Residue-by-residue listing for refined_18 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 ASP 1 - - - -59.4 - - - - - - - 174.2 - 35.1 -
* *
2 PRO 2 - - - - - -60.9 - - - - - 179.7 - 39.2 -
+* +*
3 ASN 3 A - 185.8 - - - - - - - - 178.8 - 35.1 -
4 ALA 4 l - - - - - - - - - - 177.8 - 31.0 -
5 GLU 5 S A - 191.0 - - - - - - - - 178.3 - 35.3 -
6 PHE 6 S B 53.2 - - - - - - - - - 178.0 - 35.6 -
7 ASP 7 t B - 191.0 - - - - - - - - 182.7 -2.3 34.9 -
8 PRO 8 T - - - - - -60.1 - - - - - 177.5 - 37.4 -
9 ASP 9 T A - 173.7 - - - - - - - - 182.0 - 33.8 -
10 LEU 10 g B - - -77.5 - - - - - - - 179.1 -.7 32.4 -
+* +*
11 PRO 11 G - - - - - -57.3 - - - - - 179.5 - 38.4 -
* *
12 GLY 12 G - - - - - - - - - - - 179.9 -.5 - -
** **
13 GLY 13 G - - - - - - - - - - - 183.5 -2.2 - -
14 GLY 14 G - - - - - - - - - - - 182.2 -1.5 - -
15 LEU 15 g A - - -60.1 180.4 - - - - - - 183.2 -1.4 34.7 -
16 HIS 16 t b - - -56.2 - - - - - - - 179.4 -1.3 32.5 -
17 ARG 17 B B 50.0 - - - - - - - - - 171.8 -1.6 32.6 -
* *
18 CYS 18 t B - 174.8 - - - - - - - - 183.6 -2.1 33.8 -
19 LEU 19 T A - 182.9 - - - - - - - - 179.6 -.7 35.4 -
+* +*
20 ALA 20 T A - - - - - - - - - - 179.1 - 33.5 -
Residue-by-residue listing for refined_18 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
-----------------------------------------------------------------------------------------------------------------------------------
21 CYS 21 T A - - -62.5 - - - - - - - 181.5 -1.1 31.4 -
* *
22 ALA 22 t l - - - - - - - - - - 182.6 -1.5 32.9 -
23 ARG 23 B - - -60.1 - - - - - - - 180.6 - 34.4 -
24 TYR 24 B B - - -62.5 - - - - - - - 182.4 - 37.0 -
25 PHE 25 B - - -57.7 - - - - - - - 186.5 -2.7 34.2 -
* *
26 ILE 26 S A 61.5 - - 177.2 - - - - - - 178.4 - 32.8 -
27 ASP 27 h B - 181.6 - - - - - - - - 180.3 - 33.7 -
28 SER 28 H A 52.2 - - - - -57.1 -33.2 - - - 180.3 - 35.0 -
29 THR 29 H A - - -51.0 - - -66.7 -33.2 - - - 177.2 - 34.2 -
* *
30 ASN 30 H A - - -76.4 - - -69.3 -42.0 - - - 177.6 -.9 34.4 -
+* +*
31 LEU 31 H A - 172.4 - - - -62.6 -50.5 - - - 177.1 -1.8 33.0 -
32 LYS 32 H A - - -62.9 182.7 - -59.8 -43.0 - - - 178.4 -3.2 33.0 -
+* +*
33 THR 33 H A - - -55.9 - - -64.7 -31.5 - - - 175.5 -2.5 33.4 -
34 HIS 34 H A - 159.6 - - - -59.0 -30.0 - - - 181.7 -1.8 32.8 -
* *
35 PHE 35 h A - - -50.2 - - - - - - - 177.0 -1.0 32.4 -
* * *
36 ARG 36 T A - - -65.4 - - - - - - - 169.6 -1.9 30.8 -
+* +*
37 SER 37 h b - 178.7 - - - - - - - - 182.8 -.9 35.1 -
* *
38 LYS 38 H A 62.5 - - - - -65.3 -25.8 - - - 176.3 -1.2 31.0 -
* * *
39 ASP 39 H A - 177.6 - - - -66.5 -34.6 - - - 180.5 - 35.6 -
40 HIS 40 H A - 185.7 - - - -72.9 -47.7 - - - 180.3 - 36.4 -
41 LYS 41 H A - - -60.3 192.2 - -68.7 -28.6 - - - 166.7 -2.0 28.5 -
** +* **
42 LYS 42 H A - 166.1 - - - -56.8 -50.5 - - - 176.2 -1.9 36.5 -
