
#######################################################
#                                                     #
#                        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 T0335AL333_3-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL333_3-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          3.792
LGA    K       6      K       6          0.752
LGA    I       7      I       7          1.565
LGA    A       8      A       8          2.015
LGA    R       9      R       9          1.386
LGA    I      10      I      10          0.853
LGA    N      11      N      11          0.821
LGA    E      12      E      12          0.341
LGA    L      13      L      13          0.888
LGA    A      14      A      14          1.109
LGA    A      15      A      15          1.464
LGA    K      16      K      16          1.530
LGA    A      17      A      17          1.107
LGA    K      18      K      18          1.782
LGA    A      19      A      19          2.605
LGA    G      20      G      20          1.974
LGA    V      21      V      21          2.572
LGA    I      22      I      22          2.493
LGA    T      23      T      23          4.503
LGA    E      24      E      24          3.846
LGA    E      25      E      25          2.631
LGA    E      26      E      26          2.728
LGA    K      27      K      27          2.185
LGA    A      28      A      28          2.975
LGA    E      29      E      29          5.341
LGA    Q      30      Q      30           #
LGA    Q      31      -       -           -
LGA    K      32      -       -           -
LGA    L      33      -       -           -
LGA    R      34      -       -           -
LGA    Q      35      -       -           -
LGA    E      36      -       -           -
LGA    Y      37      Q      31          4.713
LGA    L      38      K      32           #
LGA    -       -      L      33           -
LGA    K      39      R      34           #
LGA    G      40      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     26    2.58    96.15     59.257     0.970

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.469267 * X  +  -0.415229 * Y  +   0.779342 * Z  + -23.110601
  Y_new =  -0.873944 * X  +  -0.091924 * Y  +   0.477254 * Z  +  13.048152
  Z_new =  -0.126530 * X  +  -0.905061 * Y  +  -0.406024 * Z  + -34.059418 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.992498    1.149095  [ DEG:  -114.1617     65.8383 ]
  Theta =   0.126870    3.014723  [ DEG:     7.2691    172.7309 ]
  Phi   =  -1.078025    2.063568  [ DEG:   -61.7663    118.2337 ]
 
# 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: T0335AL333_3-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL333_3-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   26   2.58   96.15  59.257
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL333_3-D1
REMARK Aligment from pdb entry: 1lva_A
ATOM      1  N   ALA     5      -0.450  -7.871  -9.586  1.00  0.00              
ATOM      2  CA  ALA     5      -1.127  -8.690  -8.603  1.00  0.00              
ATOM      3  C   ALA     5      -0.785  -8.233  -7.193  1.00  0.00              
ATOM      4  O   ALA     5      -1.638  -8.240  -6.297  1.00  0.00              
ATOM      5  N   LYS     6       0.471  -7.847  -6.996  1.00  0.00              
ATOM      6  CA  LYS     6       0.921  -7.373  -5.695  1.00  0.00              
ATOM      7  C   LYS     6       0.209  -6.059  -5.380  1.00  0.00              
ATOM      8  O   LYS     6      -0.181  -5.806  -4.245  1.00  0.00              
ATOM      9  N   ILE     7       0.047  -5.216  -6.391  1.00  0.00              
