
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0299AL243_3-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299AL243_3-D1.T0299_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A      22      -       -           -
LGA    E      23      -       -           -
LGA    L      24      -       -           -
LGA    R      25      -       -           -
LGA    Q      26      -       -           -
LGA    E      27      -       -           -
LGA    L      28      -       -           -
LGA    T      29      -       -           -
LGA    N      30      -       -           -
LGA    L      31      -       -           -
LGA    G      32      -       -           -
LGA    L      33      -       -           -
LGA    E      34      -       -           -
LGA    K      35      -       -           -
LGA    V      36      M       1          4.539
LGA    E      37      T       2          1.260
LGA    S      38      R       3          1.260
LGA    Y      39      Y       4          1.445
LGA    I      40      A       5          1.731
LGA    N      41      L       6          0.936
LGA    S      42      L       7          0.680
LGA    -       -      V       8           -
LGA    -       -      R       9           -
LGA    -       -      G      10           -
LGA    -       -      I      11           -
LGA    -       -      N      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    -       -      V      19           -
LGA    -       -      V      20           -
LGA    -       -      M      21           -
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    -       -      L      24           -
LGA    -       -      R      25           -
LGA    -       -      Q      26           -
LGA    -       -      E      27           -
LGA    -       -      L      28           -
LGA    -       -      T      29           -
LGA    -       -      N      30           -
LGA    -       -      L      31           -
LGA    -       -      G      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    -       -      E      37           -
LGA    -       -      S      38           -
LGA    -       -      Y      39           -
LGA    -       -      I      40           -
LGA    -       -      N      41           -
LGA    -       -      S      42           -
LGA    G      43      G      43          1.922
LGA    N      44      N      44          1.630
LGA    I      45      I      45          2.256
LGA    F      46      F      46          2.184
LGA    F      47      F      47          2.290
LGA    T      48      T      48          1.302
LGA    S      49      S      49          1.193
LGA    I      50      I      50          2.241
LGA    D      51      D      51          1.543
LGA    S      52      S      52          1.455
LGA    K      53      K      53          3.642
LGA    A      54      A      54          3.370
LGA    Q      55      Q      55          1.300
LGA    L      56      L      56          1.648
LGA    V      57      V      57          2.166
LGA    E      58      E      58          1.000
LGA    K      59      K      59          1.392
LGA    L      60      L      60          2.293
LGA    E      61      E      61          0.662
LGA    T      62      T      62          1.716
LGA    F      63      F      63          3.241
LGA    F      64      F      64          2.455
LGA    A      65      A      65          1.661
LGA    V      66      V      66          3.845
LGA    -       -      H      67           -
LGA    H      67      Y      68          2.405
LGA    -       -      P      69           -
LGA    -       -      F      70           -
LGA    -       -      I      71           -
LGA    -       -      Q      72           -
LGA    -       -      S      73           -
LGA    -       -      F      74           -
LGA    -       -      S      75           -
LGA    -       -      L      76           -
LGA    -       -      L      77           -
LGA    -       -      S      78           -
LGA    -       -      A     168           -
LGA    -       -      K     169           -
LGA    -       -      T     170           -
