
#######################################################
#                                                     #
#                        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    9 (   75),  selected    9 , name T0372TS671_3-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS671_3-D1.T0372_D1.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       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    K     290      F      31          2.360
LGA    Y     291      S      32          1.210
LGA    M     292      N      33          2.189
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    A     293      S      36          1.264
LGA    C     294      W      37          2.441
LGA    L     295      R      38          3.800
LGA    -       -      F      39           -
LGA    K     296      L      40          0.697
LGA    D     297      Y      41          2.877
LGA    H     298      D      42          2.296
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9  126    5.0      9    2.31     0.00      5.661     0.374

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.585515 * X  +  -0.245046 * Y  +   0.772738 * Z  +  22.829985
  Y_new =   0.540061 * X  +   0.828797 * Y  +  -0.146389 * Z  +  44.462101
  Z_new =  -0.604571 * X  +   0.503038 * Y  +   0.617613 * Z  +   5.693171 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.683513   -2.458080  [ DEG:    39.1624   -140.8376 ]
  Theta =   0.649227    2.492366  [ DEG:    37.1980    142.8020 ]
  Phi   =   0.745037   -2.396556  [ DEG:    42.6875   -137.3125 ]
 
# 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: T0372TS671_3-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS671_3-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9  126   5.0    9   2.31    0.00   5.661
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS671_3-D1
PFRMAT TS
TARGET T0372
MODEL  3  REFINED
PARENT 1NE9_A
ATOM   1245  N   LYS   290      43.135  53.121  16.174  1.00  0.00
ATOM   1246  CA  LYS   290      42.302  52.225  15.427  1.00  0.00
ATOM   1247  C   LYS   290      43.074  50.931  15.168  1.00  0.00
ATOM   1248  O   LYS   290      43.949  50.867  14.292  1.00  0.00
ATOM   1249  CB  LYS   290      41.992  52.890  14.037  1.00  0.00
ATOM   1250  CG  LYS   290      40.704  53.610  13.965  1.00  0.00
ATOM   1251  CD  LYS   290      40.112  53.226  12.572  1.00  0.00
ATOM   1252  CE  LYS   290      38.752  53.882  12.359  1.00  0.00
ATOM   1253  NZ  LYS   290      38.987  55.361  12.150  1.00  0.00
ATOM   1254  N   TYR   291      42.612  49.856  15.801  1.00  0.00
ATOM   1255  CA  TYR   291      43.201  48.536  15.806  1.00  0.00
ATOM   1256  C   TYR   291      42.679  47.734  14.608  1.00  0.00
ATOM   1257  O   TYR   291      41.466  47.554  14.449  1.00  0.00
ATOM   1258  CB  TYR   291      42.713  47.834  17.083  1.00  0.00
ATOM   1259  CG  TYR   291      43.373  48.281  18.386  1.00  0.00
ATOM   1260  CD1 TYR   291      44.682  47.949  18.680  1.00  0.00
ATOM   1261  CD2 TYR   291      42.665  49.062  19.303  1.00  0.00
ATOM   1262  CE1 TYR   291      45.273  48.368  19.852  1.00  0.00
ATOM   1263  CE2 TYR   291      43.252  49.502  20.478  1.00  0.00
ATOM   1264  CZ  TYR   291      44.555  49.149  20.746  1.00  0.00
ATOM   1265  OH  TYR   291      45.162  49.551  21.946  1.00  0.00
ATOM   1266  N   MET   292      43.652  47.159  13.863  1.00  0.00
ATOM   1267  CA  MET   292      43.302  46.470  12.668  1.00  0.00
