
#######################################################
#                                                     #
#                        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   30 (  120),  selected   30 , name T0335TS383_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS383_1-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    K       6      -       -           -
LGA    I       7      -       -           -
LGA    A       8      A       5          3.119
LGA    R       9      K       6          1.972
LGA    I      10      I       7          1.275
LGA    N      11      A       8          1.549
LGA    E      12      R       9          1.520
LGA    L      13      I      10          1.922
LGA    A      14      N      11          2.027
LGA    A      15      E      12          1.215
LGA    K      16      L      13          1.501
LGA    A      17      A      14          2.106
LGA    K      18      A      15          2.110
LGA    A      19      K      16          1.949
LGA    G      20      A      17          2.574
LGA    K      27      K      18          3.970
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    A      28      V      21          3.690
LGA    E      29      I      22          1.942
LGA    Q      30      T      23          1.985
LGA    -       -      E      24           -
LGA    -       -      E      25           -
LGA    -       -      E      26           -
LGA    Q      31      K      27          2.595
LGA    K      32      A      28          2.431
LGA    L      33      E      29          2.791
LGA    R      34      Q      30          2.984
LGA    Q      35      Q      31          2.306
LGA    E      36      K      32          2.952
LGA    Y      37      L      33          3.251
LGA    L      38      R      34          2.345
LGA    K      39      Q      35          2.476
LGA    G      40      E      36          4.187
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)   30   36    5.0     27    2.52    18.52     56.465     1.032

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.650577 * X  +  -0.117364 * Y  +  -0.750317 * Z  + -10.749938
  Y_new =   0.669944 * X  +  -0.376609 * Y  +   0.639797 * Z  +   0.079262
  Z_new =  -0.357666 * X  +  -0.918908 * Y  +  -0.166386 * Z  +  20.699869 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.749925    1.391668  [ DEG:  -100.2633     79.7367 ]
  Theta =   0.365767    2.775826  [ DEG:    20.9569    159.0431 ]
  Phi   =   0.800064   -2.341529  [ DEG:    45.8403   -134.1597 ]
 
# 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: T0335TS383_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS383_1-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   30   36   5.0   27   2.52   18.52  56.465
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS383_1-D1
PFRMAT TS
TARGET T0335
MODEL 1
PARENT 1x0tA
ATOM      9  N   ALA     5       1.064 -13.008 -12.071  1.00  0.00
ATOM     10  CA  ALA     5       1.550 -12.970 -10.695  1.00  0.00
ATOM     11  C   ALA     5       1.725 -11.522 -10.261  1.00  0.00
ATOM     12  O   ALA     5       1.348 -11.141  -9.152  1.00  0.00
ATOM     13  N   LYS     6       2.306 -10.720 -11.145  1.00  0.00
ATOM     14  CA  LYS     6       2.538  -9.312 -10.858  1.00  0.00
ATOM     15  C   LYS     6       1.220  -8.613 -10.557  1.00  0.00
ATOM     16  O   LYS     6       1.120  -7.847  -9.599  1.00  0.00
ATOM     17  N   ILE     7       0.212  -8.877 -11.379  1.00  0.00
ATOM     18  CA  ILE     7      -1.092  -8.261 -11.177  1.00  0.00
ATOM     19  C   ILE     7      -1.693  -8.735  -9.856  1.00  0.00
ATOM     20  O   ILE     7      -2.309  -7.949  -9.132  1.00  0.00
