
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0309AL381_3
# Molecule2: number of CA atoms   62 (  501),  selected   62 , name T0309.pdb
# PARAMETERS: T0309AL381_3.T0309.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    D      16      A       2           -
LGA    -       -      S       3           -
LGA    -       -      K       4           -
LGA    -       -      K       5           -
LGA    -       -      V       6           -
LGA    -       -      H       7           -
LGA    -       -      Q       8           -
LGA    -       -      I       9           -
LGA    -       -      N      10           -
LGA    -       -      V      11           -
LGA    -       -      K      12           -
LGA    -       -      G      13           -
LGA    -       -      F      14           -
LGA    -       -      F      15           -
LGA    -       -      D      16           -
LGA    -       -      M      17           -
LGA    M      17      D      18          2.618
LGA    D      18      V      19          2.880
LGA    V      19      M      20          2.112
LGA    M      20      E      21          1.333
LGA    E      21      V      22          2.758
LGA    V      22      T      23          2.527
LGA    T      23      E      24          3.233
LGA    E      24      Q      25          3.115
LGA    Q      25      T      26          1.484
LGA    T      26      K      27          1.474
LGA    K      27      E      28          2.520
LGA    E      28      A      29          4.385
LGA    A      29      E      30          2.754
LGA    E      30      Y      31          1.781
LGA    Y      31      T      32          1.590
LGA    T      32      Y      33          2.226
LGA    Y      33      D      34          1.814
LGA    D      34      F      35          2.224
LGA    F      35      K      36          3.422
LGA    K      36      E      37          3.068
LGA    -       -      I      38           -
LGA    -       -      L      39           -
LGA    -       -      S      40           -
LGA    E      37      E      41          2.944
LGA    I      38      F      42          3.926
LGA    -       -      N      43           -
LGA    -       -      G      44           -
LGA    -       -      K      45           -
LGA    -       -      N      46           -
LGA    L      39      V      47           #
LGA    S      40      -       -           -
LGA    E      41      -       -           -
LGA    F      42      -       -           -
LGA    N      43      -       -           -
LGA    G      44      -       -           -
LGA    K      45      S      48          4.705
LGA    N      46      I      49          2.873
LGA    V      47      T      50           -
LGA    S      48      V      51           -
LGA    I      49      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)   34   62    5.0     24    2.80     4.17     29.900     0.829

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.205413 * X  +  -0.329136 * Y  +   0.921670 * Z  +  50.699730
  Y_new =  -0.364108 * X  +   0.899851 * Y  +   0.240195 * Z  + -52.691551
  Z_new =  -0.908422 * X  +  -0.286248 * Y  +  -0.304682 * Z  + 131.512177 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.387380    0.754212  [ DEG:  -136.7868     43.2132 ]
  Theta =   1.139494    2.002098  [ DEG:    65.2882    114.7118 ]
  Phi   =  -2.084443    1.057150  [ DEG:  -119.4298     60.5702 ]
 
# 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: T0309AL381_3                                  
REMARK     2: T0309.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0309AL381_3.T0309.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34   62   5.0   24   2.80    4.17  29.900
REMARK  ---------------------------------------------------------- 
