 +** ** +* +** 4 VAL 4 1.316 1.241 1.518 1.561 1.461 122.15 113.71 122.56 111.03 109.34 111.36 123.71 * * * 5 HIS 5 1.274 1.232 1.519 1.539 1.442 123.92 118.08 119.83 110.90 106.81 109.77 122.08 +*** * +* +*** 6 ASN 6 1.309 1.243 1.538 1.551 1.450 119.67 116.26 120.84 112.18 109.74 110.85 122.90 * * * * * 7 GLN 7 1.297 1.234 1.520 1.516 1.429 124.62 117.62 119.76 108.61 108.35 107.55 122.61 ** +* +* * +* ** 8 LEU 8 1.318 1.221 1.518 1.552 1.443 120.31 117.27 120.50 110.95 110.04 114.08 122.21 * ** ** 9 GLU 9 1.311 1.242 1.506 1.516 1.438 120.44 114.87 121.43 110.19 110.74 112.09 123.70 * * * 10 ILE 10 1.294 1.239 1.510 1.569 1.435 122.94 115.92 120.54 108.68 109.17 110.94 123.50 ** * * ** 11 LYS 11 1.302 1.249 1.518 1.539 1.442 121.93 116.24 120.71 111.01 108.77 112.61 123.05 +* * +* Residue-by-residue listing for refined_8 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 PHE 12 1.300 1.215 1.509 1.535 1.443 121.64 117.35 120.00 108.47 109.87 110.10 122.65 ** ** 13 ARG 13 1.306 1.228 1.513 1.539 1.445 120.96 115.25 121.16 112.68 110.39 112.53 123.58 +* * * +* 14 LEU 14 1.306 1.242 1.526 1.538 1.444 123.47 115.67 121.11 108.08 111.16 109.48 123.21 +* * +* 15 THR 15 1.319 1.234 1.534 1.528 1.450 123.34 115.20 121.56 110.50 110.64 109.65 123.23 * * 16 ASP 16 1.329 1.231 1.517 1.541 1.463 122.93 115.75 121.11 108.23 109.78 111.18 123.12 17 GLY 17 1.322 1.232 1.507 - 1.441 121.74 116.32 120.84 - 112.02 - 122.83 18 SER 18 1.308 1.227 1.515 1.521 1.423 121.82 116.91 120.56 112.30 110.28 109.41 122.50 +* +* * +* 19 ASP 19 1.303 1.236 1.501 1.530 1.426 121.03 114.17 121.36 111.29 112.65 112.01 124.46 +* * +* * +* 20 ILE 20 1.302 1.239 1.524 1.564 1.441 124.97 116.24 119.58 109.32 107.95 110.45 124.15 +* +* * +* 21 GLY 21 1.336 1.242 1.529 - 1.460 122.75 116.94 120.52 - 114.23 - 122.54 * * 22 PRO 22 1.344 1.240 1.519 1.529 1.462 123.55 115.66 121.38 109.58 113.56 104.26 122.96 * * 23 LYS 23 1.295 1.224 1.506 1.547 1.445 122.34 118.06 119.31 110.02 106.43 111.47 122.63 ** +* ** 24 ALA 24 1.299 1.239 1.513 1.519 1.434 120.54 115.77 120.51 110.87 109.40 110.46 123.57 ** * ** 25 PHE 25 1.311 1.225 1.515 1.536 1.442 123.23 118.37 120.16 106.54 108.24 111.28 121.37 * * +* * * +* 26 PRO 26 1.306 1.233 1.534 1.527 1.460 122.49 116.20 120.91 108.79 111.59 103.75 122.89 ** ** 27 ASP 27 1.324 1.227 1.526 1.541 1.480 122.94 115.51 121.40 107.29 109.89 110.81 123.06 * * * 28 ALA 28 1.322 1.229 1.524 1.519 1.450 122.54 117.20 120.29 110.00 112.24 109.75 122.52 29 THR 29 1.314 1.242 1.533 1.544 1.441 120.80 116.12 120.81 111.91 110.39 110.55 123.02 * * * 30 THR 30 1.318 1.234 1.517 1.546 1.428 121.53 115.98 121.03 108.87 110.81 111.50 122.99 +* +* 31 VAL 31 1.307 1.223 1.527 1.541 1.443 122.39 115.80 121.28 110.94 108.77 110.96 122.92 +* +* 32 SER 32 1.320 1.222 1.537 1.536 1.436 121.72 116.46 120.40 111.10 108.43 