
#######################################################
#                                                     #
#                        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_5_2-D1
# Molecule2: number of CA atoms  180 ( 1390),  selected  180 , name T0295_D1.pdb
# PARAMETERS: T0295TS193_5_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    P     163      A      16          2.339
LGA    K     164      K      17          3.094
LGA    V     165      I      18          1.905
LGA    D     166      K      19          3.015
LGA    -       -      S      20           -
LGA    -       -      S      21           -
LGA    S     167      D      22          0.588
LGA    V     168      I      23          1.417
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    -       -      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    -       -      A      77           -
LGA    -       -      I      78           -
LGA    -       -      K      79           -
LGA    -       -      T      80           -
LGA    -       -      V      81           -
LGA    -       -      F      82           -
LGA    -       -      P      83           -
LGA    -       -      K      84           -
LGA    I     169      F      85          3.371
LGA    V     170      D      86          4.306
LGA    K     171      V      87          4.659
LGA    L     172      C      88          3.603
LGA    I     173      T      89          3.591
LGA    P     174      A      90          3.571
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     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    K     175      A     114           #
LGA    E     176      V     115          4.475
LGA    S     177      L     116          4.512
LGA    S     178      M     117          5.014
LGA    F     179      F     118          2.352
LGA    L     180      Q     119          4.031
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    -       -      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     17    3.49    11.76      5.662     0.473

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.639055 * X  +   0.226561 * Y  +   0.735037 * Z  +   9.032313
  Y_new =   0.415901 * X  +   0.702098 * Y  +  -0.578000 * Z  +  -5.458017
  Z_new =  -0.647021 * X  +   0.675076 * Y  +   0.354452 * Z  +   5.744933 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.087306   -2.054286  [ DEG:    62.2981   -117.7019 ]
  Theta =   0.703670    2.437922  [ DEG:    40.3173    139.6827 ]
  Phi   =   0.576942   -2.564651  [ DEG:    33.0563   -146.9437 ]
 
# 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_5_2-D1                             
REMARK     2: T0295_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295TS193_5_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   17   3.49   11.76   5.662
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS193_5_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0295
PARENT N/A
ATOM   1272  N   PRO   162       5.430  -4.597  13.993  1.00  0.00
ATOM   1273  CA  PRO   162       5.380  -5.843  14.751  1.00  0.00
ATOM   1274  C   PRO   162       5.647  -5.598  16.230  1.00  0.00
ATOM   1275  O   PRO   162       6.720  -5.129  16.609  1.00  0.00
