
#######################################################
#                                                     #
#                        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_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS035_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      A       5          3.595
LGA    K       6      K       6          2.791
LGA    I       7      I       7          2.140
LGA    A       8      A       8          2.236
LGA    R       9      R       9          1.682
LGA    I      10      I      10          0.823
LGA    N      11      N      11          1.454
LGA    E      12      E      12          1.255
LGA    L      13      L      13          2.077
LGA    A      14      A      14          2.523
LGA    A      15      A      15          1.647
LGA    K      16      K      16          1.501
LGA    -       -      A      17           -
LGA    A      17      K      18          0.652
LGA    K      18      A      19          3.021
LGA    A      19      -       -           -
LGA    G      20      G      20          1.836
LGA    V      21      V      21          1.364
LGA    I      22      I      22          1.330
LGA    T      23      T      23          2.571
LGA    E      24      E      24          2.987
LGA    E      25      E      25          2.679
LGA    E      26      E      26          1.457
LGA    K      27      K      27          0.889
LGA    A      28      A      28          1.465
LGA    E      29      E      29          1.691
LGA    Q      30      Q      30          1.287
LGA    Q      31      Q      31          0.793
LGA    K      32      K      32          0.971
LGA    L      33      L      33          1.625
LGA    R      34      R      34          1.655
LGA    Q      35      Q      35          0.837
LGA    E      36      E      36          0.742
LGA    Y      37      Y      37          1.342
LGA    L      38      L      38          1.177
LGA    K      39      K      39          0.735
LGA    G      40      G      40          0.696

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     35    1.81    94.29     89.340     1.835

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.359934 * X  +  -0.676242 * Y  +   0.642763 * Z  +   1.864132
  Y_new =   0.212066 * X  +  -0.730204 * Y  +  -0.649485 * Z  +   3.506063
  Z_new =   0.908557 * X  +  -0.097464 * Y  +   0.406233 * Z  + -11.693212 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.235470    2.906122  [ DEG:   -13.4914    166.5086 ]
  Theta =  -1.139817   -2.001776  [ DEG:   -65.3067   -114.6933 ]
  Phi   =   2.609167   -0.532425  [ DEG:   149.4943    -30.5057 ]
 
# 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_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS035_1-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   35   1.81   94.29  89.340
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS035_1-D1
PFRMAT TS
TARGET T0335
MODEL  1  REFINED
PARENT N/A
ATOM     17  N   ALA     5       1.992 -10.919  -3.929  1.00  0.00
ATOM     18  CA  ALA     5       1.428 -10.640  -2.623  1.00  0.00
ATOM     19  C   ALA     5       1.455  -9.154  -2.308  1.00  0.00
