
#######################################################
#                                                     #
#                        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   20 (  152),  selected   20 , name T0356TS249_5_4-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356TS249_5_4-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N       7           -
LGA    -       -      D       8           -
LGA    -       -      L       9           -
LGA    E     328      R      10          3.405
LGA    P     329      D      11          4.938
LGA    A     330      F      12          2.603
LGA    V     331      L      13          3.976
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    -       -      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    -       -      G      47           -
LGA    L     332      P      48          4.028
LGA    G     333      A      49          1.660
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    -       -      L      63           -
LGA    -       -      C      64           -
LGA    V     334      N      65          1.568
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    A     335      G      68          1.954
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      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    L     336      E     328          2.366
LGA    -       -      P     329           -
LGA    -       -      A     330           -
LGA    N     337      V     331          2.400
LGA    E     338      L     332          2.327
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    V     339      A     335          2.109
LGA    F     340      L     336          1.740
LGA    V     341      N     337          1.764
LGA    P     342      E     338          0.749
LGA    I     343      V     339          0.736
LGA    L     344      F     340          1.648
LGA    Q     345      V     341          2.090
LGA    K     346      P     342          2.307
LGA    Q     347      I     343          1.940
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)   20  124    5.0     20    2.53     0.00     12.499     0.759

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.107037 * X  +   0.974186 * Y  +  -0.198760 * Z  +   5.743247
  Y_new =   0.174051 * X  +   0.178463 * Y  +   0.968430 * Z  +  18.061180
  Z_new =   0.978902 * X  +  -0.138252 * Y  +  -0.150456 * Z  +   3.847058 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.398438    0.743154  [ DEG:  -137.4204     42.5796 ]
  Theta =  -1.365018   -1.776575  [ DEG:   -78.2097   -101.7903 ]
  Phi   =   1.019438   -2.122154  [ DEG:    58.4095   -121.5905 ]
 
# 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: T0356TS249_5_4-D1                             
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS249_5_4-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20  124   5.0   20   2.53    0.00  12.499
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS249_5_4-D1
REMARK PARENT number 4
PFRMAT TS
TARGET T0356
PARENT 1aa6 1cr5_A 1e32_A 1g8k_A
ATOM      1  N   GLU   328      74.074  81.837  84.923  1.00  0.00
ATOM      2  CA  GLU   328      73.519  80.479  84.742  1.00  0.00
ATOM      3  CB  GLU   328      73.187  79.846  86.106  1.00  0.00
ATOM      4  CG  GLU   328      74.430  79.478  86.921  1.00  0.00
