
#######################################################
#                                                     #
#                        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   39 (  156),  selected   39 , name T0347AL242_5-D1
# Molecule2: number of CA atoms   89 (  730),  selected   89 , name T0347_D1.pdb
# PARAMETERS: T0347AL242_5-D1.T0347_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      P       7           -
LGA    -       -      R       8           -
LGA    -       -      L       9           -
LGA    -       -      S      10           -
LGA    -       -      R      11           -
LGA    -       -      I      12           -
LGA    -       -      A      13           -
LGA    -       -      I      14           -
LGA    -       -      D      15           -
LGA    -       -      K      16           -
LGA    -       -      L      17           -
LGA    -       -      R      18           -
LGA    -       -      P      19           -
LGA    -       -      T      20           -
LGA    -       -      Q      21           -
LGA    -       -      I      22           -
LGA    -       -      A      23           -
LGA    -       -      V      24           -
LGA    -       -      G      25           -
LGA    -       -      F      26           -
LGA    -       -      R      27           -
LGA    -       -      E      28           -
LGA    -       -      V      29           -
LGA    -       -      E      30           -
LGA    -       -      L      31           -
LGA    -       -      K      32           -
LGA    -       -      R      33           -
LGA    -       -      K      34           -
LGA    -       -      E      35           -
LGA    -       -      W      36           -
LGA    -       -      R      37           -
LGA    -       -      H      51           -
LGA    -       -      I      52           -
LGA    -       -      V      53           -
LGA    -       -      P      54           -
LGA    -       -      V      55           -
LGA    -       -      V      56           -
LGA    -       -      A      57           -
LGA    -       -      G      58           -
LGA    -       -      P      59           -
LGA    -       -      K      60           -
LGA    -       -      D      61           -
LGA    -       -      R      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    P       7      L      65          3.135
LGA    R       8      I      66          2.460
LGA    L       9      D      67          1.541
LGA    S      10      H      68          4.132
LGA    R      11      H      69          3.962
LGA    I      12      H      70          3.539
LGA    A      13      L      71          2.607
LGA    I      14      V      72          2.434
LGA    D      15      L      73          1.904
LGA    K      16      A      74          1.929
LGA    L      17      L      75          2.076
LGA    R      18      S      76          2.081
LGA    P      19      K      77          1.606
LGA    T      20      E      78          4.389
LGA    Q      21      G      79           #
LGA    I      22      V      80          2.710
LGA    -       -      E      81           -
LGA    A      23      H      82          3.964
LGA    V      24      V      83          1.933
LGA    G      25      L      84          1.404
LGA    F      26      T      85          1.205
LGA    R      27      S      86          0.669
LGA    E      28      E      87          1.064
LGA    E      30      V      88          3.758
LGA    -       -      A      89           -
LGA    L      31      K      90          3.551
LGA    K      32      F      91           -
LGA    R      33      S      92           -
LGA    K      34      H      93           -
LGA    E      35      L      94           -
LGA    W      36      G      95           -
LGA    R      37      K      96           -
LGA    -       -      D      97           -
LGA    -       -      E      98           -
LGA    H      51      F      99           #
LGA    I      52      -       -           -
LGA    V      53      -       -           -
LGA    P      54      W     100          4.820
LGA    V      55      S     101           -
LGA    -       -      V     102           -
LGA    V      56      M     103          4.946
LGA    A      57      D     104          2.112
LGA    G      58      H     105          1.414
LGA    P      59      R     106          5.208
LGA    -       -      N     107           -
LGA    -       -      L     108           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39   89    5.0     28    3.01    10.71     20.234     0.900

