
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms   19 (  147),  selected   19 , name T0295TS193_1_2-D1
# Molecule2: number of CA atoms  180 ( 1390),  selected  180 , name T0295_D1.pdb
# PARAMETERS: T0295TS193_1_2-D1.T0295_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      H       1           -
LGA    -       -      L       2           -
LGA    -       -      L       3           -
LGA    -       -      K       4           -
LGA    -       -      N       5           -
LGA    -       -      P       6           -
LGA    -       -      G       7           -
LGA    -       -      I       8           -
LGA    -       -      L       9           -
LGA    -       -      D      10           -
LGA    -       -      K      11           -
LGA    -       -      I      12           -
LGA    -       -      I      13           -
LGA    -       -      Y      14           -
LGA    -       -      A      15           -
LGA    -       -      A      16           -
LGA    -       -      K      17           -
LGA    -       -      I      18           -
LGA    -       -      K      19           -
LGA    -       -      S      20           -
LGA    -       -      S      21           -
LGA    -       -      D      22           -
LGA    -       -      I      23           -
LGA    -       -      V      24           -
LGA    -       -      L      25           -
LGA    -       -      E      26           -
LGA    -       -      I      27           -
LGA    -       -      G      28           -
LGA    -       -      C      29           -
LGA    -       -      G      30           -
LGA    -       -      T      31           -
LGA    -       -      G      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      T      35           -
LGA    -       -      V      36           -
LGA    -       -      K      37           -
LGA    -       -      L      38           -
LGA    -       -      L      39           -
LGA    -       -      P      40           -
LGA    -       -      L      41           -
LGA    -       -      A      42           -
LGA    -       -      K      43           -
LGA    -       -      K      44           -
LGA    -       -      V      45           -
LGA    P     162      I      46          1.986
LGA    P     163      T      47          1.756
LGA    K     164      I      48          1.224
LGA    V     165      D      49          1.137
LGA    D     166      I      50          3.060
LGA    -       -      D      51           -
LGA    -       -      S      52           -
LGA    -       -      R      53           -
LGA    -       -      M      54           -
LGA    -       -      I      55           -
LGA    -       -      S      56           -
LGA    -       -      E      57           -
LGA    -       -      V      58           -
LGA    -       -      K      59           -
LGA    -       -      K      60           -
LGA    -       -      R      61           -
LGA    -       -      C      62           -
LGA    -       -      L      63           -
LGA    -       -      Y      64           -
LGA    -       -      E      65           -
LGA    -       -      G      66           -
LGA    -       -      Y      67           -
LGA    -       -      N      68           -
LGA    -       -      N      69           -
LGA    -       -      L      70           -
LGA    -       -      E      71           -
LGA    -       -      V      72           -
LGA    -       -      Y      73           -
LGA    -       -      E      74           -
LGA    S     167      G      75          2.598
LGA    V     168      D      76          3.807
LGA    I     169      -       -           -
LGA    V     170      A      77          3.076
LGA    K     171      I      78          5.651
LGA    -       -      K      79           -
LGA    -       -      T      80           -
LGA    -       -      V      81           -
