
#######################################################
#                                                     #
#                        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   46 (  184),  selected   46 , name T0299AL381_4-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299AL381_4-D1.T0299_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    E      23      M       1           -
LGA    L      24      T       2           -
LGA    R      25      R       3           -
LGA    Q      26      Y       4           -
LGA    E      27      A       5           -
LGA    L      28      L       6           -
LGA    T      29      L       7           -
LGA    N      30      V       8           -
LGA    L      31      -       -           -
LGA    G      32      -       -           -
LGA    L      33      -       -           -
LGA    E      34      -       -           -
LGA    K      35      -       -           -
LGA    V      36      -       -           -
LGA    E      37      R       9          3.766
LGA    S      38      G      10          2.130
LGA    Y      39      I      11          4.525
LGA    -       -      N      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    -       -      V      19           -
LGA    -       -      V      20           -
LGA    -       -      M      21           -
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    -       -      L      24           -
LGA    -       -      R      25           -
LGA    -       -      Q      26           -
LGA    -       -      E      27           -
LGA    -       -      L      28           -
LGA    -       -      T      29           -
LGA    -       -      N      30           -
LGA    -       -      L      31           -
LGA    -       -      G      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    -       -      E      37           -
LGA    -       -      S      38           -
LGA    -       -      Y      39           -
LGA    -       -      I      40           -
LGA    -       -      N      41           -
LGA    -       -      S      42           -
LGA    I      40      G      43          3.432
LGA    N      41      N      44          4.843
LGA    S      42      I      45          1.569
LGA    G      43      F      46          2.793
LGA    N      44      F      47          1.733
LGA    I      45      T      48          2.919
LGA    F      46      S      49           #
LGA    F      47      I      50           -
LGA    -       -      D      51           -
LGA    T      48      S      52          5.031
LGA    S      49      K      53          2.951
LGA    I      50      A      54          2.630
LGA    D      51      Q      55          1.834
LGA    S      52      L      56          1.302
LGA    K      53      V      57          1.273
LGA    A      54      E      58          0.748
LGA    Q      55      K      59          0.707
LGA    L      56      L      60          0.769
LGA    V      57      E      61          0.960
LGA    E      58      T      62          1.166
LGA    P      69      F      63          1.159
LGA    F      70      F      64          1.821
LGA    -       -      A      65           -
LGA    -       -      V      66           -
LGA    -       -      H      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      F      70           -
LGA    I      71      I      71          1.233
LGA    Q      72      Q      72          5.129
LGA    S      73      S      73          2.946
LGA    -       -      F      74           -
LGA    F      74      S      75          2.101
LGA    S      75      L      76          3.151
LGA    L      76      L      77          5.062
LGA    L      77      S      78           #
LGA    -       -      A     168           -
LGA    -       -      K     169           -
LGA    -       -      T     170           -
LGA    -       -      F     171           -
LGA    -       -      D     172           -
LGA    -       -      K     173           -
LGA    -       -      I     174           -
LGA    -       -      G     175           -