ATOM     10  CA  ILE     7      -0.619  -3.938  -6.185  1.00  0.00              
ATOM     11  C   ILE     7      -2.066  -4.166  -5.745  1.00  0.00              
ATOM     12  O   ILE     7      -2.598  -3.445  -4.891  1.00  0.00              
ATOM     13  N   ALA     8      -2.696  -5.180  -6.326  1.00  0.00              
ATOM     14  CA  ALA     8      -4.072  -5.489  -5.973  1.00  0.00              
ATOM     15  C   ALA     8      -4.188  -5.888  -4.516  1.00  0.00              
ATOM     16  O   ALA     8      -5.118  -5.472  -3.818  1.00  0.00              
ATOM     17  N   ARG     9      -3.237  -6.690  -4.046  1.00  0.00              
ATOM     18  CA  ARG     9      -3.251  -7.141  -2.657  1.00  0.00              
ATOM     19  C   ARG     9      -2.978  -5.980  -1.721  1.00  0.00              
ATOM     20  O   ARG     9      -3.593  -5.879  -0.656  1.00  0.00              
ATOM     21  N   ILE    10      -2.058  -5.104  -2.119  1.00  0.00              
ATOM     22  CA  ILE    10      -1.709  -3.933  -1.309  1.00  0.00              
ATOM     23  C   ILE    10      -2.936  -3.049  -1.124  1.00  0.00              
ATOM     24  O   ILE    10      -3.142  -2.473  -0.052  1.00  0.00              
ATOM     25  N   ASN    11      -3.759  -2.945  -2.163  1.00  0.00              
ATOM     26  CA  ASN    11      -4.955  -2.124  -2.066  1.00  0.00              
ATOM     27  C   ASN    11      -5.934  -2.744  -1.084  1.00  0.00              
ATOM     28  O   ASN    11      -6.645  -2.026  -0.381  1.00  0.00              
ATOM     29  N   GLU    12      -5.975  -4.078  -1.032  1.00  0.00              
ATOM     30  CA  GLU    12      -6.868  -4.754  -0.096  1.00  0.00              
ATOM     31  C   GLU    12      -6.366  -4.509   1.319  1.00  0.00              
ATOM     32  O   GLU    12      -7.163  -4.374   2.253  1.00  0.00              
ATOM     33  N   LEU    13      -5.043  -4.452   1.477  1.00  0.00              
ATOM     34  CA  LEU    13      -4.459  -4.183   2.786  1.00  0.00              
ATOM     35  C   LEU    13      -4.913  -2.789   3.205  1.00  0.00              
ATOM     36  O   LEU    13      -5.291  -2.565   4.353  1.00  0.00              
ATOM     37  N   ALA    14      -4.880  -1.862   2.254  1.00  0.00              
ATOM     38  CA  ALA    14      -5.271  -0.487   2.507  1.00  0.00              
ATOM     39  C   ALA    14      -6.759  -0.358   2.818  1.00  0.00              
ATOM     40  O   ALA    14      -7.152   0.485   3.621  1.00  0.00              
ATOM     41  N   ALA    15      -7.589  -1.178   2.180  1.00  0.00              
ATOM     42  CA  ALA    15      -9.032  -1.154   2.438  1.00  0.00              
ATOM     43  C   ALA    15      -9.285  -1.571   3.880  1.00  0.00              
ATOM     44  O   ALA    15     -10.106  -0.978   4.587  1.00  0.00              
ATOM     45  N   LYS    16      -8.590  -2.624   4.298  1.00  0.00              
ATOM     46  CA  LYS    16      -8.711  -3.165   5.659  1.00  0.00              
ATOM     47  C   LYS    16      -8.238  -2.115   6.664  1.00  0.00              
ATOM     48  O   LYS    16      -8.868  -1.889   7.694  1.00  0.00              
ATOM     49  N   ALA    17      -7.115  -1.481   6.357  1.00  0.00              
ATOM     50  CA  ALA    17      -6.573  -0.445   7.227  1.00  0.00              
ATOM     51  C   ALA    17      -7.573   0.710   7.406  1.00  0.00              
ATOM     52  O   ALA    17      -7.848   1.164   8.528  1.00  0.00              
ATOM     53  N   LYS    18      -8.133   1.165   6.292  1.00  0.00              
ATOM     54  CA  LYS    18      -9.074   2.285   6.298  1.00  0.00              
