
#######################################################
#                                                     #
#                        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_3_2-D1
# Molecule2: number of CA atoms  180 ( 1390),  selected  180 , name T0295_D1.pdb
# PARAMETERS: T0295TS193_3_2-D1.T0295_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    P     162      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    P     163      S      21           #
LGA    K     164      D      22          4.596
LGA    -       -      I      23           -
LGA    V     165      V      24          3.304
LGA    D     166      L      25          2.077
LGA    S     167      E      26          2.248
LGA    V     168      I      27          1.949
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    -       -      I      46           -
LGA    -       -      T      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      I      50           -
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    -       -      G      75           -
LGA    -       -      D      76           -
LGA    I     169      A      77          3.021
LGA    V     170      I      78          4.675
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    -       -      P      93           -
LGA    -       -      Y      94           -
LGA    -       -      K      95           -
LGA    -       -      I      96           -
LGA    -       -      S      97           -
LGA    -       -      S      98           -
LGA    -       -      P      99           -
LGA    -       -      L     100           -
LGA    -       -      I     101           -
LGA    -       -      F     102           -
LGA    K     171      K     103          3.318
LGA    L     172      L     104          1.843
LGA    I     173      I     105          3.984
LGA    P     174      S     106           -
LGA    -       -      H     107           -
LGA    -       -      R     108           -
LGA    -       -      P     109           -
LGA    -       -      L     110           -
LGA    -       -      F     111           -
LGA    -       -      K     112           -
LGA    -       -      C     113           -
LGA    K     175      A     114          3.801
LGA    -       -      V     115           -
LGA    -       -      L     116           -
LGA    -       -      M     117           -
LGA    -       -      F     118           -
LGA    -       -      Q     119           -
LGA    -       -      K     120           -
LGA    -       -      E     121           -
LGA    -       -      F     122           -
LGA    -       -      A     123           -
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    E     176      L     172          2.100
LGA    S     177      I     173          1.301
LGA    S     178      P     174          3.148
LGA    F     179      K     175          4.303
LGA    L     180      E     176          1.317
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     16    3.13    25.00      5.302     0.495

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.114797 * X  +  -0.213860 * Y  +   0.970096 * Z  +   2.592820
  Y_new =   0.171031 * X  +   0.966224 * Y  +   0.192767 * Z  +   2.817538
  Z_new =  -0.978555 * X  +   0.143787 * Y  +   0.147497 * Z  +  19.162407 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.772662   -2.368930  [ DEG:    44.2703   -135.7297 ]
  Theta =   1.363326    1.778267  [ DEG:    78.1128    101.8872 ]
