
#######################################################
#                                                     #
#                        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   38 (  152),  selected   38 , name T0319AL044_1
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319AL044_1.T0319.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    G      67      M       1           -
LGA    -       -      K       2           -
LGA    -       -      F       3           -
LGA    -       -      L       4           -
LGA    -       -      T       5           -
LGA    -       -      T       6           -
LGA    -       -      N       7           -
LGA    -       -      F       8           -
LGA    N      68      L       9           #
LGA    N      69      K      10          3.021
LGA    -       -      C      11           -
LGA    -       -      S      12           -
LGA    -       -      V      13           -
LGA    -       -      K      14           -
LGA    -       -      A      15           -
LGA    -       -      C      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      N      20           -
LGA    -       -      D      21           -
LGA    -       -      N      22           -
LGA    A      70      F      23          2.063
LGA    P      73      P      24          1.833
LGA    T      74      L      25           #
LGA    -       -      Q      26           -
LGA    -       -      Y      27           -
LGA    -       -      D      28           -
LGA    -       -      G      29           -
LGA    -       -      S      30           -
LGA    -       -      K      31           -
LGA    -       -      C      32           -
LGA    -       -      Q      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      D      37           -
LGA    -       -      E      38           -
LGA    -       -      S      39           -
LGA    -       -      I      40           -
LGA    -       -      E      41           -
LGA    -       -      F      42           -
LGA    -       -      N      43           -
LGA    -       -      P      44           -
LGA    -       -      E      45           -
LGA    -       -      F      46           -
LGA    -       -      L      47           -
LGA    -       -      L      48           -
LGA    -       -      N      49           -
LGA    -       -      I      50           -
LGA    -       -      V      51           -
LGA    -       -      D      52           -
LGA    -       -      R      53           -
LGA    -       -      V      54           -
LGA    -       -      D      55           -
LGA    -       -      W      56           -
LGA    K      75      P      57          4.160
LGA    P      76      A      58          1.695
LGA    S      77      V      59          3.318
LGA    F      78      -       -           -
LGA    Q      83      L      60          3.092
LGA    E      84      T      61           -
LGA    L      85      V      62           -
LGA    -       -      A      63           -
LGA    -       -      A      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      G      67           -
LGA    -       -      N      68           -
LGA    -       -      N      69           -
LGA    -       -      A      70           -
LGA    -       -      L      71           -
LGA    -       -      P      72           -
LGA    -       -      P      73           -
LGA    D      87      T      74          5.645
LGA    A      91      K      75          5.004
LGA    I      92      P      76          0.190
LGA    L      96      -       -           -
LGA    H      97      S      77           #
LGA    T      98      F      78          4.616
LGA    -       -      P      79           -
LGA    -       -      S      80           -
LGA    -       -      S      81           -
LGA    -       -      I      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    -       -      L      85           -