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.664663 * X  +   0.169261 * Y  +   0.727718 * Z  +   5.284939
  Y_new =   0.699306 * X  +  -0.483852 * Y  +  -0.526173 * Z  +  36.697811
  Z_new =   0.263047 * X  +   0.858626 * Y  +  -0.439964 * Z  +  -2.823488 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.044318   -1.097274  [ DEG:   117.1308    -62.8692 ]
  Theta =  -0.266179   -2.875413  [ DEG:   -15.2510   -164.7490 ]
  Phi   =   0.810791   -2.330801  [ DEG:    46.4549   -133.5451 ]
 
# 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: T0347AL242_5-D1                               
REMARK     2: T0347_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0347AL242_5-D1.T0347_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39   89   5.0   28   3.01   10.71  20.234
REMARK  ---------------------------------------------------------- 
MOLECULE T0347AL242_5-D1
REMARK Aligment from pdb entry: 1hyw_A
ATOM     25  N   PRO     7       9.768  35.388  -3.556  1.00  0.00              
ATOM     26  CA  PRO     7       8.791  35.575  -4.616  1.00  0.00              
ATOM     27  C   PRO     7       8.000  36.856  -4.388  1.00  0.00              
ATOM     28  O   PRO     7       7.559  37.495  -5.341  1.00  0.00              
ATOM     29  N   ARG     8       7.846  37.253  -3.127  1.00  0.00              
ATOM     30  CA  ARG     8       7.238  38.542  -2.828  1.00  0.00              
ATOM     31  C   ARG     8       8.038  39.634  -3.543  1.00  0.00              
ATOM     32  O   ARG     8       7.506  40.672  -3.937  1.00  0.00              
ATOM     33  N   LEU     9       9.329  39.377  -3.733  1.00  0.00              
ATOM     34  CA  LEU     9      10.149  40.257  -4.538  1.00  0.00              
ATOM     35  C   LEU     9       9.694  40.110  -5.976  1.00  0.00              
ATOM     36  O   LEU     9       9.495  41.094  -6.692  1.00  0.00              
ATOM     37  N   SER    10       9.400  38.867  -6.348  1.00  0.00              
ATOM     38  CA  SER    10       8.812  38.587  -7.641  1.00  0.00              
ATOM     39  C   SER    10       7.521  39.375  -7.782  1.00  0.00              
ATOM     40  O   SER    10       7.255  39.954  -8.835  1.00  0.00              
ATOM     41  N   ARG    11       6.766  39.502  -6.676  1.00  0.00              
ATOM     42  CA  ARG    11       5.569  40.337  -6.684  1.00  0.00              
ATOM     43  C   ARG    11       5.956  41.720  -7.217  1.00  0.00              
ATOM     44  O   ARG    11       5.261  42.303  -8.049  1.00  0.00              
ATOM     45  N   ILE    12       7.091  42.211  -6.727  1.00  0.00              
ATOM     46  CA  ILE    12       7.601  43.512  -7.127  1.00  0.00              
ATOM     47  C   ILE    12       7.661  43.598  -8.644  1.00  0.00              
ATOM     48  O   ILE    12       7.194  44.568  -9.243  1.00  0.00              
ATOM     49  N   ALA    13       8.177  42.545  -9.260  1.00  0.00              
ATOM     50  CA  ALA    13       8.211  42.464 -10.709  1.00  0.00              
ATOM     51  C   ALA    13       6.795  42.356 -11.243  1.00  0.00              
ATOM     52  O   ALA    13       6.442  43.001 -12.220  1.00  0.00              
ATOM     53  N   ILE    14       5.986  41.556 -10.564  1.00  0.00              
ATOM     54  CA  ILE    14       4.600  41.346 -10.959  1.00  0.00              
ATOM     55  C   ILE    14       3.823  42.650 -11.000  1.00  0.00              
ATOM     56  O   ILE    14       3.235  42.995 -12.027  1.00  0.00              
ATOM     57  N   ASP    15       3.842  43.404  -9.902  1.00  0.00              
ATOM     58  CA  ASP    15       3.175  44.699  -9.883  1.00  0.00              
ATOM     59  C   ASP    15       3.718  45.532 -11.031  1.00  0.00              
ATOM     60  O   ASP    15       2.994  46.300 -11.664  1.00  0.00              
ATOM     61  N   LYS    16       4.989  45.298 -11.344  1.00  0.00              
ATOM     62  CA  LYS    16       5.619  45.932 -12.479  1.00  0.00              
ATOM     63  C   LYS    16       5.083  45.323 -13.773  1.00  0.00              
ATOM     64  O   LYS    16       4.870  46.027 -14.748  1.00  0.00              
ATOM     65  N   LEU    17       4.795  44.019 -13.761  1.00  0.00              
ATOM     66  CA  LEU    17       4.270  43.349 -14.944  1.00  0.00              
ATOM     67  C   LEU    17       3.081  44.113 -15.492  1.00  0.00              
ATOM     68  O   LEU    17       2.922  44.265 -16.705  1.00  0.00              
