
#######################################################
#                                                     #
#                        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_4-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL333_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      A       5           -
LGA    K       6      K       6           -
LGA    I       7      I       7           -
LGA    A       8      A       8           -
LGA    R       9      R       9           -
LGA    I      10      -       -           -
LGA    N      11      -       -           -
LGA    E      12      -       -           -
LGA    L      13      -       -           -
LGA    A      14      I      10          4.619
LGA    -       -      N      11           -
LGA    -       -      E      12           -
LGA    A      15      L      13          3.384
LGA    K      16      A      14          2.092
LGA    A      17      A      15          1.754
LGA    K      18      K      16          1.982
LGA    A      19      A      17          3.864
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    G      20      G      20          4.509
LGA    V      21      V      21          3.519
LGA    -       -      I      22           -
LGA    I      22      T      23          2.770
LGA    T      23      E      24          1.866
LGA    -       -      E      25           -
LGA    -       -      E      26           -
LGA    E      24      K      27          3.805
LGA    E      25      A      28          1.498
LGA    E      26      E      29          2.644
LGA    K      27      Q      30          2.333
LGA    A      28      Q      31          1.279
LGA    E      29      K      32          2.693
LGA    Q      30      L      33          1.699
LGA    Q      31      R      34          1.710
LGA    K      32      Q      35          2.309
LGA    L      33      E      36          1.578
LGA    -       -      Y      37           -
LGA    -       -      L      38           -
LGA    R      34      K      39           #
LGA    Q      35      G      40           -
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     20    2.78    30.00     38.020     0.694

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.750824 * X  +  -0.564914 * Y  +  -0.342252 * Z  + 125.468155
  Y_new =   0.309945 * X  +   0.156236 * Y  +  -0.937830 * Z  + 114.433998
  Z_new =   0.583265 * X  +  -0.810224 * Y  +   0.057786 * Z  +  30.197569 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.499595    1.641997  [ DEG:   -85.9205     94.0795 ]
  Theta =  -0.622742   -2.518850  [ DEG:   -35.6805   -144.3195 ]
  Phi   =   2.750095   -0.391498  [ DEG:   157.5688    -22.4312 ]
 
# 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_4-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL333_4-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   20   2.78   30.00  38.020
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL333_4-D1
REMARK Aligment from pdb entry: 2fok_A
ATOM     17  N   ALA     5     -15.743  14.834 -12.154  1.00  0.00              
ATOM     18  CA  ALA     5     -14.625  14.835 -13.083  1.00  0.00              
ATOM     19  C   ALA     5     -13.314  14.516 -12.351  1.00  0.00              
ATOM     20  O   ALA     5     -12.508  13.715 -12.825  1.00  0.00              
ATOM     21  N   LYS     6     -13.121  15.121 -11.181  1.00  0.00              
ATOM     22  CA  LYS     6     -11.916  14.900 -10.390  1.00  0.00              
ATOM     23  C   LYS     6     -11.736  13.455  -9.930  1.00  0.00              
ATOM     24  O   LYS     6     -10.657  12.898 -10.058  1.00  0.00              
