
#######################################################
#                                                     #
#                        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-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL381_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           -
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          1.106
LGA    I       7      E      24          0.611
LGA    A       8      E      25          0.673
LGA    R       9      E      26          0.759
LGA    I      10      K      27          0.290
LGA    N      11      A      28          0.302
LGA    E      12      E      29          0.621
LGA    L      13      Q      30          1.050
LGA    A      14      Q      31          1.108
LGA    A      15      K      32          1.000
LGA    K      16      L      33          0.996
LGA    A      17      R      34          0.711
LGA    K      18      Q      35          0.349
LGA    A      19      E      36          0.339
LGA    E      24      Y      37          0.723
LGA    E      25      L      38          0.637
LGA    E      26      K      39          0.436
LGA    K      27      G      40          1.258
LGA    A      28      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19   36    5.0     18    0.78     5.56     49.561     2.046

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.277901 * X  +  -0.297893 * Y  +  -0.913253 * Z  +  -1.341958
  Y_new =   0.054781 * X  +  -0.944240 * Y  +   0.324670 * Z  +   2.586011
  Z_new =  -0.959046 * X  +  -0.140255 * Y  +  -0.246086 * Z  +  22.131878 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.623567    0.518026  [ DEG:  -150.3193     29.6807 ]
  Theta =   1.283616    1.857976  [ DEG:    73.5458    106.4542 ]
  Phi   =   0.194630   -2.946963  [ DEG:    11.1514   -168.8486 ]
 
# 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-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL381_4-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   36   5.0   18   0.78    5.56  49.561
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL381_4-D1
REMARK Aligment from pdb entry: 1hj0A
ATOM      1  N   LYS     6      -1.280   2.938  12.472  1.00  0.00              
ATOM      2  CA  LYS     6      -1.703   3.650  11.223  1.00  0.00              
ATOM      3  C   LYS     6      -0.511   4.256  10.491  1.00  0.00              
ATOM      4  O   LYS     6      -0.160   3.826   9.413  1.00  0.00              
ATOM      5  N   ILE     7       0.122   5.234  11.061  1.00  0.00              
ATOM      6  CA  ILE     7       1.304   5.852  10.402  1.00  0.00              
ATOM      7  C   ILE     7       2.181   4.740   9.846  1.00  0.00              
ATOM      8  O   ILE     7       2.946   4.932   8.920  1.00  0.00              
ATOM      9  N   ALA     8       2.075   3.576  10.413  1.00  0.00              
ATOM     10  CA  ALA     8       2.904   2.438   9.929  1.00  0.00              
ATOM     11  C   ALA     8       2.363   1.903   8.603  1.00  0.00              
ATOM     12  O   ALA     8       3.001   2.005   7.573  1.00  0.00              
ATOM     13  N   ARG     9       1.200   1.319   8.623  1.00  0.00              
ATOM     14  CA  ARG     9       0.628   0.761   7.362  1.00  0.00              
ATOM     15  C   ARG     9       0.715   1.806   6.255  1.00  0.00              
ATOM     16  O   ARG     9       0.918   1.489   5.096  1.00  0.00              
ATOM     17  N   ILE    10       0.559   3.051   6.593  1.00  0.00              
ATOM     18  CA  ILE    10       0.626   4.097   5.538  1.00  0.00              
ATOM     19  C   ILE    10       2.066   4.259   5.066  1.00  0.00              
ATOM     20  O   ILE    10       2.327   4.225   3.890  1.00  0.00              
ATOM     21  N   ASN    11       3.016   4.418   5.951  1.00  0.00              
ATOM     22  CA  ASN    11       4.419   4.559   5.472  1.00  0.00              
ATOM     23  C   ASN    11       4.703   3.406   4.503  1.00  0.00              
ATOM     24  O   ASN    11       5.325   3.585   3.469  1.00  0.00              
ATOM     25  N   GLU    12       4.216   2.228   4.802  1.00  0.00              
