
#######################################################
#                                                     #
#                        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   41 (  164),  selected   41 , name T0358AL381_4-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358AL381_4-D1.T0358_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D      31      -       -           -
LGA    D      32      -       -           -
LGA    Q      33      G      10          3.280
LGA    G      34      P      11          0.762
LGA    S      35      -       -           -
LGA    H      36      F      12          3.545
LGA    F      37      T      13          2.930
LGA    R      38      R      14          3.990
LGA    L      39      R      15          4.608
LGA    V      40      Q      16          2.773
LGA    V      41      A      17          3.760
LGA    R      42      -       -           -
LGA    D      43      -       -           -
LGA    T      44      -       -           -
LGA    E      45      -       -           -
LGA    G      46      -       -           -
LGA    R      47      Q      18          2.583
LGA    M      48      A      19          4.929
LGA    V      49      V      20          4.758
LGA    W      50      T      21          3.802
LGA    R      51      T      22          4.004
LGA    A      52      T      23          3.396
LGA    W      53      Y      24          1.482
LGA    F      55      S      25          1.974
LGA    E      56      -       -           -
LGA    P      57      N      26          3.995
LGA    D      58      I      27          3.941
LGA    A      59      T      28           #
LGA    G      60      L      29           -
LGA    -       -      E      30           -
LGA    -       -      D      31           -
LGA    -       -      D      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    -       -      F      37           -
LGA    -       -      R      38           -
LGA    -       -      L      39           -
LGA    -       -      V      40           -
LGA    -       -      V      41           -
LGA    -       -      R      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    E      61      E      45          3.548
LGA    G      62      G      46          1.859
LGA    L      63      R      47          2.318
LGA    N      64      M      48          3.065
LGA    R      65      -       -           -
LGA    Y      66      V      49          1.511
LGA    I      67      W      50          3.973
LGA    R      68      R      51           -
LGA    T      69      A      52           -
LGA    S      70      W      53           -
LGA    G      71      N      54           -
LGA    I      72      F      55           -
LGA    -       -      E      56           -
LGA    -       -      P      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    -       -      N      64           -
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   41   65    5.0     24    3.38    16.67     19.845     0.690

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.270960 * X  +   0.047816 * Y  +  -0.961402 * Z  + 140.519058
  Y_new =  -0.270306 * X  +   0.954799 * Y  +   0.123670 * Z  + -19.784054
  Z_new =   0.923859 * X  +   0.293382 * Y  +  -0.245787 * Z  +   9.971416 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.268148   -0.873444  [ DEG:   129.9553    -50.0447 ]
  Theta =  -1.178044   -1.963549  [ DEG:   -67.4969   -112.5031 ]
  Phi   =  -2.357404    0.784189  [ DEG:  -135.0693     44.9307 ]
 
# 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: T0358AL381_4-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL381_4-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   41   65   5.0   24   3.38   16.67  19.845
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL381_4-D1
REMARK Aligment from pdb entry: 2cwiA
ATOM      1  N   ASP    31      11.316   6.825   6.230  1.00  0.00              
ATOM      2  CA  ASP    31      11.260   7.833   5.168  1.00  0.00              
ATOM      3  C   ASP    31      11.899   7.360   3.865  1.00  0.00              
ATOM      4  O   ASP    31      11.361   7.639   2.707  1.00  0.00              
ATOM      5  N   ASP    32      13.014   6.644   3.966  1.00  0.00              
ATOM      6  CA  ASP    32      13.711   6.253   2.689  1.00  0.00              
