
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0381AL509_1-D1
# Molecule2: number of CA atoms   61 (  477),  selected   61 , name T0381_D1.pdb
# PARAMETERS: T0381AL509_1-D1.T0381_D1.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    -       -      V      17           -
LGA    -       -      Q      18           -
LGA    -       -      S      19           -
LGA    -       -      L      20           -
LGA    -       -      A      21           -
LGA    -       -      R      22           -
LGA    -       -      G      23           -
LGA    -       -      L      24           -
LGA    -       -      A      25           -
LGA    -       -      V      26           -
LGA    -       -      I      27           -
LGA    -       -      R      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      D      31           -
LGA    -       -      H      32           -
LGA    -       -      R      33           -
LGA    -       -      N      34           -
LGA    -       -      Q      35           -
LGA    V      17      R      36          1.741
LGA    Q      18      R      37          4.792
LGA    S      19      T      38          4.623
LGA    L      20      L      39           #
LGA    -       -      S      40           -
LGA    -       -      D      41           -
LGA    A      21      V      42          2.073
LGA    -       -      A      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    V      42      T      46          2.836
LGA    A      43      D      47          0.569
LGA    R      44      L      48          2.264
LGA    A      45      T      49          2.296
LGA    T      46      R      50          2.860
LGA    -       -      A      51           -
LGA    -       -      T      52           -
LGA    D      47      A      53          2.443
LGA    -       -      R      54           -
LGA    -       -      R      55           -
LGA    L      48      F      56          4.022
LGA    T      49      L      57          2.542
LGA    -       -      L      58           -
LGA    -       -      T      59           -
LGA    -       -      L      60           -
LGA    -       -      V      61           -
LGA    -       -      E      62           -
LGA    -       -      L      63           -
LGA    -       -      G      64           -
LGA    -       -      Y      65           -
LGA    -       -      V      66           -
LGA    -       -      A      67           -
LGA    -       -      T      68           -
LGA    -       -      D      69           -
LGA    -       -      G      70           -
LGA    -       -      S      71           -
LGA    -       -      A      72           -
LGA    -       -      F      73           -
LGA    T      59      W      74          2.406
LGA    L      60      L      75          2.973
LGA    V      61      T      76          1.521
LGA    E      62      P      77          4.247
LGA    L      63      -       -           -
LGA    G      64      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19   61    5.0     16    2.98     6.25     16.889     0.519

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.300642 * X  +   0.315546 * Y  +  -0.900025 * Z  +  96.708557
  Y_new =  -0.782660 * X  +  -0.620910 * Y  +   0.043749 * Z  +  71.280624
  Z_new =  -0.545030 * X  +   0.717567 * Y  +   0.433636 * Z  +  12.869373 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.027210   -2.114383  [ DEG:    58.8548   -121.1452 ]
  Theta =   0.576424    2.565168  [ DEG:    33.0267    146.9733 ]
  Phi   =  -1.937545    1.204047  [ DEG:  -111.0132     68.9868 ]
 
# 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: T0381AL509_1-D1                               
REMARK     2: T0381_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0381AL509_1-D1.T0381_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   61   5.0   16   2.98    6.25  16.889
REMARK  ---------------------------------------------------------- 
MOLECULE T0381AL509_1-D1
REMARK Aligment from pdb entry: 1mkm_A
ATOM     65  N   VAL    17       8.308  55.733   9.448  1.00  0.00              
ATOM     66  CA  VAL    17       8.779  55.223  10.719  1.00  0.00              
ATOM     67  C   VAL    17       9.855  56.014  11.419  1.00  0.00              
ATOM     68  O   VAL    17      10.367  55.542  12.412  1.00  0.00              
ATOM     69  N   GLN    18      10.184  57.200  10.916  1.00  0.00              
ATOM     70  CA  GLN    18      11.210  58.041  11.513  1.00  0.00              
ATOM     71  C   GLN    18      10.651  58.733  12.724  1.00  0.00              
ATOM     72  O   GLN    18      11.375  59.425  13.434  1.00  0.00              
ATOM     73  N   SER    19       9.354  58.561  12.949  1.00  0.00              
ATOM     74  CA  SER    19       8.686  59.182  14.077  1.00  0.00              
ATOM     75  C   SER    19       7.611  58.247  14.630  1.00  0.00              
ATOM     76  O   SER    19       7.072  57.403  13.908  1.00  0.00              
ATOM     77  N   LEU    20       7.341  58.372  15.927  1.00  0.00              
ATOM     78  CA  LEU    20       6.352  57.546  16.594  1.00  0.00              
