
#######################################################
#                                                     #
#                        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   45 (  180),  selected   45 , name T0309AL243_2
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309AL243_2.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    Q       8      A       2           -
LGA    I       9      S       3           -
LGA    -       -      K       4           -
LGA    -       -      K       5           -
LGA    -       -      V       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      I       9           -
LGA    N      10      N      10           #
LGA    V      11      V      11          2.934
LGA    K      12      K      12          1.760
LGA    G      13      G      13          4.399
LGA    -       -      F      14           -
LGA    -       -      F      15           -
LGA    -       -      D      16           -
LGA    -       -      M      17           -
LGA    -       -      D      18           -
LGA    -       -      V      19           -
LGA    -       -      M      20           -
LGA    -       -      E      21           -
LGA    -       -      V      22           -
LGA    -       -      T      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      T      26           -
LGA    -       -      K      27           -
LGA    -       -      E      28           -
LGA    -       -      A      29           -
LGA    F      14      E      30          3.284
LGA    E      21      Y      31          3.020
LGA    V      22      T      32          2.908
LGA    T      23      Y      33          3.152
LGA    E      24      D      34          2.541
LGA    Q      25      -       -           -
LGA    T      26      -       -           -
LGA    K      27      F      35          1.281
LGA    E      28      K      36          2.153
LGA    Y      31      E      37          2.633
LGA    T      32      I      38          1.758
LGA    K      36      L      39          0.504
LGA    E      37      S      40          0.551
LGA    I      38      E      41          2.212
LGA    L      39      F      42          2.954
LGA    S      40      N      43          2.130
LGA    E      41      G      44          3.016
LGA    F      42      K      45          2.228
LGA    N      43      N      46          3.138
LGA    K      45      V      47           #
LGA    -       -      S      48           -
LGA    -       -      I      49           -
LGA    N      46      T      50          3.450
LGA    V      47      V      51          3.342
LGA    S      48      K      52          5.241
LGA    I      49      E      53           -
LGA    T      50      E      54           -
LGA    V      51      N      55           -
LGA    K      52      E      56           -
LGA    E      53      L      57           -
LGA    E      54      P      58           -
LGA    N      55      V      59           -
LGA    E      56      K      60           -
LGA    L      57      G      61           -
LGA    P      58      V      62           -
LGA    V      59      E      63           -
LGA    K      60      -       -           -
LGA    G      61      -       -           -
LGA    V      62      -       -           -
LGA    E      63      -       -           -
LGA    M      64      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45   62    5.0     23    2.84    21.74     27.013     0.783

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.928490 * X  +  -0.192903 * Y  +  -0.317325 * Z  + -34.854584
  Y_new =  -0.244610 * X  +  -0.325245 * Y  +   0.913445 * Z  + -10.758005
  Z_new =  -0.279415 * X  +   0.925745 * Y  +   0.254800 * Z  +  10.495343 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.302209   -1.839384  [ DEG:    74.6111   -105.3889 ]
