
#######################################################
#                                                     #
#                        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   19 (   76),  selected   19 , name T0335AL381_4
# Molecule2: number of CA atoms   42 (  691),  selected   42 , name T0335.pdb
# PARAMETERS: T0335AL381_4.T0335.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      S       3           -
LGA    -       -      N       4           -
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           -
LGA    -       -      A      14           -
LGA    -       -      A      15           -
LGA    -       -      K      16           -
LGA    -       -      A      17           -
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    -       -      V      21           -
LGA    -       -      I      22           -
LGA    K       6      T      23          1.137
LGA    I       7      E      24          0.698
LGA    A       8      E      25          0.759
LGA    R       9      E      26          0.789
LGA    I      10      K      27          0.290
LGA    N      11      A      28          0.280
LGA    E      12      E      29          0.635
LGA    L      13      Q      30          1.119
LGA    A      14      Q      31          1.131
LGA    A      15      K      32          0.981
LGA    K      16      L      33          1.062
LGA    A      17      R      34          0.846
LGA    K      18      Q      35          0.372
LGA    A      19      E      36          0.330
LGA    E      24      Y      37          0.650
LGA    E      25      L      38          0.472
LGA    E      26      K      39          0.368
LGA    K      27      G      40          1.110
LGA    A      28      F      41          0.811
LGA    -       -      R      42           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19   42    5.0     19    0.79     5.26     44.862     2.140

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.276545 * X  +  -0.317677 * Y  +  -0.906975 * Z  +  -1.305073
  Y_new =   0.064234 * X  +  -0.935561 * Y  +   0.347275 * Z  +   2.386262
  Z_new =  -0.958852 * X  +  -0.154296 * Y  +  -0.238318 * Z  +  22.124733 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.567022    0.574570  [ DEG:  -147.0795     32.9205 ]
  Theta =   1.282930    1.858662  [ DEG:    73.5065    106.4935 ]
  Phi   =   0.228227   -2.913365  [ DEG:    13.0765   -166.9235 ]
 
# 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: T0335AL381_4                                  
REMARK     2: T0335.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_4.T0335.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   42   5.0   19   0.79    5.26  44.862
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_4
REMARK Aligment from pdb entry: 1hj0A
ATOM      1  N   LYS     6      -1.260   2.890  12.471  1.00  0.00              
ATOM      2  CA  LYS     6      -1.672   3.630  11.235  1.00  0.00              
ATOM      3  C   LYS     6      -0.469   4.223  10.509  1.00  0.00              
ATOM      4  O   LYS     6      -0.130   3.803   9.424  1.00  0.00              
ATOM      5  N   ILE     7       0.185   5.179  11.093  1.00  0.00              
ATOM      6  CA  ILE     7       1.378   5.783  10.440  1.00  0.00              
ATOM      7  C   ILE     7       2.231   4.661   9.864  1.00  0.00              
ATOM      8  O   ILE     7       2.997   4.852   8.939  1.00  0.00              
ATOM      9  N   ALA     8       2.102   3.491  10.413  1.00  0.00              
ATOM     10  CA  ALA     8       2.906   2.345   9.909  1.00  0.00              
ATOM     11  C   ALA     8       2.351   1.841   8.576  1.00  0.00              
ATOM     12  O   ALA     8       2.988   1.947   7.546  1.00  0.00              
ATOM     13  N   ARG     9       1.176   1.281   8.590  1.00  0.00              
ATOM     14  CA  ARG     9       0.590   0.755   7.322  1.00  0.00              
ATOM     15  C   ARG     9       0.695   1.815   6.231  1.00  0.00              
ATOM     16  O   ARG     9       0.889   1.513   5.067  1.00  0.00              
ATOM     17  N   ILE    10       0.566   3.058   6.590  1.00  0.00              
ATOM     18  CA  ILE    10       0.652   4.120   5.551  1.00  0.00              
ATOM     19  C   ILE    10       2.094   4.258   5.078  1.00  0.00              
ATOM     20  O   ILE    10       2.351   4.238   3.901  1.00  0.00              
ATOM     21  N   ASN    11       3.049   4.385   5.962  1.00  0.00              