LGA    -       -      T      86           -
LGA    -       -      D      87           -
LGA    L      99      D      88          4.583
LGA    L     100      D      89          2.203
LGA    L     101      M      90          3.014
LGA    Q     102      A      91          4.034
LGA    T     103      I      92          2.914
LGA    -       -      L      93           -
LGA    -       -      N      94           -
LGA    S     104      D      95          1.247
LGA    -       -      L      96           -
LGA    -       -      H      97           -
LGA    I     105      T      98          1.133
LGA    A     106      L      99          5.610
LGA    -       -      L     100           -
LGA    -       -      L     101           -
LGA    E     107      Q     102          1.431
LGA    G     108      T     103           -
LGA    -       -      S     104           -
LGA    -       -      I     105           -
LGA    E     109      A     106           #
LGA    M     110      E     107          3.355
LGA    K     111      G     108          1.605
LGA    C     112      E     109          2.747
LGA    R     113      M     110          1.834
LGA    N     114      K     111          2.000
LGA    C     115      C     112          5.992
LGA    -       -      R     113           -
LGA    -       -      N     114           -
LGA    -       -      C     115           -
LGA    -       -      G     116           -
LGA    -       -      H     117           -
LGA    -       -      I     118           -
LGA    -       -      Y     119           -
LGA    G     116      Y     120          3.128
LGA    I     118      I     121           #
LGA    -       -      K     122           -
LGA    -       -      N     123           -
LGA    -       -      G     124           -
LGA    -       -      I     125           -
LGA    -       -      P     126           -
LGA    -       -      N     127           -
LGA    -       -      L     128           -
LGA    -       -      L     129           -
LGA    -       -      L     130           -
LGA    -       -      P     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      V     135           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   38  135    5.0     27    3.37     7.41     11.684     0.779

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.713309 * X  +  -0.150307 * Y  +   0.684542 * Z  +  72.027405
  Y_new =  -0.542065 * X  +   0.737442 * Y  +  -0.402922 * Z  +   2.206152
  Z_new =  -0.444248 * X  +  -0.658474 * Y  +  -0.607500 * Z  + 110.323898 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.315951    0.825641  [ DEG:  -132.6942     47.3058 ]
  Theta =   0.460335    2.681258  [ DEG:    26.3752    153.6248 ]
  Phi   =  -2.491767    0.649826  [ DEG:  -142.7677     37.2323 ]
 
# 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: T0319AL044_1                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319AL044_1.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   38  135   5.0   27   3.37    7.41  11.684
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL044_1
REMARK Aligment from pdb entry: 1nnq_A
ATOM      1  N   GLY    67       3.384  -1.787   9.726  1.00  0.00              
ATOM      2  CA  GLY    67       4.092  -1.001   8.724  1.00  0.00              
ATOM      3  C   GLY    67       5.398  -0.491   9.328  1.00  0.00              
ATOM      4  O   GLY    67       6.439  -0.467   8.663  1.00  0.00              
ATOM      5  N   ASN    68       5.355  -0.104  10.595  1.00  0.00              
ATOM      6  CA  ASN    68       6.574   0.324  11.273  1.00  0.00              
ATOM      7  C   ASN    68       7.602  -0.825  11.266  1.00  0.00              
ATOM      8  O   ASN    68       8.737  -0.644  10.885  1.00  0.00              
ATOM      9  N   ASN    69       7.157  -2.016  11.650  1.00  0.00              
