
#######################################################
#                                                     #
#                        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 T0372TS298_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS298_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    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    K     290      S      98          3.397
LGA    Y     291      N      99          1.758
LGA    M     292      M     100          2.781
LGA    -       -      R     101           -
LGA    A     293      A     102          1.921
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    C     294      E     105          1.564
LGA    L     295      A     106          2.994
LGA    -       -      I     107           -
LGA    K     296      L     108          2.001
LGA    D     297      P     109          1.723
LGA    -       -      E     110           -
LGA    H     298      R     111          4.492
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    2.68    22.22      5.387     0.324

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.733538 * X  +  -0.267900 * Y  +  -0.624621 * Z  +  26.564749
  Y_new =  -0.657444 * X  +  -0.046703 * Y  +  -0.752054 * Z  + 102.987076
  Z_new =   0.172304 * X  +   0.962314 * Y  +  -0.210388 * Z  + -35.022408 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.786036   -1.355556  [ DEG:   102.3324    -77.6676 ]
  Theta =  -0.173168   -2.968425  [ DEG:    -9.9218   -170.0782 ]
  Phi   =  -0.730748    2.410845  [ DEG:   -41.8688    138.1312 ]
 
# 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: T0372TS298_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS298_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   2.68   22.22   5.387
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS298_4-D1
PFRMAT TS
TARGET T0372
MODEL  4  REFINED
PARENT 2GE3_A
ATOM   1097  N   LYS   290      23.145  50.873   4.597  1.00  0.00
ATOM   1098  CA  LYS   290      22.273  51.713   3.790  1.00  0.00
ATOM   1099  C   LYS   290      21.769  52.943   4.644  1.00  0.00
ATOM   1100  O   LYS   290      20.702  53.505   4.308  1.00  0.00
ATOM   1101  CB  LYS   290      21.064  50.799   3.399  1.00  0.00
ATOM   1102  CG  LYS   290      21.411  49.546   2.585  1.00  0.00
ATOM   1103  CD  LYS   290      20.544  49.274   1.381  1.00  0.00
ATOM   1104  CE  LYS   290      20.820  47.829   1.007  1.00  0.00
ATOM   1105  NZ  LYS   290      20.359  47.525  -0.331  1.00  0.00
ATOM   1106  N   TYR   291      22.707  53.536   5.427  1.00  0.00
ATOM   1107  CA  TYR   291      22.385  54.698   6.200  1.00  0.00
ATOM   1108  C   TYR   291      22.330  55.912   5.233  1.00  0.00
ATOM   1109  O   TYR   291      21.469  56.786   5.490  1.00  0.00
ATOM   1110  CB  TYR   291      23.368  54.837   7.373  1.00  0.00
ATOM   1111  CG  TYR   291      22.890  55.648   8.507  1.00  0.00
ATOM   1112  CD1 TYR   291      21.881  55.160   9.337  1.00  0.00
ATOM   1113  CD2 TYR   291      23.408  56.916   8.782  1.00  0.00
ATOM   1114  CE1 TYR   291      21.375  55.892  10.402  1.00  0.00
ATOM   1115  CE2 TYR   291      22.938  57.663   9.860  1.00  0.00
ATOM   1116  CZ  TYR   291      21.911  57.144  10.653  1.00  0.00
ATOM   1117  OH  TYR   291      21.474  57.905  11.710  1.00  0.00
ATOM   1118  N   MET   292      23.243  56.036   4.236  1.00  0.00
ATOM   1119  CA  MET   292      23.109  57.119   3.334  1.00  0.00
