
#######################################################
#                                                     #
#                        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   45 (  180),  selected   45 , name T0309AL243_3
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309AL243_3.T0309.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    Q       8      A       2           -
LGA    I       9      S       3           -
LGA    N      10      K       4           -
LGA    V      11      K       5           -
LGA    K      12      V       6           -
LGA    G      13      H       7           -
LGA    F      14      Q       8           -
LGA    E      21      I       9           -
LGA    -       -      N      10           -
LGA    -       -      V      11           -
LGA    -       -      K      12           -
LGA    -       -      G      13           -
LGA    -       -      F      14           -
LGA    V      22      F      15           #
LGA    T      23      D      16          3.187
LGA    E      24      M      17          2.285
LGA    -       -      D      18           -
LGA    -       -      V      19           -
LGA    -       -      M      20           -
LGA    Q      25      E      21          2.241
LGA    T      26      V      22          3.951
LGA    K      27      T      23           -
LGA    -       -      E      24           -
LGA    -       -      Q      25           -
LGA    -       -      T      26           -
LGA    -       -      K      27           -
LGA    -       -      E      28           -
LGA    -       -      A      29           -
LGA    -       -      E      30           -
LGA    -       -      Y      31           -
LGA    -       -      T      32           -
LGA    -       -      Y      33           -
LGA    E      28      D      34          4.480
LGA    Y      31      F      35          1.765
LGA    T      32      -       -           -
LGA    K      36      K      36          3.568
LGA    E      37      E      37          2.517
LGA    I      38      I      38          2.087
LGA    L      39      L      39          2.822
LGA    S      40      S      40          2.574
LGA    E      41      E      41          3.902
LGA    F      42      -       -           -
LGA    N      43      F      42          4.201
LGA    K      45      N      43           -
LGA    -       -      G      44           -
LGA    -       -      K      45           -
LGA    N      46      N      46          4.037
LGA    V      47      V      47          3.486
LGA    -       -      S      48           -
LGA    S      48      I      49          2.231
LGA    I      49      T      50          2.860
LGA    T      50      V      51          1.877
LGA    V      51      K      52          2.505
LGA    K      52      E      53          1.245
LGA    E      53      E      54          2.575
LGA    E      54      N      55          2.612
LGA    N      55      E      56          3.413
LGA    E      56      L      57           -
LGA    L      57      P      58           -
LGA    P      58      V      59           -
LGA    V      59      K      60           -
LGA    K      60      G      61           -
LGA    G      61      V      62           -
LGA    V      62      E      63           -
LGA    E      63      -       -           -
LGA    M      64      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   45   62    5.0     23    3.01    39.13     24.431     0.740

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.834020 * X  +  -0.534741 * Y  +  -0.135878 * Z  +  -6.111757
  Y_new =   0.088539 * X  +   0.113366 * Y  +  -0.989600 * Z  + -15.422681
  Z_new =   0.544584 * X  +  -0.837377 * Y  +  -0.047204 * Z  +  -0.443676 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.627108    1.514485  [ DEG:   -93.2264     86.7736 ]
