
#######################################################
#                                                     #
#                        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   50 (  200),  selected   50 , name T0309TS550_1
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309TS550_1.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    V      19      A       2           -
LGA    M      20      S       3           -
LGA    E      21      K       4           -
LGA    V      22      K       5           -
LGA    T      26      V       6           -
LGA    K      27      H       7           -
LGA    E      28      Q       8           -
LGA    A      29      -       -           -
LGA    E      30      I       9          4.136
LGA    Y      31      N      10          2.818
LGA    T      32      -       -           -
LGA    Y      33      V      11          4.649
LGA    D      34      K      12          4.132
LGA    F      35      -       -           -
LGA    K      36      -       -           -
LGA    E      37      G      13          6.064
LGA    I      38      -       -           -
LGA    L      39      -       -           -
LGA    S      40      -       -           -
LGA    E      41      F      14           #
LGA    F      42      F      15          3.336
LGA    N      43      D      16          4.080
LGA    G      44      M      17          2.651
LGA    K      45      D      18          3.735
LGA    -       -      V      19           -
LGA    -       -      M      20           -
LGA    N      46      E      21          1.344
LGA    V      47      V      22          2.062
LGA    S      48      T      23          2.034
LGA    I      49      E      24          3.262
LGA    T      50      Q      25          3.000
LGA    V      51      T      26          2.750
LGA    K      52      K      27          1.769
LGA    E      53      -       -           -
LGA    E      54      -       -           -
LGA    N      55      -       -           -
LGA    E      56      E      28          1.155
LGA    L      57      A      29          1.945
LGA    P      58      E      30          1.231
LGA    V      59      Y      31          3.484
LGA    K      60      -       -           -
LGA    G      61      T      32          1.111
LGA    V      62      Y      33          0.980
LGA    E      63      D      34          1.752
LGA    G      66      F      35          2.135
LGA    D      67      K      36          1.014
LGA    P      68      E      37          1.731
LGA    L      69      I      38          1.885
LGA    E      70      L      39          1.531
LGA    H      71      S      40          1.976
LGA    H      72      E      41          2.227
LGA    H      73      F      42          1.694
LGA    -       -      N      43           -
LGA    -       -      G      44           -
LGA    -       -      K      45           -
LGA    -       -      N      46           -
LGA    -       -      V      47           -
LGA    -       -      S      48           -
LGA    -       -      I      49           -
LGA    -       -      T      50           -
LGA    -       -      V      51           -
LGA    -       -      K      52           -
LGA    -       -      E      53           -
LGA    -       -      E      54           -
LGA    -       -      N      55           -
LGA    -       -      E      56           -
LGA    -       -      L      57           -
LGA    -       -      P      58           -
LGA    -       -      V      59           -
LGA    -       -      K      60           -
LGA    -       -      G      61           -
LGA    -       -      V      62           -
