
#######################################################
#                                                     #
#                        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   37 (  148),  selected   37 , name T0353AL381_1
# Molecule2: number of CA atoms   85 ( 1334),  selected   85 , name T0353.pdb
# PARAMETERS: T0353AL381_1.T0353.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      I       3           -
LGA    -       -      H       4           -
LGA    -       -      V       5           -
LGA    -       -      Y       6           -
LGA    -       -      D       7           -
LGA    -       -      T       8           -
LGA    -       -      Y       9           -
LGA    -       -      V      10           -
LGA    -       -      K      11           -
LGA    -       -      A      12           -
LGA    -       -      K      13           -
LGA    -       -      D      14           -
LGA    -       -      G      15           -
LGA    -       -      H      16           -
LGA    -       -      V      17           -
LGA    -       -      M      18           -
LGA    -       -      H      19           -
LGA    -       -      F      20           -
LGA    -       -      D      21           -
LGA    -       -      V      22           -
LGA    -       -      F      23           -
LGA    -       -      T      24           -
LGA    -       -      D      25           -
LGA    -       -      V      26           -
LGA    -       -      R      27           -
LGA    -       -      D      28           -
LGA    -       -      D      29           -
LGA    K      30      K      30          1.678
LGA    K      31      K      31          0.818
LGA    A      32      A      32          0.815
LGA    I      33      I      33          1.379
LGA    E      34      E      34          1.052
LGA    F      35      F      35          0.472
LGA    A      36      A      36          1.455
LGA    K      37      K      37          1.370
LGA    Q      38      Q      38          0.486
LGA    W      39      W      39          0.285
LGA    L      40      L      40          0.315
LGA    S      41      S      41          0.411
LGA    S      42      S      42          0.649
LGA    I      43      I      43          1.331
LGA    G      44      G      44          1.384
LGA    E      45      E      45          1.417
LGA    E      46      E      46          2.274
LGA    G      47      G      47          5.156
LGA    A      48      A      48          2.261
LGA    T      49      T      49          4.878
LGA    V      50      V      50          4.117
LGA    T      51      T      51          3.861
LGA    S      52      S      52          3.855
LGA    E      53      E      53          1.914
LGA    E      54      E      54          2.618
LGA    C      55      C      55          2.624
LGA    R      56      -       -           -
LGA    F      57      R      56          2.715
LGA    C      58      F      57          2.094
LGA    H      59      C      58          3.299
LGA    S      60      H      59          1.291
LGA    Q      61      S      60          5.219
LGA    K      62      Q      61           -
LGA    A      63      K      62           -
LGA    P      64      A      63           -
LGA    D      65      P      64           -
LGA    E      66      D      65           -
LGA    -       -      E      66           -
LGA    -       -      V      67           -
LGA    -       -      I      68           -
LGA    -       -      E      69           -
LGA    -       -      A      70           -
LGA    -       -      I      71           -
LGA    -       -      K      72           -
LGA    -       -      Q      73           -
LGA    -       -      N      74           -
LGA    -       -      G      75           -
LGA    -       -      Y      76           -
LGA    -       -      F      77           -
LGA    -       -      I      78           -
LGA    -       -      Y      79           -
LGA    -       -      K      80           -
LGA    -       -      M      81           -
LGA    -       -      E      82           -
LGA    -       -      G      83           -
LGA    -       -      C      84           -
LGA    -       -      N      85           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   37   85    5.0     31    2.50    83.87     27.272     1.190