LGA    -       -      Q     176           -
LGA    S      78      M     177          4.024
LGA    -       -      L     178           -
LGA    -       -      K     179           -
LGA    -       -      K     180           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   91    5.0     29    2.91    24.14     21.817     0.964

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.655928 * X  +   0.365520 * Y  +  -0.660419 * Z  + -58.088207
  Y_new =   0.178737 * X  +  -0.925262 * Y  +  -0.334579 * Z  + 119.720840
  Z_new =  -0.733356 * X  +   0.101418 * Y  +  -0.672237 * Z  +  44.218716 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.991855   -0.149737  [ DEG:   171.4207     -8.5793 ]
  Theta =   0.823246    2.318347  [ DEG:    47.1685    132.8315 ]
  Phi   =   0.266036   -2.875556  [ DEG:    15.2428   -164.7572 ]
 
# 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: T0299AL381_4-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL381_4-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   91   5.0   29   2.91   24.14  21.817
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL381_4-D1
REMARK Aligment from pdb entry: 1z5oA
ATOM      1  N   GLU    23      13.928  43.801  -9.651  1.00  0.00              
ATOM      2  CA  GLU    23      14.278  45.075 -10.259  1.00  0.00              
ATOM      3  C   GLU    23      13.703  46.208  -9.419  1.00  0.00              
ATOM      4  O   GLU    23      14.384  47.194  -9.137  1.00  0.00              
ATOM      5  N   LEU    24      12.454  46.058  -8.991  1.00  0.00              
ATOM      6  CA  LEU    24      11.839  47.098  -8.178  1.00  0.00              
ATOM      7  C   LEU    24      12.615  47.294  -6.870  1.00  0.00              
ATOM      8  O   LEU    24      12.784  48.427  -6.424  1.00  0.00              
ATOM      9  N   ARG    25      13.091  46.199  -6.267  1.00  0.00              
ATOM     10  CA  ARG    25      13.840  46.271  -5.009  1.00  0.00              
ATOM     11  C   ARG    25      15.180  46.958  -5.186  1.00  0.00              
ATOM     12  O   ARG    25      15.661  47.637  -4.286  1.00  0.00              
ATOM     13  N   GLN    26      15.788  46.762  -6.345  1.00  0.00              
ATOM     14  CA  GLN    26      17.066  47.390  -6.633  1.00  0.00              
ATOM     15  C   GLN    26      16.851  48.900  -6.674  1.00  0.00              
ATOM     16  O   GLN    26      17.632  49.672  -6.115  1.00  0.00              
ATOM     17  N   GLU    27      15.773  49.317  -7.331  1.00  0.00              
ATOM     18  CA  GLU    27      15.463  50.728  -7.450  1.00  0.00              
ATOM     19  C   GLU    27      15.221  51.333  -6.074  1.00  0.00              
ATOM     20  O   GLU    27      15.696  52.433  -5.761  1.00  0.00              
ATOM     21  N   LEU    28      14.483  50.599  -5.247  1.00  0.00              
ATOM     22  CA  LEU    28      14.177  51.038  -3.893  1.00  0.00              
ATOM     23  C   LEU    28      15.463  51.300  -3.109  1.00  0.00              
ATOM     24  O   LEU    28      15.568  52.287  -2.382  1.00  0.00              
ATOM     25  N   THR    29      16.437  50.410  -3.262  1.00  0.00              
ATOM     26  CA  THR    29      17.709  50.553  -2.565  1.00  0.00              
ATOM     27  C   THR    29      18.529  51.716  -3.140  1.00  0.00              
ATOM     28  O   THR    29      19.074  52.536  -2.401  1.00  0.00              
ATOM     29  N   ASN    30      18.615  51.778  -4.463  1.00  0.00              
ATOM     30  CA  ASN    30      19.364  52.842  -5.099  1.00  0.00              
ATOM     31  C   ASN    30      18.753  54.213  -4.783  1.00  0.00              
ATOM     32  O   ASN    30      19.466  55.215  -4.723  1.00  0.00              
ATOM     33  N   LEU    31      17.441  54.261  -4.559  1.00  0.00              
ATOM     34  CA  LEU    31      16.793  55.535  -4.238  1.00  0.00              
ATOM     35  C   LEU    31      16.677  55.773  -2.723  1.00  0.00              