ATOM     55  C   LYS    18     -10.446   1.979   6.881  1.00  0.00              
ATOM     56  O   LYS    18     -11.176   2.893   7.272  1.00  0.00              
ATOM     57  N   ALA    19     -10.791   0.697   6.948  1.00  0.00              
ATOM     58  CA  ALA    19     -12.095   0.272   7.440  1.00  0.00              
ATOM     59  C   ALA    19     -12.396   0.712   8.866  1.00  0.00              
ATOM     60  O   ALA    19     -13.545   0.672   9.294  1.00  0.00              
ATOM     61  N   GLY    20     -11.378   1.131   9.606  1.00  0.00              
ATOM     62  CA  GLY    20     -11.600   1.566  10.976  1.00  0.00              
ATOM     63  C   GLY    20     -11.364   3.063  11.190  1.00  0.00              
ATOM     64  O   GLY    20     -11.435   3.549  12.319  1.00  0.00              
ATOM     65  N   VAL    21     -11.091   3.791  10.108  1.00  0.00              
ATOM     66  CA  VAL    21     -10.861   5.229  10.213  1.00  0.00              
ATOM     67  C   VAL    21      -9.763   5.725   9.286  1.00  0.00              
ATOM     68  O   VAL    21      -9.019   4.913   8.727  1.00  0.00              
ATOM     69  N   ILE    22      -6.247   6.967   7.815  1.00  0.00              
ATOM     70  CA  ILE    22      -4.936   6.473   8.232  1.00  0.00              
ATOM     71  C   ILE    22      -3.832   7.364   7.728  1.00  0.00              
ATOM     72  O   ILE    22      -3.991   8.048   6.703  1.00  0.00              
ATOM     73  N   THR    23      -2.715   7.350   8.452  1.00  0.00              
ATOM     74  CA  THR    23      -1.559   8.136   8.059  1.00  0.00              
ATOM     75  C   THR    23      -0.511   7.224   7.439  1.00  0.00              
ATOM     76  O   THR    23      -0.665   5.998   7.421  1.00  0.00              
ATOM     77  N   GLU    24       0.567   7.817   6.942  1.00  0.00              
ATOM     78  CA  GLU    24       1.632   7.064   6.300  1.00  0.00              
ATOM     79  C   GLU    24       2.255   6.002   7.190  1.00  0.00              
ATOM     80  O   GLU    24       2.543   4.890   6.737  1.00  0.00              
ATOM     81  N   GLU    25       2.470   6.341   8.458  1.00  0.00              
ATOM     82  CA  GLU    25       3.073   5.411   9.405  1.00  0.00              
ATOM     83  C   GLU    25       2.203   4.170   9.578  1.00  0.00              
ATOM     84  O   GLU    25       2.721   3.061   9.700  1.00  0.00              
ATOM     85  N   GLU    26       0.885   4.349   9.588  1.00  0.00              
ATOM     86  CA  GLU    26      -0.017   3.212   9.747  1.00  0.00              
ATOM     87  C   GLU    26      -0.013   2.329   8.505  1.00  0.00              
ATOM     88  O   GLU    26      -0.115   1.103   8.608  1.00  0.00              
ATOM     89  N   LYS    27       0.104   2.952   7.331  1.00  0.00              
ATOM     90  CA  LYS    27       0.140   2.205   6.075  1.00  0.00              
ATOM     91  C   LYS    27       1.464   1.468   6.025  1.00  0.00              
ATOM     92  O   LYS    27       1.541   0.331   5.559  1.00  0.00              
ATOM     93  N   ALA    28       2.507   2.129   6.510  1.00  0.00              
ATOM     94  CA  ALA    28       3.838   1.540   6.529  1.00  0.00              
ATOM     95  C   ALA    28       3.822   0.198   7.265  1.00  0.00              
ATOM     96  O   ALA    28       4.364  -0.799   6.779  1.00  0.00              
ATOM     97  N   GLU    29       3.190   0.178   8.438  1.00  0.00              
ATOM     98  CA  GLU    29       3.132  -1.028   9.257  1.00  0.00              
ATOM     99  C   GLU    29       2.206  -2.123   8.723  1.00  0.00              