  Theta =   0.283184    2.858408  [ DEG:    16.2253    163.7747 ]
  Phi   =  -2.883996    0.257597  [ DEG:  -165.2408     14.7592 ]
 
# 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: T0309AL243_2                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309AL243_2.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   62   5.0   23   2.84   21.74  27.013
REMARK  ---------------------------------------------------------- 
MOLECULE T0309AL243_2
REMARK Aligment from pdb entry: 1l4sA
ATOM      1  N   GLN     8       3.612 -12.072   1.869  1.00  0.00              
ATOM      2  CA  GLN     8       2.265 -11.734   2.399  1.00  0.00              
ATOM      3  C   GLN     8       1.181 -11.991   1.357  1.00  0.00              
ATOM      4  O   GLN     8       0.049 -12.335   1.697  1.00  0.00              
ATOM      5  N   ILE     9       1.537 -11.823   0.088  1.00  0.00              
ATOM      6  CA  ILE     9       0.596 -12.037  -1.005  1.00  0.00              
ATOM      7  C   ILE     9       1.313 -12.010  -2.351  1.00  0.00              
ATOM      8  O   ILE     9       1.659 -10.944  -2.858  1.00  0.00              
ATOM      9  N   ASN    10       1.534 -13.189  -2.922  1.00  0.00              
ATOM     10  CA  ASN    10       2.212 -13.298  -4.208  1.00  0.00              
ATOM     11  C   ASN    10       1.313 -13.961  -5.248  1.00  0.00              
ATOM     12  O   ASN    10       0.845 -15.084  -5.053  1.00  0.00              
ATOM     13  N   VAL    11       1.082 -13.262  -6.354  1.00  0.00              
ATOM     14  CA  VAL    11       0.244 -13.782  -7.428  1.00  0.00              
ATOM     15  C   VAL    11       1.029 -13.870  -8.735  1.00  0.00              
ATOM     16  O   VAL    11       1.608 -12.883  -9.188  1.00  0.00              
ATOM     17  N   LYS    12       1.044 -15.056  -9.337  1.00  0.00              
ATOM     18  CA  LYS    12       1.758 -15.266 -10.592  1.00  0.00              
ATOM     19  C   LYS    12       0.903 -16.036 -11.587  1.00  0.00              
ATOM     20  O   LYS    12      -0.069 -16.691 -11.211  1.00  0.00              
ATOM     21  N   GLY    13       1.264 -15.947 -12.862  1.00  0.00              
ATOM     22  CA  GLY    13       0.526 -16.627 -13.919  1.00  0.00              
ATOM     23  C   GLY    13       1.359 -16.701 -15.195  1.00  0.00              
ATOM     24  O   GLY    13       2.095 -15.770 -15.523  1.00  0.00              
ATOM     25  N   PHE    14      -1.437 -14.573 -18.188  1.00  0.00              
ATOM     26  CA  PHE    14      -1.757 -13.154 -18.080  1.00  0.00              
ATOM     27  C   PHE    14      -0.791 -12.456 -17.130  1.00  0.00              
ATOM     28  O   PHE    14       0.169 -13.059 -16.651  1.00  0.00              
ATOM     29  N   GLU    21      -1.053 -11.182 -16.858  1.00  0.00              
ATOM     30  CA  GLU    21      -0.206 -10.402 -15.962  1.00  0.00              
ATOM     31  C   GLU    21      -0.973 -10.013 -14.703  1.00  0.00              
ATOM     32  O   GLU    21      -2.194 -10.162 -14.638  1.00  0.00              
ATOM     33  N   VAL    22      -0.252  -9.524 -13.699  1.00  0.00              
ATOM     34  CA  VAL    22      -0.867  -9.127 -12.441  1.00  0.00              
ATOM     35  C   VAL    22      -1.258  -7.655 -12.463  1.00  0.00              
ATOM     36  O   VAL    22      -0.405  -6.771 -12.546  1.00  0.00              
ATOM     37  N   THR    23      -2.559  -7.403 -12.382  1.00  0.00              
ATOM     38  CA  THR    23      -3.078  -6.041 -12.387  1.00  0.00              
ATOM     39  C   THR    23      -3.403  -5.577 -10.968  1.00  0.00              
ATOM     40  O   THR    23      -3.779  -6.381 -10.116  1.00  0.00              
