
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0386TS307_4u-D2
# Molecule2: number of CA atoms   81 (  636),  selected   81 , name T0386_D2.pdb
# PARAMETERS: T0386TS307_4u-D2.T0386_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    -       -      N     219           -
LGA    -       -      P     220           -
LGA    -       -      E     221           -
LGA    -       -      K     222           -
LGA    -       -      I     223           -
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    N     219      G     237           #
LGA    E     221      R     238          1.907
LGA    K     222      N     239          3.978
LGA    I     223      V     240          0.848
LGA    -       -      N     241           -
LGA    R     224      D     242          2.289
LGA    L     225      R     243          1.904
LGA    L     226      P     244          2.409
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      G     265           -
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    K     227      K     271          4.566
LGA    E     228      G     272          4.847
LGA    F     229      A     273          4.297
LGA    M     230      Y     274          2.920
LGA    H     231      I     275          3.021
LGA    T     232      I     276          3.808
LGA    M     233      -       -           -
LGA    K     234      G     277          3.032
LGA    N     235      -       -           -
LGA    T     236      -       -           -
LGA    G     237      -       -           -
LGA    R     238      N     278          2.917
LGA    N     239      I     279          2.246
LGA    E     250      -       -           -
LGA    G     251      D     280          0.905
LGA    E     252      H     281          1.351
LGA    T     253      L     282          2.488
LGA    -       -      P     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    -       -      L     287           -
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24   81    5.0     18    2.99     5.56     13.986     0.582

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.372675 * X  +   0.073458 * Y  +  -0.925050 * Z  +   6.070703
  Y_new =  -0.719448 * X  +  -0.652484 * Y  +   0.238031 * Z  +  64.602043
  Z_new =  -0.586095 * X  +   0.754233 * Y  +   0.296015 * Z  +  76.210190 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.196797   -1.944795  [ DEG:    68.5714   -111.4286 ]
  Theta =   0.626231    2.515362  [ DEG:    35.8804    144.1196 ]
  Phi   =  -2.048742    1.092851  [ DEG:  -117.3842     62.6158 ]
 
# 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: T0386TS307_4u-D2                              
REMARK     2: T0386_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS307_4u-D2.T0386_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24   81   5.0   18   2.99    5.56  13.986
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS307_4u-D2
PFRMAT   TS
TARGET   T0386
MODEL    4  UNREFINED
PARENT   2f6s_A
ATOM   1249  N   ASN   219      20.189  72.307  75.048  1.00 62.93           N  
ATOM   1250  CA  ASN   219      21.479  71.906  74.492  1.00 63.15           C  
ATOM   1251  C   ASN   219      21.417  71.843  72.974  1.00 63.71           C  
ATOM   1252  O   ASN   219      20.374  71.479  72.407  1.00 63.95           O  
ATOM   1255  N   GLU   221      22.534  72.193  72.330  1.00 64.14           N  
ATOM   1256  CA  GLU   221      22.707  72.036  70.879  1.00 64.71           C  
ATOM   1257  C   GLU   221      23.098  70.611  70.483  1.00 64.82           C  
ATOM   1258  O   GLU   221      23.054  70.248  69.313  1.00 64.67           O  