ATOM     26  CA  GLU    12       4.430   1.088   3.871  1.00  0.00              
ATOM     27  C   GLU    12       3.690   1.382   2.561  1.00  0.00              
ATOM     28  O   GLU    12       4.176   1.098   1.488  1.00  0.00              
ATOM     29  N   LEU    13       2.511   1.948   2.648  1.00  0.00              
ATOM     30  CA  LEU    13       1.728   2.269   1.422  1.00  0.00              
ATOM     31  C   LEU    13       2.503   3.270   0.547  1.00  0.00              
ATOM     32  O   LEU    13       2.550   3.135  -0.657  1.00  0.00              
ATOM     33  N   ALA    14       3.105   4.274   1.129  1.00  0.00              
ATOM     34  CA  ALA    14       3.857   5.256   0.302  1.00  0.00              
ATOM     35  C   ALA    14       5.049   4.553  -0.351  1.00  0.00              
ATOM     36  O   ALA    14       5.247   4.635  -1.548  1.00  0.00              
ATOM     37  N   ALA    15       5.843   3.855   0.418  1.00  0.00              
ATOM     38  CA  ALA    15       7.009   3.150  -0.187  1.00  0.00              
ATOM     39  C   ALA    15       6.518   2.061  -1.163  1.00  0.00              
ATOM     40  O   ALA    15       7.229   1.669  -2.070  1.00  0.00              
ATOM     41  N   LYS    16       5.306   1.575  -1.002  1.00  0.00              
ATOM     42  CA  LYS    16       4.798   0.528  -1.931  1.00  0.00              
ATOM     43  C   LYS    16       4.415   1.179  -3.252  1.00  0.00              
ATOM     44  O   LYS    16       5.034   0.948  -4.264  1.00  0.00              
ATOM     45  N   ALA    17       3.402   1.999  -3.256  1.00  0.00              
ATOM     46  CA  ALA    17       3.011   2.661  -4.526  1.00  0.00              
ATOM     47  C   ALA    17       4.279   3.213  -5.186  1.00  0.00              
ATOM     48  O   ALA    17       4.449   3.136  -6.387  1.00  0.00              
ATOM     49  N   LYS    18       5.177   3.757  -4.402  1.00  0.00              
ATOM     50  CA  LYS    18       6.438   4.304  -4.979  1.00  0.00              
ATOM     51  C   LYS    18       7.261   3.180  -5.595  1.00  0.00              
ATOM     52  O   LYS    18       7.849   3.355  -6.634  1.00  0.00              
ATOM     53  N   ALA    19       7.331   2.031  -4.985  1.00  0.00              
ATOM     54  CA  ALA    19       8.141   0.950  -5.611  1.00  0.00              
ATOM     55  C   ALA    19       7.424   0.446  -6.855  1.00  0.00              
ATOM     56  O   ALA    19       7.955   0.479  -7.942  1.00  0.00              
ATOM     57  N   GLU    24       6.226  -0.011  -6.723  1.00  0.00              
ATOM     58  CA  GLU    24       5.504  -0.492  -7.920  1.00  0.00              
ATOM     59  C   GLU    24       5.536   0.596  -8.996  1.00  0.00              
ATOM     60  O   GLU    24       5.449   0.312 -10.170  1.00  0.00              
ATOM     61  N   GLU    25       5.646   1.845  -8.612  1.00  0.00              
ATOM     62  CA  GLU    25       5.657   2.923  -9.649  1.00  0.00              
ATOM     63  C   GLU    25       7.030   3.035 -10.307  1.00  0.00              
ATOM     64  O   GLU    25       7.142   2.965 -11.510  1.00  0.00              
ATOM     65  N   GLU    26       8.082   3.205  -9.558  1.00  0.00              
ATOM     66  CA  GLU    26       9.409   3.308 -10.220  1.00  0.00              
ATOM     67  C   GLU    26       9.617   2.055 -11.072  1.00  0.00              
ATOM     68  O   GLU    26       9.973   2.131 -12.238  1.00  0.00              
ATOM     69  N   LYS    27       9.383   0.897 -10.512  1.00  0.00              
ATOM     70  CA  LYS    27       9.566  -0.344 -11.306  1.00  0.00              
ATOM     71  C   LYS    27       8.511  -0.412 -12.420  1.00  0.00              
ATOM     72  O   LYS    27       8.764  -0.949 -13.479  1.00  0.00              
ATOM     73  N   ALA    28       7.333   0.128 -12.206  1.00  0.00              
ATOM     74  CA  ALA    28       6.300   0.079 -13.286  1.00  0.00              
ATOM     75  C   ALA    28       6.821   0.868 -14.480  1.00  0.00              
ATOM     76  O   ALA    28       7.050   0.323 -15.534  1.00  0.00              
END
