
#######################################################
#                                                     #
#                        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   44 (  176),  selected   44 , name T0319TS383_4
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319TS383_4.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    D      88      M       1           -
LGA    D      89      K       2           -
LGA    M      90      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    A      91      Y      27          5.039
LGA    I      92      D      28          1.039
LGA    -       -      G      29           -
LGA    -       -      S      30           -
LGA    L      93      K      31          3.511
LGA    N      94      C      32          2.838
LGA    D      95      Q      33          3.403
LGA    L      96      L      34          1.896
LGA    H      97      V      35           #
LGA    T      98      -       -           -
LGA    L      99      -       -           -
LGA    L     100      Q      36          3.016
LGA    L     101      D      37          2.313
LGA    Q     102      E      38          3.393
LGA    S     104      S      39          1.522
LGA    I     105      I      40          1.572
LGA    A     106      E      41          1.308
LGA    E     107      F      42           #
LGA    G     108      N      43           #
LGA    E     109      P      44          5.189
LGA    -       -      E      45           -
LGA    -       -      F      46           -
LGA    -       -      L      47           -
LGA    M     110      L      48          3.889
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    K     111      S      77           #
LGA    C     112      F      78           #
LGA    R     113      P      79          4.909
LGA    N     114      -       -           -
LGA    C     115      -       -           -
LGA    G     116      S      80          2.184
LGA    H     117      S      81          2.177
LGA    I     118      I      82          2.299
LGA    Y     119      Q      83          4.018
LGA    Y     120      E      84           #
LGA    -       -      L      85           -
LGA    I     121      T      86          4.527
LGA    -       -      D      87           -
LGA    -       -      D      88           -
LGA    -       -      D      89           -
LGA    K     122      M      90          1.476
LGA    N     123      A      91          3.060
LGA    G     124      I      92           #
LGA    I     125      L      93           -
LGA    P     126      N      94           -
LGA    N     127      D      95           -
LGA    L     128      L      96           -
LGA    L     129      H      97           -
LGA    L     130      T      98           -
LGA    P     131      L      99           -
LGA    P     132      L     100           -
LGA    -       -      L     101           -
LGA    -       -      Q     102           -
LGA    -       -      T     103           -
LGA    -       -      S     104           -
LGA    -       -      I     105           -
LGA    -       -      A     106           -
LGA    -       -      E     107           -
LGA    -       -      G     108           -
LGA    -       -      E     109           -
LGA    -       -      M     110           -
