
#######################################################
#                                                     #
#                        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 T0304AL381_2-D1
# Molecule2: number of CA atoms  101 (  799),  selected  101 , name T0304_D1.pdb
# PARAMETERS: T0304AL381_2-D1.T0304_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    R      17      R      17           -
LGA    P      18      P      18           -
LGA    W      19      W      19           -
LGA    -       -      W      20           -
LGA    -       -      G      21           -
LGA    -       -      L      22           -
LGA    -       -      P      23           -
LGA    -       -      C      24           -
LGA    -       -      T      25           -
LGA    -       -      V      26           -
LGA    -       -      T      27           -
LGA    -       -      P      28           -
LGA    -       -      C      29           -
LGA    -       -      F      30           -
LGA    -       -      G      31           -
LGA    -       -      A      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    W      20      E      37           #
LGA    G      21      G      38          3.643
LGA    -       -      N      39           -
LGA    L      22      R      40           #
LGA    P      23      L      41          3.624
LGA    C      24      H      42           #
LGA    T      25      Y      43          4.646
LGA    -       -      L      44           -
LGA    -       -      A      45           -
LGA    -       -      D      46           -
LGA    -       -      R      47           -
LGA    -       -      A      48           -
LGA    -       -      G      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      G      52           -
LGA    -       -      L      53           -
LGA    -       -      F      54           -
LGA    -       -      S      55           -
LGA    -       -      D      56           -
LGA    -       -      A      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      Y      60           -
LGA    -       -      H      61           -
LGA    -       -      L      62           -
LGA    -       -      D      63           -
LGA    -       -      Q      64           -
LGA    V      26      A      65           #
LGA    T      27      F      66          3.834
LGA    P      28      P      67          1.221
LGA    C      29      L      68          1.890
LGA    -       -      L      69           -
LGA    -       -      M      70           -
LGA    F      30      K      71          1.541
LGA    G      31      Q      72          1.428
LGA    A      32      L      73          2.306
LGA    -       -      E      74           -
LGA    -       -      L      75           -
LGA    R      33      M      76          2.156
LGA    L      34      L      77          2.718
LGA    -       -      T      78           -
LGA    -       -      S      79           -
LGA    -       -      G      80           -
LGA    -       -      E      81           -
LGA    -       -      L      82           -
LGA    V      35      N      83          2.008
LGA    -       -      P      84           -
LGA    -       -      R      85           -
LGA    -       -      H      86           -
LGA    Q      36      Q      87          5.643
LGA    E      37      H      88          2.203
LGA    G      38      -       -           -
LGA    N      39      -       -           -
LGA    R      40      T      89          3.199
LGA    L      41      V      90          2.172
LGA    H      42      T      91          3.380
LGA    Y      43      L      92          3.414
LGA    L      44      -       -           -
LGA    A      45      Y      93          3.751
LGA    D      46      A      94          4.382
LGA    R      47      K      95           #
LGA    -       -      G      96           -
LGA    -       -      L      97           -
LGA    A      48      T      98          1.307
LGA    G      49      C      99          3.017
LGA    I      50      K     100          2.803
LGA    -       -      A     101           -
LGA    -       -      D     102           -
LGA    -       -      T     103           -
LGA    -       -      L     104           -
LGA    -       -      S     105           -
LGA    -       -      S     106           -
LGA    -       -      C     107           -
LGA    -       -      D     108           -
LGA    -       -      Y     109           -
LGA    -       -      V     110           -
LGA    -       -      Y     111           -
LGA    R      51      L     112          1.780
LGA    G      52      A     113          3.496
LGA    L      53      V     114           -