ATOM     36  O   LEU    31      16.190  56.818  -2.293  1.00  0.00              
ATOM     37  N   GLY    32      17.124  54.799  -1.926  1.00  0.00              
ATOM     38  CA  GLY    32      17.088  54.882  -0.465  1.00  0.00              
ATOM     39  C   GLY    32      15.690  55.197   0.079  1.00  0.00              
ATOM     40  O   GLY    32      15.508  56.090   0.919  1.00  0.00              
ATOM     41  N   LEU    33      14.709  54.446  -0.404  1.00  0.00              
ATOM     42  CA  LEU    33      13.330  54.636  -0.002  1.00  0.00              
ATOM     43  C   LEU    33      12.919  53.555   0.985  1.00  0.00              
ATOM     44  O   LEU    33      13.517  52.477   1.020  1.00  0.00              
ATOM     45  N   GLU    34      11.916  53.841   1.806  1.00  0.00              
ATOM     46  CA  GLU    34      11.428  52.827   2.730  1.00  0.00              
ATOM     47  C   GLU    34      10.341  52.109   1.949  1.00  0.00              
ATOM     48  O   GLU    34       9.528  52.752   1.280  1.00  0.00              
ATOM     49  N   LYS    35      10.310  50.785   2.040  1.00  0.00              
ATOM     50  CA  LYS    35       9.315  50.024   1.304  1.00  0.00              
ATOM     51  C   LYS    35       9.010  48.740   2.041  1.00  0.00              
ATOM     52  O   LYS    35       9.682  48.404   3.018  1.00  0.00              
ATOM     53  N   VAL    36       7.983  48.040   1.563  1.00  0.00              
ATOM     54  CA  VAL    36       7.579  46.754   2.103  1.00  0.00              
ATOM     55  C   VAL    36       7.080  45.947   0.911  1.00  0.00              
ATOM     56  O   VAL    36       6.381  46.471   0.038  1.00  0.00              
ATOM     57  N   GLU    37       7.463  44.680   0.876  1.00  0.00              
ATOM     58  CA  GLU    37       7.093  43.779  -0.192  1.00  0.00              
ATOM     59  C   GLU    37       6.193  42.721   0.400  1.00  0.00              
ATOM     60  O   GLU    37       6.405  42.276   1.522  1.00  0.00              
ATOM     61  N   SER    38       5.182  42.316  -0.354  1.00  0.00              
ATOM     62  CA  SER    38       4.276  41.321   0.163  1.00  0.00              
ATOM     63  C   SER    38       2.965  41.331  -0.579  1.00  0.00              
ATOM     64  O   SER    38       2.889  41.793  -1.712  1.00  0.00              
ATOM     65  N   TYR    39       1.928  40.842   0.088  1.00  0.00              
ATOM     66  CA  TYR    39       0.602  40.728  -0.490  1.00  0.00              
ATOM     67  C   TYR    39      -0.186  42.008  -0.535  1.00  0.00              
ATOM     68  O   TYR    39      -0.341  42.691   0.481  1.00  0.00              
ATOM     69  N   ILE    40      -0.685  42.336  -1.720  1.00  0.00              
ATOM     70  CA  ILE    40      -1.529  43.508  -1.893  1.00  0.00              
ATOM     71  C   ILE    40      -2.901  42.953  -2.257  1.00  0.00              
ATOM     72  O   ILE    40      -3.013  42.037  -3.078  1.00  0.00              
ATOM     73  N   ASN    41      -3.940  43.485  -1.623  1.00  0.00              
ATOM     74  CA  ASN    41      -5.299  43.021  -1.857  1.00  0.00              
ATOM     75  C   ASN    41      -6.198  44.108  -2.434  1.00  0.00              
ATOM     76  O   ASN    41      -6.110  45.275  -2.042  1.00  0.00              
ATOM     77  N   SER    42      -7.068  43.713  -3.357  1.00  0.00              
ATOM     78  CA  SER    42      -7.959  44.665  -4.002  1.00  0.00              
ATOM     79  C   SER    42      -9.438  44.359  -3.792  1.00  0.00              
ATOM     80  O   SER    42      -9.828  43.223  -3.539  1.00  0.00              
ATOM     81  N   GLY    43     -10.251  45.405  -3.901  1.00  0.00              
ATOM     82  CA  GLY    43     -11.685  45.272  -3.751  1.00  0.00              
ATOM     83  C   GLY    43     -12.304  46.499  -4.386  1.00  0.00              
ATOM     84  O   GLY    43     -11.577  47.382  -4.861  1.00  0.00              
ATOM     85  N   ASN    44     -13.630  46.567  -4.407  1.00  0.00              
