
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0349AL509_2-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349AL509_2-D1.T0349_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      R       2           -
LGA    -       -      E       3           -
LGA    G      26      L       4          0.909
LGA    H      27      L       5          0.512
LGA    L      28      R       6          1.238
LGA    V      29      T       7          2.406
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    -       -      L      12           -
LGA    -       -      L      13           -
LGA    -       -      S      14           -
LGA    -       -      A      15           -
LGA    -       -      V      16           -
LGA    -       -      G      17           -
LGA    -       -      A      18           -
LGA    -       -      L      19           -
LGA    -       -      L      20           -
LGA    -       -      D      21           -
LGA    -       -      G      22           -
LGA    -       -      A      23           -
LGA    -       -      D      24           -
LGA    -       -      I      25           -
LGA    -       -      G      26           -
LGA    -       -      H      27           -
LGA    P      45      L      28          1.655
LGA    R      46      V      29          0.991
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    -       -      V      48           -
LGA    L      49      L      49          0.987
LGA    V      50      V      50          0.605
LGA    H      51      H      51          0.657
LGA    E      52      E      52          1.397
LGA    D      53      D      53          1.934
LGA    D      54      D      54          1.032
LGA    L      55      L      55          0.717
LGA    A      56      A      56          0.405
LGA    G      57      G      57          0.375
LGA    A      58      A      58          0.496
LGA    R      59      R      59          0.783
LGA    R      60      R      60          0.689
LGA    L      61      L      61          0.452
LGA    L      62      L      62          0.613
LGA    T      63      T      63          0.724
LGA    D      64      D      64          0.759
LGA    A      65      A      65          2.010
LGA    -       -      G      66           -
LGA    G      66      L      67          2.250
LGA    L      67      A      68          2.968
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   25   57    5.0     25    1.30    68.00     41.736     1.783

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.691173 * X  +  -0.598611 * Y  +   0.404901 * Z  +   2.963364
  Y_new =   0.664513 * X  +   0.746655 * Y  +  -0.030471 * Z  + -65.446121
  Z_new =  -0.284081 * X  +   0.290122 * Y  +   0.913853 * Z  + -41.706009 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.307408   -2.834185  [ DEG:    17.6132   -162.3868 ]
  Theta =   0.288048    2.853545  [ DEG:    16.5039    163.4961 ]
  Phi   =   0.765735   -2.375857  [ DEG:    43.8734   -136.1266 ]
 
# 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: T0349AL509_2-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349AL509_2-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25   57   5.0   25   1.30   68.00  41.736
REMARK  ---------------------------------------------------------- 
MOLECULE T0349AL509_2-D1
REMARK Aligment from pdb entry: 1yj7A_
ATOM      1  N   GLY    26       3.803   4.597  -1.599  1.00  0.00              
ATOM      2  CA  GLY    26       4.589   4.446  -0.356  1.00  0.00              
ATOM      3  C   GLY    26       5.030   2.994  -0.198  1.00  0.00              
ATOM      4  O   GLY    26       6.217   2.679  -0.278  1.00  0.00              
ATOM      5  N   HIS    27       4.062   2.103  -0.025  1.00  0.00              
ATOM      6  CA  HIS    27       4.311   0.696   0.233  1.00  0.00              