ATOM   1276  CB  PRO   162       6.477  -6.703  14.120  1.00  0.00
ATOM   1277  CG  PRO   162       6.625  -6.166  12.737  1.00  0.00
ATOM   1278  CD  PRO   162       6.419  -4.680  12.842  1.00  0.00
ATOM   1279  N   PRO   163       4.664  -5.921  17.065  1.00  0.00
ATOM   1280  CA  PRO   163       4.829  -5.839  18.510  1.00  0.00
ATOM   1281  C   PRO   163       5.979  -6.719  18.985  1.00  0.00
ATOM   1282  O   PRO   163       6.227  -7.787  18.426  1.00  0.00
ATOM   1283  CB  PRO   163       3.488  -6.325  19.063  1.00  0.00
ATOM   1284  CG  PRO   163       2.517  -6.081  17.958  1.00  0.00
ATOM   1285  CD  PRO   163       3.263  -6.349  16.681  1.00  0.00
ATOM   1286  N   LYS   164       6.678  -6.263  20.018  1.00  0.00
ATOM   1287  CA  LYS   164       7.737  -7.053  20.636  1.00  0.00
ATOM   1288  C   LYS   164       7.729  -6.897  22.150  1.00  0.00
ATOM   1289  O   LYS   164       7.066  -6.011  22.690  1.00  0.00
ATOM   1290  CB  LYS   164       9.108  -6.609  20.121  1.00  0.00
ATOM   1291  CG  LYS   164       9.344  -6.907  18.649  1.00  0.00
ATOM   1292  CD  LYS   164      10.753  -6.523  18.228  1.00  0.00
ATOM   1293  CE  LYS   164      10.990  -6.823  16.756  1.00  0.00
ATOM   1294  NZ  LYS   164      12.358  -6.426  16.322  1.00  0.00
ATOM   1295  N   VAL   165       7.963  -8.071  22.806  1.00  0.00
ATOM   1296  CA  VAL   165       8.285  -7.984  24.226  1.00  0.00
ATOM   1297  C   VAL   165       9.787  -7.863  24.445  1.00  0.00
ATOM   1298  O   VAL   165      10.547  -8.774  24.115  1.00  0.00
ATOM   1299  CB  VAL   165       7.803  -9.231  24.991  1.00  0.00
ATOM   1300  CG1 VAL   165       8.197  -9.142  26.457  1.00  0.00
ATOM   1301  CG2 VAL   165       6.290  -9.357  24.907  1.00  0.00
ATOM   1302  N   ASP   166      10.211  -6.735  25.003  1.00  0.00
ATOM   1303  CA  ASP   166      11.631  -6.438  25.149  1.00  0.00
ATOM   1304  C   ASP   166      12.055  -6.480  26.612  1.00  0.00
ATOM   1305  O   ASP   166      11.307  -6.065  27.497  1.00  0.00
ATOM   1306  CB  ASP   166      11.945  -5.043  24.604  1.00  0.00
ATOM   1307  CG  ASP   166      13.434  -4.756  24.561  1.00  0.00
ATOM   1308  OD1 ASP   166      14.226  -5.707  24.730  1.00  0.00
ATOM   1309  OD2 ASP   166      13.807  -3.582  24.358  1.00  0.00
ATOM   1310  N   SER   167      10.575  -4.499  26.057  1.00  0.00
ATOM   1311  CA  SER   167       9.667  -3.881  27.015  1.00  0.00
ATOM   1312  C   SER   167       8.365  -3.458  26.347  1.00  0.00
ATOM   1313  O   SER   167       8.365  -2.983  25.212  1.00  0.00
ATOM   1314  CB  SER   167      10.308  -2.637  27.635  1.00  0.00
ATOM   1315  OG  SER   167      11.468  -2.975  28.373  1.00  0.00
ATOM   1316  N   VAL   168       9.288  -1.212  26.248  1.00  0.00
ATOM   1317  CA  VAL   168       8.069  -0.413  26.211  1.00  0.00
ATOM   1318  C   VAL   168       7.657  -0.105  24.777  1.00  0.00
ATOM   1319  O   VAL   168       6.476  -0.167  24.434  1.00  0.00
ATOM   1320  CB  VAL   168       8.253   0.931  26.939  1.00  0.00
ATOM   1321  CG1 VAL   168       7.044   1.827  26.718  1.00  0.00
ATOM   1322  CG2 VAL   168       8.420   0.708  28.435  1.00  0.00
ATOM   1323  N   ILE   169       8.636   0.227  23.942  1.00  0.00
