
#######################################################
#                                                     #
#                        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   36 (  144),  selected   36 , name T0335AL242_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL242_4-D1.T0335_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    A       5      -       -           -
LGA    K       6      -       -           -
LGA    I       7      -       -           -
LGA    A       8      -       -           -
LGA    R       9      -       -           -
LGA    I      10      -       -           -
LGA    N      11      -       -           -
LGA    E      12      -       -           -
LGA    L      13      -       -           -
LGA    A      14      -       -           -
LGA    A      15      -       -           -
LGA    K      16      -       -           -
LGA    A      17      A       5           #
LGA    K      18      K       6          3.647
LGA    A      19      I       7          4.866
LGA    G      20      A       8           #
LGA    -       -      R       9           -
LGA    V      21      I      10          2.011
LGA    -       -      N      11           -
LGA    -       -      E      12           -
LGA    I      22      L      13          1.548
LGA    T      23      A      14          3.233
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    E      24      A      17          2.000
LGA    E      25      K      18           #
LGA    E      26      A      19          2.848
LGA    K      27      G      20          3.491
LGA    A      28      V      21          0.777
LGA    E      29      I      22          0.482
LGA    Q      30      T      23           #
LGA    -       -      E      24           -
LGA    -       -      E      25           -
LGA    -       -      E      26           -
LGA    Q      31      K      27          3.248
LGA    -       -      A      28           -
LGA    -       -      E      29           -
LGA    K      32      Q      30          2.712
LGA    L      33      Q      31          4.294
LGA    -       -      K      32           -
LGA    R      34      L      33          2.161
LGA    Q      35      R      34           -
LGA    E      36      Q      35           -
LGA    Y      37      E      36           -
LGA    L      38      Y      37           -
LGA    K      39      L      38           -
LGA    G      40      K      39           -
LGA    -       -      G      40           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     14    2.93     7.14     27.849     0.462

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.758508 * X  +   0.059602 * Y  +  -0.648932 * Z  +   3.077130
  Y_new =  -0.623968 * X  +   0.353649 * Y  +  -0.696847 * Z  +  -0.672661
  Z_new =   0.187961 * X  +   0.933477 * Y  +   0.305436 * Z  +   3.043233 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.254574   -1.887019  [ DEG:    71.8818   -108.1182 ]
  Theta =  -0.189086   -2.952507  [ DEG:   -10.8338   -169.1662 ]
  Phi   =  -0.688385    2.453207  [ DEG:   -39.4416    140.5584 ]
 
# 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: T0335AL242_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL242_4-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   36   36   5.0   14   2.93    7.14  27.849
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL242_4-D1
REMARK Aligment from pdb entry: 1d4b_A
ATOM     17  N   ALA     5     -31.740  -2.256 -36.779  1.00  0.00              
ATOM     18  CA  ALA     5     -32.702  -3.039 -35.952  1.00  0.00              
ATOM     19  C   ALA     5     -32.039  -3.499 -34.652  1.00  0.00              
ATOM     20  O   ALA     5     -32.492  -3.185 -33.569  1.00  0.00              
