
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0351AL381_5
# Molecule2: number of CA atoms   56 (  935),  selected   56 , name T0351.pdb
# PARAMETERS: T0351AL381_5.T0351.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      24      M       1           -
LGA    D      25      I       2           -
LGA    G      26      L       3           -
LGA    N      27      Y       4           -
LGA    G      28      D       5           #
LGA    -       -      A       6           -
LGA    -       -      I       7           -
LGA    -       -      M       8           -
LGA    S      29      Y       9          2.087
LGA    Y      30      K      10          3.213
LGA    I      31      Y      11          1.659
LGA    -       -      P      12           -
LGA    -       -      N      13           -
LGA    E      32      A      14          1.508
LGA    -       -      V      15           -
LGA    -       -      S      16           -
LGA    -       -      R      17           -
LGA    -       -      K      18           -
LGA    K      33      D      19          5.146
LGA    W      34      F      20          1.529
LGA    N      35      E      21          3.023
LGA    L      36      L      22          0.800
LGA    R      37      R      23          2.668
LGA    A      38      N      24          0.881
LGA    P      39      D      25          1.350
LGA    L      40      G      26          3.327
LGA    P      41      N      27           -
LGA    T      42      G      28           -
LGA    -       -      S      29           -
LGA    -       -      Y      30           -
LGA    -       -      I      31           -
LGA    Q      43      E      32           #
LGA    A      44      K      33          3.731
LGA    E      45      W      34          5.313
LGA    L      46      N      35          1.478
LGA    E      47      L      36          4.067
LGA    T      48      -       -           -
LGA    W      49      R      37          1.706
LGA    W      50      A      38          1.489
LGA    E      51      P      39          2.563
LGA    E      52      -       -           -
LGA    L      53      -       -           -
LGA    Q      54      -       -           -
LGA    K      55      -       -           -
LGA    N      56      L      40          3.802
LGA    P      57      P      41          2.224
LGA    -       -      T      42           -
LGA    -       -      Q      43           -
LGA    -       -      A      44           -
LGA    -       -      E      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      T      48           -
LGA    -       -      W      49           -
LGA    -       -      W      50           -
LGA    -       -      E      51           -
LGA    -       -      E      52           -
LGA    -       -      L      53           -
LGA    -       -      Q      54           -
LGA    -       -      K      55           -
LGA    -       -      N      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34   56    5.0     21    2.85    14.29     24.501     0.711

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.573988 * X  +   0.744788 * Y  +   0.340336 * Z  +  -4.574080
  Y_new =  -0.385569 * X  +  -0.612481 * Y  +   0.690075 * Z  +   6.365317
  Z_new =   0.722409 * X  +   0.264871 * Y  +   0.638724 * Z  +  -0.682057 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.393104   -2.748488  [ DEG:    22.5232   -157.4768 ]
  Theta =  -0.807279   -2.334313  [ DEG:   -46.2537   -133.7463 ]
  Phi   =  -2.550088    0.591505  [ DEG:  -146.1093     33.8907 ]
 
# 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: T0351AL381_5                                  
REMARK     2: T0351.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0351AL381_5.T0351.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34   56   5.0   21   2.85   14.29  24.501