ATOM   1324  CA  ILE   169       8.380   0.517  22.538  1.00  0.00
ATOM   1325  C   ILE   169       7.929  -0.731  21.789  1.00  0.00
ATOM   1326  O   ILE   169       7.105  -0.657  20.878  1.00  0.00
ATOM   1327  CB  ILE   169       9.641   1.051  21.833  1.00  0.00
ATOM   1328  CG1 ILE   169       9.270   1.709  20.503  1.00  0.00
ATOM   1329  CG2 ILE   169      10.614  -0.084  21.553  1.00  0.00
ATOM   1330  CD1 ILE   169      10.397   2.505  19.881  1.00  0.00
ATOM   1331  N   VAL   170       8.475  -1.878  22.180  1.00  0.00
ATOM   1332  CA  VAL   170       8.067  -3.154  21.606  1.00  0.00
ATOM   1333  C   VAL   170       6.643  -3.512  22.011  1.00  0.00
ATOM   1334  O   VAL   170       5.863  -4.010  21.199  1.00  0.00
ATOM   1335  CB  VAL   170       8.983  -4.300  22.072  1.00  0.00
ATOM   1336  CG1 VAL   170       8.431  -5.643  21.617  1.00  0.00
ATOM   1337  CG2 VAL   170      10.380  -4.136  21.495  1.00  0.00
ATOM   1338  N   LYS   171       6.309  -3.253  23.271  1.00  0.00
ATOM   1339  CA  LYS   171       4.932  -3.362  23.736  1.00  0.00
ATOM   1340  C   LYS   171       4.008  -2.450  22.938  1.00  0.00
ATOM   1341  O   LYS   171       2.979  -2.889  22.424  1.00  0.00
ATOM   1342  CB  LYS   171       4.832  -2.965  25.210  1.00  0.00
ATOM   1343  CG  LYS   171       3.432  -3.089  25.792  1.00  0.00
ATOM   1344  CD  LYS   171       3.418  -2.748  27.273  1.00  0.00
ATOM   1345  CE  LYS   171       2.012  -2.823  27.844  1.00  0.00
ATOM   1346  NZ  LYS   171       1.980  -2.469  29.290  1.00  0.00
ATOM   1347  N   LEU   172       4.381  -1.178  22.838  1.00  0.00
ATOM   1348  CA  LEU   172       3.589  -0.204  22.098  1.00  0.00
ATOM   1349  C   LEU   172       3.535  -0.550  20.614  1.00  0.00
ATOM   1350  O   LEU   172       2.476  -0.484  19.990  1.00  0.00
ATOM   1351  CB  LEU   172       4.193   1.195  22.237  1.00  0.00
ATOM   1352  CG  LEU   172       4.093   1.843  23.619  1.00  0.00
ATOM   1353  CD1 LEU   172       4.887   3.140  23.664  1.00  0.00
ATOM   1354  CD2 LEU   172       2.645   2.159  23.961  1.00  0.00
ATOM   1355  N   ILE   173       4.682  -0.921  20.056  1.00  0.00
ATOM   1356  CA  ILE   173       4.762  -1.307  18.653  1.00  0.00
ATOM   1357  C   ILE   173       3.906  -2.535  18.369  1.00  0.00
ATOM   1358  O   ILE   173       3.228  -2.607  17.344  1.00  0.00
ATOM   1359  CB  ILE   173       6.207  -1.643  18.241  1.00  0.00
ATOM   1360  CG1 ILE   173       7.110  -0.421  18.418  1.00  0.00
ATOM   1361  CG2 ILE   173       6.259  -2.075  16.784  1.00  0.00
ATOM   1362  CD1 ILE   173       8.583  -0.719  18.236  1.00  0.00
ATOM   1363  N   PRO   174       3.159  -0.393  16.953  1.00  0.00
ATOM   1364  CA  PRO   174       2.013  -0.473  16.056  1.00  0.00
ATOM   1365  C   PRO   174       2.359  -1.244  14.787  1.00  0.00
ATOM   1366  O   PRO   174       3.441  -1.080  14.226  1.00  0.00
ATOM   1367  CB  PRO   174       1.680   0.988  15.748  1.00  0.00
ATOM   1368  CG  PRO   174       2.215   1.747  16.916  1.00  0.00
ATOM   1369  CD  PRO   174       3.488   1.055  17.316  1.00  0.00
ATOM   1370  N   LYS   175       1.431  -2.086  14.342  1.00  0.00
