
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0352AL381_2
# Molecule2: number of CA atoms  109 ( 1766),  selected  109 , name T0352.pdb
# PARAMETERS: T0352AL381_2.T0352.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    R       6      M       1          3.291
LGA    V       7      T       2          1.000
LGA    R       8      T       3          1.021
LGA    L       9      H       4          1.684
LGA    Q      10      D       5          1.827
LGA    L      11      R       6          1.819
LGA    Q      12      V       7          1.957
LGA    A      13      R       8          2.761
LGA    L      14      L       9          3.617
LGA    -       -      Q      10           -
LGA    E      15      L      11          0.714
LGA    A      16      Q      12          3.341
LGA    L      17      A      13          4.448
LGA    L      18      L      14          3.713
LGA    R      19      E      15          4.913
LGA    E      20      A      16           -
LGA    -       -      L      17           -
LGA    -       -      L      18           -
LGA    -       -      R      19           -
LGA    -       -      E      20           -
LGA    -       -      H      21           -
LGA    -       -      Q      22           -
LGA    -       -      H      23           -
LGA    -       -      W      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      D      27           -
LGA    -       -      E      28           -
LGA    -       -      P      29           -
LGA    -       -      Q      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      Q      33           -
LGA    -       -      F      34           -
LGA    -       -      N      35           -
LGA    H      21      S      36           #
LGA    Q      22      T      37          3.471
LGA    H      23      Q      38          4.957
LGA    W      24      P      39          2.411
LGA    R      25      F      40          3.943
LGA    -       -      F      41           -
LGA    -       -      M      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      M      45           -
LGA    -       -      E      46           -
LGA    -       -      P      47           -
LGA    -       -      L      48           -
LGA    -       -      E      49           -
LGA    -       -      W      50           -
LGA    -       -      L      51           -
LGA    -       -      Q      52           -
LGA    -       -      W      53           -
LGA    -       -      V      54           -
LGA    N      26      L      55          3.976
LGA    D      27      I      56          5.265
LGA    -       -      P      57           -
LGA    -       -      R      58           -
LGA    -       -      M      59           -
LGA    -       -      H      60           -
LGA    -       -      D      61           -
LGA    -       -      L      62           -
LGA    -       -      L      63           -
LGA    -       -      D      64           -
LGA    -       -      N      65           -
LGA    -       -      K      66           -
LGA    -       -      Q      67           -
LGA    -       -      P      68           -
LGA    -       -      L      69           -
LGA    -       -      P      70           -
LGA    -       -      G      71           -
LGA    E      28      A      72           #
LGA    P      29      F      73          4.029
LGA    Q      30      A      74           #
LGA    H      32      V      75          3.091
LGA    Q      33      -       -           -
LGA    F      34      -       -           -
LGA    N      35      -       -           -
LGA    S      36      A      76          4.322
LGA    T      37      P      77          4.005
LGA    -       -      Y      78           -
LGA    Q      38      Y      79          2.951
LGA    P      39      E      80          1.376
LGA    -       -      M      81           -
LGA    -       -      A      82           -
LGA    F      40      L      83          3.589
LGA    -       -      A      84           -
LGA    -       -      T      85           -
LGA    -       -      D      86           -
LGA    -       -      H      87           -
LGA    -       -      P      88           -
LGA    -       -      Q      89           -
LGA    -       -      R      90           -
LGA    -       -      A      91           -
