
#######################################################
#                                                     #
#                        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 T0363AL257_2-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL257_2-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           -
LGA    Q      12      I      13          3.014
LGA    I      13      N      14          1.956
LGA    N      14      I      15          2.866
LGA    I      15      E      16          1.062
LGA    E      16      I      17          4.427
LGA    I      17      A      18          1.919
LGA    A      18      -       -           -
LGA    Y      19      -       -           -
LGA    A      20      Y      19           #
LGA    F      21      A      20          2.871
LGA    P      22      F      21          4.598
LGA    E      23      P      22          3.595
LGA    -       -      E      23           -
LGA    R      24      R      24          5.083
LGA    Y      25      Y      25          4.801
LGA    Y      26      Y      26          3.719
LGA    L      27      L      27          3.537
LGA    K      28      -       -           -
LGA    S      29      -       -           -
LGA    F      30      K      28          2.537
LGA    Q      31      S      29          1.795
LGA    V      32      F      30          0.977
LGA    D      33      Q      31          1.202
LGA    E      34      V      32          3.018
LGA    -       -      D      33           -
LGA    -       -      E      34           -
LGA    G      35      G      35           #
LGA    I      36      I      36          1.918
LGA    T      37      T      37          0.694
LGA    V      38      V      38          0.567
LGA    Q      39      Q      39          0.449
LGA    T      40      T      40          0.472
LGA    A      41      A      41          0.255
LGA    I      42      I      42          0.491
LGA    T      43      T      43          0.353
LGA    Q      44      Q      44          1.066
LGA    I      47      S      45          1.478
LGA    L      48      G      46          2.640
LGA    S      49      -       -           -
LGA    Q      50      I      47           #
LGA    F      51      L      48           #
LGA    P      52      S      49          3.812
LGA    E      53      Q      50          2.247
LGA    I      54      -       -           -
LGA    D      55      -       -           -
LGA    L      56      F      51          1.475
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)   43   46    5.0     32    2.63    40.62     48.101     1.171

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.622770 * X  +   0.767926 * Y  +   0.149826 * Z  +  12.939671
  Y_new =  -0.317608 * X  +  -0.423134 * Y  +   0.848577 * Z  +  34.119659
  Z_new =   0.715041 * X  +   0.480882 * Y  +   0.507414 * Z  + -20.150961 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.758558   -2.383034  [ DEG:    43.4622   -136.5378 ]
  Theta =  -0.796682   -2.344910  [ DEG:   -45.6465   -134.3535 ]
  Phi   =  -2.669983    0.471609  [ DEG:  -152.9788     27.0212 ]
 
# 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: T0363AL257_2-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL257_2-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   32   2.63   40.62  48.101
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL257_2-D1
REMARK Aligment from pdb entry: 1fm0_D
ATOM      1  N   GLN    12      15.025   6.674   6.105  1.00  0.00              
ATOM      2  CA  GLN    12      16.400   7.077   5.685  1.00  0.00              
ATOM      3  C   GLN    12      16.863   8.276   6.491  1.00  0.00              
ATOM      4  O   GLN    12      16.084   8.827   7.268  1.00  0.00              
ATOM      5  N   ILE    13      18.150   8.612   6.367  1.00  0.00              
ATOM      6  CA  ILE    13      18.652   9.908   6.851  1.00  0.00              
ATOM      7  C   ILE    13      18.885  10.972   5.724  1.00  0.00              
ATOM      8  O   ILE    13      19.555  10.686   4.721  1.00  0.00              
ATOM      9  N   ASN    14      18.299  12.186   5.912  1.00  0.00              
ATOM     10  CA  ASN    14      18.408  13.329   4.959  1.00  0.00              
ATOM     11  C   ASN    14      19.607  14.197   5.363  1.00  0.00              
ATOM     12  O   ASN    14      19.715  14.571   6.540  1.00  0.00              