  Theta =  -0.575893   -2.565700  [ DEG:   -32.9962   -147.0038 ]
  Phi   =   3.035829   -0.105763  [ DEG:   173.9402     -6.0598 ]
 
# 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: T0309AL243_3                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309AL243_3.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   45   62   5.0   23   3.01   39.13  24.431
REMARK  ---------------------------------------------------------- 
MOLECULE T0309AL243_3
REMARK Aligment from pdb entry: 1imuA
ATOM      1  N   GLN     8      -5.158  -7.039   6.365  1.00  0.00              
ATOM      2  CA  GLN     8      -4.264  -6.797   5.239  1.00  0.00              
ATOM      3  C   GLN     8      -3.463  -8.050   4.896  1.00  0.00              
ATOM      4  O   GLN     8      -2.872  -8.679   5.774  1.00  0.00              
ATOM      5  N   ILE     9      -3.446  -8.403   3.616  1.00  0.00              
ATOM      6  CA  ILE     9      -2.715  -9.577   3.155  1.00  0.00              
ATOM      7  C   ILE     9      -1.212  -9.335   3.209  1.00  0.00              
ATOM      8  O   ILE     9      -0.659  -8.606   2.386  1.00  0.00              
ATOM      9  N   ASN    10      -0.556  -9.943   4.192  1.00  0.00              
ATOM     10  CA  ASN    10       0.885  -9.787   4.360  1.00  0.00              
ATOM     11  C   ASN    10       1.662 -10.737   3.452  1.00  0.00              
ATOM     12  O   ASN    10       1.130 -11.743   2.971  1.00  0.00              
ATOM     13  N   VAL    11       2.930 -10.407   3.225  1.00  0.00              
ATOM     14  CA  VAL    11       3.797 -11.216   2.376  1.00  0.00              
ATOM     15  C   VAL    11       5.062 -11.630   3.117  1.00  0.00              
ATOM     16  O   VAL    11       5.441 -11.021   4.117  1.00  0.00              
ATOM     17  N   LYS    12       5.717 -12.661   2.601  1.00  0.00              
ATOM     18  CA  LYS    12       6.952 -13.160   3.187  1.00  0.00              
ATOM     19  C   LYS    12       8.039 -13.212   2.124  1.00  0.00              
ATOM     20  O   LYS    12       9.118 -12.644   2.291  1.00  0.00              
ATOM     21  N   GLY    13       7.729 -13.884   1.020  1.00  0.00              
ATOM     22  CA  GLY    13       8.652 -14.014  -0.102  1.00  0.00              
ATOM     23  C   GLY    13      10.078 -14.307   0.358  1.00  0.00              
ATOM     24  O   GLY    13      10.832 -13.397   0.702  1.00  0.00              
ATOM     25  N   PHE    14      12.420 -13.498  -4.133  1.00  0.00              
ATOM     26  CA  PHE    14      11.887 -12.340  -4.847  1.00  0.00              
ATOM     27  C   PHE    14      11.081 -11.436  -3.922  1.00  0.00              
ATOM     28  O   PHE    14      10.014 -11.816  -3.444  1.00  0.00              
ATOM     29  N   GLU    21      11.590 -10.236  -3.674  1.00  0.00              
ATOM     30  CA  GLU    21      10.902  -9.289  -2.808  1.00  0.00              
ATOM     31  C   GLU    21       9.523  -8.953  -3.369  1.00  0.00              
ATOM     32  O   GLU    21       9.164  -9.397  -4.459  1.00  0.00              
ATOM     33  N   VAL    22       8.754  -8.164  -2.625  1.00  0.00              
ATOM     34  CA  VAL    22       7.417  -7.777  -3.068  1.00  0.00              
ATOM     35  C   VAL    22       7.454  -6.429  -3.777  1.00  0.00              
ATOM     36  O   VAL    22       8.258  -5.559  -3.446  1.00  0.00              
ATOM     37  N   THR    23       6.575  -6.270  -4.754  1.00  0.00              
ATOM     38  CA  THR    23       6.491  -5.038  -5.522  1.00  0.00              
ATOM     39  C   THR    23       5.034  -4.714  -5.847  1.00  0.00              
ATOM     40  O   THR    23       4.143  -5.526  -5.596  1.00  0.00              
