
#######################################################
#                                                     #
#                        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 T0335AL242_5-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL242_5-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      -       -           -
LGA    R       9      -       -           -
LGA    I      10      -       -           -
LGA    N      11      -       -           -
LGA    E      12      -       -           -
LGA    L      13      -       -           -
LGA    A      14      A       5          2.674
LGA    A      15      K       6          1.918
LGA    K      16      I       7          1.532
LGA    A      17      A       8          1.314
LGA    K      18      R       9          1.598
LGA    A      19      I      10          1.952
LGA    G      20      N      11          1.541
LGA    V      21      E      12          0.984
LGA    I      22      L      13          1.431
LGA    T      23      A      14          1.457
LGA    E      24      A      15          0.823
LGA    E      25      K      16          0.214
LGA    E      26      A      17          1.015
LGA    K      27      K      18          1.230
LGA    A      28      A      19          1.292
LGA    E      29      G      20          1.273
LGA    Q      30      V      21          1.004
LGA    Q      31      I      22          2.043
LGA    K      32      T      23          1.958
LGA    L      33      E      24          2.225
LGA    -       -      E      25           -
LGA    R      34      E      26          3.705
LGA    Q      35      K      27          2.648
LGA    E      36      A      28          0.649
LGA    Y      37      E      29          1.666
LGA    L      38      Q      30          1.679
LGA    K      39      Q      31          1.307
LGA    G      40      K      32          2.186
LGA    -       -      L      33           -
LGA    -       -      R      34           -
LGA    -       -      Q      35           -
LGA    -       -      E      36           -
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     27    1.75    14.81     68.981     1.461

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.655768 * X  +  -0.545256 * Y  +   0.522173 * Z  +  38.271690
  Y_new =   0.601043 * X  +   0.041488 * Y  +   0.798139 * Z  + -54.047260
  Z_new =  -0.456854 * X  +   0.837242 * Y  +   0.300517 * Z  +  77.031250 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.226183   -1.915410  [ DEG:    70.2551   -109.7449 ]
  Theta =   0.474455    2.667137  [ DEG:    27.1843    152.8157 ]
  Phi   =   2.399709   -0.741883  [ DEG:   137.4932    -42.5068 ]
 
# 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: T0335AL242_5-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL242_5-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   27   1.75   14.81  68.981
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL242_5-D1
REMARK Aligment from pdb entry: 1g8x_A
ATOM     17  N   ALA     5       8.514 -14.307 -17.074  1.00  0.00              
ATOM     18  CA  ALA     5       7.763 -13.065 -17.194  1.00  0.00              
ATOM     19  C   ALA     5       6.267 -13.308 -17.381  1.00  0.00              
ATOM     20  O   ALA     5       5.496 -12.375 -17.614  1.00  0.00              
ATOM     21  N   LYS     6       5.868 -14.573 -17.275  1.00  0.00              
ATOM     22  CA  LYS     6       4.471 -14.939 -17.396  1.00  0.00              
ATOM     23  C   LYS     6       3.932 -15.111 -15.989  1.00  0.00              
ATOM     24  O   LYS     6       2.727 -15.031 -15.752  1.00  0.00              