ATOM     25  N   ILE     7     -12.796  12.851  -9.400  1.00  0.00              
ATOM     26  CA  ILE     7     -12.754  11.465  -8.930  1.00  0.00              
ATOM     27  C   ILE     7     -12.528  10.474 -10.073  1.00  0.00              
ATOM     28  O   ILE     7     -11.942   9.404  -9.884  1.00  0.00              
ATOM     29  N   ALA     8     -12.998  10.824 -11.266  1.00  0.00              
ATOM     30  CA  ALA     8     -12.813   9.958 -12.416  1.00  0.00              
ATOM     31  C   ALA     8     -11.374  10.077 -12.876  1.00  0.00              
ATOM     32  O   ALA     8     -10.760   9.098 -13.288  1.00  0.00              
ATOM     33  N   ARG     9     -10.846  11.292 -12.818  1.00  0.00              
ATOM     34  CA  ARG     9      -9.474  11.557 -13.211  1.00  0.00              
ATOM     35  C   ARG     9      -8.512  10.762 -12.332  1.00  0.00              
ATOM     36  O   ARG     9      -7.621  10.077 -12.828  1.00  0.00              
ATOM     37  N   ILE    10      -8.704  10.846 -11.020  1.00  0.00              
ATOM     38  CA  ILE    10      -7.833  10.145 -10.078  1.00  0.00              
ATOM     39  C   ILE    10      -7.958   8.626 -10.130  1.00  0.00              
ATOM     40  O   ILE    10      -7.025   7.916  -9.755  1.00  0.00              
ATOM     41  N   ASN    11      -9.101   8.128 -10.597  1.00  0.00              
ATOM     42  CA  ASN    11      -9.320   6.682 -10.690  1.00  0.00              
ATOM     43  C   ASN    11      -8.508   6.057 -11.827  1.00  0.00              
ATOM     44  O   ASN    11      -8.312   4.844 -11.875  1.00  0.00              
ATOM     45  N   GLU    12      -8.051   6.901 -12.747  1.00  0.00              
ATOM     46  CA  GLU    12      -7.237   6.470 -13.884  1.00  0.00              
ATOM     47  C   GLU    12      -5.758   6.606 -13.507  1.00  0.00              
ATOM     48  O   GLU    12      -4.870   6.391 -14.339  1.00  0.00              
ATOM     49  N   LEU    13      -5.601   3.071  -2.275  1.00  0.00              
ATOM     50  CA  LEU    13      -6.936   2.571  -1.921  1.00  0.00              
ATOM     51  C   LEU    13      -6.948   1.075  -1.629  1.00  0.00              
ATOM     52  O   LEU    13      -7.710   0.603  -0.790  1.00  0.00              
ATOM     53  N   ALA    14      -6.110   0.331  -2.340  1.00  0.00              
ATOM     54  CA  ALA    14      -6.020  -1.108  -2.144  1.00  0.00              
ATOM     55  C   ALA    14      -5.399  -1.422  -0.792  1.00  0.00              
ATOM     56  O   ALA    14      -5.778  -2.391  -0.139  1.00  0.00              
ATOM     57  N   ALA    15      -4.450  -0.589  -0.371  1.00  0.00              
ATOM     58  CA  ALA    15      -3.758  -0.778   0.904  1.00  0.00              
ATOM     59  C   ALA    15      -4.604  -0.432   2.127  1.00  0.00              
ATOM     60  O   ALA    15      -4.237  -0.762   3.247  1.00  0.00              
ATOM     61  N   LYS    16      -5.732   0.235   1.911  1.00  0.00              
ATOM     62  CA  LYS    16      -6.599   0.625   3.018  1.00  0.00              
ATOM     63  C   LYS    16      -7.947  -0.103   2.951  1.00  0.00              
ATOM     64  O   LYS    16      -8.806   0.078   3.812  1.00  0.00              
ATOM     65  N   ALA    17      -8.104  -0.947   1.935  1.00  0.00              
ATOM     66  CA  ALA    17      -9.348  -1.670   1.700  1.00  0.00              
ATOM     67  C   ALA    17      -9.953  -2.445   2.871  1.00  0.00              
ATOM     68  O   ALA    17     -11.181  -2.587   2.943  1.00  0.00              
ATOM     69  N   LYS    18      -9.114  -2.926   3.789  1.00  0.00              
ATOM     70  CA  LYS    18      -9.598  -3.696   4.938  1.00  0.00              