LGA    F      54      Y     115           -
LGA    S      55      P     116           -
LGA    -       -      T     117           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   39  101    5.0     25    3.07    16.00     15.053     0.789

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.632971 * X  +   0.742107 * Y  +   0.220511 * Z  +  53.684475
  Y_new =  -0.133989 * X  +   0.385547 * Y  +  -0.912908 * Z  +  42.317734
  Z_new =  -0.762493 * X  +   0.548298 * Y  +   0.343475 * Z  +  44.172726 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.011163   -2.130429  [ DEG:    57.9354   -122.0646 ]
  Theta =   0.867157    2.274436  [ DEG:    49.6844    130.3156 ]
  Phi   =  -0.208604    2.932989  [ DEG:   -11.9521    168.0479 ]
 
# 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: T0304AL381_2-D1                               
REMARK     2: T0304_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0304AL381_2-D1.T0304_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   39  101   5.0   25   3.07   16.00  15.053
REMARK  ---------------------------------------------------------- 
MOLECULE T0304AL381_2-D1
REMARK Aligment from pdb entry: 1x3cA
ATOM     49  N   ARG    17      61.114  36.964  52.766  1.00  0.00              
ATOM     50  CA  ARG    17      60.926  35.796  53.619  1.00  0.00              
ATOM     51  C   ARG    17      61.618  34.573  53.025  1.00  0.00              
ATOM     52  O   ARG    17      61.503  34.279  51.834  1.00  0.00              
ATOM     53  N   PRO    18      62.355  33.840  53.874  1.00  0.00              
ATOM     54  CA  PRO    18      63.079  32.637  53.457  1.00  0.00              
ATOM     55  C   PRO    18      62.142  31.482  53.120  1.00  0.00              
ATOM     56  O   PRO    18      62.340  30.778  52.130  1.00  0.00              
ATOM     57  N   TRP    19      61.120  31.295  53.949  1.00  0.00              
ATOM     58  CA  TRP    19      60.153  30.225  53.741  1.00  0.00              
ATOM     59  C   TRP    19      58.831  30.780  53.220  1.00  0.00              
ATOM     60  O   TRP    19      58.434  31.893  53.563  1.00  0.00              
ATOM     61  N   TRP    20      58.153  29.995  52.389  1.00  0.00              
ATOM     62  CA  TRP    20      56.875  30.406  51.819  1.00  0.00              
ATOM     63  C   TRP    20      55.802  29.352  52.074  1.00  0.00              
ATOM     64  O   TRP    20      55.935  28.190  51.690  1.00  0.00              
ATOM     65  N   GLY    21      54.712  29.765  52.737  1.00  0.00              
ATOM     66  CA  GLY    21      53.595  28.872  53.058  1.00  0.00              
ATOM     67  C   GLY    21      52.806  28.463  51.818  1.00  0.00              
ATOM     68  O   GLY    21      52.125  27.436  51.814  1.00  0.00              
ATOM     69  N   LEU    22      52.901  29.271  50.768  1.00  0.00              
ATOM     70  CA  LEU    22      52.195  28.993  49.523  1.00  0.00              
ATOM     71  C   LEU    22      53.115  28.315  48.514  1.00  0.00              
ATOM     72  O   LEU    22      54.114  28.891  48.082  1.00  0.00              
ATOM     73  N   PRO    23      52.771  27.086  48.142  1.00  0.00              
ATOM     74  CA  PRO    23      53.565  26.327  47.184  1.00  0.00              
ATOM     75  C   PRO    23      52.671  25.657  46.146  1.00  0.00              
ATOM     76  O   PRO    23      51.695  24.989  46.490  1.00  0.00              
ATOM     77  N   CYS    24      53.008  25.840  44.874  1.00  0.00              
ATOM     78  CA  CYS    24      52.237  25.254  43.785  1.00  0.00              
ATOM     79  C   CYS    24      51.981  23.771  44.035  1.00  0.00              
ATOM     80  O   CYS    24      52.898  23.019  44.365  1.00  0.00              
ATOM     81  N   THR    25      50.727  23.357  43.875  1.00  0.00              
ATOM     82  CA  THR    25      50.351  21.964  44.082  1.00  0.00              
ATOM     83  C   THR    25      50.701  21.113  42.868  1.00  0.00              
ATOM     84  O   THR    25      51.072  19.946  42.999  1.00  0.00              
ATOM     85  N   VAL    26      50.583  21.705  41.683  1.00  0.00              
ATOM     86  CA  VAL    26      50.888  21.001  40.442  1.00  0.00              
ATOM     87  C   VAL    26      52.088  20.078  40.623  1.00  0.00              
ATOM     88  O   VAL    26      53.202  20.536  40.879  1.00  0.00              
ATOM     89  N   THR    27      51.855  18.777  40.489  1.00  0.00              
ATOM     90  CA  THR    27      52.917  17.790  40.639  1.00  0.00              
