Residue-by-residue listing for refined_3 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 - - - -59.0 - - - - - - - 181.5 - 34.1 - 2 GLY 2 - - - - - - - - - - - 177.7 - - - 3 HIS 3 t B - - -64.2 - - - - - - - 187.8 - 33.3 - * * 4 HIS 4 T b 72.6 - - - - - - - - - 171.2 - 27.6 - +* +* +* 5 HIS 5 T a - - -58.4 - - - - - - - 185.2 -2.4 34.8 - 6 HIS 6 t B - 181.7 - - - - - - - - 182.2 -.8 35.2 - +* +* 7 HIS 7 b - - -64.9 - - - - - - - 179.4 - 34.2 - 8 HIS 8 B - 183.7 - - - - - - - - 177.8 - 33.8 - 9 LEU 9 S b 66.2 - - 172.4 - - - - - - 178.3 -.5 34.0 - ** ** 10 GLU 10 S b - - -62.8 180.8 - - - - - - 181.1 - 32.9 - 11 MET 11 b - - -54.4 179.6 - - - - - - 175.4 -1.0 36.3 - * * 12 ALA 12 B - - - - - - - - - - 181.9 - 33.7 - 13 SER 13 b - 184.5 - - - - - - - - 174.9 - 35.1 - 14 GLU 14 S b - 186.0 - 175.9 - - - - - - 188.3 - 32.9 - * * 15 GLU 15 B 57.7 - - 189.9 - - - - - - 175.1 -1.3 37.0 - 16 GLY 16 S - - - - - - - - - - - 181.0 -1.9 - - 17 GLN 17 e B 54.8 - - 173.8 - - - - - - 176.2 - 30.1 - * * 18 VAL 18 E B - 181.3 - - - - - - - - 182.9 - 35.3 - 19 ILE 19 E B - - -61.6 181.1 - - - - - - 180.1 -2.9 31.9 - * * Residue-by-residue listing for refined_3 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 ALA 20 E B - - - - - - - - - - 179.1 -.8 34.2 - +* +* 21 CYS 21 e B - - -55.6 - - - - - - - 179.3 -1.7 35.8 - 22 HIS 22 S A - - -62.1 - - - - - - - 181.3 - 33.8 - 23 THR 23 h B 55.3 - - - - - - - - - 176.2 - 35.8 - 24 VAL 24 H A - 180.7 - - - -76.1 -25.9 - - - 179.1 - 33.8 - * * 25 GLU 25 H A - - -59.4 - - -59.3 -51.7 - - - 178.0 - 35.0 - * * 26 THR 26 H A - - -52.4 - - -65.0 -45.0 - - - 181.0 - 35.6 - 27 TRP 27 H A - 172.7 - - - -54.5 -54.8 - - - 183.2 -1.7 35.1 - * * 28 ASN 28 H A - 188.4 - - - -64.9 -35.4 - - - 179.8 -3.6 35.1 - ** ** 29 GLU 29 H A - 182.9 - 178.3 - -68.2 -46.3 - - - 181.1 -1.6 34.0 - 30 GLN 30 H A - - -66.8 - - -62.5 -33.5 - - - 176.1 -2.8 33.6 - 31 LEU 31 H A - - -68.0 178.7 - -66.9 -44.0 - - - 175.9 -1.6 34.2 - 32 GLN 32 H A - 179.6 - - - -63.7 -37.5 - - - 174.1 -1.6 32.7 - * * 33 LYS 33 H A - 171.7 - 178.8 - -54.8 -45.7 - - - 180.0 -2.6 34.0 - 34 ALA 34 H A - - - - - -71.0 -45.8 - - - 181.9 -2.0 33.6 - 35 ASN 35 H A - 182.1 - - - -56.5 -55.0 - - - 185.9 -3.2 38.0 - * * +* * +* 36 GLU 36 H A - 184.6 - 175.0 - -75.6 -43.3 - - - 184.2 -3.2 33.7 - +* +* 37 SER 37 h A - - -58.1 - - - - - - - 177.5 -1.8 33.4 - 38 LYS 38 T l - 178.1 - 178.9 - - - - - - 180.4 -.6 32.5 - +* +* 39 THR 39 e B - - -46.9 - - - - - - - 178.5 -1.4 35.5 - * * 40 LEU 40 E B - 184.3 - 170.1 - - - - - - 183.9 - 34.4 - 41 VAL 41 E B 58.6 - - - - - - - - - 178.4 -1.1 33.0 - * * 42 VAL 42 E B 61.8 - - - - - - - - - 183.7 -3.0 33.5 - * * 43 VAL 43 E B - 185.8 - - - - - - - - 174.9 -2.5 34.2 - 44 ASP 44 E B - 170.1 - - - - - - - - 177.2 -2.7 33.9 - 45 PHE 45 E B - - -60.6 - - - - - - - 187.6 -3.1 36.4 - * * * 46 THR 46 E B - 188.8 - - - - - - - - 176.2 -2.6 36.1 - 47 ALA 47 t B - - - - - - - - - - 182.5 - 33.5 - 48 SER 48 T A - - -56.4 - - - - - - - 183.0 - 33.7 - 49 TRP 49 T A 55.2 - - - - - - - - - 182.2 - 32.4 - 50 CYS 50 h B 46.5 - - - - - - - -115.4 2.8 186.8 -1.1 27.9 - * +** *7.8* * * +* *7.8* 51 GLY 51 H - - - - - - -56.1 -67.1 - - - 180.3 -.6 - - ** +* ** 52 PRO 52 H - - - - - -56.5 -56.5 -30.2 - - - 180.6 - 38.5 - * * 53 CYS 53 H A - - -47.3 158.3 - -69.2 -39.5 - -115.4 2.8 177.6 - 36.2 - * * +** *7.8* *7.8* 54 ARG 54 H A - 179.9 - 178.8 - -76.2 -31.4 - - - 179.5 -1.8 33.7 - 55 PHE 55 H A - 180.6 - - - -67.0 -31.3 - - - 183.3 -2.4 34.8 - 56 ILE 56 H A - 194.3 - - - -87.3 -15.0 - - - 182.5 -1.6 34.5 - +* ** ** 57 ALA 57 H A - - - - - -60.3 -46.5 - - - 178.9 -.6 31.2 - +* +* Residue-by-residue listing for refined_3 