
#######################################################
#                                                     #
#                        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   52 (  208),  selected   52 , name T0309AL243_1
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309AL243_1.T0309.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    I       9      A       2           -
LGA    N      10      S       3           -
LGA    V      11      K       4           -
LGA    K      12      K       5           -
LGA    G      13      V       6           -
LGA    F      14      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      V      11           -
LGA    -       -      K      12           -
LGA    -       -      G      13           -
LGA    F      15      F      14           #
LGA    D      16      F      15          1.752
LGA    V      19      D      16           #
LGA    -       -      M      17           -
LGA    -       -      D      18           -
LGA    -       -      V      19           -
LGA    -       -      M      20           -
LGA    -       -      E      21           -
LGA    -       -      V      22           -
LGA    M      20      T      23          1.703
LGA    E      21      E      24          4.849
LGA    V      22      Q      25           -
LGA    T      23      T      26           -
LGA    E      24      K      27           -
LGA    Q      25      E      28           -
LGA    T      26      A      29           -
LGA    K      27      E      30           -
LGA    E      28      Y      31           -
LGA    A      29      T      32           -
LGA    E      30      -       -           -
LGA    Y      31      -       -           -
LGA    T      32      -       -           -
LGA    Y      33      Y      33          2.362
LGA    D      34      D      34          1.691
LGA    F      35      F      35          1.253
LGA    K      36      K      36          1.139
LGA    E      37      E      37          0.751
LGA    I      38      I      38          0.459
LGA    L      39      L      39          1.319
LGA    S      40      S      40          3.921
LGA    E      41      E      41           -
LGA    -       -      F      42           -
LGA    -       -      N      43           -
LGA    -       -      G      44           -
LGA    -       -      K      45           -
LGA    G      44      N      46          5.851
LGA    K      45      V      47          4.025
LGA    N      46      S      48          2.552
LGA    V      47      I      49          3.143
LGA    S      48      T      50          3.652
LGA    I      49      V      51          3.721
LGA    T      50      K      52          2.534
LGA    V      51      E      53          2.653
LGA    K      52      E      54          1.478
LGA    E      53      N      55          4.647
LGA    E      54      E      56           -
LGA    P      58      L      57           -
LGA    V      59      P      58           -
LGA    K      60      V      59           -
LGA    G      61      K      60           -
LGA    V      62      G      61           -
LGA    E      63      V      62           -
LGA    M      64      E      63           -
LGA    A      65      -       -           -
LGA    G      66      -       -           -
LGA    D      67      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   52   62    5.0     21    3.01    42.86     22.211     0.676

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.799427 * X  +  -0.440336 * Y  +   0.408680 * Z  +   1.874722
