
#######################################################
#                                                     #
#                        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   43 (  172),  selected   43 , name T0363AL316_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL316_1-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    Q      12      Q      12          0.999
LGA    I      13      I      13          1.824
LGA    N      14      N      14          0.624
LGA    I      15      I      15          0.783
LGA    E      16      E      16          2.320
LGA    I      17      I      17          2.374
LGA    A      18      A      18          2.695
LGA    Y      19      Y      19          2.722
LGA    A      20      A      20          1.729
LGA    F      21      F      21          3.600
LGA    P      22      P      22          3.297
LGA    E      23      E      23           -
LGA    R      24      R      24          3.743
LGA    Y      25      Y      25          4.809
LGA    Y      26      Y      26          6.057
LGA    L      27      L      27           #
LGA    K      28      K      28          1.755
LGA    S      29      S      29          1.035
LGA    F      30      F      30          1.142
LGA    Q      31      Q      31          1.141
LGA    V      32      V      32          1.181
LGA    D      33      D      33          1.149
LGA    E      34      E      34          2.129
LGA    G      35      G      35          0.702
LGA    I      36      I      36          0.405
LGA    T      37      T      37          0.215
LGA    V      38      V      38          0.337
LGA    Q      39      Q      39          0.758
LGA    T      40      T      40          0.939
LGA    A      41      A      41          0.955
LGA    I      42      I      42          0.819
LGA    T      43      T      43          1.134
LGA    Q      44      Q      44          2.219
LGA    I      47      S      45          2.386
LGA    L      48      G      46          1.889
LGA    S      49      -       -           -
LGA    Q      50      I      47           #
LGA    F      51      L      48           #
LGA    P      52      S      49          2.922
LGA    E      53      Q      50          1.460
LGA    I      54      F      51          2.934
LGA    D      55      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    L      56      D      55           #
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   43   46    5.0     36    2.26    86.11     58.688     1.524

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.497266 * X  +  -0.855346 * Y  +  -0.145290 * Z  +  50.557198
  Y_new =   0.794112 * X  +   0.381271 * Y  +   0.473306 * Z  + -26.335800
  Z_new =  -0.349446 * X  +  -0.350736 * Y  +   0.868834 * Z  +  32.677246 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.383679    2.757913  [ DEG:   -21.9832    158.0168 ]
  Theta =   0.356979    2.784613  [ DEG:    20.4534    159.5466 ]
  Phi   =   1.011341   -2.130252  [ DEG:    57.9456   -122.0544 ]
 
# 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: T0363AL316_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL316_1-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   43   46   5.0   36   2.26   86.11  58.688
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL316_1-D1
REMARK Aligment from pdb entry: 1vjk_A
ATOM      1  N   GLN    12      17.439   1.433   9.417  1.00  0.00              
ATOM      2  CA  GLN    12      18.158   2.534   8.682  1.00  0.00              
ATOM      3  C   GLN    12      17.728   3.939   9.136  1.00  0.00              
ATOM      4  O   GLN    12      16.577   4.160   9.554  1.00  0.00              
ATOM      5  N   ILE    13      18.671   4.879   9.064  1.00  0.00              
ATOM      6  CA  ILE    13      18.432   6.292   9.370  1.00  0.00              
ATOM      7  C   ILE    13      18.755   7.067   8.079  1.00  0.00              
ATOM      8  O   ILE    13      19.889   6.998   7.598  1.00  0.00              
ATOM      9  N   ASN    14      17.774   7.771   7.515  1.00  0.00              
ATOM     10  CA  ASN    14      18.004   8.522   6.289  1.00  0.00              
ATOM     11  C   ASN    14      18.091   9.996   6.608  1.00  0.00              
ATOM     12  O   ASN    14      17.128  10.580   7.153  1.00  0.00              
