
#######################################################
#                                                     #
#                        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   22 (  107),  selected   22 , name T0291TS261_1_2-D2
# Molecule2: number of CA atoms  181 ( 1450),  selected  181 , name T0291_D2.pdb
# PARAMETERS: T0291TS261_1_2-D2.T0291_D2.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    -       -      E     109           -
LGA    -       -      N     110           -
LGA    -       -      G     111           -
LGA    -       -      S     112           -
LGA    -       -      L     113           -
LGA    -       -      D     114           -
LGA    -       -      S     115           -
LGA    -       -      F     116           -
LGA    -       -      L     117           -
LGA    -       -      R     118           -
LGA    -       -      K     119           -
LGA    -       -      H     120           -
LGA    -       -      D     121           -
LGA    -       -      A     122           -
LGA    -       -      Q     123           -
LGA    -       -      F     124           -
LGA    -       -      T     125           -
LGA    -       -      V     126           -
LGA    -       -      I     127           -
LGA    -       -      Q     128           -
LGA    -       -      L     129           -
LGA    -       -      V     130           -
LGA    -       -      G     131           -
LGA    -       -      M     132           -
LGA    -       -      L     133           -
LGA    -       -      R     134           -
LGA    -       -      G     135           -
LGA    -       -      I     136           -
LGA    -       -      A     137           -
LGA    -       -      S     138           -
LGA    -       -      G     139           -
LGA    -       -      M     140           -
LGA    -       -      K     141           -
LGA    -       -      Y     142           -
LGA    -       -      L     143           -
LGA    -       -      S     144           -
LGA    -       -      D     145           -
LGA    L     173      M     146          4.708
LGA    G     174      G     147          3.288
LGA    R     175      Y     148          3.349
LGA    V     176      V     149          3.806
LGA    L     177      H     150          1.606
LGA    E     178      R     151          1.534
LGA    D     179      D     152          3.202
LGA    D     180      L     153          2.724
LGA    P     181      A     154          2.358
LGA    A     183      A     155          5.311
LGA    A     184      R     156           -
LGA    -       -      N     157           -
LGA    -       -      I     158           -
LGA    -       -      L     159           -
LGA    -       -      I     160           -
LGA    -       -      N     161           -
LGA    -       -      S     162           -
LGA    -       -      N     163           -
LGA    -       -      L     164           -
LGA    -       -      V     165           -
LGA    -       -      C     166           -
LGA    -       -      K     167           -
LGA    -       -      V     168           -
LGA    -       -      S     169           -
LGA    -       -      D     170           -
LGA    -       -      F     171           -
LGA    -       -      G     172           -
LGA    -       -      L     173           -
LGA    -       -      G     174           -
LGA    -       -      R     175           -
LGA    -       -      V     176           -
LGA    -       -      P     193           -
LGA    -       -      I     194           -
LGA    -       -      R     195           -
LGA    Y     185      W     196          2.209
LGA    T     186      T     197          0.847
LGA    T     187      S     198          2.189
LGA    R     188      P     199          0.628
LGA    G     189      E     200          0.949
LGA    G     190      A     201          3.853
LGA    -       -      I     202           -
LGA    -       -      A     203           -
LGA    -       -      Y     204           -
LGA    -       -      R     205           -
LGA    -       -      K     206           -
LGA    -       -      F     207           -
LGA    -       -      T     208           -