ATOM     25  N   ILE     7       4.844 -15.356 -15.053  1.00  0.00              
ATOM     26  CA  ILE     7       4.494 -15.524 -13.651  1.00  0.00              
ATOM     27  C   ILE     7       4.726 -14.187 -12.949  1.00  0.00              
ATOM     28  O   ILE     7       3.945 -13.786 -12.088  1.00  0.00              
ATOM     29  N   ALA     8       5.799 -13.497 -13.338  1.00  0.00              
ATOM     30  CA  ALA     8       6.139 -12.192 -12.771  1.00  0.00              
ATOM     31  C   ALA     8       5.366 -11.086 -13.459  1.00  0.00              
ATOM     32  O   ALA     8       5.882  -9.988 -13.666  1.00  0.00              
ATOM     33  N   ARG     9       4.129 -11.404 -13.825  1.00  0.00              
ATOM     34  CA  ARG     9       3.216 -10.470 -14.473  1.00  0.00              
ATOM     35  C   ARG     9       1.877 -10.726 -13.798  1.00  0.00              
ATOM     36  O   ARG     9       0.924  -9.958 -13.934  1.00  0.00              
ATOM     37  N   ILE    10       1.830 -11.833 -13.065  1.00  0.00              
ATOM     38  CA  ILE    10       0.645 -12.238 -12.322  1.00  0.00              
ATOM     39  C   ILE    10       0.984 -12.090 -10.843  1.00  0.00              
ATOM     40  O   ILE    10       0.138 -11.697 -10.036  1.00  0.00              
ATOM     41  N   ASN    11       2.234 -12.408 -10.503  1.00  0.00              
ATOM     42  CA  ASN    11       2.731 -12.308  -9.131  1.00  0.00              
ATOM     43  C   ASN    11       2.785 -10.832  -8.759  1.00  0.00              
ATOM     44  O   ASN    11       3.105 -10.463  -7.630  1.00  0.00              
ATOM     45  N   GLU    12       2.483  -9.998  -9.746  1.00  0.00              
ATOM     46  CA  GLU    12       2.458  -8.560  -9.577  1.00  0.00              
ATOM     47  C   GLU    12       0.978  -8.210  -9.543  1.00  0.00              
ATOM     48  O   GLU    12       0.486  -7.613  -8.593  1.00  0.00              
ATOM     49  N   LEU    13       0.268  -8.620 -10.583  1.00  0.00              
ATOM     50  CA  LEU    13      -1.153  -8.348 -10.663  1.00  0.00              
ATOM     51  C   LEU    13      -1.968  -8.929  -9.524  1.00  0.00              
ATOM     52  O   LEU    13      -3.083  -8.469  -9.269  1.00  0.00              
ATOM     53  N   ALA    14      -1.434  -9.936  -8.837  1.00  0.00              
ATOM     54  CA  ALA    14      -2.166 -10.542  -7.724  1.00  0.00              
ATOM     55  C   ALA    14      -1.698  -9.965  -6.383  1.00  0.00              
ATOM     56  O   ALA    14      -2.509  -9.743  -5.482  1.00  0.00              
ATOM     57  N   ALA    15      -0.393  -9.713  -6.272  1.00  0.00              
ATOM     58  CA  ALA    15       0.212  -9.153  -5.061  1.00  0.00              
ATOM     59  C   ALA    15      -0.202  -7.699  -4.826  1.00  0.00              
ATOM     60  O   ALA    15      -0.716  -7.342  -3.766  1.00  0.00              
ATOM     61  N   LYS    16       0.042  -6.860  -5.819  1.00  0.00              
ATOM     62  CA  LYS    16      -0.292  -5.458  -5.720  1.00  0.00              
ATOM     63  C   LYS    16      -1.794  -5.300  -5.494  1.00  0.00              
ATOM     64  O   LYS    16      -2.255  -4.308  -4.921  1.00  0.00              
ATOM     65  N   ALA    17      -2.556  -6.291  -5.934  1.00  0.00              
ATOM     66  CA  ALA    17      -4.001  -6.257  -5.761  1.00  0.00              
ATOM     67  C   ALA    17      -4.363  -6.506  -4.295  1.00  0.00              
ATOM     68  O   ALA    17      -5.332  -5.948  -3.784  1.00  0.00              
ATOM     69  N   LYS    18      -3.580  -7.353  -3.630  1.00  0.00              
ATOM     70  CA  LYS    18      -3.805  -7.675  -2.223  1.00  0.00              
