
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0363AL243_3-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL243_3-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      11           -
LGA    -       -      Q      12           -
LGA    -       -      I      13           -
LGA    -       -      N      14           -
LGA    -       -      I      15           -
LGA    -       -      E      16           -
LGA    -       -      I      17           -
LGA    -       -      A      18           -
LGA    -       -      Y      19           -
LGA    -       -      A      20           -
LGA    -       -      F      21           -
LGA    -       -      P      22           -
LGA    -       -      E      23           -
LGA    -       -      R      24           -
LGA    S      29      Y      25          3.590
LGA    F      30      Y      26          1.318
LGA    Q      31      L      27          1.974
LGA    V      32      K      28          3.170
LGA    E      34      S      29          4.922
LGA    G      35      F      30          4.006
LGA    -       -      Q      31           -
LGA    I      36      V      32          2.673
LGA    T      37      D      33           #
LGA    -       -      E      34           -
LGA    -       -      G      35           -
LGA    -       -      I      36           -
LGA    -       -      T      37           -
LGA    V      38      V      38          2.642
LGA    Q      39      Q      39          2.691
LGA    T      40      T      40          3.888
LGA    A      41      A      41          3.520
LGA    I      42      I      42          1.719
LGA    T      43      T      43          1.554
LGA    -       -      Q      44           -
LGA    -       -      S      45           -
LGA    Q      44      G      46          2.642
LGA    I      47      I      47          2.046
LGA    L      48      L      48          0.877
LGA    S      49      S      49          1.982
LGA    Q      50      Q      50          1.663
LGA    F      51      F      51          0.511
LGA    P      52      P      52          0.984
LGA    E      53      E      53          1.156
LGA    I      54      I      54          0.838
LGA    D      55      D      55          3.049
LGA    L      56      L      56           #

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   25   46    5.0     23    2.59    65.22     36.988     0.855

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.368568 * X  +   0.913748 * Y  +   0.170945 * Z  +  11.625590
  Y_new =  -0.890683 * X  +   0.294464 * Y  +   0.346375 * Z  +   6.506217
  Z_new =   0.266162 * X  +  -0.279920 * Y  +   0.922390 * Z  +  14.552223 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.294640    2.846953  [ DEG:   -16.8816    163.1184 ]
  Theta =  -0.269409   -2.872184  [ DEG:   -15.4360   -164.5640 ]
  Phi   =  -1.178447    1.963146  [ DEG:   -67.5200    112.4800 ]
 
# 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: T0363AL243_3-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL243_3-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   25   46   5.0   23   2.59   65.22  36.988
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL243_3-D1
REMARK Aligment from pdb entry: 1v8cA
ATOM      1  N   SER    29      26.367  24.018  -1.123  1.00  0.00              
ATOM      2  CA  SER    29      25.590  22.836  -0.764  1.00  0.00              
ATOM      3  C   SER    29      26.019  21.613  -1.553  1.00  0.00              
ATOM      4  O   SER    29      26.392  21.707  -2.724  1.00  0.00              
ATOM      5  N   PHE    30      25.971  20.463  -0.892  1.00  0.00              
ATOM      6  CA  PHE    30      26.354  19.201  -1.502  1.00  0.00              
ATOM      7  C   PHE    30      25.380  18.122  -1.059  1.00  0.00              
