
#######################################################
#                                                     #
#                        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   35 (  175),  selected   35 , name T0316TS239_5_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS239_5_1-D3.T0316_D3.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    M     284      M     284          3.891
LGA    S     285      S     285          3.500
LGA    T     286      -       -           -
LGA    S     287      T     286          4.625
LGA    L     288      -       -           -
LGA    E     289      -       -           -
LGA    A     290      -       -           -
LGA    S     291      S     287           #
LGA    Q     292      L     288          5.132
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    V     293      F     311          1.559
LGA    H     294      R     312           #
LGA    F     295      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    -       -      F     333           -
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    -       -      A     339           -
LGA    -       -      I     340           -
LGA    -       -      T     341           -
LGA    -       -      P     342           -
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    T     296      A     345          3.453
LGA    R     297      V     346          3.593
LGA    E     298      V     347          2.155
LGA    M     299      F     348          3.055
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    P     300      G     356          1.984
LGA    E     301      G     357          3.581
LGA    E     302      G     358          0.912
LGA    F     303      L     359          1.118
LGA    T     304      I     360          1.456
LGA    -       -      D     361           -
LGA    -       -      N     362           -
LGA    L     305      A     363          4.018
LGA    E     306      Y     364           #
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    C     307      Q     368          2.538
LGA    T     308      V     369           #
LGA    A     309      C     370           -
LGA    K     310      Q     371           -
LGA    F     311      Y     372           -
LGA    R     312      I     373           -
LGA    Y     313      -       -           -
LGA    R     314      -       -           -
LGA    Q     315      -       -           -
LGA    P     316      -       -           -
LGA    D     317      -       -           -
LGA    S     318      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35   90    5.0     16    3.16    12.50     12.526     0.491

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.665596 * X  +  -0.297657 * Y  +   0.684385 * Z  +  83.699867
  Y_new =  -0.162393 * X  +  -0.837286 * Y  +  -0.522093 * Z  + 102.366882
  Z_new =   0.728431 * X  +  -0.458642 * Y  +   0.508956 * Z  + -104.256912 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.733445    2.408147  [ DEG:   -42.0233    137.9767 ]
  Theta =  -0.816028   -2.325564  [ DEG:   -46.7550   -133.2450 ]
  Phi   =  -2.902287    0.239306  [ DEG:  -166.2888     13.7112 ]
 
# 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: T0316TS239_5_1-D3                             
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS239_5_1-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35   90   5.0   16   3.16   12.50  12.526
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS239_5_1-D3
REMARK PARENT number 1
PFRMAT TS
TARGET T0316
PARENT 1gpm_A
ATOM   1197  N   MET   284      22.650   6.686 -15.557  1.00  9.99
ATOM   1198  CA  MET   284      22.509   8.049 -16.080  1.00  9.99
ATOM   1199  C   MET   284      23.185   9.081 -15.191  1.00  9.99
ATOM   1200  O   MET   284      22.896   9.165 -14.000  1.00  9.99