* *
43 ARG 43 H A - - -80.9 - - -53.7 -36.5 - - - 178.0 -2.1 35.2 -
44 LEU 44 H A - - -84.7 - - -74.6 -37.5 - - - 174.8 -1.8 32.3 -
* *
45 LYS 45 H A - - -66.9 182.4 - -61.7 -48.3 - - - 179.8 -2.1 33.5 -
46 GLN 46 H A - - -57.0 - - -64.4 -32.8 - - - 177.3 -2.9 33.2 -
* *
47 LEU 47 H A - 185.2 - 170.9 - -65.0 -38.3 - - - 183.8 -1.5 35.1 -
48 SER 48 H A - - -55.2 - - -84.2 -11.7 - - - 179.6 -2.0 34.8 -
+* ** **
49 VAL 49 H a - 176.9 - - - -106.6 -49.8 - - - 184.9 -.9 34.1 -
*** * ***
50 GLU 50 h B - - -54.1 177.1 - - - - - - 171.4 -3.2 36.6 -
* * *
51 PRO 51 - - - - - -72.4 - - - - - 179.8 - 38.8 -
* *
52 TYR 52 B - - -67.5 - - - - - - - 175.9 - 34.4 -
53 SER 53 S A 46.5 - - - - - - - - - 173.7 - 33.3 -
* * *
54 GLN 54 t a 69.6 - - - - - - - - - 183.4 - 30.6 -
55 GLU 55 T l - 182.6 - 178.6 - - - - - - 184.8 - 32.8 -
56 GLU 56 T l - 184.3 - 184.2 - - - - - - 181.9 - 33.0 -
57 ALA 57 t b - - - - - - - - - - 174.5 -2.0 33.7 -
58 GLU 58 S A - - -61.9 181.3 - - - - - - 177.4 -1.9 33.1 -
Residue-by-residue listing for refined_18 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
-----------------------------------------------------------------------------------------------------------------------------------
59 ARG 59 b - 176.5 - 182.1 - - - - - - 179.0 - 34.8 -
60 ALA 60 S a - - - - - - - - - - 178.4 - 33.3 -
61 ALA 61 S b - - - - - - - - - - 180.8 - 33.2 -
62 GLY 62 S - - - - - - - - - - - 179.9 - - -
63 MET 63 S b - 186.4 - 182.6 - - - - - - 180.2 - 35.0 -
64 GLY 64 S - - - - - - - - - - - 180.8 - - -
65 SER 65 B - - -55.8 - - - - - - - 177.4 - 35.6 -
66 TYR 66 B 62.3 - - - - - - - - - 180.6 - 34.1 -
67 VAL 67 - 61.6 - - - - - - - - - - - 27.0 -
+* +*
-----------------------------------------------------------------------------------------------------------------------------------
Max deviations: * * * *** ** ** ** +* ***
-----------------------------------------------------------------------------------------------------------------------------------
Mean values: 57.7 179.6 -62.6 181.0 -62.7 -67.3 -37.1 - - - 179.1 -1.7 34.0
Standard deviations: 7.5 8.1 9.1 5.1 6.7 11.9 10.0 - - - 3.6 .7 2.2
Numbers of values: 9 19 24 12 4 19 19 0 0 0 66 34 62 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_18 Page 4
----------------------------------------
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 ASP 1 - 1.230 1.494 1.542 1.460 - 118.69 119.23 109.34 108.06 111.08 122.06
* * * *
2 PRO 2 1.347 1.237 1.527 1.535 1.461 121.80 117.01 120.28 109.81 109.95 103.59 122.71
3 ASN 3 1.312 1.240 1.513 1.528 1.460 121.68 114.51 121.24 110.31 108.55 109.62 124.23
* *
4 ALA 4 1.326 1.235 1.521 1.537 1.443 123.97 114.83 121.91 112.62 111.46 112.40 123.09
* * * *
5 GLU 5 1.316 1.224 1.526 1.532 1.436 122.67 113.85 122.48 110.61 107.97 109.30 123.68