ATOM      8  O   PHE    30      24.770  18.230  -0.001  1.00  0.00              
ATOM      9  N   GLN    31      25.223  17.102  -1.892  1.00  0.00              
ATOM     10  CA  GLN    31      24.371  15.966  -1.575  1.00  0.00              
ATOM     11  C   GLN    31      25.356  14.812  -1.391  1.00  0.00              
ATOM     12  O   GLN    31      26.106  14.480  -2.314  1.00  0.00              
ATOM     13  N   VAL    32      25.364  14.213  -0.203  1.00  0.00              
ATOM     14  CA  VAL    32      26.283  13.115   0.095  1.00  0.00              
ATOM     15  C   VAL    32      25.555  11.979   0.783  1.00  0.00              
ATOM     16  O   VAL    32      24.651  12.212   1.578  1.00  0.00              
ATOM     17  N   GLU    34      25.944  10.728   0.490  1.00  0.00              
ATOM     18  CA  GLU    34      25.284   9.579   1.117  1.00  0.00              
ATOM     19  C   GLU    34      25.697   9.373   2.574  1.00  0.00              
ATOM     20  O   GLU    34      26.728   9.882   3.023  1.00  0.00              
ATOM     21  N   GLY    35      24.872   8.639   3.313  1.00  0.00              
ATOM     22  CA  GLY    35      25.180   8.363   4.707  1.00  0.00              
ATOM     23  C   GLY    35      23.926   8.259   5.546  1.00  0.00              
ATOM     24  O   GLY    35      23.008   9.063   5.380  1.00  0.00              
ATOM     25  N   ILE    36      23.901   7.273   6.445  1.00  0.00              
ATOM     26  CA  ILE    36      22.759   7.028   7.322  1.00  0.00              
ATOM     27  C   ILE    36      22.934   7.616   8.724  1.00  0.00              
ATOM     28  O   ILE    36      22.026   7.527   9.555  1.00  0.00              
ATOM     29  N   THR    37      24.108   8.189   8.987  1.00  0.00              
ATOM     30  CA  THR    37      24.385   8.852  10.265  1.00  0.00              
ATOM     31  C   THR    37      25.183  10.102   9.944  1.00  0.00              
ATOM     32  O   THR    37      25.770  10.219   8.856  1.00  0.00              
ATOM     33  N   VAL    38      25.205  11.037  10.882  1.00  0.00              
ATOM     34  CA  VAL    38      25.948  12.271  10.679  1.00  0.00              
ATOM     35  C   VAL    38      27.412  11.946  10.368  1.00  0.00              
ATOM     36  O   VAL    38      28.009  12.532   9.461  1.00  0.00              
ATOM     37  N   GLN    39      27.978  10.995  11.104  1.00  0.00              
ATOM     38  CA  GLN    39      29.361  10.604  10.887  1.00  0.00              
ATOM     39  C   GLN    39      29.621  10.091   9.481  1.00  0.00              
ATOM     40  O   GLN    39      30.613  10.470   8.864  1.00  0.00              
ATOM     41  N   THR    40      28.741   9.224   8.981  1.00  0.00              
ATOM     42  CA  THR    40      28.912   8.672   7.637  1.00  0.00              
ATOM     43  C   THR    40      28.903   9.799   6.611  1.00  0.00              
ATOM     44  O   THR    40      29.725   9.819   5.689  1.00  0.00              
ATOM     45  N   ALA    41      27.987  10.745   6.777  1.00  0.00              
ATOM     46  CA  ALA    41      27.906  11.865   5.846  1.00  0.00              
ATOM     47  C   ALA    41      29.175  12.713   5.889  1.00  0.00              
ATOM     48  O   ALA    41      29.712  13.084   4.842  1.00  0.00              
ATOM     49  N   ILE    42      29.659  13.016   7.090  1.00  0.00              
ATOM     50  CA  ILE    42      30.862  13.823   7.227  1.00  0.00              
ATOM     51  C   ILE    42      32.108  13.106   6.716  1.00  0.00              
ATOM     52  O   ILE    42      33.001  13.747   6.174  1.00  0.00              
ATOM     53  N   THR    43      32.172  11.783   6.875  1.00  0.00              
ATOM     54  CA  THR    43      33.321  11.042   6.371  1.00  0.00              
