
#######################################################
#                                                     #
#                        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_4_2-D1
# Molecule2: number of CA atoms  180 ( 1390),  selected  180 , name T0295_D1.pdb
# PARAMETERS: T0295TS193_4_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    P     162      S      21          4.725
LGA    P     163      D      22          0.427
LGA    K     164      I      23          4.836
LGA    V     165      V      24          1.194
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    D     166      V      45          3.734
LGA    S     167      I      46          2.228
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    V     168      F      82          3.906
LGA    I     169      P      83          2.727
LGA    -       -      K      84           -
LGA    V     170      F      85          2.632
LGA    K     171      D      86          3.109
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    L     172      F     111          1.653
LGA    I     173      K     112          1.816
LGA    P     174      C     113          1.639
LGA    K     175      A     114          2.248
LGA    E     176      V     115          2.374
LGA    S     177      L     116          0.672
LGA    S     178      M     117          0.836
LGA    F     179      F     118          1.555
LGA    L     180      Q     119          4.745
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     19    2.82    10.53      7.188     0.651

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.859954 * X  +  -0.075266 * Y  +   0.504790 * Z  +   1.094447
  Y_new =  -0.255855 * X  +  -0.792229 * Y  +  -0.553996 * Z  +  -2.899239
  Z_new =   0.441607 * X  +  -0.605565 * Y  +   0.662024 * Z  +  32.617928 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.740887    2.400706  [ DEG:   -42.4497    137.5503 ]
  Theta =  -0.457389   -2.684204  [ DEG:   -26.2064   -153.7936 ]
  Phi   =  -2.852411    0.289182  [ DEG:  -163.4311     16.5689 ]
 
# 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_4_2-D1                             
REMARK     2: T0295_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0295TS193_4_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   19   2.82   10.53   7.188
REMARK  ---------------------------------------------------------- 
MOLECULE T0295TS193_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0295
PARENT N/A
ATOM   1272  N   PRO   162       6.061  -2.626  30.116  1.00  0.00
ATOM   1273  CA  PRO   162       7.473  -2.294  29.959  1.00  0.00
ATOM   1274  C   PRO   162       7.771  -1.812  28.546  1.00  0.00
ATOM   1275  O   PRO   162       7.084  -2.184  27.594  1.00  0.00
ATOM   1276  CB  PRO   162       8.198  -3.606  30.265  1.00  0.00
ATOM   1277  CG  PRO   162       7.269  -4.669  29.783  1.00  0.00
ATOM   1278  CD  PRO   162       5.886  -4.219  30.164  1.00  0.00
ATOM   1279  N   PRO   163       8.752  -3.687  27.713  1.00  0.00
ATOM   1280  CA  PRO   163       9.514  -3.100  26.618  1.00  0.00