ATOM     86  CA  ASN    44     -14.292  47.721  -4.989  1.00  0.00              
ATOM     87  C   ASN    44     -14.795  48.715  -3.952  1.00  0.00              
ATOM     88  O   ASN    44     -15.739  49.453  -4.210  1.00  0.00              
ATOM     89  N   ILE    45     -14.172  48.736  -2.776  1.00  0.00              
ATOM     90  CA  ILE    45     -14.579  49.675  -1.727  1.00  0.00              
ATOM     91  C   ILE    45     -13.371  50.414  -1.177  1.00  0.00              
ATOM     92  O   ILE    45     -12.265  49.852  -1.067  1.00  0.00              
ATOM     93  N   PHE    46     -13.583  51.678  -0.836  1.00  0.00              
ATOM     94  CA  PHE    46     -12.519  52.495  -0.274  1.00  0.00              
ATOM     95  C   PHE    46     -12.480  52.131   1.208  1.00  0.00              
ATOM     96  O   PHE    46     -13.470  52.303   1.909  1.00  0.00              
ATOM     97  N   PHE    47     -11.363  51.593   1.684  1.00  0.00              
ATOM     98  CA  PHE    47     -11.282  51.210   3.083  1.00  0.00              
ATOM     99  C   PHE    47     -11.035  52.422   3.976  1.00  0.00              
ATOM    100  O   PHE    47     -10.089  53.186   3.783  1.00  0.00              
ATOM    101  N   THR    48     -11.906  52.574   4.959  1.00  0.00              
ATOM    102  CA  THR    48     -11.886  53.724   5.849  1.00  0.00              
ATOM    103  C   THR    48     -12.151  53.283   7.291  1.00  0.00              
ATOM    104  O   THR    48     -13.065  53.791   7.938  1.00  0.00              
ATOM    105  N   SER    49     -11.360  52.337   7.788  1.00  0.00              
ATOM    106  CA  SER    49     -11.551  51.860   9.147  1.00  0.00              
ATOM    107  C   SER    49     -12.794  51.002   9.339  1.00  0.00              
ATOM    108  O   SER    49     -13.272  50.357   8.414  1.00  0.00              
ATOM    109  N   ILE    50     -13.310  50.987  10.565  1.00  0.00              
ATOM    110  CA  ILE    50     -14.507  50.219  10.909  1.00  0.00              
ATOM    111  C   ILE    50     -14.422  48.737  10.496  1.00  0.00              
ATOM    112  O   ILE    50     -13.338  48.149  10.471  1.00  0.00              
ATOM    113  N   ASP    51     -15.567  48.135  10.183  1.00  0.00              
ATOM    114  CA  ASP    51     -15.611  46.718   9.800  1.00  0.00              
ATOM    115  C   ASP    51     -14.867  46.466   8.486  1.00  0.00              
ATOM    116  O   ASP    51     -14.231  45.422   8.317  1.00  0.00              
ATOM    117  N   SER    52     -14.941  47.429   7.565  1.00  0.00              
ATOM    118  CA  SER    52     -14.268  47.274   6.286  1.00  0.00              
ATOM    119  C   SER    52     -12.805  46.910   6.467  1.00  0.00              
ATOM    120  O   SER    52     -12.312  45.963   5.846  1.00  0.00              
ATOM    121  N   LYS    53     -12.111  47.665   7.317  1.00  0.00              
ATOM    122  CA  LYS    53     -10.706  47.415   7.588  1.00  0.00              
ATOM    123  C   LYS    53     -10.478  46.137   8.409  1.00  0.00              
ATOM    124  O   LYS    53      -9.639  45.304   8.051  1.00  0.00              
ATOM    125  N   ALA    54     -11.237  45.961   9.490  1.00  0.00              
ATOM    126  CA  ALA    54     -11.049  44.791  10.352  1.00  0.00              
ATOM    127  C   ALA    54     -11.270  43.467   9.633  1.00  0.00              
ATOM    128  O   ALA    54     -10.525  42.513   9.837  1.00  0.00              
ATOM    129  N   GLN    55     -12.287  43.413   8.783  1.00  0.00              
ATOM    130  CA  GLN    55     -12.573  42.197   8.051  1.00  0.00              
ATOM    131  C   GLN    55     -11.351  41.869   7.194  1.00  0.00              
ATOM    132  O   GLN    55     -10.925  40.721   7.132  1.00  0.00              
ATOM    133  N   LEU    56     -10.779  42.882   6.546  1.00  0.00              
ATOM    134  CA  LEU    56      -9.599  42.658   5.716  1.00  0.00              