ATOM   1201  CB  MET   284      20.993   8.249 -16.099  1.00  9.99
ATOM   1202  N   SER   285      24.043   9.900 -15.793  1.00  9.99
ATOM   1203  CA  SER   285      24.796  10.923 -15.067  1.00  9.99
ATOM   1204  C   SER   285      23.948  11.812 -14.154  1.00  9.99
ATOM   1205  O   SER   285      24.357  12.117 -13.035  1.00  9.99
ATOM   1206  CB  SER   285      25.586  11.801 -16.039  1.00  9.99
ATOM   1207  N   THR   286      22.778  12.236 -14.618  1.00  9.99
ATOM   1208  CA  THR   286      21.922  13.098 -13.803  1.00  9.99
ATOM   1209  C   THR   286      21.483  12.359 -12.548  1.00  9.99
ATOM   1210  O   THR   286      21.436  12.925 -11.456  1.00  9.99
ATOM   1211  CB  THR   286      20.704  13.571 -14.603  1.00  9.99
ATOM   1212  N   SER   287      21.160  11.085 -12.715  1.00  9.99
ATOM   1213  CA  SER   287      20.749  10.246 -11.604  1.00  9.99
ATOM   1214  C   SER   287      21.904  10.156 -10.605  1.00  9.99
ATOM   1215  O   SER   287      21.720  10.364  -9.396  1.00  9.99
ATOM   1216  CB  SER   287      20.380   8.861 -12.137  1.00  9.99
ATOM   1217  N   LEU   288      23.097   9.880 -11.134  1.00  9.99
ATOM   1218  CA  LEU   288      24.318   9.762 -10.340  1.00  9.99
ATOM   1219  C   LEU   288      24.677  11.038  -9.587  1.00  9.99
ATOM   1220  O   LEU   288      25.139  10.992  -8.449  1.00  9.99
ATOM   1221  CB  LEU   288      25.475   9.360 -11.236  1.00  9.99
ATOM   1222  N   GLU   289      24.483  12.179 -10.232  1.00  9.99
ATOM   1223  CA  GLU   289      24.773  13.442  -9.584  1.00  9.99
ATOM   1224  C   GLU   289      23.732  13.756  -8.522  1.00  9.99
ATOM   1225  O   GLU   289      24.034  14.412  -7.521  1.00  9.99
ATOM   1226  CB  GLU   289      24.843  14.552 -10.645  1.00  9.99
ATOM   1227  N   ALA   290      22.504  13.294  -8.745  1.00  9.99
ATOM   1228  CA  ALA   290      21.396  13.508  -7.814  1.00  9.99
ATOM   1229  C   ALA   290      21.631  12.735  -6.523  1.00  9.99
ATOM   1230  O   ALA   290      21.383  13.253  -5.433  1.00  9.99
ATOM   1231  CB  ALA   290      20.085  13.043  -8.455  1.00  9.99
ATOM   1232  N   SER   291      22.096  11.489  -6.652  1.00  9.99
ATOM   1233  CA  SER   291      22.371  10.622  -5.496  1.00  9.99
ATOM   1234  C   SER   291      23.580  11.168  -4.748  1.00  9.99
ATOM   1235  O   SER   291      23.571  11.300  -3.520  1.00  9.99
ATOM   1236  CB  SER   291      22.689   9.164  -5.935  1.00  9.99
ATOM   1237  N   GLN   292      24.626  11.461  -5.514  1.00  9.99
ATOM   1238  CA  GLN   292      25.859  12.010  -4.986  1.00  9.99
ATOM   1239  C   GLN   292      25.535  13.236  -4.145  1.00  9.99
ATOM   1240  O   GLN   292      25.938  13.334  -2.981  1.00  9.99
ATOM   1241  CB  GLN   292      26.768  12.412  -6.140  1.00  9.99
ATOM   1242  N   VAL   293      24.787  14.161  -4.733  1.00  9.99
ATOM   1243  CA  VAL   293      24.402  15.368  -4.028  1.00  9.99
ATOM   1244  C   VAL   293      23.648  15.069  -2.737  1.00  9.99
ATOM   1245  O   VAL   293      24.045  15.561  -1.673  1.00  9.99
ATOM   1246  CB  VAL   293      23.554  16.271  -4.926  1.00  9.99
ATOM   1247  N   HIS   294      22.583  14.261  -2.821  1.00  9.99
ATOM   1248  CA  HIS   294      21.777  13.913  -1.641  1.00  9.99
ATOM   1249  C   HIS   294      22.608  13.319  -0.522  1.00  9.99
ATOM   1250  O   HIS   294      22.506  13.750   0.624  1.00  9.99
ATOM   1251  CB  HIS   294      20.655  12.921  -1.969  1.00  9.99
ATOM   1252  N   PHE   295      23.437  12.330  -0.851  1.00  9.99
ATOM   1253  CA  PHE   295      24.273  11.676   0.153  1.00  9.99
ATOM   1254  C   PHE   295      25.203  12.653   0.866  1.00  9.99
ATOM   1255  O   PHE   295      25.256  12.660   2.095  1.00  9.99
ATOM   1256  CB  PHE   295      25.111  10.497  -0.440  1.00  9.99
ATOM   1257  N   THR   296      25.922  13.480   0.115  1.00  9.99
