
#######################################################
#                                                     #
#                        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 T0363AL381_4-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363AL381_4-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    -       -      Y      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      S      29           -
LGA    -       -      F      30           -
LGA    Q      31      Q      31          1.270
LGA    V      32      V      32          3.064
LGA    D      33      D      33          2.757
LGA    E      34      E      34          0.824
LGA    G      35      G      35          0.263
LGA    I      36      I      36          0.657
LGA    T      37      T      37          0.343
LGA    V      38      V      38          1.238
LGA    Q      39      Q      39          0.726
LGA    T      40      T      40          0.347
LGA    A      41      A      41          0.836
LGA    I      42      I      42          0.877
LGA    T      43      T      43          0.736
LGA    Q      44      Q      44          0.629
LGA    S      45      S      45          0.713
LGA    G      46      G      46          1.459
LGA    I      47      I      47          1.530
LGA    D      55      L      48          2.538
LGA    L      56      S      49           -
LGA    -       -      Q      50           -
LGA    -       -      F      51           -
LGA    -       -      P      52           -
LGA    -       -      E      53           -
LGA    -       -      I      54           -
LGA    -       -      D      55           -
LGA    -       -      L      56           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   19   46    5.0     18    1.41    94.44     37.052     1.190

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.437190 * X  +  -0.137031 * Y  +  -0.888869 * Z  +  49.400642
  Y_new =   0.800964 * X  +   0.390185 * Y  +  -0.454106 * Z  +  -7.479899
  Z_new =   0.409049 * X  +  -0.910483 * Y  +  -0.060828 * Z  +  21.146973 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.637505    1.504087  [ DEG:   -93.8221     86.1779 ]
  Theta =  -0.421412   -2.720181  [ DEG:   -24.1451   -155.8549 ]
  Phi   =   2.070432   -1.071161  [ DEG:   118.6270    -61.3730 ]
 
# 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: T0363AL381_4-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363AL381_4-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   19   46   5.0   18   1.41   94.44  37.052
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL381_4-D1
REMARK Aligment from pdb entry: 2cu3A
ATOM      1  N   GLN    31      18.224   5.684   4.232  1.00  0.00              
ATOM      2  CA  GLN    31      19.390   4.860   4.528  1.00  0.00              
ATOM      3  C   GLN    31      19.382   4.366   5.976  1.00  0.00              
ATOM      4  O   GLN    31      19.041   5.080   6.910  1.00  0.00              
ATOM      5  N   VAL    32      19.742   3.078   6.141  1.00  0.00              
ATOM      6  CA  VAL    32      19.790   2.459   7.459  1.00  0.00              
ATOM      7  C   VAL    32      20.966   2.992   8.277  1.00  0.00              
ATOM      8  O   VAL    32      22.015   2.370   8.397  1.00  0.00              
ATOM      9  N   ASP    33      20.776   4.206   8.825  1.00  0.00              
ATOM     10  CA  ASP    33      21.884   4.876   9.494  1.00  0.00              
ATOM     11  C   ASP    33      21.666   4.999  11.005  1.00  0.00              
ATOM     12  O   ASP    33      22.506   5.495  11.743  1.00  0.00              
ATOM     13  N   GLU    34      20.475   4.560  11.456  1.00  0.00              
ATOM     14  CA  GLU    34      20.173   4.660  12.880  1.00  0.00              
ATOM     15  C   GLU    34      21.298   4.078  13.737  1.00  0.00              
ATOM     16  O   GLU    34      21.831   3.010  13.468  1.00  0.00              
ATOM     17  N   GLY    35      21.666   4.801  14.791  1.00  0.00              
ATOM     18  CA  GLY    35      22.714   4.336  15.680  1.00  0.00              
ATOM     19  C   GLY    35      24.093   4.881  15.365  1.00  0.00              
ATOM     20  O   GLY    35      24.959   4.925  16.242  1.00  0.00              
ATOM     21  N   ILE    36      24.301   5.287  14.115  1.00  0.00              
ATOM     22  CA  ILE    36      25.583   5.838  13.685  1.00  0.00              