109.94 123.04 * * 33 ALA 33 1.344 1.237 1.532 1.515 1.464 122.28 116.11 121.08 110.76 111.04 110.74 122.81 * * 34 LEU 34 1.322 1.229 1.538 1.526 1.419 123.23 115.46 121.47 111.76 108.11 107.31 123.04 ** * +* ** 35 LYS 35 1.323 1.219 1.527 1.533 1.444 122.55 116.97 119.86 112.54 111.31 111.13 123.15 * * 36 GLU 36 1.341 1.241 1.526 1.527 1.477 122.74 115.39 121.18 108.33 109.82 110.37 123.43 37 THR 37 1.326 1.236 1.531 1.545 1.447 122.70 115.60 121.26 109.46 109.30 110.51 123.10 38 VAL 38 1.327 1.192 1.519 1.554 1.443 122.07 116.77 120.24 109.55 109.54 112.27 122.92 +* +* 39 ILE 39 1.319 1.232 1.541 1.555 1.476 122.55 115.95 121.50 108.59 110.77 111.05 122.51 40 SER 40 1.310 1.240 1.553 1.526 1.441 122.05 116.90 120.46 111.34 112.17 109.15 122.60 * * * 41 GLU 41 1.329 1.236 1.533 1.530 1.453 122.67 116.84 120.70 111.77 113.89 110.26 122.46 42 TRP 42 1.295 1.243 1.508 1.546 1.445 122.40 119.08 119.31 109.64 106.34 109.00 121.54 ** * +* ** Residue-by-residue listing for refined_8 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 ----------------------------------------------------------------------------------------------------------------------------------- 43 PRO 43 1.332 1.225 1.519 1.530 1.433 121.03 116.05 121.09 110.07 110.30 105.06 122.84 ** +* ** 44 ARG 44 1.311 1.227 1.520 1.535 1.452 122.27 114.53 122.06 112.87 109.75 111.04 123.41 * * * 45 GLU 45 1.310 1.239 1.550 1.517 1.441 123.80 116.88 120.67 110.86 111.09 108.12 122.45 * * * * * 46 LYS 46 1.332 1.238 1.511 1.545 1.454 121.54 116.89 120.58 108.39 110.19 111.64 122.50 47 GLU 47 1.300 1.251 1.512 1.535 1.410 120.53 116.62 119.74 111.41 108.15 113.27 123.63 ** +** * +* +** 48 ASN 48 1.324 1.223 1.551 1.561 1.480 122.86 115.75 122.14 112.63 110.32 110.45 122.07 * +* * * +* 49 GLY 49 1.310 1.232 1.503 - 1.429 121.78 118.62 119.16 - 109.64 - 122.22 * * * * 50 PRO 50 1.333 1.240 1.530 1.531 1.473 122.84 116.29 120.58 109.64 111.58 103.02 123.13 51 LYS 51 1.312 1.217 1.510 1.535 1.444 121.67 115.54 121.24 109.09 109.73 110.61 123.22 * * 52 THR 52 1.310 1.238 1.531 1.567 1.423 122.49 114.19 121.62 111.81 112.48 113.61 124.15 * +* * * * +* 53 VAL 53 1.305 1.245 1.542 1.569 1.466 126.89 115.64 120.98 109.01 111.60 108.49 123.37 +* * +** +* +** 54 LYS 54 1.321 1.237 1.518 1.531 1.444 122.40 117.37 120.23 109.84 112.20 110.72 122.39 55 GLU 55 1.319 1.229 1.522 1.542 1.465 118.64 117.66 120.67 112.83 115.53 115.38 121.67 +* * +* +** +** 56 VAL 56 1.300 1.238 1.536 1.569 1.447 119.06 116.95 120.82 111.07 109.47 113.51 122.18 ** * * * ** 57 LYS 57 1.316 1.234 1.525 1.525 1.438 120.82 115.94 120.40 110.93 111.24 110.58 123.66 * * 58 LEU 58 1.330 1.235 1.523 1.558 1.465 122.92 115.43 120.68 109.24 110.87 112.24 123.89 * * * 59 ILE 59 1.315 1.243 1.540 1.562 1.457 124.59 116.06 120.91 109.29 110.38 109.39 123.02 +* * +* 60 SER 60 1.311 1.236 1.520 