ATOM     41  N   GLU    24       4.767  -3.521  -6.410  1.00  0.00              
ATOM     42  CA  GLU    24       3.409  -3.101  -6.766  1.00  0.00              
ATOM     43  C   GLU    24       2.591  -4.222  -7.399  1.00  0.00              
ATOM     44  O   GLU    24       1.458  -4.480  -6.992  1.00  0.00              
ATOM     45  N   GLN    25       3.171  -4.890  -8.392  1.00  0.00              
ATOM     46  CA  GLN    25       2.491  -5.987  -9.074  1.00  0.00              
ATOM     47  C   GLN    25       1.998  -7.021  -8.069  1.00  0.00              
ATOM     48  O   GLN    25       0.804  -7.102  -7.785  1.00  0.00              
ATOM     49  N   THR    26       2.927  -7.800  -7.515  1.00  0.00              
ATOM     50  CA  THR    26       2.579  -8.811  -6.522  1.00  0.00              
ATOM     51  C   THR    26       1.691  -8.201  -5.442  1.00  0.00              
ATOM     52  O   THR    26       0.525  -8.567  -5.302  1.00  0.00              
ATOM     53  N   LYS    27       2.261  -7.261  -4.686  1.00  0.00              
ATOM     54  CA  LYS    27       1.541  -6.586  -3.610  1.00  0.00              
ATOM     55  C   LYS    27       0.094  -6.300  -4.016  1.00  0.00              
ATOM     56  O   LYS    27      -0.847  -6.798  -3.398  1.00  0.00              
ATOM     57  N   GLU    28      -0.067  -5.506  -5.072  1.00  0.00              
ATOM     58  CA  GLU    28      -1.391  -5.160  -5.574  1.00  0.00              
ATOM     59  C   GLU    28      -2.166  -6.417  -5.949  1.00  0.00              
ATOM     60  O   GLU    28      -3.369  -6.514  -5.709  1.00  0.00              
ATOM     61  N   TYR    31      -1.463  -7.389  -6.528  1.00  0.00              
ATOM     62  CA  TYR    31      -2.077  -8.646  -6.919  1.00  0.00              
ATOM     63  C   TYR    31      -2.626  -9.350  -5.684  1.00  0.00              
ATOM     64  O   TYR    31      -3.840  -9.452  -5.502  1.00  0.00              
ATOM     65  N   THR    32      -1.719  -9.805  -4.824  1.00  0.00              
ATOM     66  CA  THR    32      -2.100 -10.473  -3.580  1.00  0.00              
ATOM     67  C   THR    32      -3.197  -9.688  -2.866  1.00  0.00              
ATOM     68  O   THR    32      -4.239 -10.238  -2.504  1.00  0.00              
ATOM     69  N   LYS    36      -2.957  -8.389  -2.682  1.00  0.00              
ATOM     70  CA  LYS    36      -3.930  -7.520  -2.028  1.00  0.00              
ATOM     71  C   LYS    36      -5.271  -7.597  -2.749  1.00  0.00              
ATOM     72  O   LYS    36      -6.301  -7.892  -2.141  1.00  0.00              
ATOM     73  N   GLU    37      -5.245  -7.345  -4.056  1.00  0.00              
ATOM     74  CA  GLU    37      -6.457  -7.404  -4.866  1.00  0.00              
ATOM     75  C   GLU    37      -7.148  -8.749  -4.676  1.00  0.00              
ATOM     76  O   GLU    37      -8.369  -8.817  -4.523  1.00  0.00              
ATOM     77  N   ILE    38      -6.354  -9.818  -4.668  1.00  0.00              
ATOM     78  CA  ILE    38      -6.886 -11.159  -4.475  1.00  0.00              
ATOM     79  C   ILE    38      -7.587 -11.251  -3.126  1.00  0.00              
ATOM     80  O   ILE    38      -8.702 -11.765  -3.028  1.00  0.00              
ATOM     81  N   LEU    39      -6.934 -10.730  -2.089  1.00  0.00              
ATOM     82  CA  LEU    39      -7.511 -10.732  -0.752  1.00  0.00              
ATOM     83  C   LEU    39      -8.822  -9.960  -0.760  1.00  0.00              
ATOM     84  O   LEU    39      -9.863 -10.462  -0.323  1.00  0.00              
ATOM     85  N   SER    40      -8.772  -8.738  -1.289  1.00  0.00              
ATOM     86  CA  SER    40      -9.959  -7.902  -1.387  1.00  0.00              
ATOM     87  C   SER    40     -11.043  -8.634  -2.164  1.00  0.00              
