
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0363TS307_4u-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS307_4u-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    Q      12      Q      12          1.541
LGA    I      13      I      13          2.001
LGA    N      14      N      14          0.777
LGA    I      15      I      15          0.726
LGA    E      16      E      16          2.511
LGA    I      17      I      17          2.705
LGA    A      18      A      18          3.281
LGA    Y      19      Y      19          3.213
LGA    A      20      A      20          3.451
LGA    F      21      F      21          2.003
LGA    P      22      P      22          5.861
LGA    E      23      E      23           #
LGA    R      24      R      24          2.191
LGA    Y      25      Y      25          6.008
LGA    Y      26      Y      26          2.905
LGA    L      27      L      27          2.450
LGA    K      28      K      28          1.864
LGA    S      29      S      29          0.945
LGA    F      30      F      30          1.352
LGA    Q      31      Q      31          1.440
LGA    V      32      V      32          1.599
LGA    D      33      D      33          1.853
LGA    E      34      E      34          2.624
LGA    G      35      G      35          1.067
LGA    I      36      I      36          0.312
LGA    T      37      T      37          0.216
LGA    V      38      V      38          0.378
LGA    Q      39      Q      39          0.350
LGA    T      40      T      40          0.822
LGA    A      41      A      41          1.440
LGA    I      42      I      42          1.250
LGA    T      43      T      43          0.599
LGA    Q      44      Q      44          2.547
LGA    I      47      S      45          3.227
LGA    L      48      G      46          2.798
LGA    S      49      -       -           -
LGA    Q      50      I      47          5.111
LGA    F      51      L      48           #
LGA    P      52      S      49          2.289
LGA    E      53      Q      50          2.049
LGA    I      54      F      51          2.211
LGA    D      55      P      52          3.314
LGA    L      56      E      53          3.559
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   46    5.0     40    2.57    80.00     62.328     1.499

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.440408 * X  +  -0.875468 * Y  +  -0.198989 * Z  +  26.880857
  Y_new =   0.840186 * X  +   0.323778 * Y  +   0.435035 * Z  +  15.453951
  Z_new =  -0.316431 * X  +  -0.358780 * Y  +   0.878150 * Z  +   7.060163 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.387867    2.753726  [ DEG:   -22.2232    157.7768 ]
  Theta =   0.321965    2.819628  [ DEG:    18.4472    161.5527 ]
  Phi   =   1.087993   -2.053599  [ DEG:    62.3374   -117.6626 ]
 
# 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: T0363TS307_4u-D1                              
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS307_4u-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   46   5.0   40   2.57   80.00  62.328
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS307_4u-D1
PFRMAT   TS
TARGET   T0363
MODEL    4  UNREFINED
PARENT   1vjk_A
ATOM      1  N   GLN    12      18.173   1.098   9.027  1.00 22.48           N  
ATOM      2  CA  GLN    12      18.817   2.273   8.338  1.00 23.77           C  
ATOM      3  C   GLN    12      18.270   3.626   8.822  1.00 24.58           C  