ATOM     20  O   ALA     5       0.623  -8.648  -1.556  1.00  0.00
ATOM     21  N   LYS     6       2.412  -8.423  -2.873  1.00  0.00
ATOM     22  CA  LYS     6       2.491  -7.000  -2.607  1.00  0.00
ATOM     23  C   LYS     6       1.323  -6.249  -3.227  1.00  0.00
ATOM     24  O   LYS     6       0.695  -5.409  -2.584  1.00  0.00
ATOM     25  N   ILE     7       1.008  -6.536  -4.487  1.00  0.00
ATOM     26  CA  ILE     7      -0.105  -5.862  -5.127  1.00  0.00
ATOM     27  C   ILE     7      -1.427  -6.217  -4.466  1.00  0.00
ATOM     28  O   ILE     7      -2.334  -5.389  -4.376  1.00  0.00
ATOM     29  N   ALA     8      -1.565  -7.451  -3.991  1.00  0.00
ATOM     30  CA  ALA     8      -2.809  -7.851  -3.361  1.00  0.00
ATOM     31  C   ALA     8      -3.047  -7.096  -2.064  1.00  0.00
ATOM     32  O   ALA     8      -4.164  -6.672  -1.770  1.00  0.00
ATOM     33  N   ARG     9      -2.003  -6.911  -1.260  1.00  0.00
ATOM     34  CA  ARG     9      -2.167  -6.191  -0.013  1.00  0.00
ATOM     35  C   ARG     9      -2.568  -4.744  -0.249  1.00  0.00
ATOM     36  O   ARG     9      -3.117  -4.085   0.631  1.00  0.00
ATOM     37  N   ILE    10      -2.300  -4.221  -1.443  1.00  0.00
ATOM     38  CA  ILE    10      -2.668  -2.848  -1.731  1.00  0.00
ATOM     39  C   ILE    10      -4.177  -2.675  -1.796  1.00  0.00
ATOM     40  O   ILE    10      -4.719  -1.661  -1.360  1.00  0.00
ATOM     41  N   ASN    11      -4.885  -3.661  -2.340  1.00  0.00
ATOM     42  CA  ASN    11      -6.334  -3.624  -2.292  1.00  0.00
ATOM     43  C   ASN    11      -6.845  -3.561  -0.862  1.00  0.00
ATOM     44  O   ASN    11      -7.749  -2.791  -0.543  1.00  0.00
ATOM     45  N   GLU    12      -6.277  -4.369   0.030  1.00  0.00
ATOM     46  CA  GLU    12      -6.744  -4.378   1.402  1.00  0.00
ATOM     47  C   GLU    12      -6.349  -3.106   2.135  1.00  0.00
ATOM     48  O   GLU    12      -7.143  -2.527   2.875  1.00  0.00
ATOM     49  N   LEU    13      -5.116  -2.646   1.946  1.00  0.00
ATOM     50  CA  LEU    13      -4.751  -1.331   2.435  1.00  0.00
ATOM     51  C   LEU    13      -5.774  -0.281   2.035  1.00  0.00
ATOM     52  O   LEU    13      -6.281   0.464   2.872  1.00  0.00
ATOM     53  N   ALA    14      -6.097  -0.197   0.747  1.00  0.00
ATOM     54  CA  ALA    14      -7.052   0.798   0.303  1.00  0.00
ATOM     55  C   ALA    14      -8.424   0.571   0.917  1.00  0.00
ATOM     56  O   ALA    14      -9.092   1.511   1.343  1.00  0.00
ATOM     57  N   ALA    15      -8.872  -0.680   0.975  1.00  0.00
ATOM     58  CA  ALA    15     -10.164  -0.961   1.570  1.00  0.00
ATOM     59  C   ALA    15     -10.209  -0.547   3.031  1.00  0.00
ATOM     60  O   ALA    15     -11.212  -0.024   3.513  1.00  0.00
ATOM     61  N   LYS    16      -9.124  -0.774   3.767  1.00  0.00
ATOM     62  CA  LYS    16      -9.106  -0.397   5.167  1.00  0.00
ATOM     63  C   LYS    16      -8.959   1.107   5.340  1.00  0.00
ATOM     64  O   LYS    16      -9.537   1.701   6.249  1.00  0.00
ATOM     65  N   ALA    17      -8.184   1.751   4.472  1.00  0.00
ATOM     66  CA  ALA    17      -8.021   3.189   4.575  1.00  0.00