ATOM   1371  CA  LYS   175       1.639  -2.888  13.142  1.00  0.00
ATOM   1372  C   LYS   175       2.027  -2.015  11.955  1.00  0.00
ATOM   1373  O   LYS   175       2.778  -2.441  11.079  1.00  0.00
ATOM   1374  CB  LYS   175       0.360  -3.645  12.776  1.00  0.00
ATOM   1375  CG  LYS   175       0.012  -4.773  13.733  1.00  0.00
ATOM   1376  CD  LYS   175      -1.264  -5.483  13.307  1.00  0.00
ATOM   1377  CE  LYS   175      -1.636  -6.583  14.288  1.00  0.00
ATOM   1378  NZ  LYS   175      -2.886  -7.285  13.887  1.00  0.00
ATOM   1379  N   GLU   176       1.511  -0.791  11.934  1.00  0.00
ATOM   1380  CA  GLU   176       1.765   0.129  10.832  1.00  0.00
ATOM   1381  C   GLU   176       3.057   0.906  11.049  1.00  0.00
ATOM   1382  O   GLU   176       3.528   1.610  10.156  1.00  0.00
ATOM   1383  CB  GLU   176       0.622   1.137  10.702  1.00  0.00
ATOM   1384  CG  GLU   176      -0.722   0.511  10.363  1.00  0.00
ATOM   1385  CD  GLU   176      -1.863   1.506  10.436  1.00  0.00
ATOM   1386  OE1 GLU   176      -1.610   2.675  10.798  1.00  0.00
ATOM   1387  OE2 GLU   176      -3.011   1.118  10.132  1.00  0.00
ATOM   1388  N   SER   177       3.231   3.591   9.131  1.00  0.00
ATOM   1389  CA  SER   177       1.782   3.456   9.045  1.00  0.00
ATOM   1390  C   SER   177       1.320   3.393   7.595  1.00  0.00
ATOM   1391  O   SER   177       1.516   4.337   6.829  1.00  0.00
ATOM   1392  CB  SER   177       1.093   4.649   9.711  1.00  0.00
ATOM   1393  OG  SER   177      -0.317   4.527   9.640  1.00  0.00
ATOM   1394  N   SER   178       0.705   2.276   7.223  1.00  0.00
ATOM   1395  CA  SER   178       0.239   2.076   5.855  1.00  0.00
ATOM   1396  C   SER   178      -1.189   1.547   5.832  1.00  0.00
ATOM   1397  O   SER   178      -1.527   0.612   6.559  1.00  0.00
ATOM   1398  CB  SER   178       1.131   1.069   5.127  1.00  0.00
ATOM   1399  OG  SER   178       0.684   0.858   3.799  1.00  0.00
ATOM   1400  N   PHE   179      -2.025   2.149   4.993  1.00  0.00
ATOM   1401  CA  PHE   179      -3.420   1.741   4.876  1.00  0.00
ATOM   1402  C   PHE   179      -3.536   0.242   4.636  1.00  0.00
ATOM   1403  O   PHE   179      -2.857  -0.314   3.774  1.00  0.00
ATOM   1404  CB  PHE   179      -4.092   2.463   3.707  1.00  0.00
ATOM   1405  CG  PHE   179      -4.222   3.947   3.903  1.00  0.00
ATOM   1406  CD1 PHE   179      -3.427   4.826   3.186  1.00  0.00
ATOM   1407  CD2 PHE   179      -5.137   4.463   4.803  1.00  0.00
ATOM   1408  CE1 PHE   179      -3.546   6.191   3.367  1.00  0.00
ATOM   1409  CE2 PHE   179      -5.255   5.828   4.984  1.00  0.00
ATOM   1410  CZ  PHE   179      -4.464   6.691   4.271  1.00  0.00
ATOM   1411  N   LEU   180      -4.404  -0.409   5.404  1.00  0.00
ATOM   1412  CA  LEU   180      -4.630  -1.842   5.260  1.00  0.00
ATOM   1413  C   LEU   180      -3.987  -2.619   6.402  1.00  0.00
ATOM   1414  O   LEU   180      -4.380  -3.747   6.698  1.00  0.00
ATOM   1415  CB  LEU   180      -4.033  -2.349   3.946  1.00  0.00
ATOM   1416  CG  LEU   180      -4.630  -1.771   2.662  1.00  0.00
ATOM   1417  CD1 LEU   180      -3.873  -2.275   1.442  1.00  0.00
ATOM   1418  CD2 LEU   180      -6.089  -2.178   2.518  1.00  0.00
TER
END