ATOM     21  N   ALA     8      -1.498 -10.015  -9.543  1.00  0.00
ATOM     22  CA  ALA     8      -2.007 -10.589  -8.296  1.00  0.00
ATOM     23  C   ALA     8      -1.378  -9.873  -7.103  1.00  0.00
ATOM     24  O   ALA     8      -2.062  -9.533  -6.132  1.00  0.00
ATOM     25  N   ARG     9      -0.068  -9.652  -7.180  1.00  0.00
ATOM     26  CA  ARG     9       0.665  -8.981  -6.112  1.00  0.00
ATOM     27  C   ARG     9       0.203  -7.538  -5.953  1.00  0.00
ATOM     28  O   ARG     9       0.033  -7.053  -4.833  1.00  0.00
ATOM     29  N   ILE    10       0.005  -6.854  -7.076  1.00  0.00
ATOM     30  CA  ILE    10      -0.446  -5.465  -7.051  1.00  0.00
ATOM     31  C   ILE    10      -1.807  -5.369  -6.364  1.00  0.00
ATOM     32  O   ILE    10      -2.037  -4.482  -5.540  1.00  0.00
ATOM     33  N   ASN    11      -2.708  -6.284  -6.707  1.00  0.00
ATOM     34  CA  ASN    11      -4.040  -6.294  -6.107  1.00  0.00
ATOM     35  C   ASN    11      -3.954  -6.496  -4.595  1.00  0.00
ATOM     36  O   ASN    11      -4.666  -5.845  -3.828  1.00  0.00
ATOM     37  N   GLU    12      -3.074  -7.392  -4.169  1.00  0.00
ATOM     38  CA  GLU    12      -2.900  -7.677  -2.750  1.00  0.00
ATOM     39  C   GLU    12      -2.313  -6.480  -2.000  1.00  0.00
ATOM     40  O   GLU    12      -2.749  -6.151  -0.895  1.00  0.00
ATOM     41  N   LEU    13      -1.323  -5.826  -2.600  1.00  0.00
ATOM     42  CA  LEU    13      -0.696  -4.670  -1.973  1.00  0.00
ATOM     43  C   LEU    13      -1.684  -3.520  -1.791  1.00  0.00
ATOM     44  O   LEU    13      -1.657  -2.828  -0.774  1.00  0.00
ATOM     45  N   ALA    14      -2.559  -3.316  -2.770  1.00  0.00
ATOM     46  CA  ALA    14      -3.554  -2.252  -2.667  1.00  0.00
ATOM     47  C   ALA    14      -4.616  -2.636  -1.649  1.00  0.00
ATOM     48  O   ALA    14      -5.164  -1.779  -0.962  1.00  0.00
ATOM     49  N   ALA    15      -4.914  -3.927  -1.556  1.00  0.00
ATOM     50  CA  ALA    15      -5.898  -4.384  -0.584  1.00  0.00
ATOM     51  C   ALA    15      -5.357  -4.072   0.810  1.00  0.00
ATOM     52  O   ALA    15      -6.085  -3.585   1.675  1.00  0.00
ATOM     53  N   LYS    16      -4.074  -4.349   1.023  1.00  0.00
ATOM     54  CA  LYS    16      -3.449  -4.074   2.307  1.00  0.00
ATOM     55  C   LYS    16      -3.391  -2.567   2.539  1.00  0.00
ATOM     56  O   LYS    16      -3.641  -2.096   3.645  1.00  0.00
ATOM     57  N   ALA    17      -3.070  -1.809   1.495  1.00  0.00
ATOM     58  CA  ALA    17      -3.005  -0.356   1.618  1.00  0.00
ATOM     59  C   ALA    17      -4.340   0.195   2.114  1.00  0.00
ATOM     60  O   ALA    17      -4.378   1.023   3.020  1.00  0.00
ATOM     61  N   LYS    18      -5.431  -0.272   1.520  1.00  0.00
ATOM     62  CA  LYS    18      -6.754   0.204   1.910  1.00  0.00
ATOM     63  C   LYS    18      -7.071  -0.124   3.365  1.00  0.00
ATOM     64  O   LYS    18      -7.644   0.695   4.082  1.00  0.00
ATOM     65  N   ALA    19      -6.688  -1.319   3.801  1.00  0.00
ATOM     66  CA  ALA    19      -6.946  -1.741   5.172  1.00  0.00
ATOM     67  C   ALA    19      -6.173  -0.945   6.217  1.00  0.00
ATOM     68  O   ALA    19      -6.682  -0.697   7.310  1.00  0.00
ATOM     69  N   GLY    20      -4.956  -0.525   5.884  1.00  0.00
ATOM     70  CA  GLY    20      -4.141   0.212   6.848  1.00  0.00
ATOM     71  C   GLY    20      -4.110   1.725   6.657  1.00  0.00
ATOM     72  O   GLY    20      -3.625   2.437   7.525  1.00  0.00
ATOM     73  N   LYS    27      -4.640   2.207   5.539  1.00  0.00
ATOM     74  CA  LYS    27      -4.610   3.634   5.216  1.00  0.00
