
#######################################################
#                                                     #
#                        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   33 (  132),  selected   33 , name T0360AL381_5
# Molecule2: number of CA atoms  116 (  917),  selected  116 , name T0360.pdb
# PARAMETERS: T0360AL381_5.T0360.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      T       2           -
LGA    -       -      Q       3           -
LGA    -       -      E       4           -
LGA    -       -      T       5           -
LGA    -       -      A       6           -
LGA    -       -      L       7           -
LGA    -       -      G       8           -
LGA    -       -      A       9           -
LGA    -       -      A      10           -
LGA    -       -      L      11           -
LGA    -       -      K      12           -
LGA    -       -      S      13           -
LGA    Y      35      A      14           #
LGA    D      36      V      15           -
LGA    V      37      Q      16           -
LGA    F      38      -       -           -
LGA    K      39      -       -           -
LGA    R      40      T      17          3.119
LGA    F      41      -       -           -
LGA    K      42      -       -           -
LGA    P      43      M      18          2.186
LGA    L      44      S      19          2.816
LGA    A      45      K      20          2.140
LGA    L      46      K      21          2.999
LGA    G      47      K      22          1.126
LGA    I      48      Q      23          0.763
LGA    D      49      T      24          0.731
LGA    Q      50      E      25          0.800
LGA    D      51      M      26          0.847
LGA    L      52      I      27          1.185
LGA    I      53      A      28          0.643
LGA    A      54      D      29          0.893
LGA    A      55      H      30          1.873
LGA    L      56      I      31          1.960
LGA    P      57      Y      32          1.457
LGA    -       -      G      33           -
LGA    Q      58      K      34          2.129
LGA    Y      59      Y      35          4.044
LGA    D      60      D      36          3.256
LGA    -       -      V      37           -
LGA    -       -      F      38           -
LGA    -       -      K      39           -
LGA    -       -      R      40           -
LGA    A      61      F      41          3.074
LGA    A      62      K      42          1.129
LGA    L      63      P      43          3.211
LGA    I      64      L      44          3.851
LGA    -       -      A      45           -
LGA    -       -      L      46           -
LGA    A      65      G      47           #
LGA    R      66      I      48          1.378
LGA    -       -      D      49           -
LGA    V      67      Q      50          2.729
LGA    -       -      D      51           -
LGA    -       -      L      52           -
LGA    -       -      I      53           -
LGA    -       -      A      54           -
LGA    -       -      A      55           -
LGA    -       -      L      56           -
LGA    -       -      P      57           -
LGA    -       -      Q      58           -
LGA    -       -      Y      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      A      62           -
LGA    -       -      L      63           -
LGA    -       -      I      64           -
LGA    -       -      A      65           -
LGA    -       -      R      66           -
LGA    -       -      V      67           -
LGA    -       -      L      68           -
LGA    -       -      A      69           -
LGA    -       -      N      70           -
LGA    -       -      H      71           -
LGA    -       -      C      72           -
LGA    -       -      R      73           -
LGA    -       -      R      74           -
LGA    -       -      P      75           -
LGA    -       -      R      76           -
LGA    -       -      Y      77           -
LGA    -       -      L      78           -
LGA    -       -      K      79           -
LGA    -       -      A      80           -
LGA    -       -      L      81           -
LGA    -       -      A      82           -
LGA    -       -      R      83           -
LGA    -       -      G      84           -
LGA    -       -      G      85           -
LGA    -       -      K      86           -
