
#######################################################
#                                                     #
#                        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_2_2-D1
# Molecule2: number of CA atoms  180 ( 1390),  selected  180 , name T0295_D1.pdb
# PARAMETERS: T0295TS193_2_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    P     162      I      18          4.016
LGA    -       -      K      19           -
LGA    -       -      S      20           -
LGA    -       -      S      21           -
LGA    -       -      D      22           -
LGA    P     163      I      23          4.136
LGA    K     164      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    V     165      K      43           #
LGA    D     166      K      44          2.777
LGA    S     167      V      45          3.322
LGA    V     168      I      46          1.842
LGA    I     169      T      47          2.454
LGA    V     170      I      48          1.653
LGA    K     171      D      49          0.347
LGA    L     172      I      50          1.385
LGA    I     173      D      51          1.652
LGA    P     174      -       -           -
LGA    K     175      S      52          1.045
LGA    E     176      R      53          1.819
LGA    S     177      M      54          0.958
LGA    S     178      I      55          0.953
LGA    F     179      S      56          2.781
LGA    L     180      E      57          1.487
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    -       -      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     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    -       -      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    -       -      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     16    2.31     0.00      7.318     0.665

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.086342 * X  +   0.825746 * Y  +   0.557394 * Z  +   1.917300
  Y_new =   0.976675 * X  +   0.040251 * Y  +  -0.210918 * Z  +   1.595484
  Z_new =  -0.196601 * X  +   0.562604 * Y  +  -0.803010 * Z  +  14.229335 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.530452   -0.611141  [ DEG:   144.9842    -35.0158 ]
  Theta =   0.197890    2.943703  [ DEG:    11.3383    168.6617 ]
  Phi   =   1.482622   -1.658971  [ DEG:    84.9480    -95.0520 ]
 
# 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_2_2-D1                             
REMARK     2: T0295_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295TS193_2_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   2.31    0.00   7.318
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS193_2_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0295
PARENT N/A
ATOM   1272  N   PRO   162       5.194  -6.228  21.359  1.00  0.00
ATOM   1273  CA  PRO   162       4.990  -4.976  22.077  1.00  0.00
ATOM   1274  C   PRO   162       5.083  -5.185  23.584  1.00  0.00
ATOM   1275  O   PRO   162       4.897  -6.295  24.079  1.00  0.00
ATOM   1276  CB  PRO   162       3.585  -4.535  21.660  1.00  0.00
ATOM   1277  CG  PRO   162       3.342  -5.237  20.365  1.00  0.00
