
#######################################################
#                                                     #
#                        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   23 (  205),  selected   23 , name T0303TS494_1-D2
# Molecule2: number of CA atoms   77 (  602),  selected   77 , name T0303_D2.pdb
# PARAMETERS: T0303TS494_1-D2.T0303_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      S      18           -
LGA    -       -      L      19           -
LGA    -       -      P      20           -
LGA    -       -      D      21           -
LGA    -       -      L      22           -
LGA    -       -      A      23           -
LGA    -       -      L      24           -
LGA    -       -      S      25           -
LGA    -       -      I      26           -
LGA    -       -      N      27           -
LGA    -       -      S      28           -
LGA    -       -      A      29           -
LGA    -       -      L      30           -
LGA    -       -      K      31           -
LGA    -       -      D      32           -
LGA    -       -      V      33           -
LGA    -       -      N      34           -
LGA    -       -      L      35           -
LGA    -       -      P      36           -
LGA    -       -      Q      37           -
LGA    -       -      A      38           -
LGA    -       -      S      39           -
LGA    -       -      E      40           -
LGA    -       -      N      41           -
LGA    -       -      L      42           -
LGA    -       -      V      43           -
LGA    -       -      M      44           -
LGA    -       -      T      45           -
LGA    -       -      W      46           -
LGA    -       -      I      47           -
LGA    -       -      G      48           -
LGA    -       -      N      49           -
LGA    -       -      G      50           -
LGA    E      72      A      51          2.165
LGA    D      73      D      52          2.479
LGA    E      74      V      53          1.672
LGA    F      75      L      54          2.069
LGA    -       -      S      55           -
LGA    K      76      Q      56          0.789
LGA    Y      77      R      57          1.966
LGA    F      78      A      58          2.274
LGA    K      79      V      59          1.517
LGA    R      80      D      60          1.538
LGA    Q      81      W      61          2.174
LGA    F      82      A      62          2.544
LGA    G      83      C      63          1.636
LGA    -       -      T      64           -
LGA    -       -      Q      65           -
LGA    -       -      A      66           -
LGA    -       -      E      67           -
LGA    -       -      K      68           -
LGA    F      84      E      69          3.632
LGA    Y      85      L      70          2.002
LGA    Y      86      T      71          6.381
LGA    -       -      E      72           -
LGA    -       -      D      73           -
LGA    -       -      E      74           -
LGA    G      87      F      75          2.538
LGA    E      88      K      76          0.391
LGA    N      89      Y      77          3.032
LGA    L      90      F      78          3.503
LGA    -       -      K      79           -
LGA    -       -      R      80           -
LGA    -       -      Q      81           -
LGA    -       -      F      82           -
LGA    C      91      G      83          1.868
LGA    N      92      F      84          1.848
LGA    I      93      Y      85          2.087
LGA    -       -      Y      86           -
LGA    -       -      G      87           -
LGA    S      94      E      88          1.326
LGA    -       -      N      89           -
LGA    -       -      L      90           -
LGA    -       -      C      91           -
