
#######################################################
#                                                     #
#                        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   38 (  152),  selected   38 , name T0358AL243_5-D1
# Molecule2: number of CA atoms   65 ( 1035),  selected   65 , name T0358_D1.pdb
# PARAMETERS: T0358AL243_5-D1.T0358_D1.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    G      10      -       -           -
LGA    P      11      -       -           -
LGA    F      12      -       -           -
LGA    T      13      -       -           -
LGA    R      14      -       -           -
LGA    R      15      -       -           -
LGA    Q      16      -       -           -
LGA    A      17      -       -           -
LGA    Q      18      -       -           -
LGA    A      19      -       -           -
LGA    V      20      -       -           -
LGA    T      21      -       -           -
LGA    T      22      G      10          2.924
LGA    T      23      P      11          2.658
LGA    S      25      F      12          3.413
LGA    N      26      T      13          2.856
LGA    I      27      R      14          5.278
LGA    -       -      R      15           -
LGA    T      28      Q      16          2.873
LGA    L      29      A      17          3.733
LGA    E      30      Q      18          4.550
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    -       -      T      28           -
LGA    D      31      L      29          4.777
LGA    -       -      E      30           -
LGA    -       -      D      31           -
LGA    D      32      D      32          4.316
LGA    Q      33      Q      33           #
LGA    G      34      G      34          0.919
LGA    S      35      S      35          4.150
LGA    H      36      H      36          1.673
LGA    F      37      F      37          1.868
LGA    R      38      R      38          3.204
LGA    L      39      L      39          2.698
LGA    V      40      V      40          1.746
LGA    V      41      V      41          1.432
LGA    R      42      R      42          3.400
LGA    D      43      D      43          2.240
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    E      45      R      47          3.354
LGA    G      46      M      48          2.441
LGA    R      47      V      49          2.508
LGA    M      48      W      50          3.115
LGA    -       -      R      51           -
LGA    V      49      A      52          2.733
LGA    -       -      W      53           -
LGA    -       -      N      54           -
LGA    -       -      F      55           -
LGA    -       -      E      56           -
LGA    -       -      P      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    -       -      G      62           -
LGA    -       -      L      63           -
LGA    -       -      N      64           -
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    -       -      I      67           -
LGA    -       -      R      68           -
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   38   65    5.0     25    3.17    44.00     24.452     0.764

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.448863 * X  +  -0.185216 * Y  +  -0.874195 * Z  +  40.332596
  Y_new =   0.884891 * X  +   0.044120 * Y  +  -0.463703 * Z  +  45.373077
  Z_new =   0.124455 * X  +  -0.981707 * Y  +   0.144093 * Z  +  19.607450 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.425059    1.716533  [ DEG:   -81.6499     98.3501 ]
  Theta =  -0.124778   -3.016815  [ DEG:    -7.1493   -172.8507 ]
  Phi   =   2.040229   -1.101364  [ DEG:   116.8965    -63.1035 ]
 
# 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: T0358AL243_5-D1                               
REMARK     2: T0358_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358AL243_5-D1.T0358_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   38   65   5.0   25   3.17   44.00  24.452
REMARK  ---------------------------------------------------------- 
MOLECULE T0358AL243_5-D1
REMARK Aligment from pdb entry: 1k8wA