* * * *
6 PHE 6 1.296 1.240 1.522 1.535 1.429 124.06 116.84 120.09 110.52 109.39 108.81 123.07
** +* * **
7 ASP 7 1.317 1.229 1.523 1.529 1.450 121.10 117.93 120.04 108.99 108.27 111.32 122.00
* *
8 PRO 8 1.344 1.227 1.535 1.533 1.474 123.25 118.06 119.88 110.99 115.13 103.89 122.06
* *
9 ASP 9 1.316 1.238 1.506 1.530 1.463 120.23 115.13 121.36 109.66 109.59 111.95 123.44
10 LEU 10 1.301 1.239 1.516 1.545 1.437 121.98 117.34 120.49 111.38 111.16 112.01 122.13
** * **
11 PRO 11 1.348 1.244 1.514 1.530 1.459 122.61 115.46 120.98 110.45 111.17 104.07 123.47
* *
12 GLY 12 1.321 1.241 1.497 - 1.437 121.30 115.37 121.04 - 111.35 - 123.52
* *
Residue-by-residue listing for refined_18 Page 5
----------------------------------------
...................................................................................................................................
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
-----------------------------------------------------------------------------------------------------------------------------------
13 GLY 13 1.325 1.240 1.508 - 1.433 121.92 115.50 121.17 - 111.81 - 123.33
* *
14 GLY 14 1.324 1.223 1.509 - 1.433 121.69 116.25 120.81 - 111.31 - 122.94
* *
15 LEU 15 1.321 1.230 1.511 1.524 1.430 122.00 116.00 121.16 110.21 111.00 109.85 122.80
* *
16 HIS 16 1.305 1.234 1.496 1.532 1.447 120.74 115.01 121.57 110.16 110.14 113.35 123.32
+* * +* +*
17 ARG 17 1.284 1.232 1.495 1.545 1.419 121.72 115.10 121.10 111.47 112.52 111.33 123.75
*** * ** ***
18 CYS 18 1.298 1.234 1.509 1.546 1.438 121.87 116.78 119.96 111.32 106.68 111.51 123.26
** * +* **
19 LEU 19 1.311 1.229 1.501 1.521 1.439 123.05 114.91 121.23 110.29 109.74 109.07 123.81
* * * *
20 ALA 20 1.311 1.221 1.540 1.521 1.457 122.63 117.20 120.43 110.65 112.26 110.38 122.37
* *
21 CYS 21 1.332 1.230 1.509 1.534 1.455 120.39 116.17 120.10 111.99 113.30 111.63 123.73
22 ALA 22 1.338 1.223 1.533 1.531 1.471 123.74 116.32 121.01 110.98 111.23 111.19 122.59
* *
23 ARG 23 1.319 1.243 1.491 1.536 1.442 121.82 115.00 120.82 108.91 109.54 112.10 124.18
+* +*
24 TYR 24 1.289 1.229 1.504 1.520 1.412 124.00 117.07 119.99 109.26 108.00 108.34 122.94
+** ** * * * +**
25 PHE 25 1.300 1.226 1.499 1.524 1.442 120.86 116.66 120.00 110.97 109.07 110.38 123.34
** * **
26 ILE 26 1.322 1.233 1.522 1.542 1.448 122.80 116.73 120.61 110.16 112.90 111.88 122.65
27 ASP 27 1.309 1.239 1.498 1.541 1.439 120.76 116.21 119.92 111.03 109.12 111.24 123.87
* * * *
28 SER 28 1.313 1.216 1.524 1.523 1.444 123.66 116.75 120.35 111.27 111.49 108.04 122.84
* * * *
29 THR 29 1.325 1.224 1.538 1.523 1.442 121.93 116.72 120.80 110.61 110.53 110.06 122.42
30 ASN 30 1.334 1.225 1.497 1.527 1.440 122.16 114.70 121.40 110.53 109.46 110.43 123.88