ATOM     23  C   ILE    36      25.623   7.337  13.959  1.00  0.00              
ATOM     24  O   ILE    36      24.582   7.989  14.025  1.00  0.00              
ATOM     25  N   THR    37      26.823   7.878  14.131  1.00  0.00              
ATOM     26  CA  THR    37      26.983   9.310  14.363  1.00  0.00              
ATOM     27  C   THR    37      27.246   9.977  13.020  1.00  0.00              
ATOM     28  O   THR    37      27.656   9.320  12.061  1.00  0.00              
ATOM     29  N   VAL    38      27.018  11.285  12.951  1.00  0.00              
ATOM     30  CA  VAL    38      27.251  12.018  11.715  1.00  0.00              
ATOM     31  C   VAL    38      28.701  11.894  11.250  1.00  0.00              
ATOM     32  O   VAL    38      28.961  11.734  10.059  1.00  0.00              
ATOM     33  N   GLN    39      29.646  11.960  12.183  1.00  0.00              
ATOM     34  CA  GLN    39      31.054  11.833  11.816  1.00  0.00              
ATOM     35  C   GLN    39      31.305  10.500  11.127  1.00  0.00              
ATOM     36  O   GLN    39      32.007  10.434  10.122  1.00  0.00              
ATOM     37  N   THR    40      30.738   9.437  11.685  1.00  0.00              
ATOM     38  CA  THR    40      30.905   8.110  11.114  1.00  0.00              
ATOM     39  C   THR    40      30.321   8.094   9.711  1.00  0.00              
ATOM     40  O   THR    40      30.942   7.594   8.778  1.00  0.00              
ATOM     41  N   ALA    41      29.126   8.658   9.561  1.00  0.00              
ATOM     42  CA  ALA    41      28.469   8.706   8.262  1.00  0.00              
ATOM     43  C   ALA    41      29.276   9.508   7.244  1.00  0.00              
ATOM     44  O   ALA    41      29.436   9.083   6.097  1.00  0.00              
ATOM     45  N   ILE    42      29.785  10.664   7.662  1.00  0.00              
ATOM     46  CA  ILE    42      30.561  11.511   6.761  1.00  0.00              
ATOM     47  C   ILE    42      31.836  10.820   6.278  1.00  0.00              
ATOM     48  O   ILE    42      32.246  10.990   5.125  1.00  0.00              
ATOM     49  N   THR    43      32.459  10.040   7.155  1.00  0.00              
ATOM     50  CA  THR    43      33.678   9.330   6.787  1.00  0.00              
ATOM     51  C   THR    43      33.352   8.232   5.785  1.00  0.00              
ATOM     52  O   THR    43      34.139   7.955   4.885  1.00  0.00              
ATOM     53  N   GLN    44      32.182   7.615   5.938  1.00  0.00              
ATOM     54  CA  GLN    44      31.765   6.549   5.036  1.00  0.00              
ATOM     55  C   GLN    44      31.378   7.111   3.674  1.00  0.00              
ATOM     56  O   GLN    44      31.284   6.371   2.698  1.00  0.00              
ATOM     57  N   SER    45      31.152   8.423   3.621  1.00  0.00              
ATOM     58  CA  SER    45      30.782   9.112   2.387  1.00  0.00              
ATOM     59  C   SER    45      32.035   9.659   1.696  1.00  0.00              
ATOM     60  O   SER    45      31.980  10.066   0.539  1.00  0.00              
ATOM     61  N   GLY    46      33.153   9.679   2.418  1.00  0.00              
ATOM     62  CA  GLY    46      34.392  10.196   1.855  1.00  0.00              
ATOM     63  C   GLY    46      34.338  11.710   1.766  1.00  0.00              
ATOM     64  O   GLY    46      35.009  12.323   0.942  1.00  0.00              
ATOM     65  N   ILE    47      33.529  12.315   2.628  1.00  0.00              
ATOM     66  CA  ILE    47      33.360  13.762   2.653  1.00  0.00              
ATOM     67  C   ILE    47      34.493  14.533   3.330  1.00  0.00              
ATOM     68  O   ILE    47      35.089  14.067   4.294  1.00  0.00              
ATOM     69  N   ASP    55      34.789  15.710   2.789  1.00  0.00              
ATOM     70  CA  ASP    55      35.811  16.597   3.330  1.00  0.00              
ATOM     71  C   ASP    55      35.060  17.443   4.355  1.00  0.00              
ATOM     72  O   ASP    55      34.285  18.323   3.988  1.00  0.00              
ATOM     73  N   LEU    56      35.281  17.168   5.635  1.00  0.00              
ATOM     74  CA  LEU    56      34.583  17.882   6.701  1.00  0.00              
ATOM     75  C   LEU    56      34.686  19.397   6.646  1.00  0.00              
ATOM     76  O   LEU    56      33.685  20.086   6.822  1.00  0.00              
END