LGA    -       -      F      82           -
LGA    -       -      P      83           -
LGA    -       -      K      84           -
LGA    -       -      F      85           -
LGA    -       -      D      86           -
LGA    -       -      V      87           -
LGA    -       -      C      88           -
LGA    -       -      T      89           -
LGA    -       -      A      90           -
LGA    -       -      N      91           -
LGA    -       -      I      92           -
LGA    L     172      P      93          3.022
LGA    I     173      Y      94          2.369
LGA    -       -      K      95           -
LGA    P     174      I      96          2.619
LGA    K     175      S      97          3.888
LGA    -       -      S      98           -
LGA    -       -      P      99           -
LGA    -       -      L     100           -
LGA    -       -      I     101           -
LGA    -       -      F     102           -
LGA    -       -      K     103           -
LGA    -       -      L     104           -
LGA    -       -      I     105           -
LGA    -       -      S     106           -
LGA    -       -      H     107           -
LGA    -       -      R     108           -
LGA    -       -      P     109           -
LGA    -       -      L     110           -
LGA    -       -      F     111           -
LGA    -       -      K     112           -
LGA    -       -      C     113           -
LGA    -       -      A     114           -
LGA    -       -      V     115           -
LGA    E     176      L     116          3.871
LGA    S     177      M     117          3.277
LGA    S     178      F     118          1.710
LGA    F     179      Q     119          2.815
LGA    -       -      K     120           -
LGA    -       -      E     121           -
LGA    -       -      F     122           -
LGA    L     180      A     123          0.365
LGA    -       -      E     124           -
LGA    -       -      R     125           -
LGA    -       -      M     126           -
LGA    -       -      L     127           -
LGA    -       -      A     128           -
LGA    -       -      N     129           -
LGA    -       -      V     130           -
LGA    -       -      G     131           -
LGA    -       -      D     132           -
LGA    -       -      S     133           -
LGA    -       -      N     134           -
LGA    -       -      Y     135           -
LGA    -       -      S     136           -
LGA    -       -      R     137           -
LGA    -       -      L     138           -
LGA    -       -      T     139           -
LGA    -       -      I     140           -
LGA    -       -      N     141           -
LGA    -       -      V     142           -
LGA    -       -      K     143           -
LGA    -       -      L     144           -
LGA    -       -      F     145           -
LGA    -       -      C     146           -
LGA    -       -      K     147           -
LGA    -       -      V     148           -
LGA    -       -      T     149           -
LGA    -       -      K     150           -
LGA    -       -      V     151           -
LGA    -       -      C     152           -
LGA    -       -      N     153           -
LGA    -       -      V     154           -
LGA    -       -      N     155           -
LGA    -       -      R     156           -
LGA    -       -      S     157           -
LGA    -       -      S     158           -
LGA    -       -      F     159           -
LGA    -       -      N     160           -
LGA    -       -      P     161           -
LGA    -       -      P     162           -
LGA    -       -      P     163           -
LGA    -       -      K     164           -
LGA    -       -      V     165           -
LGA    -       -      D     166           -
LGA    -       -      S     167           -