  Y_new =  -0.463852 * X  +  -0.884723 * Y  +  -0.045904 * Z  + -14.906118
  Z_new =   0.381782 * X  +  -0.152870 * Y  +  -0.911522 * Z  +  -2.850484 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.975430    0.166162  [ DEG:  -170.4796      9.5204 ]
  Theta =  -0.391724   -2.749869  [ DEG:   -22.4441   -157.5559 ]
  Phi   =  -0.525756    2.615837  [ DEG:   -30.1236    149.8764 ]
 
# 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: T0309AL243_1                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309AL243_1.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   52   62   5.0   21   3.01   42.86  22.211
REMARK  ---------------------------------------------------------- 
MOLECULE T0309AL243_1
REMARK Aligment from pdb entry: 1sljA
ATOM      1  N   ILE     9       4.613 -10.804   2.432  1.00  0.00              
ATOM      2  CA  ILE     9       4.003 -11.814   3.285  1.00  0.00              
ATOM      3  C   ILE     9       4.892 -12.082   4.487  1.00  0.00              
ATOM      4  O   ILE     9       6.112 -12.244   4.353  1.00  0.00              
ATOM      5  N   ASN    10       4.286 -12.114   5.656  1.00  0.00              
ATOM      6  CA  ASN    10       5.028 -12.311   6.886  1.00  0.00              
ATOM      7  C   ASN    10       4.855 -13.733   7.397  1.00  0.00              
ATOM      8  O   ASN    10       3.833 -14.077   7.988  1.00  0.00              
ATOM      9  N   VAL    11       5.847 -14.564   7.126  1.00  0.00              
ATOM     10  CA  VAL    11       5.866 -15.925   7.633  1.00  0.00              
ATOM     11  C   VAL    11       7.187 -16.176   8.358  1.00  0.00              
ATOM     12  O   VAL    11       7.995 -17.007   7.948  1.00  0.00              
ATOM     13  N   LYS    12      10.532 -10.733   4.516  1.00  0.00              
ATOM     14  CA  LYS    12       9.162 -10.837   3.997  1.00  0.00              
ATOM     15  C   LYS    12       9.132 -11.400   2.581  1.00  0.00              
ATOM     16  O   LYS    12       9.989 -11.104   1.754  1.00  0.00              
ATOM     17  N   GLY    13       8.138 -12.230   2.321  1.00  0.00              
ATOM     18  CA  GLY    13       7.969 -12.783   0.997  1.00  0.00              
ATOM     19  C   GLY    13       7.228 -11.825   0.096  1.00  0.00              
ATOM     20  O   GLY    13       6.151 -11.367   0.440  1.00  0.00              
ATOM     21  N   PHE    14       7.796 -11.518  -1.046  1.00  0.00              
ATOM     22  CA  PHE    14       7.218 -10.528  -1.930  1.00  0.00              
ATOM     23  C   PHE    14       6.594 -11.190  -3.157  1.00  0.00              
ATOM     24  O   PHE    14       7.289 -11.763  -4.002  1.00  0.00              
ATOM     25  N   PHE    15       5.274 -11.125  -3.221  1.00  0.00              
ATOM     26  CA  PHE    15       4.506 -11.704  -4.315  1.00  0.00              
ATOM     27  C   PHE    15       3.958 -10.607  -5.236  1.00  0.00              
ATOM     28  O   PHE    15       3.096  -9.829  -4.832  1.00  0.00              
ATOM     29  N   ASP    16       4.467 -10.524  -6.476  1.00  0.00              
ATOM     30  CA  ASP    16       3.960  -9.588  -7.494  1.00  0.00              
ATOM     31  C   ASP    16       2.559  -9.972  -7.978  1.00  0.00              
ATOM     32  O   ASP    16       2.212 -11.147  -8.085  1.00  0.00              
ATOM     33  N   VAL    19       1.768  -8.944  -8.267  1.00  0.00              
ATOM     34  CA  VAL    19       0.371  -9.089  -8.664  1.00  0.00              