ATOM     69  N   ARG    18       2.295  44.654 -14.581  1.00  0.00              
ATOM     70  CA  ARG    18       1.143  45.463 -14.945  1.00  0.00              
ATOM     71  C   ARG    18       1.543  46.590 -15.899  1.00  0.00              
ATOM     72  O   ARG    18       0.704  47.131 -16.619  1.00  0.00              
ATOM     73  N   PRO    19       2.828  46.947 -15.892  1.00  0.00              
ATOM     74  CA  PRO    19       3.322  48.041 -16.726  1.00  0.00              
ATOM     75  C   PRO    19       4.778  47.815 -17.150  1.00  0.00              
ATOM     76  O   PRO    19       5.071  47.663 -18.336  1.00  0.00              
ATOM     77  N   THR    20       5.689  47.842 -16.181  1.00  0.00              
ATOM     78  CA  THR    20       7.100  47.639 -16.468  1.00  0.00              
ATOM     79  C   THR    20       7.415  46.219 -16.901  1.00  0.00              
ATOM     80  O   THR    20       7.732  45.978 -18.066  1.00  0.00              
ATOM     81  N   GLN    21       7.347  45.282 -15.955  1.00  0.00              
ATOM     82  CA  GLN    21       7.615  43.876 -16.238  1.00  0.00              
ATOM     83  C   GLN    21       6.761  43.382 -17.404  1.00  0.00              
ATOM     84  O   GLN    21       6.169  44.165 -18.144  1.00  0.00              
ATOM     85  N   ILE    22       6.677  42.071 -17.521  1.00  0.00              
ATOM     86  CA  ILE    22       5.912  41.428 -18.574  1.00  0.00              
ATOM     87  C   ILE    22       5.637  39.975 -18.230  1.00  0.00              
ATOM     88  O   ILE    22       4.574  39.442 -18.545  1.00  0.00              
ATOM     89  N   ALA    23       6.607  39.325 -17.602  1.00  0.00              
ATOM     90  CA  ALA    23       6.453  37.938 -17.224  1.00  0.00              
ATOM     91  C   ALA    23       7.349  37.581 -16.051  1.00  0.00              
ATOM     92  O   ALA    23       8.567  37.750 -16.104  1.00  0.00              
ATOM     93  N   VAL    24       6.730  37.076 -14.994  1.00  0.00              
ATOM     94  CA  VAL    24       7.454  36.684 -13.799  1.00  0.00              
ATOM     95  C   VAL    24       7.399  35.178 -13.604  1.00  0.00              
ATOM     96  O   VAL    24       6.356  34.555 -13.793  1.00  0.00              
ATOM     97  N   GLY    25       8.531  34.598 -13.236  1.00  0.00              
ATOM     98  CA  GLY    25       8.619  33.161 -13.018  1.00  0.00              
ATOM     99  C   GLY    25       9.586  32.862 -11.881  1.00  0.00              
ATOM    100  O   GLY    25      10.782  33.134 -11.988  1.00  0.00              
ATOM    101  N   PHE    26       9.072  32.311 -10.786  1.00  0.00              
ATOM    102  CA  PHE    26       9.919  32.018  -9.634  1.00  0.00              
ATOM    103  C   PHE    26       9.724  30.596  -9.126  1.00  0.00              
ATOM    104  O   PHE    26       8.765  29.913  -9.490  1.00  0.00              
ATOM    105  N   ARG    27      10.646  30.167  -8.270  1.00  0.00              
ATOM    106  CA  ARG    27      10.603  28.834  -7.687  1.00  0.00              
ATOM    107  C   ARG    27      10.552  28.916  -6.166  1.00  0.00              
ATOM    108  O   ARG    27      11.377  29.587  -5.544  1.00  0.00              
ATOM    109  N   GLU    28       9.558  28.265  -5.575  1.00  0.00              
ATOM    110  CA  GLU    28       9.386  28.286  -4.128  1.00  0.00              
ATOM    111  C   GLU    28       9.458  26.874  -3.551  1.00  0.00              
ATOM    112  O   GLU    28       9.719  25.913  -4.273  1.00  0.00              
ATOM    113  N   GLU    30       9.222  26.759  -2.247  1.00  0.00              
ATOM    114  CA  GLU    30       9.257  25.465  -1.578  1.00  0.00              
ATOM    115  C   GLU    30       7.845  24.936  -1.345  1.00  0.00              
ATOM    116  O   GLU    30       7.484  24.578  -0.222  1.00  0.00              
ATOM    117  N   LEU    31       7.050  24.896  -2.407  1.00  0.00              
ATOM    118  CA  LEU    31       5.685  24.413  -2.298  1.00  0.00              
ATOM    119  C   LEU    31       4.867  24.697  -3.543  1.00  0.00              
ATOM    120  O   LEU    31       4.202  23.809  -4.072  1.00  0.00              
ATOM    121  N   LYS    32       4.920  25.938  -4.013  1.00  0.00              
ATOM    122  CA  LYS    32       4.186  26.336  -5.207  1.00  0.00              
ATOM    123  C   LYS    32       5.099  27.038  -6.199  1.00  0.00              
ATOM    124  O   LYS    32       6.246  27.348  -5.894  1.00  0.00              