LGA    -       -      L      92           -
LGA    -       -      I      93           -
LGA    -       -      L      94           -
LGA    -       -      A      95           -
LGA    -       -      E      96           -
LGA    -       -      L      97           -
LGA    -       -      E      98           -
LGA    -       -      K      99           -
LGA    -       -      L     100           -
LGA    -       -      D     101           -
LGA    -       -      A     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      A     105           -
LGA    -       -      D     106           -
LGA    -       -      D     107           -
LGA    -       -      A     108           -
LGA    -       -      S     109           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34  109    5.0     27    3.34     7.41     14.773     0.784

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.176152 * X  +  -0.010072 * Y  +  -0.984311 * Z  +  12.472678
  Y_new =   0.388978 * X  +   0.917853 * Y  +  -0.079003 * Z  + -90.240509
  Z_new =   0.904249 * X  +  -0.396792 * Y  +  -0.157764 * Z  + -100.259415 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.949231    1.192362  [ DEG:  -111.6827     68.3173 ]
  Theta =  -1.129618   -2.011975  [ DEG:   -64.7223   -115.2777 ]
  Phi   =   1.996025   -1.145567  [ DEG:   114.3638    -65.6362 ]
 
# 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: T0352AL381_2                                  
REMARK     2: T0352.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0352AL381_2.T0352.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34  109   5.0   27   3.34    7.41  14.773
REMARK  ---------------------------------------------------------- 
MOLECULE T0352AL381_2
REMARK Aligment from pdb entry: 1x74A
ATOM      1  N   ARG     6       2.115  -4.828  -7.034  1.00  0.00              
ATOM      2  CA  ARG     6       1.607  -4.282  -8.295  1.00  0.00              
ATOM      3  C   ARG     6       0.150  -4.713  -8.515  1.00  0.00              
ATOM      4  O   ARG     6      -0.697  -3.903  -8.857  1.00  0.00              
ATOM      5  N   VAL     7      -0.107  -6.021  -8.434  1.00  0.00              
ATOM      6  CA  VAL     7      -1.439  -6.515  -8.741  1.00  0.00              
ATOM      7  C   VAL     7      -2.488  -5.898  -7.814  1.00  0.00              
ATOM      8  O   VAL     7      -3.579  -5.539  -8.279  1.00  0.00              
ATOM      9  N   ARG     8      -2.199  -5.793  -6.514  1.00  0.00              
ATOM     10  CA  ARG     8      -3.193  -5.193  -5.605  1.00  0.00              
ATOM     11  C   ARG     8      -3.469  -3.714  -5.967  1.00  0.00              
ATOM     12  O   ARG     8      -4.616  -3.223  -5.821  1.00  0.00              
ATOM     13  N   LEU     9      -2.447  -3.010  -6.450  1.00  0.00              
ATOM     14  CA  LEU     9      -2.618  -1.629  -6.930  1.00  0.00              
ATOM     15  C   LEU     9      -3.581  -1.558  -8.120  1.00  0.00              
ATOM     16  O   LEU     9      -4.469  -0.692  -8.169  1.00  0.00              
ATOM     17  N   GLN    10      -3.420  -2.455  -9.095  1.00  0.00              
ATOM     18  CA  GLN    10      -4.388  -2.481 -10.199  1.00  0.00              
ATOM     19  C   GLN    10      -5.766  -2.918  -9.678  1.00  0.00              
ATOM     20  O   GLN    10      -6.777  -2.436 -10.164  1.00  0.00              
ATOM     21  N   LEU    11      -5.801  -3.836  -8.713  1.00  0.00              
ATOM     22  CA  LEU    11      -7.072  -4.287  -8.145  1.00  0.00              
ATOM     23  C   LEU    11      -7.860  -3.098  -7.549  1.00  0.00              
ATOM     24  O   LEU    11      -9.098  -3.065  -7.608  1.00  0.00              
ATOM     25  N   GLN    12      -7.134  -2.120  -6.991  1.00  0.00              
ATOM     26  CA  GLN    12      -7.774  -0.963  -6.381  1.00  0.00              
ATOM     27  C   GLN    12      -7.759   0.262  -7.312  1.00  0.00              
ATOM     28  O   GLN    12      -7.922   1.403  -6.870  1.00  0.00              
ATOM     29  N   ALA    13      -7.590   0.034  -8.608  1.00  0.00              
ATOM     30  CA  ALA    13      -7.486   1.182  -9.527  1.00  0.00              
ATOM     31  C   ALA    13      -8.692   2.133  -9.415  1.00  0.00              