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.460089 * X  +  -0.101043 * Y  +   0.882104 * Z  +  41.031311
  Y_new =  -0.186757 * X  +   0.982290 * Y  +   0.015110 * Z  +  12.704710
  Z_new =  -0.868009 * X  +  -0.157787 * Y  +  -0.470812 * Z  + -42.538692 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.818219    0.323373  [ DEG:  -161.4721     18.5279 ]
  Theta =   1.051179    2.090414  [ DEG:    60.2281    119.7719 ]
  Phi   =  -2.755999    0.385594  [ DEG:  -157.9071     22.0929 ]
 
# 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: T0353AL381_1                                  
REMARK     2: T0353.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0353AL381_1.T0353.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   37   85   5.0   31   2.50   83.87  27.272
REMARK  ---------------------------------------------------------- 
MOLECULE T0353AL381_1
REMARK Aligment from pdb entry: 1y8qA
ATOM      1  N   LYS    30      -5.367   6.436  -7.495  1.00  0.00              
ATOM      2  CA  LYS    30      -6.479   5.631  -7.996  1.00  0.00              
ATOM      3  C   LYS    30      -6.246   4.154  -7.672  1.00  0.00              
ATOM      4  O   LYS    30      -7.117   3.484  -7.113  1.00  0.00              
ATOM      5  N   LYS    31      -5.060   3.660  -8.021  1.00  0.00              
ATOM      6  CA  LYS    31      -4.698   2.268  -7.769  1.00  0.00              
ATOM      7  C   LYS    31      -4.635   1.963  -6.271  1.00  0.00              
ATOM      8  O   LYS    31      -5.171   0.949  -5.817  1.00  0.00              
ATOM      9  N   ALA    32      -3.975   2.836  -5.512  1.00  0.00              
ATOM     10  CA  ALA    32      -3.851   2.643  -4.075  1.00  0.00              
ATOM     11  C   ALA    32      -5.203   2.415  -3.420  1.00  0.00              
ATOM     12  O   ALA    32      -5.346   1.536  -2.568  1.00  0.00              
ATOM     13  N   ILE    33      -6.198   3.201  -3.822  1.00  0.00              
ATOM     14  CA  ILE    33      -7.538   3.068  -3.266  1.00  0.00              
ATOM     15  C   ILE    33      -8.136   1.721  -3.624  1.00  0.00              
ATOM     16  O   ILE    33      -8.816   1.097  -2.806  1.00  0.00              
ATOM     17  N   GLU    34      -7.874   1.269  -4.847  1.00  0.00              
ATOM     18  CA  GLU    34      -8.388  -0.017  -5.306  1.00  0.00              
ATOM     19  C   GLU    34      -7.698  -1.155  -4.556  1.00  0.00              
ATOM     20  O   GLU    34      -8.338  -2.126  -4.154  1.00  0.00              
ATOM     21  N   PHE    35      -6.391  -1.025  -4.360  1.00  0.00              
ATOM     22  CA  PHE    35      -5.629  -2.033  -3.638  1.00  0.00              
ATOM     23  C   PHE    35      -6.076  -2.101  -2.178  1.00  0.00              
ATOM     24  O   PHE    35      -6.097  -3.172  -1.572  1.00  0.00              
ATOM     25  N   ALA    36      -6.434  -0.949  -1.616  1.00  0.00              
ATOM     26  CA  ALA    36      -6.891  -0.887  -0.231  1.00  0.00              
ATOM     27  C   ALA    36      -8.133  -1.740  -0.059  1.00  0.00              
ATOM     28  O   ALA    36      -8.249  -2.508   0.896  1.00  0.00              
ATOM     29  N   LYS    37      -9.074  -1.579  -0.982  1.00  0.00              
ATOM     30  CA  LYS    37     -10.312  -2.333  -0.938  1.00  0.00              
ATOM     31  C   LYS    37     -10.072  -3.831  -1.086  1.00  0.00              
ATOM     32  O   LYS    37     -10.700  -4.634  -0.398  1.00  0.00              
ATOM     33  N   GLN    38      -9.159  -4.214  -1.972  1.00  0.00              
ATOM     34  CA  GLN    38      -8.876  -5.631  -2.163  1.00  0.00              
ATOM     35  C   GLN    38      -8.214  -6.254  -0.940  1.00  0.00              
ATOM     36  O   GLN    38      -8.671  -7.280  -0.434  1.00  0.00              
ATOM     37  N   TRP    39      -7.136  -5.636  -0.467  1.00  0.00              
ATOM     38  CA  TRP    39      -6.412  -6.161   0.681  1.00  0.00              
ATOM     39  C   TRP    39      -7.256  -6.241   1.947  1.00  0.00              
ATOM     40  O   TRP    39      -7.370  -7.304   2.560  1.00  0.00              
ATOM     41  N   LEU    40      -7.849  -5.123   2.346  1.00  0.00              
ATOM     42  CA  LEU    40      -8.656  -5.126   3.558  1.00  0.00              