ATOM     88  O   SER    40     -12.235  -8.481  -1.890  1.00  0.00              
ATOM     89  N   GLU    41     -10.614  -9.450  -3.124  1.00  0.00              
ATOM     90  CA  GLU    41     -11.537 -10.232  -3.931  1.00  0.00              
ATOM     91  C   GLU    41     -12.132 -11.356  -3.093  1.00  0.00              
ATOM     92  O   GLU    41     -13.320 -11.660  -3.196  1.00  0.00              
ATOM     93  N   PHE    42     -11.297 -11.960  -2.249  1.00  0.00              
ATOM     94  CA  PHE    42     -11.746 -13.037  -1.377  1.00  0.00              
ATOM     95  C   PHE    42     -12.559 -12.478  -0.209  1.00  0.00              
ATOM     96  O   PHE    42     -13.181 -13.228   0.539  1.00  0.00              
ATOM     97  N   ASN    43     -12.563 -11.152  -0.064  1.00  0.00              
ATOM     98  CA  ASN    43     -13.324 -10.527   1.006  1.00  0.00              
ATOM     99  C   ASN    43     -14.816 -10.747   0.848  1.00  0.00              
ATOM    100  O   ASN    43     -15.536 -10.919   1.832  1.00  0.00              
ATOM    101  N   LYS    45     -15.274 -10.749  -0.397  1.00  0.00              
ATOM    102  CA  LYS    45     -16.685 -10.958  -0.703  1.00  0.00              
ATOM    103  C   LYS    45     -17.130 -12.357  -0.278  1.00  0.00              
ATOM    104  O   LYS    45     -18.314 -12.601  -0.043  1.00  0.00              
ATOM    105  N   ASN    46      -5.964 -12.685   9.796  1.00  0.00              
ATOM    106  CA  ASN    46      -4.533 -12.504   9.577  1.00  0.00              
ATOM    107  C   ASN    46      -4.098 -13.288   8.342  1.00  0.00              
ATOM    108  O   ASN    46      -3.817 -14.484   8.416  1.00  0.00              
ATOM    109  N   VAL    47      -4.073 -12.617   7.181  1.00  0.00              
ATOM    110  CA  VAL    47      -3.717 -13.224   5.908  1.00  0.00              
ATOM    111  C   VAL    47      -2.258 -13.023   5.503  1.00  0.00              
ATOM    112  O   VAL    47      -1.688 -11.946   5.687  1.00  0.00              
ATOM    113  N   SER    48      -1.676 -14.071   4.929  1.00  0.00              
ATOM    114  CA  SER    48      -0.298 -14.038   4.466  1.00  0.00              
ATOM    115  C   SER    48      -0.187 -14.635   3.077  1.00  0.00              
ATOM    116  O   SER    48      -1.134 -15.228   2.559  1.00  0.00              
ATOM    117  N   ILE    49       0.991 -14.501   2.502  1.00  0.00              
ATOM    118  CA  ILE    49       1.261 -15.056   1.189  1.00  0.00              
ATOM    119  C   ILE    49       2.741 -15.384   1.032  1.00  0.00              
ATOM    120  O   ILE    49       3.572 -14.489   0.876  1.00  0.00              
ATOM    121  N   THR    50       3.060 -16.672   1.063  1.00  0.00              
ATOM    122  CA  THR    50       4.426 -17.120   0.915  1.00  0.00              
ATOM    123  C   THR    50       4.740 -17.329  -0.563  1.00  0.00              
ATOM    124  O   THR    50       4.536 -18.412  -1.117  1.00  0.00              
ATOM    125  N   VAL    51       5.205 -16.258  -1.195  1.00  0.00              
ATOM    126  CA  VAL    51       5.527 -16.260  -2.616  1.00  0.00              
ATOM    127  C   VAL    51       6.978 -16.651  -2.870  1.00  0.00              
ATOM    128  O   VAL    51       7.879 -16.221  -2.155  1.00  0.00              
ATOM    129  N   LYS    52       7.201 -17.449  -3.906  1.00  0.00              
ATOM    130  CA  LYS    52       8.553 -17.870  -4.258  1.00  0.00              
ATOM    131  C   LYS    52       8.691 -18.147  -5.750  1.00  0.00              
ATOM    132  O   LYS    52       7.710 -18.376  -6.459  1.00  0.00              
ATOM    133  N   GLU    53       9.930 -18.126  -6.208  1.00  0.00              