LGA    -       -      F     171           -
LGA    -       -      D     172           -
LGA    -       -      K     173           -
LGA    -       -      I     174           -
LGA    -       -      G     175           -
LGA    -       -      Q     176           -
LGA    -       -      M     177           -
LGA    -       -      L     178           -
LGA    -       -      K     179           -
LGA    -       -      K     180           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   91    5.0     32    2.16    78.12     29.935     1.415

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.582009 * X  +  -0.559829 * Y  +  -0.589794 * Z  +  13.215118
  Y_new =   0.423433 * X  +  -0.827843 * Y  +   0.367940 * Z  +  57.222466
  Z_new =  -0.694240 * X  +  -0.035594 * Y  +   0.718862 * Z  + -11.608220 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.049474    3.092119  [ DEG:    -2.8346    177.1654 ]
  Theta =   0.767364    2.374228  [ DEG:    43.9667    136.0333 ]
  Phi   =   2.512623   -0.628969  [ DEG:   143.9627    -36.0373 ]
 
# 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: T0299AL243_3-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL243_3-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   91   5.0   32   2.16   78.12  29.935
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL243_3-D1
REMARK Aligment from pdb entry: 1eejA
ATOM      1  N   ALA    22      -9.178  59.804 -17.100  1.00  0.00              
ATOM      2  CA  ALA    22      -9.512  58.676 -17.957  1.00  0.00              
ATOM      3  C   ALA    22      -8.715  57.434 -17.571  1.00  0.00              
ATOM      4  O   ALA    22      -9.228  56.317 -17.631  1.00  0.00              
ATOM      5  N   GLU    23      -7.461  57.631 -17.177  1.00  0.00              
ATOM      6  CA  GLU    23      -6.612  56.508 -16.792  1.00  0.00              
ATOM      7  C   GLU    23      -7.060  55.874 -15.481  1.00  0.00              
ATOM      8  O   GLU    23      -6.989  54.655 -15.322  1.00  0.00              
ATOM      9  N   LEU    24      -7.512  56.698 -14.540  1.00  0.00              
ATOM     10  CA  LEU    24      -7.977  56.177 -13.257  1.00  0.00              
ATOM     11  C   LEU    24      -9.245  55.365 -13.508  1.00  0.00              
ATOM     12  O   LEU    24      -9.441  54.295 -12.941  1.00  0.00              
ATOM     13  N   ARG    25     -10.100  55.898 -14.373  1.00  0.00              
ATOM     14  CA  ARG    25     -11.355  55.259 -14.723  1.00  0.00              
ATOM     15  C   ARG    25     -11.093  53.937 -15.445  1.00  0.00              
ATOM     16  O   ARG    25     -11.673  52.905 -15.104  1.00  0.00              
ATOM     17  N   GLN    26     -10.209  53.973 -16.438  1.00  0.00              
ATOM     18  CA  GLN    26      -9.861  52.782 -17.205  1.00  0.00              
ATOM     19  C   GLN    26      -9.324  51.677 -16.297  1.00  0.00              
ATOM     20  O   GLN    26      -9.742  50.524 -16.397  1.00  0.00              
ATOM     21  N   GLU    27      -8.394  52.029 -15.414  1.00  0.00              
ATOM     22  CA  GLU    27      -7.817  51.055 -14.495  1.00  0.00              
ATOM     23  C   GLU    27      -8.889  50.479 -13.569  1.00  0.00              
ATOM     24  O   GLU    27      -8.959  49.264 -13.355  1.00  0.00              
ATOM     25  N   LEU    28      -9.719  51.356 -13.013  1.00  0.00              
ATOM     26  CA  LEU    28     -10.775  50.898 -12.127  1.00  0.00              
ATOM     27  C   LEU    28     -11.648  49.870 -12.820  1.00  0.00              
ATOM     28  O   LEU    28     -11.896  48.787 -12.287  1.00  0.00              
ATOM     29  N   THR    29     -12.111  50.209 -14.019  1.00  0.00              
ATOM     30  CA  THR    29     -12.958  49.308 -14.796  1.00  0.00              
ATOM     31  C   THR    29     -12.290  47.944 -14.961  1.00  0.00              
ATOM     32  O   THR    29     -12.914  46.908 -14.735  1.00  0.00              
ATOM     33  N   ASN    30     -11.019  47.951 -15.344  1.00  0.00              