LGA    -       -      E      63           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   50   62    5.0     31    2.78    12.90     36.028     1.075

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.201828 * X  +  -0.872147 * Y  +   0.445674 * Z  +  13.571012
  Y_new =   0.118730 * X  +   0.473469 * Y  +   0.872771 * Z  + -32.936005
  Z_new =  -0.972198 * X  +  -0.123235 * Y  +   0.199110 * Z  + -14.892859 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.554222    2.587371  [ DEG:   -31.7546    148.2454 ]
  Theta =   1.334440    1.807152  [ DEG:    76.4578    103.5422 ]
  Phi   =   0.531753   -2.609839  [ DEG:    30.4672   -149.5328 ]
 
# 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: T0309TS550_1                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309TS550_1.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   50   62   5.0   31   2.78   12.90  36.028
REMARK  ---------------------------------------------------------- 
MOLECULE T0309TS550_1
PFRMAT TS
TARGET T0309
MODEL 1
PARENT 1pbj_A
ATOM      1  N   VAL    19       9.916   3.704 -22.524  1.00  0.00
ATOM      2  CA  VAL    19       9.413   2.626 -21.685  1.00  0.00
ATOM      3  C   VAL    19      10.092   1.280 -21.886  1.00  0.00
ATOM      4  O   VAL    19      10.171   0.490 -20.938  1.00  0.00
ATOM      5  N   MET    20      10.617   1.011 -23.082  1.00  0.00
ATOM      6  CA  MET    20      11.303  -0.269 -23.289  1.00  0.00
ATOM      7  C   MET    20      12.602  -0.356 -22.506  1.00  0.00
ATOM      8  O   MET    20      13.100  -1.455 -22.264  1.00  0.00
ATOM      9  N   GLU    21      13.156   0.778 -22.093  1.00  0.00
ATOM     10  CA  GLU    21      14.402   0.766 -21.333  1.00  0.00
ATOM     11  C   GLU    21      14.200   0.302 -19.891  1.00  0.00
ATOM     12  O   GLU    21      15.162  -0.134 -19.247  1.00  0.00
ATOM     13  N   VAL    22      12.963   0.404 -19.391  1.00  0.00
ATOM     14  CA  VAL    22      12.677   0.108 -17.987  1.00  0.00
ATOM     15  C   VAL    22      11.545  -0.893 -17.767  1.00  0.00
ATOM     16  O   VAL    22      11.294  -1.282 -16.627  1.00  0.00
ATOM     17  N   THR    26       5.602 -12.054 -14.109  1.00  0.00
ATOM     18  CA  THR    26       4.555 -12.809 -14.768  1.00  0.00
ATOM     19  C   THR    26       4.058 -13.903 -13.844  1.00  0.00
ATOM     20  O   THR    26       4.809 -14.424 -13.009  1.00  0.00
ATOM     21  N   LYS    27       2.773 -14.209 -13.969  1.00  0.00
ATOM     22  CA  LYS    27       2.185 -15.290 -13.210  1.00  0.00
ATOM     23  C   LYS    27       1.072 -15.925 -14.020  1.00  0.00
ATOM     24  O   LYS    27       0.457 -15.310 -14.896  1.00  0.00
ATOM     25  N   GLU    28       0.976 -15.932 -11.661  1.00  0.00
ATOM     26  CA  GLU    28       0.337 -16.958 -10.865  1.00  0.00
ATOM     27  C   GLU    28      -1.153 -16.724 -10.703  1.00  0.00
ATOM     28  O   GLU    28      -1.642 -15.607 -10.830  1.00  0.00
ATOM     29  N   ALA    29      -1.872 -17.812 -10.475  1.00  0.00
ATOM     30  CA  ALA    29      -3.313 -17.780 -10.255  1.00  0.00
ATOM     31  C   ALA    29      -3.438 -18.299  -8.831  1.00  0.00
ATOM     32  O   ALA    29      -2.452 -18.794  -8.271  1.00  0.00
ATOM     33  N   GLU    30      -4.630 -18.216  -8.250  1.00  0.00
ATOM     34  CA  GLU    30      -4.808 -18.668  -6.878  1.00  0.00
ATOM     35  C   GLU    30      -3.835 -17.876  -6.014  1.00  0.00
ATOM     36  O   GLU    30      -2.679 -18.249  -5.853  1.00  0.00
ATOM     37  N   TYR    31      -4.096 -17.053  -4.996  1.00  0.00
ATOM     38  CA  TYR    31      -3.911 -15.665  -4.590  1.00  0.00