ATOM   1261  N   LYS   222      23.456  69.809  71.475  1.00 64.94           N  
ATOM   1262  CA  LYS   222      23.916  68.458  71.254  1.00 65.39           C  
ATOM   1263  C   LYS   222      22.755  67.479  71.070  1.00 65.22           C  
ATOM   1264  O   LYS   222      22.578  66.536  71.851  1.00 65.11           O  
ATOM   1269  N   ILE   223      21.988  67.689  70.012  1.00 65.20           N  
ATOM   1270  CA  ILE   223      20.675  67.054  69.881  1.00 65.49           C  
ATOM   1271  C   ILE   223      20.728  65.578  69.507  1.00 66.39           C  
ATOM   1272  O   ILE   223      19.690  64.908  69.455  1.00 66.01           O  
ATOM   1276  N   ARG   224      21.930  65.082  69.232  1.00 67.48           N  
ATOM   1277  CA  ARG   224      22.083  63.766  68.635  1.00 68.99           C  
ATOM   1278  C   ARG   224      22.895  62.790  69.473  1.00 70.04           C  
ATOM   1279  O   ARG   224      22.913  61.597  69.172  1.00 70.40           O  
ATOM   1284  N   LEU   225      23.571  63.290  70.508  1.00 71.19           N  
ATOM   1285  CA  LEU   225      24.320  62.426  71.407  1.00 72.43           C  
ATOM   1286  C   LEU   225      23.397  61.413  72.122  1.00 73.54           C  
ATOM   1287  O   LEU   225      22.529  61.813  72.925  1.00 73.83           O  
ATOM   1292  N   LEU   226      23.563  60.095  71.836  1.00 74.34           N  
ATOM   1293  CA  LEU   226      22.560  59.210  72.455  1.00 74.48           C  
ATOM   1294  C   LEU   226      22.760  59.044  73.978  1.00 74.51           C  
ATOM   1295  O   LEU   226      21.780  58.755  74.678  1.00 74.65           O  
ATOM   1299  N   LYS   227      23.978  59.265  74.492  1.00 74.23           N  
ATOM   1300  CA  LYS   227      24.181  59.283  75.956  1.00 74.15           C  
ATOM   1301  C   LYS   227      23.327  60.391  76.606  1.00 73.89           C  
ATOM   1302  O   LYS   227      22.568  60.138  77.555  1.00 74.31           O  
ATOM   1307  N   GLU   228      23.446  61.606  76.069  1.00 73.11           N  
ATOM   1308  CA  GLU   228      22.658  62.757  76.500  1.00 72.12           C  
ATOM   1309  C   GLU   228      21.152  62.464  76.430  1.00 71.50           C  
ATOM   1310  O   GLU   228      20.403  62.798  77.344  1.00 70.98           O  
ATOM   1314  N   PHE   229      20.734  61.820  75.347  1.00 70.81           N  
ATOM   1315  CA  PHE   229      19.336  61.520  75.117  1.00 70.11           C  
ATOM   1316  C   PHE   229      18.815  60.483  76.113  1.00 69.45           C  
ATOM   1317  O   PHE   229      17.716  60.629  76.647  1.00 69.62           O  
ATOM   1322  N   MET   230      19.615  59.458  76.380  1.00 68.56           N  
ATOM   1323  CA  MET   230      19.246  58.421  77.340  1.00 67.80           C  
ATOM   1324  C   MET   230      19.166  58.985  78.766  1.00 66.67           C  
ATOM   1325  O   MET   230      18.205  58.707  79.481  1.00 65.86           O  
ATOM   1330  N   HIS   231      20.155  59.785  79.161  1.00 65.70           N  
ATOM   1331  CA  HIS   231      20.096  60.504  80.434  1.00 65.25           C  
ATOM   1332  C   HIS   231      18.822  61.334  80.555  1.00 65.00           C  
ATOM   1333  O   HIS   231      18.181  61.353  81.609  1.00 64.72           O  
ATOM   1339  N   THR   232      18.453  61.996  79.463  1.00 64.38           N  
ATOM   1340  CA  THR   232      17.239  62.768  79.392  1.00 63.69           C  
ATOM   1341  C   THR   232      15.994  61.932  79.616  1.00 63.86           C  
ATOM   1342  O   THR   232      15.123  62.296  80.427  1.00 63.91           O  
