
#######################################################
#                                                     #
#                        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   31 (  124),  selected   31 , name T0335AL257_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL257_1-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          1.943
LGA    K       6      K       6          0.814
LGA    I       7      I       7          1.396
LGA    A       8      A       8          1.040
LGA    R       9      R       9          0.098
LGA    I      10      I      10          1.177
LGA    N      11      N      11          0.594
LGA    E      12      E      12          0.731
LGA    L      13      L      13          0.978
LGA    A      14      A      14          2.092
LGA    A      15      A      15          2.515
LGA    K      16      K      16          2.100
LGA    A      17      A      17          2.028
LGA    K      18      K      18          2.242
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    A      19      V      21          2.021
LGA    G      20      I      22          2.720
LGA    V      21      T      23          1.831
LGA    T      23      -       -           -
LGA    E      24      E      24          1.233
LGA    E      25      E      25          1.500
LGA    E      26      E      26          1.606
LGA    K      27      K      27          1.007
LGA    A      28      A      28          1.100
LGA    E      29      E      29          1.103
LGA    Q      30      Q      30          0.661
LGA    Q      31      Q      31          0.467
LGA    K      32      K      32          0.563
LGA    L      33      L      33          0.873
LGA    L      38      R      34          0.807
LGA    K      39      Q      35          1.268
LGA    G      40      E      36          1.105
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)   31   36    5.0     30    1.47    80.00     78.058     1.911

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.384955 * X  +   0.125614 * Y  +  -0.914347 * Z  +  23.670242
  Y_new =   0.456070 * X  +   0.887176 * Y  +  -0.070131 * Z  + -31.603642
  Z_new =   0.802377 * X  +  -0.444004 * Y  +  -0.398812 * Z  + -16.810009 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.302626    0.838967  [ DEG:  -131.9307     48.0693 ]
  Theta =  -0.931268   -2.210325  [ DEG:   -53.3577   -126.6423 ]
  Phi   =   2.271837   -0.869755  [ DEG:   130.1667    -49.8333 ]
 
# 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_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL257_1-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   31   36   5.0   30   1.47   80.00  78.058
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL257_1-D1
REMARK Aligment from pdb entry: 2c5i_T
ATOM     17  N   ALA     5      -0.522  -8.712  -8.062  1.00  0.00              
ATOM     18  CA  ALA     5      -0.783  -9.271  -6.716  1.00  0.00              
ATOM     19  C   ALA     5      -0.305  -8.383  -5.543  1.00  0.00              
ATOM     20  O   ALA     5      -0.921  -8.340  -4.467  1.00  0.00              
ATOM     21  N   LYS     6       0.797  -7.677  -5.745  1.00  0.00              
ATOM     22  CA  LYS     6       1.269  -6.669  -4.769  1.00  0.00              
ATOM     23  C   LYS     6       0.277  -5.519  -4.647  1.00  0.00              
ATOM     24  O   LYS     6      -0.105  -5.128  -3.566  1.00  0.00              
ATOM     25  N   ILE     7      -0.142  -5.021  -5.777  1.00  0.00              
ATOM     26  CA  ILE     7      -1.150  -3.980  -5.864  1.00  0.00              
ATOM     27  C   ILE     7      -2.447  -4.386  -5.172  1.00  0.00              
ATOM     28  O   ILE     7      -2.991  -3.597  -4.395  1.00  0.00              
ATOM     29  N   ALA     8      -2.914  -5.603  -5.445  1.00  0.00              
ATOM     30  CA  ALA     8      -4.092  -6.122  -4.828  1.00  0.00              
ATOM     31  C   ALA     8      -4.006  -6.268  -3.356  1.00  0.00              
ATOM     32  O   ALA     8      -4.957  -5.964  -2.653  1.00  0.00              
ATOM     33  N   ARG     9      -2.863  -6.737  -2.873  1.00  0.00              
ATOM     34  CA  ARG     9      -2.605  -6.859  -1.446  1.00  0.00              
ATOM     35  C   ARG     9      -2.783  -5.555  -0.648  1.00  0.00              