  Phi   =   0.979655   -2.161938  [ DEG:    56.1301   -123.8699 ]
 
# 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_3_2-D1                             
REMARK     2: T0295_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295TS193_3_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   16   3.13   25.00   5.302
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS193_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0295
PARENT N/A
ATOM   1272  N   PRO   162       6.215   4.631  28.959  1.00  0.00
ATOM   1273  CA  PRO   162       6.649   4.761  27.574  1.00  0.00
ATOM   1274  C   PRO   162       6.679   3.408  26.875  1.00  0.00
ATOM   1275  O   PRO   162       7.150   2.419  27.436  1.00  0.00
ATOM   1276  CB  PRO   162       8.051   5.365  27.680  1.00  0.00
ATOM   1277  CG  PRO   162       8.051   6.079  28.990  1.00  0.00
ATOM   1278  CD  PRO   162       7.232   5.234  29.926  1.00  0.00
ATOM   1279  N   PRO   163       6.171   3.371  25.648  1.00  0.00
ATOM   1280  CA  PRO   163       6.151   2.141  24.864  1.00  0.00
ATOM   1281  C   PRO   163       7.537   1.806  24.328  1.00  0.00
ATOM   1282  O   PRO   163       8.290   2.695  23.931  1.00  0.00
ATOM   1283  CB  PRO   163       5.170   2.440  23.729  1.00  0.00
ATOM   1284  CG  PRO   163       4.330   3.559  24.247  1.00  0.00
ATOM   1285  CD  PRO   163       5.239   4.409  25.088  1.00  0.00
ATOM   1286  N   LYS   164       7.867   0.519  24.318  1.00  0.00
ATOM   1287  CA  LYS   164       9.158   0.063  23.819  1.00  0.00
ATOM   1288  C   LYS   164       9.000  -1.141  22.901  1.00  0.00
ATOM   1289  O   LYS   164       8.198  -2.037  23.169  1.00  0.00
ATOM   1290  CB  LYS   164      10.069  -0.342  24.980  1.00  0.00
ATOM   1291  CG  LYS   164      10.436   0.803  25.910  1.00  0.00
ATOM   1292  CD  LYS   164      11.381   0.341  27.007  1.00  0.00
ATOM   1293  CE  LYS   164      11.703   1.473  27.970  1.00  0.00
ATOM   1294  NZ  LYS   164      12.644   1.041  29.040  1.00  0.00
ATOM   1295  N   VAL   165       6.107  -2.081  22.341  1.00  0.00
ATOM   1296  CA  VAL   165       6.257  -0.841  21.588  1.00  0.00
ATOM   1297  C   VAL   165       5.116   0.124  21.885  1.00  0.00
ATOM   1298  O   VAL   165       4.052  -0.283  22.351  1.00  0.00
ATOM   1299  CB  VAL   165       6.263  -1.100  20.070  1.00  0.00
ATOM   1300  CG1 VAL   165       7.432  -1.995  19.687  1.00  0.00
ATOM   1301  CG2 VAL   165       4.974  -1.783  19.641  1.00  0.00
ATOM   1302  N   ASP   166       5.346   1.403  21.611  1.00  0.00
ATOM   1303  CA  ASP   166       4.310   2.418  21.770  1.00  0.00
ATOM   1304  C   ASP   166       3.164   2.194  20.792  1.00  0.00
ATOM   1305  O   ASP   166       3.374   1.736  19.669  1.00  0.00
ATOM   1306  CB  ASP   166       4.883   3.814  21.516  1.00  0.00
ATOM   1307  CG  ASP   166       3.872   4.914  21.769  1.00  0.00
ATOM   1308  OD1 ASP   166       3.491   5.115  22.942  1.00  0.00
ATOM   1309  OD2 ASP   166       3.458   5.575  20.792  1.00  0.00
ATOM   1310  N   SER   167       1.951   2.520  21.225  1.00  0.00
ATOM   1311  CA  SER   167       0.774   2.397  20.373  1.00  0.00
ATOM   1312  C   SER   167       0.103   3.748  20.164  1.00  0.00
ATOM   1313  O   SER   167       0.413   4.721  20.853  1.00  0.00
ATOM   1314  CB  SER   167      -0.250   1.452  21.005  1.00  0.00
ATOM   1315  OG  SER   167       0.277   0.142  21.134  1.00  0.00