LGA    -       -      R      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -
LGA    -       -      L      90           -
LGA    -       -      N      91           -
LGA    -       -      N      92           -
LGA    -       -      R      93           -
LGA    -       -      F      94           -
LGA    -       -      K      95           -
LGA    -       -      G      96           -
LGA    -       -      E      97           -
LGA    -       -      V      98           -
LGA    -       -      T      99           -
LGA    -       -      P     100           -
LGA    -       -      E     101           -
LGA    -       -      E     102           -
LGA    -       -      Q     103           -
LGA    -       -      A     104           -
LGA    -       -      I     105           -
LGA    -       -      A     106           -
LGA    -       -      Q     107           -
LGA    -       -      N     108           -
LGA    -       -      H     109           -
LGA    -       -      P     110           -
LGA    -       -      F     111           -
LGA    -       -      V     112           -
LGA    -       -      Q     113           -
LGA    -       -      Q     114           -
LGA    -       -      A     115           -
LGA    -       -      L     116           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   33  116    5.0     25    2.27     8.00     17.423     1.056

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.393694 * X  +   0.380874 * Y  +   0.836624 * Z  + -116.416855
  Y_new =  -0.696757 * X  +   0.470024 * Y  +  -0.541855 * Z  +  23.902681
  Z_new =  -0.599612 * X  +  -0.796249 * Y  +   0.080331 * Z  + -13.781468 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.470249    1.671344  [ DEG:   -84.2391     95.7609 ]
  Theta =   0.643016    2.498577  [ DEG:    36.8421    143.1579 ]
  Phi   =  -2.085111    1.056481  [ DEG:  -119.4681     60.5319 ]
 
# 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: T0360AL381_5                                  
REMARK     2: T0360.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0360AL381_5.T0360.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   33  116   5.0   25   2.27    8.00  17.423
REMARK  ---------------------------------------------------------- 
MOLECULE T0360AL381_5
REMARK Aligment from pdb entry: 2awhA
ATOM      1  N   TYR    35    -103.561  -2.650  -5.692  1.00  0.00              
ATOM      2  CA  TYR    35    -103.243  -1.567  -4.765  1.00  0.00              
ATOM      3  C   TYR    35    -103.832  -0.288  -5.340  1.00  0.00              
ATOM      4  O   TYR    35    -104.027  -0.175  -6.552  1.00  0.00              
ATOM      5  N   ASP    36    -104.160   0.657  -4.484  1.00  0.00              
ATOM      6  CA  ASP    36    -104.616   1.938  -4.978  1.00  0.00              
ATOM      7  C   ASP    36    -103.481   2.517  -5.832  1.00  0.00              
ATOM      8  O   ASP    36    -102.294   2.296  -5.547  1.00  0.00              
ATOM      9  N   VAL    37    -103.866   3.250  -6.871  1.00  0.00              
ATOM     10  CA  VAL    37    -102.946   3.814  -7.835  1.00  0.00              
ATOM     11  C   VAL    37    -101.899   4.702  -7.162  1.00  0.00              
ATOM     12  O   VAL    37    -100.756   4.753  -7.611  1.00  0.00              
ATOM     13  N   PHE    38    -102.273   5.398  -6.086  1.00  0.00              
ATOM     14  CA  PHE    38    -101.290   6.224  -5.376  1.00  0.00              
ATOM     15  C   PHE    38    -100.211   5.375  -4.703  1.00  0.00              
ATOM     16  O   PHE    38     -99.044   5.772  -4.667  1.00  0.00              
ATOM     17  N   LYS    39    -100.592   4.218  -4.161  1.00  0.00              
ATOM     18  CA  LYS    39     -99.571   3.298  -3.617  1.00  0.00              
ATOM     19  C   LYS    39     -98.665   2.705  -4.684  1.00  0.00              
ATOM     20  O   LYS    39     -97.469   2.553  -4.442  1.00  0.00              
ATOM     21  N   ARG    40     -99.221   2.347  -5.862  1.00  0.00              
ATOM     22  CA  ARG    40     -98.427   1.863  -6.981  1.00  0.00              
ATOM     23  C   ARG    40     -97.359   2.878  -7.376  1.00  0.00              
ATOM     24  O   ARG    40     -96.194   2.497  -7.611  1.00  0.00              
ATOM     25  N   PHE    41     -97.746   4.156  -7.431  1.00  0.00              