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 ----------------------------------------------------------------------------------------------------------------------------------- 58 PRO 58 H - - - - - -62.0 -62.0 -23.6 - - - 177.9 - 38.8 - * * * 59 PHE 59 H A - 180.5 - - - -78.2 -38.0 - - - 176.8 -.6 32.9 - * +* +* 60 PHE 60 H A - 184.2 - - - -68.0 -33.4 - - - 175.1 -1.6 33.6 - 61 ALA 61 H A - - - - - -69.1 -30.1 - - - 176.4 -2.3 33.9 - 62 ASP 62 H A - 182.3 - - - -68.5 -48.3 - - - 176.7 -.9 35.5 - * * 63 LEU 63 H A - - -65.9 180.4 - -52.7 -43.6 - - - 178.7 -2.6 35.5 - * * 64 ALA 64 H A - - - - - -60.5 -32.2 - - - 180.1 -1.9 33.8 - 65 LYS 65 H A - 186.1 - 177.0 - -79.7 -33.3 - - - 179.5 -.9 32.8 - * +* +* 66 LYS 66 H A - - -78.2 - - -76.5 -29.1 - - - 175.3 -2.0 31.1 - 67 LEU 67 h b - - -67.5 171.2 - - - - - - 185.1 -2.3 32.3 - 68 PRO 68 S - - - - - -72.8 - - - - - 185.2 - 39.4 - +* +* 69 ASN 69 S A - 186.9 - - - - - - - - 179.2 - 34.1 - 70 VAL 70 S B - 178.9 - - - - - - - - 183.8 - 33.8 - 71 LEU 71 E B - 185.2 - - - - - - - - 178.5 -2.7 34.9 - 72 PHE 72 E B - - -64.4 - - - - - - - 179.7 -.7 36.2 - +* +* 73 LEU 73 E B - - -71.3 - - - - - - - 177.4 -2.5 32.9 - 74 LYS 74 E B - 176.2 - - - - - - - - 177.9 -2.0 35.8 - 75 VAL 75 E B - 177.3 - - - - - - - - 177.4 -2.9 33.6 - * * 76 ASP 76 E B - 185.8 - - - - - - - - 183.2 - 33.8 - 77 THR 77 e A 41.3 - - - - - - - - - 176.2 -2.3 31.0 - * * 78 ASP 78 T A - 185.4 - - - - - - - - 172.5 -.6 34.6 - * +* +* 79 GLU 79 T a - - -69.0 - - - - - - - 180.8 - 36.4 - 80 LEU 80 h b - - -70.2 - - - - - - - 182.3 -3.3 33.3 - +* +* 81 LYS 81 H A - - -52.5 178.6 - -68.6 -39.4 - - - 181.2 -1.9 35.7 - 82 SER 82 H A - - -52.8 - - -62.9 -40.0 - - - 179.6 - 34.8 - 83 VAL 83 H A - 180.2 - - - -69.3 -39.9 - - - 178.2 - 33.8 - 84 ALA 84 H A - - - - - -61.7 -38.0 - - - 180.4 -1.8 34.2 - 85 SER 85 H A - 190.9 - - - -75.6 -34.2 - - - 184.1 -2.2 33.7 - 86 ASP 86 H A - 182.2 - - - -70.3 -37.2 - - - 179.0 -2.1 33.6 - 87 TRP 87 h A - - -64.9 - - - - - - - 182.9 -2.2 33.5 - 88 ALA 88 T l - - - - - - - - - - 180.5 - 31.1 - 89 ILE 89 t B - - -60.4 178.2 - - - - - - 182.1 -2.4 33.3 - 90 GLN 90 A - 180.8 - 182.9 - - - - - - 185.0 -.7 35.5 - +* +* 91 ALA 91 S B - - - - - - - - - - 180.5 - 34.0 - 92 MET 92 S B - - -59.9 177.7 - - - - - - 2.7 - 34.6 - 93 PRO 93 e cis - - - - - -90.7 - - - - - 175.8 - 39.5 - ** +* ** 94 THR 94 E B - - -58.5 - - - - - - - 179.4 -2.8 34.5 - * * 95 PHE 95 E B - - -62.4 - - - - - - - 181.7 -2.7 36.3 - 96 MET 96 E B - 184.6 - - - - - - - - 181.4 -3.1 34.2 - * * 97 PHE 97 E B - - -66.1 - - - - - - - 177.4 -2.5 36.3 - 98 LEU 98 E B 60.2 - - 170.0 - - - - - - 184.1 -1.7 32.1 - Residue-by-residue listing for refined_3 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 E B - 179.8 - 173.3 - - - - - - 180.4 -3.2 32.6 - +* +* 100 GLU 100 e l - - -60.3 179.6 - - - - - - 180.5 -.9 33.5 - +* +* 101 GLY 101 T - - - - - - - - - - - 177.7 - - - 102 LYS 102 E B - - -70.8 - - - - - - - 184.4 -2.2 32.0 - 103 ILE 103 E B - - -67.8 175.9 - - - - - - 175.2 - 34.3 - 104 LEU 104 E a - - -66.1 180.7 - - - - - - 184.8 -1.7 33.7 - 105 ASP 105 E B 47.0 - - - - - - - - - 180.2 -2.2 32.4 - * * 106 LYS 106 E B 51.9 - - - - - - - - - 178.4 - 31.1 - 107 VAL 107 E B - 181.6 - - - - - - - - 180.2 -2.9 34.5 - * * 108 VAL 108 E B 56.8 - - - - - - - - - 181.4 - 32.5 - 109 GLY 109 e - - - - - - - - - - - 177.4 -2.9 - - * * 110 ALA 110 B - - - - - - - - - - 180.4 - 34.9 - 111 LYS 111 h B - - -58.2 181.2 - - - - - - 185.8 -1.1 35.1 - * * 112 LYS 112 H A - 181.2 - 179.9 - -56.5 -50.8 - - - 184.4 -.5 34.4 - * ** ** 113 ASP 113 H A - 173.6 - - - -66.2 -48.7 - - - 181.2 - 33.3 - 114 GLU 114 H A - - -61.7 189.5 - -71.2 -29.6 - - - 178.6 - 30.8 - 115 LEU 115 H A - 186.5 - - - -61.9 -51.3 - - - 179.8 -2.2 34.9 - * * 116 GLN 116 H A - - -54.4 - - -56.5 -40.7 - - - 180.7 -2.0 34.7 - 117 SER 117 H A - - -55.6 - - -68.4 -38.9 - - - 177.8 -1.8 34.1 - 118 THR 118 H A - - -55.6 - - -69.2 -32.1 - - - 176.9 -2.6 34.0 - 119 ILE 119 H A - - -61.8 175.7 - -63.8 -49.0 - - - 181.4 -2.4 33.7 - 120 ALA 120 H A - - - - - -64.1 -31.7 - - - 176.8 -2.3 33.2 - 121 LYS 121 H A - 186.7 - 179.8 - -57.8 -41.7 - - - 179.4 -1.7 36.8 - 122 HIS 122 H A - - -70.4 - - -88.0 -38.1 - - - 185.8 -1.4 33.9 - +* +* 123 LEU 123 h B - 182.1 - - - - - - - - 178.8 -3.5 34.3 - ** ** 124 ALA 124 - - - - - - - - - - - - - 34.0 - ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: * * * ** +* ** +** *7.8* +* ** +* *7.8* ----------------------------------------------------------------------------------------------------------------------------------- Mean values: 56.1 182.3 -61.5 177.6 -70.5 -66.5 -39.5 - -115.4 2.8 180.1 -2.0 34.1 +** *7.8* *7.8* Standard deviations: 8.1 4.8 6.6 5.7 15.1 8.2 9.5 - .0 .0 3.3 .8 1.8 Numbers of values: 14 44 44 32 4 46 46 0 2 2 122 81 119 0 Number of cis-peptides (labelled cis): 1 Residue-by-residue listing for refined_3 Page 5 ---------------------------------------- KEY TO CODES: ------------ Regions of the Ramachandran plot Secondary structure (extended Kabsch/Sander) -------------------------------- -------------------------------------------- A - Core alpha B - residue in isolated beta-bridge a - Allowed alpha E - extended strand, participates in beta-ladder ~a - Generous alpha ** Generous G - 3-helix (3/10 helix) B - Core beta H - 4-helix (alpha-helix) b - Allowed beta I - 5-helix (pi-helix) ~b - Generous beta ** Generous S - bend L - Core left-handed alpha T - hydrogen-bonded turn l - Allowed left-handed alpha ~l - Generous left-handed alpha ** Generous e - extension of beta-strand p - Allowed epsilon g - extension of 3/10 helix ~p - Generous epsilon ** Generous h - extension of alpha-helix XX - Outside major areas **** Disallowed Residue-by-residue listing for refined_3 Page 6 ---------------------------------------- M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S ..................................... Small molecule data ......................................... <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N --------------------------------------------------------------------------------------------------- Any - 1.231 - - - - - - - - - - ( .020) Pro 1.341 - - - 1.466 122.60 116.90 - - 111.80 103.00 122.00 ( .016) ( .015) ( 5.00) ( 1.50) ( 2.50) ( 1.10) ( 1.40) Except Pro 1.329 - - - - - - - - - - 123.00 ( .014) ( 1.60) Gly - - 1.516 - 1.451 120.60 116.40 120.80 - 112.50 - - ( .018) ( .016) ( 1.70) ( 2.10) ( 2.10) ( 2.90) Except Gly - - 1.525 - - - - 120.80 - - - - ( .021) ( 1.70) Ala - - - 1.521 - - - - 110.50 - 110.40 - ( .033) ( 1.50) ( 1.50) Ile,Thr,Val - - - 1.540 - - - - 109.10 - 111.50 - ( .027) ( 2.20) ( 1.70) Except Gly,Pro - - - - 1.458 121.70 116.20 - - 111.20 - - ( .019) ( 1.80) ( 2.00) ( 2.80) The rest - - - 1.530 - - - - 110.10 - 110.50 - ( .020) ( 1.90) ( 1.70) Note. The table above shows the mean values obtained from small molecule data by Engh & Huber (1991). The values shown in brackets are standard deviations ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 1 MET 1 - 1.235 1.502 1.536 1.462 - 116.48 120.18 109.75 108.46 111.95 123.33 * * 2 GLY 2 1.314 1.231 1.502 - 1.431 120.86 115.87 120.94 - 112.03 - 123.17 * * * 3 HIS 3 1.305 1.238 1.518 1.544 1.454 122.80 117.97 119.66 111.23 107.48 111.97 122.37 +* * +* 4 HIS 4 1.327 1.228 1.540 1.560 1.460 119.78 114.73 122.08 112.92 