
#######################################################
#                                                     #
#                        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   49 (  196),  selected   49 , name T0349TS125_5u-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS125_5u-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          3.593
LGA    R       2      R       2          4.574
LGA    E       3      E       3          1.048
LGA    L       4      L       4          0.648
LGA    L       5      L       5          0.315
LGA    R       6      R       6          1.335
LGA    T       7      T       7          2.654
LGA    N       8      N       8          4.343
LGA    D       9      D       9          1.038
LGA    A      10      A      10          1.472
LGA    V      11      V      11          0.909
LGA    L      12      L      12          0.267
LGA    L      13      L      13          1.228
LGA    S      14      S      14          1.117
LGA    A      15      A      15          0.534
LGA    V      16      V      16          0.528
LGA    G      17      G      17          0.938
LGA    A      18      A      18          0.735
LGA    L      19      L      19          0.774
LGA    L      20      L      20          1.007
LGA    D      21      D      21          0.994
LGA    G      22      G      22          0.374
LGA    A      23      A      23          1.418
LGA    D      24      D      24          2.092
LGA    I      25      I      25          0.791
LGA    -       -      G      26           -
LGA    -       -      H      27           -
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      P      45           -
LGA    R      46      R      46          2.100
LGA    R      47      R      47          0.894
LGA    V      48      V      48          0.791
LGA    L      49      L      49          0.737
LGA    V      50      V      50          0.478
LGA    H      51      H      51          0.932
LGA    E      52      E      52          1.815
LGA    D      53      D      53          2.307
LGA    D      54      D      54          1.430
LGA    L      55      L      55          1.077
LGA    A      56      A      56          0.334
LGA    G      57      G      57          0.270
LGA    A      58      A      58          0.421
LGA    R      59      R      59          0.662
LGA    R      60      R      60          0.677
LGA    L      61      L      61          0.460
LGA    L      62      L      62          0.319
LGA    T      63      T      63          0.566
LGA    D      64      D      64          1.342
LGA    A      65      A      65          2.259
LGA    -       -      G      66           -
LGA    G      66      L      67          1.885
LGA    L      67      A      68          3.371
LGA    A      68      H      69          3.493
LGA    R      72      E      70           #
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   49   57    5.0     48    1.69    93.75     78.601     2.682

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.699359 * X  +  -0.617624 * Y  +   0.359776 * Z  +   0.307229
  Y_new =   0.666770 * X  +   0.745069 * Y  +  -0.017064 * Z  +   3.932716
  Z_new =  -0.257519 * X  +   0.251821 * Y  +   0.932883 * Z  +   3.286334 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.263655   -2.877938  [ DEG:    15.1063   -164.8937 ]
  Theta =   0.260454    2.881139  [ DEG:    14.9229    165.0771 ]
  Phi   =   0.761548   -2.380045  [ DEG:    43.6335   -136.3665 ]
 