ATOM     35  C   VAL    19       0.188  -9.971  -9.894  1.00  0.00              
ATOM     36  O   VAL    19      -0.759 -10.752  -9.955  1.00  0.00              
ATOM     37  N   MET    20       1.070  -9.848 -10.873  1.00  0.00              
ATOM     38  CA  MET    20       0.903 -10.587 -12.119  1.00  0.00              
ATOM     39  C   MET    20       1.075 -12.091 -11.897  1.00  0.00              
ATOM     40  O   MET    20       0.788 -12.892 -12.784  1.00  0.00              
ATOM     41  N   GLU    21       1.533 -12.468 -10.711  1.00  0.00              
ATOM     42  CA  GLU    21       1.707 -13.870 -10.372  1.00  0.00              
ATOM     43  C   GLU    21       0.449 -14.402  -9.681  1.00  0.00              
ATOM     44  O   GLU    21       0.178 -15.602  -9.707  1.00  0.00              
ATOM     45  N   VAL    22      -0.333 -13.479  -9.112  1.00  0.00              
ATOM     46  CA  VAL    22      -1.440 -13.804  -8.203  1.00  0.00              
ATOM     47  C   VAL    22      -2.379 -14.893  -8.735  1.00  0.00              
ATOM     48  O   VAL    22      -2.794 -14.880  -9.896  1.00  0.00              
ATOM     49  N   THR    23      -2.707 -15.830  -7.844  1.00  0.00              
ATOM     50  CA  THR    23      -3.609 -16.931  -8.150  1.00  0.00              
ATOM     51  C   THR    23      -5.042 -16.586  -7.756  1.00  0.00              
ATOM     52  O   THR    23      -5.277 -15.752  -6.882  1.00  0.00              
ATOM     53  N   GLU    24      -5.986 -17.262  -8.408  1.00  0.00              
ATOM     54  CA  GLU    24      -7.423 -17.102  -8.148  1.00  0.00              
ATOM     55  C   GLU    24      -7.779 -17.372  -6.680  1.00  0.00              
ATOM     56  O   GLU    24      -8.863 -17.023  -6.234  1.00  0.00              
ATOM     57  N   GLN    25      -6.888 -18.025  -5.934  1.00  0.00              
ATOM     58  CA  GLN    25      -7.141 -18.261  -4.513  1.00  0.00              
ATOM     59  C   GLN    25      -7.185 -16.945  -3.739  1.00  0.00              
ATOM     60  O   GLN    25      -7.809 -16.854  -2.684  1.00  0.00              
ATOM     61  N   THR    26      -6.526 -15.931  -4.279  1.00  0.00              
ATOM     62  CA  THR    26      -6.370 -14.665  -3.578  1.00  0.00              
ATOM     63  C   THR    26      -7.612 -13.809  -3.760  1.00  0.00              
ATOM     64  O   THR    26      -8.187 -13.298  -2.800  1.00  0.00              
ATOM     65  N   LYS    27      -8.016 -13.660  -5.006  1.00  0.00              
ATOM     66  CA  LYS    27      -9.294 -13.063  -5.321  1.00  0.00              
ATOM     67  C   LYS    27     -10.265 -14.197  -5.564  1.00  0.00              
ATOM     68  O   LYS    27     -10.274 -14.800  -6.637  1.00  0.00              
ATOM     69  N   GLU    28     -11.094 -14.479  -4.545  1.00  0.00              
ATOM     70  CA  GLU    28     -11.834 -15.733  -4.391  1.00  0.00              
ATOM     71  C   GLU    28     -12.386 -16.287  -5.688  1.00  0.00              
ATOM     72  O   GLU    28     -12.840 -15.552  -6.554  1.00  0.00              
ATOM     73  N   ALA    29     -12.329 -17.602  -5.797  1.00  0.00              
ATOM     74  CA  ALA    29     -12.869 -18.331  -6.939  1.00  0.00              
ATOM     75  C   ALA    29     -14.334 -17.976  -7.237  1.00  0.00              
ATOM     76  O   ALA    29     -14.850 -18.312  -8.298  1.00  0.00              
ATOM     77  N   GLU    30     -15.003 -17.308  -6.299  1.00  0.00              
ATOM     78  CA  GLU    30     -16.381 -16.854  -6.513  1.00  0.00              
