
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS671_4-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    K     290      D      11          1.036
LGA    Y     291      R      12          0.949
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    M     292      T      16          1.912
LGA    A     293      A      17          2.188
LGA    -       -      F      18           -
LGA    C     294      T      19          1.687
LGA    L     295      M      20          2.287
LGA    K     296      K      21          2.630
LGA    -       -      S      22           -
LGA    D     297      D      23          0.915
LGA    H     298      R      24          2.073
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
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    1.84    33.33      6.426     0.463

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.293576 * X  +   0.919677 * Y  +   0.260781 * Z  +  39.315868
  Y_new =  -0.813629 * X  +  -0.097188 * Y  +  -0.573203 * Z  +  73.967987
  Z_new =  -0.501818 * X  +  -0.380458 * Y  +   0.776808 * Z  +   1.611273 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.455430    2.686162  [ DEG:   -26.0942    153.9058 ]
  Theta =   0.525699    2.615894  [ DEG:    30.1203    149.8797 ]
  Phi   =  -1.917080    1.224513  [ DEG:  -109.8406     70.1594 ]
 
# 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_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS671_4-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   1.84   33.33   6.426
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS671_4-D1
PFRMAT TS
TARGET T0372
MODEL  4  REFINED
PARENT 1NE9_A
ATOM   1245  N   LYS   290      49.602  53.717   9.707  1.00  0.00
ATOM   1246  CA  LYS   290      48.664  54.859   9.509  1.00  0.00
ATOM   1247  C   LYS   290      47.697  54.944  10.728  1.00  0.00
ATOM   1248  O   LYS   290      46.705  54.209  10.848  1.00  0.00
ATOM   1249  CB  LYS   290      47.765  54.674   8.248  1.00  0.00
ATOM   1250  CG  LYS   290      48.278  55.347   7.033  1.00  0.00
ATOM   1251  CD  LYS   290      46.993  55.969   6.395  1.00  0.00
ATOM   1252  CE  LYS   290      47.340  56.760   5.136  1.00  0.00
ATOM   1253  NZ  LYS   290      47.715  55.763   4.061  1.00  0.00
ATOM   1254  N   TYR   291      48.034  55.917  11.592  1.00  0.00
ATOM   1255  CA  TYR   291      47.296  56.291  12.784  1.00  0.00
ATOM   1256  C   TYR   291      46.086  57.157  12.365  1.00  0.00
ATOM   1257  O   TYR   291      46.239  58.308  11.914  1.00  0.00
ATOM   1258  CB  TYR   291      48.205  57.030  13.717  1.00  0.00
ATOM   1259  CG  TYR   291      49.218  56.243  14.500  1.00  0.00
ATOM   1260  CD1 TYR   291      48.825  55.419  15.536  1.00  0.00
ATOM   1261  CD2 TYR   291      50.575  56.297  14.174  1.00  0.00
ATOM   1262  CE1 TYR   291      49.748  54.675  16.238  1.00  0.00
ATOM   1263  CE2 TYR   291      51.511  55.543  14.862  1.00  0.00
ATOM   1264  CZ  TYR   291      51.090  54.737  15.894  1.00  0.00
ATOM   1265  OH  TYR   291      52.022  53.990  16.632  1.00  0.00
ATOM   1266  N   MET   292      44.892  56.638  12.653  1.00  0.00
ATOM   1267  CA  MET   292      43.685  57.302  12.248  1.00  0.00
ATOM   1268  C   MET   292      42.967  58.059  13.351  1.00  0.00
ATOM   1269  O   MET   292      42.680  57.495  14.404  1.00  0.00