ATOM     43  C   LEU    40      -9.840  -6.076   3.439  1.00  0.00              
ATOM     44  O   LEU    40     -10.214  -6.745   4.408  1.00  0.00              
ATOM     45  N   SER    41     -10.414  -6.152   2.243  1.00  0.00              
ATOM     46  CA  SER    41     -11.554  -7.029   2.019  1.00  0.00              
ATOM     47  C   SER    41     -11.129  -8.491   2.126  1.00  0.00              
ATOM     48  O   SER    41     -11.833  -9.303   2.725  1.00  0.00              
ATOM     49  N   SER    42      -9.970  -8.823   1.567  1.00  0.00              
ATOM     50  CA  SER    42      -9.499 -10.200   1.620  1.00  0.00              
ATOM     51  C   SER    42      -9.089 -10.611   3.031  1.00  0.00              
ATOM     52  O   SER    42      -8.669 -11.747   3.247  1.00  0.00              
ATOM     53  N   ILE    43      -9.202  -9.691   3.986  1.00  0.00              
ATOM     54  CA  ILE    43      -8.849  -9.983   5.381  1.00  0.00              
ATOM     55  C   ILE    43     -10.100  -9.954   6.259  1.00  0.00              
ATOM     56  O   ILE    43     -10.044 -10.251   7.453  1.00  0.00              
ATOM     57  N   GLY    44     -11.230  -9.596   5.657  1.00  0.00              
ATOM     58  CA  GLY    44     -12.475  -9.541   6.400  1.00  0.00              
ATOM     59  C   GLY    44     -12.625  -8.265   7.208  1.00  0.00              
ATOM     60  O   GLY    44     -13.457  -8.181   8.112  1.00  0.00              
ATOM     61  N   GLU    45     -11.816  -7.265   6.879  1.00  0.00              
ATOM     62  CA  GLU    45     -11.854  -5.988   7.574  1.00  0.00              
ATOM     63  C   GLU    45     -12.431  -4.923   6.648  1.00  0.00              
ATOM     64  O   GLU    45     -12.144  -4.908   5.449  1.00  0.00              
ATOM     65  N   GLU    46     -13.248  -4.035   7.201  1.00  0.00              
ATOM     66  CA  GLU    46     -13.854  -2.984   6.398  1.00  0.00              
ATOM     67  C   GLU    46     -12.806  -2.103   5.738  1.00  0.00              
ATOM     68  O   GLU    46     -11.847  -1.667   6.375  1.00  0.00              
ATOM     69  N   GLY    47     -12.976  -1.836   4.438  1.00  0.00              
ATOM     70  CA  GLY    47     -12.033  -0.995   3.699  1.00  0.00              
ATOM     71  C   GLY    47     -12.003   0.426   4.247  1.00  0.00              
ATOM     72  O   GLY    47     -11.041   1.166   4.042  1.00  0.00              
ATOM     73  N   ALA    48     -13.070   0.801   4.945  1.00  0.00              
ATOM     74  CA  ALA    48     -13.171   2.133   5.528  1.00  0.00              
ATOM     75  C   ALA    48     -12.140   2.373   6.624  1.00  0.00              
ATOM     76  O   ALA    48     -11.795   3.517   6.913  1.00  0.00              
ATOM     77  N   THR    49     -11.646   1.290   7.215  1.00  0.00              
ATOM     78  CA  THR    49     -10.648   1.359   8.284  1.00  0.00              
ATOM     79  C   THR    49      -9.491   2.264   7.899  1.00  0.00              
ATOM     80  O   THR    49      -8.761   2.754   8.754  1.00  0.00              
ATOM     81  N   VAL    50      -9.322   2.470   6.601  1.00  0.00              
ATOM     82  CA  VAL    50      -8.250   3.308   6.091  1.00  0.00              
ATOM     83  C   VAL    50      -8.912   4.390   5.249  1.00  0.00              
ATOM     84  O   VAL    50      -9.373   4.125   4.141  1.00  0.00              
ATOM     85  N   THR    51      -8.979   5.626   5.770  1.00  0.00              
ATOM     86  CA  THR    51      -9.607   6.733   5.034  1.00  0.00              
ATOM     87  C   THR    51      -9.042   6.945   3.630  1.00  0.00              
ATOM     88  O   THR    51      -7.829   6.904   3.428  1.00  0.00              
ATOM     89  N   SER    52      -9.930   7.175   2.666  1.00  0.00              
ATOM     90  CA  SER    52      -9.518   7.383   1.286  1.00  0.00              
ATOM     91  C   SER    52      -8.467   8.476   1.206  1.00  0.00              
ATOM     92  O   SER    52      -7.723   8.573   0.229  1.00  0.00              
ATOM     93  N   GLU    53      -8.415   9.292   2.249  1.00  0.00              
ATOM     94  CA  GLU    53      -7.484  10.410   2.336  1.00  0.00              
ATOM     95  C   GLU    53      -6.027   9.978   2.530  1.00  0.00              