ATOM     67  C   ALA    17      -9.354   3.912   4.478  1.00  0.00
ATOM     68  O   ALA    17      -9.605   4.880   5.192  1.00  0.00
ATOM     69  N   LYS    18     -10.236   3.457   3.593  1.00  0.00
ATOM     70  CA  LYS    18     -11.521   4.113   3.446  1.00  0.00
ATOM     71  C   LYS    18     -12.522   3.621   4.478  1.00  0.00
ATOM     72  O   LYS    18     -13.559   4.244   4.705  1.00  0.00
ATOM     73  N   ALA    19     -12.233   2.496   5.125  1.00  0.00
ATOM     74  CA  ALA    19     -13.160   1.967   6.107  1.00  0.00
ATOM     75  C   ALA    19     -12.706   2.273   7.525  1.00  0.00
ATOM     76  O   ALA    19     -13.433   2.040   8.489  1.00  0.00
ATOM     77  N   GLY    20     -11.495   2.800   7.683  1.00  0.00
ATOM     78  CA  GLY    20     -11.007   3.113   9.012  1.00  0.00
ATOM     79  C   GLY    20      -9.586   3.649   8.974  1.00  0.00
ATOM     80  O   GLY    20      -8.862   3.462   7.997  1.00  0.00
ATOM     81  N   VAL    21      -9.156   4.326  10.035  1.00  0.00
ATOM     82  CA  VAL    21      -7.813   4.871  10.053  1.00  0.00
ATOM     83  C   VAL    21      -6.763   3.772  10.011  1.00  0.00
ATOM     84  O   VAL    21      -6.876   2.759  10.699  1.00  0.00
ATOM     85  N   ILE    22      -5.720   3.949   9.205  1.00  0.00
ATOM     86  CA  ILE    22      -4.692   2.930   9.116  1.00  0.00
ATOM     87  C   ILE    22      -3.620   3.124  10.175  1.00  0.00
ATOM     88  O   ILE    22      -3.361   4.241  10.621  1.00  0.00
ATOM     89  N   THR    23      -2.972   2.042  10.598  1.00  0.00
ATOM     90  CA  THR    23      -1.900   2.171  11.565  1.00  0.00
ATOM     91  C   THR    23      -0.633   2.720  10.927  1.00  0.00
ATOM     92  O   THR    23      -0.531   2.821   9.705  1.00  0.00
ATOM     93  N   GLU    24       0.355   3.085  11.739  1.00  0.00
ATOM     94  CA  GLU    24       1.589   3.610  11.187  1.00  0.00
ATOM     95  C   GLU    24       2.262   2.606  10.266  1.00  0.00
ATOM     96  O   GLU    24       2.756   2.957   9.196  1.00  0.00
ATOM     97  N   GLU    25       2.298   1.337  10.662  1.00  0.00
ATOM     98  CA  GLU    25       2.926   0.333   9.826  1.00  0.00
ATOM     99  C   GLU    25       2.202   0.179   8.497  1.00  0.00
ATOM    100  O   GLU    25       2.826   0.058   7.444  1.00  0.00
ATOM    101  N   GLU    26       0.872   0.181   8.518  1.00  0.00
ATOM    102  CA  GLU    26       0.128   0.051   7.281  1.00  0.00
ATOM    103  C   GLU    26       0.372   1.231   6.354  1.00  0.00
ATOM    104  O   GLU    26       0.503   1.070   5.141  1.00  0.00
ATOM    105  N   LYS    27       0.440   2.440   6.904  1.00  0.00
ATOM    106  CA  LYS    27       0.672   3.603   6.069  1.00  0.00
ATOM    107  C   LYS    27       2.015   3.526   5.362  1.00  0.00
ATOM    108  O   LYS    27       2.157   3.963   4.220  1.00  0.00
ATOM    109  N   ALA    28       3.026   2.971   6.022  1.00  0.00
ATOM    110  CA  ALA    28       4.329   2.862   5.396  1.00  0.00
ATOM    111  C   ALA    28       4.290   1.956   4.176  1.00  0.00
ATOM    112  O   ALA    28       4.934   2.225   3.164  1.00  0.00
ATOM    113  N   GLU    29       3.531   0.866   4.245  1.00  0.00
