
#######################################################
#                                                     #
#                        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 T0335TS239_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335TS239_4-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           -
LGA    K       6      -       -           -
LGA    I       7      K       6           #
LGA    A       8      I       7          4.453
LGA    -       -      A       8           -
LGA    R       9      R       9          5.362
LGA    I      10      I      10          3.916
LGA    N      11      N      11          2.408
LGA    E      12      E      12          2.359
LGA    L      13      L      13          2.146
LGA    A      14      A      14          0.963
LGA    A      15      A      15          2.407
LGA    K      16      K      16          3.495
LGA    A      17      A      17          2.669
LGA    K      18      K      18          3.959
LGA    A      19      A      19           #
LGA    G      20      -       -           -
LGA    V      21      G      20          3.867
LGA    I      22      V      21          3.661
LGA    T      23      I      22          2.788
LGA    E      24      T      23          2.288
LGA    E      25      E      24          2.582
LGA    E      26      E      25          2.597
LGA    K      27      E      26          2.980
LGA    A      28      K      27          2.088
LGA    E      29      A      28          1.879
LGA    Q      30      E      29          2.689
LGA    Q      31      Q      30          3.099
LGA    -       -      Q      31           -
LGA    K      32      K      32          4.777
LGA    L      33      L      33          2.257
LGA    -       -      R      34           -
LGA    R      34      Q      35          1.883
LGA    Q      35      E      36          1.631
LGA    E      36      Y      37          2.816
LGA    Y      37      L      38          2.716
LGA    L      38      K      39          1.363
LGA    K      39      G      40          2.260
LGA    G      40      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   36   36    5.0     30    2.98    50.00     62.943     0.974

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.572010 * X  +  -0.326721 * Y  +   0.752368 * Z  +   3.355224
  Y_new =   0.820171 * X  +   0.240297 * Y  +  -0.519208 * Z  + -39.342178
  Z_new =  -0.011156 * X  +   0.914063 * Y  +   0.405420 * Z  +  75.504410 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.153331   -1.988262  [ DEG:    66.0810   -113.9190 ]
  Theta =   0.011156    3.130437  [ DEG:     0.6392    179.3608 ]
  Phi   =   0.961799   -2.179793  [ DEG:    55.1070   -124.8930 ]
 
# 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: T0335TS239_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335TS239_4-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   30   2.98   50.00  62.943
REMARK  ---------------------------------------------------------- 
MOLECULE T0335TS239_4-D1
PFRMAT TS
TARGET T0335
MODEL 4
PARENT 1gkr_A
ATOM     21  N   ALA     5       3.733   4.700  -8.551  1.00  9.99
ATOM     22  CA  ALA     5       3.229   3.894  -7.443  1.00  9.99
ATOM     23  C   ALA     5       2.310   2.862  -8.056  1.00  9.99
ATOM     24  O   ALA     5       1.909   2.998  -9.205  1.00  9.99
ATOM     25  CB  ALA     5       2.473   4.732  -6.419  1.00  9.99
ATOM     26  N   LYS     6       1.995   1.812  -7.316  1.00  9.99
ATOM     27  CA  LYS     6       1.108   0.796  -7.857  1.00  9.99
ATOM     28  C   LYS     6      -0.302   1.035  -7.314  1.00  9.99
ATOM     29  O   LYS     6      -0.605   0.736  -6.158  1.00  9.99
ATOM     30  CB  LYS     6       1.593  -0.599  -7.482  1.00  9.99