ATOM     22  CA  ASN    11       4.453   4.503   5.481  1.00  0.00              
ATOM     23  C   ASN    11       4.711   3.360   4.493  1.00  0.00              
ATOM     24  O   ASN    11       5.334   3.543   3.461  1.00  0.00              
ATOM     25  N   GLU    12       4.201   2.188   4.776  1.00  0.00              
ATOM     26  CA  GLU    12       4.389   1.059   3.826  1.00  0.00              
ATOM     27  C   GLU    12       3.651   1.389   2.523  1.00  0.00              
ATOM     28  O   GLU    12       4.128   1.112   1.445  1.00  0.00              
ATOM     29  N   LEU    13       2.485   1.978   2.622  1.00  0.00              
ATOM     30  CA  LEU    13       1.705   2.334   1.404  1.00  0.00              
ATOM     31  C   LEU    13       2.498   3.333   0.542  1.00  0.00              
ATOM     32  O   LEU    13       2.539   3.216  -0.664  1.00  0.00              
ATOM     33  N   ALA    14       3.123   4.315   1.139  1.00  0.00              
ATOM     34  CA  ALA    14       3.893   5.294   0.325  1.00  0.00              
ATOM     35  C   ALA    14       5.068   4.577  -0.343  1.00  0.00              
ATOM     36  O   ALA    14       5.265   4.674  -1.538  1.00  0.00              
ATOM     37  N   ALA    15       5.849   3.851   0.413  1.00  0.00              
ATOM     38  CA  ALA    15       6.999   3.132  -0.206  1.00  0.00              
ATOM     39  C   ALA    15       6.483   2.069  -1.197  1.00  0.00              
ATOM     40  O   ALA    15       7.183   1.677  -2.113  1.00  0.00              
ATOM     41  N   LYS    16       5.262   1.605  -1.041  1.00  0.00              
ATOM     42  CA  LYS    16       4.730   0.584  -1.985  1.00  0.00              
ATOM     43  C   LYS    16       4.357   1.263  -3.294  1.00  0.00              
ATOM     44  O   LYS    16       4.969   1.036  -4.312  1.00  0.00              
ATOM     45  N   ALA    17       3.362   2.104  -3.282  1.00  0.00              
ATOM     46  CA  ALA    17       2.981   2.794  -4.541  1.00  0.00              
ATOM     47  C   ALA    17       4.258   3.330  -5.195  1.00  0.00              
ATOM     48  O   ALA    17       4.424   3.269  -6.398  1.00  0.00              
ATOM     49  N   LYS    18       5.170   3.843  -4.406  1.00  0.00              
ATOM     50  CA  LYS    18       6.440   4.373  -4.978  1.00  0.00              
ATOM     51  C   LYS    18       7.239   3.242  -5.614  1.00  0.00              
ATOM     52  O   LYS    18       7.827   3.421  -6.652  1.00  0.00              
ATOM     53  N   ALA    19       7.286   2.082  -5.022  1.00  0.00              
ATOM     54  CA  ALA    19       8.071   0.995  -5.667  1.00  0.00              
ATOM     55  C   ALA    19       7.341   0.526  -6.918  1.00  0.00              
ATOM     56  O   ALA    19       7.870   0.565  -8.005  1.00  0.00              
ATOM     57  N   GLU    24       6.135   0.091  -6.789  1.00  0.00              
ATOM     58  CA  GLU    24       5.400  -0.356  -7.991  1.00  0.00              
ATOM     59  C   GLU    24       5.451   0.749  -9.050  1.00  0.00              
ATOM     60  O   GLU    24       5.356   0.485 -10.229  1.00  0.00              
ATOM     61  N   GLU    25       5.588   1.989  -8.647  1.00  0.00              
ATOM     62  CA  GLU    25       5.619   3.083  -9.667  1.00  0.00              
ATOM     63  C   GLU    25       6.992   3.177 -10.327  1.00  0.00              
ATOM     64  O   GLU    25       7.100   3.124 -11.531  1.00  0.00              
ATOM     65  N   GLU    26       8.049   3.313  -9.578  1.00  0.00              
ATOM     66  CA  GLU    26       9.377   3.399 -10.242  1.00  0.00              
ATOM     67  C   GLU    26       9.557   2.156 -11.115  1.00  0.00              
ATOM     68  O   GLU    26       9.911   2.243 -12.281  1.00  0.00              
ATOM     69  N   LYS    27       9.300   0.994 -10.572  1.00  0.00              
ATOM     70  CA  LYS    27       9.455  -0.237 -11.386  1.00  0.00              
ATOM     71  C   LYS    27       8.397  -0.266 -12.498  1.00  0.00              
ATOM     72  O   LYS    27       8.636  -0.792 -13.566  1.00  0.00              
ATOM     73  N   ALA    28       7.230   0.294 -12.273  1.00  0.00              
ATOM     74  CA  ALA    28       6.194   0.284 -13.350  1.00  0.00              
ATOM     75  C   ALA    28       6.728   1.081 -14.533  1.00  0.00              
ATOM     76  O   ALA    28       6.943   0.548 -15.596  1.00  0.00              
END
