
#######################################################
#                                                     #
#                        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   32 (  128),  selected   32 , name T0335AL257_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL257_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      -       -           -
LGA    K       6      -       -           -
LGA    I       7      -       -           -
LGA    A       8      -       -           -
LGA    R       9      -       -           -
LGA    I      10      -       -           -
LGA    N      11      -       -           -
LGA    E      12      -       -           -
LGA    L      13      A       5           #
LGA    A      14      K       6          2.865
LGA    A      15      I       7          1.528
LGA    K      16      A       8          1.003
LGA    A      17      R       9          1.782
LGA    K      18      I      10          1.276
LGA    A      19      N      11          1.490
LGA    G      20      E      12          1.783
LGA    V      21      L      13          1.917
LGA    I      22      A      14          1.267
LGA    T      23      A      15          3.104
LGA    E      24      K      16          3.327
LGA    E      25      A      17          2.724
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    E      26      V      21          2.997
LGA    K      27      I      22          2.526
LGA    A      28      T      23          2.309
LGA    -       -      E      24           -
LGA    E      29      E      25          3.896
LGA    R      34      E      26          3.157
LGA    Q      35      K      27          0.534
LGA    E      36      A      28          2.786
LGA    Y      37      E      29          2.931
LGA    L      38      Q      30          0.834
LGA    K      39      Q      31          1.648
LGA    -       -      K      32           -
LGA    G      40      L      33          3.456
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)   32   36    5.0     23    2.40     4.35     50.000     0.918

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.404453 * X  +  -0.734034 * Y  +  -0.545538 * Z  +  23.768736
  Y_new =   0.178847 * X  +  -0.648468 * Y  +   0.739935 * Z  +  15.812916
  Z_new =  -0.896901 * X  +   0.201701 * Y  +   0.393554 * Z  + -17.948420 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.473607   -2.667986  [ DEG:    27.1357   -152.8643 ]
  Theta =   1.112712    2.028881  [ DEG:    63.7537    116.2463 ]
  Phi   =   2.725249   -0.416344  [ DEG:   156.1453    -23.8547 ]
 
# 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: T0335AL257_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL257_4-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   32   36   5.0   23   2.40    4.35  50.000
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL257_4-D1
REMARK Aligment from pdb entry: 1e3h_A
ATOM     13  N   ALA     5       1.114   0.097 -20.993  1.00  0.00              
ATOM     14  CA  ALA     5       2.039  -0.927 -20.528  1.00  0.00              
ATOM     15  C   ALA     5       2.361  -0.779 -19.048  1.00  0.00              
ATOM     16  O   ALA     5       2.281  -1.752 -18.295  1.00  0.00              
ATOM     17  N   LYS     6       2.702   0.431 -18.620  1.00  0.00              
ATOM     18  CA  LYS     6       3.030   0.651 -17.218  1.00  0.00              
ATOM     19  C   LYS     6       1.877   0.352 -16.254  1.00  0.00              
ATOM     20  O   LYS     6       2.101  -0.179 -15.166  1.00  0.00              
ATOM     21  N   ILE     7       0.644   0.668 -16.637  1.00  0.00              
ATOM     22  CA  ILE     7      -0.483   0.388 -15.745  1.00  0.00              
ATOM     23  C   ILE     7      -0.761  -1.110 -15.632  1.00  0.00              
ATOM     24  O   ILE     7      -1.157  -1.597 -14.573  1.00  0.00              
ATOM     25  N   ALA     8      -0.570  -1.835 -16.730  1.00  0.00              
ATOM     26  CA  ALA     8      -0.795  -3.276 -16.736  1.00  0.00              
ATOM     27  C   ALA     8       0.319  -3.968 -15.950  1.00  0.00              
ATOM     28  O   ALA     8       0.072  -4.921 -15.208  1.00  0.00              
ATOM     29  N   ARG     9       1.541  -3.467 -16.105  1.00  0.00              
ATOM     30  CA  ARG     9       2.689  -4.019 -15.403  1.00  0.00              
ATOM     31  C   ARG     9       2.483  -3.857 -13.901  1.00  0.00              
