
#######################################################
#                                                     #
#                        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   29 (  116),  selected   29 , name T0335AL257_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL257_5-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      A       5           -
LGA    A       5      K       6          1.384
LGA    K       6      I       7          1.275
LGA    I       7      A       8          2.403
LGA    A       8      R       9          1.833
LGA    R       9      I      10          1.719
LGA    I      10      N      11          2.120
LGA    N      11      E      12          1.143
LGA    E      12      L      13          1.180
LGA    L      13      A      14          2.317
LGA    A      14      A      15          1.924
LGA    A      15      K      16          0.491
LGA    K      16      A      17          1.719
LGA    A      17      K      18           -
LGA    K      18      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    -       -      I      22           -
LGA    -       -      T      23           -
LGA    -       -      E      24           -
LGA    -       -      E      25           -
LGA    A      19      E      26          0.506
LGA    K      27      K      27          1.233
LGA    A      28      A      28          1.174
LGA    E      29      E      29          1.684
LGA    Q      30      Q      30          2.514
LGA    Q      31      Q      31          1.522
LGA    K      32      K      32          1.217
LGA    L      33      L      33          2.353
LGA    -       -      R      34           -
LGA    -       -      Q      35           -
LGA    -       -      E      36           -
LGA    -       -      Y      37           -
LGA    R      34      L      38          0.784
LGA    Q      35      K      39          2.187
LGA    E      36      G      40          4.850
LGA    Y      37      -       -           -
LGA    L      38      -       -           -
LGA    K      39      -       -           -
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   29   36    5.0     23    1.93    34.78     57.773     1.133

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.071716 * X  +  -0.788416 * Y  +   0.610947 * Z  +  12.457801
  Y_new =  -0.842236 * X  +  -0.280260 * Y  +  -0.460536 * Z  +  15.860086
  Z_new =   0.534318 * X  +  -0.547590 * Y  +  -0.643933 * Z  +  -1.731698 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.436877    0.704716  [ DEG:  -139.6227     40.3773 ]
  Theta =  -0.563701   -2.577892  [ DEG:   -32.2977   -147.7023 ]
  Phi   =  -1.655741    1.485851  [ DEG:   -94.8670     85.1330 ]
 
# 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: T0335AL257_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL257_5-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   29   36   5.0   23   1.93   34.78  57.773
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL257_5-D1
REMARK Aligment from pdb entry: 1yoz_A
ATOM     17  N   ALA     5      -0.386  -8.670  -7.041  1.00  0.00              
ATOM     18  CA  ALA     5       0.304  -8.236  -5.801  1.00  0.00              
ATOM     19  C   ALA     5      -0.026  -6.809  -5.512  1.00  0.00              
ATOM     20  O   ALA     5      -0.297  -6.430  -4.382  1.00  0.00              
ATOM     21  N   LYS     6      -0.043  -5.987  -6.549  1.00  0.00              
ATOM     22  CA  LYS     6      -0.420  -4.602  -6.335  1.00  0.00              
ATOM     23  C   LYS     6      -1.817  -4.390  -5.709  1.00  0.00              
ATOM     24  O   LYS     6      -1.951  -3.616  -4.731  1.00  0.00              
ATOM     25  N   ILE     7      -2.821  -4.987  -6.349  1.00  0.00              
ATOM     26  CA  ILE     7      -4.200  -4.983  -5.901  1.00  0.00              
ATOM     27  C   ILE     7      -4.347  -5.488  -4.434  1.00  0.00              
ATOM     28  O   ILE     7      -4.941  -4.812  -3.605  1.00  0.00              
ATOM     29  N   ALA     8      -3.791  -6.655  -4.128  1.00  0.00              
ATOM     30  CA  ALA     8      -3.869  -7.181  -2.756  1.00  0.00              
