
#######################################################
#                                                     #
#                        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 (  184),  selected   46 , name T0363AL044_3
# Molecule2: number of CA atoms   80 (  645),  selected   80 , name T0363.pdb
# PARAMETERS: T0363AL044_3.T0363.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L      10           -
LGA    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    -       -      I      13           -
LGA    -       -      N      14           -
LGA    I      13      I      15          0.533
LGA    N      14      E      16          2.035
LGA    I      15      I      17          2.189
LGA    E      16      A      18          2.672
LGA    I      17      Y      19          3.078
LGA    A      18      A      20          1.767
LGA    Y      19      F      21          3.268
LGA    A      20      P      22          3.418
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    F      21      Y      25          4.512
LGA    P      22      Y      26          2.925
LGA    E      23      L      27           -
LGA    Q      31      K      28           -
LGA    -       -      S      29           -
LGA    -       -      F      30           -
LGA    -       -      Q      31           -
LGA    -       -      V      32           -
LGA    -       -      D      33           -
LGA    -       -      E      34           -
LGA    V      32      G      35          1.670
LGA    D      33      I      36          0.515
LGA    V      38      T      37          0.705
LGA    Q      39      V      38          1.004
LGA    T      40      Q      39          1.106
LGA    A      41      T      40          0.694
LGA    I      42      A      41          0.824
LGA    T      43      I      42          1.126
LGA    Q      44      T      43          1.305
LGA    S      45      Q      44          1.886
LGA    G      46      S      45          2.023
LGA    I      47      G      46          1.513
LGA    L      48      I      47           #
LGA    S      49      L      48           -
LGA    Q      50      S      49           #
LGA    F      51      Q      50          4.202
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    P      52      L      56          2.715
LGA    -       -      S      57           -
LGA    E      53      T      58          4.423
LGA    L      56      N      59           #
LGA    T      58      -       -           -
LGA    K      60      K      60          4.804
LGA    I      61      I      61           -
LGA    G      62      -       -           -
LGA    I      63      G      62          4.226
LGA    R      66      I      63          4.793
LGA    P      67      -       -           -
LGA    T      71      -       -           -
LGA    D      72      -       -           -
LGA    V      73      -       -           -
LGA    L      74      -       -           -
LGA    D      78      F      64           #
LGA    R      79      S      65          5.016
LGA    I      80      R      66           -
LGA    E      81      P      67           -
LGA    -       -      I      68           -
LGA    -       -      K      69           -
LGA    -       -      L      70           -
LGA    -       -      T      71           -
LGA    -       -      D      72           -
LGA    -       -      V      73           -
LGA    -       -      L      74           -
LGA    -       -      K      75           -
LGA    -       -      E      76           -
LGA    -       -      G      77           -
LGA    -       -      D      78           -
LGA    -       -      R      79           -
LGA    -       -      I      80           -
LGA    -       -      E      81           -
LGA    -       -      I      82           -
LGA    -       -      Y      83           -
LGA    -       -      R      84           -
LGA    -       -      P      85           -
LGA    -       -      L      86           -
LGA    -       -      L      87           -