1.536 1.435 122.83 116.59 120.03 110.54 108.46 110.64 123.31 * * * 61 ALA 61 1.328 1.237 1.536 1.532 1.476 123.52 116.02 120.83 111.19 111.75 111.03 123.07 * * 62 GLY 62 1.319 1.236 1.523 - 1.449 121.44 116.55 120.81 - 112.58 - 122.64 63 LYS 63 1.319 1.221 1.509 1.537 1.422 122.70 116.77 120.13 109.21 110.27 110.24 123.10 +* +* 64 VAL 64 1.313 1.240 1.530 1.569 1.447 121.45 116.55 120.65 111.01 108.65 112.15 122.71 * * * 65 LEU 65 1.302 1.231 1.528 1.538 1.427 121.91 116.75 120.60 109.44 111.20 110.74 122.62 +* +* +* 66 GLU 66 1.316 1.222 1.524 1.540 1.466 122.46 117.47 120.08 109.59 109.57 111.27 122.43 67 ASN 67 1.326 1.233 1.538 1.548 1.479 121.50 116.86 120.59 110.28 112.80 112.59 122.54 * * * 68 SER 68 1.319 1.235 1.542 1.523 1.460 121.73 115.92 121.38 111.24 111.82 109.29 122.70 69 LYS 69 1.312 1.234 1.516 1.520 1.433 122.67 116.19 120.68 109.68 109.88 109.55 123.10 * * * 70 THR 70 1.296 1.244 1.509 1.525 1.414 123.23 117.43 119.62 109.15 108.84 109.33 122.94 ** ** * ** 71 VAL 71 1.335 1.231 1.532 1.560 1.457 120.53 114.18 121.67 110.13 107.65 111.49 124.08 * * * 72 LYS 72 1.328 1.223 1.535 1.533 1.455 125.16 117.29 120.13 108.82 112.21 108.83 122.57 +* +* 73 ASP 73 1.330 1.234 1.530 1.535 1.475 121.49 116.46 120.84 110.53 111.40 111.49 122.69 Residue-by-residue listing for refined_8 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 ----------------------------------------------------------------------------------------------------------------------------------- 74 TYR 74 1.324 1.226 1.521 1.529 1.450 122.24 115.28 121.51 112.57 111.74 111.13 123.19 * * 75 ARG 75 1.301 1.237 1.508 1.523 1.423 123.77 116.13 120.88 110.72 109.66 109.27 122.95 +* +* * +* 76 SER 76 1.282 1.246 1.545 1.530 1.416 121.92 118.64 119.57 113.10 109.63 107.92 121.73 *** ** * +* +* *** 77 PRO 77 1.363 1.236 1.537 1.528 1.476 122.75 115.48 120.23 110.24 112.46 103.51 124.28 * +* +* 78 VAL 78 1.342 1.240 1.521 1.587 1.479 125.92 114.54 122.09 112.78 112.96 117.19 123.37 +* * ** +* *** *** 79 SER 79 1.310 1.247 1.530 1.518 1.435 122.61 114.16 122.03 112.44 111.77 110.15 123.81 * * * * * 80 ASN 80 1.295 1.232 1.515 1.539 1.428 124.05 116.51 120.15 111.45 109.10 108.15 123.32 ** +* * * ** 81 LEU 81 1.321 1.239 1.513 1.493 1.402 123.33 115.89 121.47 109.68 111.29 107.91 122.62 +* +** +* +** 82 ALA 82 1.289 1.234 1.511 1.520 1.408 121.66 115.09 121.32 111.83 111.80 112.11 123.38 +** +** * +** 83 GLY 83 1.310 1.236 1.497 - 1.439 121.24 114.00 121.90 - 107.74 - 124.10 * * * +* +* 84 ALA 84 1.309 1.239 1.508 1.524 1.422 123.83 117.81 119.91 110.33 106.51 110.24 122.27 * +* * +* +* 85 VAL 85 1.292 1.236 1.512 1.545 1.436 119.67 116.93 120.23 109.75 107.65 112.26 122.84 +** * * * +** 86 THR 86 1.301 1.228 1.517 1.542 1.425 120.80 115.89 121.12 111.74 108.81 110.17 122.94 +* +* * +* 87 THR 87 1.296 1.231 1.524 1.545 1.419 121.38 