ATOM     21  N   LYS     6     -30.971  -4.246 -34.752  1.00  0.00              
ATOM     22  CA  LYS     6     -30.282  -4.731 -33.520  1.00  0.00              
ATOM     23  C   LYS     6     -28.767  -4.763 -33.737  1.00  0.00              
ATOM     24  O   LYS     6     -28.083  -5.654 -33.273  1.00  0.00              
ATOM     25  N   ILE     7     -28.238  -3.796 -34.437  1.00  0.00              
ATOM     26  CA  ILE     7     -26.766  -3.768 -34.681  1.00  0.00              
ATOM     27  C   ILE     7     -26.053  -3.084 -33.511  1.00  0.00              
ATOM     28  O   ILE     7     -25.425  -2.054 -33.666  1.00  0.00              
ATOM     29  N   ALA     8     -26.148  -3.649 -32.336  1.00  0.00              
ATOM     30  CA  ALA     8     -25.479  -3.034 -31.151  1.00  0.00              
ATOM     31  C   ALA     8     -24.976  -4.126 -30.201  1.00  0.00              
ATOM     32  O   ALA     8     -24.994  -3.966 -28.996  1.00  0.00              
ATOM     33  N   ARG     9     -24.530  -5.231 -30.733  1.00  0.00              
ATOM     34  CA  ARG     9     -24.026  -6.332 -29.863  1.00  0.00              
ATOM     35  C   ARG     9     -22.554  -6.101 -29.514  1.00  0.00              
ATOM     36  O   ARG     9     -21.911  -5.220 -30.054  1.00  0.00              
ATOM     37  N   ILE    10     -22.017  -6.883 -28.616  1.00  0.00              
ATOM     38  CA  ILE    10     -20.586  -6.710 -28.231  1.00  0.00              
ATOM     39  C   ILE    10     -19.834  -8.033 -28.392  1.00  0.00              
ATOM     40  O   ILE    10     -19.829  -8.868 -27.507  1.00  0.00              
ATOM     41  N   ASN    11     -19.199  -8.232 -29.518  1.00  0.00              
ATOM     42  CA  ASN    11     -18.448  -9.501 -29.739  1.00  0.00              
ATOM     43  C   ASN    11     -16.971  -9.310 -29.384  1.00  0.00              
ATOM     44  O   ASN    11     -16.197  -8.789 -30.164  1.00  0.00              
ATOM     45  N   GLU    12     -16.574  -9.730 -28.213  1.00  0.00              
ATOM     46  CA  GLU    12     -15.149  -9.575 -27.804  1.00  0.00              
ATOM     47  C   GLU    12     -14.578 -10.926 -27.362  1.00  0.00              
ATOM     48  O   GLU    12     -13.774 -11.002 -26.454  1.00  0.00              
ATOM     49  N   LEU    13     -14.990 -11.990 -28.000  1.00  0.00              
ATOM     50  CA  LEU    13     -14.471 -13.338 -27.619  1.00  0.00              
ATOM     51  C   LEU    13     -13.012 -13.487 -28.060  1.00  0.00              
ATOM     52  O   LEU    13     -12.690 -14.292 -28.912  1.00  0.00              
ATOM     53  N   ALA    14     -12.127 -12.717 -27.484  1.00  0.00              
ATOM     54  CA  ALA    14     -10.687 -12.812 -27.868  1.00  0.00              
ATOM     55  C   ALA    14     -10.110 -14.157 -27.425  1.00  0.00              
ATOM     56  O   ALA    14     -10.774 -14.947 -26.780  1.00  0.00              
ATOM     57  N   ALA    15      -8.878 -14.426 -27.766  1.00  0.00              
ATOM     58  CA  ALA    15      -8.254 -15.721 -27.365  1.00  0.00              
ATOM     59  C   ALA    15      -7.122 -15.473 -26.365  1.00  0.00              
ATOM     60  O   ALA    15      -6.288 -14.613 -26.558  1.00  0.00              
ATOM     61  N   LYS    16      -7.091 -16.221 -25.294  1.00  0.00              
ATOM     62  CA  LYS    16      -6.015 -16.030 -24.277  1.00  0.00              
ATOM     63  C   LYS    16      -5.964 -17.226 -23.324  1.00  0.00              
ATOM     64  O   LYS    16      -6.983 -17.753 -22.920  1.00  0.00              
ATOM     65  N   ALA    17       8.085  -8.226  -6.447  1.00  0.00              
ATOM     66  CA  ALA    17       7.632  -7.003  -5.723  1.00  0.00              
ATOM     67  C   ALA    17       6.370  -6.439  -6.381  1.00  0.00              