LGA    -       -      A      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   80    5.0     29    2.84    13.79     25.110     0.987

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.461080 * X  +  -0.881157 * Y  +  -0.104723 * Z  +  53.106831
  Y_new =   0.789971 * X  +   0.353855 * Y  +   0.500732 * Z  + -25.325657
  Z_new =  -0.404167 * X  +  -0.313606 * Y  +   0.859244 * Z  +  32.521828 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.349957    2.791636  [ DEG:   -20.0510    159.9490 ]
  Theta =   0.416068    2.725525  [ DEG:    23.8389    156.1611 ]
  Phi   =   1.042472   -2.099120  [ DEG:    59.7293   -120.2707 ]
 
# 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: T0363AL044_3                                  
REMARK     2: T0363.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL044_3.T0363.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   80   5.0   29   2.84   13.79  25.110
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL044_3
REMARK Aligment from pdb entry: 1vjk_A
ATOM      1  N   ILE    13      19.618  10.118   6.755  1.00  0.00              
ATOM      2  CA  ILE    13      19.812  11.549   6.964  1.00  0.00              
ATOM      3  C   ILE    13      19.828  12.260   5.627  1.00  0.00              
ATOM      4  O   ILE    13      20.199  11.674   4.582  1.00  0.00              
ATOM      5  N   ASN    14      19.429  13.515   5.623  1.00  0.00              
ATOM      6  CA  ASN    14      19.447  14.345   4.446  1.00  0.00              
ATOM      7  C   ASN    14      20.664  15.223   4.543  1.00  0.00              
ATOM      8  O   ASN    14      20.759  16.050   5.461  1.00  0.00              
ATOM      9  N   ILE    15      21.595  15.072   3.622  1.00  0.00              
ATOM     10  CA  ILE    15      22.804  15.879   3.587  1.00  0.00              
ATOM     11  C   ILE    15      22.646  17.008   2.600  1.00  0.00              
ATOM     12  O   ILE    15      22.282  16.755   1.450  1.00  0.00              
ATOM     13  N   GLU    16      22.883  18.248   3.049  1.00  0.00              
ATOM     14  CA  GLU    16      22.802  19.420   2.173  1.00  0.00              
ATOM     15  C   GLU    16      24.197  19.984   2.028  1.00  0.00              
ATOM     16  O   GLU    16      24.837  20.360   3.026  1.00  0.00              
ATOM     17  N   ILE    17      24.678  20.040   0.797  1.00  0.00              
ATOM     18  CA  ILE    17      25.990  20.618   0.499  1.00  0.00              
ATOM     19  C   ILE    17      25.850  22.061   0.111  1.00  0.00              
ATOM     20  O   ILE    17      24.867  22.455  -0.543  1.00  0.00              
ATOM     21  N   ALA    18      26.866  22.849   0.482  1.00  0.00              
ATOM     22  CA  ALA    18      26.869  24.271   0.200  1.00  0.00              
ATOM     23  C   ALA    18      28.098  24.708  -0.549  1.00  0.00              
ATOM     24  O   ALA    18      29.176  24.143  -0.385  1.00  0.00              
ATOM     25  N   TYR    19      27.931  25.761  -1.348  1.00  0.00              
ATOM     26  CA  TYR    19      29.046  26.427  -2.015  1.00  0.00              
ATOM     27  C   TYR    19      29.885  25.409  -2.804  1.00  0.00              
ATOM     28  O   TYR    19      29.312  24.608  -3.555  1.00  0.00              
ATOM     29  N   ALA    20      31.216  25.419  -2.657  1.00  0.00              
ATOM     30  CA  ALA    20      32.014  24.566  -3.560  1.00  0.00              
ATOM     31  C   ALA    20      31.791  23.091  -3.318  1.00  0.00              
ATOM     32  O   ALA    20      32.074  22.272  -4.189  1.00  0.00              
ATOM     33  N   PHE    21      31.250  22.738  -2.154  1.00  0.00              
ATOM     34  CA  PHE    21      31.013  21.318  -1.838  1.00  0.00              
ATOM     35  C   PHE    21      29.879  20.732  -2.646  1.00  0.00              
ATOM     36  O   PHE    21      29.797  19.509  -2.777  1.00  0.00              
ATOM     37  N   PRO    22      29.046  21.589  -3.231  1.00  0.00              