ATOM    134  CA  GLU    53      10.250 -18.377  -7.607  1.00  0.00              
ATOM    135  C   GLU    53      11.275 -19.495  -7.704  1.00  0.00              
ATOM    136  O   GLU    53      11.904 -19.859  -6.712  1.00  0.00              
ATOM    137  N   GLU    54      11.468 -20.003  -8.909  1.00  0.00              
ATOM    138  CA  GLU    54      12.449 -21.039  -9.135  1.00  0.00              
ATOM    139  C   GLU    54      12.832 -21.135 -10.613  1.00  0.00              
ATOM    140  O   GLU    54      12.081 -20.709 -11.488  1.00  0.00              
ATOM    141  N   ASN    55      14.014 -21.693 -10.912  1.00  0.00              
ATOM    142  CA  ASN    55      14.490 -21.833 -12.291  1.00  0.00              
ATOM    143  C   ASN    55      13.449 -22.465 -13.211  1.00  0.00              
ATOM    144  O   ASN    55      13.258 -22.024 -14.344  1.00  0.00              
ATOM    145  N   GLU    56      -1.432 -18.563   2.669  1.00  0.00              
ATOM    146  CA  GLU    56      -1.816 -18.995   4.004  1.00  0.00              
ATOM    147  C   GLU    56      -2.634 -17.919   4.712  1.00  0.00              
ATOM    148  O   GLU    56      -2.092 -16.927   5.198  1.00  0.00              
ATOM    149  N   LEU    57      -3.943 -18.133   4.769  1.00  0.00              
ATOM    150  CA  LEU    57      -4.851 -17.195   5.422  1.00  0.00              
ATOM    151  C   LEU    57      -5.591 -17.887   6.563  1.00  0.00              
ATOM    152  O   LEU    57      -5.454 -19.093   6.753  1.00  0.00              
ATOM    153  N   PRO    58      -6.375 -17.127   7.318  1.00  0.00              
ATOM    154  CA  PRO    58      -7.119 -17.696   8.416  1.00  0.00              
ATOM    155  C   PRO    58      -8.596 -17.436   8.286  1.00  0.00              
ATOM    156  O   PRO    58      -9.017 -16.414   7.746  1.00  0.00              
ATOM    157  N   VAL    59      -9.380 -18.362   8.790  1.00  0.00              
ATOM    158  CA  VAL    59     -10.830 -18.243   8.743  1.00  0.00              
ATOM    159  C   VAL    59     -11.466 -18.851   9.984  1.00  0.00              
ATOM    160  O   VAL    59     -11.058 -19.924  10.427  1.00  0.00              
ATOM    161  N   LYS    60     -12.498 -18.203  10.550  1.00  0.00              
ATOM    162  CA  LYS    60     -13.185 -18.741  11.719  1.00  0.00              
ATOM    163  C   LYS    60     -13.638 -20.182  11.489  1.00  0.00              
ATOM    164  O   LYS    60     -13.951 -20.901  12.437  1.00  0.00              
ATOM    165  N   GLY    61     -13.686 -20.594  10.218  1.00  0.00              
ATOM    166  CA  GLY    61     -14.119 -21.942   9.874  1.00  0.00              
ATOM    167  C   GLY    61     -12.925 -22.866   9.643  1.00  0.00              
ATOM    168  O   GLY    61     -13.046 -24.088   9.746  1.00  0.00              
ATOM    169  N   VAL    62     -11.774 -22.279   9.334  1.00  0.00              
ATOM    170  CA  VAL    62     -10.577 -23.066   9.098  1.00  0.00              
ATOM    171  C   VAL    62      -9.511 -22.296   8.346  1.00  0.00              
ATOM    172  O   VAL    62      -9.796 -21.656   7.335  1.00  0.00              
ATOM    173  N   GLU    63      -8.280 -22.359   8.845  1.00  0.00              
ATOM    174  CA  GLU    63      -7.161 -21.663   8.224  1.00  0.00              
ATOM    175  C   GLU    63      -7.020 -22.040   6.753  1.00  0.00              
ATOM    176  O   GLU    63      -7.128 -23.210   6.388  1.00  0.00              
ATOM    177  N   MET    64      -6.762 -21.041   5.915  1.00  0.00              
ATOM    178  CA  MET    64      -6.585 -21.269   4.488  1.00  0.00              
ATOM    179  C   MET    64      -5.112 -21.450   4.155  1.00  0.00              
ATOM    180  O   MET    64      -4.256 -20.757   4.701  1.00  0.00              
END