ATOM     13  N   ILE    15      20.487  14.488   4.401  1.00  0.00              
ATOM     14  CA  ILE    15      21.720  15.290   4.616  1.00  0.00              
ATOM     15  C   ILE    15      21.681  16.560   3.753  1.00  0.00              
ATOM     16  O   ILE    15      21.497  16.493   2.528  1.00  0.00              
ATOM     17  N   GLU    16      21.822  17.711   4.419  1.00  0.00              
ATOM     18  CA  GLU    16      21.838  19.046   3.802  1.00  0.00              
ATOM     19  C   GLU    16      23.235  19.694   3.880  1.00  0.00              
ATOM     20  O   GLU    16      23.977  19.457   4.832  1.00  0.00              
ATOM     21  N   ILE    17      23.554  20.523   2.874  1.00  0.00              
ATOM     22  CA  ILE    17      24.844  21.233   2.775  1.00  0.00              
ATOM     23  C   ILE    17      24.625  22.740   2.539  1.00  0.00              
ATOM     24  O   ILE    17      23.647  23.124   1.880  1.00  0.00              
ATOM     25  N   ALA    18      25.540  23.582   3.037  1.00  0.00              
ATOM     26  CA  ALA    18      25.451  25.049   2.885  1.00  0.00              
ATOM     27  C   ALA    18      26.779  25.719   2.506  1.00  0.00              
ATOM     28  O   ALA    18      27.868  25.183   2.767  1.00  0.00              
ATOM     29  N   TYR    19      26.670  26.886   1.857  1.00  0.00              
ATOM     30  CA  TYR    19      27.800  27.756   1.517  1.00  0.00              
ATOM     31  C   TYR    19      28.927  27.018   0.760  1.00  0.00              
ATOM     32  O   TYR    19      28.632  26.284  -0.190  1.00  0.00              
ATOM     33  N   ALA    20      30.190  27.197   1.135  1.00  0.00              
ATOM     34  CA  ALA    20      31.312  26.558   0.414  1.00  0.00              
ATOM     35  C   ALA    20      31.197  25.037   0.369  1.00  0.00              
ATOM     36  O   ALA    20      31.676  24.398  -0.584  1.00  0.00              
ATOM     37  N   PHE    21      30.659  24.435   1.437  1.00  0.00              
ATOM     38  CA  PHE    21      30.499  22.984   1.476  1.00  0.00              
ATOM     39  C   PHE    21      29.556  22.525   0.350  1.00  0.00              
ATOM     40  O   PHE    21      29.873  21.596  -0.411  1.00  0.00              
ATOM     41  N   PRO    22      28.392  23.179   0.256  1.00  0.00              
ATOM     42  CA  PRO    22      27.411  22.931  -0.806  1.00  0.00              
ATOM     43  C   PRO    22      28.010  23.076  -2.210  1.00  0.00              
ATOM     44  O   PRO    22      27.778  22.230  -3.095  1.00  0.00              
ATOM     45  N   GLU    23      28.777  24.147  -2.411  1.00  0.00              
ATOM     46  CA  GLU    23      29.410  24.417  -3.715  1.00  0.00              
ATOM     47  C   GLU    23      30.374  23.285  -4.115  1.00  0.00              
ATOM     48  O   GLU    23      30.339  22.811  -5.261  1.00  0.00              
ATOM     49  N   ARG    24      31.186  22.815  -3.172  1.00  0.00              
ATOM     50  CA  ARG    24      32.176  21.780  -3.478  1.00  0.00              
ATOM     51  C   ARG    24      31.547  20.386  -3.638  1.00  0.00              
ATOM     52  O   ARG    24      31.918  19.625  -4.555  1.00  0.00              
ATOM     53  N   TYR    25      30.594  20.012  -2.778  1.00  0.00              
ATOM     54  CA  TYR    25      29.977  18.679  -2.937  1.00  0.00              
ATOM     55  C   TYR    25      29.107  18.614  -4.206  1.00  0.00              
ATOM     56  O   TYR    25      28.919  17.537  -4.779  1.00  0.00              
ATOM     57  N   TYR    26      28.568  19.758  -4.645  1.00  0.00              
ATOM     58  CA  TYR    26      27.825  19.800  -5.898  1.00  0.00              
ATOM     59  C   TYR    26      26.346  19.459  -5.871  1.00  0.00              
ATOM     60  O   TYR    26      25.743  19.246  -6.939  1.00  0.00              
ATOM     61  N   LEU    27      25.776  19.402  -4.671  1.00  0.00              
ATOM     62  CA  LEU    27      24.351  19.160  -4.478  1.00  0.00              
ATOM     63  C   LEU    27      23.929  19.863  -3.186  1.00  0.00              
ATOM     64  O   LEU    27      24.753  20.060  -2.290  1.00  0.00              
ATOM     65  N   LYS    28      22.647  20.225  -3.082  1.00  0.00              