ATOM     31  C   ALA     8      -3.188  -6.263  -1.715  1.00  0.00              
ATOM     32  O   ALA     8      -3.706  -6.090  -0.618  1.00  0.00              
ATOM     33  N   ARG     9      -2.041  -5.704  -2.048  1.00  0.00              
ATOM     34  CA  ARG     9      -1.358  -4.746  -1.176  1.00  0.00              
ATOM     35  C   ARG     9      -2.099  -3.448  -0.984  1.00  0.00              
ATOM     36  O   ARG     9      -2.013  -2.826   0.080  1.00  0.00              
ATOM     37  N   ILE    10      -2.767  -2.978  -2.033  1.00  0.00              
ATOM     38  CA  ILE    10      -3.640  -1.816  -1.883  1.00  0.00              
ATOM     39  C   ILE    10      -4.773  -2.119  -0.918  1.00  0.00              
ATOM     40  O   ILE    10      -5.082  -1.299  -0.040  1.00  0.00              
ATOM     41  N   ASN    11      -5.396  -3.281  -1.098  1.00  0.00              
ATOM     42  CA  ASN    11      -6.503  -3.748  -0.228  1.00  0.00              
ATOM     43  C   ASN    11      -6.092  -3.895   1.252  1.00  0.00              
ATOM     44  O   ASN    11      -6.862  -3.516   2.164  1.00  0.00              
ATOM     45  N   GLU    12      -4.880  -4.395   1.500  1.00  0.00              
ATOM     46  CA  GLU    12      -4.331  -4.477   2.884  1.00  0.00              
ATOM     47  C   GLU    12      -4.301  -3.091   3.563  1.00  0.00              
ATOM     48  O   GLU    12      -4.663  -2.952   4.772  1.00  0.00              
ATOM     49  N   LEU    13      -3.884  -2.082   2.812  1.00  0.00              
ATOM     50  CA  LEU    13      -3.707  -0.721   3.347  1.00  0.00              
ATOM     51  C   LEU    13      -5.074  -0.090   3.561  1.00  0.00              
ATOM     52  O   LEU    13      -5.336   0.480   4.613  1.00  0.00              
ATOM     53  N   ALA    14      -5.954  -0.226   2.575  1.00  0.00              
ATOM     54  CA  ALA    14      -7.285   0.358   2.656  1.00  0.00              
ATOM     55  C   ALA    14      -8.162  -0.275   3.768  1.00  0.00              
ATOM     56  O   ALA    14      -8.991   0.413   4.391  1.00  0.00              
ATOM     57  N   ALA    15      -8.006  -1.578   3.984  1.00  0.00              
ATOM     58  CA  ALA    15      -8.697  -2.269   5.082  1.00  0.00              
ATOM     59  C   ALA    15      -8.075  -1.958   6.467  1.00  0.00              
ATOM     60  O   ALA    15      -8.572  -2.438   7.490  1.00  0.00              
ATOM     61  N   LYS    16      -6.988  -1.186   6.489  1.00  0.00              
ATOM     62  CA  LYS    16      -6.341  -0.826   7.746  1.00  0.00              
ATOM     63  C   LYS    16      -5.635  -2.011   8.370  1.00  0.00              
ATOM     64  O   LYS    16      -5.416  -2.026   9.602  1.00  0.00              
ATOM     65  N   ALA    17      -5.269  -2.997   7.533  1.00  0.00              
ATOM     66  CA  ALA    17      -4.477  -4.151   7.999  1.00  0.00              
ATOM     67  C   ALA    17      -2.991  -3.894   7.960  1.00  0.00              
ATOM     68  O   ALA    17      -2.231  -4.604   8.596  1.00  0.00              
ATOM     69  N   LYS    18      -2.567  -2.897   7.196  1.00  0.00              
ATOM     70  CA  LYS    18      -1.154  -2.505   7.152  1.00  0.00              
ATOM     71  C   LYS    18      -1.088  -1.001   7.201  1.00  0.00              
ATOM     72  O   LYS    18      -2.014  -0.334   6.770  1.00  0.00              
ATOM     73  N   ALA    19       0.018  -0.474   7.721  1.00  0.00              
ATOM     74  CA  ALA    19       0.199   0.951   7.932  1.00  0.00              
ATOM     75  C   ALA    19       0.047   1.741   6.641  1.00  0.00              
ATOM     76  O   ALA    19       0.552   1.336   5.615  1.00  0.00              
ATOM     77  N   LYS    27      -0.610   2.886   6.707  1.00  0.00              
ATOM     78  CA  LYS    27      -0.691   3.823   5.575  1.00  0.00              
ATOM     79  C   LYS    27       0.700   4.332   5.100  1.00  0.00              
ATOM     80  O   LYS    27       0.851   4.809   3.971  1.00  0.00              
ATOM     81  N   ALA    28       1.719   4.156   5.933  1.00  0.00              
