
#######################################################
#                                                     #
#                        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   44 (  176),  selected   44 , name T0363AL257_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL257_4-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    I      13      -       -           -
LGA    N      14      -       -           -
LGA    I      15      -       -           -
LGA    E      16      -       -           -
LGA    I      17      -       -           -
LGA    A      18      -       -           -
LGA    Y      19      -       -           -
LGA    A      20      -       -           -
LGA    F      21      -       -           -
LGA    P      22      -       -           -
LGA    E      23      -       -           -
LGA    R      24      -       -           -
LGA    Y      25      -       -           -
LGA    Y      26      -       -           -
LGA    L      27      N      11           #
LGA    K      28      Q      12          3.384
LGA    -       -      I      13           -
LGA    S      29      N      14          2.005
LGA    F      30      I      15          1.422
LGA    Q      31      E      16          0.963
LGA    V      32      I      17          1.346
LGA    D      33      A      18          1.274
LGA    E      34      Y      19          1.583
LGA    G      35      A      20           #
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    -       -      Y      25           -
LGA    -       -      Y      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      S      29           -
LGA    I      36      F      30           #
LGA    T      37      -       -           -
LGA    V      38      Q      31           #
LGA    Q      39      V      32          4.090
LGA    T      40      D      33           #
LGA    A      41      E      34          2.492
LGA    I      42      G      35          2.374
LGA    T      43      I      36          1.369
LGA    Q      44      T      37          2.042
LGA    -       -      V      38           -
LGA    S      45      Q      39          3.301
LGA    G      46      T      40          1.760
LGA    I      47      A      41          1.965
LGA    L      48      I      42          0.691
LGA    S      49      T      43          2.081
LGA    Q      50      Q      44          2.761
LGA    F      51      S      45          2.271
LGA    P      52      G      46          3.877
LGA    E      53      I      47          4.672
LGA    I      54      L      48           #
LGA    D      55      S      49          5.430
LGA    L      56      Q      50          2.963
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   44   46    5.0     23    2.72     4.35     36.616     0.817

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.173076 * X  +   0.471820 * Y  +  -0.864540 * Z  +  22.018385
  Y_new =   0.968840 * X  +   0.239472 * Y  +  -0.063265 * Z  +   8.368906
  Z_new =   0.177183 * X  +  -0.848551 * Y  +  -0.498565 * Z  +   2.627717 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.102010    1.039582  [ DEG:  -120.4363     59.5637 ]
  Theta =  -0.178124   -2.963469  [ DEG:   -10.2057   -169.7943 ]
  Phi   =   1.747575   -1.394018  [ DEG:   100.1286    -79.8714 ]
 
# 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: T0363AL257_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL257_4-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   44   46   5.0   23   2.72    4.35  36.616
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL257_4-D1
REMARK Aligment from pdb entry: 2grg_A
ATOM      1  N   ILE    13      34.425  -6.252  -4.973  1.00  0.00              
ATOM      2  CA  ILE    13      33.285  -7.077  -4.504  1.00  0.00              
ATOM      3  C   ILE    13      32.180  -6.206  -3.920  1.00  0.00              
ATOM      4  O   ILE    13      31.014  -6.604  -3.891  1.00  0.00              
ATOM      5  N   ASN    14      32.544  -5.023  -3.443  1.00  0.00              
ATOM      6  CA  ASN    14      31.566  -4.091  -2.906  1.00  0.00              
ATOM      7  C   ASN    14      30.872  -3.366  -4.051  1.00  0.00              
ATOM      8  O   ASN    14      29.654  -3.463  -4.209  1.00  0.00              
ATOM      9  N   ILE    15      31.676  -2.665  -4.854  1.00  0.00              
ATOM     10  CA  ILE    15      31.199  -1.939  -6.031  1.00  0.00              
ATOM     11  C   ILE    15      30.358  -0.717  -5.658  1.00  0.00              