ATOM   1268  C   MET   292      44.218  45.287  12.312  1.00  0.00
ATOM   1269  O   MET   292      45.438  45.478  12.141  1.00  0.00
ATOM   1270  CB  MET   292      43.094  47.542  11.534  1.00  0.00
ATOM   1271  CG  MET   292      42.459  46.850  10.302  1.00  0.00
ATOM   1272  SD  MET   292      43.868  46.561   9.164  1.00  0.00
ATOM   1273  CE  MET   292      43.601  47.869   7.942  1.00  0.00
ATOM   1274  N   ALA   293      43.623  44.149  12.196  1.00  0.00
ATOM   1275  CA  ALA   293      44.340  42.993  11.744  1.00  0.00
ATOM   1276  C   ALA   293      44.043  42.819  10.224  1.00  0.00
ATOM   1277  O   ALA   293      42.855  42.529   9.898  1.00  0.00
ATOM   1278  CB  ALA   293      43.969  41.730  12.584  1.00  0.00
ATOM   1279  N   CYS   294      44.895  43.467   9.422  1.00  0.00
ATOM   1280  CA  CYS   294      44.674  43.511   7.986  1.00  0.00
ATOM   1281  C   CYS   294      44.106  42.204   7.529  1.00  0.00
ATOM   1282  O   CYS   294      43.259  42.212   6.622  1.00  0.00
ATOM   1283  CB  CYS   294      45.857  44.004   7.189  1.00  0.00
ATOM   1284  SG  CYS   294      45.640  43.850   5.458  1.00  0.00
ATOM   1285  N   LEU   295      44.865  41.200   7.763  1.00  0.00
ATOM   1286  CA  LEU   295      44.581  39.757   7.641  1.00  0.00
ATOM   1287  C   LEU   295      44.673  39.042   6.299  1.00  0.00
ATOM   1288  O   LEU   295      45.686  38.351   6.124  1.00  0.00
ATOM   1289  CB  LEU   295      43.470  39.394   8.588  1.00  0.00
ATOM   1290  CG  LEU   295      43.341  38.113   9.336  1.00  0.00
ATOM   1291  CD1 LEU   295      41.973  38.050   9.988  1.00  0.00
ATOM   1292  CD2 LEU   295      43.521  36.866   8.480  1.00  0.00
ATOM   1293  N   LYS   296      43.805  39.242   5.272  1.00  0.00
ATOM   1294  CA  LYS   296      43.975  38.313   4.151  1.00  0.00
ATOM   1295  C   LYS   296      44.710  38.884   2.985  1.00  0.00
ATOM   1296  O   LYS   296      45.900  38.651   2.927  1.00  0.00
ATOM   1297  CB  LYS   296      42.605  37.733   3.741  1.00  0.00
ATOM   1298  CG  LYS   296      41.800  37.333   4.919  1.00  0.00
ATOM   1299  CD  LYS   296      40.363  37.198   4.720  1.00  0.00
ATOM   1300  CE  LYS   296      39.578  36.625   5.982  1.00  0.00
ATOM   1301  NZ  LYS   296      40.326  37.118   7.309  1.00  0.00
ATOM   1302  N   ASP   297      44.066  39.528   2.069  1.00  0.00
ATOM   1303  CA  ASP   297      44.706  40.154   0.934  1.00  0.00
ATOM   1304  C   ASP   297      44.457  41.691   0.889  1.00  0.00
ATOM   1305  O   ASP   297      44.562  42.241  -0.232  1.00  0.00
ATOM   1306  CB  ASP   297      44.195  39.414  -0.304  1.00  0.00
ATOM   1307  CG  ASP   297      44.743  37.966  -0.362  1.00  0.00
ATOM   1308  OD1 ASP   297      45.856  37.761   0.167  1.00  0.00
ATOM   1309  OD2 ASP   297      44.137  37.085  -0.999  1.00  0.00
ATOM   1310  N   HIS   298      44.027  42.351   1.979  1.00  0.00
ATOM   1311  CA  HIS   298      43.833  43.735   1.881  1.00  0.00
ATOM   1312  C   HIS   298      45.168  44.334   1.555  1.00  0.00
ATOM   1313  O   HIS   298      46.223  43.744   2.003  1.00  0.00
ATOM   1314  CB  HIS   298      43.151  44.327   3.123  1.00  0.00
ATOM   1315  CG  HIS   298      43.173  45.812   3.342  1.00  0.00
ATOM   1316  ND1 HIS   298      42.691  46.747   2.450  1.00  0.00
ATOM   1317  CD2 HIS   298      43.647  46.524   4.397  1.00  0.00
ATOM   1318  CE1 HIS   298      42.879  47.968   2.932  1.00  0.00
ATOM   1319  NE2 HIS   298      43.466  47.864   4.110  1.00  0.00
TER
END
