
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0356TS383_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS383_3-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    S      83      N       7           -
LGA    A      84      D       8           -
LGA    L      85      L       9           -
LGA    R      86      R      10           -
LGA    E      87      D      11           -
LGA    V      88      F      12           -
LGA    G      89      L      13           -
LGA    K      90      T      14           -
LGA    L      91      L      15           -
LGA    L      92      L      16           -
LGA    A      93      E      17           -
LGA    F      94      Q      18           -
LGA    L      95      Q      19           -
LGA    K      96      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      K      23           -
LGA    -       -      R      24           -
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    I     316      G      47          4.518
LGA    Y     317      P      48          3.150
LGA    H     318      A      49          3.934
LGA    S     319      L      50          2.657
LGA    T     320      L      51          2.638
LGA    Y     321      F      52          2.532
LGA    T     322      E      53          3.301
LGA    -       -      N      54           -
LGA    G     323      P      55          2.226
LGA    R     324      K      56          1.494
LGA    P     325      G      57          2.463
LGA    P     326      Y      58          2.898
LGA    D     327      S      59          1.144
LGA    E     328      M      60          0.968
LGA    P     329      P      61          1.282
LGA    A     330      V      62          2.296
LGA    V     331      L      63          2.536
LGA    -       -      C      64           -
LGA    L     332      N      65          2.968
LGA    G     333      L      66          4.235
LGA    V     334      F      67           #
LGA    A     335      G      68          3.977
LGA    L     336      T      69          1.639
LGA    N     337      P      70          1.707
LGA    E     338      K      71          1.057
LGA    V     339      R      72          1.823
LGA    F     340      V      73          1.470
LGA    V     341      A      74          1.349
LGA    P     342      M      75          2.077
LGA    I     343      G      76          2.004
LGA    L     344      M      77          2.813
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    Q     345      L      85          4.666
LGA    K     346      R      86           #
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    -       -      A     335           -
LGA    Q     347      L     336          3.706
LGA    -       -      N     337           -
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    -       -      F     340           -
LGA    -       -      V     341           -
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46  124    5.0     30    2.72     3.33     16.735     1.062

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.243327 * X  +   0.846379 * Y  +  -0.473746 * Z  + 102.282906
  Y_new =   0.739466 * X  +  -0.477950 * Y  +  -0.474083 * Z  + 125.522614
  Z_new =  -0.627680 * X  +  -0.234962 * Y  +  -0.742166 * Z  + 163.598221 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.834987    0.306606  [ DEG:  -162.4328     17.5672 ]
  Theta =   0.678570    2.463023  [ DEG:    38.8792    141.1208 ]
  Phi   =   1.252899   -1.888694  [ DEG:    71.7858   -108.2142 ]
 
# 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: T0356TS383_3-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS383_3-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46  124   5.0   30   2.72    3.33  16.735
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS383_3-D1
PFRMAT TS
TARGET t0356
MODEL 3
PARENT 1uliA
ATOM      1  N   SER    83      88.624  79.717 114.398  1.00  0.00
ATOM      2  CA  SER    83      87.142  79.837 114.603  1.00  0.00
ATOM      3  C   SER    83      86.599  78.710 115.466  1.00  0.00
