
#######################################################
#                                                     #
#                        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 T0372TS249_3_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS249_3_2-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    K     290      L      34          2.262
LGA    Y     291      C      35          1.061
LGA    M     292      S      36          1.166
LGA    A     293      W      37          2.419
LGA    C     294      R      38          2.042
LGA    -       -      F      39           -
LGA    L     295      L      40          1.194
LGA    K     296      Y      41          2.799
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    D     297      W      57          1.460
LGA    -       -      A      58           -
LGA    H     298      G      59          2.195
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    1.94    11.11      6.429     0.441

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.582640 * X  +  -0.726667 * Y  +  -0.363986 * Z  +  49.626034
  Y_new =   0.812475 * X  +  -0.532012 * Y  +  -0.238429 * Z  +  59.872925
  Z_new =  -0.020387 * X  +  -0.434648 * Y  +   0.900370 * Z  +   9.134900 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.449747    2.691845  [ DEG:   -25.7686    154.2314 ]
  Theta =   0.020388    3.121205  [ DEG:     1.1682    178.8318 ]
  Phi   =   2.192918   -0.948674  [ DEG:   125.6450    -54.3550 ]
 
# 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: T0372TS249_3_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS249_3_2-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   1.94   11.11   6.429
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS249_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM   1035  N   LYS   290      43.282  47.867  13.383  1.00  0.00
ATOM   1036  CA  LYS   290      42.937  47.403  12.065  1.00  0.00
ATOM   1037  C   LYS   290      44.178  47.156  11.275  1.00  0.00
ATOM   1038  O   LYS   290      44.107  46.724  10.127  1.00  0.00
ATOM   1039  CB  LYS   290      42.047  48.360  11.246  1.00  0.00
ATOM   1040  CG  LYS   290      40.550  48.228  11.542  1.00  0.00
ATOM   1041  CD  LYS   290      40.139  48.711  12.927  1.00  0.00
ATOM   1042  CE  LYS   290      38.660  48.484  13.234  1.00  0.00
ATOM   1043  NZ  LYS   290      37.818  49.249  12.290  1.00  0.00
ATOM   1044  N   TYR   291      45.352  47.491  11.833  1.00  0.00
ATOM   1045  CA  TYR   291      46.569  47.266  11.116  1.00  0.00
ATOM   1046  C   TYR   291      46.616  45.822  10.750  1.00  0.00
ATOM   1047  O   TYR   291      47.138  45.466   9.695  1.00  0.00
ATOM   1048  CB  TYR   291      47.846  47.678  11.884  1.00  0.00
ATOM   1049  CG  TYR   291      47.983  46.923  13.164  1.00  0.00
ATOM   1050  CD1 TYR   291      48.536  45.664  13.181  1.00  0.00
ATOM   1051  CD2 TYR   291      47.579  47.488  14.353  1.00  0.00
ATOM   1052  CE1 TYR   291      48.669  44.974  14.364  1.00  0.00
ATOM   1053  CE2 TYR   291      47.711  46.804  15.538  1.00  0.00
ATOM   1054  CZ  TYR   291      48.255  45.543  15.545  1.00  0.00
ATOM   1055  OH  TYR   291      48.390  44.839  16.762  1.00  0.00
ATOM   1056  N   MET   292      46.100  44.933  11.617  1.00  0.00
ATOM   1057  CA  MET   292      46.042  43.581  11.161  1.00  0.00
ATOM   1058  C   MET   292      44.819  43.484  10.309  1.00  0.00
