
#######################################################
#                                                     #
#                        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 (  178),  selected   36 , name T0335TS556_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS556_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      A       5          2.283
LGA    A       8      K       6          2.292
LGA    R       9      I       7          1.610
LGA    I      10      A       8          1.515
LGA    N      11      R       9          1.893
LGA    E      12      I      10          1.768
LGA    L      13      N      11          0.963
LGA    A      14      E      12          1.230
LGA    A      15      L      13          1.906
LGA    K      16      A      14          2.253
LGA    -       -      A      15           -
LGA    A      17      K      16          1.518
LGA    K      18      A      17          2.214
LGA    A      19      K      18          2.894
LGA    G      20      A      19          1.807
LGA    V      21      G      20          1.172
LGA    I      22      V      21          2.876
LGA    T      23      -       -           -
LGA    E      24      -       -           -
LGA    E      25      -       -           -
LGA    E      26      I      22          4.251
LGA    K      27      T      23          2.819
LGA    A      28      E      24          2.824
LGA    E      29      E      25          2.166
LGA    Q      30      E      26          1.359
LGA    Q      31      K      27          1.784
LGA    K      32      A      28          1.655
LGA    L      33      E      29          0.492
LGA    R      34      Q      30          0.746
LGA    Q      35      Q      31          1.727
LGA    E      36      K      32          0.379
LGA    Y      37      L      33          1.520
LGA    L      38      R      34          2.319
LGA    K      39      Q      35          2.941
LGA    G      40      E      36          3.058
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)   36   36    5.0     31    2.11     6.45     74.118     1.404

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.991625 * X  +   0.128708 * Y  +   0.010671 * Z  +   7.094102
  Y_new =   0.028480 * X  +   0.137339 * Y  +   0.990115 * Z  + -11.725638
  Z_new =   0.125970 * X  +   0.982126 * Y  +  -0.139855 * Z  + -12.475701 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.712245   -1.429347  [ DEG:    98.1044    -81.8956 ]
  Theta =  -0.126305   -3.015287  [ DEG:    -7.2368   -172.7632 ]
  Phi   =   3.112880   -0.028713  [ DEG:   178.3549     -1.6451 ]
 
# 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: T0335TS556_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS556_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   31   2.11    6.45  74.118
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS556_1-D1
PFRMAT TS
TARGET T0335
MODEL 1
PARENT N/A
ATOM     21  N   ALA     5       3.576  -7.546  -9.384  1.00 10.00
ATOM     22  CA  ALA     5       2.841  -6.304  -9.589  1.00 10.00
ATOM     23  C   ALA     5       1.407  -6.424  -9.089  1.00 10.00
ATOM     24  O   ALA     5       0.885  -5.512  -8.448  1.00 10.00
ATOM     25  CB  ALA     5       2.862  -5.912 -11.058  1.00 10.00
ATOM     26  N   LYS     6       0.775  -7.554  -9.388  1.00 10.00
ATOM     27  CA  LYS     6      -0.598  -7.798  -8.962  1.00 10.00
ATOM     28  C   LYS     6      -0.699  -7.878  -7.444  1.00 10.00
ATOM     29  O   LYS     6      -1.614  -7.315  -6.843  1.00 10.00
ATOM     30  CB  LYS     6      -1.132  -9.073  -9.598  1.00 10.00
ATOM     31  N   ILE     7       0.249  -8.580  -6.830  1.00 10.00
ATOM     32  CA  ILE     7       0.279  -8.718  -5.379  1.00 10.00