ATOM     10  CA  ASN    69       8.006  -3.191  11.761  1.00  0.00              
ATOM     11  C   ASN    69       8.561  -3.607  10.393  1.00  0.00              
ATOM     12  O   ASN    69       9.766  -3.761  10.227  1.00  0.00              
ATOM     13  N   ALA    70       7.673  -3.733   9.416  1.00  0.00              
ATOM     14  CA  ALA    70       8.015  -4.150   8.070  1.00  0.00              
ATOM     15  C   ALA    70       9.153  -3.322   7.454  1.00  0.00              
ATOM     16  O   ALA    70      10.162  -3.885   7.014  1.00  0.00              
ATOM     17  N   PRO    73       9.002  -1.995   7.443  1.00  0.00              
ATOM     18  CA  PRO    73      10.050  -1.131   6.913  1.00  0.00              
ATOM     19  C   PRO    73      11.409  -1.316   7.604  1.00  0.00              
ATOM     20  O   PRO    73      12.433  -1.314   6.930  1.00  0.00              
ATOM     21  N   THR    74      11.419  -1.521   8.923  1.00  0.00              
ATOM     22  CA  THR    74      12.675  -1.720   9.648  1.00  0.00              
ATOM     23  C   THR    74      13.308  -3.087   9.400  1.00  0.00              
ATOM     24  O   THR    74      14.527  -3.176   9.333  1.00  0.00              
ATOM     25  N   LYS    75      13.335  -4.761   6.695  1.00  0.00              
ATOM     26  CA  LYS    75      13.979  -4.663   5.399  1.00  0.00              
ATOM     27  C   LYS    75      15.447  -4.262   5.569  1.00  0.00              
ATOM     28  O   LYS    75      16.330  -4.795   4.901  1.00  0.00              
ATOM     29  N   PRO    76      15.677  -3.323   6.483  1.00  0.00              
ATOM     30  CA  PRO    76      17.003  -2.825   6.751  1.00  0.00              
ATOM     31  C   PRO    76      17.830  -3.878   7.466  1.00  0.00              
ATOM     32  O   PRO    76      18.979  -4.116   7.100  1.00  0.00              
ATOM     33  N   SER    77      17.231  -4.531   8.450  1.00  0.00              
ATOM     34  CA  SER    77      17.930  -5.544   9.230  1.00  0.00              
ATOM     35  C   SER    77      18.469  -6.707   8.402  1.00  0.00              
ATOM     36  O   SER    77      19.588  -7.136   8.622  1.00  0.00              
ATOM     37  N   PHE    78      17.675  -7.213   7.471  1.00  0.00              
ATOM     38  CA  PHE    78      18.109  -8.313   6.601  1.00  0.00              
ATOM     39  C   PHE    78      19.378  -7.906   5.856  1.00  0.00              
ATOM     40  O   PHE    78      20.324  -8.693   5.782  1.00  0.00              
ATOM     41  N   GLN    83      19.404  -6.670   5.348  1.00  0.00              
ATOM     42  CA  GLN    83      20.555  -6.198   4.584  1.00  0.00              
ATOM     43  C   GLN    83      21.818  -5.979   5.433  1.00  0.00              
ATOM     44  O   GLN    83      22.936  -6.285   5.007  1.00  0.00              
ATOM     45  N   GLU    84      22.560  -7.607   8.199  1.00  0.00              
ATOM     46  CA  GLU    84      23.037  -8.921   8.578  1.00  0.00              
ATOM     47  C   GLU    84      23.733  -9.623   7.385  1.00  0.00              
ATOM     48  O   GLU    84      24.723 -10.329   7.570  1.00  0.00              
ATOM     49  N   LEU    85      23.207  -9.418   6.177  1.00  0.00              
ATOM     50  CA  LEU    85      23.815  -9.939   4.952  1.00  0.00              
ATOM     51  C   LEU    85      25.203  -9.363   4.818  1.00  0.00              
ATOM     52  O   LEU    85      26.156 -10.080   4.540  1.00  0.00              
ATOM     53  N   ASP    87      25.316  -8.057   5.034  1.00  0.00              
ATOM     54  CA  ASP    87      26.607  -7.403   4.898  1.00  0.00              
ATOM     55  C   ASP    87      27.567  -7.845   5.993  1.00  0.00              
ATOM     56  O   ASP    87      28.744  -8.029   5.715  1.00  0.00              
ATOM     57  N   ALA    91      27.077  -8.042   7.215  1.00  0.00              