ATOM     71  C   LYS    18      -9.989  -2.852   6.139  1.00  0.00              
ATOM     72  O   LYS    18     -10.299  -3.390   7.206  1.00  0.00              
ATOM     73  N   ALA    19      -9.979  -1.535   5.969  1.00  0.00              
ATOM     74  CA  ALA    19     -10.343  -0.655   7.063  1.00  0.00              
ATOM     75  C   ALA    19      -9.161  -0.290   7.933  1.00  0.00              
ATOM     76  O   ALA    19      -9.333   0.326   8.985  1.00  0.00              
ATOM     77  N   GLY    20      -7.965  -0.675   7.495  1.00  0.00              
ATOM     78  CA  GLY    20      -6.729  -0.388   8.222  1.00  0.00              
ATOM     79  C   GLY    20      -6.524   1.119   8.395  1.00  0.00              
ATOM     80  O   GLY    20      -7.017   1.920   7.595  1.00  0.00              
ATOM     81  N   VAL    21      -5.798   1.493   9.446  1.00  0.00              
ATOM     82  CA  VAL    21      -5.475   2.894   9.725  1.00  0.00              
ATOM     83  C   VAL    21      -3.959   2.981   9.583  1.00  0.00              
ATOM     84  O   VAL    21      -3.221   2.535  10.463  1.00  0.00              
ATOM     85  N   ILE    22      -3.481   3.555   8.486  1.00  0.00              
ATOM     86  CA  ILE    22      -2.039   3.608   8.283  1.00  0.00              
ATOM     87  C   ILE    22      -1.398   4.979   8.074  1.00  0.00              
ATOM     88  O   ILE    22      -2.041   5.930   7.603  1.00  0.00              
ATOM     89  N   THR    23      -0.115   5.057   8.438  1.00  0.00              
ATOM     90  CA  THR    23       0.683   6.266   8.293  1.00  0.00              
ATOM     91  C   THR    23       1.285   6.230   6.896  1.00  0.00              
ATOM     92  O   THR    23       1.260   5.189   6.229  1.00  0.00              
ATOM     93  N   GLU    24       1.828   7.368   6.472  1.00  0.00              
ATOM     94  CA  GLU    24       2.451   7.516   5.164  1.00  0.00              
ATOM     95  C   GLU    24       3.603   6.526   4.994  1.00  0.00              
ATOM     96  O   GLU    24       3.941   6.134   3.869  1.00  0.00              
ATOM     97  N   GLU    25       4.204   6.132   6.118  1.00  0.00              
ATOM     98  CA  GLU    25       5.328   5.189   6.120  1.00  0.00              
ATOM     99  C   GLU    25       4.876   3.763   5.868  1.00  0.00              
ATOM    100  O   GLU    25       5.555   3.009   5.160  1.00  0.00              
ATOM    101  N   GLU    26       3.747   3.391   6.472  1.00  0.00              
ATOM    102  CA  GLU    26       3.183   2.043   6.318  1.00  0.00              
ATOM    103  C   GLU    26       2.623   1.868   4.928  1.00  0.00              
ATOM    104  O   GLU    26       2.440   0.751   4.451  1.00  0.00              
ATOM    105  N   LYS    27       2.306   2.995   4.303  1.00  0.00              
ATOM    106  CA  LYS    27       1.770   3.015   2.955  1.00  0.00              
ATOM    107  C   LYS    27       2.936   3.127   1.996  1.00  0.00              
ATOM    108  O   LYS    27       3.011   2.401   1.009  1.00  0.00              
ATOM    109  N   ALA    28       3.867   4.019   2.314  1.00  0.00              
ATOM    110  CA  ALA    28       5.027   4.236   1.463  1.00  0.00              
ATOM    111  C   ALA    28       5.875   3.020   1.155  1.00  0.00              
ATOM    112  O   ALA    28       6.428   2.910   0.067  1.00  0.00              
ATOM    113  N   GLU    29       5.981   2.104   2.110  1.00  0.00              
ATOM    114  CA  GLU    29       6.775   0.897   1.936  1.00  0.00              
ATOM    115  C   GLU    29       6.220  -0.054   0.869  1.00  0.00              