LGA    -       -      K     111           -
LGA    -       -      C     112           -
LGA    -       -      R     113           -
LGA    -       -      N     114           -
LGA    -       -      C     115           -
LGA    -       -      G     116           -
LGA    -       -      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)   44  135    5.0     22    3.19    18.18     10.010     0.669

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.129881 * X  +   0.271561 * Y  +  -0.953617 * Z  +  29.506134
  Y_new =  -0.413167 * X  +  -0.889110 * Y  +  -0.196919 * Z  +  -8.850434
  Z_new =  -0.901345 * X  +   0.368427 * Y  +   0.227679 * Z  +   6.235635 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.017265   -2.124328  [ DEG:    58.2850   -121.7150 ]
  Theta =   1.122866    2.018726  [ DEG:    64.3355    115.6645 ]
  Phi   =  -1.875370    1.266222  [ DEG:  -107.4508     72.5492 ]
 
# 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: T0319TS383_4                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319TS383_4.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44  135   5.0   22   3.19   18.18  10.010
REMARK  ---------------------------------------------------------- 
MOLECULE T0319TS383_4
PFRMAT TS
TARGET T0319
MODEL 4
PARENT 2ct7A
ATOM      1  N   ASP    88       4.930  11.305  -6.167  1.00  0.00
ATOM      2  CA  ASP    88       6.318  11.219  -5.730  1.00  0.00
ATOM      3  C   ASP    88       6.416  10.557  -4.359  1.00  0.00
ATOM      4  O   ASP    88       5.403  10.287  -3.714  1.00  0.00
ATOM      5  N   ASP    89       7.644  10.297  -3.920  1.00  0.00
ATOM      6  CA  ASP    89       7.876   9.664  -2.628  1.00  0.00
ATOM      7  C   ASP    89       9.327   9.835  -2.191  1.00  0.00
ATOM      8  O   ASP    89      10.156  10.350  -2.941  1.00  0.00
ATOM      9  N   MET    90       9.627   9.400  -0.971  1.00  0.00
ATOM     10  CA  MET    90      10.979   9.514  -0.454  1.00  0.00
ATOM     11  C   MET    90      11.022  10.150   0.921  1.00  0.00
ATOM     12  O   MET    90      10.274  11.085   1.203  1.00  0.00
ATOM     13  N   ALA    91      11.899   9.640   1.780  1.00  0.00
ATOM     14  CA  ALA    91      12.033  10.161   3.135  1.00  0.00
ATOM     15  C   ALA    91      13.290   9.614   3.806  1.00  0.00
ATOM     16  O   ALA    91      13.403   8.415   4.055  1.00  0.00
ATOM     17  N   ILE    92      14.234  10.505   4.094  1.00  0.00
ATOM     18  CA  ILE    92      15.485  10.114   4.732  1.00  0.00
ATOM     19  C   ILE    92      15.997  11.220   5.649  1.00  0.00
ATOM     20  O   ILE    92      15.903  12.404   5.325  1.00  0.00
ATOM     21  N   LEU    93      16.540  10.825   6.797  1.00  0.00
ATOM     22  CA  LEU    93      17.059  11.795   7.744  1.00  0.00
ATOM     23  C   LEU    93      17.496  11.154   9.048  1.00  0.00
ATOM     24  O   LEU    93      16.680  10.585   9.771  1.00  0.00
ATOM     25  N   ASN    94      18.787  11.247   9.346  1.00  0.00
ATOM     26  CA  ASN    94      19.331  10.672  10.571  1.00  0.00
ATOM     27  C   ASN    94      20.587  11.415  11.014  1.00  0.00
ATOM     28  O   ASN    94      21.280  12.025  10.200  1.00  0.00
ATOM     29  N   ASP    95      20.874  11.361  12.311  1.00  0.00
ATOM     30  CA  ASP    95      22.046  12.029  12.863  1.00  0.00