MOLECULE T0309AL381_3
REMARK Aligment from pdb entry: 1tf7A
ATOM      1  N   ASP    16       4.170   2.429 -10.230  1.00  0.00              
ATOM      2  CA  ASP    16       2.996   1.966  -9.503  1.00  0.00              
ATOM      3  C   ASP    16       3.399   1.297  -8.179  1.00  0.00              
ATOM      4  O   ASP    16       4.388   0.576  -8.122  1.00  0.00              
ATOM      5  N   MET    17       2.636   1.534  -7.117  1.00  0.00              
ATOM      6  CA  MET    17       2.943   0.944  -5.814  1.00  0.00              
ATOM      7  C   MET    17       2.125  -0.324  -5.557  1.00  0.00              
ATOM      8  O   MET    17       2.232  -0.936  -4.492  1.00  0.00              
ATOM      9  N   ASP    18       1.310  -0.720  -6.524  1.00  0.00              
ATOM     10  CA  ASP    18       0.460  -1.889  -6.349  1.00  0.00              
ATOM     11  C   ASP    18       1.138  -3.235  -6.557  1.00  0.00              
ATOM     12  O   ASP    18       2.045  -3.377  -7.380  1.00  0.00              
ATOM     13  N   VAL    19       0.683  -4.219  -5.789  1.00  0.00              
ATOM     14  CA  VAL    19       1.186  -5.579  -5.886  1.00  0.00              
ATOM     15  C   VAL    19       0.121  -6.291  -6.712  1.00  0.00              
ATOM     16  O   VAL    19      -0.841  -6.843  -6.177  1.00  0.00              
ATOM     17  N   MET    20       0.302  -6.246  -8.030  1.00  0.00              
ATOM     18  CA  MET    20      -0.632  -6.833  -8.989  1.00  0.00              
ATOM     19  C   MET    20      -0.440  -8.322  -9.223  1.00  0.00              
ATOM     20  O   MET    20       0.683  -8.801  -9.333  1.00  0.00              
ATOM     21  N   GLU    21      -1.539  -9.059  -9.295  1.00  0.00              
ATOM     22  CA  GLU    21      -1.431 -10.484  -9.548  1.00  0.00              
ATOM     23  C   GLU    21      -1.330 -10.622 -11.053  1.00  0.00              
ATOM     24  O   GLU    21      -1.837  -9.781 -11.791  1.00  0.00              
ATOM     25  N   VAL    22      -0.663 -11.670 -11.508  1.00  0.00              
ATOM     26  CA  VAL    22      -0.525 -11.877 -12.932  1.00  0.00              
ATOM     27  C   VAL    22      -0.507 -13.361 -13.244  1.00  0.00              
ATOM     28  O   VAL    22      -0.024 -14.170 -12.451  1.00  0.00              
ATOM     29  N   THR    23      -1.066 -13.709 -14.398  1.00  0.00              
ATOM     30  CA  THR    23      -1.129 -15.087 -14.855  1.00  0.00              
ATOM     31  C   THR    23      -0.149 -15.245 -15.999  1.00  0.00              
ATOM     32  O   THR    23       0.348 -14.260 -16.544  1.00  0.00              
ATOM     33  N   GLU    24       0.130 -16.487 -16.361  1.00  0.00              
ATOM     34  CA  GLU    24       1.043 -16.768 -17.455  1.00  0.00              
ATOM     35  C   GLU    24       0.319 -17.688 -18.423  1.00  0.00              
ATOM     36  O   GLU    24      -0.255 -18.695 -18.017  1.00  0.00              
ATOM     37  N   GLN    25       0.329 -17.320 -19.701  1.00  0.00              
ATOM     38  CA  GLN    25      -0.341 -18.101 -20.735  1.00  0.00              
ATOM     39  C   GLN    25       0.549 -18.251 -21.959  1.00  0.00              
ATOM     40  O   GLN    25       1.735 -17.930 -21.921  1.00  0.00              
ATOM     41  N   THR    26      -0.035 -18.735 -23.047  1.00  0.00              
ATOM     42  CA  THR    26       0.704 -18.911 -24.288  1.00  0.00              
ATOM     43  C   THR    26       1.077 -17.531 -24.808  1.00  0.00              
ATOM     44  O   THR    26       2.137 -17.340 -25.408  1.00  0.00              
ATOM     45  N   LYS    27       0.196 -16.567 -24.565  1.00  0.00              