REMARK  ---------------------------------------------------------- 
MOLECULE T0351AL381_5
REMARK Aligment from pdb entry: 1emwA
ATOM      1  N   ASN    24       3.300  -6.889   1.126  1.00  0.00              
ATOM      2  CA  ASN    24       4.396  -6.732   2.125  1.00  0.00              
ATOM      3  C   ASN    24       5.310  -7.961   2.094  1.00  0.00              
ATOM      4  O   ASN    24       4.999  -8.963   1.480  1.00  0.00              
ATOM      5  N   ASP    25       6.435  -7.892   2.751  1.00  0.00              
ATOM      6  CA  ASP    25       7.365  -9.056   2.757  1.00  0.00              
ATOM      7  C   ASP    25       7.735  -9.426   4.197  1.00  0.00              
ATOM      8  O   ASP    25       7.562 -10.552   4.622  1.00  0.00              
ATOM      9  N   GLY    26       8.238  -8.487   4.950  1.00  0.00              
ATOM     10  CA  GLY    26       8.613  -8.787   6.360  1.00  0.00              
ATOM     11  C   GLY    26       7.823  -7.886   7.314  1.00  0.00              
ATOM     12  O   GLY    26       7.260  -8.341   8.290  1.00  0.00              
ATOM     13  N   ASN    27       7.777  -6.612   7.035  1.00  0.00              
ATOM     14  CA  ASN    27       7.023  -5.681   7.924  1.00  0.00              
ATOM     15  C   ASN    27       5.956  -4.925   7.123  1.00  0.00              
ATOM     16  O   ASN    27       4.922  -4.557   7.642  1.00  0.00              
ATOM     17  N   GLY    28       6.200  -4.690   5.861  1.00  0.00              
ATOM     18  CA  GLY    28       5.200  -3.957   5.031  1.00  0.00              
ATOM     19  C   GLY    28       5.593  -2.481   4.961  1.00  0.00              
ATOM     20  O   GLY    28       5.491  -1.755   5.930  1.00  0.00              
ATOM     21  N   SER    29       6.044  -2.031   3.821  1.00  0.00              
ATOM     22  CA  SER    29       6.444  -0.600   3.696  1.00  0.00              
ATOM     23  C   SER    29       5.976  -0.027   2.354  1.00  0.00              
ATOM     24  O   SER    29       5.891  -0.725   1.364  1.00  0.00              
ATOM     25  N   TYR    30       5.671   1.241   2.321  1.00  0.00              
ATOM     26  CA  TYR    30       5.205   1.872   1.049  1.00  0.00              
ATOM     27  C   TYR    30       6.149   3.000   0.633  1.00  0.00              
ATOM     28  O   TYR    30       6.952   3.473   1.412  1.00  0.00              
ATOM     29  N   ILE    31       6.047   3.438  -0.591  1.00  0.00              
ATOM     30  CA  ILE    31       6.926   4.544  -1.066  1.00  0.00              
ATOM     31  C   ILE    31       6.408   5.881  -0.527  1.00  0.00              
ATOM     32  O   ILE    31       7.145   6.839  -0.402  1.00  0.00              
ATOM     33  N   GLU    32       5.146   5.950  -0.206  1.00  0.00              
ATOM     34  CA  GLU    32       4.577   7.222   0.325  1.00  0.00              
ATOM     35  C   GLU    32       3.115   7.014   0.726  1.00  0.00              
ATOM     36  O   GLU    32       2.489   6.046   0.344  1.00  0.00              
ATOM     37  N   LYS    33       2.562   7.918   1.488  1.00  0.00              
ATOM     38  CA  LYS    33       1.137   7.772   1.904  1.00  0.00              
ATOM     39  C   LYS    33       0.280   8.813   1.178  1.00  0.00              
ATOM     40  O   LYS    33       0.450  10.001   1.355  1.00  0.00              
ATOM     41  N   TRP    34      -0.631   8.376   0.350  1.00  0.00              
ATOM     42  CA  TRP    34      -1.484   9.350  -0.398  1.00  0.00              
ATOM     43  C   TRP    34      -2.899   9.376   0.147  1.00  0.00              
ATOM     44  O   TRP    34      -3.540  10.409   0.187  1.00  0.00              