ATOM      4  O   SER    83      86.765  77.540 115.127  1.00  0.00
ATOM      5  N   ALA    84      85.933  79.060 116.564  1.00  0.00
ATOM      6  CA  ALA    84      85.202  78.080 117.371  1.00  0.00
ATOM      7  C   ALA    84      83.954  77.617 116.638  1.00  0.00
ATOM      8  O   ALA    84      83.380  78.369 115.857  1.00  0.00
ATOM      9  N   LEU    85      83.545  76.379 116.912  1.00  0.00
ATOM     10  CA  LEU    85      82.409  75.744 116.256  1.00  0.00
ATOM     11  C   LEU    85      81.119  76.519 116.446  1.00  0.00
ATOM     12  O   LEU    85      80.348  76.694 115.495  1.00  0.00
ATOM     13  N   ARG    86      80.883  76.995 117.663  1.00  0.00
ATOM     14  CA  ARG    86      79.669  77.747 117.959  1.00  0.00
ATOM     15  C   ARG    86      79.633  79.083 117.215  1.00  0.00
ATOM     16  O   ARG    86      78.564  79.563 116.848  1.00  0.00
ATOM     17  N   GLU    87      80.801  79.678 117.002  1.00  0.00
ATOM     18  CA  GLU    87      80.902  80.937 116.270  1.00  0.00
ATOM     19  C   GLU    87      80.563  80.764 114.786  1.00  0.00
ATOM     20  O   GLU    87      79.937  81.647 114.191  1.00  0.00
ATOM     21  N   VAL    88      80.972  79.631 114.203  1.00  0.00
ATOM     22  CA  VAL    88      80.650  79.299 112.814  1.00  0.00
ATOM     23  C   VAL    88      79.138  79.079 112.643  1.00  0.00
ATOM     24  O   VAL    88      78.542  79.550 111.664  1.00  0.00
ATOM     25  N   GLY    89      78.536  78.371 113.603  1.00  0.00
ATOM     26  CA  GLY    89      77.097  78.097 113.588  1.00  0.00
ATOM     27  C   GLY    89      76.254  79.371 113.566  1.00  0.00
ATOM     28  O   GLY    89      75.193  79.381 112.958  1.00  0.00
ATOM     29  N   LYS    90      76.730  80.436 114.216  1.00  0.00
ATOM     30  CA  LYS    90      76.025  81.730 114.235  1.00  0.00
ATOM     31  C   LYS    90      76.059  82.481 112.887  1.00  0.00
ATOM     32  O   LYS    90      75.317  83.448 112.702  1.00  0.00
ATOM     33  N   LEU    91      76.928  82.064 111.968  1.00  0.00
ATOM     34  CA  LEU    91      77.060  82.723 110.657  1.00  0.00
ATOM     35  C   LEU    91      75.908  82.400 109.704  1.00  0.00
ATOM     36  O   LEU    91      75.697  83.107 108.726  1.00  0.00
ATOM     37  N   LEU    92      75.182  81.323 109.991  1.00  0.00
ATOM     38  CA  LEU    92      74.053  80.884 109.179  1.00  0.00
ATOM     39  C   LEU    92      72.867  80.597 110.098  1.00  0.00
ATOM     40  O   LEU    92      73.009  79.878 111.091  1.00  0.00
ATOM     41  N   ALA    93      71.707  81.141 109.745  1.00  0.00
ATOM     42  CA  ALA    93      70.479  80.963 110.516  1.00  0.00
ATOM     43  C   ALA    93      69.343  80.628 109.550  1.00  0.00
ATOM     44  O   ALA    93      68.778  81.513 108.908  1.00  0.00
ATOM     45  N   PHE    94      69.035  79.341 109.426  1.00  0.00
ATOM     46  CA  PHE    94      67.953  78.885 108.552  1.00  0.00
ATOM     47  C   PHE    94      66.567  79.073 109.171  1.00  0.00
ATOM     48  O   PHE    94      65.570  78.975 108.461  1.00  0.00
ATOM     49  N   LEU    95      66.517  79.322 110.479  1.00  0.00
ATOM     50  CA  LEU    95      65.260  79.554 111.216  1.00  0.00
ATOM     51  C   LEU    95      64.622  80.899 110.816  1.00  0.00
ATOM     52  O   LEU    95      63.436  80.940 110.500  1.00  0.00
ATOM     53  N   LYS    96      65.413  81.977 110.826  1.00  0.00
ATOM     54  CA  LYS    96      64.962  83.312 110.392  1.00  0.00
ATOM     55  C   LYS    96      65.445  83.690 108.978  1.00  0.00
ATOM     56  O   LYS    96      64.942  84.642 108.390  1.00  0.00
ATOM    737  N   ILE   316      56.178  80.201  85.798  1.00  0.00
ATOM    738  CA  ILE   316      55.226  80.425  86.891  1.00  0.00
ATOM    739  C   ILE   316      54.959  79.184  87.761  1.00  0.00
ATOM    740  O   ILE   316      54.852  79.294  88.989  1.00  0.00
ATOM    741  N   TYR   317      54.782  78.023  87.132  1.00  0.00
ATOM    742  CA  TYR   317      54.588  76.785  87.881  1.00  0.00
ATOM    743  C   TYR   317      55.908  76.004  87.949  1.00  0.00
ATOM    744  O   TYR   317      56.664  75.941  86.993  1.00  0.00
