
#######################################################
#                                                     #
#                        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   46 (  228),  selected   46 , name T0363TS252_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS252_1-D1.T0363_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    N      11      N      11          3.495
LGA    Q      12      Q      12          2.698
LGA    I      13      I      13          3.876
LGA    N      14      -       -           -
LGA    I      15      -       -           -
LGA    E      16      N      14          3.626
LGA    I      17      I      15          3.691
LGA    A      18      E      16          2.773
LGA    Y      19      I      17           -
LGA    -       -      A      18           -
LGA    -       -      Y      19           -
LGA    -       -      A      20           -
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    -       -      Y      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    A      20      S      29          5.302
LGA    F      21      F      30          1.805
LGA    P      22      Q      31          3.946
LGA    E      23      -       -           -
LGA    R      24      V      32          4.012
LGA    Y      25      D      33          1.550
LGA    Y      26      -       -           -
LGA    L      27      -       -           -
LGA    K      28      -       -           -
LGA    S      29      -       -           -
LGA    F      30      E      34          1.356
LGA    Q      31      G      35          4.440
LGA    V      32      I      36           #
LGA    D      33      -       -           -
LGA    E      34      -       -           -
LGA    G      35      -       -           -
LGA    I      36      -       -           -
LGA    T      37      T      37          3.348
LGA    V      38      V      38          4.829
LGA    Q      39      Q      39          3.181
LGA    -       -      T      40           -
LGA    T      40      A      41          4.466
LGA    A      41      I      42          4.312
LGA    I      42      T      43          2.563
LGA    T      43      Q      44          3.988
LGA    Q      44      S      45          2.663
LGA    S      45      -       -           -
LGA    G      46      -       -           -
LGA    I      47      -       -           -
LGA    L      48      -       -           -
LGA    S      49      -       -           -
LGA    Q      50      -       -           -
LGA    F      51      -       -           -
LGA    P      52      -       -           -
LGA    E      53      G      46          4.166
LGA    I      54      I      47          2.266
LGA    D      55      -       -           -
LGA    L      56      L      48          2.957
LGA    -       -      S      49           -
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   46    5.0     24    3.54    41.67     27.632     0.660

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.967288 * X  +  -0.252153 * Y  +  -0.027792 * Z  +  23.008389
  Y_new =  -0.149764 * X  +   0.479191 * Y  +   0.864839 * Z  +   3.042217
  Z_new =  -0.204754 * X  +   0.840711 * Y  +  -0.501279 * Z  +   0.269360 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.108459   -1.033134  [ DEG:   120.8058    -59.1942 ]
  Theta =   0.206213    2.935380  [ DEG:    11.8151    168.1849 ]
  Phi   =  -2.987983    0.153609  [ DEG:  -171.1988      8.8012 ]
 
# 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: T0363TS252_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS252_1-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   46   5.0   24   3.54   41.67  27.632
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS252_1-D1
PFRMAT TS                                                                       
TARGET T0363                                                                    
MODEL  1                                                                        
PARENT N/A                                                                      
ATOM     51  N   ASN    11      15.113   1.274  10.051   1.0                    
ATOM     52  CA  ASN    11      14.514   2.539  10.457   1.0                    
ATOM     53  C   ASN    11      15.140   3.712   9.710   1.0                    
ATOM     54  O   ASN    11      14.434   4.581   9.197   1.0                    
ATOM     55  CB  ASN    11      14.689   2.790  12.421   0.0                    
ATOM     56  N   GLN    12      16.467   3.730   9.654   1.0                    
