
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0363AL243_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL243_1-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    -       -      Y      25           -
LGA    K      28      Y      26          2.940
LGA    S      29      L      27          1.725
LGA    F      30      K      28          1.818
LGA    Q      31      S      29          2.270
LGA    V      32      F      30          2.076
LGA    D      33      Q      31          2.978
LGA    E      34      V      32          2.070
LGA    G      35      D      33          1.769
LGA    I      36      E      34          6.086
LGA    -       -      G      35           -
LGA    -       -      I      36           -
LGA    T      37      T      37          2.909
LGA    V      38      V      38          0.857
LGA    Q      39      Q      39          1.466
LGA    T      40      T      40          2.420
LGA    A      41      A      41          2.771
LGA    I      42      I      42          2.246
LGA    T      43      T      43          1.025
LGA    -       -      Q      44           -
LGA    Q      44      S      45          2.624
LGA    -       -      G      46           -
LGA    I      47      I      47          2.762
LGA    L      48      L      48          1.033
LGA    S      49      S      49          2.765
LGA    Q      50      Q      50          2.659
LGA    F      51      F      51          1.232
LGA    P      52      P      52          1.789
LGA    E      53      E      53          1.932
LGA    I      54      I      54          1.862
LGA    D      55      D      55           -
LGA    L      56      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27   46    5.0     25    2.46    60.00     39.408     0.978

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.579222 * X  +  -0.722982 * Y  +  -0.376563 * Z  +  43.126534
  Y_new =   0.804666 * X  +   0.581017 * Y  +   0.122197 * Z  + -33.500320
  Z_new =   0.130443 * X  +  -0.373787 * Y  +   0.918296 * Z  +  20.138807 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.386564    2.755029  [ DEG:   -22.1485    157.8515 ]
  Theta =  -0.130816   -3.010777  [ DEG:    -7.4952   -172.5048 ]
  Phi   =   0.946886   -2.194707  [ DEG:    54.2526   -125.7474 ]
 
# 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_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL243_1-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27   46   5.0   25   2.46   60.00  39.408
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL243_1-D1
REMARK Aligment from pdb entry: 1vjkA
ATOM      1  N   LYS    28      25.020  21.139  -0.118  1.00  0.00              
ATOM      2  CA  LYS    28      24.963  19.926  -0.908  1.00  0.00              
ATOM      3  C   LYS    28      24.120  18.888  -0.223  1.00  0.00              
ATOM      4  O   LYS    28      24.098  18.817   1.012  1.00  0.00              
ATOM      5  N   SER    29      23.408  18.104  -1.006  1.00  0.00              
ATOM      6  CA  SER    29      22.647  16.986  -0.508  1.00  0.00              
ATOM      7  C   SER    29      23.511  15.763  -0.478  1.00  0.00              
ATOM      8  O   SER    29      24.143  15.413  -1.499  1.00  0.00              
ATOM      9  N   PHE    30      23.525  15.063   0.643  1.00  0.00              
ATOM     10  CA  PHE    30      24.325  13.870   0.778  1.00  0.00              
ATOM     11  C   PHE    30      23.443  12.694   1.161  1.00  0.00              
ATOM     12  O   PHE    30      22.797  12.685   2.228  1.00  0.00              
ATOM     13  N   GLN    31      23.386  11.710   0.280  1.00  0.00              
ATOM     14  CA  GLN    31      22.658  10.471   0.525  1.00  0.00              
ATOM     15  C   GLN    31      23.560   9.513   1.302  1.00  0.00              