ATOM   1278  CD  PRO   162       4.042  -6.563  20.473  1.00  0.00
ATOM   1279  N   PRO   163       5.372  -4.109  24.307  1.00  0.00
ATOM   1280  CA  PRO   163       5.301  -4.123  25.764  1.00  0.00
ATOM   1281  C   PRO   163       3.949  -4.637  26.245  1.00  0.00
ATOM   1282  O   PRO   163       2.914  -4.340  25.649  1.00  0.00
ATOM   1283  CB  PRO   163       5.515  -2.661  26.159  1.00  0.00
ATOM   1284  CG  PRO   163       6.317  -2.084  25.042  1.00  0.00
ATOM   1285  CD  PRO   163       5.794  -2.719  23.783  1.00  0.00
ATOM   1286  N   LYS   164       3.966  -5.410  27.324  1.00  0.00
ATOM   1287  CA  LYS   164       2.739  -5.946  27.903  1.00  0.00
ATOM   1288  C   LYS   164       1.793  -4.828  28.321  1.00  0.00
ATOM   1289  O   LYS   164       0.579  -4.928  28.138  1.00  0.00
ATOM   1290  CB  LYS   164       3.054  -6.789  29.140  1.00  0.00
ATOM   1291  CG  LYS   164       3.816  -8.070  28.842  1.00  0.00
ATOM   1292  CD  LYS   164       4.068  -8.870  30.109  1.00  0.00
ATOM   1293  CE  LYS   164       4.847 -10.142  29.813  1.00  0.00
ATOM   1294  NZ  LYS   164       5.115 -10.929  31.047  1.00  0.00
ATOM   1295  N   VAL   165       0.270  -2.703  28.261  1.00  0.00
ATOM   1296  CA  VAL   165       1.610  -2.377  27.788  1.00  0.00
ATOM   1297  C   VAL   165       2.247  -1.289  28.642  1.00  0.00
ATOM   1298  O   VAL   165       1.610  -0.738  29.539  1.00  0.00
ATOM   1299  CB  VAL   165       1.586  -1.870  26.333  1.00  0.00
ATOM   1300  CG1 VAL   165       1.032  -2.941  25.405  1.00  0.00
ATOM   1301  CG2 VAL   165       0.713  -0.631  26.215  1.00  0.00
ATOM   1302  N   ASP   166       3.509  -0.983  28.358  1.00  0.00
ATOM   1303  CA  ASP   166       4.226   0.060  29.081  1.00  0.00
ATOM   1304  C   ASP   166       3.331   1.267  29.337  1.00  0.00
ATOM   1305  O   ASP   166       2.555   1.671  28.471  1.00  0.00
ATOM   1306  CB  ASP   166       5.439   0.531  28.277  1.00  0.00
ATOM   1307  CG  ASP   166       6.325   1.480  29.061  1.00  0.00
ATOM   1308  OD1 ASP   166       5.987   1.782  30.226  1.00  0.00
ATOM   1309  OD2 ASP   166       7.356   1.922  28.511  1.00  0.00
ATOM   1310  N   SER   167       1.366   0.001  29.400  1.00  0.00
ATOM   1311  CA  SER   167       0.802   0.839  30.452  1.00  0.00
ATOM   1312  C   SER   167       0.223   2.126  29.881  1.00  0.00
ATOM   1313  O   SER   167       0.499   3.217  30.381  1.00  0.00
ATOM   1314  CB  SER   167       1.879   1.215  31.473  1.00  0.00
ATOM   1315  OG  SER   167       2.384   0.065  32.129  1.00  0.00
ATOM   1316  N   VAL   168      -0.580   1.993  28.832  1.00  0.00
ATOM   1317  CA  VAL   168      -1.195   3.147  28.187  1.00  0.00
ATOM   1318  C   VAL   168      -2.440   2.744  27.407  1.00  0.00
ATOM   1319  O   VAL   168      -2.572   1.599  26.976  1.00  0.00
ATOM   1320  CB  VAL   168      -0.227   3.823  27.198  1.00  0.00
ATOM   1321  CG1 VAL   168       0.111   2.879  26.054  1.00  0.00
ATOM   1322  CG2 VAL   168      -0.854   5.080  26.615  1.00  0.00
ATOM   1323  N   ILE   169      -3.353   3.693  27.229  1.00  0.00
ATOM   1324  CA  ILE   169      -4.565   3.455  26.455  1.00  0.00