# 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: T0349TS125_5u-D1                              
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS125_5u-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   49   57   5.0   48   1.69   93.75  78.601
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS125_5u-D1
PFRMAT   TS
TARGET   T0349
MODEL    5  UNREFINED
PARENT   1yj7a1   
ATOM      1  N   MET     1       0.983  13.859  -9.714    1.00  0.50
ATOM      2  CA  MET     1       1.824  12.632  -9.639    1.00  0.50
ATOM      3  C   MET     1       1.587  11.945  -8.302    1.00  0.50
ATOM      4  O   MET     1       1.538  12.604  -7.280    1.00  0.50
ATOM      9  N   ARG     2       1.441  10.632  -8.357    1.00  0.50
ATOM     10  CA  ARG     2       1.255   9.763  -7.199    1.00  0.50
ATOM     11  C   ARG     2       2.572   9.054  -6.954    1.00  0.50
ATOM     12  O   ARG     2       3.339   8.825  -7.891    1.00  0.50
ATOM     27  N   GLU     3       4.092   5.563  -4.819    1.00  0.50
ATOM     28  CA  GLU     3       3.831   4.376  -4.009    1.00  0.50
ATOM     29  C   GLU     3       4.604   4.522  -2.719    1.00  0.50
ATOM     30  O   GLU     3       5.729   4.989  -2.731    1.00  0.50
ATOM     36  N   LEU     4       3.988   4.149  -1.622    1.00  0.50
ATOM     37  CA  LEU     4       4.712   4.019  -0.340    1.00  0.50
ATOM     38  C   LEU     4       5.156   2.571  -0.144    1.00  0.50
ATOM     39  O   LEU     4       6.348   2.266  -0.162    1.00  0.50
ATOM     44  N   LEU     5       4.187   1.675  -0.008    1.00  0.50
ATOM     45  CA  LEU     5       4.434   0.273   0.277    1.00  0.50
ATOM     46  C   LEU     5       3.477  -0.636  -0.504    1.00  0.50
ATOM     47  O   LEU     5       2.308  -0.312  -0.671    1.00  0.50
ATOM     56  N   ARG     6       4.000  -1.764  -0.962    1.00  0.50
ATOM     57  CA  ARG     6       3.205  -2.885  -1.474    1.00  0.50
ATOM     58  C   ARG     6       3.335  -4.106  -0.560    1.00  0.50
ATOM     59  O   ARG     6       4.131  -4.118   0.398    1.00  0.50
ATOM     63  N   THR     7       2.559  -5.145  -0.865    1.00  0.50
ATOM     64  CA  THR     7       2.652  -6.410  -0.156    1.00  0.50
ATOM     65  C   THR     7       2.055  -6.399   1.235    1.00  0.50
ATOM     66  O   THR     7       2.366  -7.266   2.059    1.00  0.50
ATOM     67  N   ASN     8       1.208  -5.414   1.539    1.00  0.50
ATOM     68  CA  ASN     8       0.658  -5.284   2.888    1.00  0.50
ATOM     69  C   ASN     8      -0.572  -6.179   3.080    1.00  0.50
ATOM     70  O   ASN     8      -1.342  -6.403   2.143    1.00  0.50
ATOM     75  N   ASP     9      -0.769  -6.671   4.304    1.00  0.50
ATOM     76  CA  ASP     9      -2.044  -7.287   4.670    1.00  0.50
ATOM     77  C   ASP     9      -3.131  -6.229   4.685    1.00  0.50
ATOM     78  O   ASP     9      -2.859  -5.031   4.786    1.00  0.50
ATOM     82  N   ALA    10      -4.376  -6.676   4.595    1.00  0.50
ATOM     83  CA  ALA    10      -5.488  -5.749   4.656    1.00  0.50
ATOM     84  C   ALA    10      -5.496  -5.012   6.000    1.00  0.50
ATOM     85  O   ALA    10      -5.668  -3.797   6.037    1.00  0.50
ATOM     91  N   VAL    11      -5.258  -5.728   7.098    1.00  0.50
ATOM     92  CA  VAL    11      -5.292  -5.130   8.437    1.00  0.50
ATOM     93  C   VAL    11      -4.234  -4.032   8.603    1.00  0.50
ATOM     94  O   VAL    11      -4.534  -2.944   9.096    1.00  0.50
ATOM    100  N   LEU    12      -3.001  -4.319   8.193    1.00  0.50