ATOM    116  O   GLU    29       6.923  -0.947   0.385  1.00  0.00              
ATOM    117  N   GLN    30       4.959   0.138   0.505  1.00  0.00              
ATOM    118  CA  GLN    30       4.321  -0.701  -0.500  1.00  0.00              
ATOM    119  C   GLN    30       3.808   0.154  -1.662  1.00  0.00              
ATOM    120  O   GLN    30       2.849  -0.205  -2.346  1.00  0.00              
ATOM    121  N   GLN    31       4.485   1.279  -1.880  1.00  0.00              
ATOM    122  CA  GLN    31       4.125   2.234  -2.921  1.00  0.00              
ATOM    123  C   GLN    31       5.267   2.458  -3.915  1.00  0.00              
ATOM    124  O   GLN    31       6.409   2.734  -3.523  1.00  0.00              
ATOM    125  N   LYS    32       4.957   2.334  -5.202  1.00  0.00              
ATOM    126  CA  LYS    32       5.970   2.520  -6.224  1.00  0.00              
ATOM    127  C   LYS    32       6.943   1.356  -6.335  1.00  0.00              
ATOM    128  O   LYS    32       6.610   0.209  -6.020  1.00  0.00              
ATOM    129  N   LEU    33       8.153   1.654  -6.800  1.00  0.00              
ATOM    130  CA  LEU    33       9.186   0.643  -6.950  1.00  0.00              
ATOM    131  C   LEU    33      10.032   0.665  -5.687  1.00  0.00              
ATOM    132  O   LEU    33      11.192   1.073  -5.696  1.00  0.00              
ATOM    133  N   ARG    34       9.405   0.201  -4.605  1.00  0.00              
ATOM    134  CA  ARG    34       9.963   0.151  -3.253  1.00  0.00              
ATOM    135  C   ARG    34      11.425  -0.212  -3.040  1.00  0.00              
ATOM    136  O   ARG    34      11.938  -1.178  -3.601  1.00  0.00              
ATOM    137  N   GLN    35      12.082   0.587  -2.205  1.00  0.00              
ATOM    138  CA  GLN    35      13.463   0.343  -1.867  1.00  0.00              
ATOM    139  C   GLN    35      14.499   1.085  -2.669  1.00  0.00              
ATOM    140  O   GLN    35      15.516   1.506  -2.123  1.00  0.00              
ATOM    141  N   GLU    36      14.261   1.242  -3.965  1.00  0.00              
ATOM    142  CA  GLU    36      15.226   1.925  -4.807  1.00  0.00              
ATOM    143  C   GLU    36      15.142   3.417  -4.584  1.00  0.00              
ATOM    144  O   GLU    36      14.185   3.900  -3.973  1.00  0.00              
ATOM    145  N   TYR    37      11.340   5.417  13.029  1.00  0.00              
ATOM    146  CA  TYR    37      11.119   6.853  13.035  1.00  0.00              
ATOM    147  C   TYR    37      10.419   7.333  14.316  1.00  0.00              
ATOM    148  O   TYR    37      10.680   8.437  14.798  1.00  0.00              
ATOM    149  N   LEU    38       9.532   6.513  14.862  1.00  0.00              
ATOM    150  CA  LEU    38       8.813   6.879  16.075  1.00  0.00              
ATOM    151  C   LEU    38       9.770   6.949  17.268  1.00  0.00              
ATOM    152  O   LEU    38       9.534   7.687  18.232  1.00  0.00              
ATOM    153  N   LYS    39      10.850   6.177  17.191  1.00  0.00              
ATOM    154  CA  LYS    39      11.872   6.145  18.236  1.00  0.00              
ATOM    155  C   LYS    39      12.612   7.486  18.288  1.00  0.00              
ATOM    156  O   LYS    39      12.951   7.990  19.357  1.00  0.00              
ATOM    157  N   GLY    40      12.878   8.044  17.114  1.00  0.00              
ATOM    158  CA  GLY    40      13.573   9.312  17.004  1.00  0.00              
ATOM    159  C   GLY    40      12.651  10.425  17.466  1.00  0.00              
ATOM    160  O   GLY    40      13.102  11.475  17.907  1.00  0.00              
END