LGA    -       -      N      92           -
LGA    -       -      I      93           -
LGA    -       -      S      94           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23   77    5.0     23    2.51     4.35     22.465     0.881

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.201939 * X  +  -0.350744 * Y  +   0.914439 * Z  + -17.302954
  Y_new =  -0.454967 * X  +   0.793225 * Y  +   0.404723 * Z  +  51.423878
  Z_new =  -0.867310 * X  +  -0.497769 * Y  +   0.000607 * Z  +  74.138580 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.569578    1.572015  [ DEG:   -89.9302     90.0698 ]
  Theta =   1.049772    2.091821  [ DEG:    60.1475    119.8525 ]
  Phi   =  -1.153064    1.988529  [ DEG:   -66.0657    113.9343 ]
 
# 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: T0303TS494_1-D2                               
REMARK     2: T0303_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0303TS494_1-D2.T0303_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23   77   5.0   23   2.51    4.35  22.465
REMARK  ---------------------------------------------------------- 
MOLECULE T0303TS494_1-D2
PFRMAT     TS
TARGET     T0303
MODEL      1
PARENT     1x42_A
ATOM      1  N   GLU    72       0.372  82.497  22.976  1.00  0.02
ATOM      5  CA  GLU    72       0.243  83.954  23.146  1.00  0.03
ATOM      6  CB  GLU    72      -0.292  84.278  24.536  1.00  0.02
ATOM      7  CG  GLU    72      -1.678  83.678  24.743  1.00  0.02
ATOM      8  CD  GLU    72      -2.176  83.966  26.156  1.00  0.00
ATOM      9  OE1 GLU    72      -2.867  84.960  26.329  1.00  0.02
ATOM     10  OE2 GLU    72      -1.876  83.166  27.033  1.00  0.02
ATOM     11  C   GLU    72       1.583  84.647  22.938  1.00  0.03
ATOM     12  O   GLU    72       1.679  85.614  22.176  1.00  0.01
ATOM     13  N   ASP    73       2.635  83.986  23.395  1.00  0.02
ATOM     15  CA  ASP    73       3.998  84.544  23.317  1.00  0.02
ATOM     16  CB  ASP    73       4.870  83.872  24.373  1.00  0.02
ATOM     17  CG  ASP    73       4.366  84.209  25.776  1.00  0.02
ATOM     18  OD1 ASP    73       3.878  85.314  25.962  1.00  0.09
ATOM     19  OD2 ASP    73       4.475  83.348  26.637  1.00  0.13
ATOM     20  C   ASP    73       4.648  84.383  21.937  1.00  0.03
ATOM     21  O   ASP    73       5.788  84.811  21.733  1.00  0.03
ATOM     22  N   GLU    74       3.904  83.842  20.985  1.00  0.03
ATOM     24  CA  GLU    74       4.389  83.709  19.611  1.00  0.02
ATOM     25  CB  GLU    74       3.747  82.463  19.003  1.00  0.02
ATOM     26  CG  GLU    74       4.295  82.146  17.613  1.00  0.02
ATOM     27  CD  GLU    74       3.580  80.933  17.029  1.00  0.02
ATOM     28  OE1 GLU    74       4.064  79.831  17.248  1.00  0.03
ATOM     29  OE2 GLU    74       2.508  81.122  16.474  1.00  0.02
ATOM     30  C   GLU    74       4.028  84.949  18.787  1.00  0.02
ATOM     31  O   GLU    74       4.567  85.141  17.687  1.00  0.03
ATOM     32  N   PHE    75       3.269  85.862  19.380  1.00  0.03
ATOM     34  CA  PHE    75       2.827  87.082  18.684  1.00  0.02
ATOM     35  CB  PHE    75       1.486  87.514  19.265  1.00  0.03
ATOM     36  CG  PHE    75       0.348  86.529  19.009  1.00  0.33
ATOM     37  CD1 PHE    75      -0.575  86.264  20.013  1.00  0.95
ATOM     38  CE1 PHE    75      -1.609  85.365  19.786  1.00  1.26
ATOM     39  CZ  PHE    75      -1.721  84.733  18.554  1.00  0.98
ATOM     40  CE2 PHE    75      -0.801  85.002  17.548  1.00  0.71
ATOM     41  CD2 PHE    75       0.232  85.901  17.776  1.00  0.54
ATOM     42  C   PHE    75       3.829  88.238  18.789  1.00  0.02
ATOM     43  O   PHE    75       3.430  89.410  18.838  1.00  0.02
ATOM     44  N   LYS    76       5.094  87.921  18.547  1.00  0.02