ATOM      7  C   ASP    32      12.843   5.231   1.974  1.00  0.00              
ATOM      8  O   ASP    32      12.656   5.275   0.731  1.00  0.00              
ATOM      9  N   GLN    33      12.373   4.279   2.760  1.00  0.00              
ATOM     10  CA  GLN    33      11.481   3.231   2.230  1.00  0.00              
ATOM     11  C   GLN    33      10.255   3.859   1.494  1.00  0.00              
ATOM     12  O   GLN    33       9.838   3.420   0.421  1.00  0.00              
ATOM     13  N   GLY    34       9.606   4.829   2.128  1.00  0.00              
ATOM     14  CA  GLY    34       8.461   5.527   1.506  1.00  0.00              
ATOM     15  C   GLY    34       8.817   6.237   0.177  1.00  0.00              
ATOM     16  O   GLY    34       8.146   6.072  -0.840  1.00  0.00              
ATOM     17  N   SER    35       9.918   6.966   0.193  1.00  0.00              
ATOM     18  CA  SER    35      10.447   7.604  -1.024  1.00  0.00              
ATOM     19  C   SER    35      10.689   6.574  -2.088  1.00  0.00              
ATOM     20  O   SER    35      10.330   6.816  -3.213  1.00  0.00              
ATOM     21  N   HIS    36      11.211   5.392  -1.716  1.00  0.00              
ATOM     22  CA  HIS    36      11.429   4.357  -2.714  1.00  0.00              
ATOM     23  C   HIS    36      10.113   3.707  -3.188  1.00  0.00              
ATOM     24  O   HIS    36       9.913   3.520  -4.379  1.00  0.00              
ATOM     25  N   PHE    37       9.204   3.389  -2.256  1.00  0.00              
ATOM     26  CA  PHE    37       7.869   2.830  -2.651  1.00  0.00              
ATOM     27  C   PHE    37       7.079   3.765  -3.589  1.00  0.00              
ATOM     28  O   PHE    37       6.459   3.329  -4.536  1.00  0.00              
ATOM     29  N   ARG    38       7.190   5.046  -3.320  1.00  0.00              
ATOM     30  CA  ARG    38       6.622   6.078  -4.204  1.00  0.00              
ATOM     31  C   ARG    38       7.167   5.931  -5.633  1.00  0.00              
ATOM     32  O   ARG    38       6.462   6.120  -6.651  1.00  0.00              
ATOM     33  N   LEU    39       8.420   5.553  -5.719  1.00  0.00              
ATOM     34  CA  LEU    39       9.026   5.398  -7.030  1.00  0.00              
ATOM     35  C   LEU    39       8.636   4.057  -7.667  1.00  0.00              
ATOM     36  O   LEU    39       8.337   3.953  -8.859  1.00  0.00              
ATOM     37  N   VAL    40       8.590   3.004  -6.871  1.00  0.00              
ATOM     38  CA  VAL    40       8.213   1.688  -7.377  1.00  0.00              
ATOM     39  C   VAL    40       6.875   1.698  -8.023  1.00  0.00              
ATOM     40  O   VAL    40       6.713   1.142  -9.093  1.00  0.00              
ATOM     41  N   VAL    41       5.878   2.310  -7.366  1.00  0.00              
ATOM     42  CA  VAL    41       4.520   2.290  -7.830  1.00  0.00              
ATOM     43  C   VAL    41       4.335   3.018  -9.142  1.00  0.00              
ATOM     44  O   VAL    41       3.329   2.779  -9.855  1.00  0.00              
ATOM     45  N   ARG    42       5.312   3.894  -9.457  1.00  0.00              
ATOM     46  CA  ARG    42       5.362   4.608 -10.737  1.00  0.00              
ATOM     47  C   ARG    42       5.668   3.781 -11.954  1.00  0.00              
ATOM     48  O   ARG    42       5.475   4.238 -13.127  1.00  0.00              
ATOM     49  N   ASP    43       6.165   2.577 -11.754  1.00  0.00              
ATOM     50  CA  ASP    43       6.285   1.613 -12.829  1.00  0.00              
ATOM     51  C   ASP    43       4.974   1.083 -13.345  1.00  0.00              
ATOM     52  O   ASP    43       3.956   1.136 -12.621  1.00  0.00              
ATOM     53  N   THR    44       4.978   0.455 -14.548  1.00  0.00              
ATOM     54  CA  THR    44       3.745   0.103 -15.242  1.00  0.00              
ATOM     55  C   THR    44       2.801  -0.888 -14.508  1.00  0.00              
ATOM     56  O   THR    44       1.572  -0.841 -14.642  1.00  0.00              
ATOM     57  N   GLU    45       3.391  -1.755 -13.715  1.00  0.00              
ATOM     58  CA  GLU    45       2.678  -2.737 -12.852  1.00  0.00              