ATOM    100  O   GLU    29       2.539  -3.301   8.788  1.00  0.00              
ATOM    101  N   GLN    30       1.047  -1.736   8.199  1.00  0.00              
ATOM    102  CA  GLN    30       0.086  -2.703   7.670  1.00  0.00              
ATOM    103  C   GLN    30       0.654  -3.432   6.462  1.00  0.00              
ATOM    104  O   GLN    30       0.266  -4.563   6.177  1.00  0.00              
ATOM    105  N   GLN    31       1.569  -2.782   5.749  1.00  0.00              
ATOM    106  CA  GLN    31       2.179  -3.393   4.571  1.00  0.00              
ATOM    107  C   GLN    31       3.532  -3.987   4.913  1.00  0.00              
ATOM    108  O   GLN    31       4.126  -4.690   4.101  1.00  0.00              
ATOM    109  N   LYS    32       4.022  -3.686   6.111  1.00  0.00              
ATOM    110  CA  LYS    32       5.310  -4.215   6.522  1.00  0.00              
ATOM    111  C   LYS    32       6.406  -3.764   5.576  1.00  0.00              
ATOM    112  O   LYS    32       7.424  -4.448   5.404  1.00  0.00              
ATOM    113  N   LEU    33       6.206  -2.594   4.976  1.00  0.00              
ATOM    114  CA  LEU    33       7.164  -2.065   4.026  1.00  0.00              
ATOM    115  C   LEU    33       7.572  -0.636   4.368  1.00  0.00              
ATOM    116  O   LEU    33       6.755   0.170   4.821  1.00  0.00              
ATOM    117  N   ARG    34       8.844  -0.337   4.149  1.00  0.00              
ATOM    118  CA  ARG    34       9.420   0.977   4.402  1.00  0.00              
ATOM    119  C   ARG    34       8.698   2.123   3.679  1.00  0.00              
ATOM    120  O   ARG    34       8.115   1.934   2.600  1.00  0.00              
ATOM    121  N   GLN    35       8.728   3.312   4.277  1.00  0.00              
ATOM    122  CA  GLN    35       8.075   4.472   3.682  1.00  0.00              
ATOM    123  C   GLN    35       8.623   4.741   2.290  1.00  0.00              
ATOM    124  O   GLN    35       7.954   5.342   1.454  1.00  0.00              
ATOM    125  N   GLU    36       9.847   4.282   2.052  1.00  0.00              
ATOM    126  CA  GLU    36      10.505   4.457   0.766  1.00  0.00              
ATOM    127  C   GLU    36       9.628   3.886  -0.358  1.00  0.00              
ATOM    128  O   GLU    36       9.611   4.412  -1.476  1.00  0.00              
ATOM    129  N   TYR    37       8.921   2.800  -0.061  1.00  0.00              
ATOM    130  CA  TYR    37       8.044   2.162  -1.045  1.00  0.00              
ATOM    131  C   TYR    37       6.600   2.596  -0.880  1.00  0.00              
ATOM    132  O   TYR    37       5.879   2.760  -1.863  1.00  0.00              
ATOM    133  N   LEU    38       1.074   5.355  -2.047  1.00  0.00              
ATOM    134  CA  LEU    38      -0.060   6.169  -1.616  1.00  0.00              
ATOM    135  C   LEU    38      -0.320   7.365  -2.534  1.00  0.00              
ATOM    136  O   LEU    38      -1.470   7.729  -2.766  1.00  0.00              
ATOM    137  N   LYS    39       0.734   7.986  -3.051  1.00  0.00              
ATOM    138  CA  LYS    39       0.538   9.109  -3.961  1.00  0.00              
ATOM    139  C   LYS    39       0.009   8.572  -5.291  1.00  0.00              
ATOM    140  O   LYS    39      -0.762   9.249  -5.971  1.00  0.00              
ATOM    141  N   GLY    40       0.399   7.349  -5.656  1.00  0.00              
ATOM    142  CA  GLY    40      -0.103   6.754  -6.890  1.00  0.00              
ATOM    143  C   GLY    40      -1.581   6.430  -6.683  1.00  0.00              
ATOM    144  O   GLY    40      -2.416   6.689  -7.560  1.00  0.00              
END