114.99 114.57 122.98 * * * * ** ** 5 HIS 5 1.310 1.233 1.511 1.547 1.468 124.07 114.29 121.69 108.17 106.56 112.91 124.01 * * * +* * +* 6 HIS 6 1.320 1.225 1.521 1.548 1.445 124.08 116.21 120.73 111.79 109.38 108.19 123.06 * * * 7 HIS 7 1.308 1.234 1.509 1.539 1.454 122.25 116.29 120.69 109.86 110.57 111.09 123.02 * * 8 HIS 8 1.309 1.229 1.519 1.546 1.436 121.43 115.22 120.91 110.74 109.82 111.17 123.87 * * * 9 LEU 9 1.300 1.240 1.506 1.566 1.446 124.35 118.43 118.46 110.43 105.70 112.67 123.11 ** +* * * * +* * ** 10 GLU 10 1.314 1.229 1.532 1.531 1.453 120.75 115.69 121.27 111.12 110.40 111.43 123.00 * * 11 MET 11 1.318 1.232 1.516 1.537 1.462 122.82 117.76 120.00 108.59 108.40 109.66 122.24 Residue-by-residue listing for refined_3 Page 7 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 12 ALA 12 1.312 1.245 1.518 1.522 1.442 120.39 116.81 120.29 111.05 108.42 111.04 122.88 * * 13 SER 13 1.299 1.241 1.520 1.545 1.436 121.46 117.14 120.18 111.05 108.75 109.27 122.66 ** * ** 14 GLU 14 1.315 1.238 1.511 1.526 1.428 120.82 114.64 121.40 112.12 107.05 111.88 123.87 +* * * +* 15 GLU 15 1.302 1.248 1.520 1.541 1.426 122.98 116.29 120.57 110.23 109.81 106.97 123.13 +* +* ** ** 16 GLY 16 1.308 1.229 1.496 - 1.440 120.68 117.53 119.97 - 113.98 - 122.50 * * * 17 GLN 17 1.312 1.241 1.481 1.510 1.434 119.13 112.99 122.14 110.51 113.93 114.52 124.84 * ** * * +* ** * ** 18 VAL 18 1.285 1.231 1.524 1.555 1.434 124.07 118.38 119.74 109.33 106.86 111.27 121.87 *** * * * +* *** 19 ILE 19 1.307 1.231 1.519 1.553 1.443 119.35 115.56 121.52 111.81 111.21 112.24 122.91 +* * * +* 20 ALA 20 1.305 1.240 1.513 1.518 1.433 122.05 116.29 120.82 110.52 110.04 110.40 122.89 +* * +* 21 CYS 21 1.301 1.225 1.510 1.510 1.419 121.96 116.97 120.31 109.75 108.62 109.22 122.69 ** * ** ** 22 HIS 22 1.305 1.232 1.509 1.538 1.457 121.04 115.67 120.96 110.07 110.13 111.52 123.38 +* +* 23 THR 23 1.319 1.245 1.507 1.549 1.450 122.64 116.40 120.32 107.51 109.25 111.64 123.27 24 VAL 24 1.315 1.218 1.535 1.550 1.436 121.57 116.36 120.93 110.35 109.15 111.66 122.69 * * 25 GLU 25 1.336 1.231 1.529 1.533 1.421 123.35 116.33 120.47 109.43 110.75 110.25 123.17 +* +* 26 THR 26 1.337 1.224 1.536 1.553 1.454 121.64 114.83 121.45 109.04 108.87 110.36 123.66 27 TRP 27 1.321 1.235 1.540 1.534 1.457 124.44 116.00 120.89 110.98 112.64 107.75 123.09 +* +* +* 28 ASN 28 1.314 1.236 1.525 1.535 1.458 122.96 115.60 121.25 110.22 110.52 109.26 123.14 * * 29 GLU 29 1.312 1.230 1.535 1.525 1.447 122.28 116.64 120.41 110.56 111.02 110.25 122.93 * * 30 GLN 30 1.328 1.234 1.514 1.488 1.428 122.72 116.37 120.79 110.81 112.89 109.75 122.84 ** +* ** 31 LEU 31 1.307 1.226 1.514 1.487 1.408 122.23 116.57 120.24 111.29 111.08 109.08 123.18 +* ** +** +** 32 GLN 32 1.321 1.228 1.521 1.530 1.449 121.41 115.72 120.58 111.68 109.86 111.44 123.68 33 LYS 33 1.324 1.228 1.523 1.540 1.451 122.70 116.53 120.72 110.83 110.37 110.41 122.71 34 ALA 34 1.320 1.234 1.522 1.508 1.437 120.59 114.89 121.11 111.04 110.94 110.26 123.98 * * 35 ASN 35 1.313 1.239 1.508 1.523 1.463 124.34 114.40 121.79 107.42 111.84 107.53 123.78 * * * +* +* 36 GLU 36 1.288 1.229 1.536 1.529 1.447 122.60 117.49 120.24 111.73 112.91 108.94 122.21 +** +** 37 SER 37 1.316 1.235 1.544 1.512 1.446 121.41 117.30 120.07 111.29 113.50 109.34 122.63 38 LYS 38 1.350 1.237 1.560 1.528 1.434 123.33 115.34 122.97 114.23 111.35 108.51 121.59 +* +* * * ** * ** 39 THR 39 1.292 1.237 1.522 1.521 1.418 121.32 116.07 121.27 108.98 108.20 110.66 122.63 +** ** * +** 40 LEU 40 1.272 1.239 1.520 1.563 1.427 121.27 116.91 120.02 112.71 105.90 109.80 123.06 **** +* +* * +* **** 41 VAL 41 1.300 1.231 1.520 1.563 1.428 121.11 115.70 121.36 111.72 