ATOM      4  O   GLN    12      17.098   3.745   9.220  1.00 26.32           O  
ATOM      7  N   ILE    13      19.138   4.639   8.796  1.00 15.17           N  
ATOM      8  CA  ILE    13      18.783   6.019   9.135  1.00 17.07           C  
ATOM      9  C   ILE    13      19.070   6.854   7.874  1.00 15.76           C  
ATOM     10  O   ILE    13      20.215   6.887   7.416  1.00 20.45           O  
ATOM     14  N   ASN    14      18.049   7.496   7.308  1.00  9.10           N  
ATOM     15  CA  ASN    14      18.243   8.298   6.108  1.00  9.29           C  
ATOM     16  C   ASN    14      18.208   9.764   6.470  1.00  9.64           C  
ATOM     17  O   ASN    14      17.191  10.255   7.009  1.00 10.36           O  
ATOM     23  N   ILE    15      19.302  10.465   6.202  1.00  9.47           N  
ATOM     24  CA  ILE    15      19.391  11.887   6.514  1.00  9.07           C  
ATOM     25  C   ILE    15      19.463  12.687   5.230  1.00 10.16           C  
ATOM     26  O   ILE    15      19.945  12.195   4.182  1.00 11.73           O  
ATOM     30  N   GLU    16      18.989  13.914   5.274  1.00  8.37           N  
ATOM     31  CA  GLU    16      19.043  14.822   4.156  1.00  8.63           C  
ATOM     32  C   GLU    16      20.193  15.758   4.403  1.00 10.75           C  
ATOM     33  O   GLU    16      20.168  16.526   5.376  1.00 10.03           O  
ATOM     39  N   ILE    17      21.198  15.723   3.550  1.00  8.53           N  
ATOM     40  CA  ILE    17      22.354  16.598   3.661  1.00  8.87           C  
ATOM     41  C   ILE    17      22.200  17.780   2.737  1.00  9.59           C  
ATOM     42  O   ILE    17      21.940  17.584   1.549  1.00 12.22           O  
ATOM     46  N   ALA    18      22.327  18.998   3.280  1.00  9.65           N  
ATOM     47  CA  ALA    18      22.239  20.220   2.475  1.00 10.12           C  
ATOM     48  C   ALA    18      23.604  20.870   2.476  1.00  9.91           C  
ATOM     49  O   ALA    18      24.144  21.214   3.543  1.00 10.64           O  
ATOM     54  N   TYR    19      24.171  21.036   1.293  1.00  8.67           N  
ATOM     55  CA  TYR    19      25.464  21.706   1.135  1.00  7.65           C  
ATOM     56  C   TYR    19      25.264  23.162   0.829  1.00  7.41           C  
ATOM     57  O   TYR    19      24.310  23.542   0.126  1.00 10.51           O  
ATOM     77  N   ALA    20      27.216  27.063  -0.228  1.00  9.04           N  
ATOM     78  CA  ALA    20      28.335  27.835  -0.763  1.00  8.07           C  
ATOM     79  C   ALA    20      29.291  26.921  -1.545  1.00  9.04           C  
ATOM     80  O   ALA    20      28.826  26.142  -2.387  1.00  8.85           O  
ATOM     82  N   PHE    21      30.604  26.996  -1.294  1.00  7.97           N  
ATOM     83  CA  PHE    21      31.519  26.253  -2.184  1.00  7.44           C  
ATOM     84  C   PHE    21      31.369  24.755  -2.053  1.00  8.03           C  
ATOM     85  O   PHE    21      31.766  24.013  -2.949  1.00  8.59           O  
ATOM     93  N   PRO    22      30.765  24.294  -0.960  1.00  7.80           N  
ATOM     94  CA  PRO    22      30.593  22.845  -0.753  1.00  7.18           C  
ATOM     95  C   PRO    22      29.561  22.251  -1.683  1.00 10.09           C  
ATOM     96  O   PRO    22      29.564  21.037  -1.896  1.00 10.87           O  
ATOM    104  N   GLU    23      28.723  23.097  -2.276  1.00  9.30           N  