116.47 120.87 109.72 110.39 109.38 122.65 ** ** * ** 88 MET 88 1.304 1.235 1.491 1.532 1.440 121.25 116.23 120.55 110.99 109.03 112.81 123.19 +* +* * +* 89 HIS 89 1.296 1.219 1.491 1.533 1.432 120.99 115.91 120.70 111.17 109.67 111.97 123.37 ** +* * ** 90 VAL 90 1.286 1.235 1.490 1.548 1.429 121.93 114.57 121.45 109.56 109.39 111.68 123.98 *** +* +* *** 91 ILE 91 1.275 1.241 1.494 1.537 1.407 122.82 114.63 121.52 110.94 108.12 110.51 123.84 +*** * +** * +*** 92 ILE 92 1.287 1.243 1.499 1.552 1.412 122.20 115.58 120.97 109.31 109.81 111.12 123.40 +** * ** +** 93 GLN 93 1.292 1.222 1.497 1.533 1.406 121.36 115.47 121.14 112.62 108.62 112.53 123.30 +** * +** * * +** 94 ALA 94 1.280 1.247 1.512 1.521 1.428 122.05 118.17 119.89 109.85 109.66 109.31 121.91 +*** +* +*** 95 PRO 95 1.340 1.248 1.501 1.525 1.439 121.33 116.97 120.22 109.47 107.49 105.06 122.80 * +* +* +* +* 96 VAL 96 1.294 1.238 1.512 1.548 1.425 120.01 114.90 121.67 111.61 111.69 113.31 123.27 ** +* * * ** 97 THR 97 1.303 1.241 1.515 1.539 1.395 122.77 114.13 122.10 112.67 108.23 110.43 123.55 +* *** * +* * *** 98 GLU 98 1.301 1.245 1.512 1.524 1.425 122.95 115.04 120.23 110.95 110.23 108.80 124.74 ** +* * ** 99 LYS 99 1.329 1.235 1.515 1.546 1.456 125.17 114.94 121.32 112.81 110.96 112.93 123.71 +* * * +* 100 GLU 100 1.312 1.236 1.515 1.525 1.447 123.17 115.46 121.18 111.21 110.91 109.38 123.34 * * Residue-by-residue listing for refined_8 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 ----------------------------------------------------------------------------------------------------------------------------------- 101 LYS 101 1.304 - 1.524 1.564 1.428 122.22 - - 115.24 113.24 112.78 - +* +* +* +** * +** ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: +*** +* +* +* *** +** * * +** +* *** +* +*** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_8 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 94 1.274 1.344 1.311 .015 +*** * * C-N (Pro) 1.341 .016 6 1.306 1.363 1.336 .017 ** * C-O C-O 1.231 .020 100 1.192 1.251 1.234 .009 +* CA-C CH1E-C (except Gly) 1.525 .021 96 1.490 1.553 1.521 .014 +* * CH2G*-C (Gly) 1.516 .018 5 1.497 1.529 1.512 .012 * CA-CB CH1E-CH3E (Ala) 1.521 .033 8 1.515 1.532 1.522 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 26 1.525 1.587 1.553 .014 +* CH1E-CH2E (the rest) 1.530 .020 62 1.493 1.564 1.534 .012 +* +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 90 1.395 1.480 1.441 .019 *** * NH1-CH2G* (Gly) 1.451 .016 5 1.429 1.460 1.444 .011 * N-CH1E (Pro) 1.466 .015 6 1.433 1.476 1.457 .016 ** ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_8 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 89 113.71 119.08 116.14 1.10 * * CH2G*-C-NH1 (Gly) 116.4 2.1 5 114.00 118.62 116.49 1.48 * * CH1E-C-N (Pro) 116.9 1.5 6 115.48 116.97 116.11 .48 O-C-N O-C-NH1 (except Pro) 123.0 1.6 94 