ATOM     82  CA  ALA    28       3.093   4.482   5.590  1.00  0.00              
ATOM     83  C   ALA    28       3.568   3.655   4.399  1.00  0.00              
ATOM     84  O   ALA    28       4.357   4.107   3.578  1.00  0.00              
ATOM     85  N   GLU    29       3.047   2.443   4.301  1.00  0.00              
ATOM     86  CA  GLU    29       3.389   1.536   3.233  1.00  0.00              
ATOM     87  C   GLU    29       2.973   2.041   1.850  1.00  0.00              
ATOM     88  O   GLU    29       3.519   1.570   0.853  1.00  0.00              
ATOM     89  N   GLN    30       2.037   2.995   1.789  1.00  0.00              
ATOM     90  CA  GLN    30       1.550   3.541   0.517  1.00  0.00              
ATOM     91  C   GLN    30       2.676   4.170  -0.293  1.00  0.00              
ATOM     92  O   GLN    30       2.606   4.199  -1.532  1.00  0.00              
ATOM     93  N   GLN    31       3.717   4.625   0.416  1.00  0.00              
ATOM     94  CA  GLN    31       4.812   5.349  -0.172  1.00  0.00              
ATOM     95  C   GLN    31       5.642   4.481  -1.132  1.00  0.00              
ATOM     96  O   GLN    31       5.890   4.897  -2.284  1.00  0.00              
ATOM     97  N   LYS    32       6.092   3.313  -0.658  1.00  0.00              
ATOM     98  CA  LYS    32       6.807   2.383  -1.523  1.00  0.00              
ATOM     99  C   LYS    32       5.879   1.828  -2.595  1.00  0.00              
ATOM    100  O   LYS    32       6.292   1.635  -3.729  1.00  0.00              
ATOM    101  N   LEU    33       4.627   1.575  -2.229  1.00  0.00              
ATOM    102  CA  LEU    33       3.639   1.091  -3.192  1.00  0.00              
ATOM    103  C   LEU    33       3.364   2.104  -4.286  1.00  0.00              
ATOM    104  O   LEU    33       3.160   1.728  -5.414  1.00  0.00              
ATOM    105  N   ARG    34       6.251   4.144  -9.042  1.00  0.00              
ATOM    106  CA  ARG    34       6.021   3.433 -10.314  1.00  0.00              
ATOM    107  C   ARG    34       7.041   2.342 -10.696  1.00  0.00              
ATOM    108  O   ARG    34       6.694   1.359 -11.365  1.00  0.00              
ATOM    109  N   GLN    35       8.285   2.508 -10.250  1.00  0.00              
ATOM    110  CA  GLN    35       9.329   1.538 -10.450  1.00  0.00              
ATOM    111  C   GLN    35       9.039   0.284  -9.649  1.00  0.00              
ATOM    112  O   GLN    35       9.224  -0.820 -10.152  1.00  0.00              
ATOM    113  N   GLU    36       8.620   0.432  -8.393  1.00  0.00              
ATOM    114  CA  GLU    36       8.224  -0.746  -7.621  1.00  0.00              
ATOM    115  C   GLU    36       6.964  -1.385  -8.222  1.00  0.00              
ATOM    116  O   GLU    36       6.837  -2.590  -8.221  1.00  0.00              
ATOM    117  N   TYR    37       6.023  -0.575  -8.694  1.00  0.00              
ATOM    118  CA  TYR    37       4.796  -1.106  -9.298  1.00  0.00              
ATOM    119  C   TYR    37       5.124  -1.959 -10.537  1.00  0.00              
ATOM    120  O   TYR    37       4.719  -3.116 -10.656  1.00  0.00              
ATOM    121  N   LEU    38       5.904  -1.374 -11.445  1.00  0.00              
ATOM    122  CA  LEU    38       6.400  -2.113 -12.600  1.00  0.00              
ATOM    123  C   LEU    38       7.054  -3.436 -12.159  1.00  0.00              
ATOM    124  O   LEU    38       6.735  -4.507 -12.672  1.00  0.00              
ATOM    125  N   LYS    39       7.937  -3.385 -11.158  1.00  0.00              
ATOM    126  CA  LYS    39       8.539  -4.625 -10.655  1.00  0.00              
ATOM    127  C   LYS    39       7.555  -5.642 -10.068  1.00  0.00              
ATOM    128  O   LYS    39       7.778  -6.853 -10.197  1.00  0.00              
ATOM    129  N   GLY    40       6.527  -5.168  -9.340  1.00  0.00              
ATOM    130  CA  GLY    40       5.539  -6.066  -8.748  1.00  0.00              
ATOM    131  C   GLY    40       4.875  -6.909  -9.809  1.00  0.00              
ATOM    132  O   GLY    40       4.676  -8.097  -9.629  1.00  0.00              
END