ATOM   1258  CA  THR   296      26.838  14.417   0.756  1.00  9.99
ATOM   1259  C   THR   296      26.108  15.471   1.589  1.00  9.99
ATOM   1260  O   THR   296      26.564  15.828   2.674  1.00  9.99
ATOM   1261  CB  THR   296      27.747  15.136  -0.252  1.00  9.99
ATOM   1262  N   ARG   297      24.959  15.936   1.102  1.00  9.99
ATOM   1263  CA  ARG   297      24.191  16.959   1.805  1.00  9.99
ATOM   1264  C   ARG   297      23.341  16.441   2.969  1.00  9.99
ATOM   1265  O   ARG   297      23.113  17.161   3.948  1.00  9.99
ATOM   1266  CB  ARG   297      23.279  17.718   0.828  1.00  9.99
ATOM   1267  N   GLU   298      22.880  15.197   2.871  1.00  9.99
ATOM   1268  CA  GLU   298      22.013  14.621   3.894  1.00  9.99
ATOM   1269  C   GLU   298      22.655  13.778   4.979  1.00  9.99
ATOM   1270  O   GLU   298      22.164  13.748   6.118  1.00  9.99
ATOM   1271  CB  GLU   298      20.869  13.846   3.229  1.00  9.99
ATOM   1272  N   MET   299      23.725  13.068   4.641  1.00  9.99
ATOM   1273  CA  MET   299      24.388  12.217   5.621  1.00  9.99
ATOM   1274  C   MET   299      25.585  12.929   6.224  1.00  9.99
ATOM   1275  O   MET   299      26.639  13.021   5.603  1.00  9.99
ATOM   1276  CB  MET   299      24.835  10.866   5.005  1.00  9.99
ATOM   1277  N   PRO   300      25.415  13.430   7.442  1.00  9.99
ATOM   1278  CA  PRO   300      26.486  14.134   8.143  1.00  9.99
ATOM   1279  C   PRO   300      27.600  13.144   8.440  1.00  9.99
ATOM   1280  O   PRO   300      27.390  12.186   9.181  1.00  9.99
ATOM   1281  CB  PRO   300      25.945  14.740   9.443  1.00  9.99
ATOM   1282  N   GLU   301      28.766  13.358   7.844  1.00  9.99
ATOM   1283  CA  GLU   301      29.883  12.455   8.061  1.00  9.99
ATOM   1284  C   GLU   301      30.466  11.944   6.754  1.00  9.99
ATOM   1285  O   GLU   301      31.510  11.284   6.744  1.00  9.99
ATOM   1286  CB  GLU   301      29.418  11.290   8.951  1.00  9.99
ATOM   1287  N   GLU   302      29.763  12.209   5.652  1.00  9.99
ATOM   1288  CA  GLU   302      30.203  11.790   4.320  1.00  9.99
ATOM   1289  C   GLU   302      30.351  13.038   3.443  1.00  9.99
ATOM   1290  O   GLU   302      29.400  13.810   3.283  1.00  9.99
ATOM   1291  CB  GLU   302      29.200  10.785   3.683  1.00  9.99
ATOM   1292  N   PHE   303      31.549  13.245   2.904  1.00  9.99
ATOM   1293  CA  PHE   303      31.820  14.411   2.068  1.00  9.99
ATOM   1294  C   PHE   303      32.100  14.096   0.597  1.00  9.99
ATOM   1295  O   PHE   303      32.202  15.013  -0.229  1.00  9.99
ATOM   1296  CB  PHE   303      32.975  15.223   2.660  1.00  9.99
ATOM   1297  N   THR   304      32.213  12.814   0.258  1.00  9.99
ATOM   1298  CA  THR   304      32.483  12.431  -1.122  1.00  9.99
ATOM   1299  C   THR   304      31.855  11.101  -1.495  1.00  9.99
ATOM   1300  O   THR   304      31.804  10.175  -0.682  1.00  9.99
ATOM   1301  CB  THR   304      33.988  12.362  -1.372  1.00  9.99
ATOM   1302  N   LEU   305      31.925   6.197  -7.766  1.00  9.99
ATOM   1303  CA  LEU   305      31.192   5.127  -8.418  1.00  9.99
ATOM   1304  C   LEU   305      32.136   4.039  -8.914  1.00  9.99
ATOM   1305  O   LEU   305      33.155   4.341  -9.529  1.00  9.99
ATOM   1306  CB  LEU   305      30.372   5.685  -9.578  1.00  9.99
ATOM   1307  N   GLU   306      31.802   2.776  -8.632  1.00  9.99
ATOM   1308  CA  GLU   306      32.633   1.654  -9.056  1.00  9.99
ATOM   1309  C   GLU   306      32.470   1.390 -10.549  1.00  9.99
ATOM   1310  O   GLU   306      31.367   1.098 -11.026  1.00  9.99
ATOM   1311  CB  GLU   306      32.312   0.387  -8.258  1.00  9.99
ATOM   1312  N   CYS   307      33.569   1.511 -11.286  1.00  9.99
ATOM   1313  CA  CYS   307      33.535   1.300 -12.722  1.00  9.99
ATOM   1314  C   CYS   307      34.395   0.111 -13.099  1.00  9.99