ATOM     26  CA  PHE    41     -96.820   5.271  -7.757  1.00  0.00              
ATOM     27  C   PHE    41     -95.680   5.488  -6.731  1.00  0.00              
ATOM     28  O   PHE    41     -94.518   5.728  -7.107  1.00  0.00              
ATOM     29  N   LYS    42     -96.018   5.418  -5.444  1.00  0.00              
ATOM     30  CA  LYS    42     -95.012   5.440  -4.375  1.00  0.00              
ATOM     31  C   LYS    42     -94.028   4.258  -4.493  1.00  0.00              
ATOM     32  O   LYS    42     -92.833   4.433  -4.339  1.00  0.00              
ATOM     33  N   PRO    43     -94.540   3.059  -4.769  1.00  0.00              
ATOM     34  CA  PRO    43     -93.682   1.872  -4.919  1.00  0.00              
ATOM     35  C   PRO    43     -92.714   2.008  -6.084  1.00  0.00              
ATOM     36  O   PRO    43     -91.535   1.656  -5.977  1.00  0.00              
ATOM     37  N   LEU    44     -93.192   2.497  -7.216  1.00  0.00              
ATOM     38  CA  LEU    44     -92.312   2.711  -8.383  1.00  0.00              
ATOM     39  C   LEU    44     -91.344   3.868  -8.108  1.00  0.00              
ATOM     40  O   LEU    44     -90.136   3.756  -8.315  1.00  0.00              
ATOM     41  N   ALA    45     -91.866   4.965  -7.573  1.00  0.00              
ATOM     42  CA  ALA    45     -91.003   6.116  -7.246  1.00  0.00              
ATOM     43  C   ALA    45     -89.777   5.672  -6.476  1.00  0.00              
ATOM     44  O   ALA    45     -88.667   5.930  -6.904  1.00  0.00              
ATOM     45  N   LEU    46     -89.969   4.986  -5.356  1.00  0.00              
ATOM     46  CA  LEU    46     -88.849   4.591  -4.481  1.00  0.00              
ATOM     47  C   LEU    46     -88.142   3.287  -4.810  1.00  0.00              
ATOM     48  O   LEU    46     -87.028   3.044  -4.319  1.00  0.00              
ATOM     49  N   GLY    47     -88.758   2.462  -5.671  1.00  0.00              
ATOM     50  CA  GLY    47     -88.154   1.190  -6.070  1.00  0.00              
ATOM     51  C   GLY    47     -87.493   1.076  -7.444  1.00  0.00              
ATOM     52  O   GLY    47     -86.607   0.224  -7.614  1.00  0.00              
ATOM     53  N   ILE    48     -87.876   1.909  -8.424  1.00  0.00              
ATOM     54  CA  ILE    48     -87.377   1.702  -9.809  1.00  0.00              
ATOM     55  C   ILE    48     -85.877   1.769  -9.958  1.00  0.00              
ATOM     56  O   ILE    48     -85.307   0.912 -10.619  1.00  0.00              
ATOM     57  N   ASP    49     -85.227   2.768  -9.321  1.00  0.00              
ATOM     58  CA  ASP    49     -83.763   2.832  -9.348  1.00  0.00              
ATOM     59  C   ASP    49     -83.017   1.730  -8.590  1.00  0.00              
ATOM     60  O   ASP    49     -81.947   1.337  -9.026  1.00  0.00              
ATOM     61  N   GLN    50     -83.516   1.256  -7.452  1.00  0.00              
ATOM     62  CA  GLN    50     -82.919   0.088  -6.826  1.00  0.00              
ATOM     63  C   GLN    50     -82.979  -1.083  -7.834  1.00  0.00              
ATOM     64  O   GLN    50     -82.011  -1.833  -8.002  1.00  0.00              
ATOM     65  N   ASP    51     -84.128  -1.241  -8.482  1.00  0.00              
ATOM     66  CA  ASP    51     -84.280  -2.370  -9.438  1.00  0.00              
ATOM     67  C   ASP    51     -83.339  -2.157 -10.630  1.00  0.00              
ATOM     68  O   ASP    51     -82.674  -3.093 -11.098  1.00  0.00              
ATOM     69  N   LEU    52     -83.248  -0.908 -11.088  1.00  0.00              
ATOM     70  CA  LEU    52     -82.396  -0.562 -12.218  1.00  0.00              
ATOM     71  C   LEU    52     -80.929  -0.909 -11.955  1.00  0.00              
ATOM     72  O   LEU    52     -80.261  -1.498 -12.800  1.00  0.00              
ATOM     73  N   ILE    53     -80.429  -0.504 -10.784  1.00  0.00              
ATOM     74  CA  ILE    53     -79.029  -0.702 -10.468  1.00  0.00              
ATOM     75  C   ILE    53     -78.707  -2.157 -10.164  1.00  0.00              
ATOM     76  O   ILE    53     -77.609  -2.580 -10.410  1.00  0.00              
ATOM     77  N   ALA    54     -79.657  -2.922  -9.639  1.00  0.00              
ATOM     78  CA  ALA    54     -79.505  -4.407  -9.539  1.00  0.00              
ATOM     79  C   ALA    54     -79.378  -5.103 -10.916  1.00  0.00              