ATOM     33  C   ILE     7       0.473  -7.368  -4.701  1.00 10.00
ATOM     34  O   ILE     7      -0.172  -7.069  -3.696  1.00 10.00
ATOM     35  CB  ILE     7       1.376  -9.686  -4.962  1.00 10.00
ATOM     36  N   ALA     8       1.366  -6.555  -5.257  1.00 10.00
ATOM     37  CA  ALA     8       1.629  -5.225  -4.720  1.00 10.00
ATOM     38  C   ALA     8       0.387  -4.348  -4.787  1.00 10.00
ATOM     39  O   ALA     8       0.052  -3.655  -3.826  1.00 10.00
ATOM     40  CB  ALA     8       2.783  -4.572  -5.466  1.00 10.00
ATOM     41  N   ARG     9      -0.296  -4.382  -5.927  1.00 10.00
ATOM     42  CA  ARG     9      -1.499  -3.583  -6.124  1.00 10.00
ATOM     43  C   ARG     9      -2.612  -4.023  -5.184  1.00 10.00
ATOM     44  O   ARG     9      -3.312  -3.193  -4.603  1.00 10.00
ATOM     45  CB  ARG     9      -1.961  -3.668  -7.572  1.00 10.00
ATOM     46  N   ILE    10      -2.772  -5.334  -5.037  1.00 10.00
ATOM     47  CA  ILE    10      -3.800  -5.887  -4.162  1.00 10.00
ATOM     48  C   ILE    10      -3.536  -5.527  -2.706  1.00 10.00
ATOM     49  O   ILE    10      -4.455  -5.172  -1.968  1.00 10.00
ATOM     50  CB  ILE    10      -3.882  -7.396  -4.330  1.00 10.00
ATOM     51  N   ASN    11      -2.274  -5.618  -2.299  1.00 10.00
ATOM     52  CA  ASN    11      -1.885  -5.285  -0.933  1.00 10.00
ATOM     53  C   ASN    11      -2.232  -3.840  -0.599  1.00 10.00
ATOM     54  O   ASN    11      -2.603  -3.528   0.533  1.00 10.00
ATOM     55  CB  ASN    11      -0.398  -5.535  -0.731  1.00 10.00
ATOM     56  N   GLU    12      -2.111  -2.963  -1.589  1.00 10.00
ATOM     57  CA  GLU    12      -2.382  -1.544  -1.392  1.00 10.00
ATOM     58  C   GLU    12      -3.875  -1.284  -1.238  1.00 10.00
ATOM     59  O   GLU    12      -4.293  -0.490  -0.395  1.00 10.00
ATOM     60  CB  GLU    12      -1.817  -0.731  -2.548  1.00 10.00
ATOM     61  N   LEU    13      -4.675  -1.958  -2.057  1.00 10.00
ATOM     62  CA  LEU    13      -6.126  -1.906  -1.925  1.00 10.00
ATOM     63  C   LEU    13      -6.575  -2.437  -0.570  1.00 10.00
ATOM     64  O   LEU    13      -7.424  -1.839   0.092  1.00 10.00
ATOM     65  CB  LEU    13      -6.789  -2.686  -3.050  1.00 10.00
ATOM     66  N   ALA    14      -6.001  -3.564  -0.162  1.00 10.00
ATOM     67  CA  ALA    14      -6.273  -4.129   1.154  1.00 10.00
ATOM     68  C   ALA    14      -5.918  -3.144   2.260  1.00 10.00
ATOM     69  O   ALA    14      -6.636  -3.026   3.253  1.00 10.00
ATOM     70  CB  ALA    14      -5.512  -5.433   1.338  1.00 10.00
ATOM     71  N   ALA    15      -4.806  -2.439   2.083  1.00 10.00
ATOM     72  CA  ALA    15      -4.379  -1.427   3.043  1.00 10.00
ATOM     73  C   ALA    15      -5.428  -0.334   3.194  1.00 10.00
ATOM     74  O   ALA    15      -5.697   0.133   4.301  1.00 10.00
ATOM     75  CB  ALA    15      -3.044  -0.829   2.625  1.00 10.00
ATOM     76  N   LYS    16      -6.021   0.070   2.074  1.00 10.00
ATOM     77  CA  LYS    16      -7.079   1.073   2.086  1.00 10.00
ATOM     78  C   LYS    16      -8.235   0.643   2.980  1.00 10.00
ATOM     79  O   LYS    16      -8.813   1.458   3.698  1.00 10.00
ATOM     80  CB  LYS    16      -7.571   1.341   0.672  1.00 10.00
ATOM     81  N   ALA    17      -8.568  -0.643   2.931  1.00 10.00
ATOM     82  CA  ALA    17      -9.637  -1.190   3.758  1.00 10.00
ATOM     83  C   ALA    17      -9.239  -1.216   5.228  1.00 10.00
ATOM     84  O   ALA    17     -10.071  -1.001   6.110  1.00 10.00
ATOM     85  CB  ALA    17     -10.014  -2.585   3.282  1.00 10.00
ATOM     86  N   LYS    18      -7.963  -1.481   5.485  1.00 10.00
ATOM     87  CA  LYS    18      -7.445  -1.504   6.847  1.00 10.00