LGA    -       -      S     209           -
LGA    -       -      A     210           -
LGA    K     191      S     211          2.667
LGA    I     192      D     212          3.635
LGA    -       -      V     213           -
LGA    -       -      W     214           -
LGA    -       -      S     215           -
LGA    P     193      Y     216          1.618
LGA    I     194      G     217          1.626
LGA    R     195      I     218          3.241
LGA    -       -      V     219           -
LGA    -       -      L     220           -
LGA    -       -      W     221           -
LGA    -       -      E     222           -
LGA    -       -      V     223           -
LGA    -       -      M     224           -
LGA    -       -      S     225           -
LGA    -       -      Y     226           -
LGA    -       -      G     227           -
LGA    -       -      E     228           -
LGA    -       -      R     229           -
LGA    -       -      P     230           -
LGA    -       -      Y     231           -
LGA    -       -      W     232           -
LGA    -       -      E     233           -
LGA    -       -      M     234           -
LGA    -       -      S     235           -
LGA    -       -      N     236           -
LGA    -       -      Q     237           -
LGA    -       -      D     238           -
LGA    -       -      V     239           -
LGA    -       -      I     240           -
LGA    -       -      K     241           -
LGA    -       -      A     242           -
LGA    -       -      V     243           -
LGA    -       -      D     244           -
LGA    -       -      E     245           -
LGA    -       -      G     246           -
LGA    -       -      Y     247           -
LGA    -       -      R     248           -
LGA    -       -      L     249           -
LGA    -       -      P     250           -
LGA    -       -      P     251           -
LGA    -       -      P     252           -
LGA    -       -      M     253           -
LGA    -       -      D     254           -
LGA    -       -      C     255           -
LGA    -       -      P     256           -
LGA    -       -      A     257           -
LGA    -       -      A     258           -
LGA    -       -      L     259           -
LGA    -       -      Y     260           -
LGA    -       -      Q     261           -
LGA    -       -      L     262           -
LGA    -       -      M     263           -
LGA    -       -      L     264           -
LGA    -       -      D     265           -
LGA    -       -      C     266           -
LGA    -       -      W     267           -
LGA    -       -      Q     268           -
LGA    -       -      K     269           -
LGA    -       -      D     270           -
LGA    -       -      R     271           -
LGA    -       -      N     272           -
LGA    -       -      N     273           -
LGA    -       -      R     274           -
LGA    -       -      P     275           -
LGA    -       -      K     276           -
LGA    -       -      F     277           -
LGA    -       -      E     278           -
LGA    -       -      Q     279           -
LGA    -       -      I     280           -
LGA    -       -      V     281           -
LGA    -       -      S     282           -
LGA    -       -      I     283           -
LGA    -       -      L     284           -
LGA    -       -      D     285           -
LGA    -       -      K     286           -
LGA    -       -      L     287           -
LGA    -       -      I     288           -
LGA    -       -      R     289           -
LGA    -       -      N     290           -
LGA    -       -      P     291           -
LGA    -       -      G     292           -
LGA    -       -      S     293           -
LGA    -       -      L     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      I     297           -
LGA    -       -      T     298           -
LGA    -       -      S     299           -
LGA    -       -      S     305           -
LGA    -       -      N     306           -
LGA    -       -      L     307           -
LGA    -       -      L     308           -
LGA    -       -      L     309           -