121.37 124.74 123.03 .65 * * O-C-N (Pro) 122.0 1.4 6 122.80 124.28 123.15 .52 +* C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 89 118.64 126.89 122.34 1.42 +* +** C-NH1-CH2G* (Gly) 120.6 1.7 5 121.24 122.75 121.79 .52 * C-N-CH1E (Pro) 122.6 5.0 6 121.03 123.55 122.33 .88 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 95 119.31 122.56 120.79 .69 * CH2G*-C-O (Gly) 120.8 2.1 5 119.16 121.90 120.64 .88 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 8 109.85 111.83 110.81 .69 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 26 108.59 112.78 110.32 1.22 +* CH2E-CH1E-C (the rest) 110.1 1.9 62 106.54 115.24 110.62 1.63 +* +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 90 106.34 115.53 110.13 1.66 +* +* NH1-CH2G*-C (Gly) 112.5 2.9 5 107.74 114.23 111.24 2.29 +* N-CH1E-C (Pro) 111.8 2.5 6 107.49 113.56 111.16 1.92 +* N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 8 109.31 112.67 110.79 1.06 +* NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 26 108.49 117.19 111.28 1.74 +* *** N-CH1E-CH2E (Pro) 103.0 1.1 6 103.02 105.06 104.11 .76 +* * NH1-CH1E-CH2E (the rest) 110.5 1.7 56 107.31 115.38 110.72 1.68 +* +** ------------------------------------------------------------------------------------------------------------- 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_8 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] 78 88.6% Residues in additional allowed regions [a,b,l,p] 6 6.8% Residues in generously allowed regions [~a,~b,~l,~p] 3 3.4% Residues in disallowed regions [XX] 1 1.1% ---- ------ Number of non-glycine and non-proline residues 88 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 5 Number of proline residues 6 ---- Total number of residues 101 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 88.6 83.8 10.0 .5 Inside b. Omega angle st dev 100 3.4 6.0 3.0 -.9 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 96 2.3 3.1 1.6 -.5 Inside e. H-bond energy st dev 51 .9 .8 .2 .5 Inside f. Overall G-factor 101 -.1 -.4 .3 1.1 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 21 6.9 18.1 6.5 -1.7 BETTER b. Chi-1 trans st dev 23 6.1 19.0 5.3 -2.4 BETTER c. Chi-1 gauche plus st dev 38 8.5 17.5 4.9 -1.8 BETTER d. Chi-1 pooled st dev 82 8.9 18.2 4.8 -1.9 BETTER e. Chi-2 trans st dev 26 5.3 20.4 5.0 -3.0 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% 88.6 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 9.3 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .90 3 Residue-by-residue listing for refined_8 Page 13 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.52 Chi1-chi2 distribution -.21 Chi1 only -.06 Chi3 & chi4 .22 Omega -.05 ------ -.18 ===== Main-chain covalent forces:- Main-chain bond lengths -.07 Main-chain bond angles .34 ------ .17 ===== OVERALL AVERAGE -.06 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.