ATOM   1270  CB  MET   292      42.710  56.240  11.636  1.00  0.00
ATOM   1271  CG  MET   292      41.457  56.909  10.996  1.00  0.00
ATOM   1272  SD  MET   292      40.753  55.665   9.841  1.00  0.00
ATOM   1273  CE  MET   292      38.968  56.162   9.857  1.00  0.00
ATOM   1274  N   ALA   293      42.782  59.321  13.035  1.00  0.00
ATOM   1275  CA  ALA   293      42.014  60.205  13.837  1.00  0.00
ATOM   1276  C   ALA   293      40.545  59.946  13.403  1.00  0.00
ATOM   1277  O   ALA   293      40.122  60.529  12.388  1.00  0.00
ATOM   1278  CB  ALA   293      42.474  61.671  13.625  1.00  0.00
ATOM   1279  N   CYS   294      40.044  58.754  13.848  1.00  0.00
ATOM   1280  CA  CYS   294      38.657  58.381  13.459  1.00  0.00
ATOM   1281  C   CYS   294      37.708  59.632  13.314  1.00  0.00
ATOM   1282  O   CYS   294      36.903  59.716  12.377  1.00  0.00
ATOM   1283  CB  CYS   294      38.234  57.614  14.702  1.00  0.00
ATOM   1284  SG  CYS   294      36.634  56.949  14.799  1.00  0.00
ATOM   1285  N   LEU   295      37.621  60.323  14.444  1.00  0.00
ATOM   1286  CA  LEU   295      37.039  61.642  14.630  1.00  0.00
ATOM   1287  C   LEU   295      35.460  61.798  14.735  1.00  0.00
ATOM   1288  O   LEU   295      35.077  61.942  15.937  1.00  0.00
ATOM   1289  CB  LEU   295      37.589  62.525  13.477  1.00  0.00
ATOM   1290  CG  LEU   295      37.660  64.060  13.508  1.00  0.00
ATOM   1291  CD1 LEU   295      37.895  64.614  12.131  1.00  0.00
ATOM   1292  CD2 LEU   295      36.350  64.681  13.870  1.00  0.00
ATOM   1293  N   LYS   296      34.580  61.482  13.756  1.00  0.00
ATOM   1294  CA  LYS   296      33.242  61.874  14.091  1.00  0.00
ATOM   1295  C   LYS   296      32.327  60.722  14.517  1.00  0.00
ATOM   1296  O   LYS   296      31.995  60.612  15.706  1.00  0.00
ATOM   1297  CB  LYS   296      32.571  62.829  13.195  1.00  0.00
ATOM   1298  CG  LYS   296      33.088  64.121  12.843  1.00  0.00
ATOM   1299  CD  LYS   296      32.238  64.643  11.692  1.00  0.00
ATOM   1300  CE  LYS   296      32.367  63.677  10.505  1.00  0.00
ATOM   1301  NZ  LYS   296      31.398  63.916   9.455  1.00  0.00
ATOM   1302  N   ASP   297      31.672  60.239  13.541  1.00  0.00
ATOM   1303  CA  ASP   297      30.749  59.165  13.737  1.00  0.00
ATOM   1304  C   ASP   297      31.236  57.912  12.892  1.00  0.00
ATOM   1305  O   ASP   297      30.384  56.967  12.798  1.00  0.00
ATOM   1306  CB  ASP   297      29.376  59.678  13.147  1.00  0.00
ATOM   1307  CG  ASP   297      28.857  60.821  14.095  1.00  0.00
ATOM   1308  OD1 ASP   297      29.150  60.759  15.307  1.00  0.00
ATOM   1309  OD2 ASP   297      28.090  61.687  13.640  1.00  0.00
ATOM   1310  N   HIS   298      32.474  57.914  12.312  1.00  0.00
ATOM   1311  CA  HIS   298      32.766  56.726  11.600  1.00  0.00
ATOM   1312  C   HIS   298      32.585  55.577  12.672  1.00  0.00
ATOM   1313  O   HIS   298      32.868  55.847  13.859  1.00  0.00
ATOM   1314  CB  HIS   298      34.209  56.682  11.021  1.00  0.00
ATOM   1315  CG  HIS   298      34.798  55.425  10.535  1.00  0.00
ATOM   1316  ND1 HIS   298      34.258  54.605   9.566  1.00  0.00
ATOM   1317  CD2 HIS   298      35.941  54.810  10.936  1.00  0.00
ATOM   1318  CE1 HIS   298      35.026  53.538   9.399  1.00  0.00
ATOM   1319  NE2 HIS   298      36.052  53.631  10.226  1.00  0.00
TER
END