ATOM     58  CA  ALA    91      27.966  -8.449   8.316  1.00  0.00              
ATOM     59  C   ALA    91      28.469  -9.869   8.159  1.00  0.00              
ATOM     60  O   ALA    91      29.568 -10.179   8.622  1.00  0.00              
ATOM     61  N   ILE    92      27.658 -10.725   7.529  1.00  0.00              
ATOM     62  CA  ILE    92      28.003 -12.141   7.366  1.00  0.00              
ATOM     63  C   ILE    92      29.194 -12.360   6.417  1.00  0.00              
ATOM     64  O   ILE    92      30.058 -13.181   6.699  1.00  0.00              
ATOM     65  N   LEU    96      29.219 -11.624   5.306  1.00  0.00              
ATOM     66  CA  LEU    96      30.383 -11.568   4.421  1.00  0.00              
ATOM     67  C   LEU    96      31.656 -11.354   5.244  1.00  0.00              
ATOM     68  O   LEU    96      32.649 -12.091   5.105  1.00  0.00              
ATOM     69  N   HIS    97      31.603 -10.355   6.123  1.00  0.00              
ATOM     70  CA  HIS    97      32.726 -10.020   6.985  1.00  0.00              
ATOM     71  C   HIS    97      33.058 -11.164   7.955  1.00  0.00              
ATOM     72  O   HIS    97      34.179 -11.665   7.936  1.00  0.00              
ATOM     73  N   THR    98      32.350 -14.332   8.073  1.00  0.00              
ATOM     74  CA  THR    98      32.780 -15.546   7.391  1.00  0.00              
ATOM     75  C   THR    98      34.273 -15.506   6.991  1.00  0.00              
ATOM     76  O   THR    98      34.932 -16.546   6.963  1.00  0.00              
ATOM     77  N   LEU    99      34.783 -14.305   6.692  1.00  0.00              
ATOM     78  CA  LEU    99      36.199 -14.071   6.367  1.00  0.00              
ATOM     79  C   LEU    99      37.020 -13.774   7.621  1.00  0.00              
ATOM     80  O   LEU    99      38.154 -13.305   7.527  1.00  0.00              
ATOM     81  N   LEU   100      36.431 -14.023   8.788  1.00  0.00              
ATOM     82  CA  LEU   100      37.078 -13.782  10.072  1.00  0.00              
ATOM     83  C   LEU   100      37.266 -12.308  10.416  1.00  0.00              
ATOM     84  O   LEU   100      37.935 -11.994  11.407  1.00  0.00              
ATOM     85  N   LEU   101      36.702 -11.414   9.599  1.00  0.00              
ATOM     86  CA  LEU   101      36.742  -9.971   9.840  1.00  0.00              
ATOM     87  C   LEU   101      35.494  -9.487  10.615  1.00  0.00              
ATOM     88  O   LEU   101      34.367  -9.799  10.241  1.00  0.00              
ATOM     89  N   GLN   102      35.701  -8.732  11.695  1.00  0.00              
ATOM     90  CA  GLN   102      34.626  -7.932  12.291  1.00  0.00              
ATOM     91  C   GLN   102      34.169  -6.863  11.294  1.00  0.00              
ATOM     92  O   GLN   102      34.909  -6.529  10.374  1.00  0.00              
ATOM     93  N   THR   103      32.953  -6.342  11.452  1.00  0.00              
ATOM     94  CA  THR   103      32.509  -5.227  10.605  1.00  0.00              
ATOM     95  C   THR   103      33.119  -3.931  11.127  1.00  0.00              
ATOM     96  O   THR   103      33.546  -3.859  12.281  1.00  0.00              
ATOM     97  N   SER   104      33.173  -2.919  10.263  1.00  0.00              
ATOM     98  CA  SER   104      33.698  -1.623  10.656  1.00  0.00              
ATOM     99  C   SER   104      32.543  -0.652  10.739  1.00  0.00              
ATOM    100  O   SER   104      31.984  -0.250   9.713  1.00  0.00              
ATOM    101  N   ILE   105      32.165  -0.312  11.968  1.00  0.00              
ATOM    102  CA  ILE   105      31.096   0.660  12.207  1.00  0.00              
ATOM    103  C   ILE   105      31.371   1.509  13.448  1.00  0.00              
ATOM    104  O   ILE   105      31.914   1.022  14.443  1.00  0.00              