ATOM     38  CA  PRO    22      28.054  21.130  -4.208  1.00  0.00              
ATOM     39  C   PRO    22      28.746  20.565  -5.437  1.00  0.00              
ATOM     40  O   PRO    22      28.243  19.599  -6.031  1.00  0.00              
ATOM     41  N   GLU    23      29.865  21.169  -5.863  1.00  0.00              
ATOM     42  CA  GLU    23      30.610  20.616  -6.976  1.00  0.00              
ATOM     43  C   GLU    23      31.361  19.385  -6.617  1.00  0.00              
ATOM     44  O   GLU    23      31.428  18.474  -7.426  1.00  0.00              
ATOM     45  N   GLN    31      31.942  19.336  -5.414  1.00  0.00              
ATOM     46  CA  GLN    31      32.656  18.123  -5.012  1.00  0.00              
ATOM     47  C   GLN    31      31.722  16.924  -4.881  1.00  0.00              
ATOM     48  O   GLN    31      32.095  15.806  -5.231  1.00  0.00              
ATOM     49  N   VAL    32      22.948   3.350  15.167  1.00  0.00              
ATOM     50  CA  VAL    32      23.987   3.844  16.061  1.00  0.00              
ATOM     51  C   VAL    32      24.951   4.814  15.401  1.00  0.00              
ATOM     52  O   VAL    32      25.914   5.281  16.032  1.00  0.00              
ATOM     53  N   ASP    33      24.714   5.130  14.135  1.00  0.00              
ATOM     54  CA  ASP    33      25.627   6.007  13.425  1.00  0.00              
ATOM     55  C   ASP    33      25.796   7.331  14.107  1.00  0.00              
ATOM     56  O   ASP    33      24.834   7.925  14.622  1.00  0.00              
ATOM     57  N   VAL    38      27.040   7.804  14.065  1.00  0.00              
ATOM     58  CA  VAL    38      27.426   9.084  14.625  1.00  0.00              
ATOM     59  C   VAL    38      27.849  10.047  13.520  1.00  0.00              
ATOM     60  O   VAL    38      28.121   9.645  12.377  1.00  0.00              
ATOM     61  N   GLN    39      27.963  11.330  13.845  1.00  0.00              
ATOM     62  CA  GLN    39      28.460  12.316  12.885  1.00  0.00              
ATOM     63  C   GLN    39      29.769  11.860  12.212  1.00  0.00              
ATOM     64  O   GLN    39      29.919  11.957  10.974  1.00  0.00              
ATOM     65  N   THR    40      30.715  11.324  12.996  1.00  0.00              
ATOM     66  CA  THR    40      31.973  10.887  12.386  1.00  0.00              
ATOM     67  C   THR    40      31.763   9.783  11.318  1.00  0.00              
ATOM     68  O   THR    40      32.511   9.722  10.328  1.00  0.00              
ATOM     69  N   ALA    41      30.760   8.922  11.523  1.00  0.00              
ATOM     70  CA  ALA    41      30.482   7.846  10.545  1.00  0.00              
ATOM     71  C   ALA    41      29.918   8.437   9.288  1.00  0.00              
ATOM     72  O   ALA    41      30.252   7.979   8.187  1.00  0.00              
ATOM     73  N   ILE    42      29.087   9.456   9.426  1.00  0.00              
ATOM     74  CA  ILE    42      28.555  10.143   8.249  1.00  0.00              
ATOM     75  C   ILE    42      29.668  10.825   7.446  1.00  0.00              
ATOM     76  O   ILE    42      29.692  10.714   6.206  1.00  0.00              
ATOM     77  N   THR    43      30.609  11.473   8.133  1.00  0.00              
ATOM     78  CA  THR    43      31.734  12.096   7.446  1.00  0.00              
ATOM     79  C   THR    43      32.519  11.045   6.665  1.00  0.00              
ATOM     80  O   THR    43      32.891  11.269   5.485  1.00  0.00              
ATOM     81  N   GLN    44      32.778   9.879   7.283  1.00  0.00              
ATOM     82  CA  GLN    44      33.466   8.820   6.534  1.00  0.00              
ATOM     83  C   GLN    44      32.702   8.335   5.325  1.00  0.00              
ATOM     84  O   GLN    44      33.322   8.019   4.286  1.00  0.00              
ATOM     85  N   SER    45      31.383   8.272   5.426  1.00  0.00              
ATOM     86  CA  SER    45      30.578   7.842   4.299  1.00  0.00              