110.80 111.20 122.89 ** +* * ** Residue-by-residue listing for refined_3 Page 8 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 42 VAL 42 1.288 1.236 1.507 1.551 1.423 121.71 116.68 121.13 111.27 108.60 111.67 122.16 +** +* +** 43 VAL 43 1.288 1.239 1.503 1.546 1.426 119.38 115.27 120.74 109.28 110.93 111.83 123.98 +** * +* * +** 44 ASP 44 1.300 1.247 1.502 1.529 1.438 122.66 115.48 121.08 110.52 109.41 111.21 123.35 ** * * ** 45 PHE 45 1.298 1.225 1.501 1.510 1.412 122.31 117.11 120.21 109.10 107.03 109.48 122.65 ** * ** * ** 46 THR 46 1.282 1.218 1.523 1.567 1.426 120.61 116.95 120.21 110.55 109.13 108.50 122.84 *** +* +* *** 47 ALA 47 1.301 1.234 1.505 1.518 1.436 121.79 116.45 120.71 111.05 108.47 111.44 122.84 ** * ** 48 SER 48 1.291 1.229 1.548 1.526 1.442 122.38 116.99 120.63 111.43 112.68 109.23 122.33 +** * +** 49 TRP 49 1.326 1.237 1.534 1.539 1.466 121.46 118.17 120.14 110.39 114.43 111.41 121.69 * * 50 CYS 50 1.307 1.236 1.539 1.537 1.449 119.54 114.39 121.62 115.07 113.80 112.59 123.98 +* * +** * +** 51 GLY 51 1.335 1.234 1.515 - 1.464 124.37 119.14 119.28 - 116.03 - 121.57 ** * * ** 52 PRO 52 1.357 1.229 1.523 1.540 1.478 122.86 115.01 121.53 110.23 111.61 103.99 123.45 * * * * 53 CYS 53 1.306 1.220 1.527 1.498 1.441 123.42 116.30 121.16 109.45 110.02 108.17 122.53 +* +* * +* 54 ARG 54 1.315 1.226 1.529 1.534 1.447 121.10 115.59 121.16 110.95 109.84 110.86 123.22 * * 55 PHE 55 1.324 1.238 1.536 1.544 1.462 123.00 116.45 120.93 109.99 111.30 109.77 122.60 56 ILE 56 1.318 1.235 1.550 1.576 1.455 121.29 115.54 121.48 110.41 109.81 110.56 122.93 * * * 57 ALA 57 1.328 1.234 1.556 1.521 1.463 123.06 120.43 118.91 111.74 114.37 111.29 120.66 * ** * * * ** 58 PRO 58 1.383 1.232 1.526 1.531 1.476 122.00 115.92 121.17 109.94 111.64 103.75 122.91 +** +** 59 PHE 59 1.316 1.219 1.526 1.533 1.440 121.50 116.51 120.85 111.42 109.98 111.52 122.63 60 PHE 60 1.318 1.231 1.535 1.541 1.462 121.66 115.72 121.32 112.12 108.90 109.99 122.95 * * 61 ALA 61 1.326 1.235 1.537 1.518 1.457 121.86 115.80 121.20 110.66 110.19 110.40 123.01 62 ASP 62 1.329 1.225 1.493 1.521 1.468 122.55 114.56 121.24 108.92 108.65 110.46 124.19 +* +* 63 LEU 63 1.313 1.236 1.526 1.527 1.434 124.09 115.70 120.79 110.29 110.67 108.60 123.49 * * * * * 64 ALA 64 1.322 1.229 1.524 1.515 1.452 123.00 116.57 120.96 110.37 111.72 110.39 122.45 65 LYS 65 1.318 1.227 1.523 1.528 1.441 120.78 116.35 120.92 111.65 110.99 110.91 122.72 66 LYS 66 1.316 1.222 1.520 1.543 1.458 121.22 117.10 120.51 112.02 112.03 112.52 122.39 * * * 67 LEU 67 1.313 1.219 1.522 1.506 1.430 121.54 116.30 121.32 112.46 110.67 110.85 122.36 * * * * * 68 PRO 68 1.332 1.226 1.533 1.534 1.473 123.43 117.18 120.45 109.67 114.47 102.64 122.37 * * 69 ASN 69 1.320 1.237 1.525 1.532 1.466 120.80 115.63 121.48 111.07 110.90 109.70 122.88 70 VAL 70 1.308 1.227 1.515 1.553 1.443 122.09 116.81 120.40 110.74 108.46 111.60 122.77 * * 71 LEU 71 1.303 1.231 1.532 1.538 1.430 120.86 116.24 120.79 111.01 110.04 109.06 122.96 +* * +* Residue-by-residue listing for refined_3 Page 9 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 72 PHE 72 1.317 1.245 1.514 1.536 1.458 122.59 116.42 120.66 107.00 108.77 111.38 122.92 +* +* 73 LEU 73 1.290 1.234 1.505 1.539 1.440 122.37 114.50 121.44 108.61 112.34 113.58 124.06 +** +* +** 74 LYS 74 1.302 1.235 1.515 1.541 1.435 123.75 116.90 120.43 109.60 107.93 109.85 122.63 +* * * * +* 75 VAL 75 1.293 1.235 1.502 1.565 1.438 121.10 116.01 120.78 110.03 109.23 112.60 123.19 +** * * +** 76 ASP 76 1.300 1.230 1.508 1.524 1.427 120.92 115.76 121.18 111.03 107.58 111.33 123.00 ** +* * ** 77 THR 77 1.299 1.233 1.518 1.526 1.431 122.94 116.87 120.57 112.46 