ATOM     96  O   GLU    53      -5.110  10.773   2.340  1.00  0.00              
ATOM     97  N   GLU    54      -5.811   8.719   2.893  1.00  0.00              
ATOM     98  CA  GLU    54      -4.459   8.225   3.140  1.00  0.00              
ATOM     99  C   GLU    54      -3.498   8.389   1.967  1.00  0.00              
ATOM    100  O   GLU    54      -2.293   8.520   2.174  1.00  0.00              
ATOM    101  N   CYS    55      -4.027   8.393   0.745  1.00  0.00              
ATOM    102  CA  CYS    55      -3.195   8.517  -0.448  1.00  0.00              
ATOM    103  C   CYS    55      -2.397   9.819  -0.523  1.00  0.00              
ATOM    104  O   CYS    55      -1.365   9.889  -1.195  1.00  0.00              
ATOM    105  N   ARG    56      -2.867  10.847   0.173  1.00  0.00              
ATOM    106  CA  ARG    56      -2.186  12.136   0.168  1.00  0.00              
ATOM    107  C   ARG    56      -0.937  12.182   1.046  1.00  0.00              
ATOM    108  O   ARG    56      -0.071  13.041   0.854  1.00  0.00              
ATOM    109  N   PHE    57      -0.828  11.257   1.995  1.00  0.00              
ATOM    110  CA  PHE    57       0.303  11.278   2.909  1.00  0.00              
ATOM    111  C   PHE    57       1.331  10.152   2.818  1.00  0.00              
ATOM    112  O   PHE    57       2.229  10.069   3.659  1.00  0.00              
ATOM    113  N   CYS    58       1.226   9.295   1.804  1.00  0.00              
ATOM    114  CA  CYS    58       2.180   8.195   1.671  1.00  0.00              
ATOM    115  C   CYS    58       2.930   8.212   0.344  1.00  0.00              
ATOM    116  O   CYS    58       3.128   7.171  -0.279  1.00  0.00              
ATOM    117  N   HIS    59       3.373   9.394  -0.069  1.00  0.00              
ATOM    118  CA  HIS    59       4.087   9.561  -1.326  1.00  0.00              
ATOM    119  C   HIS    59       5.493  10.102  -1.181  1.00  0.00              
ATOM    120  O   HIS    59       5.726  11.059  -0.449  1.00  0.00              
ATOM    121  N   SER    60       6.425   9.490  -1.903  1.00  0.00              
ATOM    122  CA  SER    60       7.817   9.923  -1.912  1.00  0.00              
ATOM    123  C   SER    60       8.573   9.620  -0.636  1.00  0.00              
ATOM    124  O   SER    60       8.072   8.952   0.261  1.00  0.00              
ATOM    125  N   GLN    61       9.797  10.124  -0.572  1.00  0.00              
ATOM    126  CA  GLN    61      10.640   9.928   0.590  1.00  0.00              
ATOM    127  C   GLN    61      10.984  11.303   1.130  1.00  0.00              
ATOM    128  O   GLN    61      11.649  12.097   0.461  1.00  0.00              
ATOM    129  N   LYS    62      10.520  11.585   2.340  1.00  0.00              
ATOM    130  CA  LYS    62      10.787  12.861   2.971  1.00  0.00              
ATOM    131  C   LYS    62      12.004  12.712   3.868  1.00  0.00              
ATOM    132  O   LYS    62      12.093  11.785   4.674  1.00  0.00              
ATOM    133  N   ALA    63      12.945  13.630   3.720  1.00  0.00              
ATOM    134  CA  ALA    63      14.162  13.586   4.503  1.00  0.00              
ATOM    135  C   ALA    63      13.943  13.476   6.020  1.00  0.00              
ATOM    136  O   ALA    63      14.616  12.691   6.685  1.00  0.00              
ATOM    137  N   PRO    64      13.003  14.254   6.586  1.00  0.00              
ATOM    138  CA  PRO    64      12.771  14.174   8.035  1.00  0.00              
ATOM    139  C   PRO    64      12.299  12.783   8.463  1.00  0.00              
ATOM    140  O   PRO    64      12.694  12.273   9.512  1.00  0.00              
ATOM    141  N   ASP    65      11.459  12.168   7.642  1.00  0.00              
ATOM    142  CA  ASP    65      10.956  10.849   7.963  1.00  0.00              
ATOM    143  C   ASP    65      12.045   9.787   7.848  1.00  0.00              
ATOM    144  O   ASP    65      12.077   8.844   8.635  1.00  0.00              
ATOM    145  N   GLU    66      12.946   9.939   6.879  1.00  0.00              
ATOM    146  CA  GLU    66      14.039   8.985   6.724  1.00  0.00              
ATOM    147  C   GLU    66      14.919   9.059   7.962  1.00  0.00              
ATOM    148  O   GLU    66      15.464   8.050   8.412  1.00  0.00              
END
