
#######################################################
#                                                     #
#                        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 T0372TS028_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS028_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    -       -      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    -       -      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    K     290      M      93          0.921
LGA    Y     291      L      94          0.726
LGA    M     292      G      95          2.504
LGA    -       -      V      96           -
LGA    A     293      C      97          1.665
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    C     294      K     290          0.544
LGA    L     295      Y     291          0.536
LGA    K     296      M     292          0.374
LGA    D     297      A     293          0.421
LGA    H     298      C     294          0.922
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    1.16     0.00      6.958     0.713

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.703513 * X  +   0.709656 * Y  +  -0.038188 * Z  +  57.314159
  Y_new =   0.050348 * X  +   0.103368 * Y  +   0.993368 * Z  +  45.751133
  Z_new =   0.708897 * X  +   0.696924 * Y  +  -0.108450 * Z  + -39.780647 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.725171   -1.416422  [ DEG:    98.8450    -81.1550 ]
  Theta =  -0.787933   -2.353660  [ DEG:   -45.1452   -134.8548 ]
  Phi   =   3.070148   -0.071445  [ DEG:   175.9065     -4.0935 ]
 
# 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: T0372TS028_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS028_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   1.16    0.00   6.958
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS028_4-D1
PFRMAT TS
TARGET T0372
MODEL 4
PARENT 1s7f-A
ATOM   1236  N   LYS   290      31.552  47.561  -2.043  1.00  9.00
ATOM   1237  CA  LYS   290      31.826  48.407  -0.872  1.00  9.00
ATOM   1238  C   LYS   290      30.927  48.092   0.311  1.00  9.00
ATOM   1239  O   LYS   290      29.699  48.180   0.207  1.00  9.00
ATOM   1240  CB  LYS   290      31.658  49.871  -1.261  1.00  9.00
ATOM   1241  CG  LYS   290      32.713  50.296  -2.276  1.00  9.00
ATOM   1242  CD  LYS   290      34.121  50.105  -1.717  1.00  9.00
ATOM   1243  CE  LYS   290      35.182  50.475  -2.746  1.00  9.00
ATOM   1244  NZ  LYS   290      36.532  50.269  -2.200  1.00  9.00
ATOM   1245  N   TYR   291      31.537  47.739   1.428  1.00  9.00
ATOM   1246  CA  TYR   291      30.762  47.515   2.651  1.00  9.00
ATOM   1247  C   TYR   291      30.564  48.834   3.394  1.00  9.00
ATOM   1248  O   TYR   291      31.522  49.458   3.865  1.00  9.00
ATOM   1249  CB  TYR   291      31.483  46.505   3.539  1.00  9.00
ATOM   1250  CG  TYR   291      30.680  46.089   4.770  1.00  9.00
ATOM   1251  CD1 TYR   291      29.637  45.182   4.636  1.00  9.00
ATOM   1252  CD2 TYR   291      30.986  46.621   6.017  1.00  9.00
ATOM   1253  CE1 TYR   291      28.899  44.805   5.748  1.00  9.00
ATOM   1254  CE2 TYR   291      30.246  46.244   7.132  1.00  9.00
ATOM   1255  CZ  TYR   291      29.203  45.338   6.992  1.00  9.00
ATOM   1256  OH  TYR   291      28.441  44.997   8.088  1.00  9.00
ATOM   1257  N   MET   292      29.309  49.228   3.511  1.00  9.00
ATOM   1258  CA  MET   292      28.955  50.488   4.164  1.00  9.00
ATOM   1259  C   MET   292      27.656  50.334   4.953  1.00  9.00