ATOM     91  C   THR    27      54.019  18.014  39.609  1.00  0.00              
ATOM     92  O   THR    27      53.961  17.489  38.499  1.00  0.00              
ATOM     93  N   PRO    28      55.023  18.802  39.986  1.00  0.00              
ATOM     94  CA  PRO    28      56.123  19.083  39.083  1.00  0.00              
ATOM     95  C   PRO    28      56.304  20.567  38.834  1.00  0.00              
ATOM     96  O   PRO    28      56.574  20.988  37.708  1.00  0.00              
ATOM     97  N   CYS    29      56.152  21.366  39.886  1.00  0.00              
ATOM     98  CA  CYS    29      56.297  22.812  39.776  1.00  0.00              
ATOM     99  C   CYS    29      57.005  23.381  41.002  1.00  0.00              
ATOM    100  O   CYS    29      56.452  23.396  42.102  1.00  0.00              
ATOM    101  N   PHE    30      58.233  23.851  40.804  1.00  0.00              
ATOM    102  CA  PHE    30      59.018  24.420  41.893  1.00  0.00              
ATOM    103  C   PHE    30      58.829  25.933  41.966  1.00  0.00              
ATOM    104  O   PHE    30      59.733  26.699  41.637  1.00  0.00              
ATOM    105  N   GLY    31      57.645  26.355  42.398  1.00  0.00              
ATOM    106  CA  GLY    31      57.337  27.774  42.516  1.00  0.00              
ATOM    107  C   GLY    31      56.543  28.061  43.787  1.00  0.00              
ATOM    108  O   GLY    31      55.899  27.171  44.341  1.00  0.00              
ATOM    109  N   ALA    32      56.595  29.308  44.242  1.00  0.00              
ATOM    110  CA  ALA    32      55.879  29.711  45.447  1.00  0.00              
ATOM    111  C   ALA    32      55.915  31.225  45.626  1.00  0.00              
ATOM    112  O   ALA    32      56.811  31.900  45.117  1.00  0.00              
ATOM    113  N   ARG    33      54.934  31.754  46.351  1.00  0.00              
ATOM    114  CA  ARG    33      54.853  33.189  46.595  1.00  0.00              
ATOM    115  C   ARG    33      54.310  33.473  47.992  1.00  0.00              
ATOM    116  O   ARG    33      53.212  33.041  48.344  1.00  0.00              
ATOM    117  N   LEU    34      55.088  34.203  48.786  1.00  0.00              
ATOM    118  CA  LEU    34      54.686  34.544  50.145  1.00  0.00              
ATOM    119  C   LEU    34      53.264  35.090  50.178  1.00  0.00              
ATOM    120  O   LEU    34      52.455  34.691  51.016  1.00  0.00              
ATOM    121  N   VAL    35      52.965  36.005  49.261  1.00  0.00              
ATOM    122  CA  VAL    35      51.639  36.604  49.186  1.00  0.00              
ATOM    123  C   VAL    35      50.689  35.736  48.366  1.00  0.00              
ATOM    124  O   VAL    35      51.038  35.272  47.282  1.00  0.00              
ATOM    125  N   GLN    36      49.488  35.522  48.895  1.00  0.00              
ATOM    126  CA  GLN    36      48.488  34.711  48.212  1.00  0.00              
ATOM    127  C   GLN    36      48.177  35.278  46.830  1.00  0.00              
ATOM    128  O   GLN    36      47.947  34.530  45.880  1.00  0.00              
ATOM    129  N   GLU    37      48.173  36.603  46.727  1.00  0.00              
ATOM    130  CA  GLU    37      47.890  37.269  45.462  1.00  0.00              
ATOM    131  C   GLU    37      48.963  36.949  44.426  1.00  0.00              
ATOM    132  O   GLU    37      48.671  36.395  43.366  1.00  0.00              
ATOM    133  N   GLY    38      50.205  37.302  44.739  1.00  0.00              
ATOM    134  CA  GLY    38      51.322  37.053  43.835  1.00  0.00              
ATOM    135  C   GLY    38      51.366  35.587  43.417  1.00  0.00              
ATOM    136  O   GLY    38      52.040  35.225  42.451  1.00  0.00              
ATOM    137  N   ASN    39      50.646  34.746  44.151  1.00  0.00              
ATOM    138  CA  ASN    39      50.602  33.318  43.856  1.00  0.00              
ATOM    139  C   ASN    39      49.540  33.011  42.805  1.00  0.00              
ATOM    140  O   ASN    39      49.650  32.032  42.066  1.00  0.00              
ATOM    141  N   ARG    40      48.514  33.852  42.746  1.00  0.00              
ATOM    142  CA  ARG    40      47.433  33.672  41.784  1.00  0.00              
ATOM    143  C   ARG    40      47.947  33.791  40.353  1.00  0.00              
ATOM    144  O   ARG    40      47.853  32.846  39.568  1.00  0.00              
ATOM    145  N   LEU    41      48.490  34.956  40.020  1.00  0.00              
ATOM    146  CA  LEU    41      49.021  35.199  38.683  1.00  0.00              
ATOM    147  C   LEU    41      49.940  34.062  38.247  1.00  0.00              