ATOM     87  C   SER    45      30.583   8.890   3.185  1.00  0.00              
ATOM     88  O   SER    45      30.618   8.513   2.008  1.00  0.00              
ATOM     89  N   GLY    46      30.567  10.193   3.526  1.00  0.00              
ATOM     90  CA  GLY    46      30.662  11.235   2.496  1.00  0.00              
ATOM     91  C   GLY    46      31.969  11.077   1.716  1.00  0.00              
ATOM     92  O   GLY    46      31.965  11.122   0.467  1.00  0.00              
ATOM     93  N   ILE    47      33.056  10.844   2.444  1.00  0.00              
ATOM     94  CA  ILE    47      34.369  10.638   1.823  1.00  0.00              
ATOM     95  C   ILE    47      34.412   9.378   0.945  1.00  0.00              
ATOM     96  O   ILE    47      35.089   9.371  -0.109  1.00  0.00              
ATOM     97  N   LEU    48      33.698   8.334   1.356  1.00  0.00              
ATOM     98  CA  LEU    48      33.637   7.101   0.589  1.00  0.00              
ATOM     99  C   LEU    48      32.851   7.297  -0.703  1.00  0.00              
ATOM    100  O   LEU    48      33.216   6.739  -1.749  1.00  0.00              
ATOM    101  N   SER    49      31.762   8.062  -0.653  1.00  0.00              
ATOM    102  CA  SER    49      30.944   8.282  -1.833  1.00  0.00              
ATOM    103  C   SER    49      31.580   9.264  -2.805  1.00  0.00              
ATOM    104  O   SER    49      31.359   9.201  -4.013  1.00  0.00              
ATOM    105  N   GLN    50      32.303  10.225  -2.249  1.00  0.00              
ATOM    106  CA  GLN    50      32.813  11.351  -3.022  1.00  0.00              
ATOM    107  C   GLN    50      34.261  11.567  -2.666  1.00  0.00              
ATOM    108  O   GLN    50      34.586  12.345  -1.734  1.00  0.00              
ATOM    109  N   PHE    51      35.140  10.906  -3.418  1.00  0.00              
ATOM    110  CA  PHE    51      36.556  10.839  -3.048  1.00  0.00              
ATOM    111  C   PHE    51      37.240  12.195  -2.947  1.00  0.00              
ATOM    112  O   PHE    51      38.238  12.314  -2.243  1.00  0.00              
ATOM    113  N   PRO    52      36.060  19.979  10.317  1.00  0.00              
ATOM    114  CA  PRO    52      36.177  20.444  11.678  1.00  0.00              
ATOM    115  C   PRO    52      35.160  19.774  12.575  1.00  0.00              
ATOM    116  O   PRO    52      34.141  19.200  12.135  1.00  0.00              
ATOM    117  N   GLU    53      35.450  19.843  13.866  1.00  0.00              
ATOM    118  CA  GLU    53      34.515  19.391  14.870  1.00  0.00              
ATOM    119  C   GLU    53      33.854  20.617  15.461  1.00  0.00              
ATOM    120  O   GLU    53      34.549  21.503  16.014  1.00  0.00              
ATOM    121  N   LEU    56      32.533  20.682  15.358  1.00  0.00              
ATOM    122  CA  LEU    56      31.789  21.881  15.702  1.00  0.00              
ATOM    123  C   LEU    56      32.203  23.041  14.822  1.00  0.00              
ATOM    124  O   LEU    56      32.593  22.864  13.651  1.00  0.00              
ATOM    125  N   THR    58      32.155  24.244  15.375  1.00  0.00              
ATOM    126  CA  THR    58      32.631  25.398  14.657  1.00  0.00              
ATOM    127  C   THR    58      34.164  25.410  14.642  1.00  0.00              
ATOM    128  O   THR    58      34.811  25.291  15.696  1.00  0.00              
ATOM    129  N   LYS    60      34.735  25.552  13.448  1.00  0.00              
ATOM    130  CA  LYS    60      36.176  25.613  13.276  1.00  0.00              
ATOM    131  C   LYS    60      36.526  26.352  12.000  1.00  0.00              
ATOM    132  O   LYS    60      36.336  25.841  10.909  1.00  0.00              
ATOM    133  N   ILE    61      37.055  27.568  12.138  1.00  0.00              
ATOM    134  CA  ILE    61      37.340  28.405  10.966  1.00  0.00              
ATOM    135  C   ILE    61      38.570  27.940  10.193  1.00  0.00              