ATOM   1260  O   MET   292      26.617  49.941   4.407  1.00  9.00
ATOM   1261  CB  MET   292      28.821  51.569   3.089  1.00  9.00
ATOM   1262  CG  MET   292      28.493  52.944   3.668  1.00  9.00
ATOM   1263  SD  MET   292      29.690  53.620   4.845  1.00  9.00
ATOM   1264  CE  MET   292      31.142  53.722   3.772  1.00  9.00
ATOM   1265  N   ALA   293      27.762  50.595   6.250  1.00  9.00
ATOM   1266  CA  ALA   293      26.627  50.548   7.191  1.00  9.00
ATOM   1267  C   ALA   293      25.784  49.285   7.047  1.00  9.00
ATOM   1268  O   ALA   293      24.682  49.323   6.486  1.00  9.00
ATOM   1269  CB  ALA   293      25.758  51.785   6.982  1.00  9.00
ATOM   1270  N   CYS   294      26.406  48.169   7.404  1.00  9.00
ATOM   1271  CA  CYS   294      25.809  46.816   7.410  1.00  9.00
ATOM   1272  C   CYS   294      25.560  46.161   6.041  1.00  9.00
ATOM   1273  O   CYS   294      25.361  44.941   6.005  1.00  9.00
ATOM   1274  CB  CYS   294      24.494  46.845   8.186  1.00  9.00
ATOM   1275  SG  CYS   294      24.606  47.380   9.910  1.00  9.00
ATOM   1276  N   LEU   295      25.625  46.897   4.942  1.00  9.00
ATOM   1277  CA  LEU   295      25.366  46.277   3.636  1.00  9.00
ATOM   1278  C   LEU   295      26.529  46.390   2.661  1.00  9.00
ATOM   1279  O   LEU   295      27.506  47.112   2.889  1.00  9.00
ATOM   1280  CB  LEU   295      24.146  46.936   3.007  1.00  9.00
ATOM   1281  CG  LEU   295      22.866  46.590   3.757  1.00  9.00
ATOM   1282  CD1 LEU   295      21.676  47.342   3.172  1.00  9.00
ATOM   1283  CD2 LEU   295      22.614  45.086   3.728  1.00  9.00
ATOM   1284  N   LYS   296      26.470  45.543   1.649  1.00  9.00
ATOM   1285  CA  LYS   296      27.393  45.636   0.517  1.00  9.00
ATOM   1286  C   LYS   296      26.711  46.383  -0.626  1.00  9.00
ATOM   1287  O   LYS   296      25.587  46.061  -1.021  1.00  9.00
ATOM   1288  CB  LYS   296      27.766  44.237   0.054  1.00  9.00
ATOM   1289  CG  LYS   296      28.447  43.422   1.144  1.00  9.00
ATOM   1290  CD  LYS   296      28.756  42.020   0.631  1.00  9.00
ATOM   1291  CE  LYS   296      29.416  41.152   1.696  1.00  9.00
ATOM   1292  NZ  LYS   296      29.677  39.800   1.177  1.00  9.00
ATOM   1293  N   ASP   297      27.375  47.412  -1.112  1.00  9.00
ATOM   1294  CA  ASP   297      26.800  48.269  -2.158  1.00  9.00
ATOM   1295  C   ASP   297      27.460  48.062  -3.519  1.00  9.00
ATOM   1296  O   ASP   297      28.636  47.689  -3.602  1.00  9.00
ATOM   1297  CB  ASP   297      26.994  49.719  -1.726  1.00  9.00
ATOM   1298  CG  ASP   297      26.294  49.991  -0.396  1.00  9.00
ATOM   1299  OD1 ASP   297      25.194  49.485  -0.218  1.00  9.00
ATOM   1300  OD2 ASP   297      26.828  50.776   0.375  1.00  9.00
ATOM   1301  N   HIS   298      26.664  48.215  -4.568  1.00  9.00
ATOM   1302  CA  HIS   298      27.174  48.213  -5.954  1.00  9.00
ATOM   1303  C   HIS   298      27.687  49.592  -6.362  1.00  9.00
ATOM   1304  O   HIS   298      26.882  50.526  -6.395  1.00  9.00
ATOM   1305  CB  HIS   298      26.020  47.923  -6.911  1.00  9.00
ATOM   1306  CG  HIS   298      25.338  46.578  -6.808  1.00  9.00
ATOM   1307  ND1 HIS   298      25.698  45.458  -7.457  1.00  9.00
ATOM   1308  CD2 HIS   298      24.218  46.273  -6.070  1.00  9.00
ATOM   1309  CE1 HIS   298      24.849  44.461  -7.134  1.00  9.00
ATOM   1310  NE2 HIS   298      23.934  44.967  -6.275  1.00  9.00
TER
END