ATOM     66  CA  LYS    28      22.107  20.883  -1.890  1.00  0.00              
ATOM     67  C   LYS    28      21.645  19.890  -0.811  1.00  0.00              
ATOM     68  O   LYS    28      21.565  20.252   0.385  1.00  0.00              
ATOM     69  N   SER    29      21.342  18.655  -1.217  1.00  0.00              
ATOM     70  CA  SER    29      20.715  17.682  -0.323  1.00  0.00              
ATOM     71  C   SER    29      20.804  16.282  -0.908  1.00  0.00              
ATOM     72  O   SER    29      20.736  16.123  -2.138  1.00  0.00              
ATOM     73  N   PHE    30      20.919  15.275  -0.047  1.00  0.00              
ATOM     74  CA  PHE    30      20.882  13.871  -0.489  1.00  0.00              
ATOM     75  C   PHE    30      20.382  12.964   0.643  1.00  0.00              
ATOM     76  O   PHE    30      20.245  13.392   1.788  1.00  0.00              
ATOM     77  N   GLN    31      20.067  11.715   0.315  1.00  0.00              
ATOM     78  CA  GLN    31      19.568  10.739   1.290  1.00  0.00              
ATOM     79  C   GLN    31      20.545   9.585   1.456  1.00  0.00              
ATOM     80  O   GLN    31      21.181   9.171   0.479  1.00  0.00              
ATOM     81  N   VAL    32      20.658   9.070   2.682  1.00  0.00              
ATOM     82  CA  VAL    32      21.500   7.920   3.000  1.00  0.00              
ATOM     83  C   VAL    32      20.730   6.926   3.897  1.00  0.00              
ATOM     84  O   VAL    32      19.887   7.315   4.703  1.00  0.00              
ATOM     85  N   ASP    33      20.977   5.626   3.756  1.00  0.00              
ATOM     86  CA  ASP    33      20.338   4.660   4.656  1.00  0.00              
ATOM     87  C   ASP    33      20.757   4.930   6.119  1.00  0.00              
ATOM     88  O   ASP    33      21.787   5.560   6.380  1.00  0.00              
ATOM     89  N   GLU    34      22.417   3.467   8.412  1.00  0.00              
ATOM     90  CA  GLU    34      23.420   2.475   8.800  1.00  0.00              
ATOM     91  C   GLU    34      24.689   3.074   9.400  1.00  0.00              
ATOM     92  O   GLU    34      25.771   2.532   9.182  1.00  0.00              
ATOM     93  N   GLY    35      24.583   4.185  10.119  1.00  0.00              
ATOM     94  CA  GLY    35      25.763   4.785  10.741  1.00  0.00              
ATOM     95  C   GLY    35      25.468   5.163  12.195  1.00  0.00              
ATOM     96  O   GLY    35      24.456   5.805  12.473  1.00  0.00              
ATOM     97  N   ILE    36      26.341   4.757  13.122  1.00  0.00              
ATOM     98  CA  ILE    36      26.095   5.007  14.548  1.00  0.00              
ATOM     99  C   ILE    36      26.128   6.481  14.994  1.00  0.00              
ATOM    100  O   ILE    36      25.385   6.853  15.892  1.00  0.00              
ATOM    101  N   THR    37      26.950   7.301  14.343  1.00  0.00              
ATOM    102  CA  THR    37      27.149   8.703  14.738  1.00  0.00              
ATOM    103  C   THR    37      27.311   9.642  13.546  1.00  0.00              
ATOM    104  O   THR    37      27.505   9.201  12.406  1.00  0.00              
ATOM    105  N   VAL    38      27.242  10.947  13.832  1.00  0.00              
ATOM    106  CA  VAL    38      27.524  11.976  12.829  1.00  0.00              
ATOM    107  C   VAL    38      28.926  11.753  12.207  1.00  0.00              
ATOM    108  O   VAL    38      29.112  11.874  10.989  1.00  0.00              
ATOM    109  N   GLN    39      29.927  11.470  13.046  1.00  0.00              
ATOM    110  CA  GLN    39      31.302  11.246  12.548  1.00  0.00              
ATOM    111  C   GLN    39      31.398  10.068  11.569  1.00  0.00              
ATOM    112  O   GLN    39      32.087  10.165  10.545  1.00  0.00              
ATOM    113  N   THR    40      30.737   8.954  11.881  1.00  0.00              
ATOM    114  CA  THR    40      30.733   7.803  10.966  1.00  0.00              
ATOM    115  C   THR    40      30.104   8.167   9.612  1.00  0.00              
ATOM    116  O   THR    40      30.605   7.757   8.563  1.00  0.00              
ATOM    117  N   ALA    41      29.001   8.932   9.645  1.00  0.00              
ATOM    118  CA  ALA    41      28.381   9.434   8.406  1.00  0.00              
ATOM    119  C   ALA    41      29.341  10.379   7.626  1.00  0.00              