ATOM     88  C   LYS    18      -7.443  -0.110   7.460  1.00 10.00
ATOM     89  O   LYS    18      -7.769   0.064   8.634  1.00 10.00
ATOM     90  CB  LYS    18      -6.044  -2.097   6.873  1.00 10.00
ATOM     91  N   ALA    19      -7.073   0.883   6.658  1.00 10.00
ATOM     92  CA  ALA    19      -6.992   2.260   7.131  1.00 10.00
ATOM     93  C   ALA    19      -8.377   2.842   7.374  1.00 10.00
ATOM     94  O   ALA    19      -8.578   3.623   8.304  1.00 10.00
ATOM     95  CB  ALA    19      -6.222   3.117   6.136  1.00 10.00
ATOM     96  N   GLY    20      -9.332   2.458   6.532  1.00 10.00
ATOM     97  CA  GLY    20     -10.716   2.887   6.695  1.00 10.00
ATOM     98  C   GLY    20     -11.324   2.313   7.969  1.00 10.00
ATOM     99  O   GLY    20     -12.075   2.992   8.670  1.00 10.00
ATOM    100  N   VAL    21     -10.995   1.060   8.263  1.00 10.00
ATOM    101  CA  VAL    21     -11.497   0.396   9.460  1.00 10.00
ATOM    102  C   VAL    21     -10.592   0.660  10.657  1.00 10.00
ATOM    103  O   VAL    21     -11.008   0.510  11.807  1.00 10.00
ATOM    104  CB  VAL    21     -11.638  -1.099   9.219  1.00 10.00
ATOM    105  N   ILE    22      -9.353   1.053  10.381  1.00 10.00
ATOM    106  CA  ILE    22      -8.363   1.259  11.431  1.00 10.00
ATOM    107  C   ILE    22      -8.325   2.716  11.874  1.00 10.00
ATOM    108  O   ILE    22      -9.002   3.568  11.298  1.00 10.00
ATOM    109  CB  ILE    22      -6.989   0.812  10.958  1.00 10.00
ATOM    110  N   THR    23      -7.530   2.996  12.901  1.00 10.00
ATOM    111  CA  THR    23      -7.421   4.347  13.439  1.00 10.00
ATOM    112  C   THR    23      -6.636   5.253  12.499  1.00 10.00
ATOM    113  O   THR    23      -5.980   4.780  11.571  1.00 10.00
ATOM    114  CB  THR    23      -6.774   4.320  14.815  1.00 10.00
ATOM    115  N   GLU    24      -6.707   6.557  12.745  1.00 10.00
ATOM    116  CA  GLU    24      -5.992   7.530  11.929  1.00 10.00
ATOM    117  C   GLU    24      -4.485   7.315  12.008  1.00 10.00
ATOM    118  O   GLU    24      -3.783   7.407  11.002  1.00 10.00
ATOM    119  CB  GLU    24      -6.351   8.945  12.355  1.00 10.00
ATOM    120  N   GLU    25      -3.996   7.029  13.210  1.00 10.00
ATOM    121  CA  GLU    25      -2.573   6.790  13.421  1.00 10.00
ATOM    122  C   GLU    25      -2.119   5.517  12.720  1.00 10.00
ATOM    123  O   GLU    25      -1.033   5.469  12.143  1.00 10.00
ATOM    124  CB  GLU    25      -2.263   6.719  14.908  1.00 10.00
ATOM    125  N   GLU    26      -2.957   4.486  12.774  1.00 10.00
ATOM    126  CA  GLU    26      -2.640   3.209  12.147  1.00 10.00
ATOM    127  C   GLU    26      -2.712   3.306  10.630  1.00 10.00
ATOM    128  O   GLU    26      -1.925   2.682   9.920  1.00 10.00
ATOM    129  CB  GLU    26      -3.577   2.123  12.656  1.00 10.00
ATOM    130  N   LYS    27      -3.663   4.094  10.137  1.00 10.00
ATOM    131  CA  LYS    27      -3.823   4.295   8.702  1.00 10.00
ATOM    132  C   LYS    27      -2.616   5.007   8.107  1.00 10.00
ATOM    133  O   LYS    27      -2.145   4.654   7.025  1.00 10.00
ATOM    134  CB  LYS    27      -5.097   5.077   8.415  1.00 10.00
ATOM    135  N   ALA    28      -2.117   6.012   8.819  1.00 10.00
ATOM    136  CA  ALA    28      -0.957   6.770   8.368  1.00 10.00
ATOM    137  C   ALA    28       0.241   5.859   8.139  1.00 10.00
ATOM    138  O   ALA    28       0.880   5.909   7.087  1.00 10.00
ATOM    139  CB  ALA    28      -0.613   7.862   9.371  1.00 10.00
ATOM    140  N   GLU    29       0.544   5.028   9.131  1.00 10.00
ATOM    141  CA  GLU    29       1.664   4.099   9.036  1.00 10.00
ATOM    142  C   GLU    29       1.449   3.088   7.918  1.00 10.00
ATOM    143  O   GLU    29       2.373   2.770   7.169  1.00 10.00