ATOM     71  C   LYS    18      -3.288  -6.552  -1.345  1.00  0.00              
ATOM     72  O   LYS    18      -3.930  -6.163  -0.369  1.00  0.00              
ATOM     73  N   ALA    19      -2.111  -6.046  -1.697  1.00  0.00              
ATOM     74  CA  ALA    19      -1.509  -4.964  -0.951  1.00  0.00              
ATOM     75  C   ALA    19      -2.476  -3.793  -0.900  1.00  0.00              
ATOM     76  O   ALA    19      -2.630  -3.156   0.143  1.00  0.00              
ATOM     77  N   GLY    20      -3.142  -3.524  -2.019  1.00  0.00              
ATOM     78  CA  GLY    20      -4.101  -2.431  -2.063  1.00  0.00              
ATOM     79  C   GLY    20      -5.338  -2.769  -1.234  1.00  0.00              
ATOM     80  O   GLY    20      -5.820  -1.942  -0.460  1.00  0.00              
ATOM     81  N   VAL    21      -5.840  -3.990  -1.389  1.00  0.00              
ATOM     82  CA  VAL    21      -7.025  -4.433  -0.659  1.00  0.00              
ATOM     83  C   VAL    21      -6.789  -4.366   0.845  1.00  0.00              
ATOM     84  O   VAL    21      -7.707  -4.092   1.609  1.00  0.00              
ATOM     85  N   ILE    22      -5.553  -4.633   1.257  1.00  0.00              
ATOM     86  CA  ILE    22      -5.178  -4.573   2.661  1.00  0.00              
ATOM     87  C   ILE    22      -5.149  -3.100   3.075  1.00  0.00              
ATOM     88  O   ILE    22      -5.658  -2.727   4.137  1.00  0.00              
ATOM     89  N   THR    23      -4.550  -2.267   2.226  1.00  0.00              
ATOM     90  CA  THR    23      -4.442  -0.839   2.497  1.00  0.00              
ATOM     91  C   THR    23      -5.798  -0.175   2.654  1.00  0.00              
ATOM     92  O   THR    23      -6.008   0.595   3.583  1.00  0.00              
ATOM     93  N   GLU    24      -6.723  -0.481   1.752  1.00  0.00              
ATOM     94  CA  GLU    24      -8.052   0.107   1.820  1.00  0.00              
ATOM     95  C   GLU    24      -8.690  -0.240   3.160  1.00  0.00              
ATOM     96  O   GLU    24      -9.332   0.593   3.797  1.00  0.00              
ATOM     97  N   GLU    25      -8.510  -1.486   3.581  1.00  0.00              
ATOM     98  CA  GLU    25      -9.062  -1.940   4.845  1.00  0.00              
ATOM     99  C   GLU    25      -8.501  -1.120   5.998  1.00  0.00              
ATOM    100  O   GLU    25      -9.257  -0.526   6.769  1.00  0.00              
ATOM    101  N   GLU    26      -7.175  -1.112   6.118  1.00  0.00              
ATOM    102  CA  GLU    26      -6.501  -0.358   7.162  1.00  0.00              
ATOM    103  C   GLU    26      -6.979   1.088   7.109  1.00  0.00              
ATOM    104  O   GLU    26      -7.105   1.756   8.143  1.00  0.00              
ATOM    105  N   LYS    27      -7.241   1.572   5.903  1.00  0.00              
ATOM    106  CA  LYS    27      -7.714   2.930   5.745  1.00  0.00              
ATOM    107  C   LYS    27      -9.109   3.012   6.343  1.00  0.00              
ATOM    108  O   LYS    27      -9.446   3.995   7.004  1.00  0.00              
ATOM    109  N   ALA    28      -9.903   1.963   6.128  1.00  0.00              
ATOM    110  CA  ALA    28     -11.269   1.877   6.646  1.00  0.00              
ATOM    111  C   ALA    28     -11.285   1.740   8.178  1.00  0.00              
ATOM    112  O   ALA    28     -12.319   1.907   8.822  1.00  0.00              
ATOM    113  N   GLU    29     -10.134   1.420   8.756  1.00  0.00              
ATOM    114  CA  GLU    29     -10.017   1.299  10.199  1.00  0.00              
ATOM    115  C   GLU    29      -9.271   2.534  10.682  1.00  0.00              