ATOM     32  O   ALA    13      -8.558   3.347  -9.654  1.00  0.00              
ATOM     33  N   LEU    14      -9.869   1.576  -9.088  1.00  0.00              
ATOM     34  CA  LEU    14     -11.055   2.419  -9.003  1.00  0.00              
ATOM     35  C   LEU    14     -10.866   3.552  -7.982  1.00  0.00              
ATOM     36  O   LEU    14     -11.321   4.689  -8.217  1.00  0.00              
ATOM     37  N   GLU    15     -10.209   3.252  -6.858  1.00  0.00              
ATOM     38  CA  GLU    15      -9.940   4.306  -5.864  1.00  0.00              
ATOM     39  C   GLU    15      -8.921   5.312  -6.351  1.00  0.00              
ATOM     40  O   GLU    15      -9.084   6.503  -6.096  1.00  0.00              
ATOM     41  N   ALA    16      -7.872   4.851  -7.043  1.00  0.00              
ATOM     42  CA  ALA    16      -6.920   5.797  -7.660  1.00  0.00              
ATOM     43  C   ALA    16      -7.610   6.728  -8.662  1.00  0.00              
ATOM     44  O   ALA    16      -7.302   7.923  -8.725  1.00  0.00              
ATOM     45  N   LEU    17      -8.545   6.172  -9.433  1.00  0.00              
ATOM     46  CA  LEU    17      -9.319   6.955 -10.413  1.00  0.00              
ATOM     47  C   LEU    17     -10.185   7.980  -9.679  1.00  0.00              
ATOM     48  O   LEU    17     -10.176   9.170 -10.003  1.00  0.00              
ATOM     49  N   LEU    18     -10.921   7.508  -8.684  1.00  0.00              
ATOM     50  CA  LEU    18     -11.789   8.385  -7.871  1.00  0.00              
ATOM     51  C   LEU    18     -11.033   9.440  -7.070  1.00  0.00              
ATOM     52  O   LEU    18     -11.487  10.559  -6.961  1.00  0.00              
ATOM     53  N   ARG    19      -9.873   9.100  -6.513  1.00  0.00              
ATOM     54  CA  ARG    19      -9.060  10.130  -5.853  1.00  0.00              
ATOM     55  C   ARG    19      -8.752  11.334  -6.743  1.00  0.00              
ATOM     56  O   ARG    19      -8.774  12.476  -6.293  1.00  0.00              
ATOM     57  N   GLU    20      -8.476  11.074  -8.015  1.00  0.00              
ATOM     58  CA  GLU    20      -8.137  12.114  -8.965  1.00  0.00              
ATOM     59  C   GLU    20      -9.276  13.084  -9.259  1.00  0.00              
ATOM     60  O   GLU    20      -9.024  14.212  -9.667  1.00  0.00              
ATOM     61  N   HIS    21     -10.522  12.643  -9.056  1.00  0.00              
ATOM     62  CA  HIS    21     -11.688  13.492  -9.362  1.00  0.00              
ATOM     63  C   HIS    21     -12.455  13.936  -8.119  1.00  0.00              
ATOM     64  O   HIS    21     -13.589  14.436  -8.229  1.00  0.00              
ATOM     65  N   GLN    22     -11.854  13.799  -6.945  1.00  0.00              
ATOM     66  CA  GLN    22     -12.536  14.244  -5.732  1.00  0.00              
ATOM     67  C   GLN    22     -13.577  13.271  -5.203  1.00  0.00              
ATOM     68  O   GLN    22     -14.317  13.605  -4.262  1.00  0.00              
ATOM     69  N   HIS    23     -13.647  12.071  -5.778  1.00  0.00              
ATOM     70  CA  HIS    23     -14.672  11.085  -5.401  1.00  0.00              
ATOM     71  C   HIS    23     -14.245  10.094  -4.321  1.00  0.00              
ATOM     72  O   HIS    23     -15.016   9.211  -3.914  1.00  0.00              
ATOM     73  N   TRP    24     -13.017  10.233  -3.842  1.00  0.00              
ATOM     74  CA  TRP    24     -12.520   9.375  -2.769  1.00  0.00              
ATOM     75  C   TRP    24     -11.464  10.154  -2.000  1.00  0.00              
ATOM     76  O   TRP    24     -10.682  10.892  -2.589  1.00  0.00              
ATOM     77  N   ARG    25     -11.432   9.969  -0.680  1.00  0.00              
ATOM     78  CA  ARG    25     -10.486  10.706   0.140  1.00  0.00              
ATOM     79  C   ARG    25      -9.620   9.703   0.887  1.00  0.00              
ATOM     80  O   ARG    25     -10.006   8.548   1.093  1.00  0.00              
ATOM     81  N   ASN    26      -8.462  10.185   1.331  1.00  0.00              
ATOM     82  CA  ASN    26      -7.529   9.407   2.143  1.00  0.00              
ATOM     83  C   ASN    26      -7.947   9.199   3.594  1.00  0.00              