ATOM    136  O   ILE    61      38.757  28.321   9.030  1.00  0.00              
ATOM    137  N   GLY    62      39.394  27.099  10.816  1.00  0.00              
ATOM    138  CA  GLY    62      40.637  26.643  10.173  1.00  0.00              
ATOM    139  C   GLY    62      40.445  25.394   9.303  1.00  0.00              
ATOM    140  O   GLY    62      41.310  25.052   8.493  1.00  0.00              
ATOM    141  N   ILE    63      20.659  22.419  12.113  1.00  0.00              
ATOM    142  CA  ILE    63      20.997  23.799  12.387  1.00  0.00              
ATOM    143  C   ILE    63      21.913  24.010  13.566  1.00  0.00              
ATOM    144  O   ILE    63      22.108  25.163  13.949  1.00  0.00              
ATOM    145  N   ARG    66      22.479  22.942  14.138  1.00  0.00              
ATOM    146  CA  ARG    66      23.307  23.066  15.345  1.00  0.00              
ATOM    147  C   ARG    66      24.695  22.483  15.166  1.00  0.00              
ATOM    148  O   ARG    66      24.846  21.429  14.540  1.00  0.00              
ATOM    149  N   PRO    67      25.716  23.143  15.687  1.00  0.00              
ATOM    150  CA  PRO    67      27.039  22.549  15.745  1.00  0.00              
ATOM    151  C   PRO    67      27.016  21.468  16.815  1.00  0.00              
ATOM    152  O   PRO    67      26.431  21.651  17.917  1.00  0.00              
ATOM    153  N   THR    71      27.638  20.341  16.489  1.00  0.00              
ATOM    154  CA  THR    71      27.658  19.185  17.385  1.00  0.00              
ATOM    155  C   THR    71      29.022  18.503  17.354  1.00  0.00              
ATOM    156  O   THR    71      29.879  18.808  16.510  1.00  0.00              
ATOM    157  N   ASP    72      29.212  17.558  18.279  1.00  0.00              
ATOM    158  CA  ASP    72      30.453  16.812  18.329  1.00  0.00              
ATOM    159  C   ASP    72      30.481  15.705  17.261  1.00  0.00              
ATOM    160  O   ASP    72      29.437  15.324  16.697  1.00  0.00              
ATOM    161  N   VAL    73      28.269  12.740  18.198  1.00  0.00              
ATOM    162  CA  VAL    73      26.828  12.946  18.288  1.00  0.00              
ATOM    163  C   VAL    73      26.113  11.862  17.495  1.00  0.00              
ATOM    164  O   VAL    73      26.456  11.616  16.325  1.00  0.00              
ATOM    165  N   LEU    74      15.928  11.032   9.873  1.00  0.00              
ATOM    166  CA  LEU    74      15.354  12.280   9.430  1.00  0.00              
ATOM    167  C   LEU    74      16.215  13.514   9.709  1.00  0.00              
ATOM    168  O   LEU    74      15.874  14.603   9.270  1.00  0.00              
ATOM    169  N   ASP    78      17.348  13.353  10.395  1.00  0.00              
ATOM    170  CA  ASP    78      18.200  14.519  10.660  1.00  0.00              
ATOM    171  C   ASP    78      18.661  15.148   9.355  1.00  0.00              
ATOM    172  O   ASP    78      18.898  14.433   8.355  1.00  0.00              
ATOM    173  N   ARG    79      18.832  16.460   9.366  1.00  0.00              
ATOM    174  CA  ARG    79      19.335  17.205   8.216  1.00  0.00              
ATOM    175  C   ARG    79      20.730  17.704   8.541  1.00  0.00              
ATOM    176  O   ARG    79      20.932  18.402   9.532  1.00  0.00              
ATOM    177  N   ILE    80      21.713  17.334   7.733  1.00  0.00              
ATOM    178  CA  ILE    80      23.096  17.679   8.009  1.00  0.00              
ATOM    179  C   ILE    80      23.638  18.588   6.932  1.00  0.00              
ATOM    180  O   ILE    80      23.697  18.186   5.760  1.00  0.00              
ATOM    181  N   GLU    81      24.035  19.807   7.290  1.00  0.00              
ATOM    182  CA  GLU    81      24.641  20.720   6.344  1.00  0.00              
ATOM    183  C   GLU    81      26.145  20.493   6.310  1.00  0.00              
ATOM    184  O   GLU    81      26.772  20.182   7.335  1.00  0.00              
END