ATOM     12  O   ILE    15      29.505  -0.765  -4.772  1.00  0.00              
ATOM     13  N   GLU    16      30.628   0.390  -6.329  1.00  0.00              
ATOM     14  CA  GLU    16      29.841   1.593  -6.156  1.00  0.00              
ATOM     15  C   GLU    16      28.583   1.506  -7.016  1.00  0.00              
ATOM     16  O   GLU    16      28.634   1.662  -8.233  1.00  0.00              
ATOM     17  N   ILE    17      27.462   1.247  -6.364  1.00  0.00              
ATOM     18  CA  ILE    17      26.212   0.915  -7.042  1.00  0.00              
ATOM     19  C   ILE    17      25.379   2.173  -7.280  1.00  0.00              
ATOM     20  O   ILE    17      25.317   3.043  -6.415  1.00  0.00              
ATOM     21  N   ALA    18      24.743   2.297  -8.460  1.00  0.00              
ATOM     22  CA  ALA    18      23.964   3.487  -8.815  1.00  0.00              
ATOM     23  C   ALA    18      22.753   3.698  -7.909  1.00  0.00              
ATOM     24  O   ALA    18      22.193   2.745  -7.357  1.00  0.00              
ATOM     25  N   TYR    19      22.340   4.955  -7.783  1.00  0.00              
ATOM     26  CA  TYR    19      21.262   5.327  -6.873  1.00  0.00              
ATOM     27  C   TYR    19      19.928   4.736  -7.325  1.00  0.00              
ATOM     28  O   TYR    19      19.051   4.477  -6.507  1.00  0.00              
ATOM     29  N   ALA    20      19.798   4.490  -8.623  1.00  0.00              
ATOM     30  CA  ALA    20      18.584   3.901  -9.173  1.00  0.00              
ATOM     31  C   ALA    20      18.301   2.541  -8.532  1.00  0.00              
ATOM     32  O   ALA    20      17.150   2.111  -8.439  1.00  0.00              
ATOM     33  N   PHE    21      19.356   1.882  -8.073  1.00  0.00              
ATOM     34  CA  PHE    21      19.226   0.594  -7.416  1.00  0.00              
ATOM     35  C   PHE    21      19.208   0.767  -5.900  1.00  0.00              
ATOM     36  O   PHE    21      18.340   0.232  -5.212  1.00  0.00              
ATOM     37  N   PRO    22      20.152   1.546  -5.387  1.00  0.00              
ATOM     38  CA  PRO    22      20.334   1.674  -3.946  1.00  0.00              
ATOM     39  C   PRO    22      19.149   2.373  -3.281  1.00  0.00              
ATOM     40  O   PRO    22      18.759   2.007  -2.175  1.00  0.00              
ATOM     41  N   GLU    23      18.570   3.359  -3.961  1.00  0.00              
ATOM     42  CA  GLU    23      17.446   4.119  -3.414  1.00  0.00              
ATOM     43  C   GLU    23      16.302   3.199  -2.944  1.00  0.00              
ATOM     44  O   GLU    23      15.973   3.190  -1.756  1.00  0.00              
ATOM     45  N   ARG    24      15.676   2.415  -3.847  1.00  0.00              
ATOM     46  CA  ARG    24      14.588   1.510  -3.466  1.00  0.00              
ATOM     47  C   ARG    24      15.045   0.383  -2.535  1.00  0.00              
ATOM     48  O   ARG    24      14.271  -0.087  -1.700  1.00  0.00              
ATOM     49  N   TYR    25      16.302  -0.040  -2.666  1.00  0.00              
ATOM     50  CA  TYR    25      16.830  -1.126  -1.844  1.00  0.00              
ATOM     51  C   TYR    25      17.168  -0.649  -0.431  1.00  0.00              
ATOM     52  O   TYR    25      17.417  -1.459   0.462  1.00  0.00              
ATOM     53  N   TYR    26      17.187   0.663  -0.235  1.00  0.00              
ATOM     54  CA  TYR    26      17.566   1.236   1.049  1.00  0.00              
ATOM     55  C   TYR    26      16.393   1.261   2.019  1.00  0.00              
ATOM     56  O   TYR    26      15.234   1.381   1.615  1.00  0.00              
ATOM     57  N   LEU    27      16.707   1.145   3.301  1.00  0.00              
ATOM     58  CA  LEU    27      15.705   1.182   4.358  1.00  0.00              
ATOM     59  C   LEU    27      15.983   2.340   5.312  1.00  0.00              
ATOM     60  O   LEU    27      15.332   2.490   6.345  1.00  0.00              
ATOM     61  N   LYS    28      16.962   3.153   4.953  1.00  0.00              
ATOM     62  CA  LYS    28      17.319   4.300   5.753  1.00  0.00              
ATOM     63  C   LYS    28      18.080   5.299   4.922  1.00  0.00              
ATOM     64  O   LYS    28      18.737   4.917   3.956  1.00  0.00              
ATOM     65  N   SER    29      17.984   6.571   5.253  1.00  0.00              
ATOM     66  CA  SER    29      18.647   7.597   4.467  1.00  0.00              