ATOM     31  N   ILE     7      -1.153   1.590  -8.168  1.00  9.99
ATOM     32  CA  ILE     7      -2.526   1.918  -7.803  1.00  9.99
ATOM     33  C   ILE     7      -3.299   0.787  -7.149  1.00  9.99
ATOM     34  O   ILE     7      -3.871   0.930  -6.074  1.00  9.99
ATOM     35  CB  ILE     7      -3.278   2.380  -9.045  1.00  9.99
ATOM     36  N   ALA     8      -3.298  -0.344  -7.826  1.00  9.99
ATOM     37  CA  ALA     8      -4.007  -1.528  -7.400  1.00  9.99
ATOM     38  C   ALA     8      -3.581  -2.150  -6.082  1.00  9.99
ATOM     39  O   ALA     8      -4.414  -2.678  -5.352  1.00  9.99
ATOM     40  CB  ALA     8      -3.929  -2.544  -8.524  1.00  9.99
ATOM     41  N   ARG     9      -2.287  -2.103  -5.787  1.00  9.99
ATOM     42  CA  ARG     9      -1.774  -2.662  -4.542  1.00  9.99
ATOM     43  C   ARG     9      -2.120  -1.720  -3.409  1.00  9.99
ATOM     44  O   ARG     9      -2.472  -2.154  -2.314  1.00  9.99
ATOM     45  CB  ARG     9      -0.251  -2.863  -4.612  1.00  9.99
ATOM     46  N   ILE    10      -2.033  -0.423  -3.675  1.00  9.99
ATOM     47  CA  ILE    10      -2.372   0.554  -2.661  1.00  9.99
ATOM     48  C   ILE    10      -3.820   0.340  -2.242  1.00  9.99
ATOM     49  O   ILE    10      -4.128   0.340  -1.052  1.00  9.99
ATOM     50  CB  ILE    10      -2.180   1.976  -3.174  1.00  9.99
ATOM     51  N   ASN    11      -4.711   0.140  -3.208  1.00  9.99
ATOM     52  CA  ASN    11      -6.113  -0.090  -2.878  1.00  9.99
ATOM     53  C   ASN    11      -6.274  -1.318  -1.995  1.00  9.99
ATOM     54  O   ASN    11      -6.969  -1.267  -0.978  1.00  9.99
ATOM     55  CB  ASN    11      -6.938  -0.298  -4.136  1.00  9.99
ATOM     56  N   GLU    12      -5.640  -2.421  -2.383  1.00  9.99
ATOM     57  CA  GLU    12      -5.737  -3.651  -1.607  1.00  9.99
ATOM     58  C   GLU    12      -5.230  -3.441  -0.191  1.00  9.99
ATOM     59  O   GLU    12      -5.889  -3.828   0.777  1.00  9.99
ATOM     60  CB  GLU    12      -4.956  -4.769  -2.277  1.00  9.99
ATOM     61  N   LEU    13      -4.061  -2.831  -0.061  1.00  9.99
ATOM     62  CA  LEU    13      -3.516  -2.586   1.258  1.00  9.99
ATOM     63  C   LEU    13      -4.408  -1.641   2.077  1.00  9.99
ATOM     64  O   LEU    13      -4.560  -1.821   3.285  1.00  9.99
ATOM     65  CB  LEU    13      -2.106  -2.021   1.138  1.00  9.99
ATOM     66  N   ALA    14      -5.002  -0.639   1.433  1.00  9.99
ATOM     67  CA  ALA    14      -5.872   0.285   2.155  1.00  9.99
ATOM     68  C   ALA    14      -7.000  -0.468   2.825  1.00  9.99
ATOM     69  O   ALA    14      -7.317  -0.219   3.989  1.00  9.99
ATOM     70  CB  ALA    14      -6.479   1.311   1.214  1.00  9.99
ATOM     71  N   ALA    15      -7.615  -1.381   2.075  1.00  9.99
ATOM     72  CA  ALA    15      -8.714  -2.169   2.602  1.00  9.99
ATOM     73  C   ALA    15      -8.253  -3.015   3.765  1.00  9.99
ATOM     74  O   ALA    15      -8.894  -3.014   4.806  1.00  9.99
ATOM     75  CB  ALA    15      -9.332  -3.051   1.514  1.00  9.99
ATOM     76  N   LYS    16      -7.139  -3.719   3.612  1.00  9.99
ATOM     77  CA  LYS    16      -6.660  -4.553   4.705  1.00  9.99
ATOM     78  C   LYS    16      -6.409  -3.695   5.943  1.00  9.99
ATOM     79  O   LYS    16      -6.902  -4.007   7.026  1.00  9.99
ATOM     80  CB  LYS    16      -5.364  -5.281   4.330  1.00  9.99
ATOM     81  N   ALA    17      -5.656  -2.610   5.774  1.00  9.99
ATOM     82  CA  ALA    17      -5.322  -1.715   6.880  1.00  9.99
ATOM     83  C   ALA    17      -6.526  -1.026   7.514  1.00  9.99
ATOM     84  O   ALA    17      -6.602  -0.920   8.740  1.00  9.99
ATOM     85  CB  ALA    17      -4.280  -0.661   6.435  1.00  9.99
ATOM     86  N   LYS    18      -7.462  -0.553   6.697  1.00  9.99