ATOM      5  CD  GLU   328      75.047  80.768  87.445  1.00  0.00
ATOM      6  OE1 GLU   328      74.323  81.523  88.146  1.00  0.00
ATOM      7  OE2 GLU   328      76.246  81.018  87.146  1.00  0.00
ATOM      8  C   GLU   328      72.277  80.522  83.914  1.00  0.00
ATOM      9  O   GLU   328      71.817  81.575  83.492  1.00  0.00
ATOM     10  N   PRO   329      71.755  79.360  83.653  1.00  0.00
ATOM     11  CA  PRO   329      70.553  79.272  82.878  1.00  0.00
ATOM     12  CD  PRO   329      72.590  78.184  83.500  1.00  0.00
ATOM     13  CB  PRO   329      70.515  77.850  82.306  1.00  0.00
ATOM     14  CG  PRO   329      71.604  77.085  83.081  1.00  0.00
ATOM     15  C   PRO   329      69.377  79.630  83.722  1.00  0.00
ATOM     16  O   PRO   329      69.462  79.528  84.944  1.00  0.00
ATOM     17  N   ALA   330      68.274  80.072  83.091  1.00  0.00
ATOM     18  CA  ALA   330      67.107  80.432  83.837  1.00  0.00
ATOM     19  CB  ALA   330      66.043  81.162  83.002  1.00  0.00
ATOM     20  C   ALA   330      66.499  79.169  84.340  1.00  0.00
ATOM     21  O   ALA   330      66.656  78.106  83.740  1.00  0.00
ATOM     22  N   VAL   331      65.799  79.253  85.487  1.00  0.00
ATOM     23  CA  VAL   331      65.193  78.074  86.023  1.00  0.00
ATOM     24  CB  VAL   331      65.801  77.632  87.321  1.00  0.00
ATOM     25  CG1 VAL   331      65.590  78.741  88.366  1.00  0.00
ATOM     26  CG2 VAL   331      65.183  76.280  87.714  1.00  0.00
ATOM     27  C   VAL   331      63.753  78.368  86.282  1.00  0.00
ATOM     28  O   VAL   331      63.383  79.486  86.637  1.00  0.00
ATOM     29  N   LEU   332      62.900  77.348  86.075  1.00  0.00
ATOM     30  CA  LEU   332      61.493  77.474  86.304  1.00  0.00
ATOM     31  CB  LEU   332      60.642  77.409  85.026  1.00  0.00
ATOM     32  CG  LEU   332      60.853  78.607  84.085  1.00  0.00
ATOM     33  CD1 LEU   332      62.295  78.659  83.558  1.00  0.00
ATOM     34  CD2 LEU   332      59.803  78.620  82.961  1.00  0.00
ATOM     35  C   LEU   332      61.089  76.319  87.153  1.00  0.00
ATOM     36  O   LEU   332      61.934  75.586  87.666  1.00  0.00
ATOM     37  N   GLY   333      59.768  76.139  87.332  1.00  0.00
ATOM     38  CA  GLY   333      59.296  75.046  88.126  1.00  0.00
ATOM     39  C   GLY   333      59.611  73.814  87.348  1.00  0.00
ATOM     40  O   GLY   333      60.067  73.894  86.208  1.00  0.00
ATOM     41  N   VAL   334      59.384  72.630  87.946  1.00  0.00
ATOM     42  CA  VAL   334      59.735  71.434  87.242  1.00  0.00
ATOM     43  CB  VAL   334      59.780  70.220  88.121  1.00  0.00
ATOM     44  CG1 VAL   334      60.029  68.985  87.242  1.00  0.00
ATOM     45  CG2 VAL   334      60.850  70.442  89.203  1.00  0.00
ATOM     46  C   VAL   334      58.702  71.188  86.196  1.00  0.00
ATOM     47  O   VAL   334      57.539  70.921  86.495  1.00  0.00
ATOM     48  N   ALA   335      59.122  71.285  84.920  1.00  0.00
ATOM     49  CA  ALA   335      58.230  71.040  83.830  1.00  0.00
ATOM     50  CB  ALA   335      57.503  72.300  83.333  1.00  0.00
ATOM     51  C   ALA   335      59.060  70.542  82.694  1.00  0.00
ATOM     52  O   ALA   335      60.240  70.879  82.583  1.00  0.00
ATOM     53  N   LEU   336      58.463  69.703  81.828  1.00  0.00