ATOM     34  CA  ASN    30     -10.269  46.713 -15.532  1.00  0.00              
ATOM     35  C   ASN    30     -10.184  45.894 -14.245  1.00  0.00              
ATOM     36  O   ASN    30     -10.326  44.670 -14.270  1.00  0.00              
ATOM     37  N   LEU    31      -9.954  46.570 -13.121  1.00  0.00              
ATOM     38  CA  LEU    31      -9.860  45.891 -11.831  1.00  0.00              
ATOM     39  C   LEU    31     -11.223  45.357 -11.392  1.00  0.00              
ATOM     40  O   LEU    31     -11.319  44.574 -10.445  1.00  0.00              
ATOM     41  N   GLY    32     -12.272  45.795 -12.082  1.00  0.00              
ATOM     42  CA  GLY    32     -13.614  45.338 -11.766  1.00  0.00              
ATOM     43  C   GLY    32     -14.471  46.284 -10.942  1.00  0.00              
ATOM     44  O   GLY    32     -15.467  45.855 -10.365  1.00  0.00              
ATOM     45  N   LEU    33     -14.096  47.558 -10.871  1.00  0.00              
ATOM     46  CA  LEU    33     -14.874  48.530 -10.099  1.00  0.00              
ATOM     47  C   LEU    33     -16.291  48.668 -10.654  1.00  0.00              
ATOM     48  O   LEU    33     -16.489  49.127 -11.780  1.00  0.00              
ATOM     49  N   GLU    34     -17.272  48.281  -9.843  1.00  0.00              
ATOM     50  CA  GLU    34     -18.677  48.329 -10.241  1.00  0.00              
ATOM     51  C   GLU    34     -19.493  49.278  -9.370  1.00  0.00              
ATOM     52  O   GLU    34     -20.689  49.064  -9.162  1.00  0.00              
ATOM     53  N   LYS    35     -18.842  50.320  -8.863  1.00  0.00              
ATOM     54  CA  LYS    35     -19.515  51.279  -8.006  1.00  0.00              
ATOM     55  C   LYS    35     -18.499  51.907  -7.069  1.00  0.00              
ATOM     56  O   LYS    35     -17.359  51.446  -7.000  1.00  0.00              
ATOM     57  N   VAL    36     -18.897  52.950  -6.347  1.00  0.00              
ATOM     58  CA  VAL    36     -17.979  53.621  -5.431  1.00  0.00              
ATOM     59  C   VAL    36     -18.588  53.828  -4.050  1.00  0.00              
ATOM     60  O   VAL    36     -19.806  53.974  -3.913  1.00  0.00              
ATOM     61  N   GLU    37     -17.747  53.826  -2.999  1.00  0.00              
ATOM     62  CA  GLU    37     -16.296  53.633  -3.083  1.00  0.00              
ATOM     63  C   GLU    37     -15.930  52.165  -3.270  1.00  0.00              
ATOM     64  O   GLU    37     -16.660  51.270  -2.840  1.00  0.00              
ATOM     65  N   SER    38     -14.800  51.931  -3.924  1.00  0.00              
ATOM     66  CA  SER    38     -14.308  50.581  -4.162  1.00  0.00              
ATOM     67  C   SER    38     -12.871  50.535  -3.666  1.00  0.00              
ATOM     68  O   SER    38     -12.033  51.367  -4.039  1.00  0.00              
ATOM     69  N   TYR    39     -12.596  49.555  -2.821  1.00  0.00              
ATOM     70  CA  TYR    39     -11.281  49.389  -2.230  1.00  0.00              
ATOM     71  C   TYR    39     -10.420  48.359  -2.953  1.00  0.00              
ATOM     72  O   TYR    39     -10.884  47.269  -3.273  1.00  0.00              
ATOM     73  N   ILE    40      -9.169  48.717  -3.225  1.00  0.00              
ATOM     74  CA  ILE    40      -8.245  47.781  -3.849  1.00  0.00              
ATOM     75  C   ILE    40      -7.200  47.478  -2.786  1.00  0.00              
ATOM     76  O   ILE    40      -6.512  48.381  -2.303  1.00  0.00              
ATOM     77  N   ASN    41      -7.097  46.208  -2.408  1.00  0.00              
ATOM     78  CA  ASN    41      -6.138  45.799  -1.391  1.00  0.00              
ATOM     79  C   ASN    41      -4.727  45.758  -1.958  1.00  0.00              
ATOM     80  O   ASN    41      -4.538  45.733  -3.176  1.00  0.00              
ATOM     81  N   SER    42      -3.738  45.755  -1.069  1.00  0.00              
ATOM     82  CA  SER    42      -2.337  45.738  -1.472  1.00  0.00              
ATOM     83  C   SER    42      -1.943  44.523  -2.312  1.00  0.00              
ATOM     84  O   SER    42      -0.838  44.480  -2.854  1.00  0.00              