ATOM     13  N   ILE    15      19.230  10.601   6.298  1.00  0.00              
ATOM     14  CA  ILE    15      19.436  12.020   6.567  1.00  0.00              
ATOM     15  C   ILE    15      19.542  12.776   5.259  1.00  0.00              
ATOM     16  O   ILE    15      19.961  12.219   4.217  1.00  0.00              
ATOM     17  N   GLU    16      19.165  14.038   5.276  1.00  0.00              
ATOM     18  CA  GLU    16      19.265  14.907   4.131  1.00  0.00              
ATOM     19  C   GLU    16      20.489  15.757   4.329  1.00  0.00              
ATOM     20  O   GLU    16      20.546  16.550   5.279  1.00  0.00              
ATOM     21  N   ILE    17      21.470  15.620   3.457  1.00  0.00              
ATOM     22  CA  ILE    17      22.693  16.404   3.519  1.00  0.00              
ATOM     23  C   ILE    17      22.611  17.569   2.565  1.00  0.00              
ATOM     24  O   ILE    17      22.310  17.361   1.388  1.00  0.00              
ATOM     25  N   ALA    18      22.843  18.787   3.069  1.00  0.00              
ATOM     26  CA  ALA    18      22.833  19.990   2.231  1.00  0.00              
ATOM     27  C   ALA    18      24.244  20.531   2.186  1.00  0.00              
ATOM     28  O   ALA    18      24.832  20.861   3.232  1.00  0.00              
ATOM     29  N   TYR    19      24.796  20.620   0.987  1.00  0.00              
ATOM     30  CA  TYR    19      26.133  21.182   0.785  1.00  0.00              
ATOM     31  C   TYR    19      26.040  22.640   0.440  1.00  0.00              
ATOM     32  O   TYR    19      25.104  23.074  -0.254  1.00  0.00              
ATOM     33  N   ALA    20      27.047  23.395   0.896  1.00  0.00              
ATOM     34  CA  ALA    20      27.091  24.825   0.664  1.00  0.00              
ATOM     35  C   ALA    20      28.368  25.264   0.002  1.00  0.00              
ATOM     36  O   ALA    20      29.426  24.673   0.207  1.00  0.00              
ATOM     37  N   PHE    21      28.266  26.346  -0.768  1.00  0.00              
ATOM     38  CA  PHE    21      29.430  27.012  -1.347  1.00  0.00              
ATOM     39  C   PHE    21      30.294  26.005  -2.122  1.00  0.00              
ATOM     40  O   PHE    21      29.752  25.242  -2.931  1.00  0.00              
ATOM     41  N   PRO    22      31.614  25.985  -1.899  1.00  0.00              
ATOM     42  CA  PRO    22      32.449  25.148  -2.785  1.00  0.00              
ATOM     43  C   PRO    22      32.186  23.670  -2.607  1.00  0.00              
ATOM     44  O   PRO    22      32.504  22.875  -3.488  1.00  0.00              
ATOM     45  N   GLU    23      31.573  23.288  -1.489  1.00  0.00              
ATOM     46  CA  GLU    23      31.293  21.863  -1.237  1.00  0.00              
ATOM     47  C   GLU    23      30.198  21.327  -2.128  1.00  0.00              
ATOM     48  O   GLU    23      30.102  20.111  -2.306  1.00  0.00              
ATOM     49  N   ARG    24      29.415  22.219  -2.729  1.00  0.00              
ATOM     50  CA  ARG    24      28.473  21.812  -3.777  1.00  0.00              
ATOM     51  C   ARG    24      29.224  21.277  -4.983  1.00  0.00              
ATOM     52  O   ARG    24      28.740  20.341  -5.638  1.00  0.00              
ATOM     53  N   TYR    25      30.377  21.873  -5.324  1.00  0.00              
ATOM     54  CA  TYR    25      31.174  21.343  -6.411  1.00  0.00              
ATOM     55  C   TYR    25      31.882  20.087  -6.052  1.00  0.00              
ATOM     56  O   TYR    25      31.980  19.202  -6.888  1.00  0.00              
ATOM     57  N   TYR    26      32.392  19.986  -4.821  1.00  0.00              
ATOM     58  CA  TYR    26      33.060  18.746  -4.421  1.00  0.00              
ATOM     59  C   TYR    26      32.100  17.562  -4.386  1.00  0.00              
ATOM     60  O   TYR    26      32.473  16.449  -4.753  1.00  0.00              
ATOM     61  N   LEU    27      30.873  17.787  -3.901  1.00  0.00              
ATOM     62  CA  LEU    27      29.888  16.715  -3.853  1.00  0.00              
ATOM     63  C   LEU    27      29.255  16.446  -5.213  1.00  0.00              
ATOM     64  O   LEU    27      28.711  15.357  -5.445  1.00  0.00              
ATOM     65  N   LYS    28      21.805  15.716  -0.917  1.00  0.00              