ATOM    105  CA  GLU    23      27.836  22.649  -3.355  1.00  9.47           C  
ATOM    106  C   GLU    23      28.651  22.209  -4.559  1.00 11.38           C  
ATOM    107  O   GLU    23      28.255  21.258  -5.249  1.00 11.20           O  
ATOM    115  N   ARG    24      29.760  22.902  -4.857  1.00  9.70           N  
ATOM    116  CA  ARG    24      30.618  22.468  -5.941  1.00 10.10           C  
ATOM    117  C   ARG    24      31.414  21.261  -5.602  1.00 11.11           C  
ATOM    118  O   ARG    24      31.598  20.411  -6.459  1.00 13.28           O  
ATOM    124  N   TYR    25      31.907  21.164  -4.363  1.00 11.22           N  
ATOM    125  CA  TYR    25      32.661  19.968  -3.983  1.00 12.02           C  
ATOM    126  C   TYR    25      31.796  18.713  -4.001  1.00 12.43           C  
ATOM    127  O   TYR    25      32.262  17.643  -4.391  1.00 15.60           O  
ATOM    132  N   TYR    26      30.546  18.828  -3.538  1.00  9.99           N  
ATOM    133  CA  TYR    26      29.647  17.681  -3.541  1.00  9.15           C  
ATOM    134  C   TYR    26      29.064  17.404  -4.921  1.00 11.80           C  
ATOM    135  O   TYR    26      28.612  16.283  -5.195  1.00 15.07           O  
ATOM    156  N   LEU    27      22.037  19.133  -2.467  1.00 11.04           N  
ATOM    157  CA  LEU    27      21.552  18.305  -1.372  1.00 11.95           C  
ATOM    158  C   LEU    27      21.586  16.865  -1.794  1.00  8.62           C  
ATOM    159  O   LEU    27      21.587  16.550  -2.989  1.00 11.37           O  
ATOM    165  N   LYS    28      21.611  15.973  -0.811  1.00  9.61           N  
ATOM    166  CA  LYS    28      21.613  14.549  -1.076  1.00  9.51           C  
ATOM    167  C   LYS    28      21.125  13.788   0.124  1.00  9.57           C  
ATOM    168  O   LYS    28      21.366  14.200   1.266  1.00 10.47           O  
ATOM    174  N   SER    29      20.421  12.702  -0.120  1.00 10.46           N  
ATOM    175  CA  SER    29      19.989  11.801   0.920  1.00  8.15           C  
ATOM    176  C   SER    29      21.045  10.768   1.162  1.00 10.02           C  
ATOM    177  O   SER    29      21.511  10.107   0.208  1.00 12.23           O  
ATOM    183  N   PHE    30      21.410  10.563   2.415  1.00  8.11           N  
ATOM    184  CA  PHE    30      22.421   9.592   2.758  1.00  8.94           C  
ATOM    185  C   PHE    30      21.859   8.583   3.745  1.00  9.61           C  
ATOM    186  O   PHE    30      21.454   8.931   4.872  1.00 10.15           O  
ATOM    191  N   GLN    31      21.802   7.333   3.317  1.00  8.73           N  
ATOM    192  CA  GLN    31      21.372   6.227   4.164  1.00  8.64           C  
ATOM    193  C   GLN    31      22.568   5.730   4.973  1.00  9.55           C  
ATOM    194  O   GLN    31      23.636   5.456   4.419  1.00 12.64           O  
ATOM    200  N   VAL    32      22.379   5.638   6.287  1.00  9.34           N  
ATOM    201  CA  VAL    32      23.424   5.266   7.215  1.00 11.38           C  
ATOM    202  C   VAL    32      22.957   4.084   8.041  1.00 12.09           C  
ATOM    203  O   VAL    32      21.761   3.913   8.232  1.00 12.32           O  
ATOM    208  N   ASP    33      23.877   3.248   8.533  1.00 12.02           N  
ATOM    209  CA  ASP    33      23.490   2.124   9.381  1.00 12.22           C  
ATOM    210  C   ASP    33      22.920   2.579  10.715  1.00 13.09           C  