ATOM     59  C   GLU    45       2.059  -2.181 -11.553  1.00  0.00              
ATOM     60  O   GLU    45       1.380  -2.897 -10.869  1.00  0.00              
ATOM     61  N   GLY    46       2.308  -0.920 -11.216  1.00  0.00              
ATOM     62  CA  GLY    46       1.650  -0.246 -10.102  1.00  0.00              
ATOM     63  C   GLY    46       2.019  -1.011  -8.838  1.00  0.00              
ATOM     64  O   GLY    46       3.165  -1.595  -8.681  1.00  0.00              
ATOM     65  N   ARG    47       1.034  -1.093  -7.930  1.00  0.00              
ATOM     66  CA  ARG    47       1.233  -1.884  -6.731  1.00  0.00              
ATOM     67  C   ARG    47       1.404  -3.398  -6.962  1.00  0.00              
ATOM     68  O   ARG    47       1.760  -4.089  -6.011  1.00  0.00              
ATOM     69  N   MET    48       1.177  -3.914  -8.163  1.00  0.00              
ATOM     70  CA  MET    48       1.333  -5.338  -8.454  1.00  0.00              
ATOM     71  C   MET    48       2.775  -5.774  -8.405  1.00  0.00              
ATOM     72  O   MET    48       3.077  -6.995  -8.395  1.00  0.00              
ATOM     73  N   VAL    49       3.674  -4.803  -8.247  1.00  0.00              
ATOM     74  CA  VAL    49       5.074  -5.077  -7.950  1.00  0.00              
ATOM     75  C   VAL    49       5.229  -5.745  -6.666  1.00  0.00              
ATOM     76  O   VAL    49       6.247  -6.410  -6.456  1.00  0.00              
ATOM     77  N   TRP    50       4.268  -5.532  -5.742  1.00  0.00              
ATOM     78  CA  TRP    50       4.298  -6.212  -4.521  1.00  0.00              
ATOM     79  C   TRP    50       3.411  -7.434  -4.623  1.00  0.00              
ATOM     80  O   TRP    50       2.190  -7.302  -4.513  1.00  0.00              
ATOM     81  N   ARG    51       4.007  -8.636  -4.705  1.00  0.00              
ATOM     82  CA  ARG    51       3.228  -9.838  -4.744  1.00  0.00              
ATOM     83  C   ARG    51       2.301 -10.078  -3.576  1.00  0.00              
ATOM     84  O   ARG    51       1.164 -10.583  -3.756  1.00  0.00              
ATOM     85  N   ALA    52       2.705  -9.682  -2.378  1.00  0.00              
ATOM     86  CA  ALA    52       1.793  -9.995  -1.269  1.00  0.00              
ATOM     87  C   ALA    52       0.546  -9.109  -1.252  1.00  0.00              
ATOM     88  O   ALA    52      -0.496  -9.521  -0.767  1.00  0.00              
ATOM     89  N   TRP    53       0.643  -7.924  -1.849  1.00  0.00              
ATOM     90  CA  TRP    53      -0.483  -7.004  -2.062  1.00  0.00              
ATOM     91  C   TRP    53      -1.484  -7.625  -3.110  1.00  0.00              
ATOM     92  O   TRP    53      -2.719  -7.655  -2.921  1.00  0.00              
ATOM     93  N   PHE    55      -0.930  -8.087  -4.226  1.00  0.00              
ATOM     94  CA  PHE    55      -1.700  -8.834  -5.245  1.00  0.00              
ATOM     95  C   PHE    55      -2.437 -10.022  -4.583  1.00  0.00              
ATOM     96  O   PHE    55      -3.620 -10.275  -4.814  1.00  0.00              
ATOM     97  N   GLU    56      -1.743 -10.750  -3.721  1.00  0.00              
ATOM     98  CA  GLU    56      -2.352 -11.948  -3.126  1.00  0.00              
ATOM     99  C   GLU    56      -3.392 -11.617  -2.007  1.00  0.00              
ATOM    100  O   GLU    56      -4.417 -12.317  -1.833  1.00  0.00              
ATOM    101  N   PRO    57      -3.111 -10.582  -1.230  1.00  0.00              
ATOM    102  CA  PRO    57      -3.750 -10.372   0.118  1.00  0.00              
ATOM    103  C   PRO    57      -4.531  -9.071   0.271  1.00  0.00              
ATOM    104  O   PRO    57      -5.300  -8.922   1.194  1.00  0.00              
ATOM    105  N   ASP    58      -4.500  -8.224  -0.740  1.00  0.00              
ATOM    106  CA  ASP    58      -5.046  -6.898  -0.696  1.00  0.00              
ATOM    107  C   ASP    58      -5.844  -6.519  -1.892  1.00  0.00              
ATOM    108  O   ASP    58      -6.919  -5.923  -1.729  1.00  0.00              
ATOM    109  N   ALA    59      -5.330  -6.812  -3.083  1.00  0.00              
ATOM    110  CA  ALA    59      -5.901  -6.311  -4.326  1.00  0.00              
ATOM    111  C   ALA    59      -7.327  -6.798  -4.480  1.00  0.00              