ATOM    144  CB  GLU    29       1.875   3.387  10.364  1.00 10.00
ATOM    145  N   GLN    30       0.223   2.586   7.809  1.00 10.00
ATOM    146  CA  GLN    30      -0.119   1.619   6.772  1.00 10.00
ATOM    147  C   GLN    30       0.015   2.231   5.384  1.00 10.00
ATOM    148  O   GLN    30       0.491   1.581   4.452  1.00 10.00
ATOM    149  CB  GLN    30      -1.527   1.089   6.987  1.00 10.00
ATOM    150  N   GLN    31      -0.408   3.483   5.251  1.00 10.00
ATOM    151  CA  GLN    31      -0.320   4.191   3.979  1.00 10.00
ATOM    152  C   GLN    31       1.129   4.358   3.540  1.00 10.00
ATOM    153  O   GLN    31       1.451   4.218   2.360  1.00 10.00
ATOM    154  CB  GLN    31      -1.007   5.544   4.076  1.00 10.00
ATOM    155  N   LYS    32       2.000   4.658   4.497  1.00 10.00
ATOM    156  CA  LYS    32       3.419   4.835   4.213  1.00 10.00
ATOM    157  C   LYS    32       4.053   3.533   3.743  1.00 10.00
ATOM    158  O   LYS    32       4.737   3.498   2.720  1.00 10.00
ATOM    159  CB  LYS    32       4.144   5.367   5.441  1.00 10.00
ATOM    160  N   LEU    33       3.823   2.462   4.496  1.00 10.00
ATOM    161  CA  LEU    33       4.387   1.158   4.169  1.00 10.00
ATOM    162  C   LEU    33       3.865   0.654   2.830  1.00 10.00
ATOM    163  O   LEU    33       4.600   0.037   2.059  1.00 10.00
ATOM    164  CB  LEU    33       4.083   0.157   5.271  1.00 10.00
ATOM    165  N   ARG    34       2.591   0.917   2.560  1.00 10.00
ATOM    166  CA  ARG    34       1.973   0.506   1.306  1.00 10.00
ATOM    167  C   ARG    34       2.582   1.248   0.122  1.00 10.00
ATOM    168  O   ARG    34       2.852   0.655  -0.921  1.00 10.00
ATOM    169  CB  ARG    34       0.469   0.731   1.357  1.00 10.00
ATOM    170  N   GLN    35       2.795   2.549   0.292  1.00 10.00
ATOM    171  CA  GLN    35       3.389   3.370  -0.756  1.00 10.00
ATOM    172  C   GLN    35       4.797   2.899  -1.093  1.00 10.00
ATOM    173  O   GLN    35       5.201   2.902  -2.256  1.00 10.00
ATOM    174  CB  GLN    35       3.404   4.833  -0.338  1.00 10.00
ATOM    175  N   GLU    36       5.542   2.494  -0.070  1.00 10.00
ATOM    176  CA  GLU    36       6.901   2.001  -0.260  1.00 10.00
ATOM    177  C   GLU    36       6.909   0.701  -1.055  1.00 10.00
ATOM    178  O   GLU    36       7.726   0.521  -1.958  1.00 10.00
ATOM    179  CB  GLU    36       7.587   1.807   1.084  1.00 10.00
ATOM    180  N   TYR    37       5.996  -0.201  -0.713  1.00 10.00
ATOM    181  CA  TYR    37       5.897  -1.487  -1.394  1.00 10.00
ATOM    182  C   TYR    37       5.529  -1.305  -2.861  1.00 10.00
ATOM    183  O   TYR    37       6.042  -2.008  -3.731  1.00 10.00
ATOM    184  CB  TYR    37       4.880  -2.378  -0.698  1.00 10.00
ATOM    185  N   LEU    38       4.638  -0.357  -3.130  1.00 10.00
ATOM    186  CA  LEU    38       4.198  -0.082  -4.492  1.00 10.00
ATOM    187  C   LEU    38       5.359   0.378  -5.364  1.00 10.00
ATOM    188  O   LEU    38       5.438   0.035  -6.543  1.00 10.00
ATOM    189  CB  LEU    38       3.087   0.957  -4.492  1.00 10.00
ATOM    190  N   LYS    39       6.260   1.159  -4.775  1.00 10.00
ATOM    191  CA  LYS    39       7.435   1.644  -5.489  1.00 10.00
ATOM    192  C   LYS    39       8.386   0.503  -5.826  1.00 10.00
ATOM    193  O   LYS    39       8.907   0.424  -6.938  1.00 10.00
ATOM    194  CB  LYS    39       8.150   2.709  -4.670  1.00 10.00
ATOM    195  N   GLY    40       8.608  -0.381  -4.857  1.00 10.00
ATOM    196  CA  GLY    40       9.455  -1.549  -5.066  1.00 10.00
ATOM    197  C   GLY    40       8.927  -2.416  -6.200  1.00 10.00
ATOM    198  O   GLY    40       9.688  -2.861  -7.060  1.00 10.00
TER
END