ATOM    211  O   ASP    33      23.216   3.677  11.201  1.00 13.18           O  
ATOM    215  N   GLU    34      22.098   1.716  11.296  1.00 13.61           N  
ATOM    216  CA  GLU    34      21.593   1.890  12.640  1.00 15.20           C  
ATOM    217  C   GLU    34      22.712   2.343  13.584  1.00 11.76           C  
ATOM    218  O   GLU    34      23.815   1.808  13.547  1.00 13.53           O  
ATOM    224  N   GLY    35      22.407   3.346  14.406  1.00 10.81           N  
ATOM    225  CA  GLY    35      23.344   3.837  15.408  1.00 10.42           C  
ATOM    226  C   GLY    35      24.292   4.901  14.888  1.00 11.39           C  
ATOM    227  O   GLY    35      25.175   5.379  15.621  1.00 10.63           O  
ATOM    228  N   ILE    36      24.131   5.288  13.630  1.00  9.83           N  
ATOM    229  CA  ILE    36      25.039   6.261  13.050  1.00  8.36           C  
ATOM    230  C   ILE    36      25.075   7.544  13.824  1.00  8.18           C  
ATOM    231  O   ILE    36      24.043   8.047  14.299  1.00  9.72           O  
ATOM    233  N   THR    37      26.287   8.088  13.910  1.00  6.91           N  
ATOM    234  CA  THR    37      26.551   9.347  14.578  1.00  6.25           C  
ATOM    235  C   THR    37      26.995  10.405  13.572  1.00  6.53           C  
ATOM    236  O   THR    37      27.375  10.096  12.431  1.00  7.65           O  
ATOM    244  N   VAL    38      27.006  11.667  13.985  1.00  7.59           N  
ATOM    245  CA  VAL    38      27.510  12.742  13.131  1.00  8.27           C  
ATOM    246  C   VAL    38      28.892  12.408  12.535  1.00  7.47           C  
ATOM    247  O   VAL    38      29.127  12.596  11.320  1.00  8.26           O  
ATOM    251  N   GLN    39      29.808  11.875  13.355  1.00  7.56           N  
ATOM    252  CA  GLN    39      31.132  11.551  12.820  1.00  6.87           C  
ATOM    253  C   GLN    39      31.071  10.512  11.671  1.00  7.52           C  
ATOM    254  O   GLN    39      31.893  10.559  10.740  1.00  7.60           O  
ATOM    262  N   THR    40      30.110   9.583  11.742  1.00  7.45           N  
ATOM    263  CA  THR    40      29.972   8.561  10.680  1.00  6.77           C  
ATOM    264  C   THR    40      29.469   9.203   9.422  1.00 10.11           C  
ATOM    265  O   THR    40      29.911   8.840   8.325  1.00  8.59           O  
ATOM    270  N   ALA    41      28.568  10.162   9.559  1.00  7.40           N  
ATOM    271  CA  ALA    41      28.084  10.895   8.389  1.00  7.10           C  
ATOM    272  C   ALA    41      29.210  11.692   7.720  1.00  8.12           C  
ATOM    273  O   ALA    41      29.332  11.666   6.481  1.00  8.17           O  
ATOM    278  N   ILE    42      30.055  12.344   8.517  1.00  8.03           N  
ATOM    279  CA  ILE    42      31.187  13.074   7.961  1.00  8.12           C  
ATOM    280  C   ILE    42      32.091  12.124   7.180  1.00  8.50           C  
ATOM    281  O   ILE    42      32.536  12.448   6.049  1.00  8.93           O  
ATOM    286  N   THR    43      32.376  10.936   7.742  1.00  8.07           N  
ATOM    287  CA  THR    43      33.181   9.971   6.984  1.00  8.57           C  
ATOM    288  C   THR    43      32.541   9.526   5.691  1.00  9.86           C  
ATOM    289  O   THR    43      33.254   9.316   4.685  1.00  9.51           O  
ATOM    295  N   GLN    44      31.224   9.381   5.685  1.00  7.79           N  
ATOM    296  CA  GLN    44      30.533   8.984   4.472  1.00  7.03           C  