ATOM    745  N   HIS   318      56.171  75.418  89.102  1.00  0.00
ATOM    746  CA  HIS   318      57.331  74.581  89.280  1.00  0.00
ATOM    747  C   HIS   318      57.561  74.288  90.735  1.00  0.00
ATOM    748  O   HIS   318      56.856  74.799  91.602  1.00  0.00
ATOM    749  N   SER   319      58.556  73.457  91.006  1.00  0.00
ATOM    750  CA  SER   319      58.895  73.119  92.372  1.00  0.00
ATOM    751  C   SER   319      60.392  73.098  92.627  1.00  0.00
ATOM    752  O   SER   319      61.207  73.132  91.714  1.00  0.00
ATOM    753  N   THR   320      60.737  73.039  93.898  1.00  0.00
ATOM    754  CA  THR   320      62.120  73.015  94.327  1.00  0.00
ATOM    755  C   THR   320      62.320  71.976  95.402  1.00  0.00
ATOM    756  O   THR   320      61.599  71.940  96.384  1.00  0.00
ATOM    757  N   TYR   321      63.362  71.183  95.219  1.00  0.00
ATOM    758  CA  TYR   321      63.764  70.145  96.133  1.00  0.00
ATOM    759  C   TYR   321      64.921  70.622  97.002  1.00  0.00
ATOM    760  O   TYR   321      65.909  71.146  96.496  1.00  0.00
ATOM    761  N   THR   322      64.763  70.458  98.310  1.00  0.00
ATOM    762  CA  THR   322      65.847  70.535  99.272  1.00  0.00
ATOM    763  C   THR   322      66.060  69.135  99.855  1.00  0.00
ATOM    764  O   THR   322      65.115  68.509 100.339  1.00  0.00
ATOM    765  N   GLY   323      67.305  68.670  99.840  1.00  0.00
ATOM    766  CA  GLY   323      67.633  67.368 100.379  1.00  0.00
ATOM    767  C   GLY   323      67.371  67.347 101.890  1.00  0.00
ATOM    768  O   GLY   323      67.694  68.299 102.620  1.00  0.00
ATOM    769  N   ARG   324      66.742  66.262 102.324  1.00  0.00
ATOM    770  CA  ARG   324      66.449  65.996 103.727  1.00  0.00
ATOM    771  C   ARG   324      67.710  66.220 104.539  1.00  0.00
ATOM    772  O   ARG   324      67.688  66.857 105.585  1.00  0.00
ATOM    773  N   PRO   325      68.815  65.699 104.018  1.00  0.00
ATOM    774  CA  PRO   325      70.138  65.946 104.567  1.00  0.00
ATOM    775  C   PRO   325      71.153  65.943 103.440  1.00  0.00
ATOM    776  O   PRO   325      70.995  65.202 102.474  1.00  0.00
ATOM    777  N   PRO   326      72.185  66.772 103.557  1.00  0.00
ATOM    778  CA  PRO   326      73.345  66.668 102.677  1.00  0.00
ATOM    779  C   PRO   326      73.636  67.886 101.814  1.00  0.00
ATOM    780  O   PRO   326      74.677  67.947 101.167  1.00  0.00
ATOM    781  N   ASP   327      72.714  68.841 101.804  1.00  0.00
ATOM    782  CA  ASP   327      72.921  70.125 101.166  1.00  0.00
ATOM    783  C   ASP   327      72.633  70.179  99.681  1.00  0.00
ATOM    784  O   ASP   327      72.885  71.202  99.069  1.00  0.00
ATOM    785  N   GLU   328      72.106  69.102  99.098  1.00  0.00
ATOM    786  CA  GLU   328      71.795  69.095  97.662  1.00  0.00
ATOM    787  C   GLU   328      70.512  69.863  97.436  1.00  0.00
ATOM    788  O   GLU   328      69.708  70.051  98.360  1.00  0.00
ATOM    789  N   PRO   329      70.323  70.322  96.204  1.00  0.00
ATOM    790  CA  PRO   329      69.109  71.028  95.844  1.00  0.00
ATOM    791  C   PRO   329      68.865  71.002  94.353  1.00  0.00
ATOM    792  O   PRO   329      69.791  70.892  93.555  1.00  0.00
ATOM    793  N   ALA   330      67.603  71.090  93.971  1.00  0.00
ATOM    794  CA  ALA   330      67.239  71.199  92.563  1.00  0.00
ATOM    795  C   ALA   330      65.882  71.871  92.385  1.00  0.00
ATOM    796  O   ALA   330      64.963  71.650  93.162  1.00  0.00
ATOM    797  N   VAL   331      65.751  72.681  91.348  1.00  0.00
ATOM    798  CA  VAL   331      64.464  73.254  91.005  1.00  0.00
ATOM    799  C   VAL   331      64.180  73.157  89.522  1.00  0.00
ATOM    800  O   VAL   331      65.082  73.005  88.707  1.00  0.00
ATOM    801  N   LEU   332      62.908  73.243  89.171  1.00  0.00
ATOM    802  CA  LEU   332      62.497  73.152  87.775  1.00  0.00
ATOM    803  C   LEU   332      61.083  73.659  87.584  1.00  0.00
ATOM    804  O   LEU   332      60.228  73.542  88.466  1.00  0.00