ATOM     39  C   TYR    31      -2.709 -15.537  -3.674  1.00  0.00
ATOM     40  O   TYR    31      -1.953 -14.569  -3.776  1.00  0.00
ATOM     41  N   THR    32      -2.521 -16.514  -2.787  1.00  0.00
ATOM     42  CA  THR    32      -1.381 -16.512  -1.878  1.00  0.00
ATOM     43  C   THR    32      -0.097 -16.604  -2.692  1.00  0.00
ATOM     44  O   THR    32       0.886 -15.920  -2.395  1.00  0.00
ATOM     45  N   TYR    33      -0.093 -17.448  -3.726  1.00  0.00
ATOM     46  CA  TYR    33       1.095 -17.554  -4.566  1.00  0.00
ATOM     47  C   TYR    33       1.377 -16.230  -5.281  1.00  0.00
ATOM     48  O   TYR    33       2.538 -15.847  -5.439  1.00  0.00
ATOM     49  N   ASP    34       0.324 -15.536  -5.707  1.00  0.00
ATOM     50  CA  ASP    34       0.508 -14.237  -6.362  1.00  0.00
ATOM     51  C   ASP    34       1.110 -13.258  -5.334  1.00  0.00
ATOM     52  O   ASP    34       2.032 -12.499  -5.676  1.00  0.00
ATOM     53  N   PHE    35       0.593 -13.252  -4.105  1.00  0.00
ATOM     54  CA  PHE    35       1.134 -12.358  -3.071  1.00  0.00
ATOM     55  C   PHE    35       2.607 -12.715  -2.817  1.00  0.00
ATOM     56  O   PHE    35       3.452 -11.829  -2.635  1.00  0.00
ATOM     57  N   LYS    36       2.923 -14.010  -2.782  1.00  0.00
ATOM     58  CA  LYS    36       4.309 -14.407  -2.559  1.00  0.00
ATOM     59  C   LYS    36       5.224 -13.890  -3.671  1.00  0.00
ATOM     60  O   LYS    36       6.333 -13.426  -3.372  1.00  0.00
ATOM     61  N   GLU    37       4.779 -13.954  -4.926  1.00  0.00
ATOM     62  CA  GLU    37       5.621 -13.465  -6.029  1.00  0.00
ATOM     63  C   GLU    37       5.775 -11.945  -5.957  1.00  0.00
ATOM     64  O   GLU    37       6.851 -11.395  -6.221  1.00  0.00
ATOM     65  N   ILE    38       4.689 -11.248  -5.637  1.00  0.00
ATOM     66  CA  ILE    38       4.783  -9.790  -5.448  1.00  0.00
ATOM     67  C   ILE    38       5.782  -9.430  -4.345  1.00  0.00
ATOM     68  O   ILE    38       6.592  -8.508  -4.517  1.00  0.00
ATOM     69  N   LEU    39       5.733 -10.143  -3.227  1.00  0.00
ATOM     70  CA  LEU    39       6.635  -9.861  -2.123  1.00  0.00
ATOM     71  C   LEU    39       8.091 -10.197  -2.479  1.00  0.00
ATOM     72  O   LEU    39       8.991  -9.398  -2.209  1.00  0.00
ATOM     73  N   SER    40       8.315 -11.345  -3.114  1.00  0.00
ATOM     74  CA  SER    40       9.675 -11.745  -3.497  1.00  0.00
ATOM     75  C   SER    40      10.312 -10.749  -4.470  1.00  0.00
ATOM     76  O   SER    40      11.506 -10.462  -4.378  1.00  0.00
ATOM     77  N   GLU    41       9.517 -10.229  -5.403  1.00  0.00
ATOM     78  CA  GLU    41      10.002  -9.281  -6.417  1.00  0.00
ATOM     79  C   GLU    41       9.733  -7.820  -6.103  1.00  0.00
ATOM     80  O   GLU    41      10.035  -6.920  -6.898  1.00  0.00
ATOM     81  N   PHE    42       8.315  -7.889  -7.423  1.00  0.00
ATOM     82  CA  PHE    42       7.391  -6.772  -7.567  1.00  0.00
ATOM     83  C   PHE    42       5.937  -7.177  -7.398  1.00  0.00
ATOM     84  O   PHE    42       5.037  -6.532  -7.930  1.00  0.00
ATOM     85  N   ASN    43       5.702  -8.244  -6.651  1.00  0.00
ATOM     86  CA  ASN    43       4.344  -8.710  -6.437  1.00  0.00
ATOM     87  C   ASN    43       3.440  -7.599  -5.913  1.00  0.00
ATOM     88  O   ASN    43       2.406  -7.315  -6.499  1.00  0.00
ATOM     89  N   GLY    44       3.840  -6.972  -4.811  1.00  0.00
ATOM     90  CA  GLY    44       3.057  -5.896  -4.204  1.00  0.00
ATOM     91  C   GLY    44       2.659  -4.808  -5.195  1.00  0.00
ATOM     92  O   GLY    44       1.586  -4.217  -5.071  1.00  0.00