ATOM     68  O   ALA    17       6.362  -6.121  -7.554  1.00  0.00              
ATOM     69  N   LYS    18       5.304  -6.316  -5.636  1.00  0.00              
ATOM     70  CA  LYS    18       4.042  -5.776  -6.221  1.00  0.00              
ATOM     71  C   LYS    18       3.440  -4.711  -5.293  1.00  0.00              
ATOM     72  O   LYS    18       3.458  -4.864  -4.087  1.00  0.00              
ATOM     73  N   ALA    19       2.923  -3.660  -5.883  1.00  0.00              
ATOM     74  CA  ALA    19       2.312  -2.569  -5.083  1.00  0.00              
ATOM     75  C   ALA    19       0.979  -3.024  -4.483  1.00  0.00              
ATOM     76  O   ALA    19      -0.048  -2.987  -5.131  1.00  0.00              
ATOM     77  N   GLY    20       0.989  -3.454  -3.248  1.00  0.00              
ATOM     78  CA  GLY    20      -0.275  -3.912  -2.604  1.00  0.00              
ATOM     79  C   GLY    20      -0.895  -2.775  -1.788  1.00  0.00              
ATOM     80  O   GLY    20      -0.202  -2.002  -1.155  1.00  0.00              
ATOM     81  N   VAL    21      -2.198  -2.668  -1.798  1.00  0.00              
ATOM     82  CA  VAL    21      -2.867  -1.582  -1.024  1.00  0.00              
ATOM     83  C   VAL    21      -3.466  -2.147   0.267  1.00  0.00              
ATOM     84  O   VAL    21      -4.351  -2.982   0.239  1.00  0.00              
ATOM     85  N   ILE    22      -2.992  -1.696   1.397  1.00  0.00              
ATOM     86  CA  ILE    22      -3.531  -2.203   2.694  1.00  0.00              
ATOM     87  C   ILE    22      -4.428  -1.143   3.341  1.00  0.00              
ATOM     88  O   ILE    22      -4.081   0.020   3.405  1.00  0.00              
ATOM     89  N   THR    23      -5.576  -1.539   3.822  1.00  0.00              
ATOM     90  CA  THR    23      -6.497  -0.557   4.467  1.00  0.00              
ATOM     91  C   THR    23      -6.950  -1.079   5.832  1.00  0.00              
ATOM     92  O   THR    23      -7.170  -2.259   6.011  1.00  0.00              
ATOM     93  N   GLU    24      -7.090  -0.208   6.796  1.00  0.00              
ATOM     94  CA  GLU    24      -7.525  -0.654   8.153  1.00  0.00              
ATOM     95  C   GLU    24      -9.043  -0.860   8.180  1.00  0.00              
ATOM     96  O   GLU    24      -9.721  -0.636   7.196  1.00  0.00              
ATOM     97  N   GLU    25      -9.570  -1.311   9.294  1.00  0.00              
ATOM     98  CA  GLU    25     -11.045  -1.566   9.403  1.00  0.00              
ATOM     99  C   GLU    25     -11.864  -0.545   8.591  1.00  0.00              
ATOM    100  O   GLU    25     -12.201  -0.791   7.450  1.00  0.00              
ATOM    101  N   GLU    26     -12.198   0.593   9.156  1.00  0.00              
ATOM    102  CA  GLU    26     -12.999   1.587   8.378  1.00  0.00              
ATOM    103  C   GLU    26     -12.088   2.591   7.659  1.00  0.00              
ATOM    104  O   GLU    26     -11.976   2.580   6.450  1.00  0.00              
ATOM    105  N   LYS    27     -11.441   3.460   8.393  1.00  0.00              
ATOM    106  CA  LYS    27     -10.541   4.463   7.742  1.00  0.00              
ATOM    107  C   LYS    27      -9.436   4.923   8.703  1.00  0.00              
ATOM    108  O   LYS    27      -8.799   5.934   8.479  1.00  0.00              
ATOM    109  N   ALA    28      -9.208   4.209   9.775  1.00  0.00              
ATOM    110  CA  ALA    28      -8.151   4.637  10.743  1.00  0.00              
ATOM    111  C   ALA    28      -6.795   4.764  10.040  1.00  0.00              
ATOM    112  O   ALA    28      -6.135   5.781  10.127  1.00  0.00              
ATOM    113  N   GLU    29      -6.374   3.741   9.346  1.00  0.00              
ATOM    114  CA  GLU    29      -5.059   3.809   8.639  1.00  0.00              