ATOM     46  CA  LYS    76       6.184  88.893  18.660  1.00  0.02
ATOM     47  CB  LYS    76       7.493  88.130  18.812  1.00  0.02
ATOM     48  CG  LYS    76       7.480  87.315  20.100  1.00  0.01
ATOM     49  CD  LYS    76       8.837  86.685  20.381  1.00  0.03
ATOM     50  CE  LYS    76       8.842  85.978  21.731  1.00  1.12
ATOM     51  NZ  LYS    76      10.164  85.404  22.024  1.00  1.33
ATOM     52  C   LYS    76       6.262  89.829  17.460  1.00  0.03
ATOM     53  O   LYS    76       6.787  90.943  17.586  1.00  0.02
ATOM     54  N   TYR    77       5.492  89.509  16.432  1.00  0.02
ATOM     56  CA  TYR    77       5.382  90.379  15.268  1.00  0.02
ATOM     57  CB  TYR    77       4.649  89.625  14.162  1.00  0.03
ATOM     58  CG  TYR    77       4.225  90.514  12.996  1.00  0.02
ATOM     59  CD1 TYR    77       2.875  90.673  12.713  1.00  0.18
ATOM     60  CE1 TYR    77       2.477  91.496  11.668  1.00  0.22
ATOM     61  CZ  TYR    77       3.434  92.158  10.911  1.00  0.21
ATOM     62  OH  TYR    77       3.033  93.092   9.981  1.00  0.30
ATOM     63  CE2 TYR    77       4.785  91.987  11.178  1.00  0.26
ATOM     64  CD2 TYR    77       5.182  91.161  12.222  1.00  0.20
ATOM     65  C   TYR    77       4.632  91.674  15.575  1.00  0.02
ATOM     66  O   TYR    77       5.049  92.710  15.051  1.00  0.02
ATOM     67  N   PHE    78       3.798  91.697  16.602  1.00  0.04
ATOM     69  CA  PHE    78       3.085  92.940  16.914  1.00  0.02
ATOM     70  CB  PHE    78       1.891  92.619  17.804  1.00  0.03
ATOM     71  CG  PHE    78       0.837  91.735  17.143  1.00  0.03
ATOM     72  CD1 PHE    78       0.252  90.701  17.861  1.00  0.02
ATOM     73  CE1 PHE    78      -0.706  89.894  17.261  1.00  0.31
ATOM     74  CZ  PHE    78      -1.078  90.120  15.943  1.00  0.22
ATOM     75  CE2 PHE    78      -0.493  91.156  15.225  1.00  0.17
ATOM     76  CD2 PHE    78       0.463  91.964  15.825  1.00  0.02
ATOM     77  C   PHE    78       3.999  93.934  17.623  1.00  0.02
ATOM     78  O   PHE    78       4.034  95.112  17.244  1.00  0.02
ATOM     79  N   LYS    79       4.956  93.401  18.366  1.00  0.02
ATOM     81  CA  LYS    79       5.894  94.263  19.076  1.00  0.02
ATOM     82  CB  LYS    79       6.550  93.458  20.181  1.00  0.03
ATOM     83  CG  LYS    79       5.526  92.746  21.053  1.00  1.37
ATOM     84  CD  LYS    79       6.158  91.906  22.165  1.00  1.50
ATOM     85  CE  LYS    79       6.860  90.639  21.662  1.00  2.71
ATOM     86  NZ  LYS    79       8.223  90.877  21.141  1.00  3.56
ATOM     87  C   LYS    79       6.979  94.750  18.132  1.00  0.03
ATOM     88  O   LYS    79       7.311  95.940  18.144  1.00  0.02
ATOM     89  N   ARG    80       7.281  93.928  17.141  1.00  0.03
ATOM     91  CA  ARG    80       8.280  94.281  16.131  1.00  0.02
ATOM     92  CB  ARG    80       8.755  92.962  15.536  1.00  0.03
ATOM     93  CG  ARG    80       9.781  93.128  14.426  1.00  0.03
ATOM     94  CD  ARG    80      10.387  91.778  14.052  1.00  0.04
ATOM     95  NE  ARG    80       9.356  90.799  13.662  1.00  0.57
ATOM     96  CZ  ARG    80       9.192  89.623  14.277  1.00  0.37
ATOM     97  NH1 ARG    80       9.891  89.343  15.378  1.00  0.72
ATOM     98  NH2 ARG    80       8.269  88.765  13.839  1.00  0.90
ATOM     99  C   ARG    80       7.711  95.203  15.047  1.00  0.03
ATOM    100  O   ARG    80       8.448  96.017  14.479  1.00  0.02
ATOM    101  N   GLN    81       6.393  95.226  14.932  1.00  0.02
ATOM    103  CA  GLN    81       5.720  96.104  13.977  1.00  0.03
ATOM    104  CB  GLN    81       4.382  95.449  13.647  1.00  0.02
ATOM    105  CG  GLN    81       3.569  96.238  12.630  1.00  0.02
ATOM    106  CD  GLN    81       2.204  95.583  12.453  1.00  0.03