ATOM    105  N   ALA   106      30.994   2.783  13.371  1.00  0.00              
ATOM    106  CA  ALA   106      31.165   3.719  14.475  1.00  0.00              
ATOM    107  C   ALA   106      29.977   3.662  15.435  1.00  0.00              
ATOM    108  O   ALA   106      30.174   3.519  16.648  1.00  0.00              
ATOM    109  N   GLU   107      28.755   3.777  14.895  1.00  0.00              
ATOM    110  CA  GLU   107      27.540   3.855  15.718  1.00  0.00              
ATOM    111  C   GLU   107      26.263   3.369  15.001  1.00  0.00              
ATOM    112  O   GLU   107      26.226   3.273  13.772  1.00  0.00              
ATOM    113  N   GLY   108      11.370   2.104  15.120  1.00  0.00              
ATOM    114  CA  GLY   108      12.438   1.123  14.996  1.00  0.00              
ATOM    115  C   GLY   108      13.311   1.181  13.755  1.00  0.00              
ATOM    116  O   GLY   108      14.172   0.306  13.558  1.00  0.00              
ATOM    117  N   GLU   109      19.406  10.324   8.644  1.00  0.00              
ATOM    118  CA  GLU   109      18.750  11.554   8.177  1.00  0.00              
ATOM    119  C   GLU   109      18.316  12.392   9.368  1.00  0.00              
ATOM    120  O   GLU   109      18.282  11.859  10.474  1.00  0.00              
ATOM    121  N   MET   110      18.012  13.674   9.161  1.00  0.00              
ATOM    122  CA  MET   110      17.613  14.558  10.266  1.00  0.00              
ATOM    123  C   MET   110      16.254  14.155  10.842  1.00  0.00              
ATOM    124  O   MET   110      15.934  14.465  11.985  1.00  0.00              
ATOM    125  N   LYS   111      15.454  13.478  10.031  1.00  0.00              
ATOM    126  CA  LYS   111      14.137  13.020  10.449  1.00  0.00              
ATOM    127  C   LYS   111      14.006  11.592  10.008  1.00  0.00              
ATOM    128  O   LYS   111      14.482  11.220   8.930  1.00  0.00              
ATOM    129  N   CYS   112      13.375  10.789  10.854  1.00  0.00              
ATOM    130  CA  CYS   112      13.060   9.419  10.520  1.00  0.00              
ATOM    131  C   CYS   112      12.212   9.402   9.263  1.00  0.00              
ATOM    132  O   CYS   112      11.184  10.057   9.204  1.00  0.00              
ATOM    133  N   ARG   113      12.646   8.676   8.246  1.00  0.00              
ATOM    134  CA  ARG   113      11.881   8.597   6.996  1.00  0.00              
ATOM    135  C   ARG   113      10.559   7.823   7.143  1.00  0.00              
ATOM    136  O   ARG   113       9.733   7.878   6.218  1.00  0.00              
ATOM    137  N   ASN   114      10.365   7.107   8.259  1.00  0.00              
ATOM    138  CA  ASN   114       9.138   6.314   8.411  1.00  0.00              
ATOM    139  C   ASN   114       8.083   7.067   9.212  1.00  0.00              
ATOM    140  O   ASN   114       6.948   7.200   8.758  1.00  0.00              
ATOM    141  N   CYS   115       8.469   7.587  10.369  1.00  0.00              
ATOM    142  CA  CYS   115       7.518   8.239  11.269  1.00  0.00              
ATOM    143  C   CYS   115       7.707   9.752  11.416  1.00  0.00              
ATOM    144  O   CYS   115       6.848  10.413  12.005  1.00  0.00              
ATOM    145  N   GLY   116       8.820  10.298  10.913  1.00  0.00              
ATOM    146  CA  GLY   116       9.069  11.729  11.012  1.00  0.00              
ATOM    147  C   GLY   116       9.762  12.220  12.278  1.00  0.00              
ATOM    148  O   GLY   116      10.096  13.394  12.349  1.00  0.00              
ATOM    149  N   ILE   118      10.009  11.343  13.256  1.00  0.00              
ATOM    150  CA  ILE   118      10.755  11.710  14.475  1.00  0.00              
ATOM    151  C   ILE   118      12.131  12.334  14.181  1.00  0.00              
ATOM    152  O   ILE   118      12.797  11.938  13.229  1.00  0.00              
END