ATOM     57  CA  GLN    12      17.191   4.795   8.970   1.0                    
ATOM     58  C   GLN    12      16.897   4.789   7.474   1.0                    
ATOM     59  O   GLN    12      16.734   5.844   6.859   1.0                    
ATOM     60  CB  GLN    12      19.646   4.583   9.380   0.0                    
ATOM     61  N   ILE    13      16.829   3.596   6.893   1.0                    
ATOM     62  CA  ILE    13      16.555   3.450   5.469   1.0                    
ATOM     63  C   ILE    13      15.233   4.112   5.092   1.0                    
ATOM     64  O   ILE    13      15.135   4.781   4.062   1.0                    
ATOM     65  CB  ILE    13      16.544   1.721   5.008   0.0                    
ATOM     66  N   ASN    14      14.221   3.922   5.932   1.0                    
ATOM     67  CA  ASN    14      12.905   4.501   5.688   1.0                    
ATOM     68  C   ASN    14      12.983   6.019   5.563   1.0                    
ATOM     69  O   ASN    14      12.291   6.619   4.741   1.0                    
ATOM     70  CB  ASN    14      11.643   3.985   7.134   0.0                    
ATOM     71  N   ILE    15      13.830   6.631   6.384   1.0                    
ATOM     72  CA  ILE    15      14.000   8.079   6.367   1.0                    
ATOM     73  C   ILE    15      14.648   8.543   5.067   1.0                    
ATOM     74  O   ILE    15      15.080   7.729   4.253   1.0                    
ATOM     75  CB  ILE    15      14.970   8.610   7.776   0.0                    
ATOM     76  N   GLU    16      14.710   9.858   4.879   1.0                    
ATOM     77  CA  GLU    16      15.306  10.433   3.678   1.0                    
ATOM     78  C   GLU    16      16.365  11.472   4.031   1.0                    
ATOM     79  O   GLU    16      17.439  11.505   3.430   1.0                    
ATOM     80  CB  GLU    16      13.528  11.448   2.221   0.0                    
ATOM     81  N   ILE    17      16.057  12.317   5.009   1.0                    
ATOM     82  CA  ILE    17      16.981  13.357   5.443   1.0                    
ATOM     83  C   ILE    17      18.181  12.760   6.170   1.0                    
ATOM     84  O   ILE    17      18.054  12.255   7.285   1.0                    
ATOM     85  CB  ILE    17      16.140  14.544   6.487   0.0                    
ATOM     86  N   ALA    18      19.345  12.825   5.532   1.0                    
ATOM     87  CA  ALA    18      20.569  12.291   6.117   1.0                    
ATOM     88  C   ALA    18      20.394  10.834   6.532   1.0                    
ATOM     89  O   ALA    18      21.345  10.054   6.511   1.0                    
ATOM     90  CB  ALA    18      20.786  12.715   6.713   0.0                    
ATOM     91  N   TYR    19      19.170  10.475   6.908   1.0                    
ATOM     92  CA  TYR    19      18.867   9.112   7.329   1.0                    
ATOM     93  C   TYR    19      19.002   8.134   6.168   1.0                    
ATOM     94  O   TYR    19      19.254   6.946   6.371   1.0                    
ATOM     95  CB  TYR    19      15.791   8.953   8.647   0.0                    
ATOM     96  N   ALA    20      18.833   8.640   4.951   1.0                    
ATOM     97  CA  ALA    20      18.935   7.812   3.755   1.0                    
ATOM     98  C   ALA    20      20.338   7.234   3.603   1.0                    
ATOM     99  O   ALA    20      20.503   6.062   3.264   1.0                    
ATOM    100  CB  ALA    20      18.742   8.214   3.136   0.0                    
ATOM    101  N   PHE    21      21.345   8.063   3.856   1.0                    
ATOM    102  CA  PHE    21      22.735   7.636   3.748   1.0                    
ATOM    103  C   PHE    21      22.995   6.388   4.585   1.0                    
ATOM    104  O   PHE    21      22.731   6.369   5.786   1.0                    
ATOM    105  CB  PHE    21      24.568   9.845   4.565   0.0                    
ATOM    106  N   PRO    22      23.517   5.349   3.941   1.0                    
ATOM    107  CA  PRO    22      23.813   4.096   4.624   1.0                    
ATOM    108  C   PRO    22      25.050   4.228   5.507   1.0                    
ATOM    109  O   PRO    22      25.370   3.327   6.282   1.0                    
ATOM    110  CB  PRO    22      23.983   3.058   3.692   0.0                    
ATOM    111  N   GLU    23      25.741   5.356   5.383   1.0                    
ATOM    112  CA  GLU    23      26.943   5.608   6.168   1.0                    