ATOM    107  OE1 GLN    81       1.996  94.427  12.844  1.00  0.28
ATOM    108  NE2 GLN    81       1.282  96.337  11.882  1.00  0.43
ATOM    111  C   GLN    81       5.472  97.496  14.555  1.00  0.03
ATOM    112  O   GLN    81       5.394  98.476  13.803  1.00  0.03
ATOM    113  N   PHE    82       5.396  97.595  15.872  1.00  0.04
ATOM    115  CA  PHE    82       5.183  98.911  16.489  1.00  0.02
ATOM    116  CB  PHE    82       4.063  98.793  17.516  1.00  0.03
ATOM    117  CG  PHE    82       2.716  98.381  16.921  1.00  0.02
ATOM    118  CD1 PHE    82       2.248  98.992  15.764  1.00  0.02
ATOM    119  CE1 PHE    82       1.028  98.613  15.221  1.00  0.03
ATOM    120  CZ  PHE    82       0.270  97.626  15.839  1.00  0.02
ATOM    121  CE2 PHE    82       0.731  97.023  17.002  1.00  0.04
ATOM    122  CD2 PHE    82       1.951  97.403  17.544  1.00  0.03
ATOM    123  C   PHE    82       6.453  99.479  17.126  1.00  0.02
ATOM    124  O   PHE    82       6.497 100.665  17.474  1.00  0.02
ATOM    125  N   GLY    83       7.464  98.641  17.281  1.00  0.02
ATOM    127  CA  GLY    83       8.776  99.097  17.752  1.00  0.00
ATOM    128  C   GLY    83       8.923  99.051  19.274  1.00  0.03
ATOM    129  O   GLY    83       9.395 100.020  19.880  1.00  0.03
ATOM    130  N   PHE    84       8.518  97.949  19.886  1.00  0.03
ATOM    132  CA  PHE    84       8.675  97.826  21.343  1.00  0.02
ATOM    133  CB  PHE    84       7.409  98.293  22.067  1.00  0.03
ATOM    134  CG  PHE    84       6.122  97.492  21.871  1.00  0.03
ATOM    135  CD1 PHE    84       5.270  97.776  20.812  1.00  0.02
ATOM    136  CE1 PHE    84       4.093  97.057  20.654  1.00  0.03
ATOM    137  CZ  PHE    84       3.759  96.062  21.561  1.00  0.02
ATOM    138  CE2 PHE    84       4.603  95.787  22.630  1.00  0.02
ATOM    139  CD2 PHE    84       5.781  96.505  22.787  1.00  0.03
ATOM    140  C   PHE    84       9.091  96.421  21.783  1.00  0.03
ATOM    141  O   PHE    84       8.857  95.420  21.096  1.00  0.03
ATOM    142  N   TYR    85       9.743  96.385  22.934  1.00  0.03
ATOM    144  CA  TYR    85      10.292  95.144  23.505  1.00  0.03
ATOM    145  CB  TYR    85      11.302  95.503  24.590  1.00  0.03
ATOM    146  CG  TYR    85      12.742  95.611  24.100  1.00  0.02
ATOM    147  CD1 TYR    85      13.561  94.490  24.157  1.00  1.01
ATOM    148  CE1 TYR    85      14.876  94.567  23.718  1.00  1.62
ATOM    149  CZ  TYR    85      15.367  95.766  23.223  1.00  1.85
ATOM    150  OH  TYR    85      16.674  95.842  22.791  1.00  2.56
ATOM    151  CE2 TYR    85      14.552  96.890  23.164  1.00  1.60
ATOM    152  CD2 TYR    85      13.237  96.812  23.606  1.00  0.97
ATOM    153  C   TYR    85       9.248  94.201  24.097  1.00  0.02
ATOM    154  O   TYR    85       8.097  94.570  24.359  1.00  0.02
ATOM    155  N   TYR    86       9.685  92.965  24.279  1.00  0.02
ATOM    157  CA  TYR    86       8.836  91.915  24.850  1.00  0.02
ATOM    158  CB  TYR    86       9.388  90.560  24.403  1.00  0.02
ATOM    159  CG  TYR    86       8.619  89.338  24.913  1.00  0.02
ATOM    160  CD1 TYR    86       7.230  89.319  24.899  1.00  0.01
ATOM    161  CE1 TYR    86       6.544  88.214  25.386  1.00  0.02
ATOM    162  CZ  TYR    86       7.251  87.123  25.875  1.00  0.03
ATOM    163  OH  TYR    86       6.589  86.153  26.593  1.00  0.03
ATOM    164  CE2 TYR    86       8.638  87.120  25.843  1.00  0.02
ATOM    165  CD2 TYR    86       9.322  88.226  25.356  1.00  0.02
ATOM    166  C   TYR    86       8.803  91.953  26.376  1.00  0.03
ATOM    167  O   TYR    86       9.841  91.887  27.049  1.00  0.02
ATOM    168  N   GLY    87       7.599  92.060  26.909  1.00  0.02