ATOM     84  O   ASN    26      -7.252   8.520   4.344  1.00  0.00              
ATOM     85  N   ASP    27      -9.069   9.780   3.988  1.00  0.00              
ATOM     86  CA  ASP    27      -9.602   9.581   5.325  1.00  0.00              
ATOM     87  C   ASP    27     -10.247   8.179   5.457  1.00  0.00              
ATOM     88  O   ASP    27     -11.233   7.865   4.786  1.00  0.00              
ATOM     89  N   GLU    28      -9.690   7.345   6.323  1.00  0.00              
ATOM     90  CA  GLU    28     -10.242   6.004   6.557  1.00  0.00              
ATOM     91  C   GLU    28     -11.635   6.100   7.186  1.00  0.00              
ATOM     92  O   GLU    28     -11.878   6.928   8.079  1.00  0.00              
ATOM     93  N   PRO    29     -12.548   5.296   6.662  1.00  0.00              
ATOM     94  CA  PRO    29     -13.880   5.114   7.214  1.00  0.00              
ATOM     95  C   PRO    29     -14.810   6.278   6.896  1.00  0.00              
ATOM     96  O   PRO    29     -15.757   6.495   7.619  1.00  0.00              
ATOM     97  N   GLN    30     -14.522   7.054   5.852  1.00  0.00              
ATOM     98  CA  GLN    30     -15.280   8.287   5.596  1.00  0.00              
ATOM     99  C   GLN    30     -15.641   8.452   4.122  1.00  0.00              
ATOM    100  O   GLN    30     -15.704   9.596   3.598  1.00  0.00              
ATOM    101  N   HIS    32     -15.858   7.323   3.451  1.00  0.00              
ATOM    102  CA  HIS    32     -16.147   7.353   2.013  1.00  0.00              
ATOM    103  C   HIS    32     -17.331   6.463   1.687  1.00  0.00              
ATOM    104  O   HIS    32     -17.918   5.833   2.595  1.00  0.00              
ATOM    105  N   GLN    33     -17.702   6.425   0.409  1.00  0.00              
ATOM    106  CA  GLN    33     -18.925   5.704   0.045  1.00  0.00              
ATOM    107  C   GLN    33     -18.887   4.194   0.308  1.00  0.00              
ATOM    108  O   GLN    33     -19.919   3.613   0.606  1.00  0.00              
ATOM    109  N   PHE    34     -17.724   3.559   0.143  1.00  0.00              
ATOM    110  CA  PHE    34     -17.635   2.106   0.064  1.00  0.00              
ATOM    111  C   PHE    34     -16.798   1.497   1.175  1.00  0.00              
ATOM    112  O   PHE    34     -16.485   0.308   1.122  1.00  0.00              
ATOM    113  N   ASN    35     -16.450   2.292   2.179  1.00  0.00              
ATOM    114  CA  ASN    35     -15.553   1.792   3.238  1.00  0.00              
ATOM    115  C   ASN    35     -16.231   1.680   4.593  1.00  0.00              
ATOM    116  O   ASN    35     -15.579   1.419   5.599  1.00  0.00              
ATOM    117  N   SER    36     -17.543   1.899   4.624  1.00  0.00              
ATOM    118  CA  SER    36     -18.259   1.922   5.874  1.00  0.00              
ATOM    119  C   SER    36     -18.683   3.307   6.285  1.00  0.00              
ATOM    120  O   SER    36     -19.519   3.446   7.189  1.00  0.00              
ATOM    121  N   THR    37     -18.138   4.334   5.624  1.00  0.00              
ATOM    122  CA  THR    37     -18.501   5.712   5.932  1.00  0.00              
ATOM    123  C   THR    37     -19.960   6.079   5.658  1.00  0.00              
ATOM    124  O   THR    37     -20.512   6.957   6.326  1.00  0.00              
ATOM    125  N   GLN    38     -20.571   5.447   4.655  1.00  0.00              
ATOM    126  CA  GLN    38     -21.939   5.785   4.229  1.00  0.00              
ATOM    127  C   GLN    38     -22.948   4.889   4.969  1.00  0.00              
ATOM    128  O   GLN    38     -22.755   3.678   4.985  1.00  0.00              
ATOM    129  N   PRO    39     -23.992   5.479   5.575  1.00  0.00              
ATOM    130  CA  PRO    39     -25.035   4.698   6.279  1.00  0.00              
ATOM    131  C   PRO    39     -25.791   3.727   5.381  1.00  0.00              
ATOM    132  O   PRO    39     -26.376   2.754   5.896  1.00  0.00              
ATOM    133  N   PHE    40     -25.761   3.951   4.064  1.00  0.00              
ATOM    134  CA  PHE    40     -26.408   3.022   3.126  1.00  0.00              
ATOM    135  C   PHE    40     -25.459   1.999   2.532  1.00  0.00              
ATOM    136  O   PHE    40     -25.834   1.224   1.638  1.00  0.00              
END