ATOM    101  CA  LEU    12      -1.927  -3.345   8.355    1.00  0.50
ATOM    102  C   LEU    12      -2.086  -2.156   7.400    1.00  0.50
ATOM    103  O   LEU    12      -1.853  -1.021   7.808    1.00  0.50
ATOM    109  N   LEU    13      -2.478  -2.398   6.149    1.00  0.50
ATOM    110  CA  LEU    13      -2.735  -1.293   5.233    1.00  0.50
ATOM    111  C   LEU    13      -3.810  -0.407   5.837    1.00  0.50
ATOM    112  O   LEU    13      -3.711   0.805   5.758    1.00  0.50
ATOM    114  N   SER    14      -4.852  -1.001   6.430    1.00  0.50
ATOM    115  CA  SER    14      -5.885  -0.197   7.073    1.00  0.50
ATOM    116  C   SER    14      -5.369   0.648   8.227    1.00  0.50
ATOM    117  O   SER    14      -5.757   1.800   8.371    1.00  0.50
ATOM    122  N   ALA    15      -4.497   0.074   9.043    1.00  0.50
ATOM    123  CA  ALA    15      -3.916   0.808  10.156    1.00  0.50
ATOM    124  C   ALA    15      -3.083   1.991   9.640    1.00  0.50
ATOM    125  O   ALA    15      -3.194   3.107  10.140    1.00  0.50
ATOM    131  N   VAL    16      -2.295   1.743   8.613    1.00  0.50
ATOM    132  CA  VAL    16      -1.439   2.779   8.022    1.00  0.50
ATOM    133  C   VAL    16      -2.258   3.878   7.332    1.00  0.50
ATOM    134  O   VAL    16      -1.947   5.072   7.463    1.00  0.50
ATOM    139  N   GLY    17      -3.301   3.475   6.593    1.00  0.50
ATOM    140  CA  GLY    17      -4.179   4.403   5.898    1.00  0.50
ATOM    141  C   GLY    17      -4.926   5.284   6.890    1.00  0.50
ATOM    142  O   GLY    17      -4.972   6.503   6.747    1.00  0.50
ATOM    148  N   ALA    18      -5.466   4.685   7.948    1.00  0.50
ATOM    149  CA  ALA    18      -6.165   5.468   8.955    1.00  0.50
ATOM    150  C   ALA    18      -5.217   6.410   9.697    1.00  0.50
ATOM    151  O   ALA    18      -5.574   7.546   9.974    1.00  0.50
ATOM    153  N   LEU    19      -4.002   5.956   9.993    1.00  0.50
ATOM    154  CA  LEU    19      -3.007   6.800  10.636    1.00  0.50
ATOM    155  C   LEU    19      -2.675   8.044   9.795    1.00  0.50
ATOM    156  O   LEU    19      -2.619   9.165  10.299    1.00  0.50
ATOM    161  N   LEU    20      -2.459   7.835   8.504    1.00  0.50
ATOM    162  CA  LEU    20      -2.137   8.943   7.598    1.00  0.50
ATOM    163  C   LEU    20      -3.310   9.891   7.486    1.00  0.50
ATOM    164  O   LEU    20      -3.146  11.105   7.647    1.00  0.50
ATOM    169  N   ASP    21      -4.508   9.367   7.235    1.00  0.50
ATOM    170  CA  ASP    21      -5.660  10.244   7.085    1.00  0.50
ATOM    171  C   ASP    21      -5.886  11.064   8.353    1.00  0.50
ATOM    172  O   ASP    21      -6.203  12.249   8.288    1.00  0.50
ATOM    177  N   GLY    22      -5.696  10.446   9.513    1.00  0.50
ATOM    178  CA  GLY    22      -5.980  11.147  10.766    1.00  0.50
ATOM    179  C   GLY    22      -4.900  12.172  11.117    1.00  0.50
ATOM    180  O   GLY    22      -5.119  13.049  11.960    1.00  0.50
ATOM    183  N   ALA    23      -3.760  12.080  10.435    1.00  0.50
ATOM    184  CA  ALA    23      -2.666  13.025  10.529    1.00  0.50
ATOM    185  C   ALA    23      -2.583  13.928   9.276    1.00  0.50
ATOM    186  O   ALA    23      -1.518  14.446   8.911    1.00  0.50
ATOM    191  N   ASP    24      -3.723  14.085   8.619    1.00  0.50
ATOM    192  CA  ASP    24      -3.907  15.052   7.543    1.00  0.50
ATOM    193  C   ASP    24      -2.974  14.836   6.358    1.00  0.50