ATOM     79  C   LEU    20       5.367  58.413  17.357  1.00  0.00              
ATOM     80  O   LEU    20       5.758  59.349  18.063  1.00  0.00              
ATOM     81  N   ALA    21       4.083  58.116  17.224  1.00  0.00              
ATOM     82  CA  ALA    21       3.115  58.908  17.945  1.00  0.00              
ATOM     83  C   ALA    21       2.648  58.123  19.162  1.00  0.00              
ATOM     84  O   ALA    21       2.141  57.004  19.034  1.00  0.00              
ATOM     85  N   VAL    42       2.845  58.710  20.340  1.00  0.00              
ATOM     86  CA  VAL    42       2.461  58.096  21.599  1.00  0.00              
ATOM     87  C   VAL    42       0.952  58.175  21.836  1.00  0.00              
ATOM     88  O   VAL    42       0.258  58.948  21.184  1.00  0.00              
ATOM     89  N   ALA    43       0.449  57.383  22.775  1.00  0.00              
ATOM     90  CA  ALA    43      -0.979  57.386  23.081  1.00  0.00              
ATOM     91  C   ALA    43      -1.529  58.801  23.327  1.00  0.00              
ATOM     92  O   ALA    43      -2.633  59.125  22.884  1.00  0.00              
ATOM     93  N   ARG    44      -0.764  59.636  24.030  1.00  0.00              
ATOM     94  CA  ARG    44      -1.189  60.999  24.324  1.00  0.00              
ATOM     95  C   ARG    44      -1.043  61.928  23.113  1.00  0.00              
ATOM     96  O   ARG    44      -1.113  63.154  23.246  1.00  0.00              
ATOM     97  N   ALA    45      -0.829  61.331  21.943  1.00  0.00              
ATOM     98  CA  ALA    45      -0.685  62.047  20.676  1.00  0.00              
ATOM     99  C   ALA    45       0.637  62.775  20.425  1.00  0.00              
ATOM    100  O   ALA    45       0.942  63.092  19.276  1.00  0.00              
ATOM    101  N   THR    46       1.401  63.068  21.478  1.00  0.00              
ATOM    102  CA  THR    46       2.699  63.735  21.325  1.00  0.00              
ATOM    103  C   THR    46       3.632  62.801  20.559  1.00  0.00              
ATOM    104  O   THR    46       3.524  61.582  20.675  1.00  0.00              
ATOM    105  N   ASP    47       4.553  63.375  19.788  1.00  0.00              
ATOM    106  CA  ASP    47       5.503  62.586  19.003  1.00  0.00              
ATOM    107  C   ASP    47       6.909  62.475  19.595  1.00  0.00              
ATOM    108  O   ASP    47       7.411  63.368  20.280  1.00  0.00              
ATOM    109  N   LEU    48       7.549  61.363  19.284  1.00  0.00              
ATOM    110  CA  LEU    48       8.885  61.090  19.766  1.00  0.00              
ATOM    111  C   LEU    48       9.610  60.411  18.597  1.00  0.00              
ATOM    112  O   LEU    48       8.961  59.932  17.669  1.00  0.00              
ATOM    113  N   THR    49      10.958  60.392  18.598  1.00  0.00              
ATOM    114  CA  THR    49      11.642  59.734  17.471  1.00  0.00              
ATOM    115  C   THR    49      11.341  58.236  17.329  1.00  0.00              
ATOM    116  O   THR    49      11.089  57.543  18.323  1.00  0.00              
ATOM    117  N   THR    59      13.055  53.340  13.387  1.00  0.00              
ATOM    118  CA  THR    59      13.711  53.270  12.091  1.00  0.00              
ATOM    119  C   THR    59      15.053  54.005  12.088  1.00  0.00              
ATOM    120  O   THR    59      15.966  53.601  11.396  1.00  0.00              
ATOM    121  N   LEU    60      15.160  55.095  12.835  1.00  0.00              
ATOM    122  CA  LEU    60      16.412  55.844  12.908  1.00  0.00              
ATOM    123  C   LEU    60      17.521  54.954  13.481  1.00  0.00              
ATOM    124  O   LEU    60      18.689  55.099  13.138  1.00  0.00              
ATOM    125  N   VAL    61      17.149  54.019  14.345  1.00  0.00              
ATOM    126  CA  VAL    61      18.142  53.112  14.902  1.00  0.00              
ATOM    127  C   VAL    61      18.438  52.099  13.824  1.00  0.00              
ATOM    128  O   VAL    61      19.595  51.782  13.552  1.00  0.00              
ATOM    129  N   GLU    62      17.392  51.609  13.174  1.00  0.00              
ATOM    130  CA  GLU    62      17.584  50.607  12.118  1.00  0.00              
ATOM    131  C   GLU    62      18.543  51.115  11.053  1.00  0.00              
ATOM    132  O   GLU    62      19.477  50.411  10.649  1.00  0.00              
ATOM    133  N   LEU    63      18.313  52.349  10.607  1.00  0.00              
ATOM    134  CA  LEU    63      19.156  52.986   9.597  1.00  0.00              
ATOM    135  C   LEU    63      20.538  53.298  10.150  1.00  0.00              
ATOM    136  O   LEU    63      21.542  53.163   9.450  1.00  0.00              
ATOM    137  N   GLY    64      20.563  53.763  11.400  1.00  0.00              
ATOM    138  CA  GLY    64      21.816  54.122  12.033  1.00  0.00              
ATOM    139  C   GLY    64      22.807  52.981  12.068  1.00  0.00              
ATOM    140  O   GLY    64      23.928  53.094  11.588  1.00  0.00              
END