ATOM    113  C   GLU    23      26.635   5.615   7.663   1.0                    
ATOM    114  O   GLU    23      27.523   5.409   8.490   1.0                    
ATOM    115  CB  GLU    23      28.001   7.783   5.480   0.0                    
ATOM    116  N   ARG    24      25.371   5.851   8.000   1.0                    
ATOM    117  CA  ARG    24      24.943   5.883   9.393   1.0                    
ATOM    118  C   ARG    24      24.400   4.528   9.835   1.0                    
ATOM    119  O   ARG    24      24.684   4.065  10.940   1.0                    
ATOM    120  CB  ARG    24      22.423   8.510   9.900   0.0                    
ATOM    121  N   TYR    25      23.615   3.899   8.966   1.0                    
ATOM    122  CA  TYR    25      23.031   2.597   9.265   1.0                    
ATOM    123  C   TYR    25      24.105   1.520   9.370   1.0                    
ATOM    124  O   TYR    25      24.071   0.682  10.270   1.0                    
ATOM    125  CB  TYR    25      20.765   1.772   6.938   0.0                    
ATOM    126  N   TYR    26      25.058   1.549   8.444   1.0                    
ATOM    127  CA  TYR    26      26.144   0.576   8.431   1.0                    
ATOM    128  C   TYR    26      26.852   0.522   9.780   1.0                    
ATOM    129  O   TYR    26      27.085  -0.555  10.326   1.0                    
ATOM    130  CB  TYR    26      28.323   1.291   5.988   0.0                    
ATOM    131  N   LEU    27      27.192   1.692  10.312   1.0                    
ATOM    132  CA  LEU    27      27.874   1.780  11.597   1.0                    
ATOM    133  C   LEU    27      27.048   1.136  12.705   1.0                    
ATOM    134  O   LEU    27      26.267   0.217  12.457   1.0                    
ATOM    135  CB  LEU    27      28.282   3.701  12.046   0.0                    
ATOM    136  N   LYS    28      27.226   1.624  13.929   1.0                    
ATOM    137  CA  LYS    28      26.498   1.097  15.077   1.0                    
ATOM    138  C   LYS    28      25.205   1.871  15.313   1.0                    
ATOM    139  O   LYS    28      24.154   1.281  15.564   1.0                    
ATOM    140  CB  LYS    28      28.160   1.159  17.439   0.0                    
ATOM    141  N   SER    29      25.290   3.195  15.230   1.0                    
ATOM    142  CA  SER    29      24.128   4.052  15.434   1.0                    
ATOM    143  C   SER    29      23.052   3.780  14.389   1.0                    
ATOM    144  O   SER    29      23.353   3.569  13.214   1.0                    
ATOM    145  CB  SER    29      24.470   5.270  15.413   0.0                    
ATOM    146  N   PHE    30      21.796   3.788  14.824   1.0                    
ATOM    147  CA  PHE    30      20.674   3.543  13.926   1.0                    
ATOM    148  C   PHE    30      20.107   4.850  13.381   1.0                    
ATOM    149  O   PHE    30      19.850   4.974  12.184   1.0                    
ATOM    150  CB  PHE    30      18.547   1.983  15.324   0.0                    
ATOM    151  N   GLN    31      19.915   5.821  14.268   1.0                    
ATOM    152  CA  GLN    31      19.379   7.119  13.877   1.0                    
ATOM    153  C   GLN    31      20.263   7.790  12.831   1.0                    
ATOM    154  O   GLN    31      21.489   7.714  12.902   1.0                    
ATOM    155  CB  GLN    31      19.121   8.592  15.879   0.0                    
ATOM    156  N   VAL    32      19.632   8.444  11.862   1.0                    
ATOM    157  CA  VAL    32      20.360   9.128  10.801   1.0                    
ATOM    158  C   VAL    32      19.973  10.601  10.726   1.0                    
ATOM    159  O   VAL    32      20.827  11.468  10.538   1.0                    
ATOM    160  CB  VAL    32      20.122   8.468   9.507   0.0                    
ATOM    161  N   ASP    33      18.682  10.877  10.877   1.0                    
ATOM    162  CA  ASP    33      18.179  12.245  10.827   1.0                    
ATOM    163  C   ASP    33      18.752  13.084  11.965   1.0                    
ATOM    164  O   ASP    33      18.921  14.297  11.831   1.0                    
ATOM    165  CB  ASP    33      16.196  12.256  10.886   0.0                    
ATOM    166  N   GLU    34      19.051  12.431  13.084   1.0                    
ATOM    167  CA  GLU    34      19.605  13.115  14.246   1.0                    
ATOM    168  C   GLU    34      20.722  12.298  14.886   1.0                    