ATOM      7  C   HIS    27       3.310  -0.197  -0.510  1.00  0.00              
ATOM      8  O   HIS    27       2.137   0.137  -0.616  1.00  0.00              
ATOM      9  N   LEU    28       3.800  -1.324  -1.007  1.00  0.00              
ATOM     10  CA  LEU    28       2.973  -2.432  -1.491  1.00  0.00              
ATOM     11  C   LEU    28       3.138  -3.665  -0.599  1.00  0.00              
ATOM     12  O   LEU    28       3.980  -3.694   0.320  1.00  0.00              
ATOM     13  N   VAL    29       2.340  -4.695  -0.877  1.00  0.00              
ATOM     14  CA  VAL    29       2.457  -5.968  -0.187  1.00  0.00              
ATOM     15  C   VAL    29       1.930  -5.969   1.232  1.00  0.00              
ATOM     16  O   VAL    29       2.274  -6.848   2.029  1.00  0.00              
ATOM     53  N   PRO    45      -4.326   7.338  -0.613  1.00  0.00              
ATOM     54  CA  PRO    45      -5.139   6.492  -1.448  1.00  0.00              
ATOM     55  C   PRO    45      -4.664   5.051  -1.319  1.00  0.00              
ATOM     56  O   PRO    45      -3.502   4.788  -1.037  1.00  0.00              
ATOM     57  N   ARG    46      -5.584   4.116  -1.519  1.00  0.00              
ATOM     58  CA  ARG    46      -5.324   2.710  -1.314  1.00  0.00              
ATOM     59  C   ARG    46      -5.853   1.905  -2.485  1.00  0.00              
ATOM     60  O   ARG    46      -6.906   2.233  -3.036  1.00  0.00              
ATOM     61  N   LEU    49      -0.592   4.948  -1.364  1.00  0.00              
ATOM     62  CA  LEU    49       0.057   6.047  -2.082  1.00  0.00              
ATOM     63  C   LEU    49      -0.345   7.389  -1.492  1.00  0.00              
ATOM     64  O   LEU    49      -1.362   7.492  -0.810  1.00  0.00              
ATOM     65  N   VAL    50       0.439   8.419  -1.778  1.00  0.00              
ATOM     66  CA  VAL    50       0.118   9.785  -1.396  1.00  0.00              
ATOM     67  C   VAL    50       0.352  10.714  -2.585  1.00  0.00              
ATOM     68  O   VAL    50       1.004  10.346  -3.558  1.00  0.00              
ATOM     69  N   HIS    51      -0.169  11.926  -2.492  1.00  0.00              
ATOM     70  CA  HIS    51       0.192  12.965  -3.451  1.00  0.00              
ATOM     71  C   HIS    51       1.686  13.175  -3.320  1.00  0.00              
ATOM     72  O   HIS    51       2.233  13.132  -2.205  1.00  0.00              
ATOM     73  N   GLU    52       2.383  13.363  -4.442  1.00  0.00              
ATOM     74  CA  GLU    52       3.846  13.422  -4.393  1.00  0.00              
ATOM     75  C   GLU    52       4.400  14.471  -3.443  1.00  0.00              
ATOM     76  O   GLU    52       5.433  14.241  -2.815  1.00  0.00              
ATOM     77  N   ASP    53       3.718  15.610  -3.319  1.00  0.00              
ATOM     78  CA  ASP    53       4.178  16.706  -2.497  1.00  0.00              
ATOM     79  C   ASP    53       4.158  16.340  -1.023  1.00  0.00              
ATOM     80  O   ASP    53       4.861  16.956  -0.229  1.00  0.00              
ATOM     81  N   ASP    54       3.367  15.330  -0.681  1.00  0.00              
ATOM     82  CA  ASP    54       3.194  14.898   0.701  1.00  0.00              
ATOM     83  C   ASP    54       4.129  13.753   1.102  1.00  0.00              
ATOM     84  O   ASP    54       4.051  13.246   2.239  1.00  0.00              
ATOM     85  N   LEU    55       5.012  13.333   0.194  1.00  0.00              
ATOM     86  CA  LEU    55       5.795  12.136   0.431  1.00  0.00              
ATOM     87  C   LEU    55       6.670  12.239   1.696  1.00  0.00              
ATOM     88  O   LEU    55       6.677  11.324   2.525  1.00  0.00              
ATOM     89  N   ALA    56       7.379  13.338   1.858  1.00  0.00              
