
#######################################################
#                                                     #
#                        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_2
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319AL044_2.T0319.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    -       -      L       9           -
LGA    -       -      K      10           -
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    -       -      F      23           -
LGA    -       -      P      24           -
LGA    -       -      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    -       -      P      57           -
LGA    -       -      A      58           -
LGA    -       -      V      59           -
LGA    -       -      L      60           -
LGA    -       -      T      61           -
LGA    -       -      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    -       -      T      74           -
LGA    -       -      K      75           -
LGA    -       -      P      76           -
LGA    -       -      S      77           -
LGA    -       -      F      78           -
LGA    -       -      P      79           -
LGA    -       -      S      80           -
LGA    -       -      S      81           -
LGA    -       -      I      82           -
LGA    -       -      Q      83           -
LGA    N      68      E      84           #
LGA    N      69      L      85          3.778
LGA    A      70      T      86           #
LGA    -       -      D      87           -
LGA    -       -      D      88           -
LGA    P      73      D      89          2.625
LGA    T      74      M      90          1.716
LGA    -       -      A      91           -
LGA    -       -      I      92           -
LGA    K      75      L      93          1.963
LGA    P      76      N      94          2.467
LGA    S      77      D      95          1.535
LGA    F      78      L      96          0.931
LGA    Q      83      H      97          1.811
LGA    E      84      T      98          1.721
LGA    L      85      L      99          2.610
LGA    D      87      L     100          4.625
LGA    A      91      L     101          5.163
LGA    I      92      Q     102          4.875
LGA    L      96      T     103          4.201
LGA    H      97      S     104          4.252
LGA    T      98      I     105          2.387
LGA    L      99      A     106          5.400
LGA    L     100      -       -           -
LGA    L     101      E     107           #
LGA    Q     102      G     108          4.173
LGA    T     103      E     109           -
LGA    S     104      -       -           -
LGA    I     105      -       -           -
LGA    A     106      -       -           -
LGA    E     107      -       -           -
LGA    G     108      -       -           -
LGA    E     109      M     110          2.028
LGA    M     110      K     111          3.338
LGA    K     111      C     112          2.334
LGA    C     112      -       -           -
LGA    R     113      R     113          3.823
LGA    N     114      N     114          3.307
LGA    C     115      C     115          5.655
LGA    G     116      G     116          5.556
LGA    I     118      H     117           #
LGA    -       -      I     118           -
LGA    -       -      Y     119           -
LGA    -       -      Y     120           -
LGA    -       -      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     25    3.57    20.00     11.199     0.681

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.399893 * X  +   0.737931 * Y  +   0.543640 * Z  +  12.275406
  Y_new =   0.670852 * X  +  -0.168504 * Y  +   0.722193 * Z  + -18.460705
  Z_new =   0.624534 * X  +   0.653502 * Y  +  -0.427659 * Z  +   9.586207 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.150266   -0.991326  [ DEG:   123.2012    -56.7988 ]
  Theta =  -0.674535   -2.467058  [ DEG:   -38.6480   -141.3520 ]
  Phi   =   2.108341   -1.033252  [ DEG:   120.7990    -59.2010 ]
 
# 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_2                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319AL044_2.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   25   3.57   20.00  11.199
REMARK  ---------------------------------------------------------- 