ATOM     31  C   ASP    95      23.329  11.323  12.433  1.00  0.00
ATOM     32  O   ASP    95      24.433  11.783  12.727  1.00  0.00
ATOM     33  N   LEU    96      23.176  10.203  11.735  1.00  0.00
ATOM     34  CA  LEU    96      24.321   9.433  11.264  1.00  0.00
ATOM     35  C   LEU    96      24.778   9.923   9.893  1.00  0.00
ATOM     36  O   LEU    96      24.913   9.137   8.953  1.00  0.00
ATOM     37  N   HIS    97      25.015  11.226   9.785  1.00  0.00
ATOM     38  CA  HIS    97      25.457  11.822   8.530  1.00  0.00
ATOM     39  C   HIS    97      26.659  12.734   8.755  1.00  0.00
ATOM     40  O   HIS    97      27.673  12.624   8.066  1.00  0.00
ATOM     41  N   THR    98      26.539  13.635   9.724  1.00  0.00
ATOM     42  CA  THR    98      27.615  14.567  10.042  1.00  0.00
ATOM     43  C   THR    98      27.970  14.502  11.523  1.00  0.00
ATOM     44  O   THR    98      28.418  15.489  12.108  1.00  0.00
ATOM     45  N   LEU    99      27.771  13.335  12.125  1.00  0.00
ATOM     46  CA  LEU    99      28.073  13.140  13.537  1.00  0.00
ATOM     47  C   LEU    99      29.108  12.036  13.725  1.00  0.00
ATOM     48  O   LEU    99      28.857  10.874  13.401  1.00  0.00
ATOM     49  N   LEU   100      30.272  12.405  14.249  1.00  0.00
ATOM     50  CA  LEU   100      31.345  11.444  14.481  1.00  0.00
ATOM     51  C   LEU   100      31.139  10.705  15.799  1.00  0.00
ATOM     52  O   LEU   100      30.660  11.279  16.778  1.00  0.00
ATOM     53  N   LEU   101      31.507   9.428  15.819  1.00  0.00
ATOM     54  CA  LEU   101      31.363   8.610  17.017  1.00  0.00
ATOM     55  C   LEU   101      32.237   9.136  18.150  1.00  0.00
ATOM     56  O   LEU   101      33.302   9.704  17.911  1.00  0.00
ATOM     57  N   GLN   102      31.779   8.942  19.383  1.00  0.00
ATOM     58  CA  GLN   102      32.521   9.398  20.553  1.00  0.00
ATOM     59  C   GLN   102      32.263   8.488  21.750  1.00  0.00
ATOM     60  O   GLN   102      31.135   8.052  21.980  1.00  0.00
ATOM     61  N   SER   104      33.317   8.204  22.510  1.00  0.00
ATOM     62  CA  SER   104      33.183   7.348  23.673  1.00  0.00
ATOM     63  C   SER   104      32.238   6.187  23.433  1.00  0.00
ATOM     64  O   SER   104      31.424   5.852  24.294  1.00  0.00
ATOM     65  N   ILE   105      32.343   5.573  22.259  1.00  0.00
ATOM     66  CA  ILE   105      31.490   4.444  21.909  1.00  0.00
ATOM     67  C   ILE   105      32.289   3.146  21.858  1.00  0.00
ATOM     68  O   ILE   105      32.902   2.821  20.839  1.00  0.00
ATOM     69  N   ALA   106      32.278   2.408  22.961  1.00  0.00
ATOM     70  CA  ALA   106      33.002   1.144  23.044  1.00  0.00
ATOM     71  C   ALA   106      32.098   0.032  23.565  1.00  0.00
ATOM     72  O   ALA   106      32.542  -0.848  24.303  1.00  0.00
ATOM     73  N   GLU   107      30.827   0.077  23.176  1.00  0.00
ATOM     74  CA  GLU   107      29.862  -0.930  23.602  1.00  0.00
ATOM     75  C   GLU   107      29.482  -1.844  22.442  1.00  0.00
ATOM     76  O   GLU   107      29.497  -3.068  22.574  1.00  0.00
ATOM     77  N   GLY   108      31.959  -5.526  17.350  1.00  0.00
ATOM     78  CA  GLY   108      32.591  -5.470  16.028  1.00  0.00