ATOM     54  CA  LEU   336      59.198  69.222  80.699  1.00  0.00
ATOM     55  CB  LEU   336      59.199  67.680  80.604  1.00  0.00
ATOM     56  CG  LEU   336      60.158  67.061  79.560  1.00  0.00
ATOM     57  CD1 LEU   336      60.057  65.529  79.580  1.00  0.00
ATOM     58  CD2 LEU   336      59.952  67.617  78.141  1.00  0.00
ATOM     59  C   LEU   336      58.500  69.779  79.503  1.00  0.00
ATOM     60  O   LEU   336      57.357  69.425  79.219  1.00  0.00
ATOM     61  N   ASN   337      59.176  70.691  78.781  1.00  0.00
ATOM     62  CA  ASN   337      58.580  71.262  77.612  1.00  0.00
ATOM     63  CB  ASN   337      58.120  72.714  77.821  1.00  0.00
ATOM     64  CG  ASN   337      57.060  72.721  78.914  1.00  0.00
ATOM     65  OD1 ASN   337      56.244  71.807  79.021  1.00  0.00
ATOM     66  ND2 ASN   337      57.076  73.784  79.763  1.00  0.00
ATOM     67  C   ASN   337      59.663  71.294  76.591  1.00  0.00
ATOM     68  O   ASN   337      60.822  71.527  76.930  1.00  0.00
ATOM     69  N   GLU   338      59.341  71.043  75.307  1.00  0.00
ATOM     70  CA  GLU   338      60.444  71.096  74.401  1.00  0.00
ATOM     71  CB  GLU   338      60.862  69.733  73.829  1.00  0.00
ATOM     72  CG  GLU   338      61.435  68.789  74.890  1.00  0.00
ATOM     73  CD  GLU   338      62.104  67.629  74.166  1.00  0.00
ATOM     74  OE1 GLU   338      63.204  67.853  73.592  1.00  0.00
ATOM     75  OE2 GLU   338      61.528  66.510  74.169  1.00  0.00
ATOM     76  C   GLU   338      60.144  72.001  73.256  1.00  0.00
ATOM     77  O   GLU   338      59.216  71.778  72.482  1.00  0.00
ATOM     78  N   VAL   339      60.927  73.090  73.192  1.00  0.00
ATOM     79  CA  VAL   339      61.022  74.048  72.131  1.00  0.00
ATOM     80  CB  VAL   339      61.840  75.251  72.497  1.00  0.00
ATOM     81  CG1 VAL   339      63.280  74.797  72.784  1.00  0.00
ATOM     82  CG2 VAL   339      61.727  76.284  71.363  1.00  0.00
ATOM     83  C   VAL   339      61.705  73.356  71.022  1.00  0.00
ATOM     84  O   VAL   339      61.601  73.763  69.871  1.00  0.00
ATOM     85  N   PHE   340      62.504  72.337  71.400  1.00  0.00
ATOM     86  CA  PHE   340      63.333  71.575  70.520  1.00  0.00
ATOM     87  CB  PHE   340      64.096  70.459  71.257  1.00  0.00
ATOM     88  CG  PHE   340      64.963  71.104  72.285  1.00  0.00
ATOM     89  CD1 PHE   340      64.457  71.422  73.525  1.00  0.00
ATOM     90  CD2 PHE   340      66.280  71.393  72.016  1.00  0.00
ATOM     91  CE1 PHE   340      65.250  72.017  74.479  1.00  0.00
ATOM     92  CE2 PHE   340      67.079  71.988  72.966  1.00  0.00
ATOM     93  CZ  PHE   340      66.565  72.303  74.200  1.00  0.00
ATOM     94  C   PHE   340      62.467  70.911  69.498  1.00  0.00
ATOM     95  O   PHE   340      62.815  70.884  68.319  1.00  0.00
ATOM     96  N   VAL   341      61.330  70.330  69.914  1.00  0.00
ATOM     97  CA  VAL   341      60.490  69.649  68.970  1.00  0.00
ATOM     98  CB  VAL   341      59.324  68.957  69.614  1.00  0.00
ATOM     99  CG1 VAL   341      58.490  68.271  68.519  1.00  0.00
ATOM    100  CG2 VAL   341      59.858  67.990  70.683  1.00  0.00
ATOM    101  C   VAL   341      59.961  70.611  67.951  1.00  0.00
ATOM    102  O   VAL   341      59.921  70.281  66.763  1.00  0.00
ATOM    103  N   PRO   342      59.520  71.775  68.373  1.00  0.00