ATOM    135  C   LEU    56      -8.389  42.141   6.519  1.00  0.00              
ATOM    136  O   LEU    56      -7.751  41.150   6.141  1.00  0.00              
ATOM    137  N   VAL    57      -8.086  42.796   7.632  1.00  0.00              
ATOM    138  CA  VAL    57      -6.959  42.375   8.455  1.00  0.00              
ATOM    139  C   VAL    57      -7.160  40.952   8.945  1.00  0.00              
ATOM    140  O   VAL    57      -6.200  40.191   9.066  1.00  0.00              
ATOM    141  N   GLU    58      -8.409  40.584   9.213  1.00  0.00              
ATOM    142  CA  GLU    58      -8.706  39.232   9.673  1.00  0.00              
ATOM    143  C   GLU    58      -8.548  38.175   8.582  1.00  0.00              
ATOM    144  O   GLU    58      -7.944  37.120   8.815  1.00  0.00              
ATOM    145  N   PRO    69      -9.091  38.429   7.396  1.00  0.00              
ATOM    146  CA  PRO    69      -8.956  37.434   6.333  1.00  0.00              
ATOM    147  C   PRO    69      -7.563  37.420   5.718  1.00  0.00              
ATOM    148  O   PRO    69      -7.132  36.407   5.180  1.00  0.00              
ATOM    149  N   PHE    70      -6.854  38.542   5.790  1.00  0.00              
ATOM    150  CA  PHE    70      -5.515  38.622   5.210  1.00  0.00              
ATOM    151  C   PHE    70      -4.562  39.283   6.200  1.00  0.00              
ATOM    152  O   PHE    70      -4.150  40.430   6.029  1.00  0.00              
ATOM    153  N   ILE    71      -1.556  38.931   6.604  1.00  0.00              
ATOM    154  CA  ILE    71      -0.285  39.243   5.975  1.00  0.00              
ATOM    155  C   ILE    71      -0.362  40.335   4.901  1.00  0.00              
ATOM    156  O   ILE    71       0.677  40.756   4.388  1.00  0.00              
ATOM    157  N   GLN    72      -1.568  40.797   4.554  1.00  0.00              
ATOM    158  CA  GLN    72      -1.704  41.845   3.531  1.00  0.00              
ATOM    159  C   GLN    72      -0.963  43.097   3.981  1.00  0.00              
ATOM    160  O   GLN    72      -1.100  43.498   5.119  1.00  0.00              
ATOM    161  N   SER    73      -0.178  43.705   3.092  1.00  0.00              
ATOM    162  CA  SER    73       0.575  44.914   3.433  1.00  0.00              
ATOM    163  C   SER    73      -0.078  46.209   2.944  1.00  0.00              
ATOM    164  O   SER    73       0.267  47.291   3.417  1.00  0.00              
ATOM    165  N   PHE    74      -1.013  46.114   2.004  1.00  0.00              
ATOM    166  CA  PHE    74      -1.680  47.311   1.491  1.00  0.00              
ATOM    167  C   PHE    74      -2.980  46.943   0.795  1.00  0.00              
ATOM    168  O   PHE    74      -3.146  45.796   0.353  1.00  0.00              
ATOM    169  N   SER    75      -3.895  47.914   0.700  1.00  0.00              
ATOM    170  CA  SER    75      -5.189  47.681   0.060  1.00  0.00              
ATOM    171  C   SER    75      -5.536  48.777  -0.939  1.00  0.00              
ATOM    172  O   SER    75      -5.326  49.967  -0.685  1.00  0.00              
ATOM    173  N   LEU    76      -6.063  48.371  -2.088  1.00  0.00              
ATOM    174  CA  LEU    76      -6.466  49.338  -3.084  1.00  0.00              
ATOM    175  C   LEU    76      -7.574  48.754  -3.945  1.00  0.00              
ATOM    176  O   LEU    76      -8.258  47.837  -3.506  1.00  0.00              
ATOM    177  N   LEU    77      -7.755  49.253  -5.160  1.00  0.00              
ATOM    178  CA  LEU    77      -8.891  48.811  -5.969  1.00  0.00              
ATOM    179  C   LEU    77      -8.670  48.323  -7.412  1.00  0.00              
ATOM    180  O   LEU    77      -9.644  48.102  -8.145  1.00  0.00              
ATOM    181  N   SER    78      -7.422  48.139  -7.830  1.00  0.00              
ATOM    182  CA  SER    78      -7.183  47.723  -9.212  1.00  0.00              
ATOM    183  C   SER    78      -6.169  46.618  -9.426  1.00  0.00              
ATOM    184  O   SER    78      -6.307  45.821 -10.350  1.00  0.00              
END