ATOM     46  CA  LYS    27       0.422 -15.198 -24.999  1.00  0.00              
ATOM     47  C   LYS    27       1.585 -14.570 -24.227  1.00  0.00              
ATOM     48  O   LYS    27       2.332 -13.749 -24.763  1.00  0.00              
ATOM     49  N   GLU    28       1.746 -14.978 -22.971  1.00  0.00              
ATOM     50  CA  GLU    28       2.812 -14.444 -22.142  1.00  0.00              
ATOM     51  C   GLU    28       2.296 -14.015 -20.780  1.00  0.00              
ATOM     52  O   GLU    28       1.486 -14.715 -20.178  1.00  0.00              
ATOM     53  N   ALA    29       2.744 -12.864 -20.266  1.00  0.00              
ATOM     54  CA  ALA    29       2.319 -12.349 -18.958  1.00  0.00              
ATOM     55  C   ALA    29       1.178 -11.331 -18.979  1.00  0.00              
ATOM     56  O   ALA    29       1.226 -10.344 -19.709  1.00  0.00              
ATOM     57  N   GLU    30       0.165 -11.563 -18.154  1.00  0.00              
ATOM     58  CA  GLU    30      -0.962 -10.648 -18.083  1.00  0.00              
ATOM     59  C   GLU    30      -1.097 -10.094 -16.679  1.00  0.00              
ATOM     60  O   GLU    30      -1.550 -10.791 -15.779  1.00  0.00              
ATOM     61  N   TYR    31      -0.709  -8.837 -16.496  1.00  0.00              
ATOM     62  CA  TYR    31      -0.797  -8.198 -15.184  1.00  0.00              
ATOM     63  C   TYR    31      -2.199  -7.679 -14.905  1.00  0.00              
ATOM     64  O   TYR    31      -2.656  -6.721 -15.529  1.00  0.00              
ATOM     65  N   THR    32      -2.868  -8.305 -13.947  1.00  0.00              
ATOM     66  CA  THR    32      -4.221  -7.920 -13.578  1.00  0.00              
ATOM     67  C   THR    32      -4.277  -6.892 -12.443  1.00  0.00              
ATOM     68  O   THR    32      -3.551  -5.894 -12.465  1.00  0.00              
ATOM     69  N   TYR    33      -5.142  -7.133 -11.459  1.00  0.00              
ATOM     70  CA  TYR    33      -5.301  -6.205 -10.344  1.00  0.00              
ATOM     71  C   TYR    33      -4.599  -6.627  -9.068  1.00  0.00              
ATOM     72  O   TYR    33      -4.051  -7.728  -8.974  1.00  0.00              
ATOM     73  N   ASP    34      -4.631  -5.733  -8.085  1.00  0.00              
ATOM     74  CA  ASP    34      -4.020  -5.978  -6.786  1.00  0.00              
ATOM     75  C   ASP    34      -5.024  -6.698  -5.893  1.00  0.00              
ATOM     76  O   ASP    34      -6.201  -6.799  -6.231  1.00  0.00              
ATOM     77  N   PHE    35      -4.554  -7.208  -4.760  1.00  0.00              
ATOM     78  CA  PHE    35      -5.436  -7.888  -3.826  1.00  0.00              
ATOM     79  C   PHE    35      -5.773  -6.868  -2.751  1.00  0.00              
ATOM     80  O   PHE    35      -5.268  -6.936  -1.632  1.00  0.00              
ATOM     81  N   LYS    36      -6.625  -5.913  -3.101  1.00  0.00              
ATOM     82  CA  LYS    36      -7.004  -4.862  -2.169  1.00  0.00              
ATOM     83  C   LYS    36      -7.655  -5.386  -0.895  1.00  0.00              
ATOM     84  O   LYS    36      -7.550  -4.767   0.162  1.00  0.00              
ATOM     85  N   GLU    37      -8.318  -6.528  -0.997  1.00  0.00              
ATOM     86  CA  GLU    37      -9.015  -7.111   0.140  1.00  0.00              
ATOM     87  C   GLU    37      -8.234  -8.146   0.951  1.00  0.00              
ATOM     88  O   GLU    37      -8.825  -9.016   1.592  1.00  0.00              
ATOM     89  N   ILE    38      -6.910  -8.047   0.938  1.00  0.00              
ATOM     90  CA  ILE    38      -6.080  -8.985   1.682  1.00  0.00              