ATOM     25  N   GLY    10     -10.233  14.218   4.840  1.00  0.00              
ATOM     26  CA  GLY    10      -9.679  15.482   4.342  1.00  0.00              
ATOM     27  C   GLY    10      -8.972  15.319   2.990  1.00  0.00              
ATOM     28  O   GLY    10      -8.843  16.279   2.222  1.00  0.00              
ATOM     29  N   PRO    11      -3.987   1.127  -3.345  1.00  0.00              
ATOM     30  CA  PRO    11      -3.910   0.042  -2.381  1.00  0.00              
ATOM     31  C   PRO    11      -2.650  -0.784  -2.590  1.00  0.00              
ATOM     32  O   PRO    11      -2.279  -1.096  -3.721  1.00  0.00              
ATOM     33  N   PHE    12      -1.996  -1.128  -1.488  1.00  0.00              
ATOM     34  CA  PHE    12      -0.769  -1.914  -1.531  1.00  0.00              
ATOM     35  C   PHE    12      -0.932  -3.215  -0.767  1.00  0.00              
ATOM     36  O   PHE    12      -1.513  -3.236   0.318  1.00  0.00              
ATOM     37  N   THR    13      -0.426  -4.325  -1.327  1.00  0.00              
ATOM     38  CA  THR    13      -0.550  -5.593  -0.608  1.00  0.00              
ATOM     39  C   THR    13       0.361  -5.453   0.610  1.00  0.00              
ATOM     40  O   THR    13       1.356  -4.729   0.554  1.00  0.00              
ATOM     41  N   ARG    14       0.027  -6.124   1.706  1.00  0.00              
ATOM     42  CA  ARG    14       0.833  -6.023   2.918  1.00  0.00              
ATOM     43  C   ARG    14       2.320  -6.290   2.684  1.00  0.00              
ATOM     44  O   ARG    14       3.170  -5.785   3.421  1.00  0.00              
ATOM     45  N   ARG    15       2.633  -7.074   1.655  1.00  0.00              
ATOM     46  CA  ARG    15       4.020  -7.394   1.334  1.00  0.00              
ATOM     47  C   ARG    15       4.767  -6.177   0.796  1.00  0.00              
ATOM     48  O   ARG    15       5.997  -6.155   0.776  1.00  0.00              
ATOM     49  N   GLN    16       4.019  -5.168   0.359  1.00  0.00              
ATOM     50  CA  GLN    16       4.617  -3.944  -0.164  1.00  0.00              
ATOM     51  C   GLN    16       4.555  -2.823   0.871  1.00  0.00              
ATOM     52  O   GLN    16       5.473  -2.010   0.970  1.00  0.00              
ATOM     53  N   ALA    17       3.472  -2.786   1.642  1.00  0.00              
ATOM     54  CA  ALA    17       3.293  -1.747   2.649  1.00  0.00              
ATOM     55  C   ALA    17       4.336  -1.790   3.762  1.00  0.00              
ATOM     56  O   ALA    17       4.630  -0.768   4.378  1.00  0.00              
ATOM     57  N   GLN    18       4.891  -2.966   4.033  1.00  0.00              
ATOM     58  CA  GLN    18       5.896  -3.068   5.085  1.00  0.00              
ATOM     59  C   GLN    18       7.114  -2.205   4.737  1.00  0.00              
ATOM     60  O   GLN    18       7.689  -1.540   5.604  1.00  0.00              
ATOM     61  N   ALA    19       7.492  -2.196   3.464  1.00  0.00              
ATOM     62  CA  ALA    19       8.620  -1.387   3.025  1.00  0.00              
ATOM     63  C   ALA    19       8.204   0.081   2.992  1.00  0.00              
ATOM     64  O   ALA    19       8.965   0.966   3.386  1.00  0.00              
ATOM     65  N   VAL    20       6.981   0.322   2.528  1.00  0.00              
ATOM     66  CA  VAL    20       6.423   1.668   2.438  1.00  0.00              
ATOM     67  C   VAL    20       6.454   2.354   3.800  1.00  0.00              
ATOM     68  O   VAL    20       6.866   3.509   3.918  1.00  0.00              
ATOM     69  N   THR    21       6.015   1.635   4.829  1.00  0.00              
ATOM     70  CA  THR    21       5.987   2.186   6.178  1.00  0.00              
ATOM     71  C   THR    21       7.373   2.357   6.786  1.00  0.00              
ATOM     72  O   THR    21       7.513   2.927   7.866  1.00  0.00              
ATOM     73  N   THR    22       8.392   1.854   6.096  1.00  0.00              
ATOM     74  CA  THR    22       9.770   1.999   6.557  1.00  0.00              
ATOM     75  C   THR    22      10.422   3.160   5.808  1.00  0.00              