ATOM     32  O   ARG     9       2.433  -4.838 -13.159  1.00  0.00              
ATOM     33  N   ILE    10       2.355  -2.609 -13.466  1.00  0.00              
ATOM     34  CA  ILE    10       2.156  -2.288 -12.059  1.00  0.00              
ATOM     35  C   ILE    10       1.008  -3.063 -11.422  1.00  0.00              
ATOM     36  O   ILE    10       1.139  -3.572 -10.306  1.00  0.00              
ATOM     37  N   ASN    11      -0.118  -3.146 -12.124  1.00  0.00              
ATOM     38  CA  ASN    11      -1.275  -3.861 -11.598  1.00  0.00              
ATOM     39  C   ASN    11      -0.905  -5.305 -11.320  1.00  0.00              
ATOM     40  O   ASN    11      -1.068  -5.792 -10.204  1.00  0.00              
ATOM     41  N   GLU    12      -0.403  -5.983 -12.345  1.00  0.00              
ATOM     42  CA  GLU    12       0.001  -7.379 -12.223  1.00  0.00              
ATOM     43  C   GLU    12       1.047  -7.565 -11.118  1.00  0.00              
ATOM     44  O   GLU    12       1.108  -8.617 -10.482  1.00  0.00              
ATOM     45  N   LEU    13       1.854  -6.533 -10.890  1.00  0.00              
ATOM     46  CA  LEU    13       2.903  -6.581  -9.877  1.00  0.00              
ATOM     47  C   LEU    13       2.439  -6.380  -8.433  1.00  0.00              
ATOM     48  O   LEU    13       2.980  -7.017  -7.528  1.00  0.00              
ATOM     49  N   ALA    14       1.448  -5.516  -8.200  1.00  0.00              
ATOM     50  CA  ALA    14       0.999  -5.260  -6.826  1.00  0.00              
ATOM     51  C   ALA    14      -0.502  -5.084  -6.598  1.00  0.00              
ATOM     52  O   ALA    14      -0.915  -4.647  -5.528  1.00  0.00              
ATOM     53  N   ALA    15      -1.318  -5.432  -7.583  1.00  0.00              
ATOM     54  CA  ALA    15      -2.762  -5.259  -7.457  1.00  0.00              
ATOM     55  C   ALA    15      -3.379  -5.888  -6.201  1.00  0.00              
ATOM     56  O   ALA    15      -4.201  -5.262  -5.530  1.00  0.00              
ATOM     57  N   LYS    16      -2.998  -7.133  -5.866  1.00  0.00              
ATOM     58  CA  LYS    16      -3.568  -7.769  -4.668  1.00  0.00              
ATOM     59  C   LYS    16      -3.044  -7.181  -3.355  1.00  0.00              
ATOM     60  O   LYS    16      -3.784  -7.078  -2.374  1.00  0.00              
ATOM     61  N   ALA    17      -1.767  -6.805  -3.343  1.00  0.00              
ATOM     62  CA  ALA    17      -1.151  -6.223  -2.154  1.00  0.00              
ATOM     63  C   ALA    17      -1.755  -4.856  -1.880  1.00  0.00              
ATOM     64  O   ALA    17      -2.201  -4.570  -0.768  1.00  0.00              
ATOM     65  N   LYS    18      -1.753  -4.014  -2.909  1.00  0.00              
ATOM     66  CA  LYS    18      -2.302  -2.671  -2.812  1.00  0.00              
ATOM     67  C   LYS    18      -3.761  -2.742  -2.383  1.00  0.00              
ATOM     68  O   LYS    18      -4.216  -1.968  -1.542  1.00  0.00              
ATOM     69  N   ALA    19      -4.490  -3.682  -2.968  1.00  0.00              
ATOM     70  CA  ALA    19      -5.895  -3.859  -2.642  1.00  0.00              
ATOM     71  C   ALA    19      -6.059  -4.194  -1.162  1.00  0.00              
ATOM     72  O   ALA    19      -7.017  -3.760  -0.517  1.00  0.00              
ATOM     73  N   GLY    20      -5.115  -4.966  -0.631  1.00  0.00              
ATOM     74  CA  GLY    20      -5.140  -5.371   0.771  1.00  0.00              
ATOM     75  C   GLY    20      -4.750  -4.204   1.670  1.00  0.00              
ATOM     76  O   GLY    20      -5.387  -3.955   2.698  1.00  0.00              
ATOM     77  N   VAL    21      -3.700  -3.493   1.273  1.00  0.00              
ATOM     78  CA  VAL    21      -3.217  -2.345   2.026  1.00  0.00              
ATOM     79  C   VAL    21      -4.320  -1.302   2.233  1.00  0.00              
ATOM     80  O   VAL    21      -4.457  -0.745   3.323  1.00  0.00              
ATOM     81  N   ILE    22      -5.111  -1.049   1.193  1.00  0.00              
ATOM     82  CA  ILE    22      -6.185  -0.065   1.275  1.00  0.00              
ATOM     83  C   ILE    22      -7.324  -0.489   2.197  1.00  0.00              
ATOM     84  O   ILE    22      -8.312   0.236   2.342  1.00  0.00              
ATOM     85  N   THR    23      -7.191  -1.655   2.824  1.00  0.00              