ATOM     93  N   LYS    45       3.517  -4.539  -6.176  1.00  0.00
ATOM     94  CA  LYS    45       3.229  -3.513  -7.180  1.00  0.00
ATOM     95  C   LYS    45       2.274  -4.011  -8.275  1.00  0.00
ATOM     96  O   LYS    45       1.368  -3.286  -8.702  1.00  0.00
ATOM     97  N   ASN    46       2.225  -5.180  -8.813  1.00  0.00
ATOM     98  CA  ASN    46       1.429  -5.759  -9.884  1.00  0.00
ATOM     99  C   ASN    46       2.153  -6.846 -10.626  1.00  0.00
ATOM    100  O   ASN    46       3.372  -6.796 -10.776  1.00  0.00
ATOM    101  N   VAL    47       1.384  -7.823 -11.103  1.00  0.00
ATOM    102  CA  VAL    47       1.911  -8.927 -11.916  1.00  0.00
ATOM    103  C   VAL    47       1.126  -9.016 -13.210  1.00  0.00
ATOM    104  O   VAL    47      -0.091  -8.800 -13.245  1.00  0.00
ATOM    105  N   SER    48       1.839  -9.322 -14.287  1.00  0.00
ATOM    106  CA  SER    48       1.219  -9.575 -15.587  1.00  0.00
ATOM    107  C   SER    48       0.713 -11.029 -15.518  1.00  0.00
ATOM    108  O   SER    48       1.421 -11.916 -15.039  1.00  0.00
ATOM    109  N   ILE    49      -0.498 -11.270 -16.003  1.00  0.00
ATOM    110  CA  ILE    49      -1.025 -12.642 -16.009  1.00  0.00
ATOM    111  C   ILE    49      -0.870 -13.158 -17.442  1.00  0.00
ATOM    112  O   ILE    49      -1.336 -12.526 -18.382  1.00  0.00
ATOM    113  N   THR    50      -0.189 -14.291 -17.584  1.00  0.00
ATOM    114  CA  THR    50       0.068 -14.872 -18.895  1.00  0.00
ATOM    115  C   THR    50      -0.577 -16.253 -19.066  1.00  0.00
ATOM    116  O   THR    50      -0.500 -17.090 -18.157  1.00  0.00
ATOM    117  N   VAL    51      -1.177 -16.473 -20.214  1.00  0.00
ATOM    118  CA  VAL    51      -1.809 -17.764 -20.540  1.00  0.00
ATOM    119  C   VAL    51      -1.570 -17.986 -22.024  1.00  0.00
ATOM    120  O   VAL    51      -1.728 -17.070 -22.833  1.00  0.00
ATOM    121  N   LYS    52      -0.950 -19.491 -21.729  1.00  0.00
ATOM    122  CA  LYS    52       0.011 -20.141 -22.595  1.00  0.00
ATOM    123  C   LYS    52      -0.820 -20.819 -23.675  1.00  0.00
ATOM    124  O   LYS    52      -0.749 -20.465 -24.851  1.00  0.00
ATOM    125  N   GLU    53      -1.636 -21.778 -23.251  1.00  0.00
ATOM    126  CA  GLU    53      -2.475 -22.544 -24.165  1.00  0.00
ATOM    127  C   GLU    53      -3.486 -21.720 -24.951  1.00  0.00
ATOM    128  O   GLU    53      -3.600 -21.868 -26.164  1.00  0.00
ATOM    129  N   GLU    54      -4.210 -20.846 -24.266  1.00  0.00
ATOM    130  CA  GLU    54      -5.227 -20.035 -24.921  1.00  0.00
ATOM    131  C   GLU    54      -4.760 -18.712 -25.523  1.00  0.00
ATOM    132  O   GLU    54      -4.694 -18.569 -26.741  1.00  0.00
ATOM    133  N   ASN    55      -4.439 -17.747 -24.667  1.00  0.00
ATOM    134  CA  ASN    55      -4.024 -16.423 -25.122  1.00  0.00
ATOM    135  C   ASN    55      -2.631 -16.370 -25.750  1.00  0.00
ATOM    136  O   ASN    55      -2.375 -15.569 -26.650  1.00  0.00
ATOM    137  N   GLU    56      -1.729 -17.219 -25.275  1.00  0.00
ATOM    138  CA  GLU    56      -0.384 -17.217 -25.812  1.00  0.00
ATOM    139  C   GLU    56       0.399 -15.985 -25.382  1.00  0.00
ATOM    140  O   GLU    56       1.323 -15.567 -26.079  1.00  0.00
ATOM    141  N   LEU    57       0.694 -15.506 -23.890  1.00  0.00
ATOM    142  CA  LEU    57       0.302 -14.108 -24.072  1.00  0.00
ATOM    143  C   LEU    57      -0.190 -13.463 -22.781  1.00  0.00
ATOM    144  O   LEU    57      -0.721 -14.142 -21.901  1.00  0.00
ATOM    145  N   PRO    58      -0.005 -12.149 -22.671  1.00  0.00
ATOM    146  CA  PRO    58      -0.456 -11.422 -21.485  1.00  0.00