ATOM   1281  C   PRO   163       8.822  -3.327  25.280  1.00  0.00
ATOM   1282  O   PRO   163       9.194  -2.735  24.268  1.00  0.00
ATOM   1283  CB  PRO   163      10.863  -3.820  26.677  1.00  0.00
ATOM   1284  CG  PRO   163      10.560  -5.129  27.327  1.00  0.00
ATOM   1285  CD  PRO   163       9.489  -4.850  28.344  1.00  0.00
ATOM   1286  N   LYS   164       7.811  -4.189  25.283  1.00  0.00
ATOM   1287  CA  LYS   164       6.970  -4.387  24.108  1.00  0.00
ATOM   1288  C   LYS   164       5.914  -3.294  23.995  1.00  0.00
ATOM   1289  O   LYS   164       5.332  -3.089  22.931  1.00  0.00
ATOM   1290  CB  LYS   164       6.250  -5.735  24.185  1.00  0.00
ATOM   1291  CG  LYS   164       7.174  -6.938  24.089  1.00  0.00
ATOM   1292  CD  LYS   164       6.396  -8.241  24.186  1.00  0.00
ATOM   1293  CE  LYS   164       7.316  -9.444  24.063  1.00  0.00
ATOM   1294  NZ  LYS   164       6.565 -10.727  24.133  1.00  0.00
ATOM   1295  N   VAL   165       5.674  -2.594  25.099  1.00  0.00
ATOM   1296  CA  VAL   165       4.603  -1.607  25.162  1.00  0.00
ATOM   1297  C   VAL   165       5.162  -0.198  25.320  1.00  0.00
ATOM   1298  O   VAL   165       4.688   0.743  24.686  1.00  0.00
ATOM   1299  CB  VAL   165       3.663  -1.869  26.352  1.00  0.00
ATOM   1300  CG1 VAL   165       2.515  -0.871  26.354  1.00  0.00
ATOM   1301  CG2 VAL   165       3.079  -3.271  26.271  1.00  0.00
ATOM   1302  N   ASP   166       4.408   0.414  26.894  1.00  0.00
ATOM   1303  CA  ASP   166       3.654   1.646  27.097  1.00  0.00
ATOM   1304  C   ASP   166       4.505   2.870  26.788  1.00  0.00
ATOM   1305  O   ASP   166       4.008   3.870  26.272  1.00  0.00
ATOM   1306  CB  ASP   166       3.180   1.752  28.548  1.00  0.00
ATOM   1307  CG  ASP   166       2.195   2.884  28.758  1.00  0.00
ATOM   1308  OD1 ASP   166       1.787   3.510  27.757  1.00  0.00
ATOM   1309  OD2 ASP   166       1.831   3.146  29.923  1.00  0.00
ATOM   1310  N   SER   167       2.464   4.471  27.795  1.00  0.00
ATOM   1311  CA  SER   167       1.375   4.542  26.828  1.00  0.00
ATOM   1312  C   SER   167       1.553   5.722  25.882  1.00  0.00
ATOM   1313  O   SER   167       1.215   5.639  24.700  1.00  0.00
ATOM   1314  CB  SER   167       0.033   4.707  27.544  1.00  0.00
ATOM   1315  OG  SER   167      -0.032   5.947  28.227  1.00  0.00
ATOM   1316  N   VAL   168       2.087   6.820  26.407  1.00  0.00
ATOM   1317  CA  VAL   168       2.330   8.013  25.605  1.00  0.00
ATOM   1318  C   VAL   168       3.402   7.761  24.553  1.00  0.00
ATOM   1319  O   VAL   168       3.286   8.212  23.414  1.00  0.00
ATOM   1320  CB  VAL   168       2.803   9.191  26.477  1.00  0.00
ATOM   1321  CG1 VAL   168       3.230  10.361  25.603  1.00  0.00
ATOM   1322  CG2 VAL   168       1.683   9.659  27.393  1.00  0.00
ATOM   1323  N   ILE   169       4.446   7.037  24.941  1.00  0.00
ATOM   1324  CA  ILE   169       5.532   6.706  24.025  1.00  0.00
ATOM   1325  C   ILE   169       5.042   5.820  22.887  1.00  0.00
ATOM   1326  O   ILE   169       5.417   6.015  21.731  1.00  0.00