ATOM     41  N   GLU    24      -3.277  -4.265 -10.698  1.00  0.00              
ATOM     42  CA  GLU    24      -3.576  -3.705  -9.378  1.00  0.00              
ATOM     43  C   GLU    24      -4.998  -4.026  -8.932  1.00  0.00              
ATOM     44  O   GLU    24      -5.310  -3.975  -7.744  1.00  0.00              
ATOM     45  N   GLN    25      -5.854  -4.372  -9.889  1.00  0.00              
ATOM     46  CA  GLN    25      -7.232  -4.715  -9.576  1.00  0.00              
ATOM     47  C   GLN    25      -7.309  -6.126  -9.016  1.00  0.00              
ATOM     48  O   GLN    25      -8.024  -6.387  -8.047  1.00  0.00              
ATOM     49  N   THR    26      -6.545  -7.029  -9.624  1.00  0.00              
ATOM     50  CA  THR    26      -6.500  -8.411  -9.182  1.00  0.00              
ATOM     51  C   THR    26      -5.721  -8.502  -7.878  1.00  0.00              
ATOM     52  O   THR    26      -5.983  -9.366  -7.040  1.00  0.00              
ATOM     53  N   LYS    27      -4.777  -7.581  -7.707  1.00  0.00              
ATOM     54  CA  LYS    27      -3.975  -7.528  -6.503  1.00  0.00              
ATOM     55  C   LYS    27      -4.820  -6.978  -5.360  1.00  0.00              
ATOM     56  O   LYS    27      -4.832  -7.527  -4.260  1.00  0.00              
ATOM     57  N   GLU    28      -5.546  -5.898  -5.645  1.00  0.00              
ATOM     58  CA  GLU    28      -6.420  -5.277  -4.659  1.00  0.00              
ATOM     59  C   GLU    28      -7.587  -6.199  -4.324  1.00  0.00              
ATOM     60  O   GLU    28      -8.003  -6.281  -3.170  1.00  0.00              
ATOM     61  N   TYR    31      -8.101  -6.908  -5.320  1.00  0.00              
ATOM     62  CA  TYR    31      -9.204  -7.833  -5.086  1.00  0.00              
ATOM     63  C   TYR    31      -8.786  -8.888  -4.061  1.00  0.00              
ATOM     64  O   TYR    31      -9.353  -8.966  -2.965  1.00  0.00              
ATOM     65  N   THR    32      -7.777  -9.679  -4.402  1.00  0.00              
ATOM     66  CA  THR    32      -7.282 -10.699  -3.493  1.00  0.00              
ATOM     67  C   THR    32      -6.773 -10.065  -2.204  1.00  0.00              
ATOM     68  O   THR    32      -7.095 -10.527  -1.110  1.00  0.00              
ATOM     69  N   LYS    36      -5.982  -9.005  -2.337  1.00  0.00              
ATOM     70  CA  LYS    36      -5.438  -8.311  -1.173  1.00  0.00              
ATOM     71  C   LYS    36      -6.542  -7.825  -0.234  1.00  0.00              
ATOM     72  O   LYS    36      -6.429  -7.969   0.983  1.00  0.00              
ATOM     73  N   GLU    37      -7.604  -7.247  -0.791  1.00  0.00              
ATOM     74  CA  GLU    37      -8.704  -6.751   0.033  1.00  0.00              
ATOM     75  C   GLU    37      -9.317  -7.884   0.849  1.00  0.00              
ATOM     76  O   GLU    37      -9.774  -7.678   1.973  1.00  0.00              
ATOM     77  N   ILE    38      -9.321  -9.080   0.272  1.00  0.00              
ATOM     78  CA  ILE    38      -9.877 -10.250   0.947  1.00  0.00              
ATOM     79  C   ILE    38      -8.942 -10.745   2.048  1.00  0.00              
ATOM     80  O   ILE    38      -9.392 -11.324   3.036  1.00  0.00              
ATOM     81  N   LEU    39      -7.644 -10.507   1.888  1.00  0.00              
ATOM     82  CA  LEU    39      -6.673 -10.931   2.891  1.00  0.00              
ATOM     83  C   LEU    39      -6.860 -10.135   4.176  1.00  0.00              
ATOM     84  O   LEU    39      -7.002 -10.700   5.259  1.00  0.00              
ATOM     85  N   SER    40      -6.864  -8.815   4.037  1.00  0.00              
ATOM     86  CA  SER    40      -7.039  -7.920   5.175  1.00  0.00              
ATOM     87  C   SER    40      -8.382  -8.156   5.861  1.00  0.00              
