
#######################################################
#                                                     #
#                        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 T0335TS035_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS035_3-D1.T0335_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    A       5      A       5          2.490
LGA    K       6      K       6          1.864
LGA    I       7      I       7          0.891
LGA    A       8      A       8          1.666
LGA    R       9      R       9          2.007
LGA    I      10      I      10          1.253
LGA    N      11      N      11          0.304
LGA    E      12      E      12          1.294
LGA    L      13      L      13          2.255
LGA    A      14      A      14          2.005
LGA    A      15      A      15          1.031
LGA    K      16      K      16          1.324
LGA    A      17      A      17          2.945
LGA    K      18      K      18          2.666
LGA    A      19      A      19          1.103
LGA    G      20      G      20          1.190
LGA    V      21      V      21          0.641
LGA    I      22      I      22          2.132
LGA    T      23      T      23          2.200
LGA    E      24      E      24          1.370
LGA    E      25      E      25          1.213
LGA    E      26      E      26          0.941
LGA    K      27      K      27          0.809
LGA    A      28      A      28          0.551
LGA    E      29      E      29          0.430
LGA    Q      30      Q      30          0.753
LGA    Q      31      Q      31          1.319
LGA    K      32      K      32          1.034
LGA    L      33      L      33          0.169
LGA    R      34      R      34          0.369
LGA    Q      35      Q      35          0.711
LGA    E      36      E      36          0.737
LGA    Y      37      Y      37          0.725
LGA    L      38      L      38          0.944
LGA    K      39      K      39          0.986
LGA    G      40      G      40          1.065

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     36    1.44   100.00     93.458     2.344

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.516798 * X  +  -0.692079 * Y  +   0.503930 * Z  +   1.478612
  Y_new =   0.001761 * X  +  -0.589488 * Y  +  -0.807775 * Z  +   3.831883
  Z_new =   0.856105 * X  +  -0.416569 * Y  +   0.305865 * Z  + -13.574304 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.937452    2.204140  [ DEG:   -53.7121    126.2879 ]
  Theta =  -1.027686   -2.113907  [ DEG:   -58.8821   -121.1179 ]
  Phi   =   3.138185   -0.003408  [ DEG:   179.8047     -0.1953 ]
 
# 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: T0335TS035_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS035_3-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   36   1.44  100.00  93.458
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS035_3-D1
PFRMAT TS
TARGET T0335
MODEL  3  REFINED
PARENT N/A
ATOM     17  N   ALA     5       1.556  -9.751  -6.614  1.00  0.00
ATOM     18  CA  ALA     5       1.445  -9.773  -5.169  1.00  0.00
ATOM     19  C   ALA     5       1.511  -8.373  -4.581  1.00  0.00