ATOM     55  C   THR    43      33.289  11.150   4.851  1.00  0.00              
ATOM     56  O   THR    43      34.330  11.311   4.207  1.00  0.00              
ATOM     57  N   GLN    44      32.096  11.076   4.262  1.00  0.00              
ATOM     58  CA  GLN    44      32.016  11.202   2.812  1.00  0.00              
ATOM     59  C   GLN    44      32.353  12.615   2.359  1.00  0.00              
ATOM     60  O   GLN    44      32.940  12.807   1.291  1.00  0.00              
ATOM     61  N   ILE    47      32.012  13.604   3.176  1.00  0.00              
ATOM     62  CA  ILE    47      32.310  14.989   2.833  1.00  0.00              
ATOM     63  C   ILE    47      33.816  15.189   2.652  1.00  0.00              
ATOM     64  O   ILE    47      34.251  15.835   1.692  1.00  0.00              
ATOM     65  N   LEU    48      34.614  14.623   3.559  1.00  0.00              
ATOM     66  CA  LEU    48      36.059  14.786   3.461  1.00  0.00              
ATOM     67  C   LEU    48      36.679  13.883   2.394  1.00  0.00              
ATOM     68  O   LEU    48      37.801  14.119   1.952  1.00  0.00              
ATOM     69  N   SER    49      35.952  12.849   1.982  1.00  0.00              
ATOM     70  CA  SER    49      36.437  11.982   0.912  1.00  0.00              
ATOM     71  C   SER    49      36.228  12.762  -0.387  1.00  0.00              
ATOM     72  O   SER    49      36.974  12.592  -1.356  1.00  0.00              
ATOM     73  N   GLN    50      35.216  13.629  -0.390  1.00  0.00              
ATOM     74  CA  GLN    50      34.901  14.447  -1.568  1.00  0.00              
ATOM     75  C   GLN    50      35.726  15.736  -1.614  1.00  0.00              
ATOM     76  O   GLN    50      36.161  16.167  -2.687  1.00  0.00              
ATOM     77  N   PHE    51      35.929  16.344  -0.450  1.00  0.00              
ATOM     78  CA  PHE    51      36.686  17.587  -0.325  1.00  0.00              
ATOM     79  C   PHE    51      37.641  17.468   0.850  1.00  0.00              
ATOM     80  O   PHE    51      37.392  18.000   1.931  1.00  0.00              
ATOM     81  N   PRO    52      38.769  16.776   0.639  1.00  0.00              
ATOM     82  CA  PRO    52      39.771  16.579   1.690  1.00  0.00              
ATOM     83  C   PRO    52      40.341  17.846   2.321  1.00  0.00              
ATOM     84  O   PRO    52      40.910  17.790   3.411  1.00  0.00              
ATOM     85  N   GLU    53      40.181  18.987   1.652  1.00  0.00              
ATOM     86  CA  GLU    53      40.667  20.255   2.177  1.00  0.00              
ATOM     87  C   GLU    53      39.966  20.587   3.494  1.00  0.00              
ATOM     88  O   GLU    53      40.478  21.353   4.305  1.00  0.00              
ATOM     89  N   ILE    54      38.797  19.991   3.708  1.00  0.00              
ATOM     90  CA  ILE    54      38.026  20.221   4.928  1.00  0.00              
ATOM     91  C   ILE    54      38.396  19.300   6.086  1.00  0.00              
ATOM     92  O   ILE    54      37.973  19.525   7.219  1.00  0.00              
ATOM     93  N   ASP    55      39.186  18.268   5.813  1.00  0.00              
ATOM     94  CA  ASP    55      39.547  17.312   6.856  1.00  0.00              
ATOM     95  C   ASP    55      40.203  17.942   8.081  1.00  0.00              
ATOM     96  O   ASP    55      39.819  17.653   9.219  1.00  0.00              
ATOM     97  N   LEU    56      41.188  18.797   7.833  1.00  0.00              
ATOM     98  CA  LEU    56      41.940  19.476   8.882  1.00  0.00              
ATOM     99  C   LEU    56      41.074  20.329   9.799  1.00  0.00              
ATOM    100  O   LEU    56      41.357  20.450  10.988  1.00  0.00              
END