ATOM    297  C   GLN    44      30.556  10.102   3.430  1.00  8.01           C  
ATOM    298  O   GLN    44      30.702   9.808   2.238  1.00  7.40           O  
ATOM    304  N   ILE    47      30.435  11.376   3.850  1.00  8.16           N  
ATOM    305  CA  ILE    47      30.542  12.490   2.898  1.00  6.89           C  
ATOM    306  C   ILE    47      31.910  12.458   2.215  1.00  7.57           C  
ATOM    307  O   ILE    47      31.997  12.587   0.975  1.00  8.03           O  
ATOM    312  N   LEU    48      32.953  12.238   3.010  1.00  7.56           N  
ATOM    313  CA  LEU    48      34.319  12.149   2.481  1.00  7.86           C  
ATOM    314  C   LEU    48      34.504  10.956   1.532  1.00  9.12           C  
ATOM    315  O   LEU    48      35.257  11.058   0.536  1.00 10.55           O  
ATOM    321  N   SER    49      33.828   9.847   1.820  1.00  8.48           N  
ATOM    322  CA  SER    49      33.900   8.667   0.975  1.00 10.79           C  
ATOM    323  C   SER    49      33.201   8.906  -0.361  1.00  9.40           C  
ATOM    324  O   SER    49      33.676   8.441  -1.407  1.00 12.40           O  
ATOM    330  N   GLN    50      32.067   9.603  -0.348  1.00  7.33           N  
ATOM    331  CA  GLN    50      31.327   9.855  -1.572  1.00  7.36           C  
ATOM    332  C   GLN    50      31.972  10.934  -2.428  1.00  8.69           C  
ATOM    333  O   GLN    50      31.846  10.941  -3.651  1.00  9.70           O  
ATOM    341  N   PHE    51      32.590  11.895  -1.758  1.00  8.04           N  
ATOM    342  CA  PHE    51      33.087  13.098  -2.416  1.00  7.19           C  
ATOM    343  C   PHE    51      34.488  13.371  -1.935  1.00  8.23           C  
ATOM    344  O   PHE    51      34.694  14.101  -0.934  1.00  8.76           O  
ATOM    351  N   PRO    52      35.460  12.813  -2.656  1.00  8.97           N  
ATOM    352  CA  PRO    52      36.845  12.801  -2.181  1.00 10.47           C  
ATOM    353  C   PRO    52      37.435  14.184  -1.942  1.00 10.69           C  
ATOM    354  O   PRO    52      38.369  14.311  -1.156  1.00 12.35           O  
ATOM    360  N   GLU    53      36.890  15.212  -2.589  1.00  9.37           N  
ATOM    361  CA  GLU    53      37.415  16.580  -2.371  1.00 11.21           C  
ATOM    362  C   GLU    53      37.194  17.050  -0.933  1.00 11.29           C  
ATOM    363  O   GLU    53      37.872  17.980  -0.474  1.00 11.42           O  
ATOM    369  N   ILE    54      36.279  16.404  -0.192  1.00  9.10           N  
ATOM    370  CA  ILE    54      36.082  16.748   1.216  1.00  8.29           C  
ATOM    371  C   ILE    54      37.134  16.151   2.151  1.00  9.69           C  
ATOM    372  O   ILE    54      37.207  16.531   3.327  1.00 10.46           O  
ATOM    380  N   ASP    55      37.932  15.207   1.663  1.00 12.30           N  
ATOM    381  CA  ASP    55      38.927  14.569   2.537  1.00 11.50           C  
ATOM    382  C   ASP    55      39.913  15.597   3.088  1.00 14.66           C  
ATOM    383  O   ASP    55      40.366  15.466   4.234  1.00 20.06           O  
ATOM    388  N   LEU    56      40.203  16.617   2.278  1.00 13.79           N  
ATOM    389  CA  LEU    56      41.211  17.649   2.559  1.00 16.53           C  
ATOM    390  C   LEU    56      40.612  18.834   3.349  1.00 17.88           C  
ATOM    391  O   LEU    56      41.339  19.766   3.749  1.00 21.20           O  
TER
END