ATOM     20  O   ALA     5       0.920  -8.093  -3.539  1.00  0.00
ATOM     21  N   LYS     6       2.232  -7.467  -5.234  1.00  0.00
ATOM     22  CA  LYS     6       2.350  -6.120  -4.710  1.00  0.00
ATOM     23  C   LYS     6       1.055  -5.339  -4.874  1.00  0.00
ATOM     24  O   LYS     6       0.614  -4.643  -3.962  1.00  0.00
ATOM     25  N   ILE     7       0.420  -5.441  -6.039  1.00  0.00
ATOM     26  CA  ILE     7      -0.821  -4.723  -6.252  1.00  0.00
ATOM     27  C   ILE     7      -1.901  -5.173  -5.282  1.00  0.00
ATOM     28  O   ILE     7      -2.732  -4.379  -4.843  1.00  0.00
ATOM     29  N   ALA     8      -1.914  -6.455  -4.927  1.00  0.00
ATOM     30  CA  ALA     8      -2.908  -6.938  -3.989  1.00  0.00
ATOM     31  C   ALA     8      -2.725  -6.320  -2.613  1.00  0.00
ATOM     32  O   ALA     8      -3.691  -5.934  -1.956  1.00  0.00
ATOM     33  N   ARG     9      -1.484  -6.214  -2.147  1.00  0.00
ATOM     34  CA  ARG     9      -1.245  -5.611  -0.850  1.00  0.00
ATOM     35  C   ARG     9      -1.625  -4.140  -0.838  1.00  0.00
ATOM     36  O   ARG     9      -2.192  -3.638   0.132  1.00  0.00
ATOM     37  N   ILE    10      -1.325  -3.418  -1.914  1.00  0.00
ATOM     38  CA  ILE    10      -1.697  -2.018  -1.975  1.00  0.00
ATOM     39  C   ILE    10      -3.206  -1.837  -1.958  1.00  0.00
ATOM     40  O   ILE    10      -3.732  -0.946  -1.294  1.00  0.00
ATOM     41  N   ASN    11      -3.933  -2.680  -2.686  1.00  0.00
ATOM     42  CA  ASN    11      -5.381  -2.627  -2.627  1.00  0.00
ATOM     43  C   ASN    11      -5.893  -2.898  -1.221  1.00  0.00
ATOM     44  O   ASN    11      -6.821  -2.245  -0.746  1.00  0.00
ATOM     45  N   GLU    12      -5.301  -3.865  -0.527  1.00  0.00
ATOM     46  CA  GLU    12      -5.753  -4.176   0.815  1.00  0.00
ATOM     47  C   GLU    12      -5.487  -3.028   1.775  1.00  0.00
ATOM     48  O   GLU    12      -6.295  -2.736   2.655  1.00  0.00
ATOM     49  N   LEU    13      -4.350  -2.353   1.626  1.00  0.00
ATOM     50  CA  LEU    13      -4.089  -1.185   2.444  1.00  0.00
ATOM     51  C   LEU    13      -5.120  -0.092   2.204  1.00  0.00
ATOM     52  O   LEU    13      -5.622   0.523   3.143  1.00  0.00
ATOM     53  N   ALA    14      -5.455   0.170   0.944  1.00  0.00
ATOM     54  CA  ALA    14      -6.447   1.187   0.655  1.00  0.00
ATOM     55  C   ALA    14      -7.781   0.869   1.309  1.00  0.00
ATOM     56  O   ALA    14      -8.407   1.730   1.927  1.00  0.00
ATOM     57  N   ALA    15      -8.246  -0.371   1.188  1.00  0.00
ATOM     58  CA  ALA    15      -9.514  -0.733   1.789  1.00  0.00
ATOM     59  C   ALA    15      -9.498  -0.528   3.295  1.00  0.00
ATOM     60  O   ALA    15     -10.452  -0.014   3.877  1.00  0.00
ATOM     61  N   LYS    16      -8.414  -0.923   3.957  1.00  0.00
ATOM     62  CA  LYS    16      -8.341  -0.751   5.396  1.00  0.00
ATOM     63  C   LYS    16      -8.299   0.719   5.781  1.00  0.00
ATOM     64  O   LYS    16      -8.881   1.129   6.784  1.00  0.00
ATOM     65  N   ALA    17      -7.609   1.541   4.996  1.00  0.00
ATOM     66  CA  ALA    17      -7.545   2.956   5.306  1.00  0.00