LGA    -       -      V     168           -
LGA    -       -      I     169           -
LGA    -       -      V     170           -
LGA    -       -      K     171           -
LGA    -       -      L     172           -
LGA    -       -      I     173           -
LGA    -       -      P     174           -
LGA    -       -      K     175           -
LGA    -       -      E     176           -
LGA    -       -      S     177           -
LGA    -       -      S     178           -
LGA    -       -      F     179           -
LGA    -       -      L     180           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19  180    5.0     18    2.94     0.00      6.183     0.593

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.045474 * X  +  -0.197514 * Y  +   0.979245 * Z  +   1.496762
  Y_new =  -0.558758 * X  +  -0.807547 * Y  +  -0.188830 * Z  +   2.065626
  Z_new =   0.828083 * X  +  -0.555748 * Y  +  -0.073640 * Z  +  27.327208 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.702535    1.439058  [ DEG:   -97.5481     82.4519 ]
  Theta =  -0.975680   -2.165913  [ DEG:   -55.9023   -124.0977 ]
  Phi   =  -1.652002    1.489591  [ DEG:   -94.6527     85.3473 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0295TS193_1_2-D1                             
REMARK     2: T0295_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295TS193_1_2-D1.T0295_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19  180   5.0   18   2.94    0.00   6.183
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS193_1_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0295
PARENT N/A
ATOM   1272  N   PRO   162      -2.425   4.664  27.308  1.00  0.00
ATOM   1273  CA  PRO   162      -0.994   4.401  27.221  1.00  0.00
ATOM   1274  C   PRO   162      -0.320   5.348  26.235  1.00  0.00
ATOM   1275  O   PRO   162      -0.934   5.786  25.263  1.00  0.00
ATOM   1276  CB  PRO   162      -0.912   2.949  26.745  1.00  0.00
ATOM   1277  CG  PRO   162      -2.107   2.776  25.868  1.00  0.00
ATOM   1278  CD  PRO   162      -3.232   3.508  26.547  1.00  0.00
ATOM   1279  N   PRO   163      -1.917   3.815  24.806  1.00  0.00
ATOM   1280  CA  PRO   163      -2.504   4.271  23.551  1.00  0.00
ATOM   1281  C   PRO   163      -3.726   5.146  23.801  1.00  0.00
ATOM   1282  O   PRO   163      -4.532   4.864  24.688  1.00  0.00
ATOM   1283  CB  PRO   163      -2.882   2.977  22.828  1.00  0.00
ATOM   1284  CG  PRO   163      -1.964   1.948  23.396  1.00  0.00
ATOM   1285  CD  PRO   163      -1.803   2.292  24.851  1.00  0.00
ATOM   1286  N   LYS   164      -3.858   6.207  23.013  1.00  0.00
ATOM   1287  CA  LYS   164      -5.005   7.101  23.117  1.00  0.00
ATOM   1288  C   LYS   164      -6.206   6.547  22.360  1.00  0.00
ATOM   1289  O   LYS   164      -6.060   5.696  21.483  1.00  0.00
ATOM   1290  CB  LYS   164      -4.669   8.474  22.533  1.00  0.00
ATOM   1291  CG  LYS   164      -3.497   9.167  23.210  1.00  0.00
ATOM   1292  CD  LYS   164      -3.830   9.539  24.646  1.00  0.00
ATOM   1293  CE  LYS   164      -2.735  10.394  25.262  1.00  0.00
ATOM   1294  NZ  LYS   164      -3.076  10.821  26.647  1.00  0.00
ATOM   1295  N   VAL   165      -7.393   7.036  22.703  1.00  0.00
ATOM   1296  CA  VAL   165      -8.620   6.600  22.047  1.00  0.00
ATOM   1297  C   VAL   165      -8.629   6.999  20.577  1.00  0.00
ATOM   1298  O   VAL   165      -8.521   8.178  20.242  1.00  0.00
ATOM   1299  CB  VAL   165      -9.864   7.224  22.705  1.00  0.00
ATOM   1300  CG1 VAL   165     -11.123   6.820  21.954  1.00  0.00
ATOM   1301  CG2 VAL   165      -9.995   6.759  24.147  1.00  0.00
ATOM   1302  N   ASP   166      -8.306   8.914  22.357  1.00  0.00
ATOM   1303  CA  ASP   166      -8.205  10.319  21.977  1.00  0.00
ATOM   1304  C   ASP   166      -6.997  10.561  21.081  1.00  0.00