ATOM     80  O   ALA    54     -78.508  -5.998 -11.093  1.00  0.00              
ATOM     81  N   ALA    55     -80.230  -4.721 -11.870  1.00  0.00              
ATOM     82  CA  ALA    55     -80.210  -5.287 -13.253  1.00  0.00              
ATOM     83  C   ALA    55     -79.041  -4.801 -14.103  1.00  0.00              
ATOM     84  O   ALA    55     -78.580  -5.507 -15.017  1.00  0.00              
ATOM     85  N   LEU    56     -78.549  -3.599 -13.795  1.00  0.00              
ATOM     86  CA  LEU    56     -77.296  -3.100 -14.361  1.00  0.00              
ATOM     87  C   LEU    56     -76.157  -4.132 -14.281  1.00  0.00              
ATOM     88  O   LEU    56     -75.405  -4.317 -15.243  1.00  0.00              
ATOM     89  N   PRO    57     -76.029  -4.791 -13.137  1.00  0.00              
ATOM     90  CA  PRO    57     -74.989  -5.794 -12.929  1.00  0.00              
ATOM     91  C   PRO    57     -74.975  -6.850 -14.036  1.00  0.00              
ATOM     92  O   PRO    57     -73.920  -7.326 -14.411  1.00  0.00              
ATOM     93  N   GLN    58     -76.154  -7.192 -14.552  1.00  0.00              
ATOM     94  CA  GLN    58     -76.321  -8.164 -15.639  1.00  0.00              
ATOM     95  C   GLN    58     -75.563  -7.823 -16.915  1.00  0.00              
ATOM     96  O   GLN    58     -75.194  -8.726 -17.668  1.00  0.00              
ATOM     97  N   TYR    59     -72.857  -5.619 -17.040  1.00  0.00              
ATOM     98  CA  TYR    59     -71.589  -5.035 -16.614  1.00  0.00              
ATOM     99  C   TYR    59     -70.519  -6.132 -16.439  1.00  0.00              
ATOM    100  O   TYR    59     -70.835  -7.282 -16.097  1.00  0.00              
ATOM    101  N   ASP    60     -69.276  -5.792 -16.765  1.00  0.00              
ATOM    102  CA  ASP    60     -68.120  -6.476 -16.200  1.00  0.00              
ATOM    103  C   ASP    60     -67.149  -5.390 -15.673  1.00  0.00              
ATOM    104  O   ASP    60     -67.444  -4.180 -15.795  1.00  0.00              
ATOM    105  N   ALA    61     -66.024  -5.801 -15.078  1.00  0.00              
ATOM    106  CA  ALA    61     -65.033  -4.865 -14.521  1.00  0.00              
ATOM    107  C   ALA    61     -64.560  -3.819 -15.540  1.00  0.00              
ATOM    108  O   ALA    61     -64.042  -2.772 -15.159  1.00  0.00              
ATOM    109  N   ALA    62     -64.752  -4.127 -16.827  1.00  0.00              
ATOM    110  CA  ALA    62     -64.245  -3.330 -17.957  1.00  0.00              
ATOM    111  C   ALA    62     -65.236  -2.308 -18.541  1.00  0.00              
ATOM    112  O   ALA    62     -64.842  -1.408 -19.289  1.00  0.00              
ATOM    113  N   LEU    63     -66.526  -2.470 -18.262  1.00  0.00              
ATOM    114  CA  LEU    63     -67.524  -1.643 -18.962  1.00  0.00              
ATOM    115  C   LEU    63     -68.902  -2.256 -19.027  1.00  0.00              
ATOM    116  O   LEU    63     -69.195  -3.195 -18.301  1.00  0.00              
ATOM    117  N   ILE    64     -69.764  -1.707 -19.878  1.00  0.00              
ATOM    118  CA  ILE    64     -71.156  -2.153 -19.898  1.00  0.00              
ATOM    119  C   ILE    64     -71.742  -2.211 -21.294  1.00  0.00              
ATOM    120  O   ILE    64     -71.434  -1.363 -22.128  1.00  0.00              
ATOM    121  N   ALA    65     -72.580  -3.213 -21.541  1.00  0.00              
ATOM    122  CA  ALA    65     -73.343  -3.285 -22.797  1.00  0.00              
ATOM    123  C   ALA    65     -74.397  -2.192 -22.913  1.00  0.00              
ATOM    124  O   ALA    65     -75.136  -1.945 -21.960  1.00  0.00              
ATOM    125  N   ARG    66     -74.486  -1.569 -24.087  1.00  0.00              
ATOM    126  CA  ARG    66     -75.526  -0.589 -24.376  1.00  0.00              
ATOM    127  C   ARG    66     -76.311  -0.981 -25.637  1.00  0.00              
ATOM    128  O   ARG    66     -75.893  -1.884 -26.389  1.00  0.00              
ATOM    129  N   VAL    67     -77.454  -0.327 -25.837  1.00  0.00              
ATOM    130  CA  VAL    67     -78.321  -0.549 -27.006  1.00  0.00              
ATOM    131  C   VAL    67     -78.513  -2.012 -27.399  1.00  0.00              
ATOM    132  O   VAL    67     -78.152  -2.432 -28.499  1.00  0.00              
END