ATOM   1316  N   VAL   168      -1.185   5.791  19.685  1.00  0.00
ATOM   1317  CA  VAL   168      -1.045   4.946  18.505  1.00  0.00
ATOM   1318  C   VAL   168      -0.395   5.709  17.356  1.00  0.00
ATOM   1319  O   VAL   168       0.205   5.111  16.464  1.00  0.00
ATOM   1320  CB  VAL   168      -2.412   4.437  18.009  1.00  0.00
ATOM   1321  CG1 VAL   168      -3.088   3.597  19.083  1.00  0.00
ATOM   1322  CG2 VAL   168      -3.324   5.605  17.668  1.00  0.00
ATOM   1323  N   ILE   169      -0.521   7.032  17.386  1.00  0.00
ATOM   1324  CA  ILE   169       0.032   7.876  16.334  1.00  0.00
ATOM   1325  C   ILE   169       1.298   8.582  16.803  1.00  0.00
ATOM   1326  O   ILE   169       2.397   8.284  16.333  1.00  0.00
ATOM   1327  CB  ILE   169      -0.969   8.962  15.897  1.00  0.00
ATOM   1328  CG1 ILE   169      -2.237   8.321  15.330  1.00  0.00
ATOM   1329  CG2 ILE   169      -0.358   9.851  14.826  1.00  0.00
ATOM   1330  CD1 ILE   169      -3.344   9.310  15.039  1.00  0.00
ATOM   1331  N   VAL   170       1.139   9.519  17.731  1.00  0.00
ATOM   1332  CA  VAL   170       2.258  10.320  18.213  1.00  0.00
ATOM   1333  C   VAL   170       3.447   9.440  18.577  1.00  0.00
ATOM   1334  O   VAL   170       4.545   9.614  18.047  1.00  0.00
ATOM   1335  CB  VAL   170       1.876  11.127  19.468  1.00  0.00
ATOM   1336  CG1 VAL   170       3.084  11.874  20.009  1.00  0.00
ATOM   1337  CG2 VAL   170       0.790  12.140  19.138  1.00  0.00
ATOM   1338  N   LYS   171       4.047  10.600  16.087  1.00  0.00
ATOM   1339  CA  LYS   171       4.465   9.462  15.279  1.00  0.00
ATOM   1340  C   LYS   171       5.953   9.182  15.449  1.00  0.00
ATOM   1341  O   LYS   171       6.370   8.029  15.554  1.00  0.00
ATOM   1342  CB  LYS   171       4.199   9.730  13.797  1.00  0.00
ATOM   1343  CG  LYS   171       2.725   9.813  13.436  1.00  0.00
ATOM   1344  CD  LYS   171       2.534  10.053  11.947  1.00  0.00
ATOM   1345  CE  LYS   171       1.060  10.155  11.589  1.00  0.00
ATOM   1346  NZ  LYS   171       0.857  10.404  10.135  1.00  0.00
ATOM   1347  N   LEU   172       7.372   9.004  13.790  1.00  0.00
ATOM   1348  CA  LEU   172       7.035   7.930  12.863  1.00  0.00
ATOM   1349  C   LEU   172       7.943   6.723  13.065  1.00  0.00
ATOM   1350  O   LEU   172       7.601   5.606  12.679  1.00  0.00
ATOM   1351  CB  LEU   172       7.190   8.403  11.416  1.00  0.00
ATOM   1352  CG  LEU   172       6.202   9.472  10.943  1.00  0.00
ATOM   1353  CD1 LEU   172       6.554   9.945   9.541  1.00  0.00
ATOM   1354  CD2 LEU   172       4.785   8.921  10.918  1.00  0.00
ATOM   1355  N   ILE   173       9.102   6.957  13.671  1.00  0.00
ATOM   1356  CA  ILE   173      10.095   5.905  13.857  1.00  0.00
ATOM   1357  C   ILE   173       9.494   4.699  14.566  1.00  0.00
ATOM   1358  O   ILE   173       9.909   3.563  14.339  1.00  0.00
ATOM   1359  CB  ILE   173      11.284   6.394  14.703  1.00  0.00
ATOM   1360  CG1 ILE   173      12.435   5.389  14.637  1.00  0.00
ATOM   1361  CG2 ILE   173      10.871   6.559  16.158  1.00  0.00
ATOM   1362  CD1 ILE   173      13.040   5.243  13.258  1.00  0.00
ATOM   1363  N   PRO   174       8.513   4.953  15.426  1.00  0.00
ATOM   1364  CA  PRO   174       7.863   3.889  16.183  1.00  0.00
ATOM   1365  C   PRO   174       7.056   2.977  15.269  1.00  0.00
ATOM   1366  O   PRO   174       6.761   1.834  15.620  1.00  0.00
ATOM   1367  CB  PRO   174       6.959   4.635  17.168  1.00  0.00