* *
31 LEU 31 1.301 1.231 1.538 1.559 1.430 123.04 116.07 120.74 114.38 110.72 108.37 123.19
** * * ** * **
32 LYS 32 1.306 1.241 1.534 1.528 1.475 122.21 117.00 120.37 109.77 112.27 111.91 122.63
+* +*
33 THR 33 1.333 1.231 1.535 1.538 1.460 121.51 115.56 121.38 110.77 110.11 111.27 123.02
34 HIS 34 1.320 1.234 1.534 1.560 1.451 122.98 117.72 120.61 111.68 112.01 110.82 121.67
+* +*
35 PHE 35 1.314 1.205 1.515 1.521 1.439 118.45 117.95 120.02 108.92 111.04 114.13 122.02
* * * +* ** **
36 ARG 36 1.336 1.240 1.523 1.529 1.470 120.16 114.87 121.44 112.49 111.04 112.66 123.69
* * *
37 SER 37 1.316 1.244 1.544 1.544 1.416 123.31 115.57 121.61 111.51 106.92 109.26 122.70
** +* **
38 LYS 38 1.316 1.229 1.529 1.557 1.457 122.96 116.51 120.50 112.06 112.45 112.57 122.98
* * * *
39 ASP 39 1.324 1.232 1.510 1.527 1.473 122.46 114.36 121.92 108.97 109.20 110.00 123.71
40 HIS 40 1.299 1.195 1.476 1.495 1.444 123.42 117.04 120.47 108.52 110.28 108.99 122.47
** +* ** +* **
41 LYS 41 1.284 1.229 1.524 1.492 1.420 118.96 115.61 120.80 115.24 111.45 112.76 123.59
*** +* +* +* +** * ***
42 LYS 42 1.324 1.229 1.536 1.527 1.459 122.94 115.15 121.22 109.21 108.73 108.49 123.63
* *
Residue-by-residue listing for refined_18 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
-----------------------------------------------------------------------------------------------------------------------------------
43 ARG 43 1.330 1.226 1.529 1.532 1.456 124.25 116.05 120.90 110.40 111.65 108.63 123.05
* * *
44 LEU 44 1.312 1.235 1.517 1.523 1.439 123.06 116.64 120.44 111.79 112.16 111.03 122.91
* *
45 LYS 45 1.319 1.220 1.511 1.535 1.459 121.10 115.96 120.74 109.44 109.41 112.71 123.25
* *
46 GLN 46 1.324 1.204 1.522 1.524 1.450 121.74 116.25 120.70 111.16 110.67 110.98 123.00
* *
47 LEU 47 1.323 1.232 1.537 1.551 1.463 122.95 115.77 121.30 111.62 109.67 108.26 122.91
* * *
48 SER 48 1.315 1.235 1.541 1.529 1.450 122.27 116.47 120.90 110.56 111.86 108.89 122.62
49 VAL 49 1.314 1.229 1.524 1.557 1.454 121.77 115.92 121.14 109.63 110.77 111.41 122.91
* *
50 GLU 50 1.306 1.236 1.518 1.525 1.437 122.20 117.77 120.54 107.69 110.49 109.70 121.67
+* * * +*
51 PRO 51 1.323 1.246 1.542 1.535 1.450 121.77 117.39 120.42 110.68 109.25 103.57 122.18
* * * *
52 TYR 52 1.305 1.227 1.515 1.531 1.452 121.03 115.84 120.94 108.29 110.86 112.10 123.22
+* +*
53 SER 53 1.308 1.232 1.531 1.518 1.436 122.41 115.04 121.61 113.51 110.61 108.47 123.34
+* * +* * +*
54 GLN 54 1.286 1.205 1.513 1.588 1.468 123.26 115.52 121.27 112.33 109.35 114.50 123.21
*** * +** * ** ***
55 GLU 55 1.341 1.232 1.549 1.567 1.490 123.94 114.84 121.95 112.26 109.52 110.81 123.15
* +* +* * * +*
56 GLU 56 1.351 1.235 1.548 1.551 1.470 124.09 114.80 122.48 112.29 108.63 110.80 122.66