114.14 111.40 122.55 ** * +* * ** 78 ASP 78 1.315 1.244 1.511 1.518 1.449 120.90 114.06 121.76 110.61 107.03 110.51 124.18 * * * * 79 GLU 79 1.319 1.240 1.530 1.513 1.421 124.14 116.02 120.89 109.07 110.00 108.61 123.08 +* * * +* 80 LEU 80 1.331 1.243 1.520 1.536 1.419 123.37 114.81 121.62 110.74 111.06 111.33 123.54 ** ** 81 LYS 81 1.306 1.236 1.518 1.528 1.452 123.54 115.08 121.47 109.60 109.71 109.15 123.43 +* * +* 82 SER 82 1.314 1.239 1.532 1.512 1.435 123.07 116.26 120.81 110.87 111.02 108.67 122.89 * * * * 83 VAL 83 1.324 1.234 1.527 1.557 1.454 121.60 115.66 121.19 110.45 109.26 111.63 123.08 84 ALA 84 1.329 1.228 1.520 1.519 1.454 122.19 116.39 120.96 110.10 110.90 110.34 122.65 85 SER 85 1.312 1.230 1.542 1.541 1.431 120.88 116.85 120.57 111.23 110.82 110.37 122.54 * * * 86 ASP 86 1.333 1.232 1.526 1.534 1.477 121.75 116.79 120.65 110.26 112.26 110.62 122.53 * * 87 TRP 87 1.319 1.233 1.516 1.528 1.457 121.49 115.51 120.62 110.23 111.47 111.19 123.85 88 ALA 88 1.331 1.239 1.519 1.529 1.460 123.75 114.93 121.87 111.98 111.08 112.86 123.05 * +* +* 89 ILE 89 1.296 1.237 1.509 1.548 1.430 122.35 114.71 121.55 111.82 109.62 110.88 123.68 ** * * ** 90 GLN 90 1.301 1.232 1.520 1.532 1.437 122.76 116.20 120.74 110.00 110.26 109.10 123.03 ** * ** 91 ALA 91 1.318 1.229 1.513 1.519 1.448 121.17 115.98 121.00 110.59 111.12 110.15 123.02 92 MET 92 1.303 1.233 1.526 1.531 1.447 122.03 118.78 119.89 111.04 109.18 109.51 121.33 +* * * +* 93 PRO 93 1.339 1.227 1.528 1.525 1.447 124.15 116.01 121.42 110.10 112.65 102.40 122.51 * * 94 THR 94 1.278 1.229 1.512 1.527 1.412 121.74 116.71 120.52 110.15 108.46 111.13 122.77 +*** ** +*** 95 PHE 95 1.299 1.234 1.490 1.532 1.408 121.38 116.22 120.52 108.80 106.58 110.44 123.24 ** +* +** +* +** 96 MET 96 1.290 1.241 1.496 1.521 1.426 120.77 115.21 120.99 110.35 109.49 110.93 123.79 +** * +* +** 97 PHE 97 1.292 1.246 1.512 1.516 1.396 123.15 115.91 121.65 109.10 109.60 109.09 122.43 +** *** *** 98 LEU 98 1.278 1.224 1.509 1.569 1.415 121.31 117.99 120.14 112.40 108.01 113.00 121.87 +*** +* ** * * * +*** 99 LYS 99 1.286 1.233 1.479 1.526 1.428 119.58 113.92 121.37 111.35 111.06 111.80 124.65 *** ** +* * * * *** 100 GLU 100 1.323 1.218 1.537 1.524 1.440 124.48 116.16 120.98 110.41 110.60 111.28 122.85 +* +* 101 GLY 101 1.326 1.229 1.528 - 1.448 121.32 117.27 120.05 - 113.26 - 122.67 Residue-by-residue listing for refined_3 Page 10 ---------------------------------------- ................................................................................................................................... Residue ------------- <---------- Bond lengths ----------> <---------------------- Bond angles ----------------------> No. Type Seq Max Chain no. C-N C-O CA-C CA-CB N-CA C-N-CA CA-C-N CA-C-O CB-CA-C N-CA-C N-CA-CB O-C-N dev ----------------------------------------------------------------------------------------------------------------------------------- 102 LYS 102 1.329 1.232 1.526 1.556 1.463 121.59 115.80 120.60 110.88 110.68 113.13 123.60 * +* +* 103 ILE 103 1.320 1.234 1.529 1.567 1.468 124.25 115.62 121.26 109.71 113.10 110.32 123.11 * * * 104 LEU 104 1.327 1.232 1.526 1.528 1.428 122.26 116.43 120.66 110.41 110.86 111.06 122.89 +* +* 105 ASP 105 1.320 1.218 1.510 1.535 1.452 122.21 116.40 120.84 111.00 112.30 111.68 122.71 106 LYS 106 1.313 1.237 1.523 1.558 1.454 121.55 115.74 120.99 112.49 112.95 111.81 123.27 * * * * 107 VAL 107 1.319 1.236 1.520 1.561 1.456 122.97 116.49 120.38 109.08 109.13 111.97 123.12 108 VAL 108 1.311 1.245 1.539 1.563 1.437 121.75 115.37 121.52 112.00 111.09 111.30 123.10 * * * * 109 GLY 109 1.316 1.242 1.506 - 1.432 121.68 117.48 120.18 - 110.46 - 122.32 * * 110 ALA 110 1.320 1.235 1.494 1.524 1.433 119.16 115.21 121.32 110.32 107.42 110.58 123.44 * * * * * 111 LYS 111 1.291 1.229 1.490 1.510 1.403 122.49 116.54 119.82 111.72 108.25 108.73 123.63 +** +* * +** * * +** 112 LYS 112 1.313 1.225 1.534 1.527 1.436 122.53 116.41 120.37 110.57 112.24 109.44 123.15 * * * 113 ASP 113 1.319 1.245 1.531 1.523 1.471 122.35 117.32 120.49 110.28 113.60 110.50 122.18 114 GLU 114 1.324 1.221 1.507 1.530 1.456 119.57 117.13 120.14 111.04 111.74 113.97 122.72 * ** ** 115 LEU 115 1.325 1.215 1.503 1.512 1.448 120.75 115.40 120.60 108.79 109.19 111.29 123.97 * * 116 GLN 116 1.325 1.244 1.516 1.532 1.482 122.45 115.51 120.94 108.07 110.61 111.75 123.55 * * * 117 SER 117 1.311 1.234 1.538 1.523 1.437 121.96 116.15 121.04 111.95 110.17 108.95 122.76 * * * 118 THR 118 1.323 1.239 1.544 1.549 1.443 121.97 116.42 121.06 110.70 109.71 110.80 122.51 119 ILE 119 1.335 1.208 1.513 1.549 1.444 121.21 116.80 120.13 109.86 109.78 112.20 123.01 * * 120 ALA 120 1.328 1.239 1.526 1.510 1.467 121.90 115.25 121.02 110.98 111.51 110.47 123.74 121 LYS 121 1.319 1.228 1.525 1.500 1.453 123.72 115.16 121.65 109.07 109.74 107.63 123.19 * * +* +* 122 HIS 122 1.312 1.237 1.522 1.521 1.441 122.52 116.60 120.21 109.61 112.96 110.75 123.18 * * 123 LEU 123 1.318 1.238 1.519 1.509 1.424 123.34 115.43 121.23 111.09 112.19 108.92 123.33 * +* +* 124 ALA 124 1.301 - 1.500 1.521 1.431 122.94 - - 110.90 108.14 111.09 - +* * * * +* ----------------------------------------------------------------------------------------------------------------------------------- Max deviations: **** * ** ** *** ** ** * +** +* ** * **** ----------------------------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 Page 11 ---------------------------------------- A N A L Y S I S O F M A I N C H A I N B O N D L E N G T H S A N D B O N D A N G L E S +------------------+ | BOND LENGTHS | +------------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Bond X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- C-N C-NH1 (except Pro) 1.329 .014 119 1.272 1.350 1.312 .014 **** +* * C-N (Pro) 1.341 .016 4 1.332 1.383 1.353 .020 +** C-O C-O 1.231 .020 123 1.208 1.248 1.233 .007 * CA-C CH1E-C (except Gly) 1.525 .021 119 1.479 1.560 1.520 .014 ** +* CH2G*-C (Gly) 1.516 .018 5 1.496 1.528 1.509 .011 * CA-CB CH1E-CH3E (Ala) 1.521 .033 13 1.508 1.529 1.519 .005 CH1E-CH1E (Ile,Thr,Val) 1.540 .027 22 1.521 1.576 1.552 .013 * CH1E-CH2E (the rest) 1.530 .020 84 1.487 1.569 1.530 .015 ** +* N-CA NH1-CH1E (except Gly,Pro)1.458 .019 115 1.396 1.482 1.442 .016 *** * NH1-CH2G* (Gly) 1.451 .016 5 1.431 1.464 1.443 .012 * N-CH1E (Pro) 1.466 .015 4 1.447 1.478 1.468 .012 * ------------------------------------------------------------------------------------------------------------- Residue-by-residue listing for refined_3 Page 12 ---------------------------------------- +-----------------+ | BOND ANGLES | +-----------------+ ------------------------------------------------------------------------------------------------------------- (Small molecule data) Number of Min Max Mean Standard Angle X-PLOR labelling Mean St. dev values value value value deviation ------------------------------------------------------------------------------------------------------------- CA-C-N CH1E-C-NH1 (except Gly,Pro)116.2 2.0 114 112.99 120.43 116.12 1.06 +* ** CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.87 119.14 117.46 1.04 * CH1E-C-N (Pro) 116.9 1.5 4 115.01 117.18 116.03 .77 * O-C-N O-C-NH1 (except Pro) 123.0 1.6 119 120.66 124.84 122.99 .64 * * O-C-N (Pro) 122.0 1.4 4 122.37 123.45 122.81 .42 * C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 