ATOM     85  N   GLY    43      -2.840  43.545  -2.422  1.00  0.00              
ATOM     86  CA  GLY    43      -2.577  42.340  -3.208  1.00  0.00              
ATOM     87  C   GLY    43      -3.396  42.324  -4.503  1.00  0.00              
ATOM     88  O   GLY    43      -3.324  41.369  -5.282  1.00  0.00              
ATOM     89  N   ASN    44      -4.184  43.374  -4.721  1.00  0.00              
ATOM     90  CA  ASN    44      -4.986  43.447  -5.931  1.00  0.00              
ATOM     91  C   ASN    44      -6.453  43.093  -5.764  1.00  0.00              
ATOM     92  O   ASN    44      -7.253  43.337  -6.664  1.00  0.00              
ATOM     93  N   ILE    45      -6.812  42.518  -4.619  1.00  0.00              
ATOM     94  CA  ILE    45      -8.199  42.150  -4.361  1.00  0.00              
ATOM     95  C   ILE    45      -9.100  43.383  -4.354  1.00  0.00              
ATOM     96  O   ILE    45      -8.836  44.347  -3.636  1.00  0.00              
ATOM     97  N   PHE    46     -10.162  43.351  -5.148  1.00  0.00              
ATOM     98  CA  PHE    46     -11.098  44.467  -5.203  1.00  0.00              
ATOM     99  C   PHE    46     -12.264  44.201  -4.252  1.00  0.00              
ATOM    100  O   PHE    46     -12.923  43.163  -4.340  1.00  0.00              
ATOM    101  N   PHE    47     -12.506  45.136  -3.338  1.00  0.00              
ATOM    102  CA  PHE    47     -13.602  45.003  -2.380  1.00  0.00              
ATOM    103  C   PHE    47     -14.529  46.204  -2.526  1.00  0.00              
ATOM    104  O   PHE    47     -14.329  47.244  -1.896  1.00  0.00              
ATOM    105  N   THR    48     -15.557  46.078  -3.376  1.00  0.00              
ATOM    106  CA  THR    48     -16.507  47.170  -3.595  1.00  0.00              
ATOM    107  C   THR    48     -17.334  47.496  -2.360  1.00  0.00              
ATOM    108  O   THR    48     -17.677  46.604  -1.578  1.00  0.00              
ATOM    109  N   SER    49     -17.639  48.777  -2.181  1.00  0.00              
ATOM    110  CA  SER    49     -18.468  49.172  -1.060  1.00  0.00              
ATOM    111  C   SER    49     -17.855  49.959   0.080  1.00  0.00              
ATOM    112  O   SER    49     -16.644  49.955   0.310  1.00  0.00              
ATOM    113  N   ILE    50     -18.737  50.632   0.807  1.00  0.00              
ATOM    114  CA  ILE    50     -18.368  51.438   1.951  1.00  0.00              
ATOM    115  C   ILE    50     -18.364  50.610   3.234  1.00  0.00              
ATOM    116  O   ILE    50     -19.259  49.794   3.469  1.00  0.00              
ATOM    117  N   ASP    51     -17.349  50.837   4.059  1.00  0.00              
ATOM    118  CA  ASP    51     -17.218  50.169   5.345  1.00  0.00              
ATOM    119  C   ASP    51     -16.733  51.223   6.329  1.00  0.00              
ATOM    120  O   ASP    51     -15.772  51.939   6.049  1.00  0.00              
ATOM    121  N   SER    52     -17.408  51.351   7.482  1.00  0.00              
ATOM    122  CA  SER    52     -17.015  52.334   8.495  1.00  0.00              
ATOM    123  C   SER    52     -15.622  51.969   8.990  1.00  0.00              
ATOM    124  O   SER    52     -15.217  50.812   8.895  1.00  0.00              
ATOM    125  N   LYS    53     -14.877  52.947   9.526  1.00  0.00              
ATOM    126  CA  LYS    53     -13.520  52.742  10.039  1.00  0.00              
ATOM    127  C   LYS    53     -13.315  51.471  10.863  1.00  0.00              
ATOM    128  O   LYS    53     -12.404  50.689  10.587  1.00  0.00              
ATOM    129  N   ALA    54     -14.156  51.264  11.872  1.00  0.00              
ATOM    130  CA  ALA    54     -14.028  50.083  12.720  1.00  0.00              
ATOM    131  C   ALA    54     -14.165  48.794  11.924  1.00  0.00              
ATOM    132  O   ALA    54     -13.314  47.907  12.010  1.00  0.00              
ATOM    133  N   GLN    55     -15.240  48.691  11.152  1.00  0.00              
ATOM    134  CA  GLN    55     -15.482  47.501  10.347  1.00  0.00              