MOLECULE T0319AL044_2
REMARK Aligment from pdb entry: 1b71_A
ATOM      1  N   GLY    67      42.204 -18.459  10.555  1.00  0.00              
ATOM      2  CA  GLY    67      42.547 -17.154   9.988  1.00  0.00              
ATOM      3  C   GLY    67      41.377 -16.635   9.155  1.00  0.00              
ATOM      4  O   GLY    67      41.085 -15.433   9.158  1.00  0.00              
ATOM      5  N   ASN    68      40.708 -17.548   8.444  1.00  0.00              
ATOM      6  CA  ASN    68      39.600 -17.108   7.588  1.00  0.00              
ATOM      7  C   ASN    68      38.443 -16.556   8.399  1.00  0.00              
ATOM      8  O   ASN    68      37.944 -15.468   8.117  1.00  0.00              
ATOM      9  N   ASN    69      37.996 -17.255   9.436  1.00  0.00              
ATOM     10  CA  ASN    69      37.018 -16.715  10.373  1.00  0.00              
ATOM     11  C   ASN    69      37.410 -15.361  10.949  1.00  0.00              
ATOM     12  O   ASN    69      36.571 -14.477  11.182  1.00  0.00              
ATOM     13  N   ALA    70      36.246 -12.641   8.804  1.00  0.00              
ATOM     14  CA  ALA    70      34.815 -12.378   8.955  1.00  0.00              
ATOM     15  C   ALA    70      34.552 -11.559  10.203  1.00  0.00              
ATOM     16  O   ALA    70      33.717 -10.651  10.272  1.00  0.00              
ATOM     17  N   PRO    73      35.361 -11.943  11.217  1.00  0.00              
ATOM     18  CA  PRO    73      35.122 -11.257  12.487  1.00  0.00              
ATOM     19  C   PRO    73      35.573  -9.812  12.367  1.00  0.00              
ATOM     20  O   PRO    73      35.049  -8.924  13.047  1.00  0.00              
ATOM     21  N   THR    74      36.556  -9.543  11.507  1.00  0.00              
ATOM     22  CA  THR    74      36.915  -8.126  11.412  1.00  0.00              
ATOM     23  C   THR    74      35.790  -7.317  10.773  1.00  0.00              
ATOM     24  O   THR    74      35.487  -6.200  11.197  1.00  0.00              
ATOM     25  N   LYS    75      32.717  -8.099  10.850  1.00  0.00              
ATOM     26  CA  LYS    75      31.628  -8.042  11.817  1.00  0.00              
ATOM     27  C   LYS    75      31.866  -6.853  12.736  1.00  0.00              
ATOM     28  O   LYS    75      31.012  -6.065  13.105  1.00  0.00              
ATOM     29  N   PRO    76      33.127  -6.743  13.155  1.00  0.00              
ATOM     30  CA  PRO    76      33.469  -5.632  14.026  1.00  0.00              
ATOM     31  C   PRO    76      33.180  -4.292  13.350  1.00  0.00              
ATOM     32  O   PRO    76      32.504  -3.450  13.935  1.00  0.00              
ATOM     33  N   SER    77      33.720  -4.188  12.139  1.00  0.00              
ATOM     34  CA  SER    77      33.579  -2.966  11.349  1.00  0.00              
ATOM     35  C   SER    77      32.121  -2.517  11.325  1.00  0.00              
ATOM     36  O   SER    77      31.796  -1.374  11.653  1.00  0.00              
ATOM     37  N   PHE    78      31.287  -3.476  10.934  1.00  0.00              
ATOM     38  CA  PHE    78      29.846  -3.273  10.838  1.00  0.00              
ATOM     39  C   PHE    78      29.257  -2.794  12.154  1.00  0.00              
ATOM     40  O   PHE    78      28.529  -1.798  12.236  1.00  0.00              
ATOM     41  N   GLN    83      29.572  -3.503  13.243  1.00  0.00              
ATOM     42  CA  GLN    83      29.007  -3.137  14.529  1.00  0.00              
ATOM     43  C   GLN    83      29.407  -1.732  14.930  1.00  0.00              
ATOM     44  O   GLN    83      28.652  -1.003  15.564  1.00  0.00              
ATOM     45  N   GLU    84      30.385   0.904  12.816  1.00  0.00              
ATOM     46  CA  GLU    84      29.677   1.951  12.073  1.00  0.00              
ATOM     47  C   GLU    84      28.273   2.144  12.602  1.00  0.00              
ATOM     48  O   GLU    84      27.785   3.264  12.695  1.00  0.00              
ATOM     49  N   LEU    85      27.637   1.005  12.927  1.00  0.00              