114 119.13 124.48 122.03 1.23 * +* C-NH1-CH2G* (Gly) 120.6 1.7 5 120.68 124.37 121.78 1.34 ** C-N-CH1E (Pro) 122.6 5.0 4 122.00 124.15 123.11 .79 CA-C-O CH1E-C-O (except Gly) 120.8 1.7 118 118.46 122.97 120.85 .62 * * CH2G*-C-O (Gly) 120.8 2.1 5 119.28 120.94 120.09 .53 CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 13 110.10 111.98 110.87 .52 CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 22 107.51 112.46 110.33 1.18 +* CH2E-CH1E-C (the rest) 110.1 1.9 84 107.00 115.07 110.58 1.32 +* +** N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 115 105.70 114.99 110.24 1.91 +* * NH1-CH2G*-C (Gly) 112.5 2.9 5 110.46 116.03 113.15 1.87 * N-CH1E-C (Pro) 111.8 2.5 4 111.61 114.47 112.59 1.16 * N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 13 110.15 112.86 110.82 .71 +* NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 22 108.50 112.60 111.25 .85 +* N-CH1E-CH2E (Pro) 103.0 1.1 4 102.40 103.99 103.19 .68 NH1-CH1E-CH2E (the rest) 110.5 1.7 80 106.97 114.57 110.49 1.61 ** ** ------------------------------------------------------------------------------------------------------------- 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_3 Page 13 ---------------------------------------- R A M A C H A N D R A N P L O T S T A T I S T I C S Residues in most favoured regions [A,B,L] 98 86.7% Residues in additional allowed regions [a,b,l,p] 15 13.3% Residues in generously allowed regions [~a,~b,~l,~p] 0 .0% Residues in disallowed regions [XX] 0 .0% ---- ------ Number of non-glycine and non-proline residues 113 100.0% Number of end-residues (excl. Gly and Pro) 2 Number of glycine residues 5 Number of proline residues 4 ---- Total number of residues 124 Based on the analysis of 118 structures of resolution of at least 2.0 Angstroms and R-factor no greater than 20%, a good quality model would be expected to have over 90% in the most favoured regions [E,H,L]. S T E R E O C H E M I S T R Y O F M A I N - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. %-tage residues in A, B, L 113 86.7 83.8 10.0 .3 Inside b. Omega angle st dev 122 3.3 6.0 3.0 -.9 Inside c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside d. Zeta angle st dev 119 1.8 3.1 1.6 -.8 Inside e. H-bond energy st dev 81 .8 .8 .2 .1 Inside f. Overall G-factor 124 .1 -.4 .3 1.5 BETTER S T E R E O C H E M I S T R Y O F S I D E - C H A I N Comparison values No. of No. of Parameter Typical Band band widths Stereochemical parameter data pts value value width from mean ------------------------ -------- ----- ----- ----- --------- a. Chi-1 gauche minus st dev 14 8.1 18.1 6.5 -1.5 BETTER b. Chi-1 trans st dev 44 4.8 19.0 5.3 -2.7 BETTER c. Chi-1 gauche plus st dev 44 6.6 17.5 4.9 -2.2 BETTER d. Chi-1 pooled st dev 102 7.4 18.2 4.8 -2.2 BETTER e. Chi-2 trans st dev 32 5.7 20.4 5.0 -2.9 BETTER M O R R I S E T A L . C L A S S I F I C A T I O N Mean St.dev Classification Parameter m s 1 2 3 4 Value Class --------- ---- --- ------------------------------------ ----- ----- Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 86.7 1 Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 8.4 1 H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .83 2 Residue-by-residue listing for refined_3 Page 14 ---------------------------------------- G - F A C T O R S Average Parameter Score Score --------- ----- ----- Dihedral angles:- Phi-psi distribution -.22 Chi1-chi2 distribution .01 Chi1 only -.15 Chi3 & chi4 .30 Omega .00 ------ -.04 ===== Main-chain covalent forces:- Main-chain bond lengths .00 Main-chain bond angles .42 ------ .24 ===== OVERALL AVERAGE .05 ===== Ideally, scores should be above -0.5. Values below -1.0 may need investigation.