+* * * * * +*
57 ALA 57 1.315 1.224 1.516 1.527 1.426 122.89 115.49 121.51 111.06 111.26 110.41 122.87
+* +*
58 GLU 58 1.306 1.226 1.510 1.526 1.442 121.73 114.12 122.34 111.64 108.49 111.44 123.53
+* * +*
59 ARG 59 1.302 1.230 1.520 1.534 1.423 123.93 116.79 120.54 110.48 108.23 110.34 122.53
+* +* * * +*
60 ALA 60 1.307 1.238 1.516 1.525 1.444 120.78 115.53 120.67 111.20 109.78 111.09 123.76
+* +*
61 ALA 61 1.315 1.245 1.510 1.531 1.446 124.26 115.50 121.13 110.53 108.48 112.40 123.20
* * *
62 GLY 62 1.296 1.235 1.487 - 1.426 121.02 116.16 120.37 - 110.95 - 123.45
** +* +* **
63 MET 63 1.301 1.239 1.523 1.530 1.434 121.97 116.18 121.07 110.05 109.17 110.08 122.75
** * **
64 GLY 64 1.293 1.235 1.494 - 1.431 121.41 115.89 120.66 - 110.98 - 123.42
+** * * +**
65 SER 65 1.298 1.245 1.526 1.518 1.429 122.11 116.80 120.52 109.62 110.40 109.16 122.68
** +* **
66 TYR 66 1.309 1.239 1.530 1.534 1.406 121.49 116.05 119.63 111.56 109.20 110.03 124.31
* +** +**
67 VAL 67 1.333 - 1.551 1.589 1.479 125.43 - - 113.51 114.29 115.16 -
* +* * ** ** * ** **
-----------------------------------------------------------------------------------------------------------------------------------
Max deviations: *** +* ** +** +** ** * +** +* ** * ***
-----------------------------------------------------------------------------------------------------------------------------------
Residue-by-residue listing for refined_18 Page 7
----------------------------------------
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 62 1.284 1.351 1.314 .014
*** +* *
C-N (Pro) 1.341 .016 4 1.323 1.348 1.340 .010
*
C-O C-O 1.231 .020 66 1.195 1.246 1.231 .010
+*
CA-C CH1E-C (except Gly) 1.525 .021 62 1.476 1.551 1.520 .016
** *
CH2G*-C (Gly) 1.516 .018 5 1.487 1.509 1.499 .008
+*
CA-CB CH1E-CH3E (Ala) 1.521 .033 6 1.521 1.537 1.529 .005
CH1E-CH1E (Ile,Thr,Val) 1.540 .027 5 1.523 1.589 1.550 .022
+*
CH1E-CH2E (the rest) 1.530 .020 51 1.492 1.588 1.533 .016
+* +**
N-CA NH1-CH1E (except Gly,Pro)1.458 .019 58 1.406 1.490 1.446 .017
+** +*
NH1-CH2G* (Gly) 1.451 .016 5 1.426 1.437 1.432 .003
+* *
N-CH1E (Pro) 1.466 .015 4 1.450 1.474 1.461 .009
*
-------------------------------------------------------------------------------------------------------------
Residue-by-residue listing for refined_18 Page 8
----------------------------------------
+-----------------+
| 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 57 113.85 118.69 116.02 1.04
* *
CH2G*-C-NH1 (Gly) 116.4 2.1 5 115.37 116.25 115.83 .35
CH1E-C-N (Pro) 116.9 1.5 4 115.46 118.06 116.98 .95
O-C-N O-C-NH1 (except Pro) 123.0 1.6 62 121.67 124.31 123.08 .59
O-C-N (Pro) 122.0 1.4 4 122.06 123.47 122.61 .56
*
C-N-CA C-NH1-CH1E (except Gly,Pro)121.7 1.8 57 118.45 125.43 122.30 1.34