ATOM    805  N   GLY   333      60.854  74.214  86.407  1.00  0.00
ATOM    806  CA  GLY   333      59.529  74.563  85.963  1.00  0.00
ATOM    807  C   GLY   333      58.793  73.294  85.489  1.00  0.00
ATOM    808  O   GLY   333      59.424  72.329  85.054  1.00  0.00
ATOM    809  N   VAL   334      57.465  73.310  85.576  1.00  0.00
ATOM    810  CA  VAL   334      56.612  72.217  85.106  1.00  0.00
ATOM    811  C   VAL   334      55.619  72.785  84.090  1.00  0.00
ATOM    812  O   VAL   334      54.888  73.711  84.407  1.00  0.00
ATOM    813  N   ALA   335      55.638  72.264  82.863  1.00  0.00
ATOM    814  CA  ALA   335      54.609  72.542  81.872  1.00  0.00
ATOM    815  C   ALA   335      54.964  73.590  80.836  1.00  0.00
ATOM    816  O   ALA   335      54.714  73.395  79.655  1.00  0.00
ATOM    817  N   LEU   336      55.570  74.688  81.268  1.00  0.00
ATOM    818  CA  LEU   336      55.807  75.856  80.406  1.00  0.00
ATOM    819  C   LEU   336      57.222  75.848  79.787  1.00  0.00
ATOM    820  O   LEU   336      58.202  75.998  80.528  1.00  0.00
ATOM    821  N   ASN   337      57.338  75.693  78.457  1.00  0.00
ATOM    822  CA  ASN   337      58.647  75.606  77.782  1.00  0.00
ATOM    823  C   ASN   337      59.360  76.930  77.416  1.00  0.00
ATOM    824  O   ASN   337      60.338  76.864  76.677  1.00  0.00
ATOM    825  N   GLU   338      58.930  78.077  77.931  1.00  0.00
ATOM    826  CA  GLU   338      59.487  79.365  77.495  1.00  0.00
ATOM    827  C   GLU   338      60.973  79.559  77.810  1.00  0.00
ATOM    828  O   GLU   338      61.722  80.017  76.952  1.00  0.00
ATOM    829  N   VAL   339      61.399  79.240  79.032  1.00  0.00
ATOM    830  CA  VAL   339      62.820  79.349  79.372  1.00  0.00
ATOM    831  C   VAL   339      63.673  78.317  78.616  1.00  0.00
ATOM    832  O   VAL   339      64.778  78.644  78.184  1.00  0.00
ATOM    833  N   PHE   340      63.171  77.087  78.468  1.00  0.00
ATOM    834  CA  PHE   340      63.905  76.028  77.762  1.00  0.00
ATOM    835  C   PHE   340      64.047  76.327  76.260  1.00  0.00
ATOM    836  O   PHE   340      65.103  76.111  75.682  1.00  0.00
ATOM    837  N   VAL   341      62.972  76.814  75.647  1.00  0.00
ATOM    838  CA  VAL   341      62.955  77.185  74.236  1.00  0.00
ATOM    839  C   VAL   341      63.933  78.338  74.002  1.00  0.00
ATOM    840  O   VAL   341      64.644  78.372  72.998  1.00  0.00
ATOM    841  N   PRO   342      63.956  79.274  74.949  1.00  0.00
ATOM    842  CA  PRO   342      64.742  80.497  74.824  1.00  0.00
ATOM    843  C   PRO   342      66.217  80.201  74.941  1.00  0.00
ATOM    844  O   PRO   342      67.033  80.867  74.289  1.00  0.00
ATOM    845  N   ILE   343      66.552  79.211  75.777  1.00  0.00
ATOM    846  CA  ILE   343      67.930  78.794  75.996  1.00  0.00
ATOM    847  C   ILE   343      68.425  77.841  74.911  1.00  0.00
ATOM    848  O   ILE   343      69.517  78.036  74.364  1.00  0.00
ATOM    849  N   LEU   344      67.649  76.783  74.648  1.00  0.00
ATOM    850  CA  LEU   344      68.128  75.632  73.865  1.00  0.00
ATOM    851  C   LEU   344      67.515  75.498  72.468  1.00  0.00
ATOM    852  O   LEU   344      67.924  74.635  71.696  1.00  0.00
ATOM    853  N   GLN   345      66.534  76.334  72.152  1.00  0.00
ATOM    854  CA  GLN   345      65.927  76.349  70.830  1.00  0.00
ATOM    855  C   GLN   345      64.937  75.214  70.583  1.00  0.00
ATOM    856  O   GLN   345      64.803  74.302  71.406  1.00  0.00
ATOM    857  N   LYS   346      64.250  75.262  69.442  1.00  0.00
ATOM    858  CA  LYS   346      63.146  74.320  69.155  1.00  0.00
ATOM    859  C   LYS   346      63.532  72.847  69.027  1.00  0.00
ATOM    860  O   LYS   346      62.779  72.017  69.504  1.00  0.00
ATOM    861  N   GLN   347      64.667  72.522  68.416  1.00  0.00
ATOM    862  CA  GLN   347      65.032  71.116  68.204  1.00  0.00
ATOM    863  C   GLN   347      65.232  70.337  69.529  1.00  0.00
ATOM    864  O   GLN   347      64.702  69.239  69.700  1.00  0.00
TER
END