ATOM     16  O   GLN    31      24.705   9.268   0.913  1.00  0.00              
ATOM     17  N   VAL    32      23.035   8.995   2.410  1.00  0.00              
ATOM     18  CA  VAL    32      23.772   8.137   3.311  1.00  0.00              
ATOM     19  C   VAL    32      23.007   6.842   3.500  1.00  0.00              
ATOM     20  O   VAL    32      21.792   6.831   3.364  1.00  0.00              
ATOM     21  N   ASP    33      23.694   5.736   3.804  1.00  0.00              
ATOM     22  CA  ASP    33      23.005   4.472   4.052  1.00  0.00              
ATOM     23  C   ASP    33      22.157   4.518   5.314  1.00  0.00              
ATOM     24  O   ASP    33      22.416   5.299   6.236  1.00  0.00              
ATOM     25  N   GLU    34      21.141   3.666   5.335  1.00  0.00              
ATOM     26  CA  GLU    34      20.328   3.437   6.508  1.00  0.00              
ATOM     27  C   GLU    34      21.206   3.317   7.760  1.00  0.00              
ATOM     28  O   GLU    34      22.230   2.642   7.742  1.00  0.00              
ATOM     29  N   GLY    35      20.791   3.999   8.827  1.00  0.00              
ATOM     30  CA  GLY    35      21.482   3.926  10.107  1.00  0.00              
ATOM     31  C   GLY    35      22.623   4.918  10.244  1.00  0.00              
ATOM     32  O   GLY    35      23.329   4.938  11.267  1.00  0.00              
ATOM     33  N   ILE    36      22.822   5.749   9.230  1.00  0.00              
ATOM     34  CA  ILE    36      23.931   6.686   9.270  1.00  0.00              
ATOM     35  C   ILE    36      23.882   7.580  10.471  1.00  0.00              
ATOM     36  O   ILE    36      22.812   8.057  10.885  1.00  0.00              
ATOM     37  N   THR    37      25.075   7.832  11.004  1.00  0.00              
ATOM     38  CA  THR    37      25.271   8.703  12.147  1.00  0.00              
ATOM     39  C   THR    37      26.049   9.952  11.742  1.00  0.00              
ATOM     40  O   THR    37      26.678  10.007  10.673  1.00  0.00              
ATOM     41  N   VAL    38      26.066  10.961  12.606  1.00  0.00              
ATOM     42  CA  VAL    38      26.865  12.161  12.357  1.00  0.00              
ATOM     43  C   VAL    38      28.317  11.820  11.970  1.00  0.00              
ATOM     44  O   VAL    38      28.869  12.383  10.998  1.00  0.00              
ATOM     45  N   GLN    39      28.943  10.875  12.685  1.00  0.00              
ATOM     46  CA  GLN    39      30.326  10.533  12.346  1.00  0.00              
ATOM     47  C   GLN    39      30.468   9.998  10.897  1.00  0.00              
ATOM     48  O   GLN    39      31.500  10.226  10.245  1.00  0.00              
ATOM     49  N   THR    40      29.442   9.293  10.407  1.00  0.00              
ATOM     50  CA  THR    40      29.489   8.758   9.028  1.00  0.00              
ATOM     51  C   THR    40      29.380   9.884   8.044  1.00  0.00              
ATOM     52  O   THR    40      30.054   9.862   7.005  1.00  0.00              
ATOM     53  N   ALA    41      28.564  10.876   8.357  1.00  0.00              
ATOM     54  CA  ALA    41      28.460  12.051   7.491  1.00  0.00              
ATOM     55  C   ALA    41      29.786  12.819   7.426  1.00  0.00              
ATOM     56  O   ALA    41      30.216  13.214   6.328  1.00  0.00              
ATOM     57  N   ILE    42      30.455  12.983   8.568  1.00  0.00              
ATOM     58  CA  ILE    42      31.751  13.648   8.579  1.00  0.00              
ATOM     59  C   ILE    42      32.736  12.893   7.691  1.00  0.00              
ATOM     60  O   ILE    42      33.481  13.513   6.889  1.00  0.00              
ATOM     61  N   THR    43      32.761  11.552   7.793  1.00  0.00              