ATOM   1120  C   MET   292      21.673  57.110   2.803  1.00  0.00
ATOM   1121  O   MET   292      21.147  56.061   2.385  1.00  0.00
ATOM   1122  CB  MET   292      24.140  57.034   2.209  1.00  0.00
ATOM   1123  CG  MET   292      23.983  58.145   1.183  1.00  0.00
ATOM   1124  SD  MET   292      25.078  59.523   1.691  1.00  0.00
ATOM   1125  CE  MET   292      23.825  60.716   2.114  1.00  0.00
ATOM   1126  N   ALA   293      21.206  58.324   2.652  1.00  0.00
ATOM   1127  CA  ALA   293      19.909  58.696   2.106  1.00  0.00
ATOM   1128  C   ALA   293      19.886  58.497   0.563  1.00  0.00
ATOM   1129  O   ALA   293      19.405  59.391  -0.148  1.00  0.00
ATOM   1130  CB  ALA   293      19.593  60.126   2.544  1.00  0.00
ATOM   1131  N   CYS   294      20.882  57.696   0.142  1.00  0.00
ATOM   1132  CA  CYS   294      21.181  57.179  -1.176  1.00  0.00
ATOM   1133  C   CYS   294      21.860  58.104  -2.225  1.00  0.00
ATOM   1134  O   CYS   294      22.332  57.486  -3.210  1.00  0.00
ATOM   1135  CB  CYS   294      19.783  56.592  -1.552  1.00  0.00
ATOM   1136  SG  CYS   294      20.035  55.754  -3.165  1.00  0.00
ATOM   1137  N   LEU   295      22.425  59.243  -1.874  1.00  0.00
ATOM   1138  CA  LEU   295      23.034  59.993  -2.998  1.00  0.00
ATOM   1139  C   LEU   295      21.974  59.883  -4.157  1.00  0.00
ATOM   1140  O   LEU   295      21.040  60.690  -4.106  1.00  0.00
ATOM   1141  CB  LEU   295      24.362  59.475  -3.423  1.00  0.00
ATOM   1142  CG  LEU   295      25.678  59.573  -2.805  1.00  0.00
ATOM   1143  CD1 LEU   295      26.730  59.222  -3.848  1.00  0.00
ATOM   1144  CD2 LEU   295      25.799  61.041  -2.396  1.00  0.00
ATOM   1145  N   LYS   296      22.266  59.300  -5.306  1.00  0.00
ATOM   1146  CA  LYS   296      21.221  59.122  -6.320  1.00  0.00
ATOM   1147  C   LYS   296      21.013  57.594  -6.638  1.00  0.00
ATOM   1148  O   LYS   296      21.724  57.043  -7.495  1.00  0.00
ATOM   1149  CB  LYS   296      21.695  59.927  -7.576  1.00  0.00
ATOM   1150  CG  LYS   296      21.753  61.404  -7.296  1.00  0.00
ATOM   1151  CD  LYS   296      22.720  62.025  -8.272  1.00  0.00
ATOM   1152  CE  LYS   296      22.766  63.550  -8.024  1.00  0.00
ATOM   1153  NZ  LYS   296      21.389  64.040  -8.409  1.00  0.00
ATOM   1154  N   ASP   297      19.967  57.049  -6.056  1.00  0.00
ATOM   1155  CA  ASP   297      19.620  55.698  -6.262  1.00  0.00
ATOM   1156  C   ASP   297      20.644  54.587  -5.840  1.00  0.00
ATOM   1157  O   ASP   297      20.324  53.415  -6.063  1.00  0.00
ATOM   1158  CB  ASP   297      19.071  55.514  -7.706  1.00  0.00
ATOM   1159  CG  ASP   297      17.886  56.353  -8.065  1.00  0.00
ATOM   1160  OD1 ASP   297      16.998  56.579  -7.200  1.00  0.00
ATOM   1161  OD2 ASP   297      17.826  56.821  -9.227  1.00  0.00
ATOM   1162  N   HIS   298      21.756  54.899  -5.167  1.00  0.00
ATOM   1163  CA  HIS   298      22.591  53.845  -4.742  1.00  0.00
ATOM   1164  C   HIS   298      22.778  53.839  -3.166  1.00  0.00
ATOM   1165  O   HIS   298      23.282  54.886  -2.668  1.00  0.00
ATOM   1166  CB  HIS   298      23.984  54.073  -5.388  1.00  0.00
ATOM   1167  CG  HIS   298      23.956  53.929  -6.884  1.00  0.00
ATOM   1168  ND1 HIS   298      23.193  52.980  -7.545  1.00  0.00
ATOM   1169  CD2 HIS   298      24.569  54.664  -7.850  1.00  0.00
ATOM   1170  CE1 HIS   298      23.338  53.132  -8.853  1.00  0.00
ATOM   1171  NE2 HIS   298      24.172  54.143  -9.063  1.00  0.00
TER
END