ATOM   1315  O   CYS   307      34.957   0.053 -14.192  1.00  9.99
ATOM   1316  CB  CYS   307      33.970   2.572 -13.521  1.00  9.99
ATOM   1317  N   THR   308      34.492  -0.841 -12.179  1.00  9.99
ATOM   1318  CA  THR   308      35.265  -2.053 -12.400  1.00  9.99
ATOM   1319  C   THR   308      34.274  -3.181 -12.651  1.00  9.99
ATOM   1320  O   THR   308      33.339  -3.380 -11.873  1.00  9.99
ATOM   1321  CB  THR   308      36.100  -2.368 -11.164  1.00  9.99
ATOM   1322  N   ALA   309      34.455  -3.900 -13.750  1.00  9.99
ATOM   1323  CA  ALA   309      33.561  -4.990 -14.077  1.00  9.99
ATOM   1324  C   ALA   309      34.046  -6.326 -13.557  1.00  9.99
ATOM   1325  O   ALA   309      35.069  -6.417 -12.872  1.00  9.99
ATOM   1326  CB  ALA   309      33.374  -5.033 -15.603  1.00  9.99
ATOM   1327  N   LYS   310      33.285  -7.366 -13.857  1.00  9.99
ATOM   1328  CA  LYS   310      33.640  -8.716 -13.460  1.00  9.99
ATOM   1329  C   LYS   310      33.681  -9.585 -14.710  1.00  9.99
ATOM   1330  O   LYS   310      32.661  -9.766 -15.386  1.00  9.99
ATOM   1331  CB  LYS   310      32.639  -9.292 -12.460  1.00  9.99
ATOM   1332  N   PHE   311      34.885 -10.005 -15.116  1.00  9.99
ATOM   1333  CA  PHE   311      36.151  -9.685 -14.454  1.00  9.99
ATOM   1334  C   PHE   311      36.632  -8.310 -14.947  1.00  9.99
ATOM   1335  O   PHE   311      35.941  -7.651 -15.730  1.00  9.99
ATOM   1336  CB  PHE   311      37.060 -10.815 -14.935  1.00  9.99
ATOM   1337  N   ARG   312      37.817  -7.857 -14.504  1.00  9.99
ATOM   1338  CA  ARG   312      38.764  -8.493 -13.588  1.00  9.99
ATOM   1339  C   ARG   312      38.488  -8.281 -12.103  1.00  9.99
ATOM   1340  O   ARG   312      39.232  -8.782 -11.256  1.00  9.99
ATOM   1341  CB  ARG   312      40.092  -7.881 -14.006  1.00  9.99
ATOM   1342  N   TYR   313      37.440  -7.534 -11.775  1.00  9.99
ATOM   1343  CA  TYR   313      37.114  -7.308 -10.372  1.00  9.99
ATOM   1344  C   TYR   313      35.904  -8.157 -10.000  1.00  9.99
ATOM   1345  O   TYR   313      35.269  -8.751 -10.868  1.00  9.99
ATOM   1346  CB  TYR   313      36.821  -5.844 -10.127  1.00  9.99
ATOM   1347  N   ARG   314      35.633  -8.268  -8.704  1.00  9.99
ATOM   1348  CA  ARG   314      34.482  -9.015  -8.216  1.00  9.99
ATOM   1349  C   ARG   314      33.367  -8.008  -7.956  1.00  9.99
ATOM   1350  O   ARG   314      33.603  -6.784  -7.980  1.00  9.99
ATOM   1351  CB  ARG   314      34.803  -9.762  -6.907  1.00  9.99
ATOM   1352  N   GLN   315      32.152  -8.513  -7.737  1.00  9.99
ATOM   1353  CA  GLN   315      30.999  -7.651  -7.465  1.00  9.99
ATOM   1354  C   GLN   315      31.160  -6.985  -6.105  1.00  9.99
ATOM   1355  O   GLN   315      31.054  -5.760  -5.996  1.00  9.99
ATOM   1356  CB  GLN   315      29.673  -8.426  -7.515  1.00  9.99
ATOM   1357  N   PRO   316      31.443  -7.787  -5.084  1.00  9.99
ATOM   1358  CA  PRO   316      31.648  -7.274  -3.742  1.00  9.99
ATOM   1359  C   PRO   316      33.126  -6.914  -3.637  1.00  9.99
ATOM   1360  O   PRO   316      33.931  -7.363  -4.444  1.00  9.99
ATOM   1361  CB  PRO   316      31.257  -8.319  -2.697  1.00  9.99
ATOM   1362  N   ASP   317      33.460  -6.027  -2.704  1.00  9.99
ATOM   1363  CA  ASP   317      34.832  -5.585  -2.503  1.00  9.99
ATOM   1364  C   ASP   317      35.619  -6.455  -1.534  1.00  9.99
ATOM   1365  O   ASP   317      36.853  -6.375  -1.501  1.00  9.99
ATOM   1366  CB  ASP   317      34.859  -4.157  -1.981  1.00  9.99
ATOM   1367  N   SER   318      34.911  -7.256  -0.738  1.00  9.99
ATOM   1368  CA  SER   318      35.533  -8.141   0.247  1.00  9.99
ATOM   1369  C   SER   318      34.901  -9.533   0.190  1.00  9.99
ATOM   1370  O   SER   318      33.714  -9.640  -0.192  1.00  9.99
ATOM   1371  CB  SER   318      35.397  -7.566   1.673  1.00  9.99
TER
END