ATOM     87  CA  LYS    18      -8.650   0.090   7.244  1.00  9.99
ATOM     88  C   LYS    18      -9.435  -0.932   8.053  1.00  9.99
ATOM     89  O   LYS    18      -9.891  -0.647   9.159  1.00  9.99
ATOM     90  CB  LYS    18      -9.527   0.673   6.128  1.00  9.99
ATOM     91  N   ALA    19      -9.578  -2.135   7.510  1.00  9.99
ATOM     92  CA  ALA    19     -10.303  -3.192   8.200  1.00  9.99
ATOM     93  C   ALA    19      -9.714  -3.465   9.586  1.00  9.99
ATOM     94  O   ALA    19     -10.443  -3.707  10.539  1.00  9.99
ATOM     95  CB  ALA    19     -10.286  -4.456   7.373  1.00  9.99
ATOM     96  N   GLY    20      -8.394  -3.437   9.698  1.00  9.99
ATOM     97  CA  GLY    20      -7.748  -3.679  10.979  1.00  9.99
ATOM     98  C   GLY    20      -7.874  -2.438  11.850  1.00  9.99
ATOM     99  O   GLY    20      -7.260  -2.346  12.909  1.00  9.99
ATOM    100  N   VAL    21      -8.657  -1.470  11.388  1.00  9.99
ATOM    101  CA  VAL    21      -8.849  -0.252  12.153  1.00  9.99
ATOM    102  C   VAL    21      -7.692   0.735  12.222  1.00  9.99
ATOM    103  O   VAL    21      -7.518   1.411  13.231  1.00  9.99
ATOM    104  CB  VAL    21      -9.257  -0.669  13.576  1.00  9.99
ATOM    105  N   ILE    22      -6.895   0.828  11.163  1.00  9.99
ATOM    106  CA  ILE    22      -5.796   1.777  11.172  1.00  9.99
ATOM    107  C   ILE    22      -6.276   3.137  10.698  1.00  9.99
ATOM    108  O   ILE    22      -6.946   3.229   9.670  1.00  9.99
ATOM    109  CB  ILE    22      -4.652   1.246  10.293  1.00  9.99
ATOM    110  N   THR    23      -5.960   4.190  11.445  1.00  9.99
ATOM    111  CA  THR    23      -6.359   5.547  11.075  1.00  9.99
ATOM    112  C   THR    23      -5.189   6.503  11.282  1.00  9.99
ATOM    113  O   THR    23      -5.345   7.715  11.172  1.00  9.99
ATOM    114  CB  THR    23      -7.545   6.009  11.925  1.00  9.99
ATOM    115  N   GLU    24      -4.031   5.914  11.592  1.00  9.99
ATOM    116  CA  GLU    24      -2.740   6.578  11.842  1.00  9.99
ATOM    117  C   GLU    24      -2.133   7.255  10.629  1.00  9.99
ATOM    118  O   GLU    24      -2.641   7.176   9.519  1.00  9.99
ATOM    119  CB  GLU    24      -1.680   5.545  12.214  1.00  9.99
ATOM    120  N   GLU    25      -0.991   7.890  10.869  1.00  9.99
ATOM    121  CA  GLU    25      -0.207   8.465   9.799  1.00  9.99
ATOM    122  C   GLU    25       0.620   7.213   9.481  1.00  9.99
ATOM    123  O   GLU    25       0.966   6.934   8.328  1.00  9.99
ATOM    124  CB  GLU    25       0.703   9.579  10.306  1.00  9.99
ATOM    125  N   GLU    26       0.903   6.444  10.529  1.00  9.99
ATOM    126  CA  GLU    26       1.651   5.206  10.399  1.00  9.99
ATOM    127  C   GLU    26       0.855   4.262   9.513  1.00  9.99
ATOM    128  O   GLU    26       1.409   3.598   8.633  1.00  9.99
ATOM    129  CB  GLU    26       1.859   4.586  11.748  1.00  9.99
ATOM    130  N   LYS    27      -0.448   4.203   9.751  1.00  9.99
ATOM    131  CA  LYS    27      -1.314   3.348   8.956  1.00  9.99
ATOM    132  C   LYS    27      -1.269   3.778   7.481  1.00  9.99
ATOM    133  O   LYS    27      -1.298   2.942   6.564  1.00  9.99
ATOM    134  CB  LYS    27      -2.734   3.430   9.481  1.00  9.99
ATOM    135  N   ALA    28      -1.208   5.088   7.261  1.00  9.99
ATOM    136  CA  ALA    28      -1.158   5.618   5.917  1.00  9.99
ATOM    137  C   ALA    28       0.107   5.130   5.208  1.00  9.99
ATOM    138  O   ALA    28       0.032   4.495   4.157  1.00  9.99
ATOM    139  CB  ALA    28      -1.180   7.145   5.955  1.00  9.99
ATOM    140  N   GLU    29       1.262   5.429   5.792  1.00  9.99
ATOM    141  CA  GLU    29       2.548   5.036   5.224  1.00  9.99
ATOM    142  C   GLU    29       2.544   3.555   4.842  1.00  9.99