ATOM   1305  O   ASP   166      -7.084  11.282  20.087  1.00  0.00
ATOM   1306  CB  ASP   166      -8.060  11.201  23.219  1.00  0.00
ATOM   1307  CG  ASP   166      -9.351  11.313  24.007  1.00  0.00
ATOM   1308  OD1 ASP   166     -10.408  10.911  23.476  1.00  0.00
ATOM   1309  OD2 ASP   166      -9.305  11.804  25.155  1.00  0.00
ATOM   1310  N   SER   167      -5.870   9.956  21.439  1.00  0.00
ATOM   1311  CA  SER   167      -4.645  10.093  20.659  1.00  0.00
ATOM   1312  C   SER   167      -4.747   9.346  19.336  1.00  0.00
ATOM   1313  O   SER   167      -4.113   9.720  18.350  1.00  0.00
ATOM   1314  CB  SER   167      -3.452   9.528  21.433  1.00  0.00
ATOM   1315  OG  SER   167      -3.573   8.128  21.607  1.00  0.00
ATOM   1316  N   VAL   168      -5.548   8.286  19.322  1.00  0.00
ATOM   1317  CA  VAL   168      -5.790   7.524  18.102  1.00  0.00
ATOM   1318  C   VAL   168      -6.411   8.399  17.021  1.00  0.00
ATOM   1319  O   VAL   168      -6.090   8.266  15.840  1.00  0.00
ATOM   1320  CB  VAL   168      -6.749   6.345  18.353  1.00  0.00
ATOM   1321  CG1 VAL   168      -6.150   5.377  19.361  1.00  0.00
ATOM   1322  CG2 VAL   168      -8.078   6.846  18.898  1.00  0.00
ATOM   1323  N   ILE   169      -6.783   9.708  17.422  1.00  0.00
ATOM   1324  CA  ILE   169      -7.202  10.730  16.470  1.00  0.00
ATOM   1325  C   ILE   169      -6.022  11.235  15.649  1.00  0.00
ATOM   1326  O   ILE   169      -6.135  11.435  14.440  1.00  0.00
ATOM   1327  CB  ILE   169      -7.824  11.945  17.185  1.00  0.00
ATOM   1328  CG1 ILE   169      -9.152  11.557  17.838  1.00  0.00
ATOM   1329  CG2 ILE   169      -8.084  13.068  16.193  1.00  0.00
ATOM   1330  CD1 ILE   169      -9.699  12.610  18.777  1.00  0.00
ATOM   1331  N   VAL   170      -4.889  11.438  16.313  1.00  0.00
ATOM   1332  CA  VAL   170      -3.676  11.886  15.640  1.00  0.00
ATOM   1333  C   VAL   170      -3.098  10.787  14.756  1.00  0.00
ATOM   1334  O   VAL   170      -2.544  11.060  13.692  1.00  0.00
ATOM   1335  CB  VAL   170      -2.586  12.290  16.650  1.00  0.00
ATOM   1336  CG1 VAL   170      -1.276  12.578  15.933  1.00  0.00
ATOM   1337  CG2 VAL   170      -3.001  13.539  17.412  1.00  0.00
ATOM   1338  N   LYS   171      -3.233   9.543  15.204  1.00  0.00
ATOM   1339  CA  LYS   171      -2.727   8.400  14.453  1.00  0.00
ATOM   1340  C   LYS   171      -3.529   8.182  13.175  1.00  0.00
ATOM   1341  O   LYS   171      -2.987   7.751  12.158  1.00  0.00
ATOM   1342  CB  LYS   171      -2.818   7.124  15.294  1.00  0.00
ATOM   1343  CG  LYS   171      -1.842   7.078  16.459  1.00  0.00
ATOM   1344  CD  LYS   171      -1.989   5.790  17.251  1.00  0.00
ATOM   1345  CE  LYS   171      -1.014   5.743  18.416  1.00  0.00
ATOM   1346  NZ  LYS   171      -1.166   4.498  19.218  1.00  0.00
ATOM   1347  N   LEU   172      -4.821   8.483  13.236  1.00  0.00
ATOM   1348  CA  LEU   172      -5.743   8.116  12.167  1.00  0.00
ATOM   1349  C   LEU   172      -5.952   9.272  11.198  1.00  0.00
ATOM   1350  O   LEU   172      -6.700   9.155  10.228  1.00  0.00
ATOM   1351  CB  LEU   172      -7.107   7.730  12.745  1.00  0.00
ATOM   1352  CG  LEU   172      -7.117   6.564  13.736  1.00  0.00
ATOM   1353  CD1 LEU   172      -8.520   6.331  14.276  1.00  0.00
ATOM   1354  CD2 LEU   172      -6.648   5.283  13.065  1.00  0.00
ATOM   1355  N   ILE   173      -6.785   8.084   8.251  1.00  0.00
ATOM   1356  CA  ILE   173      -5.575   7.308   8.492  1.00  0.00
ATOM   1357  C   ILE   173      -4.337   8.195   8.467  1.00  0.00
ATOM   1358  O   ILE   173      -4.262   9.152   7.696  1.00  0.00
ATOM   1359  CB  ILE   173      -5.383   6.216   7.423  1.00  0.00
ATOM   1360  CG1 ILE   173      -6.530   5.203   7.485  1.00  0.00
ATOM   1361  CG2 ILE   173      -4.074   5.475   7.648  1.00  0.00