ATOM    194  O   ASP    24      -2.448  15.775   5.748    1.00  0.50
ATOM    199  N   ILE    25      -2.832  13.567   5.998    1.00  0.50
ATOM    200  CA  ILE    25      -2.213  13.167   4.750    1.00  0.50
ATOM    201  C   ILE    25      -3.171  12.283   3.963    1.00  0.50
ATOM    202  O   ILE    25      -3.596  11.224   4.438    1.00  0.50
ATOM    288  N   ARG    46      -2.064  -5.433  -0.488    1.00  0.50
ATOM    289  CA  ARG    46      -2.477  -4.042  -0.559    1.00  0.50
ATOM    290  C   ARG    46      -1.295  -3.118  -0.799    1.00  0.50
ATOM    291  O   ARG    46      -0.215  -3.333  -0.260    1.00  0.50
ATOM    296  N   ARG    47      -1.532  -2.103  -1.622    1.00  0.50
ATOM    297  CA  ARG    47      -0.565  -1.057  -1.921    1.00  0.50
ATOM    298  C   ARG    47      -1.131   0.285  -1.478    1.00  0.50
ATOM    299  O   ARG    47      -2.283   0.602  -1.772    1.00  0.50
ATOM    303  N   VAL    48      -0.327   1.070  -0.763    1.00  0.50
ATOM    304  CA  VAL    48      -0.694   2.421  -0.364    1.00  0.50
ATOM    305  C   VAL    48       0.195   3.399  -1.105    1.00  0.50
ATOM    306  O   VAL    48       1.397   3.171  -1.235    1.00  0.50
ATOM    311  N   LEU    49      -0.417   4.468  -1.607    1.00  0.50
ATOM    312  CA  LEU    49       0.259   5.564  -2.305    1.00  0.50
ATOM    313  C   LEU    49      -0.181   6.909  -1.750    1.00  0.50
ATOM    314  O   LEU    49      -1.231   7.011  -1.121    1.00  0.50
ATOM    317  N   VAL    50       0.609   7.943  -2.009    1.00  0.50
ATOM    318  CA  VAL    50       0.259   9.310  -1.659    1.00  0.50
ATOM    319  C   VAL    50       0.544  10.227  -2.846    1.00  0.50
ATOM    320  O   VAL    50       1.245   9.853  -3.782    1.00  0.50
ATOM    324  N   HIS    51       0.010  11.436  -2.793    1.00  0.50
ATOM    325  CA  HIS    51       0.410  12.467  -3.745    1.00  0.50
ATOM    326  C   HIS    51       1.894  12.690  -3.544    1.00  0.50
ATOM    327  O   HIS    51       2.386  12.664  -2.402    1.00  0.50
ATOM    329  N   GLU    52       2.644  12.872  -4.632    1.00  0.50
ATOM    330  CA  GLU    52       4.103  12.942  -4.512    1.00  0.50
ATOM    331  C   GLU    52       4.602  14.006  -3.548    1.00  0.50
ATOM    332  O   GLU    52       5.604  13.792  -2.868    1.00  0.50
ATOM    334  N   ASP    53       3.906  15.141  -3.471    1.00  0.50
ATOM    335  CA  ASP    53       4.316  16.250  -2.640    1.00  0.50
ATOM    336  C   ASP    53       4.228  15.901  -1.165    1.00  0.50
ATOM    337  O   ASP    53       4.886  16.531  -0.344    1.00  0.50
ATOM    339  N   ASP    54       3.427  14.888  -0.850    1.00  0.50
ATOM    340  CA  ASP    54       3.190  14.471   0.527    1.00  0.50
ATOM    341  C   ASP    54       4.113  13.337   0.986    1.00  0.50
ATOM    342  O   ASP    54       3.983  12.842   2.124    1.00  0.50
ATOM    347  N   LEU    55       5.042  12.915   0.127    1.00  0.50
ATOM    348  CA  LEU    55       5.821  11.726   0.416    1.00  0.50
ATOM    349  C   LEU    55       6.633  11.850   1.722    1.00  0.50
ATOM    350  O   LEU    55       6.606  10.944   2.560    1.00  0.50
ATOM    358  N   ALA    56       7.325  12.956   1.905    1.00  0.50
ATOM    359  CA  ALA    56       8.168  13.105   3.108    1.00  0.50
ATOM    360  C   ALA    56       7.315  13.123   4.386    1.00  0.50
ATOM    361  O   ALA    56       7.619  12.419   5.340    1.00  0.50
ATOM    365  N   GLY    57       6.233  13.891   4.393    1.00  0.50
ATOM    366  CA  GLY    57       5.306  13.939   5.523    1.00  0.50