ATOM   1325  C   ILE   169      -4.633   4.370  25.240  1.00  0.00
ATOM   1326  O   ILE   169      -4.539   5.591  25.364  1.00  0.00
ATOM   1327  CB  ILE   169      -5.830   3.708  27.296  1.00  0.00
ATOM   1328  CG1 ILE   169      -5.868   2.763  28.500  1.00  0.00
ATOM   1329  CG2 ILE   169      -7.081   3.474  26.461  1.00  0.00
ATOM   1330  CD1 ILE   169      -6.954   3.093  29.500  1.00  0.00
ATOM   1331  N   VAL   170      -4.796   3.774  24.063  1.00  0.00
ATOM   1332  CA  VAL   170      -4.831   4.532  22.818  1.00  0.00
ATOM   1333  C   VAL   170      -6.247   4.606  22.258  1.00  0.00
ATOM   1334  O   VAL   170      -6.952   3.600  22.195  1.00  0.00
ATOM   1335  CB  VAL   170      -3.938   3.889  21.740  1.00  0.00
ATOM   1336  CG1 VAL   170      -4.031   4.669  20.438  1.00  0.00
ATOM   1337  CG2 VAL   170      -2.486   3.875  22.191  1.00  0.00
ATOM   1338  N   LYS   171      -6.655   5.803  21.853  1.00  0.00
ATOM   1339  CA  LYS   171      -7.978   6.006  21.276  1.00  0.00
ATOM   1340  C   LYS   171      -7.888   6.675  19.910  1.00  0.00
ATOM   1341  O   LYS   171      -7.134   7.631  19.725  1.00  0.00
ATOM   1342  CB  LYS   171      -8.827   6.897  22.185  1.00  0.00
ATOM   1343  CG  LYS   171      -9.113   6.296  23.552  1.00  0.00
ATOM   1344  CD  LYS   171     -10.013   7.202  24.377  1.00  0.00
ATOM   1345  CE  LYS   171      -9.288   8.471  24.792  1.00  0.00
ATOM   1346  NZ  LYS   171     -10.177   9.398  25.546  1.00  0.00
ATOM   1347  N   LEU   172      -8.544   8.449  18.175  1.00  0.00
ATOM   1348  CA  LEU   172      -9.517   8.927  19.150  1.00  0.00
ATOM   1349  C   LEU   172     -10.844   8.195  19.007  1.00  0.00
ATOM   1350  O   LEU   172     -11.416   8.130  17.919  1.00  0.00
ATOM   1351  CB  LEU   172      -9.777  10.423  18.959  1.00  0.00
ATOM   1352  CG  LEU   172     -10.716  11.082  19.971  1.00  0.00
ATOM   1353  CD1 LEU   172     -10.101  11.069  21.362  1.00  0.00
ATOM   1354  CD2 LEU   172     -10.991  12.528  19.585  1.00  0.00
ATOM   1355  N   ILE   173     -11.333   7.644  20.114  1.00  0.00
ATOM   1356  CA  ILE   173     -12.608   6.937  20.121  1.00  0.00
ATOM   1357  C   ILE   173     -13.770   7.899  20.331  1.00  0.00
ATOM   1358  O   ILE   173     -13.567   9.078  20.621  1.00  0.00
ATOM   1359  CB  ILE   173     -12.665   5.887  21.248  1.00  0.00
ATOM   1360  CG1 ILE   173     -11.570   4.837  21.053  1.00  0.00
ATOM   1361  CG2 ILE   173     -14.012   5.183  21.251  1.00  0.00
ATOM   1362  CD1 ILE   173     -11.367   3.938  22.253  1.00  0.00
ATOM   1363  N   PRO   174     -15.258   7.598  20.738  1.00  0.00
ATOM   1364  CA  PRO   174     -15.662   7.996  22.081  1.00  0.00
ATOM   1365  C   PRO   174     -14.650   7.535  23.121  1.00  0.00
ATOM   1366  O   PRO   174     -14.514   6.339  23.381  1.00  0.00
ATOM   1367  CB  PRO   174     -17.017   7.312  22.279  1.00  0.00
ATOM   1368  CG  PRO   174     -17.547   7.128  20.896  1.00  0.00
ATOM   1369  CD  PRO   174     -16.362   6.783  20.038  1.00  0.00
ATOM   1370  N   LYS   175     -13.940   8.489  23.713  1.00  0.00
ATOM   1371  CA  LYS   175     -12.901   8.179  24.688  1.00  0.00