ATOM   1362  CD1 ILE   173      -6.560   4.393   8.763  1.00  0.00
ATOM   1363  N   PRO   174      -3.366   7.872   9.315  1.00  0.00
ATOM   1364  CA  PRO   174      -2.130   8.641   9.393  1.00  0.00
ATOM   1365  C   PRO   174      -0.916   7.725   9.478  1.00  0.00
ATOM   1366  O   PRO   174       0.103   7.967   8.832  1.00  0.00
ATOM   1367  CB  PRO   174      -2.293   9.473  10.668  1.00  0.00
ATOM   1368  CG  PRO   174      -3.769   9.591  10.851  1.00  0.00
ATOM   1369  CD  PRO   174      -4.351   8.278  10.406  1.00  0.00
ATOM   1370  N   LYS   175      -1.030   6.671  10.280  1.00  0.00
ATOM   1371  CA  LYS   175       0.069   5.734  10.475  1.00  0.00
ATOM   1372  C   LYS   175      -0.210   4.407   9.782  1.00  0.00
ATOM   1373  O   LYS   175      -1.353   4.096   9.451  1.00  0.00
ATOM   1374  CB  LYS   175       0.279   5.457  11.965  1.00  0.00
ATOM   1375  CG  LYS   175       0.504   6.706  12.803  1.00  0.00
ATOM   1376  CD  LYS   175       1.824   7.374  12.454  1.00  0.00
ATOM   1377  CE  LYS   175       2.089   8.573  13.350  1.00  0.00
ATOM   1378  NZ  LYS   175       1.195   9.719  13.024  1.00  0.00
ATOM   1379  N   GLU   176       0.843   3.625   9.567  1.00  0.00
ATOM   1380  CA  GLU   176       0.713   2.327   8.916  1.00  0.00
ATOM   1381  C   GLU   176      -0.124   1.371   9.757  1.00  0.00
ATOM   1382  O   GLU   176      -0.761   0.460   9.229  1.00  0.00
ATOM   1383  CB  GLU   176       2.089   1.692   8.706  1.00  0.00
ATOM   1384  CG  GLU   176       2.999   2.478   7.777  1.00  0.00
ATOM   1385  CD  GLU   176       4.384   1.870   7.665  1.00  0.00
ATOM   1386  OE1 GLU   176       4.638   0.845   8.331  1.00  0.00
ATOM   1387  OE2 GLU   176       5.215   2.419   6.911  1.00  0.00
ATOM   1388  N   SER   177      -1.977   2.097  10.177  1.00  0.00
ATOM   1389  CA  SER   177      -3.103   1.945   9.263  1.00  0.00
ATOM   1390  C   SER   177      -2.886   2.745   7.985  1.00  0.00
ATOM   1391  O   SER   177      -3.634   3.678   7.692  1.00  0.00
ATOM   1392  CB  SER   177      -4.395   2.437   9.918  1.00  0.00
ATOM   1393  OG  SER   177      -4.315   3.816  10.232  1.00  0.00
ATOM   1394  N   SER   178      -1.860   2.374   7.228  1.00  0.00
ATOM   1395  CA  SER   178      -1.551   3.049   5.972  1.00  0.00
ATOM   1396  C   SER   178      -1.448   2.055   4.823  1.00  0.00
ATOM   1397  O   SER   178      -1.159   0.877   5.034  1.00  0.00
ATOM   1398  CB  SER   178      -0.218   3.794   6.077  1.00  0.00
ATOM   1399  OG  SER   178       0.120   4.408   4.846  1.00  0.00
ATOM   1400  N   PHE   179      -1.687   2.536   3.608  1.00  0.00
ATOM   1401  CA  PHE   179      -1.616   1.690   2.422  1.00  0.00
ATOM   1402  C   PHE   179      -0.271   0.981   2.330  1.00  0.00
ATOM   1403  O   PHE   179      -0.189  -0.157   1.867  1.00  0.00
ATOM   1404  CB  PHE   179      -1.797   2.528   1.155  1.00  0.00
ATOM   1405  CG  PHE   179      -1.786   1.721  -0.112  1.00  0.00
ATOM   1406  CD1 PHE   179      -2.901   0.998  -0.499  1.00  0.00
ATOM   1407  CD2 PHE   179      -0.661   1.685  -0.917  1.00  0.00
ATOM   1408  CE1 PHE   179      -2.891   0.256  -1.665  1.00  0.00
ATOM   1409  CE2 PHE   179      -0.650   0.943  -2.083  1.00  0.00
ATOM   1410  CZ  PHE   179      -1.759   0.230  -2.458  1.00  0.00
ATOM   1411  N   LEU   180       0.781   1.659   2.776  1.00  0.00
ATOM   1412  CA  LEU   180       2.123   1.087   2.761  1.00  0.00
ATOM   1413  C   LEU   180       2.321   0.117   3.917  1.00  0.00
ATOM   1414  O   LEU   180       3.360  -0.534   4.023  1.00  0.00
ATOM   1415  CB  LEU   180       3.177   2.190   2.882  1.00  0.00
ATOM   1416  CG  LEU   180       3.225   3.210   1.741  1.00  0.00
ATOM   1417  CD1 LEU   180       4.237   4.304   2.041  1.00  0.00
ATOM   1418  CD2 LEU   180       3.622   2.539   0.436  1.00  0.00
TER
END