ATOM    367  C   GLY    57       4.767  12.557   5.846    1.00  0.50
ATOM    368  O   GLY    57       4.704  12.156   7.013    1.00  0.50
ATOM    376  N   ALA    58       4.384  11.811   4.805    1.00  0.50
ATOM    377  CA  ALA    58       3.848  10.463   4.977    1.00  0.50
ATOM    378  C   ALA    58       4.841   9.478   5.579    1.00  0.50
ATOM    379  O   ALA    58       4.511   8.762   6.529    1.00  0.50
ATOM    381  N   ARG    59       6.054   9.435   5.038    1.00  0.50
ATOM    382  CA  ARG    59       7.074   8.539   5.557    1.00  0.50
ATOM    383  C   ARG    59       7.435   8.933   6.997    1.00  0.50
ATOM    384  O   ARG    59       7.667   8.052   7.819    1.00  0.50
ATOM    389  N   ARG    60       7.441  10.219   7.288    1.00  0.50
ATOM    390  CA  ARG    60       7.709  10.708   8.649    1.00  0.50
ATOM    391  C   ARG    60       6.698  10.156   9.649    1.00  0.50
ATOM    392  O   ARG    60       7.079   9.571  10.674    1.00  0.50
ATOM    396  N   LEU    61       5.407  10.291   9.325    1.00  0.50
ATOM    397  CA  LEU    61       4.332   9.788  10.149    1.00  0.50
ATOM    398  C   LEU    61       4.426   8.267  10.322    1.00  0.50
ATOM    399  O   LEU    61       4.262   7.750  11.429    1.00  0.50
ATOM    404  N   LEU    62       4.669   7.551   9.227    1.00  0.50
ATOM    405  CA  LEU    62       4.759   6.105   9.295    1.00  0.50
ATOM    406  C   LEU    62       5.960   5.682  10.158    1.00  0.50
ATOM    407  O   LEU    62       5.797   4.810  11.034    1.00  0.50
ATOM    412  N   THR    63       7.119   6.287   9.910    1.00  0.50
ATOM    413  CA  THR    63       8.350   6.001  10.666    1.00  0.50
ATOM    414  C   THR    63       8.117   6.238  12.162    1.00  0.50
ATOM    415  O   THR    63       8.523   5.411  13.007    1.00  0.50
ATOM    420  N   ASP    64       7.460   7.351  12.478    1.00  0.50
ATOM    421  CA  ASP    64       7.180   7.734  13.871    1.00  0.50
ATOM    422  C   ASP    64       6.224   6.805  14.578    1.00  0.50
ATOM    423  O   ASP    64       6.108   6.864  15.808    1.00  0.50
ATOM    428  N   ALA    65       5.500   5.970  13.826    1.00  0.50
ATOM    429  CA  ALA    65       4.588   5.000  14.393    1.00  0.50
ATOM    430  C   ALA    65       5.019   3.556  14.178    1.00  0.50
ATOM    431  O   ALA    65       4.264   2.629  14.454    1.00  0.50
ATOM    436  N   GLY    66       6.244   3.368  13.689    1.00  0.50
ATOM    437  CA  GLY    66       6.816   2.048  13.505    1.00  0.50
ATOM    438  C   GLY    66       6.253   1.214  12.366    1.00  0.50
ATOM    439  O   GLY    66       6.276  -0.002  12.436    1.00  0.50
ATOM    440  N   LEU    67       5.710   1.870  11.338    1.00  0.50
ATOM    441  CA  LEU    67       5.150   1.170  10.178    1.00  0.50
ATOM    442  C   LEU    67       6.111   1.263   9.005    1.00  0.50
ATOM    443  O   LEU    67       6.764   2.297   8.824    1.00  0.50
ATOM    451  N   ALA    68       6.191   0.215   8.178    1.00  0.50
ATOM    452  CA  ALA    68       5.485  -1.058   8.374    1.00  0.50
ATOM    453  C   ALA    68       6.080  -1.824   9.553    1.00  0.50
ATOM    454  O   ALA    68       7.262  -1.690   9.821    1.00  0.50
ATOM    458  N   ARG    72       5.242  -2.601  10.219    1.00  0.50
ATOM    459  CA  ARG    72       5.597  -3.223  11.494    1.00  0.50
ATOM    460  C   ARG    72       6.612  -4.330  11.318    1.00  0.50
ATOM    461  O   ARG    72       6.506  -5.175  10.425    1.00  0.50
TER
END