ATOM     66  CA  LYS    28      21.691  14.290  -1.140  1.00  0.00              
ATOM     67  C   LYS    28      21.172  13.603   0.092  1.00  0.00              
ATOM     68  O   LYS    28      21.469  14.026   1.216  1.00  0.00              
ATOM     69  N   SER    29      20.381  12.569  -0.107  1.00  0.00              
ATOM     70  CA  SER    29      19.903  11.734   0.967  1.00  0.00              
ATOM     71  C   SER    29      20.880  10.628   1.218  1.00  0.00              
ATOM     72  O   SER    29      21.272   9.907   0.274  1.00  0.00              
ATOM     73  N   PHE    30      21.256  10.429   2.470  1.00  0.00              
ATOM     74  CA  PHE    30      22.195   9.392   2.820  1.00  0.00              
ATOM     75  C   PHE    30      21.579   8.457   3.848  1.00  0.00              
ATOM     76  O   PHE    30      21.227   8.868   4.972  1.00  0.00              
ATOM     77  N   GLN    31      21.415   7.205   3.458  1.00  0.00              
ATOM     78  CA  GLN    31      20.919   6.160   4.344  1.00  0.00              
ATOM     79  C   GLN    31      22.091   5.593   5.144  1.00  0.00              
ATOM     80  O   GLN    31      23.122   5.221   4.578  1.00  0.00              
ATOM     81  N   VAL    32      21.924   5.553   6.464  1.00  0.00              
ATOM     82  CA  VAL    32      22.957   5.126   7.381  1.00  0.00              
ATOM     83  C   VAL    32      22.418   4.006   8.251  1.00  0.00              
ATOM     84  O   VAL    32      21.217   3.935   8.470  1.00  0.00              
ATOM     85  N   ASP    33      23.281   3.115   8.748  1.00  0.00              
ATOM     86  CA  ASP    33      22.826   2.048   9.637  1.00  0.00              
ATOM     87  C   ASP    33      22.323   2.584  10.967  1.00  0.00              
ATOM     88  O   ASP    33      22.714   3.668  11.415  1.00  0.00              
ATOM     89  N   GLU    34      21.449   1.804  11.589  1.00  0.00              
ATOM     90  CA  GLU    34      20.989   2.054  12.937  1.00  0.00              
ATOM     91  C   GLU    34      22.160   2.444  13.846  1.00  0.00              
ATOM     92  O   GLU    34      23.218   1.823  13.803  1.00  0.00              
ATOM     93  N   GLY    35      21.952   3.490  14.644  1.00  0.00              
ATOM     94  CA  GLY    35      22.946   3.933  15.613  1.00  0.00              
ATOM     95  C   GLY    35      23.963   4.906  15.043  1.00  0.00              
ATOM     96  O   GLY    35      24.896   5.333  15.744  1.00  0.00              
ATOM     97  N   ILE    36      23.804   5.269  13.777  1.00  0.00              
ATOM     98  CA  ILE    36      24.772   6.152  13.151  1.00  0.00              
ATOM     99  C   ILE    36      24.924   7.448  13.887  1.00  0.00              
ATOM    100  O   ILE    36      23.945   8.043  14.367  1.00  0.00              
ATOM    101  N   THR    37      26.177   7.898  13.933  1.00  0.00              
ATOM    102  CA  THR    37      26.553   9.151  14.559  1.00  0.00              
ATOM    103  C   THR    37      27.055  10.143  13.513  1.00  0.00              
ATOM    104  O   THR    37      27.385   9.774  12.375  1.00  0.00              
ATOM    105  N   VAL    38      27.173  11.411  13.890  1.00  0.00              
ATOM    106  CA  VAL    38      27.740  12.419  12.994  1.00  0.00              
ATOM    107  C   VAL    38      29.078  11.961  12.381  1.00  0.00              
ATOM    108  O   VAL    38      29.301  12.097  11.158  1.00  0.00              
ATOM    109  N   GLN    39      29.968  11.381  13.198  1.00  0.00              
ATOM    110  CA  GLN    39      31.251  10.941  12.647  1.00  0.00              
ATOM    111  C   GLN    39      31.084   9.878  11.530  1.00  0.00              
ATOM    112  O   GLN    39      31.886   9.835  10.583  1.00  0.00              
ATOM    113  N   THR    40      30.056   9.029  11.648  1.00  0.00              
ATOM    114  CA  THR    40      29.816   7.993  10.619  1.00  0.00              
ATOM    115  C   THR    40      29.336   8.637   9.353  1.00  0.00              
ATOM    116  O   THR    40      29.725   8.210   8.258  1.00  0.00              
ATOM    117  N   ALA    41      28.516   9.666   9.479  1.00  0.00              
ATOM    118  CA  ALA    41      28.065  10.403   8.298  1.00  0.00              
ATOM    119  C   ALA    41      29.234  11.090   7.584  1.00  0.00              