ATOM    143  O   GLU    29       3.020   3.174   3.768  1.00  9.99
ATOM    144  CB  GLU    29       3.664   5.315   6.242  1.00  9.99
ATOM    145  N   GLN    30       1.992   2.721   5.718  1.00  9.99
ATOM    146  CA  GLN    30       1.957   1.287   5.463  1.00  9.99
ATOM    147  C   GLN    30       1.072   0.905   4.297  1.00  9.99
ATOM    148  O   GLN    30       1.282  -0.142   3.693  1.00  9.99
ATOM    149  CB  GLN    30       1.509   0.551   6.695  1.00  9.99
ATOM    150  N   GLN    31       0.083   1.742   3.983  1.00  9.99
ATOM    151  CA  GLN    31      -0.830   1.445   2.878  1.00  9.99
ATOM    152  C   GLN    31      -0.187   1.705   1.510  1.00  9.99
ATOM    153  O   GLN    31      -0.691   1.253   0.480  1.00  9.99
ATOM    154  CB  GLN    31      -2.138   2.245   3.022  1.00  9.99
ATOM    155  N   LYS    32       7.908  -1.133  -1.127  1.00  9.99
ATOM    156  CA  LYS    32       7.954  -2.201  -2.111  1.00  9.99
ATOM    157  C   LYS    32       7.050  -1.929  -3.306  1.00  9.99
ATOM    158  O   LYS    32       7.385  -2.306  -4.430  1.00  9.99
ATOM    159  CB  LYS    32       7.670  -3.556  -1.453  1.00  9.99
ATOM    160  N   LEU    33       5.924  -1.252  -3.093  1.00  9.99
ATOM    161  CA  LEU    33       5.063  -0.960  -4.232  1.00  9.99
ATOM    162  C   LEU    33       5.566   0.271  -4.981  1.00  9.99
ATOM    163  O   LEU    33       5.448   0.346  -6.205  1.00  9.99
ATOM    164  CB  LEU    33       3.583  -0.814  -3.819  1.00  9.99
ATOM    165  N   ARG    34       6.160   1.224  -4.267  1.00  9.99
ATOM    166  CA  ARG    34       6.687   2.404  -4.945  1.00  9.99
ATOM    167  C   ARG    34       7.823   1.933  -5.838  1.00  9.99
ATOM    168  O   ARG    34       7.946   2.330  -6.999  1.00  9.99
ATOM    169  CB  ARG    34       7.241   3.423  -3.948  1.00  9.99
ATOM    170  N   GLN    35       8.659   1.070  -5.286  1.00  9.99
ATOM    171  CA  GLN    35       9.793   0.573  -6.032  1.00  9.99
ATOM    172  C   GLN    35       9.414  -0.345  -7.182  1.00  9.99
ATOM    173  O   GLN    35      10.119  -0.412  -8.180  1.00  9.99
ATOM    174  CB  GLN    35      10.767  -0.092  -5.069  1.00  9.99
ATOM    175  N   GLU    36       8.295  -1.043  -7.060  1.00  9.99
ATOM    176  CA  GLU    36       7.863  -1.908  -8.147  1.00  9.99
ATOM    177  C   GLU    36       7.488  -1.014  -9.331  1.00  9.99
ATOM    178  O   GLU    36       7.838  -1.296 -10.480  1.00  9.99
ATOM    179  CB  GLU    36       6.663  -2.744  -7.706  1.00  9.99
ATOM    180  N   TYR    37       6.782   0.075  -9.048  1.00  9.99
ATOM    181  CA  TYR    37       6.365   0.989 -10.100  1.00  9.99
ATOM    182  C   TYR    37       7.588   1.611 -10.770  1.00  9.99
ATOM    183  O   TYR    37       7.620   1.800 -11.994  1.00  9.99
ATOM    184  CB  TYR    37       5.469   2.070  -9.528  1.00  9.99
ATOM    185  N   LEU    38       8.600   1.933  -9.973  1.00  9.99
ATOM    186  CA  LEU    38       9.795   2.521 -10.543  1.00  9.99
ATOM    187  C   LEU    38      10.419   1.498 -11.497  1.00  9.99
ATOM    188  O   LEU    38      10.789   1.820 -12.634  1.00  9.99
ATOM    189  CB  LEU    38      10.781   2.918  -9.430  1.00  9.99
ATOM    190  N   LYS    39      10.505   0.257 -11.031  1.00  9.99
ATOM    191  CA  LYS    39      11.073  -0.839 -11.811  1.00  9.99
ATOM    192  C   LYS    39      10.330  -1.007 -13.135  1.00  9.99
ATOM    193  O   LYS    39      10.939  -1.206 -14.182  1.00  9.99
ATOM    194  CB  LYS    39      10.970  -2.120 -11.007  1.00  9.99
ATOM    195  N   GLY    40       9.005  -0.922 -13.067  1.00  9.99
ATOM    196  CA  GLY    40       8.146  -1.053 -14.235  1.00  9.99
ATOM    197  C   GLY    40       8.353   0.089 -15.241  1.00  9.99
ATOM    198  O   GLY    40       8.469  -0.144 -16.446  1.00  9.99
TER
END