ATOM   1327  CB  ILE   169       6.667   5.953  24.744  1.00  0.00
ATOM   1328  CG1 ILE   169       7.268   6.822  25.848  1.00  0.00
ATOM   1329  CG2 ILE   169       7.770   5.589  23.762  1.00  0.00
ATOM   1330  CD1 ILE   169       8.245   6.089  26.740  1.00  0.00
ATOM   1331  N   VAL   170       5.111   3.786  21.720  1.00  0.00
ATOM   1332  CA  VAL   170       6.311   3.503  22.497  1.00  0.00
ATOM   1333  C   VAL   170       7.195   2.480  21.795  1.00  0.00
ATOM   1334  O   VAL   170       6.840   1.307  21.692  1.00  0.00
ATOM   1335  CB  VAL   170       5.964   2.939  23.887  1.00  0.00
ATOM   1336  CG1 VAL   170       7.232   2.613  24.662  1.00  0.00
ATOM   1337  CG2 VAL   170       5.159   3.952  24.687  1.00  0.00
ATOM   1338  N   LYS   171       8.347   2.933  21.312  1.00  0.00
ATOM   1339  CA  LYS   171       9.217   2.097  20.495  1.00  0.00
ATOM   1340  C   LYS   171      10.686   2.405  20.759  1.00  0.00
ATOM   1341  O   LYS   171      11.047   3.547  21.046  1.00  0.00
ATOM   1342  CB  LYS   171       8.943   2.330  19.008  1.00  0.00
ATOM   1343  CG  LYS   171       7.557   1.900  18.557  1.00  0.00
ATOM   1344  CD  LYS   171       7.386   2.074  17.057  1.00  0.00
ATOM   1345  CE  LYS   171       5.975   1.720  16.616  1.00  0.00
ATOM   1346  NZ  LYS   171       5.809   1.831  15.142  1.00  0.00
ATOM   1347  N   LEU   172      12.867   2.536  21.900  1.00  0.00
ATOM   1348  CA  LEU   172      13.183   1.819  20.671  1.00  0.00
ATOM   1349  C   LEU   172      12.739   0.365  20.753  1.00  0.00
ATOM   1350  O   LEU   172      12.988  -0.315  21.748  1.00  0.00
ATOM   1351  CB  LEU   172      14.691   1.841  20.410  1.00  0.00
ATOM   1352  CG  LEU   172      15.162   1.198  19.104  1.00  0.00
ATOM   1353  CD1 LEU   172      14.648   1.977  17.904  1.00  0.00
ATOM   1354  CD2 LEU   172      16.681   1.169  19.037  1.00  0.00
ATOM   1355  N   ILE   173      12.082  -0.108  19.699  1.00  0.00
ATOM   1356  CA  ILE   173      11.605  -1.485  19.648  1.00  0.00
ATOM   1357  C   ILE   173      12.183  -2.223  18.448  1.00  0.00
ATOM   1358  O   ILE   173      11.806  -1.961  17.305  1.00  0.00
ATOM   1359  CB  ILE   173      10.070  -1.548  19.537  1.00  0.00
ATOM   1360  CG1 ILE   173       9.422  -0.693  20.627  1.00  0.00
ATOM   1361  CG2 ILE   173       9.583  -2.980  19.693  1.00  0.00
ATOM   1362  CD1 ILE   173       9.732  -1.158  22.033  1.00  0.00
ATOM   1363  N   PRO   174      11.697  -0.002  16.205  1.00  0.00
ATOM   1364  CA  PRO   174      10.241   0.077  16.263  1.00  0.00
ATOM   1365  C   PRO   174       9.597  -0.998  15.397  1.00  0.00
ATOM   1366  O   PRO   174      10.154  -1.406  14.378  1.00  0.00
ATOM   1367  CB  PRO   174       9.926   1.479  15.739  1.00  0.00
ATOM   1368  CG  PRO   174      11.174   2.260  15.984  1.00  0.00
ATOM   1369  CD  PRO   174      12.312   1.306  15.756  1.00  0.00
ATOM   1370  N   LYS   175       8.418  -1.454  15.808  1.00  0.00
ATOM   1371  CA  LYS   175       7.695  -2.483  15.071  1.00  0.00
ATOM   1372  C   LYS   175       6.626  -1.870  14.176  1.00  0.00