ATOM     45  N   ASN    35      -3.410   8.250   0.530  1.00  0.00              
ATOM     46  CA  ASN    35      -4.799   8.225   1.022  1.00  0.00              
ATOM     47  C   ASN    35      -4.880   7.689   2.441  1.00  0.00              
ATOM     48  O   ASN    35      -3.938   7.148   2.986  1.00  0.00              
ATOM     49  N   LEU    36      -6.037   7.804   3.010  1.00  0.00              
ATOM     50  CA  LEU    36      -6.280   7.273   4.381  1.00  0.00              
ATOM     51  C   LEU    36      -7.666   6.632   4.397  1.00  0.00              
ATOM     52  O   LEU    36      -8.586   7.132   3.779  1.00  0.00              
ATOM     53  N   ARG    37      -7.838   5.537   5.084  1.00  0.00              
ATOM     54  CA  ARG    37      -9.186   4.904   5.094  1.00  0.00              
ATOM     55  C   ARG    37      -9.576   4.480   6.516  1.00  0.00              
ATOM     56  O   ARG    37      -8.758   4.009   7.281  1.00  0.00              
ATOM     57  N   ALA    38     -10.825   4.622   6.863  1.00  0.00              
ATOM     58  CA  ALA    38     -11.277   4.204   8.222  1.00  0.00              
ATOM     59  C   ALA    38     -12.660   3.543   8.122  1.00  0.00              
ATOM     60  O   ALA    38     -13.650   4.214   7.928  1.00  0.00              
ATOM     61  N   PRO    39     -12.693   2.245   8.245  1.00  0.00              
ATOM     62  CA  PRO    39     -13.985   1.528   8.145  1.00  0.00              
ATOM     63  C   PRO    39     -14.847   1.788   9.386  1.00  0.00              
ATOM     64  O   PRO    39     -15.052   0.916  10.207  1.00  0.00              
ATOM     65  N   LEU    40     -15.357   2.983   9.528  1.00  0.00              
ATOM     66  CA  LEU    40     -16.205   3.295  10.708  1.00  0.00              
ATOM     67  C   LEU    40     -17.685   3.242  10.323  1.00  0.00              
ATOM     68  O   LEU    40     -18.101   3.822   9.339  1.00  0.00              
ATOM     69  N   PRO    41     -18.483   2.548  11.086  1.00  0.00              
ATOM     70  CA  PRO    41     -19.934   2.458  10.760  1.00  0.00              
ATOM     71  C   PRO    41     -20.730   3.482  11.574  1.00  0.00              
ATOM     72  O   PRO    41     -21.794   3.191  12.083  1.00  0.00              
ATOM     73  N   THR    42     -20.227   4.680  11.700  1.00  0.00              
ATOM     74  CA  THR    42     -20.960   5.719  12.480  1.00  0.00              
ATOM     75  C   THR    42     -21.452   6.828  11.546  1.00  0.00              
ATOM     76  O   THR    42     -22.638   7.004  11.345  1.00  0.00              
ATOM     77  N   GLN    43      -5.466  12.479  -0.407  1.00  0.00              
ATOM     78  CA  GLN    43      -4.884  13.677  -1.046  1.00  0.00              
ATOM     79  C   GLN    43      -4.831  13.378  -2.539  1.00  0.00              
ATOM     80  O   GLN    43      -3.775  13.127  -3.084  1.00  0.00              
ATOM     81  N   ALA    44      -5.982  13.342  -3.182  1.00  0.00              
ATOM     82  CA  ALA    44      -6.055  13.000  -4.647  1.00  0.00              
ATOM     83  C   ALA    44      -4.837  13.537  -5.414  1.00  0.00              
ATOM     84  O   ALA    44      -4.401  12.935  -6.368  1.00  0.00              
ATOM     85  N   GLU    45      -4.264  14.634  -5.001  1.00  0.00              
ATOM     86  CA  GLU    45      -3.064  15.132  -5.723  1.00  0.00              
ATOM     87  C   GLU    45      -1.966  14.075  -5.638  1.00  0.00              
ATOM     88  O   GLU    45      -1.449  13.617  -6.637  1.00  0.00              
ATOM     89  N   LEU    46      -1.626  13.663  -4.449  1.00  0.00              
ATOM     90  CA  LEU    46      -0.590  12.612  -4.289  1.00  0.00              