ATOM     50  CA  LEU    85      26.282   1.154  13.451  1.00  0.00              
ATOM     51  C   LEU    85      26.293   1.837  14.811  1.00  0.00              
ATOM     52  O   LEU    85      25.443   2.696  15.059  1.00  0.00              
ATOM     53  N   ASP    87      27.216   1.464  15.689  1.00  0.00              
ATOM     54  CA  ASP    87      27.313   2.141  16.983  1.00  0.00              
ATOM     55  C   ASP    87      27.536   3.642  16.785  1.00  0.00              
ATOM     56  O   ASP    87      26.921   4.483  17.438  1.00  0.00              
ATOM     57  N   ALA    91      28.428   3.968  15.856  1.00  0.00              
ATOM     58  CA  ALA    91      28.706   5.372  15.532  1.00  0.00              
ATOM     59  C   ALA    91      27.455   6.077  15.032  1.00  0.00              
ATOM     60  O   ALA    91      27.093   7.111  15.612  1.00  0.00              
ATOM     61  N   ILE    92      26.741   5.613  14.008  1.00  0.00              
ATOM     62  CA  ILE    92      25.496   6.300  13.641  1.00  0.00              
ATOM     63  C   ILE    92      24.517   6.449  14.789  1.00  0.00              
ATOM     64  O   ILE    92      23.788   7.419  14.953  1.00  0.00              
ATOM     65  N   LEU    96      24.471   5.453  15.671  1.00  0.00              
ATOM     66  CA  LEU    96      23.533   5.570  16.783  1.00  0.00              
ATOM     67  C   LEU    96      24.037   6.719  17.652  1.00  0.00              
ATOM     68  O   LEU    96      23.269   7.580  18.044  1.00  0.00              
ATOM     69  N   HIS    97      25.336   6.671  17.914  1.00  0.00              
ATOM     70  CA  HIS    97      25.994   7.740  18.654  1.00  0.00              
ATOM     71  C   HIS    97      25.734   9.095  17.985  1.00  0.00              
ATOM     72  O   HIS    97      25.260  10.017  18.655  1.00  0.00              
ATOM     73  N   THR    98      23.486  10.169  15.950  1.00  0.00              
ATOM     74  CA  THR    98      22.107  10.305  15.520  1.00  0.00              
ATOM     75  C   THR    98      21.947  10.305  14.012  1.00  0.00              
ATOM     76  O   THR    98      21.252  11.157  13.463  1.00  0.00              
ATOM     77  N   LEU    99      22.572   9.375  13.294  1.00  0.00              
ATOM     78  CA  LEU    99      22.527   9.423  11.837  1.00  0.00              
ATOM     79  C   LEU    99      21.894   8.152  11.279  1.00  0.00              
ATOM     80  O   LEU    99      22.090   7.814  10.108  1.00  0.00              
ATOM     81  N   LEU   100      21.153   7.462  12.156  1.00  0.00              
ATOM     82  CA  LEU   100      20.578   6.180  11.738  1.00  0.00              
ATOM     83  C   LEU   100      19.510   6.431  10.675  1.00  0.00              
ATOM     84  O   LEU   100      19.549   5.822   9.621  1.00  0.00              
ATOM     85  N   LEU   101      18.611   7.338  11.019  1.00  0.00              
ATOM     86  CA  LEU   101      17.413   7.689  10.282  1.00  0.00              
ATOM     87  C   LEU   101      17.447   9.130   9.788  1.00  0.00              
ATOM     88  O   LEU   101      16.415   9.759   9.555  1.00  0.00              
ATOM     89  N   GLN   102      18.653   9.662   9.630  1.00  0.00              
ATOM     90  CA  GLN   102      18.831  11.049   9.231  1.00  0.00              
ATOM     91  C   GLN   102      20.228  11.266   8.672  1.00  0.00              
ATOM     92  O   GLN   102      21.226  10.928   9.305  1.00  0.00              
ATOM     93  N   THR   103      20.292  11.819   7.465  1.00  0.00              
ATOM     94  CA  THR   103      21.596  12.102   6.860  1.00  0.00              
ATOM     95  C   THR   103      21.653  13.565   6.444  1.00  0.00              
ATOM     96  O   THR   103      20.640  14.264   6.396  1.00  0.00              
ATOM     97  N   SER   104      22.856  14.060   6.159  1.00  0.00              
ATOM     98  CA  SER   104      23.002  15.511   5.984  1.00  0.00              
ATOM     99  C   SER   104      22.661  15.926   4.569  1.00  0.00              
ATOM    100  O   SER   104      22.316  17.074   4.297  1.00  0.00              
ATOM    101  N   ILE   105      22.692  15.022   3.594  1.00  0.00              