ATOM    112  O   ALA    59      -8.204  -6.002  -4.893  1.00  0.00              
ATOM    113  N   GLY    60      -7.554  -8.025  -4.082  1.00  0.00              
ATOM    114  CA  GLY    60      -8.868  -8.710  -4.202  1.00  0.00              
ATOM    115  C   GLY    60      -9.896  -8.429  -3.105  1.00  0.00              
ATOM    116  O   GLY    60     -11.057  -8.846  -3.211  1.00  0.00              
ATOM    117  N   GLU    61      -9.503  -7.581  -2.152  1.00  0.00              
ATOM    118  CA  GLU    61     -10.233  -7.416  -0.924  1.00  0.00              
ATOM    119  C   GLU    61     -11.002  -6.099  -0.894  1.00  0.00              
ATOM    120  O   GLU    61     -10.587  -5.049  -1.469  1.00  0.00              
ATOM    121  N   GLY    62     -12.102  -6.156  -0.178  1.00  0.00              
ATOM    122  CA  GLY    62     -12.834  -4.981   0.258  1.00  0.00              
ATOM    123  C   GLY    62     -12.095  -4.388   1.468  1.00  0.00              
ATOM    124  O   GLY    62     -12.156  -4.915   2.642  1.00  0.00              
ATOM    125  N   LEU    63     -11.408  -3.282   1.233  1.00  0.00              
ATOM    126  CA  LEU    63     -10.614  -2.634   2.325  1.00  0.00              
ATOM    127  C   LEU    63     -11.279  -1.444   2.959  1.00  0.00              
ATOM    128  O   LEU    63     -10.640  -0.670   3.696  1.00  0.00              
ATOM    129  N   ASN    64     -12.586  -1.304   2.719  1.00  0.00              
ATOM    130  CA  ASN    64     -13.281  -0.141   3.190  1.00  0.00              
ATOM    131  C   ASN    64     -13.245  -0.008   4.727  1.00  0.00              
ATOM    132  O   ASN    64     -13.374   1.123   5.238  1.00  0.00              
ATOM    133  N   ARG    65     -13.054  -1.086   5.436  1.00  0.00              
ATOM    134  CA  ARG    65     -13.091  -1.098   6.911  1.00  0.00              
ATOM    135  C   ARG    65     -11.771  -1.391   7.528  1.00  0.00              
ATOM    136  O   ARG    65     -11.621  -1.394   8.747  1.00  0.00              
ATOM    137  N   TYR    66     -10.765  -1.545   6.671  1.00  0.00              
ATOM    138  CA  TYR    66      -9.462  -2.007   7.123  1.00  0.00              
ATOM    139  C   TYR    66      -8.825  -1.036   8.124  1.00  0.00              
ATOM    140  O   TYR    66      -8.233  -1.508   9.088  1.00  0.00              
ATOM    141  N   ILE    67      -8.926   0.288   7.890  1.00  0.00              
ATOM    142  CA  ILE    67      -8.455   1.310   8.782  1.00  0.00              
ATOM    143  C   ILE    67      -9.532   1.975   9.717  1.00  0.00              
ATOM    144  O   ILE    67      -9.263   3.045  10.305  1.00  0.00              
ATOM    145  N   ARG    68     -10.691   1.347   9.849  1.00  0.00              
ATOM    146  CA  ARG    68     -11.782   1.885  10.635  1.00  0.00              
ATOM    147  C   ARG    68     -11.412   1.959  12.154  1.00  0.00              
ATOM    148  O   ARG    68     -11.870   2.848  12.791  1.00  0.00              
ATOM    149  N   THR    69     -10.628   1.044  12.726  1.00  0.00              
ATOM    150  CA  THR    69     -10.246   1.177  14.106  1.00  0.00              
ATOM    151  C   THR    69      -9.267   2.344  14.315  1.00  0.00              
ATOM    152  O   THR    69      -9.134   2.873  15.455  1.00  0.00              
ATOM    153  N   SER    70      -8.682   2.846  13.241  1.00  0.00              
ATOM    154  CA  SER    70      -7.655   3.872  13.373  1.00  0.00              
ATOM    155  C   SER    70      -8.231   5.266  13.652  1.00  0.00              
ATOM    156  O   SER    70      -9.175   5.742  12.953  1.00  0.00              
ATOM    157  N   GLY    71      -7.584   5.934  14.625  1.00  0.00              
ATOM    158  CA  GLY    71      -7.688   7.392  14.833  1.00  0.00              
ATOM    159  C   GLY    71      -6.664   8.098  13.986  1.00  0.00              
ATOM    160  O   GLY    71      -5.474   8.010  14.204  1.00  0.00              
ATOM    161  N   ILE    72      -7.121   8.774  12.956  1.00  0.00              
ATOM    162  CA  ILE    72      -6.203   9.262  11.955  1.00  0.00              
ATOM    163  C   ILE    72      -6.427  10.775  11.830  1.00  0.00              
ATOM    164  O   ILE    72      -5.692  11.448  11.130  1.00  0.00              
END