LGA    -       -      D     310           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   22  181    5.0     21    2.91    23.81      7.156     0.698

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.216522 * X  +  -0.323521 * Y  +  -0.921115 * Z  +  57.105381
  Y_new =  -0.976097 * X  +   0.053565 * Y  +   0.210633 * Z  +  41.504601
  Z_new =  -0.018805 * X  +   0.944704 * Y  +  -0.327385 * Z  +  34.162403 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.904393   -1.237200  [ DEG:   109.1137    -70.8863 ]
  Theta =   0.018806    3.122787  [ DEG:     1.0775    178.9225 ]
  Phi   =  -1.789086    1.352506  [ DEG:  -102.5071     77.4929 ]
 
# 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: T0291TS261_1_2-D2                             
REMARK     2: T0291_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0291TS261_1_2-D2.T0291_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   22  181   5.0   21   2.91   23.81   7.156
REMARK  ---------------------------------------------------------- 
MOLECULE T0291TS261_1_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0291
PARENT 1t46_A
ATOM   1328  N   LEU   173       3.333  27.244  53.278  1.00  3.03
ATOM   1329  CA  LEU   173       2.139  27.722  53.984  1.00  3.03
ATOM   1330  C   LEU   173       0.856  26.988  53.580  1.00  3.03
ATOM   1331  O   LEU   173      -0.124  26.978  54.332  1.00  3.03
ATOM   1332  CB  LEU   173       1.944  29.225  53.746  1.00  3.03
ATOM   1333  N   GLY   174       0.872  26.379  52.397  1.00  5.08
ATOM   1334  CA  GLY   174      -0.328  25.773  51.830  1.00  5.08
ATOM   1335  C   GLY   174      -0.463  24.266  52.063  1.00  5.08
ATOM   1336  O   GLY   174      -1.270  23.616  51.411  1.00  5.08
ATOM   1337  N   ARG   175       0.304  23.708  52.994  1.00  3.25
ATOM   1338  CA  ARG   175       0.024  22.341  53.428  1.00  3.25
ATOM   1339  C   ARG   175      -0.461  22.289  54.862  1.00  3.25
ATOM   1340  O   ARG   175       0.057  23.002  55.720  1.00  3.25
ATOM   1341  CB  ARG   175       1.214  21.403  53.248  1.00  3.25
ATOM   1342  N   VAL   176      -1.457  21.435  55.092  1.00  4.40
ATOM   1343  CA  VAL   176      -2.071  21.233  56.396  1.00  4.40
ATOM   1344  C   VAL   176      -1.238  20.235  57.200  1.00  4.40
ATOM   1345  O   VAL   176      -1.644  19.082  57.390  1.00  4.40
ATOM   1346  CB  VAL   176      -3.506  20.722  56.213  1.00  4.40
ATOM   1347  N   LEU   177      -0.075  20.690  57.665  1.00  3.71
ATOM   1348  CA  LEU   177       0.883  19.830  58.363  1.00  3.71
ATOM   1349  C   LEU   177       0.343  19.314  59.698  1.00  3.71
ATOM   1350  O   LEU   177       0.838  18.324  60.235  1.00  3.71
ATOM   1351  CB  LEU   177       2.256  20.537  58.546  1.00  3.71
ATOM   1352  N   GLU   178      -0.682  19.987  60.214  1.00  5.14
ATOM   1353  CA  GLU   178      -1.347  19.567  61.444  1.00  5.14
ATOM   1354  C   GLU   178      -2.057  18.223  61.272  1.00  5.14
ATOM   1355  O   GLU   178      -2.032  17.384  62.174  1.00  5.14
ATOM   1356  CB  GLU   178      -2.328  20.647  61.908  1.00  5.14
ATOM   1357  N   ASP   179      -2.660  18.016  60.105  1.00  4.57
ATOM   1358  CA  ASP   179      -3.415  16.793  59.830  1.00  4.57
ATOM   1359  C   ASP   179      -2.763  15.860  58.810  1.00  4.57
ATOM   1360  O   ASP   179      -3.402  14.933  58.302  1.00  4.57
ATOM   1361  CB  ASP   179      -4.850  17.138  59.420  1.00  4.57
ATOM   1362  N   ASP   180      -1.491  16.114  58.514  1.00  4.66
ATOM   1363  CA  ASP   180      -0.696  15.216  57.690  1.00  4.66
ATOM   1364  C   ASP   180       0.194  14.408  58.622  1.00  4.66
ATOM   1365  O   ASP   180       1.089  14.961  59.266  1.00  4.66
ATOM   1366  CB  ASP   180       0.146  16.003  56.675  1.00  4.66
ATOM   1367  N   PRO   181      -0.069  13.104  58.695  1.00  5.45
ATOM   1368  CA  PRO   181       0.634  12.203  59.615  1.00  5.45
ATOM   1369  C   PRO   181       2.102  11.988  59.235  1.00  5.45
ATOM   1370  O   PRO   181       2.881  11.422  60.010  1.00  5.45
ATOM   1371  CB  PRO   181      -0.096  10.859  59.718  1.00  5.45
ATOM   1372  N   ALA   183       2.468  12.441  58.037  1.00  5.08