ATOM    169  O   GLU    34      20.553  11.110  15.165   1.0                    
ATOM    170  CB  GLU    34      17.797  13.603  15.921   0.0                    
ATOM    171  N   GLY    35      21.861  12.941  15.118   1.0                    
ATOM    172  CA  GLY    35      23.007  12.274  15.726   1.0                    
ATOM    173  C   GLY    35      24.283  13.087  15.534   1.0                    
ATOM    174  O   GLY    35      24.385  13.889  14.606   1.0                    
ATOM    175  N   ILE    36      25.253  12.873  16.418   1.0                    
ATOM    176  CA  ILE    36      26.524  13.584  16.347   1.0                    
ATOM    177  C   ILE    36      27.701  12.619  16.426   1.0                    
ATOM    178  O   ILE    36      28.796  12.919  15.949   1.0                    
ATOM    179  CB  ILE    36      26.627  14.809  17.649   0.0                    
ATOM    180  N   THR    37      27.469  11.458  17.031   1.0                    
ATOM    181  CA  THR    37      28.510  10.447  17.174   1.0                    
ATOM    182  C   THR    37      28.453   9.433  16.038   1.0                    
ATOM    183  O   THR    37      29.486   9.017  15.511   1.0                    
ATOM    184  CB  THR    37      28.393   9.778  18.461   0.0                    
ATOM    185  N   VAL    38      27.240   9.038  15.663   1.0                    
ATOM    186  CA  VAL    38      27.046   8.072  14.588   1.0                    
ATOM    187  C   VAL    38      27.787   8.497  13.324   1.0                    
ATOM    188  O   VAL    38      28.379   7.669  12.632   1.0                    
ATOM    189  CB  VAL    38      25.613   7.894  14.311   0.0                    
ATOM    190  N   GLN    39      27.749   9.793  13.029   1.0                    
ATOM    191  CA  GLN    39      28.416  10.329  11.850   1.0                    
ATOM    192  C   GLN    39      29.922  10.104  11.916   1.0                    
ATOM    193  O   GLN    39      30.525  10.189  12.986   1.0                    
ATOM    194  CB  GLN    39      27.905  12.762  11.592   0.0                    
ATOM    195  N   THR    40      30.523   9.817  10.766   1.0                    
ATOM    196  CA  THR    40      31.960   9.578  10.692   1.0                    
ATOM    197  C   THR    40      32.555  10.188   9.427   1.0                    
ATOM    198  O   THR    40      31.861  10.855   8.661   1.0                    
ATOM    199  CB  THR    40      32.242   8.152  10.752   0.0                    
ATOM    200  N   ALA    41      33.847   9.954   9.215   1.0                    
ATOM    201  CA  ALA    41      34.538  10.479   8.044   1.0                    
ATOM    202  C   ALA    41      33.839  10.058   6.756   1.0                    
ATOM    203  O   ALA    41      33.661  10.864   5.843   1.0                    
ATOM    204  CB  ALA    41      35.267  10.251   8.040   0.0                    
ATOM    205  N   ILE    42      33.445   8.790   6.689   1.0                    
ATOM    206  CA  ILE    42      32.765   8.260   5.513   1.0                    
ATOM    207  C   ILE    42      31.426   8.954   5.291   1.0                    
ATOM    208  O   ILE    42      30.621   9.080   6.213   1.0                    
ATOM    209  CB  ILE    42      32.538   6.491   5.669   0.0                    
ATOM    210  N   THR    43      31.193   9.401   4.061   1.0                    
ATOM    211  CA  THR    43      29.952  10.082   3.715   1.0                    
ATOM    212  C   THR    43      29.192   9.326   2.629   1.0                    
ATOM    213  O   THR    43      27.962   9.349   2.590   1.0                    
ATOM    214  CB  THR    43      30.224  11.448   3.291   0.0                    
ATOM    215  N   GLN    44      29.933   8.659   1.751   1.0                    
ATOM    216  CA  GLN    44      29.331   7.897   0.664   1.0                    
ATOM    217  C   GLN    44      28.427   6.792   1.200   1.0                    
ATOM    218  O   GLN    44      28.786   6.085   2.142   1.0                    
ATOM    219  CB  GLN    44      31.104   6.938  -0.813   0.0                    
ATOM    220  N   SER    45      27.252   6.650   0.595   1.0                    
ATOM    221  CA  SER    45      26.295   5.631   1.009   1.0                    
ATOM    222  C   SER    45      26.267   4.467   0.025   1.0                    
ATOM    223  O   SER    45      26.190   3.306   0.426   1.0                    