ATOM    120  O   ALA    41      29.487  10.256   6.408  1.00  0.00              
ATOM    121  N   ILE    42      29.981  11.315   8.333  1.00  0.00              
ATOM    122  CA  ILE    42      30.950  12.240   7.718  1.00  0.00              
ATOM    123  C   ILE    42      32.061  11.461   6.982  1.00  0.00              
ATOM    124  O   ILE    42      32.399  11.756   5.812  1.00  0.00              
ATOM    125  N   THR    43      32.615  10.441   7.645  1.00  0.00              
ATOM    126  CA  THR    43      33.698   9.625   7.036  1.00  0.00              
ATOM    127  C   THR    43      33.194   8.892   5.769  1.00  0.00              
ATOM    128  O   THR    43      33.893   8.813   4.763  1.00  0.00              
ATOM    129  N   GLN    44      31.995   8.307   5.843  1.00  0.00              
ATOM    130  CA  GLN    44      31.406   7.626   4.681  1.00  0.00              
ATOM    131  C   GLN    44      31.247   8.570   3.477  1.00  0.00              
ATOM    132  O   GLN    44      31.599   8.212   2.338  1.00  0.00              
ATOM    133  N   ILE    47      30.709   9.766   3.729  1.00  0.00              
ATOM    134  CA  ILE    47      30.497  10.727   2.641  1.00  0.00              
ATOM    135  C   ILE    47      31.835  11.259   2.076  1.00  0.00              
ATOM    136  O   ILE    47      31.988  11.407   0.843  1.00  0.00              
ATOM    137  N   LEU    48      32.812  11.530   2.955  1.00  0.00              
ATOM    138  CA  LEU    48      34.137  11.985   2.511  1.00  0.00              
ATOM    139  C   LEU    48      34.814  10.963   1.582  1.00  0.00              
ATOM    140  O   LEU    48      35.605  11.331   0.698  1.00  0.00              
ATOM    141  N   SER    49      34.505   9.678   1.768  1.00  0.00              
ATOM    142  CA  SER    49      35.143   8.623   1.008  1.00  0.00              
ATOM    143  C   SER    49      34.580   8.448  -0.403  1.00  0.00              
ATOM    144  O   SER    49      35.122   7.631  -1.162  1.00  0.00              
ATOM    145  N   GLN    50      33.543   9.216  -0.777  1.00  0.00              
ATOM    146  CA  GLN    50      32.898   9.042  -2.096  1.00  0.00              
ATOM    147  C   GLN    50      33.695   9.601  -3.271  1.00  0.00              
ATOM    148  O   GLN    50      33.601   9.066  -4.391  1.00  0.00              
ATOM    149  N   PHE    51      34.468  10.664  -3.034  1.00  0.00              
ATOM    150  CA  PHE    51      35.282  11.309  -4.071  1.00  0.00              
ATOM    151  C   PHE    51      36.285  12.289  -3.483  1.00  0.00              
ATOM    152  O   PHE    51      36.157  12.685  -2.334  1.00  0.00              
ATOM    153  N   PRO    52      37.250  12.741  -4.295  1.00  0.00              
ATOM    154  CA  PRO    52      38.248  13.698  -3.833  1.00  0.00              
ATOM    155  C   PRO    52      37.603  15.053  -3.478  1.00  0.00              
ATOM    156  O   PRO    52      38.034  15.702  -2.524  1.00  0.00              
ATOM    157  N   GLU    53      36.579  15.473  -4.232  1.00  0.00              
ATOM    158  CA  GLU    53      35.866  16.732  -3.934  1.00  0.00              
ATOM    159  C   GLU    53      35.086  16.626  -2.619  1.00  0.00              
ATOM    160  O   GLU    53      35.077  17.575  -1.832  1.00  0.00              
ATOM    161  N   ILE    54      34.401  15.497  -2.401  1.00  0.00              
ATOM    162  CA  ILE    54      33.660  15.285  -1.149  1.00  0.00              
ATOM    163  C   ILE    54      34.624  15.239   0.060  1.00  0.00              
ATOM    164  O   ILE    54      34.315  15.766   1.121  1.00  0.00              
ATOM    165  N   ASP    55      35.811  14.640  -0.123  1.00  0.00              
ATOM    166  CA  ASP    55      36.808  14.602   0.963  1.00  0.00              
ATOM    167  C   ASP    55      37.306  16.009   1.331  1.00  0.00              
ATOM    168  O   ASP    55      37.422  16.356   2.510  1.00  0.00              
ATOM    169  N   LEU    56      37.590  16.833   0.322  1.00  0.00              
ATOM    170  CA  LEU    56      38.040  18.191   0.582  1.00  0.00              
ATOM    171  C   LEU    56      36.973  19.011   1.320  1.00  0.00              
ATOM    172  O   LEU    56      37.277  19.747   2.269  1.00  0.00              
END