ATOM     36  O   ARG     9      -3.224  -5.577   0.509  1.00  0.00              
ATOM     37  N   ILE    10      -2.357  -4.442  -1.255  1.00  0.00              
ATOM     38  CA  ILE    10      -2.420  -3.120  -0.655  1.00  0.00              
ATOM     39  C   ILE    10      -3.834  -2.596  -0.787  1.00  0.00              
ATOM     40  O   ILE    10      -4.362  -1.959   0.114  1.00  0.00              
ATOM     41  N   ASN    11      -4.460  -2.918  -1.893  1.00  0.00              
ATOM     42  CA  ASN    11      -5.867  -2.622  -2.060  1.00  0.00              
ATOM     43  C   ASN    11      -6.782  -3.244  -1.058  1.00  0.00              
ATOM     44  O   ASN    11      -7.660  -2.597  -0.569  1.00  0.00              
ATOM     45  N   GLU    12      -6.557  -4.519  -0.761  1.00  0.00              
ATOM     46  CA  GLU    12      -7.297  -5.234   0.254  1.00  0.00              
ATOM     47  C   GLU    12      -7.033  -4.656   1.595  1.00  0.00              
ATOM     48  O   GLU    12      -7.967  -4.550   2.380  1.00  0.00              
ATOM     49  N   LEU    13      -5.788  -4.281   1.883  1.00  0.00              
ATOM     50  CA  LEU    13      -5.462  -3.655   3.156  1.00  0.00              
ATOM     51  C   LEU    13      -6.231  -2.322   3.348  1.00  0.00              
ATOM     52  O   LEU    13      -6.846  -2.084   4.387  1.00  0.00              
ATOM     53  N   ALA    14      -6.163  -1.447   2.353  1.00  0.00              
ATOM     54  CA  ALA    14      -6.952  -0.220   2.381  1.00  0.00              
ATOM     55  C   ALA    14      -8.430  -0.507   2.632  1.00  0.00              
ATOM     56  O   ALA    14      -9.063   0.202   3.382  1.00  0.00              
ATOM     57  N   ALA    15      -8.987  -1.545   2.020  1.00  0.00              
ATOM     58  CA  ALA    15     -10.368  -1.854   2.277  1.00  0.00              
ATOM     59  C   ALA    15     -10.633  -2.288   3.713  1.00  0.00              
ATOM     60  O   ALA    15     -11.645  -1.900   4.276  1.00  0.00              
ATOM     61  N   LYS    16      -9.738  -3.062   4.314  1.00  0.00              
ATOM     62  CA  LYS    16      -9.939  -3.465   5.705  1.00  0.00              
ATOM     63  C   LYS    16      -9.588  -2.415   6.767  1.00  0.00              
ATOM     64  O   LYS    16     -10.090  -2.494   7.873  1.00  0.00              
ATOM     65  N   ALA    17      -8.710  -1.469   6.470  1.00  0.00              
ATOM     66  CA  ALA    17      -8.298  -0.482   7.450  1.00  0.00              
ATOM     67  C   ALA    17      -8.540   0.914   6.873  1.00  0.00              
ATOM     68  O   ALA    17      -7.638   1.732   6.807  1.00  0.00              
ATOM     69  N   LYS    18      -9.791   1.163   6.459  1.00  0.00              
ATOM     70  CA  LYS    18     -10.322   2.511   6.061  1.00  0.00              
ATOM     71  C   LYS    18      -9.684   3.741   6.710  1.00  0.00              
ATOM     72  O   LYS    18      -9.638   4.832   6.116  1.00  0.00              
ATOM     73  N   ALA    19      -9.246   3.547   7.952  1.00  0.00              
ATOM     74  CA  ALA    19      -8.717   4.600   8.802  1.00  0.00              
ATOM     75  C   ALA    19      -7.245   4.820   8.454  1.00  0.00              
ATOM     76  O   ALA    19      -6.445   3.872   8.449  1.00  0.00              
ATOM     77  N   GLY    20      -6.912   6.078   8.159  1.00  0.00              
ATOM     78  CA  GLY    20      -5.607   6.460   7.612  1.00  0.00              
ATOM     79  C   GLY    20      -4.555   6.580   8.721  1.00  0.00              
ATOM     80  O   GLY    20      -3.929   7.639   8.879  1.00  0.00              
ATOM     81  N   VAL    21      -4.343   5.487   9.464  1.00  0.00              
ATOM     82  CA  VAL    21      -3.618   5.550  10.741  1.00  0.00              
ATOM     83  C   VAL    21      -2.134   5.173  10.759  1.00  0.00              
ATOM     84  O   VAL    21      -1.253   6.014  10.482  1.00  0.00              
ATOM     85  N   THR    23      -1.879   3.914  11.135  1.00  0.00              
ATOM     86  CA  THR    23      -0.543   3.337  11.276  1.00  0.00              
ATOM     87  C   THR    23       0.404   4.145  10.392  1.00  0.00              