ATOM    114  CA  GLU    29       3.451  -0.034   3.110  1.00  0.00
ATOM    115  C   GLU    29       2.727   0.607   1.939  1.00  0.00
ATOM    116  O   GLU    29       3.049   0.357   0.777  1.00  0.00
ATOM    117  N   GLN    30       1.733   1.447   2.215  1.00  0.00
ATOM    118  CA  GLN    30       1.014   2.101   1.138  1.00  0.00
ATOM    119  C   GLN    30       1.922   3.021   0.339  1.00  0.00
ATOM    120  O   GLN    30       1.925   2.998  -0.891  1.00  0.00
ATOM    121  N   GLN    31       2.711   3.848   1.018  1.00  0.00
ATOM    122  CA  GLN    31       3.596   4.752   0.310  1.00  0.00
ATOM    123  C   GLN    31       4.692   4.000  -0.427  1.00  0.00
ATOM    124  O   GLN    31       5.107   4.387  -1.519  1.00  0.00
ATOM    125  N   LYS    32       5.185   2.909   0.154  1.00  0.00
ATOM    126  CA  LYS    32       6.239   2.155  -0.496  1.00  0.00
ATOM    127  C   LYS    32       5.737   1.454  -1.748  1.00  0.00
ATOM    128  O   LYS    32       6.469   1.294  -2.723  1.00  0.00
ATOM    129  N   LEU    33       4.479   1.023  -1.747  1.00  0.00
ATOM    130  CA  LEU    33       3.928   0.391  -2.930  1.00  0.00
ATOM    131  C   LEU    33       3.824   1.369  -4.090  1.00  0.00
ATOM    132  O   LEU    33       4.185   1.053  -5.222  1.00  0.00
ATOM    133  N   ARG    34       3.327   2.576  -3.832  1.00  0.00
ATOM    134  CA  ARG    34       3.224   3.559  -4.892  1.00  0.00
ATOM    135  C   ARG    34       4.586   3.900  -5.474  1.00  0.00
ATOM    136  O   ARG    34       4.778   3.892  -6.689  1.00  0.00
ATOM    137  N   GLN    35       5.559   4.204  -4.620  1.00  0.00
ATOM    138  CA  GLN    35       6.853   4.630  -5.119  1.00  0.00
ATOM    139  C   GLN    35       7.475   3.582  -6.028  1.00  0.00
ATOM    140  O   GLN    35       7.975   3.896  -7.107  1.00  0.00
ATOM    141  N   GLU    36       7.456   2.320  -5.613  1.00  0.00
ATOM    142  CA  GLU    36       8.026   1.275  -6.442  1.00  0.00
ATOM    143  C   GLU    36       7.272   1.128  -7.753  1.00  0.00
ATOM    144  O   GLU    36       7.871   0.984  -8.818  1.00  0.00
ATOM    145  N   TYR    37       5.944   1.161  -7.705  1.00  0.00
ATOM    146  CA  TYR    37       5.171   1.038  -8.925  1.00  0.00
ATOM    147  C   TYR    37       5.493   2.154  -9.906  1.00  0.00
ATOM    148  O   TYR    37       5.689   1.915 -11.097  1.00  0.00
ATOM    149  N   LEU    38       5.555   3.393  -9.428  1.00  0.00
ATOM    150  CA  LEU    38       5.869   4.497 -10.314  1.00  0.00
ATOM    151  C   LEU    38       7.244   4.337 -10.942  1.00  0.00
ATOM    152  O   LEU    38       7.432   4.587 -12.131  1.00  0.00
ATOM    153  N   LYS    39       8.233   3.916 -10.157  1.00  0.00
ATOM    154  CA  LYS    39       9.562   3.728 -10.704  1.00  0.00
ATOM    155  C   LYS    39       9.562   2.720 -11.841  1.00  0.00
ATOM    156  O   LYS    39      10.131   2.961 -12.905  1.00  0.00
ATOM    157  N   GLY    40       8.924   1.569 -11.642  1.00  0.00
ATOM    158  CA  GLY    40       8.865   0.580 -12.701  1.00  0.00
ATOM    159  C   GLY    40       8.085   1.090 -13.901  1.00  0.00
ATOM    160  O   GLY    40       8.371   0.734 -15.043  1.00  0.00
TER
END