ATOM     67  C   SER    29      19.001   8.814   5.318  1.00  0.00              
ATOM     68  O   SER    29      18.155   9.366   6.028  1.00  0.00              
ATOM     69  N   PHE    30      20.262   9.211   5.252  1.00  0.00              
ATOM     70  CA  PHE    30      20.749  10.377   5.971  1.00  0.00              
ATOM     71  C   PHE    30      21.051  11.521   5.016  1.00  0.00              
ATOM     72  O   PHE    30      21.895  11.387   4.133  1.00  0.00              
ATOM     73  N   GLN    31      20.372  12.639   5.194  1.00  0.00              
ATOM     74  CA  GLN    31      20.636  13.814   4.384  1.00  0.00              
ATOM     75  C   GLN    31      21.635  14.724   5.092  1.00  0.00              
ATOM     76  O   GLN    31      21.345  15.272   6.155  1.00  0.00              
ATOM     77  N   VAL    32      22.812  14.851   4.509  1.00  0.00              
ATOM     78  CA  VAL    32      23.856  15.719   5.031  1.00  0.00              
ATOM     79  C   VAL    32      24.027  16.942   4.139  1.00  0.00              
ATOM     80  O   VAL    32      23.687  16.922   2.953  1.00  0.00              
ATOM     81  N   ASP    33      24.542  18.006   4.720  1.00  0.00              
ATOM     82  CA  ASP    33      24.887  19.196   3.964  1.00  0.00              
ATOM     83  C   ASP    33      26.300  19.052   3.412  1.00  0.00              
ATOM     84  O   ASP    33      27.023  18.139   3.805  1.00  0.00              
ATOM     85  N   GLU    34      26.700  19.939   2.507  1.00  0.00              
ATOM     86  CA  GLU    34      28.029  19.878   1.928  1.00  0.00              
ATOM     87  C   GLU    34      29.087  20.226   2.972  1.00  0.00              
ATOM     88  O   GLU    34      30.266  19.914   2.805  1.00  0.00              
ATOM     89  N   GLY    35      28.657  20.867   4.058  1.00  0.00              
ATOM     90  CA  GLY    35      29.527  21.127   5.196  1.00  0.00              
ATOM     91  C   GLY    35      29.543  19.920   6.124  1.00  0.00              
ATOM     92  O   GLY    35      30.018  19.994   7.257  1.00  0.00              
ATOM     93  N   ILE    36      16.209   9.719   8.179  1.00  0.00              
ATOM     94  CA  ILE    36      15.024   8.949   7.840  1.00  0.00              
ATOM     95  C   ILE    36      15.332   7.454   7.802  1.00  0.00              
ATOM     96  O   ILE    36      16.457   7.048   7.501  1.00  0.00              
ATOM     97  N   THR    37      14.332   6.648   8.132  1.00  0.00              
ATOM     98  CA  THR    37      14.476   5.208   8.071  1.00  0.00              
ATOM     99  C   THR    37      15.301   4.660   9.215  1.00  0.00              
ATOM    100  O   THR    37      15.362   5.253  10.294  1.00  0.00              
ATOM    101  N   VAL    38      15.960   3.535   8.970  1.00  0.00              
ATOM    102  CA  VAL    38      16.786   2.881   9.984  1.00  0.00              
ATOM    103  C   VAL    38      17.967   3.765  10.386  1.00  0.00              
ATOM    104  O   VAL    38      18.583   3.568  11.432  1.00  0.00              
ATOM    105  N   GLN    39      18.253   4.764   9.565  1.00  0.00              
ATOM    106  CA  GLN    39      19.358   5.675   9.825  1.00  0.00              
ATOM    107  C   GLN    39      19.159   6.431  11.137  1.00  0.00              
ATOM    108  O   GLN    39      20.088   7.042  11.655  1.00  0.00              
ATOM    109  N   THR    40      17.940   6.388  11.667  1.00  0.00              
ATOM    110  CA  THR    40      17.625   7.053  12.920  1.00  0.00              
ATOM    111  C   THR    40      18.244   6.313  14.106  1.00  0.00              
ATOM    112  O   THR    40      18.668   6.935  15.080  1.00  0.00              
ATOM    113  N   ALA    41      18.304   4.988  14.017  1.00  0.00              
ATOM    114  CA  ALA    41      18.847   4.177  15.105  1.00  0.00              
ATOM    115  C   ALA    41      20.330   3.887  14.881  1.00  0.00              
ATOM    116  O   ALA    41      21.050   3.505  15.805  1.00  0.00              
ATOM    117  N   ILE    42      20.777   4.064  13.645  1.00  0.00              
ATOM    118  CA  ILE    42      22.188   3.943  13.305  1.00  0.00              
ATOM    119  C   ILE    42      22.932   5.221  13.702  1.00  0.00              
ATOM    120  O   ILE    42      22.360   6.311  13.657  1.00  0.00              
ATOM    121  N   THR    43      24.188   5.088  14.116  1.00  0.00              