ATOM    116  O   GLU    29      -8.562   2.494  11.689  1.00  0.00              
ATOM    117  N   GLN    30      -9.443   3.630   9.945  1.00  0.00              
ATOM    118  CA  GLN    30      -8.792   4.901  10.253  1.00  0.00              
ATOM    119  C   GLN    30      -7.425   4.660  10.896  1.00  0.00              
ATOM    120  O   GLN    30      -7.070   5.313  11.875  1.00  0.00              
ATOM    121  N   GLN    31      -6.670   3.713  10.342  1.00  0.00              
ATOM    122  CA  GLN    31      -5.337   3.372  10.847  1.00  0.00              
ATOM    123  C   GLN    31      -4.308   4.406  10.410  1.00  0.00              
ATOM    124  O   GLN    31      -3.823   4.384   9.279  1.00  0.00              
ATOM    125  N   LYS    32      -3.958   5.307  11.313  1.00  0.00              
ATOM    126  CA  LYS    32      -3.002   6.337  10.965  1.00  0.00              
ATOM    127  C   LYS    32      -1.599   5.756  10.951  1.00  0.00              
ATOM    128  O   LYS    32      -0.873   5.793  11.944  1.00  0.00              
ATOM    129  N   LEU    33      -1.257   5.199   9.794  1.00  0.00              
ATOM    130  CA  LEU    33       0.031   4.575   9.566  1.00  0.00              
ATOM    131  C   LEU    33       0.065   4.094   8.122  1.00  0.00              
ATOM    132  O   LEU    33       1.047   3.510   7.657  1.00  0.00              
ATOM    133  N   ARG    34      -1.033   4.349   7.413  1.00  0.00              
ATOM    134  CA  ARG    34      -1.171   3.968   6.015  1.00  0.00              
ATOM    135  C   ARG    34      -0.101   4.587   5.116  1.00  0.00              
ATOM    136  O   ARG    34       0.482   3.899   4.279  1.00  0.00              
ATOM    137  N   GLN    35       0.179   5.896   5.276  1.00  0.00              
ATOM    138  CA  GLN    35       1.186   6.590   4.460  1.00  0.00              
ATOM    139  C   GLN    35       2.519   5.865   4.305  1.00  0.00              
ATOM    140  O   GLN    35       2.937   5.559   3.192  1.00  0.00              
ATOM    141  N   GLU    36       3.177   5.595   5.426  1.00  0.00              
ATOM    142  CA  GLU    36       4.466   4.917   5.415  1.00  0.00              
ATOM    143  C   GLU    36       4.340   3.532   4.803  1.00  0.00              
ATOM    144  O   GLU    36       5.304   2.996   4.261  1.00  0.00              
ATOM    145  N   TYR    37       3.153   2.940   4.892  1.00  0.00              
ATOM    146  CA  TYR    37       2.948   1.627   4.294  1.00  0.00              
ATOM    147  C   TYR    37       2.960   1.816   2.794  1.00  0.00              
ATOM    148  O   TYR    37       3.841   1.316   2.101  1.00  0.00              
ATOM    149  N   LEU    38       1.984   2.563   2.298  1.00  0.00              
ATOM    150  CA  LEU    38       1.892   2.814   0.877  1.00  0.00              
ATOM    151  C   LEU    38       3.266   3.195   0.299  1.00  0.00              
ATOM    152  O   LEU    38       3.575   2.856  -0.842  1.00  0.00              
ATOM    153  N   LYS    39       4.104   3.869   1.083  1.00  0.00              
ATOM    154  CA  LYS    39       5.424   4.253   0.591  1.00  0.00              
ATOM    155  C   LYS    39       6.387   3.090   0.483  1.00  0.00              
ATOM    156  O   LYS    39       7.014   2.901  -0.560  1.00  0.00              
ATOM    157  N   GLY    40       6.522   2.316   1.555  1.00  0.00              
ATOM    158  CA  GLY    40       7.429   1.174   1.534  1.00  0.00              
ATOM    159  C   GLY    40       7.092   0.300   0.321  1.00  0.00              
ATOM    160  O   GLY    40       7.979  -0.270  -0.321  1.00  0.00              
END