ATOM     79  C   GLU    30     -16.395 -15.490  -7.208  1.00  0.00              
ATOM     80  O   GLU    30     -17.437 -15.014  -7.662  1.00  0.00              
ATOM     81  N   TYR    31     -15.229 -14.873  -7.281  1.00  0.00              
ATOM     82  CA  TYR    31     -15.072 -13.555  -7.876  1.00  0.00              
ATOM     83  C   TYR    31     -14.760 -13.698  -9.361  1.00  0.00              
ATOM     84  O   TYR    31     -14.003 -14.585  -9.754  1.00  0.00              
ATOM     85  N   THR    32     -15.353 -12.838 -10.175  1.00  0.00              
ATOM     86  CA  THR    32     -15.171 -12.890 -11.619  1.00  0.00              
ATOM     87  C   THR    32     -13.725 -12.576 -12.006  1.00  0.00              
ATOM     88  O   THR    32     -13.181 -11.538 -11.624  1.00  0.00              
ATOM     89  N   TYR    33      -5.765 -10.026 -12.422  1.00  0.00              
ATOM     90  CA  TYR    33      -6.310  -9.438 -11.192  1.00  0.00              
ATOM     91  C   TYR    33      -5.647  -8.098 -10.831  1.00  0.00              
ATOM     92  O   TYR    33      -4.610  -7.737 -11.388  1.00  0.00              
ATOM     93  N   ASP    34      -6.262  -7.362  -9.906  1.00  0.00              
ATOM     94  CA  ASP    34      -5.688  -6.115  -9.396  1.00  0.00              
ATOM     95  C   ASP    34      -5.422  -6.225  -7.892  1.00  0.00              
ATOM     96  O   ASP    34      -6.345  -6.195  -7.085  1.00  0.00              
ATOM     97  N   PHE    35      -4.143  -6.330  -7.529  1.00  0.00              
ATOM     98  CA  PHE    35      -3.731  -6.757  -6.183  1.00  0.00              
ATOM     99  C   PHE    35      -4.309  -5.883  -5.076  1.00  0.00              
ATOM    100  O   PHE    35      -4.690  -6.389  -4.020  1.00  0.00              
ATOM    101  N   LYS    36      -4.388  -4.586  -5.334  1.00  0.00              
ATOM    102  CA  LYS    36      -4.940  -3.634  -4.377  1.00  0.00              
ATOM    103  C   LYS    36      -6.368  -3.989  -3.935  1.00  0.00              
ATOM    104  O   LYS    36      -6.791  -3.610  -2.844  1.00  0.00              
ATOM    105  N   GLU    37      -7.096  -4.727  -4.769  1.00  0.00              
ATOM    106  CA  GLU    37      -8.447  -5.164  -4.419  1.00  0.00              
ATOM    107  C   GLU    37      -8.559  -6.686  -4.544  1.00  0.00              
ATOM    108  O   GLU    37      -9.647  -7.250  -4.664  1.00  0.00              
ATOM    109  N   ILE    38      -7.414  -7.349  -4.501  1.00  0.00              
ATOM    110  CA  ILE    38      -7.359  -8.801  -4.596  1.00  0.00              
ATOM    111  C   ILE    38      -6.790  -9.382  -3.314  1.00  0.00              
ATOM    112  O   ILE    38      -7.353 -10.298  -2.723  1.00  0.00              
ATOM    113  N   LEU    39      -5.678  -8.824  -2.878  1.00  0.00              
ATOM    114  CA  LEU    39      -5.071  -9.241  -1.638  1.00  0.00              
ATOM    115  C   LEU    39      -5.363  -8.223  -0.557  1.00  0.00              
ATOM    116  O   LEU    39      -5.564  -7.040  -0.835  1.00  0.00              
ATOM    117  N   SER    40      -5.409  -8.695   0.669  1.00  0.00              
ATOM    118  CA  SER    40      -5.595  -7.835   1.818  1.00  0.00              
ATOM    119  C   SER    40      -4.838  -8.400   3.007  1.00  0.00              
ATOM    120  O   SER    40      -4.802  -9.612   3.208  1.00  0.00              
ATOM    121  N   GLU    41      -4.200  -7.510   3.754  1.00  0.00              