ATOM     86  CA  THR    23      -8.231  -2.140   3.729  1.00  0.00              
ATOM     87  C   THR    23      -7.934  -1.723   5.163  1.00  0.00              
ATOM     88  O   THR    23      -8.768  -1.890   6.057  1.00  0.00              
ATOM     89  N   GLU    24      -6.740  -1.175   5.370  1.00  0.00              
ATOM     90  CA  GLU    24      -6.311  -0.724   6.688  1.00  0.00              
ATOM     91  C   GLU    24      -6.883   0.660   7.010  1.00  0.00              
ATOM     92  O   GLU    24      -6.464   1.670   6.438  1.00  0.00              
ATOM     93  N   GLU    25      -7.837   0.695   7.937  1.00  0.00              
ATOM     94  CA  GLU    25      -8.490   1.936   8.342  1.00  0.00              
ATOM     95  C   GLU    25      -7.545   2.970   8.953  1.00  0.00              
ATOM     96  O   GLU    25      -7.629   4.155   8.628  1.00  0.00              
ATOM     97  N   GLU    26      -6.659   2.524   9.843  1.00  0.00              
ATOM     98  CA  GLU    26      -5.720   3.434  10.480  1.00  0.00              
ATOM     99  C   GLU    26      -4.878   4.180   9.466  1.00  0.00              
ATOM    100  O   GLU    26      -4.244   3.561   8.614  1.00  0.00              
ATOM    101  N   LYS    27      -4.860   5.507   9.554  1.00  0.00              
ATOM    102  CA  LYS    27      -4.100   6.315   8.608  1.00  0.00              
ATOM    103  C   LYS    27      -2.602   6.018   8.597  1.00  0.00              
ATOM    104  O   LYS    27      -2.057   5.586   7.582  1.00  0.00              
ATOM    105  N   ALA    28      -1.937   6.256   9.721  1.00  0.00              
ATOM    106  CA  ALA    28      -0.501   6.020   9.820  1.00  0.00              
ATOM    107  C   ALA    28      -0.137   4.541   9.699  1.00  0.00              
ATOM    108  O   ALA    28       0.970   4.193   9.287  1.00  0.00              
ATOM    109  N   GLU    29      -1.082   3.675  10.046  1.00  0.00              
ATOM    110  CA  GLU    29      -0.859   2.237   9.984  1.00  0.00              
ATOM    111  C   GLU    29      -1.006   1.698   8.554  1.00  0.00              
ATOM    112  O   GLU    29      -0.331   0.742   8.166  1.00  0.00              
ATOM    113  N   ARG    34      -1.896   2.315   7.779  1.00  0.00              
ATOM    114  CA  ARG    34      -2.134   1.921   6.392  1.00  0.00              
ATOM    115  C   ARG    34      -1.100   2.559   5.477  1.00  0.00              
ATOM    116  O   ARG    34      -0.740   1.999   4.442  1.00  0.00              
ATOM    117  N   GLN    35      -0.625   3.737   5.865  1.00  0.00              
ATOM    118  CA  GLN    35       0.370   4.443   5.075  1.00  0.00              
ATOM    119  C   GLN    35       1.692   3.692   5.145  1.00  0.00              
ATOM    120  O   GLN    35       2.611   3.953   4.370  1.00  0.00              
ATOM    121  N   GLU    36       1.779   2.759   6.088  1.00  0.00              
ATOM    122  CA  GLU    36       2.976   1.945   6.253  1.00  0.00              
ATOM    123  C   GLU    36       3.024   0.990   5.070  1.00  0.00              
ATOM    124  O   GLU    36       3.981   0.988   4.297  1.00  0.00              
ATOM    125  N   TYR    37       1.973   0.186   4.940  1.00  0.00              
ATOM    126  CA  TYR    37       1.854  -0.775   3.851  1.00  0.00              
ATOM    127  C   TYR    37       2.046  -0.096   2.505  1.00  0.00              
ATOM    128  O   TYR    37       2.841  -0.543   1.681  1.00  0.00              
ATOM    129  N   LEU    38       1.310   0.990   2.290  1.00  0.00              
ATOM    130  CA  LEU    38       1.386   1.733   1.040  1.00  0.00              
ATOM    131  C   LEU    38       2.823   2.108   0.673  1.00  0.00              
ATOM    132  O   LEU    38       3.252   1.890  -0.460  1.00  0.00              
ATOM    133  N   LYS    39       3.571   2.664   1.623  1.00  0.00              
ATOM    134  CA  LYS    39       4.959   3.034   1.354  1.00  0.00              
ATOM    135  C   LYS    39       5.794   1.792   1.060  1.00  0.00              
ATOM    136  O   LYS    39       6.860   1.880   0.445  1.00  0.00              
ATOM    137  N   GLY    40       5.301   0.637   1.500  1.00  0.00              
ATOM    138  CA  GLY    40       5.987  -0.627   1.271  1.00  0.00              
ATOM    139  C   GLY    40       5.636  -1.181  -0.103  1.00  0.00              
ATOM    140  O   GLY    40       6.525  -1.452  -0.909  1.00  0.00              
END