ATOM    122  CA  THR    43      24.967   6.237  14.571  1.00  0.00              
ATOM    123  C   THR    43      25.581   6.998  13.396  1.00  0.00              
ATOM    124  O   THR    43      25.751   6.452  12.307  1.00  0.00              
ATOM    125  N   GLN    44      25.927   8.258  13.641  1.00  0.00              
ATOM    126  CA  GLN    44      26.385   9.163  12.589  1.00  0.00              
ATOM    127  C   GLN    44      27.871   9.478  12.755  1.00  0.00              
ATOM    128  O   GLN    44      28.442  10.229  11.964  1.00  0.00              
ATOM    129  N   SER    45      28.479   8.877  13.774  1.00  0.00              
ATOM    130  CA  SER    45      29.824   9.237  14.230  1.00  0.00              
ATOM    131  C   SER    45      30.862   9.350  13.091  1.00  0.00              
ATOM    132  O   SER    45      31.358  10.450  12.823  1.00  0.00              
ATOM    133  N   GLY    46      31.209   8.248  12.391  1.00  0.00              
ATOM    134  CA  GLY    46      32.309   8.253  11.428  1.00  0.00              
ATOM    135  C   GLY    46      31.862   8.531   9.996  1.00  0.00              
ATOM    136  O   GLY    46      32.677   8.540   9.074  1.00  0.00              
ATOM    137  N   ILE    47      30.575   8.778   9.815  1.00  0.00              
ATOM    138  CA  ILE    47      30.002   8.871   8.481  1.00  0.00              
ATOM    139  C   ILE    47      30.435  10.147   7.760  1.00  0.00              
ATOM    140  O   ILE    47      30.733  10.111   6.570  1.00  0.00              
ATOM    141  N   LEU    48      30.504  11.260   8.485  1.00  0.00              
ATOM    142  CA  LEU    48      30.846  12.546   7.880  1.00  0.00              
ATOM    143  C   LEU    48      32.233  12.501   7.236  1.00  0.00              
ATOM    144  O   LEU    48      32.433  12.990   6.119  1.00  0.00              
ATOM    145  N   SER    49      33.175  11.888   7.939  1.00  0.00              
ATOM    146  CA  SER    49      34.538  11.739   7.449  1.00  0.00              
ATOM    147  C   SER    49      34.567  10.883   6.185  1.00  0.00              
ATOM    148  O   SER    49      35.327  11.145   5.255  1.00  0.00              
ATOM    149  N   GLN    50      33.733   9.860   6.141  1.00  0.00              
ATOM    150  CA  GLN    50      33.703   8.986   4.985  1.00  0.00              
ATOM    151  C   GLN    50      32.950   9.650   3.831  1.00  0.00              
ATOM    152  O   GLN    50      33.226   9.374   2.666  1.00  0.00              
ATOM    153  N   PHE    51      32.014  10.545   4.153  1.00  0.00              
ATOM    154  CA  PHE    51      31.261  11.260   3.129  1.00  0.00              
ATOM    155  C   PHE    51      32.186  12.116   2.270  1.00  0.00              
ATOM    156  O   PHE    51      32.083  12.109   1.041  1.00  0.00              
ATOM    157  N   PRO    52      33.094  12.843   2.914  1.00  0.00              
ATOM    158  CA  PRO    52      34.054  13.668   2.194  1.00  0.00              
ATOM    159  C   PRO    52      35.014  12.799   1.386  1.00  0.00              
ATOM    160  O   PRO    52      35.302  13.087   0.220  1.00  0.00              
ATOM    161  N   GLU    53      35.480  11.718   2.000  1.00  0.00              
ATOM    162  CA  GLU    53      36.354  10.772   1.315  1.00  0.00              
ATOM    163  C   GLU    53      35.654  10.208   0.085  1.00  0.00              
ATOM    164  O   GLU    53      36.223  10.167  -1.007  1.00  0.00              
ATOM    165  N   ILE    54      34.403   9.815   0.264  1.00  0.00              
ATOM    166  CA  ILE    54      33.607   9.266  -0.814  1.00  0.00              
ATOM    167  C   ILE    54      33.253  10.344  -1.832  1.00  0.00              
ATOM    168  O   ILE    54      33.015  10.049  -2.991  1.00  0.00              
ATOM    169  N   ASP    55      33.221  11.597  -1.394  1.00  0.00              
ATOM    170  CA  ASP    55      32.955  12.712  -2.299  1.00  0.00              
ATOM    171  C   ASP    55      34.009  12.757  -3.396  1.00  0.00              
ATOM    172  O   ASP    55      33.707  13.037  -4.552  1.00  0.00              
ATOM    173  N   LEU    56      35.243  12.458  -3.020  1.00  0.00              
ATOM    174  CA  LEU    56      36.339  12.405  -3.977  1.00  0.00              
ATOM    175  C   LEU    56      36.324  11.092  -4.760  1.00  0.00              
ATOM    176  O   LEU    56      36.724  11.047  -5.924  1.00  0.00              
END