ATOM    170  CA  GLY    87       7.391  91.843  28.342  1.00  0.03
ATOM    171  C   GLY    87       7.398  90.335  28.585  1.00  0.02
ATOM    172  O   GLY    87       6.466  89.627  28.189  1.00  0.02
ATOM    173  N   GLU    88       8.425  89.865  29.277  1.00  0.02
ATOM    175  CA  GLU    88       8.648  88.416  29.425  1.00  0.03
ATOM    176  CB  GLU    88      10.005  88.217  30.094  1.00  0.02
ATOM    177  CG  GLU    88      11.142  88.910  29.343  1.00  0.02
ATOM    178  CD  GLU    88      11.450  88.215  28.018  1.00  0.02
ATOM    179  OE1 GLU    88      11.897  88.900  27.109  1.00  0.03
ATOM    180  OE2 GLU    88      11.301  87.003  27.965  1.00  0.03
ATOM    181  C   GLU    88       7.570  87.751  30.281  1.00  0.03
ATOM    182  O   GLU    88       7.021  86.706  29.906  1.00  0.02
ATOM    183  N   ASN    89       7.103  88.494  31.268  1.00  0.03
ATOM    185  CA  ASN    89       6.036  88.049  32.173  1.00  0.01
ATOM    186  CB  ASN    89       6.379  88.578  33.571  1.00  0.02
ATOM    187  CG  ASN    89       7.000  89.985  33.518  1.00  0.02
ATOM    188  OD1 ASN    89       8.227  90.134  33.492  1.00  0.03
ATOM    189  ND2 ASN    89       6.149  90.995  33.498  1.00  0.03
ATOM    192  C   ASN    89       4.664  88.548  31.708  1.00  0.02
ATOM    193  O   ASN    89       3.932  89.201  32.466  1.00  0.02
ATOM    194  N   LEU    90       4.289  88.148  30.505  1.00  0.03
ATOM    196  CA  LEU    90       3.105  88.713  29.851  1.00  0.02
ATOM    197  CB  LEU    90       3.351  88.565  28.345  1.00  0.02
ATOM    198  CG  LEU    90       2.678  89.635  27.488  1.00  0.03
ATOM    199  CD1 LEU    90       1.183  89.398  27.287  1.00  0.02
ATOM    200  CD2 LEU    90       2.963  91.035  28.020  1.00  0.02
ATOM    201  C   LEU    90       1.800  88.011  30.239  1.00  0.03
ATOM    202  O   LEU    90       0.799  88.686  30.514  1.00  0.03
ATOM    203  N   CYS    91       1.849  86.705  30.436  1.00  0.02
ATOM    205  CA  CYS    91       0.607  85.932  30.618  1.00  0.02
ATOM    206  CB  CYS    91       0.821  84.557  29.999  1.00  0.02
ATOM    207  SG  CYS    91       1.229  84.566  28.239  1.00  1.13
ATOM    208  C   CYS    91       0.184  85.769  32.081  1.00  0.02
ATOM    209  O   CYS    91       0.440  84.728  32.693  1.00  0.03
ATOM    210  N   ASN    92      -0.468  86.787  32.624  1.00  0.03
ATOM    212  CA  ASN    92      -0.930  86.730  34.024  1.00  0.02
ATOM    213  CB  ASN    92      -0.027  87.616  34.882  1.00  0.02
ATOM    214  CG  ASN    92       1.330  86.954  35.127  1.00  0.02
ATOM    215  OD1 ASN    92       1.410  85.922  35.803  1.00  0.29
ATOM    216  ND2 ASN    92       2.384  87.574  34.619  1.00  0.35
ATOM    219  C   ASN    92      -2.386  87.163  34.229  1.00  0.02
ATOM    220  O   ASN    92      -2.856  87.195  35.375  1.00  0.01
ATOM    221  N   ILE    93      -3.095  87.484  33.158  1.00  0.03
ATOM    223  CA  ILE    93      -4.448  88.059  33.299  1.00  0.02
ATOM    224  CB  ILE    93      -4.571  89.148  32.237  1.00  0.02
ATOM    225  CG2 ILE    93      -5.893  89.903  32.337  1.00  0.03
ATOM    226  CG1 ILE    93      -3.406  90.132  32.360  1.00  0.03
ATOM    227  CD1 ILE    93      -3.456  91.193  31.268  1.00  0.02
ATOM    228  C   ILE    93      -5.573  87.023  33.136  1.00  0.01
ATOM    229  O   ILE    93      -5.583  86.262  32.163  1.00  0.02
ATOM    230  N   SER    94      -6.490  86.992  34.094  1.00  0.02
ATOM    232  CA  SER    94      -7.682  86.124  34.006  1.00  0.01
ATOM    233  CB  SER    94      -7.424  84.841  34.794  1.00  0.94
ATOM    234  OG  SER    94      -7.205  85.198  36.153  1.00  0.88
ATOM    235  C   SER    94      -8.948  86.817  34.547  1.00  0.02
ATOM    236  O   SER    94      -8.867  87.647  35.458  1.00  0.02
TER  
END