ATOM   1373  CA  ALA   183       3.862  12.439  57.607  1.00  5.08
ATOM   1374  C   ALA   183       4.661  13.554  58.279  1.00  5.08
ATOM   1375  O   ALA   183       5.894  13.595  58.189  1.00  5.08
ATOM   1376  CB  ALA   183       3.948  12.536  56.084  1.00  5.08
ATOM   1377  N   ALA   184       3.952  14.461  58.949  1.00  5.15
ATOM   1378  CA  ALA   184       4.587  15.495  59.751  1.00  5.15
ATOM   1379  C   ALA   184       4.331  15.178  61.210  1.00  5.15
ATOM   1380  O   ALA   184       3.180  15.069  61.636  1.00  5.15
ATOM   1381  CB  ALA   184       4.054  16.884  59.393  1.00  5.15
ATOM   1382  N   TYR   185       5.416  15.019  61.956  1.00  4.63
ATOM   1383  CA  TYR   185       5.354  14.581  63.348  1.00  4.63
ATOM   1384  C   TYR   185       5.879  15.670  64.277  1.00  4.63
ATOM   1385  O   TYR   185       6.873  16.331  63.973  1.00  4.63
ATOM   1386  CB  TYR   185       6.166  13.271  63.544  1.00  4.63
ATOM   1387  N   THR   186       5.213  15.857  65.416  1.00  4.53
ATOM   1388  CA  THR   186       5.699  16.797  66.418  1.00  4.53
ATOM   1389  C   THR   186       7.057  16.339  66.951  1.00  4.53
ATOM   1390  O   THR   186       7.222  15.195  67.377  1.00  4.53
ATOM   1391  CB  THR   186       4.700  16.994  67.597  1.00  4.53
ATOM   1392  N   THR   187       8.027  17.241  66.883  1.00  5.18
ATOM   1393  CA  THR   187       9.340  17.043  67.477  1.00  5.18
ATOM   1394  C   THR   187       9.751  18.396  68.034  1.00  5.18
ATOM   1395  O   THR   187       9.979  19.348  67.278  1.00  5.18
ATOM   1396  CB  THR   187      10.345  16.537  66.436  1.00  5.18
ATOM   1397  N   ARG   188       9.820  18.476  69.361  1.00  4.72
ATOM   1398  CA  ARG   188       9.975  19.743  70.048  1.00  4.72
ATOM   1399  C   ARG   188       8.738  20.588  69.816  1.00  4.72
ATOM   1400  O   ARG   188       7.611  20.106  69.970  1.00  4.72
ATOM   1401  CB  ARG   188      11.247  20.452  69.554  1.00  4.72
ATOM   1402  N   GLY   189       8.946  21.840  69.426  1.00  5.82
ATOM   1403  CA  GLY   189       7.839  22.746  69.135  1.00  5.82
ATOM   1404  C   GLY   189       7.673  22.978  67.632  1.00  5.82
ATOM   1405  O   GLY   189       7.504  24.110  67.170  1.00  5.82
ATOM   1406  N   GLY   190       7.726  21.881  66.877  1.00  5.51
ATOM   1407  CA  GLY   190       7.554  21.906  65.426  1.00  5.51
ATOM   1408  C   GLY   190       6.947  20.600  64.931  1.00  5.51
ATOM   1409  O   GLY   190       7.104  19.556  65.569  1.00  5.51
ATOM   1410  N   LYS   191       6.246  20.672  63.802  1.00  4.83
ATOM   1411  CA  LYS   191       5.744  19.489  63.114  1.00  4.83
ATOM   1412  C   LYS   191       6.628  19.263  61.893  1.00  4.83
ATOM   1413  O   LYS   191       6.626  20.062  60.955  1.00  4.83
ATOM   1414  CB  LYS   191       4.282  19.668  62.705  1.00  4.83
ATOM   1415  N   ILE   192       7.392  18.176  61.924  1.00  7.89
ATOM   1416  CA  ILE   192       8.467  17.967  60.959  1.00  7.89
ATOM   1417  C   ILE   192       8.312  16.678  60.162  1.00  7.89
ATOM   1418  O   ILE   192       7.790  15.685  60.673  1.00  7.89
ATOM   1419  CB  ILE   192       9.818  17.985  61.680  1.00  7.89
ATOM   1420  N   PRO   193       8.777  16.690  58.912  1.00  3.50
ATOM   1421  CA  PRO   193       8.716  15.498  58.057  1.00  3.50
ATOM   1422  C   PRO   193       9.806  14.489  58.434  1.00  3.50
ATOM   1423  O   PRO   193      10.699  14.193  57.646  1.00  3.50
ATOM   1424  CB  PRO   193       8.957  16.068  56.654  1.00  3.50
ATOM   1425  N   ILE   194       9.723  13.971  59.656  1.00  3.76
ATOM   1426  CA  ILE   194      10.811  13.201  60.252  1.00  3.76
ATOM   1427  C   ILE   194      11.303  12.023  59.400  1.00  3.76
ATOM   1428  O   ILE   194      12.513  11.807  59.300  1.00  3.76
ATOM   1429  CB  ILE   194      10.435  12.740  61.681  1.00  3.76
ATOM   1430  N   ARG   195      10.379  11.271  58.798  1.00  4.72
ATOM   1431  CA  ARG   195      10.751  10.093  57.999  1.00  4.72
ATOM   1432  C   ARG   195      11.558  10.428  56.736  1.00  4.72
ATOM   1433  O   ARG   195      12.175   9.542  56.142  1.00  4.72
ATOM   1434  CB  ARG   195       9.529   9.242  57.651  1.00  4.72
TER
END