ATOM   1373  O   LYS   175       6.008  -0.865  14.529  1.00  0.00
ATOM   1374  CB  LYS   175       7.007  -3.450  16.037  1.00  0.00
ATOM   1375  CG  LYS   175       7.967  -4.258  16.895  1.00  0.00
ATOM   1376  CD  LYS   175       7.219  -5.169  17.854  1.00  0.00
ATOM   1377  CE  LYS   175       8.179  -5.988  18.701  1.00  0.00
ATOM   1378  NZ  LYS   175       7.459  -6.914  19.618  1.00  0.00
ATOM   1379  N   GLU   176       6.372  -2.492  13.018  1.00  0.00
ATOM   1380  CA  GLU   176       5.676  -1.802  11.939  1.00  0.00
ATOM   1381  C   GLU   176       4.209  -1.579  12.283  1.00  0.00
ATOM   1382  O   GLU   176       3.594  -2.391  12.974  1.00  0.00
ATOM   1383  CB  GLU   176       5.742  -2.621  10.648  1.00  0.00
ATOM   1384  CG  GLU   176       7.133  -2.716  10.044  1.00  0.00
ATOM   1385  CD  GLU   176       7.159  -3.532   8.767  1.00  0.00
ATOM   1386  OE1 GLU   176       6.096  -4.058   8.376  1.00  0.00
ATOM   1387  OE2 GLU   176       8.243  -3.647   8.157  1.00  0.00
ATOM   1388  N   SER   177       3.653  -0.475  11.798  1.00  0.00
ATOM   1389  CA  SER   177       2.252  -0.152  12.038  1.00  0.00
ATOM   1390  C   SER   177       1.356  -0.753  10.963  1.00  0.00
ATOM   1391  O   SER   177       1.839  -1.319   9.983  1.00  0.00
ATOM   1392  CB  SER   177       2.043   1.363  12.037  1.00  0.00
ATOM   1393  OG  SER   177       2.262   1.908  10.747  1.00  0.00
ATOM   1394  N   SER   178       0.047  -0.626  11.152  1.00  0.00
ATOM   1395  CA  SER   178      -0.920  -1.145  10.192  1.00  0.00
ATOM   1396  C   SER   178      -0.585  -0.696   8.776  1.00  0.00
ATOM   1397  O   SER   178      -0.011   0.373   8.572  1.00  0.00
ATOM   1398  CB  SER   178      -2.328  -0.647  10.527  1.00  0.00
ATOM   1399  OG  SER   178      -2.429   0.755  10.347  1.00  0.00
ATOM   1400  N   PHE   179      -1.493  -1.042   7.644  1.00  0.00
ATOM   1401  CA  PHE   179      -2.131  -0.017   6.827  1.00  0.00
ATOM   1402  C   PHE   179      -2.703   1.099   7.693  1.00  0.00
ATOM   1403  O   PHE   179      -3.203   0.853   8.790  1.00  0.00
ATOM   1404  CB  PHE   179      -3.277  -0.618   6.011  1.00  0.00
ATOM   1405  CG  PHE   179      -2.821  -1.529   4.907  1.00  0.00
ATOM   1406  CD1 PHE   179      -2.829  -2.903   5.076  1.00  0.00
ATOM   1407  CD2 PHE   179      -2.385  -1.012   3.699  1.00  0.00
ATOM   1408  CE1 PHE   179      -2.410  -3.740   4.060  1.00  0.00
ATOM   1409  CE2 PHE   179      -1.966  -1.850   2.683  1.00  0.00
ATOM   1410  CZ  PHE   179      -1.977  -3.209   2.859  1.00  0.00
ATOM   1411  N   LEU   180      -2.625   2.328   7.193  1.00  0.00
ATOM   1412  CA  LEU   180      -3.124   3.486   7.924  1.00  0.00
ATOM   1413  C   LEU   180      -4.585   3.302   8.314  1.00  0.00
ATOM   1414  O   LEU   180      -5.039   3.836   9.327  1.00  0.00
ATOM   1415  CB  LEU   180      -3.018   4.748   7.065  1.00  0.00
ATOM   1416  CG  LEU   180      -1.603   5.250   6.770  1.00  0.00
ATOM   1417  CD1 LEU   180      -1.637   6.402   5.779  1.00  0.00
ATOM   1418  CD2 LEU   180      -0.930   5.740   8.045  1.00  0.00
TER
END