+* **
C-NH1-CH2G* (Gly) 120.6 1.7 5 121.02 121.92 121.47 .31
C-N-CH1E (Pro) 122.6 5.0 4 121.77 123.25 122.36 .62
CA-C-O CH1E-C-O (except Gly) 120.8 1.7 61 119.23 122.48 120.86 .68
CH2G*-C-O (Gly) 120.8 2.1 5 120.37 121.17 120.81 .28
CB-CA-C CH3E-CH1E-C (Ala) 110.5 1.5 6 110.53 112.62 111.17 .69
*
CH1E-CH1E-C (Ile,Thr,Val) 109.1 2.2 5 109.63 113.51 110.94 1.35
**
CH2E-CH1E-C (the rest) 110.1 1.9 51 107.69 115.24 110.74 1.46
* +**
N-CA-C NH1-CH1E-C (except Gly,Pro)111.2 2.8 58 106.68 114.29 110.22 1.58
+* *
NH1-CH2G*-C (Gly) 112.5 2.9 5 110.95 111.81 111.28 .31
N-CH1E-C (Pro) 111.8 2.5 4 109.25 115.13 111.37 2.28
* *
N-CA-CB NH1-CH1E-CH3E (Ala) 110.4 1.5 6 110.38 112.40 111.31 .83
*
NH1-CH1E-CH1E (Ile,Thr,Val) 111.5 1.7 5 110.06 115.16 111.96 1.71
**
N-CH1E-CH2E (Pro) 103.0 1.1 4 103.57 104.07 103.78 .21
NH1-CH1E-CH2E (the rest) 110.5 1.7 47 108.04 114.50 110.62 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_18 Page 9
----------------------------------------
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] 43 76.8%
Residues in additional allowed regions [a,b,l,p] 13 23.2%
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 56 100.0%
Number of end-residues (excl. Gly and Pro) 2
Number of glycine residues 5
Number of proline residues 4
----
Total number of residues 67
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 56 76.8 83.8 10.0 -.7 Inside
b. Omega angle st dev 66 3.6 6.0 3.0 -.8 Inside
c. Bad contacts / 100 residues 0 .0 4.2 10.0 -.4 Inside
d. Zeta angle st dev 62 2.2 3.1 1.6 -.6 Inside
e. H-bond energy st dev 34 .7 .8 .2 -.6 Inside
f. Overall G-factor 67 .0 -.4 .3 1.4 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 9 7.5 18.1 6.5 -1.6 BETTER
b. Chi-1 trans st dev 19 8.1 19.0 5.3 -2.1 BETTER
c. Chi-1 gauche plus st dev 24 9.1 17.5 4.9 -1.7 BETTER
d. Chi-1 pooled st dev 52 9.7 18.2 4.8 -1.7 BETTER
e. Chi-2 trans st dev 12 5.1 20.4 5.0 -3.1 BETTER
M O R R I S E T A L . C L A S S I F I C A T I O N
Mean St.dev Classification
Parameter m s 1 2 3 4 Value Class
--------- ---- --- ------------------------------------ ----- -----
Phi-psi distribution - - >75.0% >65.0% >55.0% <55.0% 76.8 1
Chi-1 st.dev. 18.2 6.2 <12.0 <18.2 <24.4 >24.4 10.1 1
H-bond energy st dev .87 .24 < .63 < .87 <1.11 >1.11 .76 2
Residue-by-residue listing for refined_18 Page 10
----------------------------------------
G - F A C T O R S
Average
Parameter Score Score
--------- ----- -----
Dihedral angles:-
Phi-psi distribution -.42
Chi1-chi2 distribution -.26
Chi1 only .08
Chi3 & chi4 .38
Omega .10
------ -.09
=====
Main-chain covalent forces:-
Main-chain bond lengths .03
Main-chain bond angles .39
------ .24
=====
OVERALL AVERAGE .02
=====
Ideally, scores should be above -0.5. Values below -1.0 may need investigation.