ATOM    125  N   ARG    33       4.579  27.264  -7.395  1.00  0.00              
ATOM    126  CA  ARG    33       5.325  27.918  -8.457  1.00  0.00              
ATOM    127  C   ARG    33       4.601  29.174  -8.931  1.00  0.00              
ATOM    128  O   ARG    33       3.387  29.154  -9.125  1.00  0.00              
ATOM    129  N   LYS    34       5.338  30.263  -9.132  1.00  0.00              
ATOM    130  CA  LYS    34       4.727  31.479  -9.651  1.00  0.00              
ATOM    131  C   LYS    34       5.309  31.843 -11.006  1.00  0.00              
ATOM    132  O   LYS    34       6.375  32.444 -11.091  1.00  0.00              
ATOM    133  N   GLU    35       4.563  31.514 -12.053  1.00  0.00              
ATOM    134  CA  GLU    35       4.947  31.841 -13.421  1.00  0.00              
ATOM    135  C   GLU    35       3.801  32.579 -14.088  1.00  0.00              
ATOM    136  O   GLU    35       2.740  32.001 -14.326  1.00  0.00              
ATOM    137  N   TRP    36       3.982  33.868 -14.323  1.00  0.00              
ATOM    138  CA  TRP    36       2.896  34.677 -14.852  1.00  0.00              
ATOM    139  C   TRP    36       3.360  35.699 -15.873  1.00  0.00              
ATOM    140  O   TRP    36       4.536  36.059 -15.931  1.00  0.00              
ATOM    141  N   ARG    37       2.405  36.185 -16.656  1.00  0.00              
ATOM    142  CA  ARG    37       2.673  37.211 -17.644  1.00  0.00              
ATOM    143  C   ARG    37       1.742  38.397 -17.432  1.00  0.00              
ATOM    144  O   ARG    37       1.270  38.626 -16.319  1.00  0.00              
ATOM    197  N   HIS    51       0.952  36.276  -0.714  1.00  0.00              
ATOM    198  CA  HIS    51       2.349  35.949  -0.515  1.00  0.00              
ATOM    199  C   HIS    51       3.072  37.077   0.183  1.00  0.00              
ATOM    200  O   HIS    51       3.693  36.890   1.229  1.00  0.00              
ATOM    201  N   ILE    52       2.973  38.257  -0.401  1.00  0.00              
ATOM    202  CA  ILE    52       3.584  39.452   0.154  1.00  0.00              
ATOM    203  C   ILE    52       3.344  39.540   1.641  1.00  0.00              
ATOM    204  O   ILE    52       4.251  39.410   2.459  1.00  0.00              
ATOM    205  N   VAL    53       2.078  39.641   1.968  1.00  0.00              
ATOM    206  CA  VAL    53       1.659  39.731   3.366  1.00  0.00              
ATOM    207  C   VAL    53       2.241  38.600   4.202  1.00  0.00              
ATOM    208  O   VAL    53       2.377  38.722   5.420  1.00  0.00              
ATOM    209  N   PRO    54       2.630  37.527   3.538  1.00  0.00              
ATOM    210  CA  PRO    54       3.223  36.384   4.218  1.00  0.00              
ATOM    211  C   PRO    54       4.714  36.598   4.468  1.00  0.00              
ATOM    212  O   PRO    54       5.301  35.970   5.349  1.00  0.00              
ATOM    213  N   VAL    55       5.321  37.487   3.686  1.00  0.00              
ATOM    214  CA  VAL    55       6.745  37.787   3.816  1.00  0.00              
ATOM    215  C   VAL    55       7.146  37.988   5.276  1.00  0.00              
ATOM    216  O   VAL    55       6.306  38.295   6.123  1.00  0.00              
ATOM    217  N   VAL    56       8.438  37.825   5.559  1.00  0.00              
ATOM    218  CA  VAL    56       8.939  38.011   6.913  1.00  0.00              
ATOM    219  C   VAL    56       8.030  37.417   7.973  1.00  0.00              
ATOM    220  O   VAL    56       7.871  37.985   9.054  1.00  0.00              
ATOM    221  N   ALA    57       7.429  36.272   7.663  1.00  0.00              
ATOM    222  CA  ALA    57       6.528  35.603   8.593  1.00  0.00              
ATOM    223  C   ALA    57       7.162  35.475   9.974  1.00  0.00              
ATOM    224  O   ALA    57       6.462  35.395  10.984  1.00  0.00              
ATOM    225  N   GLY    58       8.490  35.463  10.012  1.00  0.00              
ATOM    226  CA  GLY    58       9.218  35.351  11.272  1.00  0.00              
ATOM    227  C   GLY    58      10.001  36.627  11.561  1.00  0.00              
ATOM    228  O   GLY    58      11.131  36.577  12.048  1.00  0.00              
ATOM    229  N   PRO    59       9.395  37.770  11.254  1.00  0.00              
ATOM    230  CA  PRO    59      10.038  39.060  11.480  1.00  0.00              
ATOM    231  C   PRO    59      10.254  39.797  10.163  1.00  0.00              
ATOM    232  O   PRO    59       9.898  40.966  10.038  1.00  0.00              
END