ATOM   1059  O   MET   292      43.874  42.776  10.650  1.00  0.00
ATOM   1060  CB  MET   292      45.873  42.570  12.305  1.00  0.00
ATOM   1061  CG  MET   292      47.071  42.526  13.251  1.00  0.00
ATOM   1062  SD  MET   292      48.568  41.797  12.526  1.00  0.00
ATOM   1063  CE  MET   292      47.944  40.092  12.606  1.00  0.00
ATOM   1064  N   ALA   293      44.798  44.216   9.174  1.00  0.00
ATOM   1065  CA  ALA   293      43.711  44.052   8.252  1.00  0.00
ATOM   1066  C   ALA   293      44.344  43.315   7.115  1.00  0.00
ATOM   1067  O   ALA   293      44.601  43.882   6.054  1.00  0.00
ATOM   1068  CB  ALA   293      43.175  45.377   7.690  1.00  0.00
ATOM   1069  N   CYS   294      44.655  42.028   7.364  1.00  0.00
ATOM   1070  CA  CYS   294      45.384  41.186   6.462  1.00  0.00
ATOM   1071  C   CYS   294      44.649  40.581   5.282  1.00  0.00
ATOM   1072  O   CYS   294      45.139  40.646   4.158  1.00  0.00
ATOM   1073  CB  CYS   294      46.047  40.025   7.218  1.00  0.00
ATOM   1074  SG  CYS   294      47.136  40.626   8.545  1.00  0.00
ATOM   1075  N   LEU   295      43.469  39.982   5.553  1.00  0.00
ATOM   1076  CA  LEU   295      42.728  38.994   4.783  1.00  0.00
ATOM   1077  C   LEU   295      41.959  39.205   3.481  1.00  0.00
ATOM   1078  O   LEU   295      42.015  38.324   2.626  1.00  0.00
ATOM   1079  CB  LEU   295      41.759  38.222   5.692  1.00  0.00
ATOM   1080  CG  LEU   295      42.500  37.349   6.715  1.00  0.00
ATOM   1081  CD1 LEU   295      41.523  36.580   7.617  1.00  0.00
ATOM   1082  CD2 LEU   295      43.509  36.431   6.007  1.00  0.00
ATOM   1083  N   LYS   296      41.244  40.322   3.264  1.00  0.00
ATOM   1084  CA  LYS   296      40.109  40.402   2.351  1.00  0.00
ATOM   1085  C   LYS   296      40.170  40.088   0.855  1.00  0.00
ATOM   1086  O   LYS   296      39.303  39.359   0.377  1.00  0.00
ATOM   1087  CB  LYS   296      39.424  41.776   2.456  1.00  0.00
ATOM   1088  CG  LYS   296      38.079  41.845   1.735  1.00  0.00
ATOM   1089  CD  LYS   296      37.019  40.933   2.355  1.00  0.00
ATOM   1090  CE  LYS   296      35.609  41.172   1.814  1.00  0.00
ATOM   1091  NZ  LYS   296      35.034  42.390   2.429  1.00  0.00
ATOM   1092  N   ASP   297      41.151  40.566   0.066  1.00  0.00
ATOM   1093  CA  ASP   297      40.989  40.646  -1.377  1.00  0.00
ATOM   1094  C   ASP   297      40.628  39.396  -2.142  1.00  0.00
ATOM   1095  O   ASP   297      39.528  39.314  -2.684  1.00  0.00
ATOM   1096  CB  ASP   297      42.255  41.212  -2.042  1.00  0.00
ATOM   1097  CG  ASP   297      41.930  41.528  -3.489  1.00  0.00
ATOM   1098  OD1 ASP   297      40.720  41.632  -3.820  1.00  0.00
ATOM   1099  OD2 ASP   297      42.892  41.679  -4.285  1.00  0.00
ATOM   1100  N   HIS   298      41.505  38.377  -2.205  1.00  0.00
ATOM   1101  CA  HIS   298      41.225  37.240  -3.041  1.00  0.00
ATOM   1102  C   HIS   298      41.199  36.072  -2.117  1.00  0.00
ATOM   1103  O   HIS   298      41.420  36.232  -0.921  1.00  0.00
ATOM   1104  CB  HIS   298      42.337  36.960  -4.075  1.00  0.00
ATOM   1105  CG  HIS   298      42.615  38.089  -5.034  1.00  0.00
ATOM   1106  ND1 HIS   298      41.912  38.314  -6.197  1.00  0.00
ATOM   1107  CD2 HIS   298      43.569  39.063  -4.988  1.00  0.00
ATOM   1108  CE1 HIS   298      42.470  39.400  -6.793  1.00  0.00
ATOM   1109  NE2 HIS   298      43.480  39.887  -6.096  1.00  0.00
TER
END