ATOM     75  C   LYS    27      -5.116   4.634   6.252  1.00  0.00
ATOM     76  O   LYS    27      -4.456   5.636   6.517  1.00  0.00
ATOM     77  N   ALA    28      -6.282   4.383   6.829  1.00  0.00
ATOM     78  CA  ALA    28      -6.841   5.324   7.791  1.00  0.00
ATOM     79  C   ALA    28      -6.020   5.476   9.066  1.00  0.00
ATOM     80  O   ALA    28      -5.892   6.581   9.599  1.00  0.00
ATOM     81  N   GLU    29      -5.447   4.375   9.534  1.00  0.00
ATOM     82  CA  GLU    29      -4.657   4.368  10.762  1.00  0.00
ATOM     83  C   GLU    29      -3.165   4.598  10.519  1.00  0.00
ATOM     84  O   GLU    29      -2.494   5.270  11.308  1.00  0.00
ATOM     85  N   GLN    30      -2.651   4.036   9.429  1.00  0.00
ATOM     86  CA  GLN    30      -1.232   4.145   9.106  1.00  0.00
ATOM     87  C   GLN    30      -1.023   4.564   7.653  1.00  0.00
ATOM     88  O   GLN    30      -0.600   3.756   6.820  1.00  0.00
ATOM     89  N   GLN    31      -1.298   5.840   7.334  1.00  0.00
ATOM     90  CA  GLN    31      -1.134   6.342   5.965  1.00  0.00
ATOM     91  C   GLN    31       0.268   6.192   5.386  1.00  0.00
ATOM     92  O   GLN    31       0.418   5.988   4.183  1.00  0.00
ATOM     93  N   LYS    32       1.295   6.292   6.224  1.00  0.00
ATOM     94  CA  LYS    32       2.652   6.137   5.716  1.00  0.00
ATOM     95  C   LYS    32       2.868   4.707   5.235  1.00  0.00
ATOM     96  O   LYS    32       3.533   4.478   4.224  1.00  0.00
ATOM     97  N   LEU    33       2.305   3.744   5.959  1.00  0.00
ATOM     98  CA  LEU    33       2.435   2.345   5.571  1.00  0.00
ATOM     99  C   LEU    33       1.658   2.106   4.277  1.00  0.00
ATOM    100  O   LEU    33       2.117   1.377   3.398  1.00  0.00
ATOM    101  N   ARG    34       0.483   2.720   4.154  1.00  0.00
ATOM    102  CA  ARG    34      -0.313   2.550   2.941  1.00  0.00
ATOM    103  C   ARG    34       0.457   3.100   1.746  1.00  0.00
ATOM    104  O   ARG    34       0.446   2.509   0.668  1.00  0.00
ATOM    105  N   GLN    35       1.132   4.227   1.945  1.00  0.00
ATOM    106  CA  GLN    35       1.919   4.831   0.873  1.00  0.00
ATOM    107  C   GLN    35       3.038   3.865   0.468  1.00  0.00
ATOM    108  O   GLN    35       3.351   3.720  -0.715  1.00  0.00
ATOM    109  N   GLU    36       3.637   3.198   1.451  1.00  0.00
ATOM    110  CA  GLU    36       4.691   2.236   1.162  1.00  0.00
ATOM    111  C   GLU    36       4.139   1.096   0.305  1.00  0.00
ATOM    112  O   GLU    36       4.771   0.683  -0.668  1.00  0.00
ATOM    113  N   TYR    37       2.959   0.588   0.655  1.00  0.00
ATOM    114  CA  TYR    37       2.372  -0.499  -0.122  1.00  0.00
ATOM    115  C   TYR    37       2.053  -0.057  -1.542  1.00  0.00
ATOM    116  O   TYR    37       2.226  -0.821  -2.486  1.00  0.00
ATOM    117  N   LEU    38       1.588   1.178  -1.693  1.00  0.00
ATOM    118  CA  LEU    38       1.277   1.698  -3.016  1.00  0.00
ATOM    119  C   LEU    38       2.558   1.736  -3.847  1.00  0.00
ATOM    120  O   LEU    38       2.572   1.333  -5.012  1.00  0.00
ATOM    121  N   LYS    39       3.643   2.205  -3.242  1.00  0.00
ATOM    122  CA  LYS    39       4.901   2.280  -3.973  1.00  0.00
ATOM    123  C   LYS    39       5.442   0.902  -4.342  1.00  0.00
ATOM    124  O   LYS    39       6.034   0.737  -5.409  1.00  0.00
ATOM    125  N   GLY    40       5.248  -0.090  -3.477  1.00  0.00
ATOM    126  CA  GLY    40       5.715  -1.435  -3.802  1.00  0.00
ATOM    127  C   GLY    40       4.920  -1.941  -5.004  1.00  0.00
ATOM    128  O   GLY    40       5.460  -2.618  -5.881  1.00  0.00
TER
END