ATOM    120  O   ALA    41      29.327  11.021   6.345  1.00  0.00              
ATOM    121  N   ILE    42      30.145  11.696   8.345  1.00  0.00              
ATOM    122  CA  ILE    42      31.318  12.320   7.746  1.00  0.00              
ATOM    123  C   ILE    42      32.128  11.281   6.975  1.00  0.00              
ATOM    124  O   ILE    42      32.571  11.538   5.826  1.00  0.00              
ATOM    125  N   THR    43      32.331  10.090   7.566  1.00  0.00              
ATOM    126  CA  THR    43      33.043   9.044   6.820  1.00  0.00              
ATOM    127  C   THR    43      32.341   8.615   5.553  1.00  0.00              
ATOM    128  O   THR    43      33.014   8.322   4.541  1.00  0.00              
ATOM    129  N   GLN    44      31.018   8.574   5.578  1.00  0.00              
ATOM    130  CA  GLN    44      30.271   8.198   4.392  1.00  0.00              
ATOM    131  C   GLN    44      30.358   9.283   3.317  1.00  0.00              
ATOM    132  O   GLN    44      30.455   8.945   2.131  1.00  0.00              
ATOM    133  N   ILE    47      30.346  10.573   3.702  1.00  0.00              
ATOM    134  CA  ILE    47      30.518  11.648   2.716  1.00  0.00              
ATOM    135  C   ILE    47      31.865  11.491   2.007  1.00  0.00              
ATOM    136  O   ILE    47      31.934  11.579   0.762  1.00  0.00              
ATOM    137  N   LEU    48      32.904  11.212   2.787  1.00  0.00              
ATOM    138  CA  LEU    48      34.247  11.002   2.234  1.00  0.00              
ATOM    139  C   LEU    48      34.318   9.772   1.317  1.00  0.00              
ATOM    140  O   LEU    48      35.055   9.788   0.304  1.00  0.00              
ATOM    141  N   SER    49      33.564   8.728   1.651  1.00  0.00              
ATOM    142  CA  SER    49      33.526   7.524   0.839  1.00  0.00              
ATOM    143  C   SER    49      32.819   7.779  -0.489  1.00  0.00              
ATOM    144  O   SER    49      33.233   7.250  -1.531  1.00  0.00              
ATOM    145  N   GLN    50      31.743   8.562  -0.474  1.00  0.00              
ATOM    146  CA  GLN    50      30.997   8.838  -1.690  1.00  0.00              
ATOM    147  C   GLN    50      31.705   9.840  -2.590  1.00  0.00              
ATOM    148  O   GLN    50      31.554   9.822  -3.810  1.00  0.00              
ATOM    149  N   PHE    51      32.411  10.767  -1.961  1.00  0.00              
ATOM    150  CA  PHE    51      32.985  11.909  -2.663  1.00  0.00              
ATOM    151  C   PHE    51      34.413  12.084  -2.218  1.00  0.00              
ATOM    152  O   PHE    51      34.697  12.824  -1.243  1.00  0.00              
ATOM    153  N   PRO    52      35.323  11.433  -2.941  1.00  0.00              
ATOM    154  CA  PRO    52      36.714  11.326  -2.494  1.00  0.00              
ATOM    155  C   PRO    52      37.414  12.664  -2.307  1.00  0.00              
ATOM    156  O   PRO    52      38.372  12.739  -1.543  1.00  0.00              
ATOM    157  N   GLU    53      36.936  13.714  -2.972  1.00  0.00              
ATOM    158  CA  GLU    53      37.570  15.041  -2.805  1.00  0.00              
ATOM    159  C   GLU    53      37.418  15.567  -1.377  1.00  0.00              
ATOM    160  O   GLU    53      38.177  16.453  -0.959  1.00  0.00              
ATOM    161  N   ILE    54      36.472  15.015  -0.600  1.00  0.00              
ATOM    162  CA  ILE    54      36.334  15.412   0.801  1.00  0.00              
ATOM    163  C   ILE    54      37.356  14.761   1.732  1.00  0.00              
ATOM    164  O   ILE    54      37.484  15.166   2.895  1.00  0.00              
ATOM    165  N   ASP    55      36.629  27.519  13.271  1.00  0.00              
ATOM    166  CA  ASP    55      36.995  28.389  12.146  1.00  0.00              
ATOM    167  C   ASP    55      38.259  27.926  11.429  1.00  0.00              
ATOM    168  O   ASP    55      38.520  28.343  10.292  1.00  0.00              
ATOM    169  N   LEU    56      39.031  27.049  12.068  1.00  0.00              
ATOM    170  CA  LEU    56      40.301  26.591  11.481  1.00  0.00              
ATOM    171  C   LEU    56      40.138  25.376  10.559  1.00  0.00              
ATOM    172  O   LEU    56      41.042  25.045   9.788  1.00  0.00              
END