ATOM    122  CA  GLU    41      -3.410  -7.877   4.920  1.00  0.00              
ATOM    123  C   GLU    41      -4.235  -8.705   5.891  1.00  0.00              
ATOM    124  O   GLU    41      -5.280  -8.269   6.368  1.00  0.00              
ATOM    125  N   GLY    44      -3.758  -9.905   6.167  1.00  0.00              
ATOM    126  CA  GLY    44      -4.514 -10.844   6.963  1.00  0.00              
ATOM    127  C   GLY    44      -4.992 -12.020   6.141  1.00  0.00              
ATOM    128  O   GLY    44      -5.530 -12.986   6.682  1.00  0.00              
ATOM    129  N   LYS    45      -4.803 -11.941   4.830  1.00  0.00              
ATOM    130  CA  LYS    45      -5.099 -13.063   3.951  1.00  0.00              
ATOM    131  C   LYS    45      -3.862 -13.934   3.792  1.00  0.00              
ATOM    132  O   LYS    45      -2.784 -13.430   3.489  1.00  0.00              
ATOM    133  N   ASN    46      -4.022 -15.229   4.006  1.00  0.00              
ATOM    134  CA  ASN    46      -2.914 -16.168   3.893  1.00  0.00              
ATOM    135  C   ASN    46      -2.724 -16.614   2.454  1.00  0.00              
ATOM    136  O   ASN    46      -3.654 -16.566   1.646  1.00  0.00              
ATOM    137  N   VAL    47      -1.520 -17.060   2.152  1.00  0.00              
ATOM    138  CA  VAL    47      -1.209 -17.600   0.844  1.00  0.00              
ATOM    139  C   VAL    47      -0.317 -18.827   0.974  1.00  0.00              
ATOM    140  O   VAL    47       0.376 -18.995   1.982  1.00  0.00              
ATOM    141  N   SER    48      -0.354 -19.687  -0.031  1.00  0.00              
ATOM    142  CA  SER    48       0.563 -20.810  -0.112  1.00  0.00              
ATOM    143  C   SER    48       1.640 -20.465  -1.128  1.00  0.00              
ATOM    144  O   SER    48       1.367 -20.404  -2.322  1.00  0.00              
ATOM    145  N   ILE    49       2.859 -20.249  -0.663  1.00  0.00              
ATOM    146  CA  ILE    49       3.915 -19.713  -1.516  1.00  0.00              
ATOM    147  C   ILE    49       5.279 -20.246  -1.136  1.00  0.00              
ATOM    148  O   ILE    49       5.548 -20.516   0.025  1.00  0.00              
ATOM    149  N   THR    50       6.136 -20.396  -2.125  1.00  0.00              
ATOM    150  CA  THR    50       7.514 -20.768  -1.882  1.00  0.00              
ATOM    151  C   THR    50       8.419 -19.778  -2.596  1.00  0.00              
ATOM    152  O   THR    50       7.987 -19.090  -3.526  1.00  0.00              
ATOM    153  N   VAL    51       9.659 -19.689  -2.151  1.00  0.00              
ATOM    154  CA  VAL    51      10.586 -18.695  -2.667  1.00  0.00              
ATOM    155  C   VAL    51      11.255 -19.164  -3.945  1.00  0.00              
ATOM    156  O   VAL    51      12.073 -20.086  -3.941  1.00  0.00              
ATOM    157  N   LYS    52      10.869 -18.524  -5.041  1.00  0.00              
ATOM    158  CA  LYS    52      11.407 -18.831  -6.358  1.00  0.00              
ATOM    159  C   LYS    52      12.698 -18.054  -6.572  1.00  0.00              
ATOM    160  O   LYS    52      13.679 -18.575  -7.108  1.00  0.00              
ATOM    161  N   GLU    53      12.692 -16.798  -6.132  1.00  0.00              
ATOM    162  CA  GLU    53      13.878 -15.962  -6.210  1.00  0.00              
ATOM    163  C   GLU    53      14.398 -15.698  -4.805  1.00  0.00              
ATOM    164  O   GLU    53      13.663 -15.212  -3.947  1.00  0.00              
ATOM    165  N   GLU    54      15.664 -15.998  -4.591  1.00  0.00              