ATOM    148  O   LEU    41      49.875  33.600  37.108  1.00  0.00              
ATOM    149  N   HIS    42      50.794  33.614  39.162  1.00  0.00              
ATOM    150  CA  HIS    42      51.725  32.530  38.873  1.00  0.00              
ATOM    151  C   HIS    42      51.038  31.422  38.079  1.00  0.00              
ATOM    152  O   HIS    42      51.595  30.899  37.114  1.00  0.00              
ATOM    153  N   TYR    43      49.826  31.068  38.493  1.00  0.00              
ATOM    154  CA  TYR    43      49.065  30.021  37.823  1.00  0.00              
ATOM    155  C   TYR    43      48.576  30.492  36.457  1.00  0.00              
ATOM    156  O   TYR    43      48.386  29.690  35.544  1.00  0.00              
ATOM    157  N   LEU    44      48.373  31.799  36.327  1.00  0.00              
ATOM    158  CA  LEU    44      47.906  32.378  35.073  1.00  0.00              
ATOM    159  C   LEU    44      49.080  32.756  34.176  1.00  0.00              
ATOM    160  O   LEU    44      48.908  33.015  32.986  1.00  0.00              
ATOM    161  N   ALA    45      50.276  32.787  34.757  1.00  0.00              
ATOM    162  CA  ALA    45      51.480  33.131  34.011  1.00  0.00              
ATOM    163  C   ALA    45      52.247  31.880  33.598  1.00  0.00              
ATOM    164  O   ALA    45      53.030  31.904  32.649  1.00  0.00              
ATOM    165  N   ASP    46      52.018  30.787  34.319  1.00  0.00              
ATOM    166  CA  ASP    46      52.688  29.525  34.028  1.00  0.00              
ATOM    167  C   ASP    46      51.742  28.545  33.345  1.00  0.00              
ATOM    168  O   ASP    46      52.033  28.036  32.262  1.00  0.00              
ATOM    169  N   ARG    47      50.605  28.285  33.984  1.00  0.00              
ATOM    170  CA  ARG    47      49.613  27.366  33.438  1.00  0.00              
ATOM    171  C   ARG    47      48.387  28.124  32.937  1.00  0.00              
ATOM    172  O   ARG    47      47.323  27.540  32.733  1.00  0.00              
ATOM    173  N   ALA    48      48.543  29.428  32.743  1.00  0.00              
ATOM    174  CA  ALA    48      47.451  30.268  32.267  1.00  0.00              
ATOM    175  C   ALA    48      46.111  29.774  32.804  1.00  0.00              
ATOM    176  O   ALA    48      45.168  29.556  32.043  1.00  0.00              
ATOM    177  N   GLY    49      46.034  29.602  34.119  1.00  0.00              
ATOM    178  CA  GLY    49      44.810  29.132  34.759  1.00  0.00              
ATOM    179  C   GLY    49      44.682  29.698  36.170  1.00  0.00              
ATOM    180  O   GLY    49      45.603  30.337  36.680  1.00  0.00              
ATOM    181  N   ILE    50      43.534  29.459  36.794  1.00  0.00              
ATOM    182  CA  ILE    50      43.284  29.944  38.146  1.00  0.00              
ATOM    183  C   ILE    50      43.346  28.800  39.153  1.00  0.00              
ATOM    184  O   ILE    50      43.033  27.654  38.828  1.00  0.00              
ATOM    185  N   ARG    51      43.754  29.117  40.377  1.00  0.00              
ATOM    186  CA  ARG    51      43.859  28.116  41.433  1.00  0.00              
ATOM    187  C   ARG    51      42.600  27.256  41.495  1.00  0.00              
ATOM    188  O   ARG    51      41.511  27.677  41.104  1.00  0.00              
ATOM    189  N   GLY    52      42.751  26.022  41.998  1.00  0.00              
ATOM    190  CA  GLY    52      41.637  25.077  42.126  1.00  0.00              
ATOM    191  C   GLY    52      40.639  25.500  43.199  1.00  0.00              
ATOM    192  O   GLY    52      40.733  26.596  43.750  1.00  0.00              
ATOM    193  N   LEU    53      39.685  24.623  43.492  1.00  0.00              
ATOM    194  CA  LEU    53      38.672  24.904  44.500  1.00  0.00              
ATOM    195  C   LEU    53      38.601  23.786  45.535  1.00  0.00              
ATOM    196  O   LEU    53      38.204  22.663  45.225  1.00  0.00              
ATOM    197  N   PHE    54      38.991  24.101  46.766  1.00  0.00              
ATOM    198  CA  PHE    54      38.975  23.121  47.847  1.00  0.00              
ATOM    199  C   PHE    54      38.212  23.658  49.055  1.00  0.00              
ATOM    200  O   PHE    54      38.580  23.398  50.201  1.00  0.00              
ATOM    201  N   SER    55      37.147  24.408  48.789  1.00  0.00              
ATOM    202  CA  SER    55      36.335  24.986  49.853  1.00  0.00              
ATOM    203  C   SER    55      34.996  25.474  49.310  1.00  0.00              
ATOM    204  O   SER    55      34.729  25.382  48.112  1.00  0.00              
END