ATOM     67  C   ALA    17      -8.889   3.636   5.098  1.00  0.00
ATOM     68  O   ALA    17      -9.263   4.542   5.841  1.00  0.00
ATOM     69  N   LYS    18      -9.640   3.215   4.085  1.00  0.00
ATOM     70  CA  LYS    18     -10.926   3.833   3.829  1.00  0.00
ATOM     71  C   LYS    18     -12.018   3.234   4.700  1.00  0.00
ATOM     72  O   LYS    18     -13.101   3.801   4.842  1.00  0.00
ATOM     73  N   ALA    19     -11.758   2.076   5.300  1.00  0.00
ATOM     74  CA  ALA    19     -12.769   1.445   6.128  1.00  0.00
ATOM     75  C   ALA    19     -12.498   1.665   7.606  1.00  0.00
ATOM     76  O   ALA    19     -13.323   1.338   8.459  1.00  0.00
ATOM     77  N   GLY    20     -11.338   2.223   7.942  1.00  0.00
ATOM     78  CA  GLY    20     -11.023   2.457   9.338  1.00  0.00
ATOM     79  C   GLY    20      -9.632   3.044   9.506  1.00  0.00
ATOM     80  O   GLY    20      -8.791   2.954   8.614  1.00  0.00
ATOM     81  N   VAL    21      -9.359   3.659  10.654  1.00  0.00
ATOM     82  CA  VAL    21      -8.052   4.248  10.870  1.00  0.00
ATOM     83  C   VAL    21      -6.958   3.193  10.881  1.00  0.00
ATOM     84  O   VAL    21      -7.106   2.130  11.480  1.00  0.00
ATOM     85  N   ILE    22      -5.837   3.464  10.218  1.00  0.00
ATOM     86  CA  ILE    22      -4.722   2.537  10.268  1.00  0.00
ATOM     87  C   ILE    22      -3.500   3.167  10.916  1.00  0.00
ATOM     88  O   ILE    22      -3.376   4.388  10.985  1.00  0.00
ATOM     89  N   THR    23      -2.573   2.346  11.403  1.00  0.00
ATOM     90  CA  THR    23      -1.376   2.889  12.016  1.00  0.00
ATOM     91  C   THR    23      -0.472   3.552  10.988  1.00  0.00
ATOM     92  O   THR    23      -0.548   3.262   9.795  1.00  0.00
ATOM     93  N   GLU    24       0.401   4.454  11.428  1.00  0.00
ATOM     94  CA  GLU    24       1.339   5.065  10.507  1.00  0.00
ATOM     95  C   GLU    24       2.187   4.022   9.799  1.00  0.00
ATOM     96  O   GLU    24       2.510   4.160   8.619  1.00  0.00
ATOM     97  N   GLU    25       2.567   2.958  10.501  1.00  0.00
ATOM     98  CA  GLU    25       3.370   1.925   9.876  1.00  0.00
ATOM     99  C   GLU    25       2.633   1.266   8.721  1.00  0.00
ATOM    100  O   GLU    25       3.187   1.076   7.640  1.00  0.00
ATOM    101  N   GLU    26       1.370   0.903   8.926  1.00  0.00
ATOM    102  CA  GLU    26       0.587   0.355   7.836  1.00  0.00
ATOM    103  C   GLU    26       0.472   1.336   6.681  1.00  0.00
ATOM    104  O   GLU    26       0.570   0.958   5.514  1.00  0.00
ATOM    105  N   LYS    27       0.263   2.615   6.979  1.00  0.00
ATOM    106  CA  LYS    27       0.226   3.610   5.925  1.00  0.00
ATOM    107  C   LYS    27       1.552   3.691   5.186  1.00  0.00
ATOM    108  O   LYS    27       1.598   3.661   3.958  1.00  0.00
ATOM    109  N   ALA    28       2.657   3.796   5.919  1.00  0.00
ATOM    110  CA  ALA    28       3.945   3.954   5.269  1.00  0.00
ATOM    111  C   ALA    28       4.334   2.708   4.491  1.00  0.00
ATOM    112  O   ALA    28       4.953   2.789   3.431  1.00  0.00
ATOM    113  N   GLU    29       3.980   1.531   4.998  1.00  0.00