ATOM    224  CB  SER    45      25.141   6.135   1.133   0.0                    
ATOM    225  N   GLY    46      26.331   4.786  -1.264   1.0                    
ATOM    226  CA  GLY    46      26.312   3.767  -2.306   1.0                    
ATOM    227  C   GLY    46      27.612   2.970  -2.322   1.0                    
ATOM    228  O   GLY    46      27.850   2.169  -3.225   1.0                    
ATOM    229  N   ILE    47      28.451   3.195  -1.315   1.0                    
ATOM    230  CA  ILE    47      29.727   2.499  -1.210   1.0                    
ATOM    231  C   ILE    47      30.248   2.513   0.223   1.0                    
ATOM    232  O   ILE    47      30.282   3.559   0.871   1.0                    
ATOM    233  CB  ILE    47      30.928   3.227  -2.321   0.0                    
ATOM    234  N   LEU    48      30.652   1.345   0.712   1.0                    
ATOM    235  CA  LEU    48      31.172   1.221   2.068   1.0                    
ATOM    236  C   LEU    48      32.689   1.374   2.095   1.0                    
ATOM    237  O   LEU    48      33.349   0.946   3.042   1.0                    
ATOM    238  CB  LEU    48      30.626  -0.545   2.871   0.0                    
ATOM    239  N   SER    49      33.235   1.985   1.049   1.0                    
ATOM    240  CA  SER    49      34.675   2.195   0.949   1.0                    
ATOM    241  C   SER    49      35.043   3.642   1.256   1.0                    
ATOM    242  O   SER    49      34.309   4.567   0.907   1.0                    
ATOM    243  CB  SER    49      35.091   1.864  -0.198   0.0                    
ATOM    244  N   GLN    50      36.184   3.831   1.910   1.0                    
ATOM    245  CA  GLN    50      36.652   5.166   2.264   1.0                    
ATOM    246  C   GLN    50      37.071   5.951   1.025   1.0                    
ATOM    247  O   GLN    50      37.755   5.424   0.147   1.0                    
ATOM    248  CB  GLN    50      38.543   5.024   3.891   0.0                    
ATOM    249  N   PHE    51      36.657   7.212   0.961   1.0                    
ATOM    250  CA  PHE    51      36.989   8.070  -0.170   1.0                    
ATOM    251  C   PHE    51      37.270   9.498   0.285   1.0                    
ATOM    252  O   PHE    51      36.637  10.000   1.214   1.0                    
ATOM    253  CB  PHE    51      34.789   8.031  -2.187   0.0                    
ATOM    254  N   PRO    52      38.224  10.148  -0.374   1.0                    
ATOM    255  CA  PRO    52      38.591  11.518  -0.038   1.0                    
ATOM    256  C   PRO    52      37.414  12.468  -0.234   1.0                    
ATOM    257  O   PRO    52      37.301  13.482   0.455   1.0                    
ATOM    258  CB  PRO    52      39.692  11.933  -0.808   0.0                    
ATOM    259  N   GLU    53      36.540  12.133  -1.177   1.0                    
ATOM    260  CA  GLU    53      35.371  12.955  -1.465   1.0                    
ATOM    261  C   GLU    53      34.380  12.930  -0.306   1.0                    
ATOM    262  O   GLU    53      33.508  13.794  -0.204   1.0                    
ATOM    263  CB  GLU    53      34.262  12.190  -3.588   0.0                    
ATOM    264  N   ILE    54      34.521  11.936   0.564   1.0                    
ATOM    265  CA  ILE    54      33.639  11.797   1.718   1.0                    
ATOM    266  C   ILE    54      34.068  12.720   2.855   1.0                    
ATOM    267  O   ILE    54      33.237  13.372   3.484   1.0                    
ATOM    268  CB  ILE    54      33.599  10.095   2.271   0.0                    
ATOM    269  N   ASP    55      35.371  12.767   3.111   1.0                    
ATOM    270  CA  ASP    55      35.913  13.607   4.172   1.0                    
ATOM    271  C   ASP    55      35.582  15.077   3.934   1.0                    
ATOM    272  O   ASP    55      35.309  15.822   4.876   1.0                    
ATOM    273  CB  ASP    55      37.876  13.352   4.324   0.0                    
ATOM    274  N   LEU    56      35.609  15.487   2.671   1.0                    
ATOM    275  CA  LEU    56      35.312  16.868   2.306   1.0                    
ATOM    276  C   LEU    56      33.875  17.235   2.662   1.0                    
ATOM    277  O   LEU    56      33.604  18.344   3.123   1.0                    
ATOM    278  CB  LEU    56      35.653  17.166   0.344   0.0                    
TER                                                                             
END