ATOM    166  CA  GLU    54      16.249 -15.987  -3.274  1.00  0.00              
ATOM    167  C   GLU    54      16.722 -14.601  -2.906  1.00  0.00              
ATOM    168  O   GLU    54      16.965 -13.760  -3.776  1.00  0.00              
ATOM    169  N   PRO    58      16.857 -14.368  -1.613  1.00  0.00              
ATOM    170  CA  PRO    58      17.356 -13.104  -1.141  1.00  0.00              
ATOM    171  C   PRO    58      18.811 -12.935  -1.539  1.00  0.00              
ATOM    172  O   PRO    58      19.640 -13.826  -1.352  1.00  0.00              
ATOM    173  N   VAL    59      19.094 -11.785  -2.103  1.00  0.00              
ATOM    174  CA  VAL    59      20.409 -11.461  -2.605  1.00  0.00              
ATOM    175  C   VAL    59      20.678  -9.986  -2.358  1.00  0.00              
ATOM    176  O   VAL    59      21.627  -9.409  -2.886  1.00  0.00              
ATOM    177  N   LYS    60      16.288  -8.458  -4.422  1.00  0.00              
ATOM    178  CA  LYS    60      14.972  -8.896  -4.861  1.00  0.00              
ATOM    179  C   LYS    60      14.185  -9.416  -3.688  1.00  0.00              
ATOM    180  O   LYS    60      12.986  -9.174  -3.565  1.00  0.00              
ATOM    181  N   GLY    61      14.878 -10.109  -2.821  1.00  0.00              
ATOM    182  CA  GLY    61      14.302 -10.462  -1.562  1.00  0.00              
ATOM    183  C   GLY    61      13.791 -11.870  -1.562  1.00  0.00              
ATOM    184  O   GLY    61      14.208 -12.697  -2.373  1.00  0.00              
ATOM    185  N   VAL    62      12.896 -12.142  -0.648  1.00  0.00              
ATOM    186  CA  VAL    62      12.219 -13.419  -0.607  1.00  0.00              
ATOM    187  C   VAL    62      11.039 -13.378  -1.570  1.00  0.00              
ATOM    188  O   VAL    62       9.943 -12.990  -1.197  1.00  0.00              
ATOM    189  N   GLU    63      11.268 -13.762  -2.820  1.00  0.00              
ATOM    190  CA  GLU    63      10.236 -13.650  -3.844  1.00  0.00              
ATOM    191  C   GLU    63       9.317 -14.861  -3.851  1.00  0.00              
ATOM    192  O   GLU    63       9.769 -16.001  -3.985  1.00  0.00              
ATOM    193  N   MET    64       8.024 -14.603  -3.750  1.00  0.00              
ATOM    194  CA  MET    64       7.039 -15.668  -3.679  1.00  0.00              
ATOM    195  C   MET    64       6.565 -16.045  -5.072  1.00  0.00              
ATOM    196  O   MET    64       6.299 -15.178  -5.905  1.00  0.00              
ATOM    197  N   ALA    65      -5.621 -21.206  -6.220  1.00  0.00              
ATOM    198  CA  ALA    65      -6.754 -20.928  -7.088  1.00  0.00              
ATOM    199  C   ALA    65      -7.717 -22.101  -7.071  1.00  0.00              
ATOM    200  O   ALA    65      -7.710 -22.948  -7.965  1.00  0.00              
ATOM    201  N   GLY    66      -8.537 -22.152  -6.030  1.00  0.00              
ATOM    202  CA  GLY    66      -9.464 -23.248  -5.863  1.00  0.00              
ATOM    203  C   GLY    66     -10.683 -23.133  -6.753  1.00  0.00              
ATOM    204  O   GLY    66     -11.816 -23.269  -6.289  1.00  0.00              
ATOM    205  N   ASP    67     -10.451 -22.888  -8.029  1.00  0.00              
ATOM    206  CA  ASP    67     -11.517 -22.820  -9.007  1.00  0.00              
ATOM    207  C   ASP    67     -11.407 -24.005  -9.963  1.00  0.00              
ATOM    208  O   ASP    67     -10.725 -23.878 -11.000  1.00  0.00              
END