ATOM     91  C   ILE    38      -5.069  -8.310   2.597  1.00  0.00              
ATOM     92  O   ILE    38      -4.743  -7.130   2.436  1.00  0.00              
ATOM     93  N   LEU    39      -4.575  -9.085   3.557  1.00  0.00              
ATOM     94  CA  LEU    39      -3.571  -8.626   4.504  1.00  0.00              
ATOM     95  C   LEU    39      -2.403  -9.606   4.487  1.00  0.00              
ATOM     96  O   LEU    39      -2.584 -10.789   4.180  1.00  0.00              
ATOM     97  N   SER    40      -1.210  -9.117   4.816  1.00  0.00              
ATOM     98  CA  SER    40      -0.014  -9.960   4.841  1.00  0.00              
ATOM     99  C   SER    40       0.131 -10.710   3.530  1.00  0.00              
ATOM    100  O   SER    40       0.100 -11.937   3.509  1.00  0.00              
ATOM    101  N   GLU    41       0.278  -9.969   2.439  1.00  0.00              
ATOM    102  CA  GLU    41       0.425 -10.577   1.127  1.00  0.00              
ATOM    103  C   GLU    41       1.901 -10.838   0.864  1.00  0.00              
ATOM    104  O   GLU    41       2.275 -11.863   0.283  1.00  0.00              
ATOM    105  N   PHE    42       2.738  -9.909   1.313  1.00  0.00              
ATOM    106  CA  PHE    42       4.182 -10.032   1.142  1.00  0.00              
ATOM    107  C   PHE    42       4.664 -11.387   1.641  1.00  0.00              
ATOM    108  O   PHE    42       5.620 -11.950   1.106  1.00  0.00              
ATOM    109  N   ASN    43       3.978 -11.903   2.656  1.00  0.00              
ATOM    110  CA  ASN    43       4.320 -13.178   3.270  1.00  0.00              
ATOM    111  C   ASN    43       4.083 -14.416   2.402  1.00  0.00              
ATOM    112  O   ASN    43       4.720 -15.447   2.606  1.00  0.00              
ATOM    113  N   GLY    44       3.177 -14.328   1.439  1.00  0.00              
ATOM    114  CA  GLY    44       2.927 -15.482   0.595  1.00  0.00              
ATOM    115  C   GLY    44       1.660 -16.232   0.965  1.00  0.00              
ATOM    116  O   GLY    44       1.129 -16.992   0.156  1.00  0.00              
ATOM    117  N   LYS    45       1.185 -16.038   2.194  1.00  0.00              
ATOM    118  CA  LYS    45      -0.043 -16.679   2.658  1.00  0.00              
ATOM    119  C   LYS    45      -0.906 -15.594   3.277  1.00  0.00              
ATOM    120  O   LYS    45      -0.901 -15.396   4.494  1.00  0.00              
ATOM    121  N   ASN    46      -1.667 -14.872   2.433  1.00  0.00              
ATOM    122  CA  ASN    46      -2.557 -13.778   2.832  1.00  0.00              
ATOM    123  C   ASN    46      -3.677 -14.171   3.769  1.00  0.00              
ATOM    124  O   ASN    46      -3.862 -15.339   4.095  1.00  0.00              
ATOM    125  N   VAL    47      -4.424 -13.162   4.188  1.00  0.00              
ATOM    126  CA  VAL    47      -5.560 -13.339   5.068  1.00  0.00              
ATOM    127  C   VAL    47      -6.706 -12.541   4.458  1.00  0.00              
ATOM    128  O   VAL    47      -6.770 -11.320   4.611  1.00  0.00              
ATOM    129  N   SER    48      -7.590 -13.230   3.744  1.00  0.00              
ATOM    130  CA  SER    48      -8.737 -12.585   3.114  1.00  0.00              
ATOM    131  C   SER    48      -9.526 -11.832   4.170  1.00  0.00              
ATOM    132  O   SER    48      -9.641 -12.282   5.309  1.00  0.00              
ATOM    133  N   ILE    49     -10.064 -10.681   3.794  1.00  0.00              
ATOM    134  CA  ILE    49     -10.845  -9.884   4.726  1.00  0.00              
ATOM    135  C   ILE    49     -11.940  -9.101   4.001  1.00  0.00              
ATOM    136  O   ILE    49     -13.063  -9.012   4.551  1.00  0.00              
END