ATOM    135  C   GLN    55     -14.381  47.304   9.309  1.00  0.00              
ATOM    136  O   GLN    55     -13.894  46.188   9.110  1.00  0.00              
ATOM    137  N   LEU    56     -13.993  48.392   8.651  1.00  0.00              
ATOM    138  CA  LEU    56     -12.943  48.354   7.637  1.00  0.00              
ATOM    139  C   LEU    56     -11.668  47.760   8.230  1.00  0.00              
ATOM    140  O   LEU    56     -11.046  46.870   7.640  1.00  0.00              
ATOM    141  N   VAL    57     -11.283  48.268   9.398  1.00  0.00              
ATOM    142  CA  VAL    57     -10.083  47.799  10.082  1.00  0.00              
ATOM    143  C   VAL    57     -10.165  46.304  10.374  1.00  0.00              
ATOM    144  O   VAL    57      -9.209  45.563  10.142  1.00  0.00              
ATOM    145  N   GLU    58     -11.308  45.866  10.887  1.00  0.00              
ATOM    146  CA  GLU    58     -11.497  44.459  11.204  1.00  0.00              
ATOM    147  C   GLU    58     -11.416  43.622   9.934  1.00  0.00              
ATOM    148  O   GLU    58     -10.835  42.534   9.932  1.00  0.00              
ATOM    149  N   LYS    59     -11.996  44.132   8.852  1.00  0.00              
ATOM    150  CA  LYS    59     -11.973  43.424   7.579  1.00  0.00              
ATOM    151  C   LYS    59     -10.541  43.243   7.081  1.00  0.00              
ATOM    152  O   LYS    59     -10.145  42.154   6.663  1.00  0.00              
ATOM    153  N   LEU    60      -9.763  44.316   7.116  1.00  0.00              
ATOM    154  CA  LEU    60      -8.386  44.252   6.663  1.00  0.00              
ATOM    155  C   LEU    60      -7.575  43.274   7.510  1.00  0.00              
ATOM    156  O   LEU    60      -6.806  42.473   6.978  1.00  0.00              
ATOM    157  N   GLU    61      -7.747  43.334   8.826  1.00  0.00              
ATOM    158  CA  GLU    61      -7.020  42.436   9.717  1.00  0.00              
ATOM    159  C   GLU    61      -7.328  40.977   9.420  1.00  0.00              
ATOM    160  O   GLU    61      -6.421  40.153   9.318  1.00  0.00              
ATOM    161  N   THR    62      -8.609  40.656   9.287  1.00  0.00              
ATOM    162  CA  THR    62      -9.006  39.284   9.006  1.00  0.00              
ATOM    163  C   THR    62      -8.547  38.857   7.621  1.00  0.00              
ATOM    164  O   THR    62      -8.231  37.687   7.399  1.00  0.00              
ATOM    165  N   PHE    63      -8.507  39.804   6.691  1.00  0.00              
ATOM    166  CA  PHE    63      -8.070  39.492   5.338  1.00  0.00              
ATOM    167  C   PHE    63      -6.602  39.087   5.347  1.00  0.00              
ATOM    168  O   PHE    63      -6.194  38.189   4.612  1.00  0.00              
ATOM    169  N   PHE    64      -5.814  39.753   6.186  1.00  0.00              
ATOM    170  CA  PHE    64      -4.393  39.451   6.305  1.00  0.00              
ATOM    171  C   PHE    64      -4.215  38.011   6.774  1.00  0.00              
ATOM    172  O   PHE    64      -3.510  37.219   6.148  1.00  0.00              
ATOM    173  N   ALA    65      -4.869  37.678   7.881  1.00  0.00              
ATOM    174  CA  ALA    65      -4.786  36.341   8.454  1.00  0.00              
ATOM    175  C   ALA    65      -5.318  35.257   7.518  1.00  0.00              
ATOM    176  O   ALA    65      -4.684  34.217   7.342  1.00  0.00              
ATOM    177  N   VAL    66      -6.476  35.501   6.916  1.00  0.00              
ATOM    178  CA  VAL    66      -7.075  34.528   6.010  1.00  0.00              
ATOM    179  C   VAL    66      -6.284  34.364   4.715  1.00  0.00              
ATOM    180  O   VAL    66      -6.402  33.345   4.033  1.00  0.00              
ATOM    181  N   HIS    67      -5.478  35.367   4.379  1.00  0.00              
ATOM    182  CA  HIS    67      -4.669  35.324   3.165  1.00  0.00              
ATOM    183  C   HIS    67      -3.256  34.844   3.490  1.00  0.00              
ATOM    184  O   HIS    67      -2.531  34.372   2.614  1.00  0.00              
END