ATOM     88  O   SER    40      -8.544  -7.877   7.049  1.00  0.00              
ATOM     89  N   GLU    41      -9.343  -8.672   5.100  1.00  0.00              
ATOM     90  CA  GLU    41     -10.674  -8.950   5.624  1.00  0.00              
ATOM     91  C   GLU    41     -10.686 -10.249   6.422  1.00  0.00              
ATOM     92  O   GLU    41     -11.492 -10.418   7.337  1.00  0.00              
ATOM     93  N   PHE    42      -9.792 -11.163   6.066  1.00  0.00              
ATOM     94  CA  PHE    42      -9.702 -12.449   6.748  1.00  0.00              
ATOM     95  C   PHE    42      -9.006 -12.305   8.099  1.00  0.00              
ATOM     96  O   PHE    42      -7.971 -12.925   8.348  1.00  0.00              
ATOM     97  N   ASN    43      -9.584 -11.483   8.968  1.00  0.00              
ATOM     98  CA  ASN    43      -9.028 -11.252  10.297  1.00  0.00              
ATOM     99  C   ASN    43      -9.227 -12.475  11.189  1.00  0.00              
ATOM    100  O   ASN    43      -8.275 -12.983  11.782  1.00  0.00              
ATOM    101  N   LYS    45     -10.468 -12.947  11.276  1.00  0.00              
ATOM    102  CA  LYS    45     -10.794 -14.117  12.091  1.00  0.00              
ATOM    103  C   LYS    45      -9.885 -15.293  11.744  1.00  0.00              
ATOM    104  O   LYS    45      -9.647 -16.183  12.558  1.00  0.00              
ATOM    105  N   ASN    46       4.147 -16.045   3.949  1.00  0.00              
ATOM    106  CA  ASN    46       4.497 -15.851   2.548  1.00  0.00              
ATOM    107  C   ASN    46       3.687 -16.772   1.637  1.00  0.00              
ATOM    108  O   ASN    46       4.210 -17.754   1.111  1.00  0.00              
ATOM    109  N   VAL    47       2.396 -16.461   1.432  1.00  0.00              
ATOM    110  CA  VAL    47       1.519 -17.257   0.573  1.00  0.00              
ATOM    111  C   VAL    47       1.777 -16.994  -0.907  1.00  0.00              
ATOM    112  O   VAL    47       2.271 -15.930  -1.281  1.00  0.00              
ATOM    113  N   SER    48       1.446 -17.972  -1.744  1.00  0.00              
ATOM    114  CA  SER    48       1.650 -17.845  -3.183  1.00  0.00              
ATOM    115  C   SER    48       0.445 -18.366  -3.960  1.00  0.00              
ATOM    116  O   SER    48      -0.034 -19.474  -3.718  1.00  0.00              
ATOM    117  N   ILE    49      -0.034 -17.555  -4.896  1.00  0.00              
ATOM    118  CA  ILE    49      -1.180 -17.923  -5.720  1.00  0.00              
ATOM    119  C   ILE    49      -0.812 -17.910  -7.200  1.00  0.00              
ATOM    120  O   ILE    49      -0.166 -16.978  -7.682  1.00  0.00              
ATOM    121  N   THR    50      -1.225 -18.950  -7.913  1.00  0.00              
ATOM    122  CA  THR    50      -0.943 -19.066  -9.338  1.00  0.00              
ATOM    123  C   THR    50      -2.232 -19.062 -10.153  1.00  0.00              
ATOM    124  O   THR    50      -3.261 -19.574  -9.709  1.00  0.00              
ATOM    125  N   VAL    51      -2.170 -18.482 -11.346  1.00  0.00              
ATOM    126  CA  VAL    51      -3.331 -18.410 -12.226  1.00  0.00              
ATOM    127  C   VAL    51      -3.040 -19.067 -13.570  1.00  0.00              
ATOM    128  O   VAL    51      -2.048 -18.754 -14.228  1.00  0.00              
ATOM    129  N   LYS    52      -3.922 -19.976 -13.974  1.00  0.00              
ATOM    130  CA  LYS    52      -3.778 -20.680 -15.241  1.00  0.00              
ATOM    131  C   LYS    52      -5.026 -20.491 -16.095  1.00  0.00              
ATOM    132  O   LYS    52      -5.920 -19.721 -15.741  1.00  0.00              
ATOM    133  N   GLU    53      -5.082 -21.190 -17.223  1.00  0.00              