ATOM    114  CA  GLU    29       4.186   0.318   4.229  1.00  0.00
ATOM    115  C   GLU    29       3.402   0.342   2.926  1.00  0.00
ATOM    116  O   GLU    29       3.881  -0.112   1.889  1.00  0.00
ATOM    117  N   GLN    30       2.182   0.872   2.954  1.00  0.00
ATOM    118  CA  GLN    30       1.353   0.843   1.764  1.00  0.00
ATOM    119  C   GLN    30       1.791   1.887   0.751  1.00  0.00
ATOM    120  O   GLN    30       1.677   1.687  -0.457  1.00  0.00
ATOM    121  N   GLN    31       2.299   3.023   1.221  1.00  0.00
ATOM    122  CA  GLN    31       2.841   4.008   0.304  1.00  0.00
ATOM    123  C   GLN    31       4.150   3.541  -0.310  1.00  0.00
ATOM    124  O   GLN    31       4.439   3.814  -1.473  1.00  0.00
ATOM    125  N   LYS    32       4.969   2.828   0.458  1.00  0.00
ATOM    126  CA  LYS    32       6.231   2.352  -0.073  1.00  0.00
ATOM    127  C   LYS    32       6.023   1.378  -1.221  1.00  0.00
ATOM    128  O   LYS    32       6.655   1.489  -2.271  1.00  0.00
ATOM    129  N   LEU    33       5.135   0.404  -1.047  1.00  0.00
ATOM    130  CA  LEU    33       4.898  -0.560  -2.104  1.00  0.00
ATOM    131  C   LEU    33       4.336   0.104  -3.351  1.00  0.00
ATOM    132  O   LEU    33       4.672  -0.268  -4.474  1.00  0.00
ATOM    133  N   ARG    34       3.472   1.101  -3.179  1.00  0.00
ATOM    134  CA  ARG    34       2.903   1.771  -4.332  1.00  0.00
ATOM    135  C   ARG    34       3.968   2.490  -5.145  1.00  0.00
ATOM    136  O   ARG    34       3.943   2.480  -6.374  1.00  0.00
ATOM    137  N   GLN    35       4.925   3.127  -4.475  1.00  0.00
ATOM    138  CA  GLN    35       5.982   3.808  -5.196  1.00  0.00
ATOM    139  C   GLN    35       6.859   2.830  -5.962  1.00  0.00
ATOM    140  O   GLN    35       7.327   3.122  -7.060  1.00  0.00
ATOM    141  N   GLU    36       7.097   1.649  -5.399  1.00  0.00
ATOM    142  CA  GLU    36       7.917   0.670  -6.086  1.00  0.00
ATOM    143  C   GLU    36       7.275   0.214  -7.384  1.00  0.00
ATOM    144  O   GLU    36       7.938   0.087  -8.411  1.00  0.00
ATOM    145  N   TYR    37       5.969  -0.044  -7.366  1.00  0.00
ATOM    146  CA  TYR    37       5.298  -0.471  -8.578  1.00  0.00
ATOM    147  C   TYR    37       5.414   0.571  -9.679  1.00  0.00
ATOM    148  O   TYR    37       5.711   0.250 -10.828  1.00  0.00
ATOM    149  N   LEU    38       5.183   1.839  -9.352  1.00  0.00
ATOM    150  CA  LEU    38       5.290   2.879 -10.357  1.00  0.00
ATOM    151  C   LEU    38       6.693   2.957 -10.934  1.00  0.00
ATOM    152  O   LEU    38       6.876   3.108 -12.141  1.00  0.00
ATOM    153  N   LYS    39       7.713   2.857 -10.086  1.00  0.00
ATOM    154  CA  LYS    39       9.075   2.908 -10.580  1.00  0.00
ATOM    155  C   LYS    39       9.347   1.803 -11.588  1.00  0.00
ATOM    156  O   LYS    39       9.897   2.044 -12.661  1.00  0.00
ATOM    157  N   GLY    40       8.966   0.571 -11.265  1.00  0.00
ATOM    158  CA  GLY    40       9.190  -0.523 -12.190  1.00  0.00
ATOM    159  C   GLY    40       8.375  -0.354 -13.463  1.00  0.00
ATOM    160  O   GLY    40       8.872  -0.568 -14.568  1.00  0.00
TER
END