ATOM     76  O   THR    22      11.633   3.366   5.889  1.00  0.00              
ATOM     77  N   THR    23       9.605   3.906   5.066  1.00  0.00              
ATOM     78  CA  THR    23      10.104   5.057   4.330  1.00  0.00              
ATOM     79  C   THR    23      10.577   4.783   2.917  1.00  0.00              
ATOM     80  O   THR    23      11.158   5.661   2.274  1.00  0.00              
ATOM     81  N   SER    25      10.322   3.577   2.422  1.00  0.00              
ATOM     82  CA  SER    25      10.747   3.203   1.078  1.00  0.00              
ATOM     83  C   SER    25       9.655   3.364   0.028  1.00  0.00              
ATOM     84  O   SER    25       8.513   2.970   0.243  1.00  0.00              
ATOM     85  N   ASN    26       9.994   3.964  -1.123  1.00  0.00              
ATOM     86  CA  ASN    26       9.005   4.140  -2.189  1.00  0.00              
ATOM     87  C   ASN    26       8.742   2.740  -2.745  1.00  0.00              
ATOM     88  O   ASN    26       9.651   1.908  -2.771  1.00  0.00              
ATOM     89  N   ILE    27       7.516   2.468  -3.178  1.00  0.00              
ATOM     90  CA  ILE    27       7.193   1.148  -3.708  1.00  0.00              
ATOM     91  C   ILE    27       6.405   1.206  -5.012  1.00  0.00              
ATOM     92  O   ILE    27       5.713   2.186  -5.289  1.00  0.00              
ATOM     93  N   THR    28       6.520   0.150  -5.812  1.00  0.00              
ATOM     94  CA  THR    28       5.799   0.076  -7.076  1.00  0.00              
ATOM     95  C   THR    28       4.503  -0.696  -6.895  1.00  0.00              
ATOM     96  O   THR    28       4.452  -1.679  -6.153  1.00  0.00              
ATOM     97  N   LEU    29       3.455  -0.242  -7.573  1.00  0.00              
ATOM     98  CA  LEU    29       2.153  -0.891  -7.489  1.00  0.00              
ATOM     99  C   LEU    29       1.420  -0.778  -8.818  1.00  0.00              
ATOM    100  O   LEU    29       1.675   0.137  -9.601  1.00  0.00              
ATOM    101  N   GLU    30       0.512  -1.716  -9.066  1.00  0.00              
ATOM    102  CA  GLU    30      -0.262  -1.738 -10.302  1.00  0.00              
ATOM    103  C   GLU    30      -1.012  -0.431 -10.539  1.00  0.00              
ATOM    104  O   GLU    30      -0.580   0.411 -11.326  1.00  0.00              
ATOM    105  N   ASP    31      -2.141  -0.269  -9.855  1.00  0.00              
ATOM    106  CA  ASP    31      -2.934   0.936 -10.012  1.00  0.00              
ATOM    107  C   ASP    31      -2.325   2.135  -9.312  1.00  0.00              
ATOM    108  O   ASP    31      -2.460   2.288  -8.098  1.00  0.00              
ATOM    109  N   ASP    32      -1.403   6.486 -10.243  1.00  0.00              
ATOM    110  CA  ASP    32      -1.362   7.619 -11.173  1.00  0.00              
ATOM    111  C   ASP    32       0.060   7.986 -11.579  1.00  0.00              
ATOM    112  O   ASP    32       1.026   7.558 -10.950  1.00  0.00              
ATOM    113  N   GLN    33       0.181   8.782 -12.635  1.00  0.00              
ATOM    114  CA  GLN    33       1.486   9.197 -13.128  1.00  0.00              
ATOM    115  C   GLN    33       2.144  10.232 -12.223  1.00  0.00              
ATOM    116  O   GLN    33       3.354  10.442 -12.293  1.00  0.00              
ATOM    117  N   GLY    34       1.348  10.881 -11.378  1.00  0.00              
ATOM    118  CA  GLY    34       1.889  11.890 -10.473  1.00  0.00              
ATOM    119  C   GLY    34       0.874  12.372  -9.442  1.00  0.00              
ATOM    120  O   GLY    34      -0.260  11.892  -9.388  1.00  0.00              
ATOM    121  N   SER    35       1.302  13.327  -8.623  1.00  0.00              
ATOM    122  CA  SER    35       0.437  13.885  -7.601  1.00  0.00              
ATOM    123  C   SER    35       0.383  13.081  -6.317  1.00  0.00              
ATOM    124  O   SER    35       0.997  12.017  -6.202  1.00  0.00              
ATOM    125  N   HIS    36      -0.356  13.604  -5.344  1.00  0.00              
ATOM    126  CA  HIS    36      -0.523  12.949  -4.056  1.00  0.00              