ATOM    115  C   GLU    29      -5.206   3.315   7.196  1.00  0.00              
ATOM    116  O   GLU    29      -5.844   2.313   6.934  1.00  0.00              
ATOM    117  N   GLN    30      -4.615   4.008   6.259  1.00  0.00              
ATOM    118  CA  GLN    30      -4.715   3.583   4.834  1.00  0.00              
ATOM    119  C   GLN    30      -3.369   3.783   4.130  1.00  0.00              
ATOM    120  O   GLN    30      -3.012   4.885   3.758  1.00  0.00              
ATOM    121  N   GLN    31      -2.622   2.728   3.944  1.00  0.00              
ATOM    122  CA  GLN    31      -1.300   2.859   3.264  1.00  0.00              
ATOM    123  C   GLN    31      -1.129   1.747   2.225  1.00  0.00              
ATOM    124  O   GLN    31      -1.491   0.610   2.454  1.00  0.00              
ATOM    125  N   LYS    32      -0.580   2.067   1.083  1.00  0.00              
ATOM    126  CA  LYS    32      -0.385   1.030   0.029  1.00  0.00              
ATOM    127  C   LYS    32       1.046   1.106  -0.505  1.00  0.00              
ATOM    128  O   LYS    32       1.399   2.017  -1.229  1.00  0.00              
ATOM    129  N   LEU    33       1.871   0.159  -0.152  1.00  0.00              
ATOM    130  CA  LEU    33       3.282   0.175  -0.638  1.00  0.00              
ATOM    131  C   LEU    33       3.647  -1.177  -1.258  1.00  0.00              
ATOM    132  O   LEU    33       2.973  -2.166  -1.052  1.00  0.00              
ATOM    133  N   ARG    34       4.711  -1.224  -2.015  1.00  0.00              
ATOM    134  CA  ARG    34       5.123  -2.511  -2.648  1.00  0.00              
ATOM    135  C   ARG    34       5.864  -3.384  -1.632  1.00  0.00              
ATOM    136  O   ARG    34       6.804  -2.949  -0.997  1.00  0.00              
ATOM    137  N   GLN    35       5.446  -4.612  -1.474  1.00  0.00              
ATOM    138  CA  GLN    35       6.126  -5.513  -0.498  1.00  0.00              
ATOM    139  C   GLN    35       6.318  -6.905  -1.106  1.00  0.00              
ATOM    140  O   GLN    35       5.518  -7.363  -1.899  1.00  0.00              
ATOM    141  N   GLU    36       7.369  -7.582  -0.732  1.00  0.00              
ATOM    142  CA  GLU    36       7.618  -8.948  -1.281  1.00  0.00              
ATOM    143  C   GLU    36       7.919  -9.920  -0.136  1.00  0.00              
ATOM    144  O   GLU    36       9.021  -9.972   0.371  1.00  0.00              
ATOM    145  N   TYR    37       6.944 -10.688   0.274  1.00  0.00              
ATOM    146  CA  TYR    37       7.171 -11.652   1.388  1.00  0.00              
ATOM    147  C   TYR    37       6.207 -12.837   1.273  1.00  0.00              
ATOM    148  O   TYR    37       5.060 -12.683   0.901  1.00  0.00              
ATOM    149  N   LEU    38       6.666 -14.021   1.585  1.00  0.00              
ATOM    150  CA  LEU    38       5.778 -15.218   1.488  1.00  0.00              
ATOM    151  C   LEU    38       5.052 -15.468   2.817  1.00  0.00              
ATOM    152  O   LEU    38       3.880 -15.172   2.955  1.00  0.00              
ATOM    153  N   LYS    39       5.731 -16.021   3.788  1.00  0.00              
ATOM    154  CA  LYS    39       5.074 -16.302   5.098  1.00  0.00              
ATOM    155  C   LYS    39       5.223 -15.110   6.049  1.00  0.00              
ATOM    156  O   LYS    39       4.279 -14.703   6.697  1.00  0.00              
ATOM    157  N   GLY    40       6.400 -14.550   6.140  1.00  0.00              
ATOM    158  CA  GLY    40       6.605 -13.387   7.054  1.00  0.00              
ATOM    159  C   GLY    40       5.691 -12.221   6.659  1.00  0.00              
ATOM    160  O   GLY    40       5.467 -11.310   7.433  1.00  0.00              
END