ATOM     91  C   LEU    46      -1.164  11.277  -4.762  1.00  0.00              
ATOM     92  O   LEU    46      -0.505  10.496  -5.419  1.00  0.00              
ATOM     93  N   GLU    47      -2.406  11.023  -4.460  1.00  0.00              
ATOM     94  CA  GLU    47      -3.032   9.764  -4.914  1.00  0.00              
ATOM     95  C   GLU    47      -3.117   9.795  -6.448  1.00  0.00              
ATOM     96  O   GLU    47      -3.256   8.773  -7.095  1.00  0.00              
ATOM     97  N   THR    48      -2.995  10.968  -7.037  1.00  0.00              
ATOM     98  CA  THR    48      -3.029  11.064  -8.516  1.00  0.00              
ATOM     99  C   THR    48      -1.613  10.863  -9.075  1.00  0.00              
ATOM    100  O   THR    48      -1.426  10.436 -10.197  1.00  0.00              
ATOM    101  N   TRP    49      -0.613  11.152  -8.279  1.00  0.00              
ATOM    102  CA  TRP    49       0.795  10.967  -8.723  1.00  0.00              
ATOM    103  C   TRP    49       0.991   9.506  -9.053  1.00  0.00              
ATOM    104  O   TRP    49       1.595   9.120 -10.035  1.00  0.00              
ATOM    105  N   TRP    50       0.491   8.706  -8.185  1.00  0.00              
ATOM    106  CA  TRP    50       0.622   7.245  -8.334  1.00  0.00              
ATOM    107  C   TRP    50      -0.222   6.763  -9.491  1.00  0.00              
ATOM    108  O   TRP    50       0.273   6.168 -10.427  1.00  0.00              
ATOM    109  N   GLU    51      -1.483   7.050  -9.471  1.00  0.00              
ATOM    110  CA  GLU    51      -2.340   6.642 -10.617  1.00  0.00              
ATOM    111  C   GLU    51      -1.705   7.171 -11.911  1.00  0.00              
ATOM    112  O   GLU    51      -1.941   6.658 -12.988  1.00  0.00              
ATOM    113  N   GLU    52      -0.887   8.194 -11.804  1.00  0.00              
ATOM    114  CA  GLU    52      -0.223   8.751 -13.011  1.00  0.00              
ATOM    115  C   GLU    52       1.023   7.926 -13.367  1.00  0.00              
ATOM    116  O   GLU    52       1.466   7.925 -14.498  1.00  0.00              
ATOM    117  N   LEU    53       1.593   7.217 -12.420  1.00  0.00              
ATOM    118  CA  LEU    53       2.795   6.404 -12.736  1.00  0.00              
ATOM    119  C   LEU    53       2.386   4.947 -12.955  1.00  0.00              
ATOM    120  O   LEU    53       3.120   4.026 -12.654  1.00  0.00              
ATOM    121  N   GLN    54       1.215   4.744 -13.479  1.00  0.00              
ATOM    122  CA  GLN    54       0.734   3.357 -13.729  1.00  0.00              
ATOM    123  C   GLN    54       0.477   2.649 -12.397  1.00  0.00              
ATOM    124  O   GLN    54       0.587   1.443 -12.297  1.00  0.00              
ATOM    125  N   LYS    55       0.130   3.383 -11.371  1.00  0.00              
ATOM    126  CA  LYS    55      -0.135   2.736 -10.057  1.00  0.00              
ATOM    127  C   LYS    55      -1.450   1.957 -10.120  1.00  0.00              
ATOM    128  O   LYS    55      -2.477   2.487 -10.497  1.00  0.00              
ATOM    129  N   ASN    56      -1.431   0.707  -9.754  1.00  0.00              
ATOM    130  CA  ASN    56      -2.685  -0.093  -9.799  1.00  0.00              
ATOM    131  C   ASN    56      -3.335  -0.143  -8.406  1.00  0.00              
ATOM    132  O   ASN    56      -2.807  -0.763  -7.504  1.00  0.00              
ATOM    133  N   PRO    57      -4.461   0.516  -8.272  1.00  0.00              
ATOM    134  CA  PRO    57      -5.174   0.531  -6.979  1.00  0.00              
ATOM    135  C   PRO    57      -6.082  -0.696  -6.859  1.00  0.00              
ATOM    136  O   PRO    57      -6.866  -0.984  -7.742  1.00  0.00              
END