ATOM    127  C   HIS    36      -1.556  11.839  -4.188  1.00  0.00              
ATOM    128  O   HIS    36      -2.410  11.883  -5.073  1.00  0.00              
ATOM    129  N   PHE    37      -1.476  10.849  -3.306  1.00  0.00              
ATOM    130  CA  PHE    37      -2.421   9.738  -3.311  1.00  0.00              
ATOM    131  C   PHE    37      -2.620   9.183  -1.909  1.00  0.00              
ATOM    132  O   PHE    37      -1.705   9.207  -1.085  1.00  0.00              
ATOM    133  N   ARG    38      -3.827   8.702  -1.636  1.00  0.00              
ATOM    134  CA  ARG    38      -4.120   8.096  -0.349  1.00  0.00              
ATOM    135  C   ARG    38      -3.674   6.648  -0.498  1.00  0.00              
ATOM    136  O   ARG    38      -3.920   6.026  -1.532  1.00  0.00              
ATOM    137  N   LEU    39      -3.010   6.115   0.520  1.00  0.00              
ATOM    138  CA  LEU    39      -2.522   4.742   0.461  1.00  0.00              
ATOM    139  C   LEU    39      -3.183   3.841   1.493  1.00  0.00              
ATOM    140  O   LEU    39      -3.279   4.194   2.669  1.00  0.00              
ATOM    141  N   VAL    40      -3.637   2.673   1.044  1.00  0.00              
ATOM    142  CA  VAL    40      -4.275   1.704   1.927  1.00  0.00              
ATOM    143  C   VAL    40      -3.532   0.369   1.897  1.00  0.00              
ATOM    144  O   VAL    40      -2.753   0.106   0.981  1.00  0.00              
ATOM    145  N   VAL    41      -3.779  -0.465   2.906  1.00  0.00              
ATOM    146  CA  VAL    41      -3.153  -1.783   3.010  1.00  0.00              
ATOM    147  C   VAL    41      -4.128  -2.920   2.738  1.00  0.00              
ATOM    148  O   VAL    41      -5.341  -2.731   2.750  1.00  0.00              
ATOM    149  N   ARG    42      -3.559  -4.105   2.528  1.00  0.00              
ATOM    150  CA  ARG    42      -4.315  -5.323   2.285  1.00  0.00              
ATOM    151  C   ARG    42      -5.721  -5.267   1.718  1.00  0.00              
ATOM    152  O   ARG    42      -6.088  -4.346   0.987  1.00  0.00              
ATOM    153  N   ASP    43      -6.505  -6.287   2.062  1.00  0.00              
ATOM    154  CA  ASP    43      -7.883  -6.419   1.603  1.00  0.00              
ATOM    155  C   ASP    43      -8.831  -5.486   2.348  1.00  0.00              
ATOM    156  O   ASP    43      -9.718  -4.881   1.743  1.00  0.00              
ATOM    157  N   GLU    45      -8.643  -5.374   3.660  1.00  0.00              
ATOM    158  CA  GLU    45      -9.481  -4.512   4.486  1.00  0.00              
ATOM    159  C   GLU    45      -9.405  -3.055   4.029  1.00  0.00              
ATOM    160  O   GLU    45     -10.181  -2.214   4.485  1.00  0.00              
ATOM    161  N   GLY    46      -8.466  -2.767   3.129  1.00  0.00              
ATOM    162  CA  GLY    46      -8.304  -1.417   2.615  1.00  0.00              
ATOM    163  C   GLY    46      -8.041  -0.374   3.688  1.00  0.00              
ATOM    164  O   GLY    46      -8.573   0.734   3.629  1.00  0.00              
ATOM    165  N   ARG    47      -7.214  -0.725   4.668  1.00  0.00              
ATOM    166  CA  ARG    47      -6.887   0.187   5.757  1.00  0.00              
ATOM    167  C   ARG    47      -6.020   1.346   5.273  1.00  0.00              
ATOM    168  O   ARG    47      -5.032   1.142   4.571  1.00  0.00              
ATOM    169  N   MET    48      -6.407   2.562   5.648  1.00  0.00              
ATOM    170  CA  MET    48      -5.668   3.764   5.275  1.00  0.00              
ATOM    171  C   MET    48      -4.406   3.846   6.130  1.00  0.00              
ATOM    172  O   MET    48      -4.481   3.745   7.352  1.00  0.00              
ATOM    173  N   VAL    49      -3.251   4.029   5.498  1.00  0.00              
ATOM    174  CA  VAL    49      -2.010   4.125   6.255  1.00  0.00              
ATOM    175  C   VAL    49      -1.308   5.470   6.086  1.00  0.00              
ATOM    176  O   VAL    49      -0.284   5.722   6.719  1.00  0.00              
END