ATOM     62  CA  THR    43      33.645  10.793   6.899  1.00  0.00              
ATOM     63  C   THR    43      33.317  10.959   5.434  1.00  0.00              
ATOM     64  O   THR    43      34.242  10.997   4.593  1.00  0.00              
ATOM     65  N   GLN    44      32.038  11.064   5.107  1.00  0.00              
ATOM     66  CA  GLN    44      31.646  11.254   3.723  1.00  0.00              
ATOM     67  C   GLN    44      32.033  12.647   3.224  1.00  0.00              
ATOM     68  O   GLN    44      32.451  12.775   2.067  1.00  0.00              
ATOM     69  N   ILE    47      31.922  13.688   4.072  1.00  0.00              
ATOM     70  CA  ILE    47      32.367  15.028   3.669  1.00  0.00              
ATOM     71  C   ILE    47      33.856  14.998   3.319  1.00  0.00              
ATOM     72  O   ILE    47      34.266  15.542   2.272  1.00  0.00              
ATOM     73  N   LEU    48      34.638  14.327   4.159  1.00  0.00              
ATOM     74  CA  LEU    48      36.080  14.190   3.925  1.00  0.00              
ATOM     75  C   LEU    48      36.394  13.400   2.646  1.00  0.00              
ATOM     76  O   LEU    48      37.382  13.713   1.942  1.00  0.00              
ATOM     77  N   SER    49      35.571  12.401   2.338  1.00  0.00              
ATOM     78  CA  SER    49      35.751  11.607   1.135  1.00  0.00              
ATOM     79  C   SER    49      35.439  12.425  -0.115  1.00  0.00              
ATOM     80  O   SER    49      36.122  12.286  -1.140  1.00  0.00              
ATOM     81  N   GLN    50      34.405  13.263  -0.062  1.00  0.00              
ATOM     82  CA  GLN    50      34.026  14.061  -1.215  1.00  0.00              
ATOM     83  C   GLN    50      34.961  15.241  -1.435  1.00  0.00              
ATOM     84  O   GLN    50      35.152  15.705  -2.557  1.00  0.00              
ATOM     85  N   PHE    51      35.472  15.774  -0.335  1.00  0.00              
ATOM     86  CA  PHE    51      36.224  17.023  -0.359  1.00  0.00              
ATOM     87  C   PHE    51      37.475  16.851   0.462  1.00  0.00              
ATOM     88  O   PHE    51      37.483  17.129   1.688  1.00  0.00              
ATOM     89  N   PRO    52      38.545  16.423  -0.206  1.00  0.00              
ATOM     90  CA  PRO    52      39.757  15.996   0.496  1.00  0.00              
ATOM     91  C   PRO    52      40.387  17.074   1.366  1.00  0.00              
ATOM     92  O   PRO    52      41.098  16.744   2.312  1.00  0.00              
ATOM     93  N   GLU    53      40.118  18.344   1.074  1.00  0.00              
ATOM     94  CA  GLU    53      40.689  19.427   1.907  1.00  0.00              
ATOM     95  C   GLU    53      40.152  19.387   3.337  1.00  0.00              
ATOM     96  O   GLU    53      40.771  19.955   4.249  1.00  0.00              
ATOM     97  N   ILE    54      39.025  18.694   3.568  1.00  0.00              
ATOM     98  CA  ILE    54      38.508  18.544   4.928  1.00  0.00              
ATOM     99  C   ILE    54      39.230  17.476   5.750  1.00  0.00              
ATOM    100  O   ILE    54      39.034  17.393   6.970  1.00  0.00              
ATOM    101  N   ASP    55      35.424  24.904  20.808  1.00  0.00              
ATOM    102  CA  ASP    55      36.091  26.088  20.251  1.00  0.00              
ATOM    103  C   ASP    55      37.501  25.790  19.752  1.00  0.00              
ATOM    104  O   ASP    55      38.068  26.574  18.978  1.00  0.00              
ATOM    105  N   LEU    56      38.062  24.654  20.163  1.00  0.00              
ATOM    106  CA  LEU    56      39.441  24.310  19.783  1.00  0.00              
ATOM    107  C   LEU    56      39.532  23.562  18.446  1.00  0.00              
ATOM    108  O   LEU    56      40.611  23.446  17.861  1.00  0.00              
END