ATOM   1372  C   LYS   175     -13.454   7.335  25.830  1.00  0.00
ATOM   1373  O   LYS   175     -12.698   6.710  26.575  1.00  0.00
ATOM   1374  CB  LYS   175     -12.324   9.465  25.284  1.00  0.00
ATOM   1375  CG  LYS   175     -13.294  10.227  26.172  1.00  0.00
ATOM   1376  CD  LYS   175     -12.673  11.513  26.691  1.00  0.00
ATOM   1377  CE  LYS   175     -13.630  12.258  27.608  1.00  0.00
ATOM   1378  NZ  LYS   175     -13.035  13.522  28.123  1.00  0.00
ATOM   1379  N   GLU   176     -14.775   7.321  25.964  1.00  0.00
ATOM   1380  CA  GLU   176     -15.431   6.552  27.015  1.00  0.00
ATOM   1381  C   GLU   176     -15.398   5.060  26.708  1.00  0.00
ATOM   1382  O   GLU   176     -15.885   4.244  27.489  1.00  0.00
ATOM   1383  CB  GLU   176     -16.896   6.974  27.154  1.00  0.00
ATOM   1384  CG  GLU   176     -17.086   8.380  27.699  1.00  0.00
ATOM   1385  CD  GLU   176     -18.533   8.829  27.658  1.00  0.00
ATOM   1386  OE1 GLU   176     -19.376   8.071  27.133  1.00  0.00
ATOM   1387  OE2 GLU   176     -18.826   9.940  28.150  1.00  0.00
ATOM   1388  N   SER   177     -14.819   4.709  25.564  1.00  0.00
ATOM   1389  CA  SER   177     -14.728   3.315  25.146  1.00  0.00
ATOM   1390  C   SER   177     -13.387   2.708  25.539  1.00  0.00
ATOM   1391  O   SER   177     -13.262   1.491  25.673  1.00  0.00
ATOM   1392  CB  SER   177     -14.875   3.199  23.628  1.00  0.00
ATOM   1393  OG  SER   177     -16.148   3.649  23.202  1.00  0.00
ATOM   1394  N   SER   178     -12.387   3.564  25.723  1.00  0.00
ATOM   1395  CA  SER   178     -11.045   3.112  26.068  1.00  0.00
ATOM   1396  C   SER   178     -11.088   2.021  27.131  1.00  0.00
ATOM   1397  O   SER   178     -10.589   0.916  26.921  1.00  0.00
ATOM   1398  CB  SER   178     -10.212   4.273  26.615  1.00  0.00
ATOM   1399  OG  SER   178     -10.811   4.831  27.771  1.00  0.00
ATOM   1400  N   PHE   179     -11.689   2.338  28.273  1.00  0.00
ATOM   1401  CA  PHE   179     -11.797   1.386  29.372  1.00  0.00
ATOM   1402  C   PHE   179     -12.503   0.111  28.927  1.00  0.00
ATOM   1403  O   PHE   179     -12.169  -0.985  29.379  1.00  0.00
ATOM   1404  CB  PHE   179     -12.595   1.991  30.528  1.00  0.00
ATOM   1405  CG  PHE   179     -12.743   1.074  31.709  1.00  0.00
ATOM   1406  CD1 PHE   179     -11.677   0.840  32.559  1.00  0.00
ATOM   1407  CD2 PHE   179     -13.948   0.445  31.968  1.00  0.00
ATOM   1408  CE1 PHE   179     -11.812  -0.004  33.646  1.00  0.00
ATOM   1409  CE2 PHE   179     -14.084  -0.399  33.055  1.00  0.00
ATOM   1410  CZ  PHE   179     -13.023  -0.625  33.891  1.00  0.00
ATOM   1411  N   LEU   180     -13.888   0.227  28.583  1.00  0.00
ATOM   1412  CA  LEU   180     -14.147  -0.670  27.463  1.00  0.00
ATOM   1413  C   LEU   180     -13.419  -0.208  26.207  1.00  0.00
ATOM   1414  O   LEU   180     -13.712   0.858  25.665  1.00  0.00
ATOM   1415  CB  LEU   180     -15.644  -0.720  27.152  1.00  0.00
ATOM   1416  CG  LEU   180     -16.075  -1.690  26.050  1.00  0.00
ATOM   1417  CD1 LEU   180     -15.788  -3.127  26.456  1.00  0.00
ATOM   1418  CD2 LEU   180     -17.566  -1.563  25.775  1.00  0.00
TER
END