ATOM    104  CA  PRO   342      59.023  72.741  67.441  1.00  0.00
ATOM    105  CD  PRO   342      58.924  71.953  69.686  1.00  0.00
ATOM    106  CB  PRO   342      58.427  73.869  68.277  1.00  0.00
ATOM    107  CG  PRO   342      57.966  73.149  69.557  1.00  0.00
ATOM    108  C   PRO   342      60.050  73.177  66.449  1.00  0.00
ATOM    109  O   PRO   342      59.697  73.352  65.281  1.00  0.00
ATOM    110  N   ILE   343      61.316  73.343  66.885  1.00  0.00
ATOM    111  CA  ILE   343      62.343  73.793  65.987  1.00  0.00
ATOM    112  CB  ILE   343      63.658  74.135  66.631  1.00  0.00
ATOM    113  CG2 ILE   343      64.312  72.854  67.165  1.00  0.00
ATOM    114  CG1 ILE   343      64.551  74.864  65.613  1.00  0.00
ATOM    115  CD1 ILE   343      64.009  76.223  65.174  1.00  0.00
ATOM    116  C   ILE   343      62.582  72.756  64.944  1.00  0.00
ATOM    117  O   ILE   343      62.784  73.083  63.775  1.00  0.00
ATOM    118  N   LEU   344      62.595  71.467  65.348  1.00  0.00
ATOM    119  CA  LEU   344      62.837  70.429  64.386  1.00  0.00
ATOM    120  CB  LEU   344      62.946  69.014  64.984  1.00  0.00
ATOM    121  CG  LEU   344      64.319  68.711  65.611  1.00  0.00
ATOM    122  CD1 LEU   344      65.399  68.599  64.523  1.00  0.00
ATOM    123  CD2 LEU   344      64.693  69.733  66.693  1.00  0.00
ATOM    124  C   LEU   344      61.750  70.409  63.353  1.00  0.00
ATOM    125  O   LEU   344      62.024  70.232  62.163  1.00  0.00
ATOM    126  N   GLN   345      60.483  70.589  63.777  1.00  0.00
ATOM    127  CA  GLN   345      59.410  70.517  62.823  1.00  0.00
ATOM    128  CB  GLN   345      58.018  70.638  63.465  1.00  0.00
ATOM    129  CG  GLN   345      57.668  69.469  64.387  1.00  0.00
ATOM    130  CD  GLN   345      57.606  68.199  63.551  1.00  0.00
ATOM    131  OE1 GLN   345      58.594  67.793  62.943  1.00  0.00
ATOM    132  NE2 GLN   345      56.413  67.548  63.521  1.00  0.00
ATOM    133  C   GLN   345      59.544  71.626  61.817  1.00  0.00
ATOM    134  O   GLN   345      59.314  71.408  60.629  1.00  0.00
ATOM    135  N   LYS   346      59.928  72.841  62.265  1.00  0.00
ATOM    136  CA  LYS   346      60.050  73.992  61.401  1.00  0.00
ATOM    137  CB  LYS   346      60.397  75.279  62.166  1.00  0.00
ATOM    138  CG  LYS   346      60.231  76.545  61.322  1.00  0.00
ATOM    139  CD  LYS   346      60.251  77.837  62.142  1.00  0.00
ATOM    140  CE  LYS   346      59.993  79.098  61.313  1.00  0.00
ATOM    141  NZ  LYS   346      61.040  79.253  60.280  1.00  0.00
ATOM    142  C   LYS   346      61.134  73.751  60.390  1.00  0.00
ATOM    143  O   LYS   346      61.048  74.214  59.252  1.00  0.00
ATOM    144  N   GLN   347      62.198  73.022  60.774  1.00  0.00
ATOM    145  CA  GLN   347      63.273  72.790  59.847  1.00  0.00
ATOM    146  CB  GLN   347      64.380  71.893  60.428  1.00  0.00
ATOM    147  CG  GLN   347      65.527  71.645  59.448  1.00  0.00
ATOM    148  CD  GLN   347      66.501  70.664  60.081  1.00  0.00
ATOM    149  OE1 GLN   347      67.308  71.018  60.939  1.00  0.00
ATOM    150  NE2 GLN   347      66.423  69.381  59.639  1.00  0.00
ATOM    151  C   GLN   347      62.665  72.077  58.679  1.00  0.00
ATOM    152  O   GLN   347      63.091  72.291  57.548  1.00  0.00
TER
END