ATOM     88  O   THR    23       0.357   4.038   9.154  1.00  0.00              
ATOM     89  N   GLU    24       1.204   5.008  11.023  1.00  0.00              
ATOM     90  CA  GLU    24       2.285   5.718  10.322  1.00  0.00              
ATOM     91  C   GLU    24       3.304   4.746   9.695  1.00  0.00              
ATOM     92  O   GLU    24       3.827   5.004   8.610  1.00  0.00              
ATOM     93  N   GLU    25       3.538   3.630  10.389  1.00  0.00              
ATOM     94  CA  GLU    25       4.295   2.500   9.868  1.00  0.00              
ATOM     95  C   GLU    25       3.746   2.104   8.499  1.00  0.00              
ATOM     96  O   GLU    25       4.401   2.329   7.486  1.00  0.00              
ATOM     97  N   GLU    26       2.529   1.566   8.460  1.00  0.00              
ATOM     98  CA  GLU    26       1.993   1.023   7.207  1.00  0.00              
ATOM     99  C   GLU    26       1.800   2.116   6.169  1.00  0.00              
ATOM    100  O   GLU    26       1.960   1.883   4.989  1.00  0.00              
ATOM    101  N   LYS    27       1.467   3.308   6.600  1.00  0.00              
ATOM    102  CA  LYS    27       1.435   4.430   5.689  1.00  0.00              
ATOM    103  C   LYS    27       2.789   4.609   4.964  1.00  0.00              
ATOM    104  O   LYS    27       2.825   4.926   3.771  1.00  0.00              
ATOM    105  N   ALA    28       3.890   4.424   5.697  1.00  0.00              
ATOM    106  CA  ALA    28       5.241   4.549   5.120  1.00  0.00              
ATOM    107  C   ALA    28       5.505   3.340   4.221  1.00  0.00              
ATOM    108  O   ALA    28       5.941   3.490   3.087  1.00  0.00              
ATOM    109  N   GLU    29       5.232   2.163   4.766  1.00  0.00              
ATOM    110  CA  GLU    29       5.383   0.908   4.076  1.00  0.00              
ATOM    111  C   GLU    29       4.584   0.907   2.762  1.00  0.00              
ATOM    112  O   GLU    29       5.124   0.631   1.724  1.00  0.00              
ATOM    113  N   GLN    30       3.316   1.288   2.811  1.00  0.00              
ATOM    114  CA  GLN    30       2.522   1.454   1.593  1.00  0.00              
ATOM    115  C   GLN    30       3.140   2.446   0.628  1.00  0.00              
ATOM    116  O   GLN    30       3.124   2.254  -0.573  1.00  0.00              
ATOM    117  N   GLN    31       3.679   3.534   1.125  1.00  0.00              
ATOM    118  CA  GLN    31       4.308   4.475   0.228  1.00  0.00              
ATOM    119  C   GLN    31       5.611   3.926  -0.403  1.00  0.00              
ATOM    120  O   GLN    31       5.826   4.118  -1.584  1.00  0.00              
ATOM    121  N   LYS    32       6.416   3.210   0.376  1.00  0.00              
ATOM    122  CA  LYS    32       7.578   2.473  -0.079  1.00  0.00              
ATOM    123  C   LYS    32       7.264   1.471  -1.202  1.00  0.00              
ATOM    124  O   LYS    32       7.874   1.479  -2.244  1.00  0.00              
ATOM    125  N   LEU    33       6.293   0.598  -0.978  1.00  0.00              
ATOM    126  CA  LEU    33       5.870  -0.413  -1.981  1.00  0.00              
ATOM    127  C   LEU    33       5.364   0.263  -3.262  1.00  0.00              
ATOM    128  O   LEU    33       5.755  -0.079  -4.332  1.00  0.00              
ATOM    129  N   LEU    38       4.566   1.306  -3.140  1.00  0.00              
ATOM    130  CA  LEU    38       3.997   1.955  -4.306  1.00  0.00              
ATOM    131  C   LEU    38       5.088   2.602  -5.180  1.00  0.00              
ATOM    132  O   LEU    38       4.997   2.677  -6.403  1.00  0.00              
ATOM    133  N   LYS    39       6.124   3.086  -4.514  1.00  0.00              
ATOM    134  CA  LYS    39       7.264   3.625  -5.191  1.00  0.00              
ATOM    135  C   LYS    39       8.025   2.524  -5.949  1.00  0.00              
ATOM    136  O   LYS    39       8.429   2.734  -7.069  1.00  0.00              
ATOM    137  N   GLY    40       8.234   1.395  -5.284  1.00  0.00              
ATOM    138  CA  GLY    40       8.848   0.237  -5.833  1.00  0.00              
ATOM    139  C   GLY    40       8.095  -0.193  -7.102  1.00  0.00              
ATOM    140  O   GLY    40       8.727  -0.362  -8.141  1.00  0.00              
END