ATOM     79  C   GLY   108      32.109  -6.586  15.108  1.00  0.00
ATOM     80  O   GLY   108      31.122  -6.430  14.389  1.00  0.00
ATOM     81  N   GLU   109      32.812  -7.714  15.136  1.00  0.00
ATOM     82  CA  GLU   109      32.456  -8.858  14.306  1.00  0.00
ATOM     83  C   GLU   109      32.732 -10.168  15.037  1.00  0.00
ATOM     84  O   GLU   109      33.886 -10.534  15.260  1.00  0.00
ATOM     85  N   MET   110      31.667 -10.870  15.407  1.00  0.00
ATOM     86  CA  MET   110      31.796 -12.140  16.113  1.00  0.00
ATOM     87  C   MET   110      31.955 -13.296  15.130  1.00  0.00
ATOM     88  O   MET   110      30.972 -13.823  14.609  1.00  0.00
ATOM     89  N   LYS   111      33.201 -13.683  14.879  1.00  0.00
ATOM     90  CA  LYS   111      33.491 -14.777  13.957  1.00  0.00
ATOM     91  C   LYS   111      33.937 -16.023  14.714  1.00  0.00
ATOM     92  O   LYS   111      34.936 -16.000  15.433  1.00  0.00
ATOM     93  N   CYS   112      33.625 -20.738  14.715  1.00  0.00
ATOM     94  CA  CYS   112      33.356 -21.954  13.957  1.00  0.00
ATOM     95  C   CYS   112      31.855 -22.202  13.841  1.00  0.00
ATOM     96  O   CYS   112      31.047 -21.450  14.385  1.00  0.00
ATOM     97  N   ARG   113      31.489 -23.264  13.129  1.00  0.00
ATOM     98  CA  ARG   113      30.086 -23.612  12.944  1.00  0.00
ATOM     99  C   ARG   113      29.718 -24.854  13.750  1.00  0.00
ATOM    100  O   ARG   113      28.558 -25.262  13.780  1.00  0.00
ATOM    101  N   ASN   114      30.713 -25.449  14.398  1.00  0.00
ATOM    102  CA  ASN   114      30.494 -26.645  15.203  1.00  0.00
ATOM    103  C   ASN   114      30.944 -26.423  16.643  1.00  0.00
ATOM    104  O   ASN   114      30.169 -26.609  17.582  1.00  0.00
ATOM    105  N   CYS   115      32.201 -26.025  16.810  1.00  0.00
ATOM    106  CA  CYS   115      32.755 -25.778  18.136  1.00  0.00
ATOM    107  C   CYS   115      32.290 -24.429  18.677  1.00  0.00
ATOM    108  O   CYS   115      32.121 -24.259  19.885  1.00  0.00
ATOM    109  N   GLY   116      32.085 -23.475  17.776  1.00  0.00
ATOM    110  CA  GLY   116      31.643 -22.141  18.163  1.00  0.00
ATOM    111  C   GLY   116      32.592 -21.530  19.191  1.00  0.00
ATOM    112  O   GLY   116      32.170 -21.108  20.267  1.00  0.00
ATOM    113  N   HIS   117      33.876 -21.490  18.851  1.00  0.00
ATOM    114  CA  HIS   117      34.885 -20.933  19.743  1.00  0.00
ATOM    115  C   HIS   117      34.481 -19.542  20.222  1.00  0.00
ATOM    116  O   HIS   117      34.150 -19.348  21.391  1.00  0.00
ATOM    117  N   ILE   118      34.511 -18.576  19.309  1.00  0.00
ATOM    118  CA  ILE   118      34.146 -17.216  19.656  1.00  0.00
ATOM    119  C   ILE   118      35.347 -16.291  19.720  1.00  0.00
ATOM    120  O   ILE   118      35.926 -16.087  20.786  1.00  0.00
ATOM    121  N   TYR   119      35.723 -15.734  18.573  1.00  0.00
ATOM    122  CA  TYR   119      36.865 -14.829  18.502  1.00  0.00
ATOM    123  C   TYR   119      36.636 -13.747  17.450  1.00  0.00
ATOM    124  O   TYR   119      36.119 -14.020  16.366  1.00  0.00
ATOM    125  N   TYR   120      37.024 -12.520  17.778  1.00  0.00
ATOM    126  CA  TYR   120      36.863 -11.397  16.862  1.00  0.00
ATOM    127  C   TYR   120      37.978 -11.371  15.823  1.00  0.00