ATOM    147  C   PRO    58      -1.964 -11.215 -21.604  1.00  0.00
ATOM    148  O   PRO    58      -2.433 -10.549 -22.532  1.00  0.00
ATOM    149  N   VAL    59      -2.717 -11.784 -20.661  1.00  0.00
ATOM    150  CA  VAL    59      -4.178 -11.684 -20.689  1.00  0.00
ATOM    151  C   VAL    59      -4.783 -10.768 -19.630  1.00  0.00
ATOM    152  O   VAL    59      -5.992 -10.531 -19.623  1.00  0.00
ATOM    153  N   LYS    60      -3.954 -10.239 -18.733  1.00  0.00
ATOM    154  CA  LYS    60      -4.481  -9.353 -17.713  1.00  0.00
ATOM    155  C   LYS    60      -3.403  -8.945 -16.737  1.00  0.00
ATOM    156  O   LYS    60      -2.223  -9.280 -16.922  1.00  0.00
ATOM    157  N   GLY    61      -3.814  -8.246 -15.686  1.00  0.00
ATOM    158  CA  GLY    61      -2.899  -7.798 -14.651  1.00  0.00
ATOM    159  C   GLY    61      -3.571  -8.016 -13.307  1.00  0.00
ATOM    160  O   GLY    61      -4.790  -7.834 -13.182  1.00  0.00
ATOM    161  N   VAL    62      -2.814  -8.446 -12.320  1.00  0.00
ATOM    162  CA  VAL    62      -3.377  -8.577 -10.985  1.00  0.00
ATOM    163  C   VAL    62      -2.550  -7.674 -10.084  1.00  0.00
ATOM    164  O   VAL    62      -1.319  -7.630 -10.170  1.00  0.00
ATOM    165  N   GLU    63      -3.210  -6.929  -9.203  1.00  0.00
ATOM    166  CA  GLU    63      -2.451  -6.080  -8.304  1.00  0.00
ATOM    167  C   GLU    63      -2.706  -6.431  -6.855  1.00  0.00
ATOM    168  O   GLU    63      -3.639  -7.160  -6.507  1.00  0.00
ATOM    169  N   GLY    66      -1.865  -5.889  -6.006  1.00  0.00
ATOM    170  CA  GLY    66      -1.996  -6.120  -4.575  1.00  0.00
ATOM    171  C   GLY    66      -3.337  -5.543  -4.087  1.00  0.00
ATOM    172  O   GLY    66      -3.935  -6.098  -3.161  1.00  0.00
ATOM    173  N   ASP    67      -3.812  -4.456  -4.700  1.00  0.00
ATOM    174  CA  ASP    67      -5.102  -3.868  -4.313  1.00  0.00
ATOM    175  C   ASP    67      -6.214  -4.897  -4.466  1.00  0.00
ATOM    176  O   ASP    67      -7.083  -5.029  -3.596  1.00  0.00
ATOM    177  N   PRO    68      -6.176  -5.623  -5.577  1.00  0.00
ATOM    178  CA  PRO    68      -7.176  -6.650  -5.891  1.00  0.00
ATOM    179  C   PRO    68      -7.153  -7.763  -4.848  1.00  0.00
ATOM    180  O   PRO    68      -8.193  -8.262  -4.391  1.00  0.00
ATOM    181  N   LEU    69      -5.945  -8.164  -4.485  1.00  0.00
ATOM    182  CA  LEU    69      -5.746  -9.227  -3.514  1.00  0.00
ATOM    183  C   LEU    69      -6.222  -8.782  -2.140  1.00  0.00
ATOM    184  O   LEU    69      -6.927  -9.535  -1.441  1.00  0.00
ATOM    185  N   GLU    70      -5.884  -7.557  -1.746  1.00  0.00
ATOM    186  CA  GLU    70      -6.334  -7.084  -0.438  1.00  0.00
ATOM    187  C   GLU    70      -7.858  -6.989  -0.369  1.00  0.00
ATOM    188  O   GLU    70      -8.452  -7.374   0.641  1.00  0.00
ATOM    189  N   HIS    71      -8.483  -6.500  -1.433  1.00  0.00
ATOM    190  CA  HIS    71      -9.941  -6.397  -1.444  1.00  0.00
ATOM    191  C   HIS    71     -10.572  -7.778  -1.360  1.00  0.00
ATOM    192  O   HIS    71     -11.561  -7.975  -0.638  1.00  0.00
ATOM    193  N   HIS    72      -9.994  -8.753  -2.064  1.00  0.00
ATOM    194  CA  HIS    72     -10.543 -10.113  -2.032  1.00  0.00
ATOM    195  C   HIS    72     -10.403 -10.754  -0.656  1.00  0.00
ATOM    196  O   HIS    72     -11.262 -11.528  -0.232  1.00  0.00
ATOM    197  N   HIS    73      -9.322 -10.436   0.054  1.00  0.00
ATOM    198  CA  HIS    73      -9.087 -10.982   1.384  1.00  0.00
ATOM    199  C   HIS    73     -10.108 -10.396   2.357  1.00  0.00
ATOM    200  O   HIS    73     -10.650 -11.099   3.215  1.00  0.00
TER
END