ATOM    134  CA  GLU    53      -6.224 -21.085 -18.122  1.00  0.00              
ATOM    135  C   GLU    53      -6.330 -22.302 -19.030  1.00  0.00              
ATOM    136  O   GLU    53      -5.329 -22.827 -19.519  1.00  0.00              
ATOM    137  N   GLU    54      -7.562 -22.725 -19.257  1.00  0.00              
ATOM    138  CA  GLU    54      -7.856 -23.861 -20.111  1.00  0.00              
ATOM    139  C   GLU    54      -8.965 -23.481 -21.086  1.00  0.00              
ATOM    140  O   GLU    54      -9.745 -22.569 -20.813  1.00  0.00              
ATOM    141  N   ASN    55      -9.061 -24.161 -22.233  1.00  0.00              
ATOM    142  CA  ASN    55     -10.096 -23.861 -23.226  1.00  0.00              
ATOM    143  C   ASN    55     -11.492 -23.835 -22.619  1.00  0.00              
ATOM    144  O   ASN    55     -12.407 -23.206 -23.152  1.00  0.00              
ATOM    145  N   GLU    56      -1.119 -21.897  -2.544  1.00  0.00              
ATOM    146  CA  GLU    56      -0.440 -22.691  -1.527  1.00  0.00              
ATOM    147  C   GLU    56       0.065 -21.791  -0.406  1.00  0.00              
ATOM    148  O   GLU    56       0.655 -20.742  -0.664  1.00  0.00              
ATOM    149  N   LEU    57      -0.167 -22.198   0.838  1.00  0.00              
ATOM    150  CA  LEU    57       0.266 -21.413   1.987  1.00  0.00              
ATOM    151  C   LEU    57       0.973 -22.287   3.016  1.00  0.00              
ATOM    152  O   LEU    57       0.485 -23.357   3.382  1.00  0.00              
ATOM    153  N   PRO    58       2.118 -21.812   3.495  1.00  0.00              
ATOM    154  CA  PRO    58       2.894 -22.529   4.502  1.00  0.00              
ATOM    155  C   PRO    58       2.700 -21.896   5.873  1.00  0.00              
ATOM    156  O   PRO    58       2.818 -20.681   6.026  1.00  0.00              
ATOM    157  N   VAL    59       2.403 -22.724   6.869  1.00  0.00              
ATOM    158  CA  VAL    59       2.197 -22.233   8.227  1.00  0.00              
ATOM    159  C   VAL    59       3.051 -23.016   9.221  1.00  0.00              
ATOM    160  O   VAL    59       3.581 -24.077   8.893  1.00  0.00              
ATOM    161  N   LYS    60       3.197 -22.503  10.453  1.00  0.00              
ATOM    162  CA  LYS    60       3.994 -23.158  11.493  1.00  0.00              
ATOM    163  C   LYS    60       3.345 -24.444  12.006  1.00  0.00              
ATOM    164  O   LYS    60       3.957 -25.194  12.765  1.00  0.00              
ATOM    165  N   GLY    61       2.103 -24.691  11.597  1.00  0.00              
ATOM    166  CA  GLY    61       1.383 -25.885  12.030  1.00  0.00              
ATOM    167  C   GLY    61       0.918 -26.726  10.842  1.00  0.00              
ATOM    168  O   GLY    61      -0.023 -27.509  10.961  1.00  0.00              
ATOM    169  N   VAL    62       1.583 -26.566   9.701  1.00  0.00              
ATOM    170  CA  VAL    62       1.213 -27.330   8.520  1.00  0.00              
ATOM    171  C   VAL    62       1.102 -26.475   7.275  1.00  0.00              
ATOM    172  O   VAL    62       1.533 -25.323   7.261  1.00  0.00              
ATOM    173  N   GLU    63       0.521 -27.046   6.222  1.00  0.00              
ATOM    174  CA  GLU    63       0.353 -26.337   4.960  1.00  0.00              
ATOM    175  C   GLU    63      -1.040 -26.572   4.383  1.00  0.00              
ATOM    176  O   GLU    63      -1.593 -27.665   4.497  1.00  0.00              
ATOM    177  N   MET    64      -1.603 -25.539   3.761  1.00  0.00              
ATOM    178  CA  MET    64      -2.931 -25.634   3.166  1.00  0.00              
ATOM    179  C   MET    64      -2.864 -25.466   1.651  1.00  0.00              
ATOM    180  O   MET    64      -1.930 -24.859   1.124  1.00  0.00              
END