ATOM    128  O   TYR   120      39.153 -11.539  16.154  1.00  0.00
ATOM    129  N   ILE   121      37.605 -11.157  14.567  1.00  0.00
ATOM    130  CA  ILE   121      38.573 -11.109  13.478  1.00  0.00
ATOM    131  C   ILE   121      38.562  -9.743  12.800  1.00  0.00
ATOM    132  O   ILE   121      39.610  -9.211  12.433  1.00  0.00
ATOM    133  N   LYS   122      37.369  -9.180  12.635  1.00  0.00
ATOM    134  CA  LYS   122      37.221  -7.877  12.000  1.00  0.00
ATOM    135  C   LYS   122      38.334  -7.636  10.985  1.00  0.00
ATOM    136  O   LYS   122      38.908  -6.549  10.922  1.00  0.00
ATOM    137  N   ASN   123      38.633  -8.659  10.191  1.00  0.00
ATOM    138  CA  ASN   123      39.679  -8.561   9.179  1.00  0.00
ATOM    139  C   ASN   123      39.074  -8.457   7.782  1.00  0.00
ATOM    140  O   ASN   123      37.909  -8.791   7.574  1.00  0.00
ATOM    141  N   GLY   124      39.876  -7.990   6.829  1.00  0.00
ATOM    142  CA  GLY   124      39.419  -7.841   5.453  1.00  0.00
ATOM    143  C   GLY   124      39.846  -9.036   4.605  1.00  0.00
ATOM    144  O   GLY   124      40.383  -8.872   3.510  1.00  0.00
ATOM    145  N   ILE   125      39.603 -10.237   5.121  1.00  0.00
ATOM    146  CA  ILE   125      39.964 -11.460   4.413  1.00  0.00
ATOM    147  C   ILE   125      38.919 -12.547   4.639  1.00  0.00
ATOM    148  O   ILE   125      38.015 -12.394   5.460  1.00  0.00
ATOM    149  N   PRO   126      39.051 -13.648   3.906  1.00  0.00
ATOM    150  CA  PRO   126      38.118 -14.764   4.026  1.00  0.00
ATOM    151  C   PRO   126      38.853 -16.050   4.388  1.00  0.00
ATOM    152  O   PRO   126      38.380 -17.148   4.096  1.00  0.00
ATOM    153  N   ASN   127      40.009 -15.906   5.026  1.00  0.00
ATOM    154  CA  ASN   127      40.808 -17.058   5.428  1.00  0.00
ATOM    155  C   ASN   127      40.982 -17.097   6.944  1.00  0.00
ATOM    156  O   ASN   127      42.098 -17.010   7.454  1.00  0.00
ATOM    157  N   LEU   128      39.868 -17.227   7.658  1.00  0.00
ATOM    158  CA  LEU   128      39.897 -17.278   9.115  1.00  0.00
ATOM    159  C   LEU   128      40.286 -18.668   9.608  1.00  0.00
ATOM    160  O   LEU   128      39.923 -19.678   9.002  1.00  0.00
ATOM    161  N   LEU   129      41.028 -18.715  10.710  1.00  0.00
ATOM    162  CA  LEU   129      41.467 -19.981  11.283  1.00  0.00
ATOM    163  C   LEU   129      41.124 -20.062  12.766  1.00  0.00
ATOM    164  O   LEU   129      41.478 -19.176  13.545  1.00  0.00
ATOM    165  N   LEU   130      40.432 -21.129  13.151  1.00  0.00
ATOM    166  CA  LEU   130      40.041 -21.327  14.541  1.00  0.00
ATOM    167  C   LEU   130      41.258 -21.624  15.412  1.00  0.00
ATOM    168  O   LEU   130      42.119 -22.433  15.064  1.00  0.00
ATOM    169  N   PRO   131      41.332 -20.956  16.572  1.00  0.00
ATOM    170  CA  PRO   131      42.438 -21.132  17.517  1.00  0.00
ATOM    171  C   PRO   131      42.411 -22.499  18.194  1.00  0.00
ATOM    172  O   PRO   131      43.252 -22.797  19.042  1.00  0.00
ATOM    173  N   PRO   132      41.442 -23.323  17.813  1.00  0.00
ATOM    174  CA  PRO   132      41.305 -24.658  18.384  1.00  0.00
ATOM    175  C   PRO   132      41.342 -25.723  17.292  1.00  0.00
ATOM    176  O   PRO   132      42.216 -26.590  17.285  1.00  0.00
TER
END