ATOM     90  CA  ALA    56       8.281  13.466   3.019  1.00  0.00              
ATOM     91  C   ALA    56       7.492  13.476   4.338  1.00  0.00              
ATOM     92  O   ALA    56       7.837  12.759   5.268  1.00  0.00              
ATOM     93  N   GLY    57       6.418  14.251   4.407  1.00  0.00              
ATOM     94  CA  GLY    57       5.548  14.294   5.581  1.00  0.00              
ATOM     95  C   GLY    57       5.014  12.912   5.915  1.00  0.00              
ATOM     96  O   GLY    57       5.005  12.498   7.079  1.00  0.00              
ATOM     97  N   ALA    58       4.574  12.181   4.886  1.00  0.00              
ATOM     98  CA  ALA    58       4.037  10.835   5.069  1.00  0.00              
ATOM     99  C   ALA    58       5.050   9.836   5.610  1.00  0.00              
ATOM    100  O   ALA    58       4.762   9.111   6.567  1.00  0.00              
ATOM    101  N   ARG    59       6.236   9.790   5.010  1.00  0.00              
ATOM    102  CA  ARG    59       7.272   8.880   5.468  1.00  0.00              
ATOM    103  C   ARG    59       7.706   9.255   6.894  1.00  0.00              
ATOM    104  O   ARG    59       7.971   8.363   7.693  1.00  0.00              
ATOM    105  N   ARG    60       7.737  10.537   7.198  1.00  0.00              
ATOM    106  CA  ARG    60       8.075  11.009   8.549  1.00  0.00              
ATOM    107  C   ARG    60       7.110  10.453   9.592  1.00  0.00              
ATOM    108  O   ARG    60       7.536   9.854  10.590  1.00  0.00              
ATOM    109  N   LEU    61       5.806  10.601   9.333  1.00  0.00              
ATOM    110  CA  LEU    61       4.769  10.097  10.203  1.00  0.00              
ATOM    111  C   LEU    61       4.859   8.573  10.354  1.00  0.00              
ATOM    112  O   LEU    61       4.745   8.045  11.462  1.00  0.00              
ATOM    113  N   LEU    62       5.042   7.868   9.240  1.00  0.00              
ATOM    114  CA  LEU    62       5.124   6.421   9.288  1.00  0.00              
ATOM    115  C   LEU    62       6.362   5.979  10.086  1.00  0.00              
ATOM    116  O   LEU    62       6.236   5.098  10.960  1.00  0.00              
ATOM    117  N   THR    63       7.513   6.578   9.789  1.00  0.00              
ATOM    118  CA  THR    63       8.777   6.274  10.480  1.00  0.00              
ATOM    119  C   THR    63       8.619   6.496  11.988  1.00  0.00              
ATOM    120  O   THR    63       9.060   5.656  12.803  1.00  0.00              
ATOM    121  N   ASP    64       7.987   7.610  12.349  1.00  0.00              
ATOM    122  CA  ASP    64       7.779   7.979  13.758  1.00  0.00              
ATOM    123  C   ASP    64       6.851   7.049  14.500  1.00  0.00              
ATOM    124  O   ASP    64       6.797   7.095  15.735  1.00  0.00              
ATOM    125  N   ALA    65       6.085   6.228  13.776  1.00  0.00              
ATOM    126  CA  ALA    65       5.194   5.258  14.375  1.00  0.00              
ATOM    127  C   ALA    65       5.602   3.814  14.123  1.00  0.00              
ATOM    128  O   ALA    65       4.855   2.889  14.426  1.00  0.00              
ATOM    129  N   GLY    66       6.800   3.622  13.573  1.00  0.00              
ATOM    130  CA  GLY    66       7.353   2.301  13.347  1.00  0.00              
ATOM    131  C   GLY    66       6.727   1.484  12.228  1.00  0.00              
ATOM    132  O   GLY    66       6.744   0.267  12.282  1.00  0.00              
ATOM    133  N   LEU    67       6.140   2.156  11.234  1.00  0.00              
ATOM    134  CA  LEU    67       5.519   1.473  10.096  1.00  0.00              
ATOM    135  C   LEU    67       6.422   1.572   8.878  1.00  0.00              
ATOM    136  O   LEU    67       7.073   2.604   8.677  1.00  0.00              
END