ATOM   1368  CG  PRO   174       7.550   6.002  17.254  1.00  0.00
ATOM   1369  CD  PRO   174       8.134   6.291  15.901  1.00  0.00
ATOM   1370  N   LYS   175       6.701   3.487  14.095  1.00  0.00
ATOM   1371  CA  LYS   175       5.896   2.733  13.142  1.00  0.00
ATOM   1372  C   LYS   175       6.773   2.021  12.121  1.00  0.00
ATOM   1373  O   LYS   175       6.275   1.461  11.144  1.00  0.00
ATOM   1374  CB  LYS   175       4.949   3.666  12.385  1.00  0.00
ATOM   1375  CG  LYS   175       3.910   4.343  13.264  1.00  0.00
ATOM   1376  CD  LYS   175       2.944   5.174  12.437  1.00  0.00
ATOM   1377  CE  LYS   175       1.876   5.811  13.310  1.00  0.00
ATOM   1378  NZ  LYS   175       0.952   6.672  12.521  1.00  0.00
ATOM   1379  N   GLU   176       7.473   0.787  12.926  1.00  0.00
ATOM   1380  CA  GLU   176       8.691   0.548  12.161  1.00  0.00
ATOM   1381  C   GLU   176       9.806   0.015  13.052  1.00  0.00
ATOM   1382  O   GLU   176       9.705   0.055  14.279  1.00  0.00
ATOM   1383  CB  GLU   176       9.182   1.845  11.513  1.00  0.00
ATOM   1384  CG  GLU   176       8.294   2.350  10.388  1.00  0.00
ATOM   1385  CD  GLU   176       8.160   1.348   9.258  1.00  0.00
ATOM   1386  OE1 GLU   176       9.197   0.970   8.672  1.00  0.00
ATOM   1387  OE2 GLU   176       7.018   0.939   8.958  1.00  0.00
ATOM   1388  N   SER   177      10.869  -0.482  12.429  1.00  0.00
ATOM   1389  CA  SER   177      12.073  -0.865  13.155  1.00  0.00
ATOM   1390  C   SER   177      12.679   0.328  13.883  1.00  0.00
ATOM   1391  O   SER   177      12.636   1.456  13.392  1.00  0.00
ATOM   1392  CB  SER   177      13.126  -1.418  12.193  1.00  0.00
ATOM   1393  OG  SER   177      14.329  -1.726  12.875  1.00  0.00
ATOM   1394  N   SER   178      13.245   0.072  15.059  1.00  0.00
ATOM   1395  CA  SER   178      13.752   1.139  15.913  1.00  0.00
ATOM   1396  C   SER   178      14.878   1.905  15.228  1.00  0.00
ATOM   1397  O   SER   178      15.623   1.345  14.425  1.00  0.00
ATOM   1398  CB  SER   178      14.298   0.564  17.222  1.00  0.00
ATOM   1399  OG  SER   178      15.453  -0.224  16.991  1.00  0.00
ATOM   1400  N   PHE   179      14.997   3.188  15.552  1.00  0.00
ATOM   1401  CA  PHE   179      16.081   4.012  15.034  1.00  0.00
ATOM   1402  C   PHE   179      17.436   3.496  15.500  1.00  0.00
ATOM   1403  O   PHE   179      17.588   3.068  16.644  1.00  0.00
ATOM   1404  CB  PHE   179      15.932   5.457  15.514  1.00  0.00
ATOM   1405  CG  PHE   179      14.783   6.191  14.883  1.00  0.00
ATOM   1406  CD1 PHE   179      14.072   5.625  13.838  1.00  0.00
ATOM   1407  CD2 PHE   179      14.413   7.445  15.334  1.00  0.00
ATOM   1408  CE1 PHE   179      13.015   6.300  13.258  1.00  0.00
ATOM   1409  CE2 PHE   179      13.356   8.121  14.752  1.00  0.00
ATOM   1410  CZ  PHE   179      12.658   7.553  13.719  1.00  0.00
ATOM   1411  N   LEU   180      18.420   3.541  14.607  1.00  0.00
ATOM   1412  CA  LEU   180      19.744   3.006  14.899  1.00  0.00
ATOM   1413  C   LEU   180      20.816   4.078  14.753  1.00  0.00
ATOM   1414  O   LEU   180      22.004   3.811  14.933  1.00  0.00
ATOM   1415  CB  LEU   180      20.084   1.863  13.940  1.00  0.00
ATOM   1416  CG  LEU   180      19.174   0.634  14.001  1.00  0.00
ATOM   1417  CD1 LEU   180      19.516  -0.344  12.887  1.00  0.00
ATOM   1418  CD2 LEU   180      19.332  -0.086  15.331  1.00  0.00
TER
END