ATOM    102  CA  ILE   105      22.098  15.417   2.314  1.00  0.00              
ATOM    103  C   ILE   105      20.845  14.584   2.076  1.00  0.00              
ATOM    104  O   ILE   105      20.593  13.557   2.706  1.00  0.00              
ATOM    105  N   ALA   106      20.013  15.047   1.146  1.00  0.00              
ATOM    106  CA  ALA   106      18.861  14.213   0.804  1.00  0.00              
ATOM    107  C   ALA   106      19.400  12.927   0.190  1.00  0.00              
ATOM    108  O   ALA   106      20.279  12.970  -0.676  1.00  0.00              
ATOM    109  N   GLU   107      18.895  11.783   0.638  1.00  0.00              
ATOM    110  CA  GLU   107      19.302  10.517   0.021  1.00  0.00              
ATOM    111  C   GLU   107      18.139   9.543  -0.030  1.00  0.00              
ATOM    112  O   GLU   107      17.006   9.870   0.352  1.00  0.00              
ATOM    113  N   GLY   108       9.591  -2.375   0.969  1.00  0.00              
ATOM    114  CA  GLY   108      10.395  -2.020  -0.189  1.00  0.00              
ATOM    115  C   GLY   108      10.166  -0.610  -0.695  1.00  0.00              
ATOM    116  O   GLY   108      10.720  -0.137  -1.693  1.00  0.00              
ATOM    117  N   GLU   109      11.045   8.394   6.643  1.00  0.00              
ATOM    118  CA  GLU   109       9.739   8.934   7.059  1.00  0.00              
ATOM    119  C   GLU   109       9.301   8.354   8.398  1.00  0.00              
ATOM    120  O   GLU   109       9.752   7.277   8.786  1.00  0.00              
ATOM    121  N   MET   110       8.417   9.041   9.108  1.00  0.00              
ATOM    122  CA  MET   110       7.984   8.572  10.417  1.00  0.00              
ATOM    123  C   MET   110       7.067   7.352  10.311  1.00  0.00              
ATOM    124  O   MET   110       6.775   6.725  11.329  1.00  0.00              
ATOM    125  N   LYS   111       6.644   7.075   9.097  1.00  0.00              
ATOM    126  CA  LYS   111       5.710   6.022   8.746  1.00  0.00              
ATOM    127  C   LYS   111       5.808   5.728   7.256  1.00  0.00              
ATOM    128  O   LYS   111       5.872   6.611   6.398  1.00  0.00              
ATOM    129  N   CYS   112       5.824   4.426   6.948  1.00  0.00              
ATOM    130  CA  CYS   112       5.901   4.110   5.532  1.00  0.00              
ATOM    131  C   CYS   112       4.574   4.420   4.845  1.00  0.00              
ATOM    132  O   CYS   112       3.510   3.897   5.197  1.00  0.00              
ATOM    133  N   ARG   113       4.650   5.289   3.837  1.00  0.00              
ATOM    134  CA  ARG   113       3.469   5.590   3.032  1.00  0.00              
ATOM    135  C   ARG   113       2.872   4.311   2.447  1.00  0.00              
ATOM    136  O   ARG   113       1.666   4.272   2.209  1.00  0.00              
ATOM    137  N   ASN   114       3.698   3.295   2.213  1.00  0.00              
ATOM    138  CA  ASN   114       3.198   2.081   1.563  1.00  0.00              
ATOM    139  C   ASN   114       2.628   1.092   2.575  1.00  0.00              
ATOM    140  O   ASN   114       1.429   0.777   2.524  1.00  0.00              
ATOM    141  N   CYS   115       3.434   0.594   3.507  1.00  0.00              
ATOM    142  CA  CYS   115       2.973  -0.425   4.450  1.00  0.00              
ATOM    143  C   CYS   115       2.564   0.121   5.801  1.00  0.00              
ATOM    144  O   CYS   115       2.083  -0.624   6.666  1.00  0.00              
ATOM    145  N   GLY   116       2.735   1.416   6.045  1.00  0.00              
ATOM    146  CA  GLY   116       2.312   2.015   7.307  1.00  0.00              
ATOM    147  C   GLY   116       3.104   1.513   8.507  1.00  0.00              
ATOM    148  O   GLY   116       2.727   1.714   9.667  1.00  0.00              
ATOM    149  N   ILE   118       4.239   0.862   8.277  1.00  0.00              
ATOM    150  CA  ILE   118       5.159   0.561   9.371  1.00  0.00              
ATOM    151  C   ILE   118       6.007   1.778   9.724  1.00  0.00              
ATOM    152  O   ILE   118       6.232   2.687   8.924  1.00  0.00              
END