ATOM   1343  N   MET   233      15.896  60.809  78.911  1.00 63.19           N  
ATOM   1344  CA  MET   233      14.697  59.986  78.995  1.00 63.11           C  
ATOM   1345  C   MET   233      14.605  59.284  80.339  1.00 62.21           C  
ATOM   1346  O   MET   233      13.519  59.115  80.862  1.00 62.63           O  
ATOM   1351  N   LYS   234      15.745  58.896  80.908  1.00 61.31           N  
ATOM   1352  CA  LYS   234      15.777  58.312  82.238  1.00 59.89           C  
ATOM   1353  C   LYS   234      15.186  59.308  83.244  1.00 59.33           C  
ATOM   1354  O   LYS   234      14.442  58.925  84.136  1.00 59.82           O  
ATOM   1358  N   ASN   235      15.501  60.589  83.093  1.00 58.27           N  
ATOM   1359  CA  ASN   235      14.996  61.595  84.008  1.00 57.05           C  
ATOM   1360  C   ASN   235      13.498  61.791  83.797  1.00 57.20           C  
ATOM   1361  O   ASN   235      12.740  61.925  84.766  1.00 56.76           O  
ATOM   1367  N   THR   236      13.074  61.783  82.530  1.00 56.67           N  
ATOM   1368  CA  THR   236      11.669  61.888  82.203  1.00 56.17           C  
ATOM   1369  C   THR   236      10.873  60.803  82.945  1.00 56.09           C  
ATOM   1370  O   THR   236       9.827  61.086  83.530  1.00 55.94           O  
ATOM   1373  N   GLY   237      11.375  59.568  82.921  1.00 55.99           N  
ATOM   1374  CA  GLY   237      10.727  58.451  83.621  1.00 56.07           C  
ATOM   1375  C   GLY   237      10.824  58.593  85.136  1.00 56.64           C  
ATOM   1376  O   GLY   237       9.924  58.171  85.873  1.00 56.41           O  
ATOM   1385  N   ARG   238      11.910  59.214  85.588  1.00 56.89           N  
ATOM   1386  CA  ARG   238      12.071  59.511  86.988  1.00 58.07           C  
ATOM   1387  C   ARG   238      11.010  60.484  87.496  1.00 58.46           C  
ATOM   1388  O   ARG   238      10.617  60.406  88.665  1.00 58.66           O  
ATOM   1397  N   ASN   239      10.552  61.394  86.620  1.00 58.72           N  
ATOM   1398  CA  ASN   239       9.548  62.391  86.972  1.00 58.74           C  
ATOM   1399  C   ASN   239       8.240  61.696  87.359  1.00 59.64           C  
ATOM   1400  O   ASN   239       7.454  62.236  88.125  1.00 59.30           O  
ATOM   1409  N   GLU   250       8.018  60.511  86.786  1.00 60.28           N  
ATOM   1410  CA  GLU   250       6.829  59.721  87.018  1.00 61.04           C  
ATOM   1411  C   GLU   250       6.998  58.744  88.189  1.00 62.24           C  
ATOM   1412  O   GLU   250       6.106  57.932  88.446  1.00 62.04           O  
ATOM   1418  N   GLY   251       8.138  58.812  88.890  1.00 62.89           N  
ATOM   1419  CA  GLY   251       8.393  57.963  90.058  1.00 63.73           C  
ATOM   1420  C   GLY   251       9.202  56.688  89.835  1.00 64.77           C  
ATOM   1421  O   GLY   251       9.262  55.826  90.716  1.00 64.76           O  
ATOM   1422  N   GLU   252       9.825  56.549  88.666  1.00 65.76           N  
ATOM   1423  CA  GLU   252      10.700  55.403  88.408  1.00 66.54           C  
ATOM   1424  C   GLU   252      12.116  55.694  88.904  1.00 67.68           C  
ATOM   1425  O   GLU   252      12.772  56.614  88.409  1.00 67.71           O  
ATOM   1430  N   THR   253      12.584  54.907  89.878  1.00 68.80           N  
ATOM   1431  CA  THR   253      13.846  55.186  90.574  1.00 69.58           C  
ATOM   1432  C   THR   253      14.916  54.143  90.307  1.00 70.63           C  
ATOM   1433  O   THR   253      15.503  54.104  89.220  1.00 71.02           O  
TER
END
