
#######################################################
#                                                     #
#                        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   13 (   52),  selected   13 , name T0378AL316_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378AL316_5-D1.T0378_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      K       8           -
LGA    -       -      F       9           -
LGA    -       -      L      10           -
LGA    -       -      R      11           -
LGA    -       -      S      12           -
LGA    -       -      L      13           -
LGA    -       -      R      14           -
LGA    -       -      E      15           -
LGA    -       -      R      16           -
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    S      56      A      26          3.074
LGA    T      57      V      27          3.780
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    -       -      R      41           -
LGA    P      58      C      42          3.917
LGA    H      59      R      43          4.836
LGA    D      60      M      44          5.485
LGA    A      61      -       -           -
LGA    E      62      L      45          2.968
LGA    V      63      V      46          3.540
LGA    V      64      G      47          3.919
LGA    E      65      T      48          4.049
LGA    L      66      A      49          3.968
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    P      67      E      65          0.107
LGA    E      68      L      66          1.100
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   13   89    5.0     12    3.68     8.33      8.205     0.317

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.919719 * X  +  -0.124756 * Y  +   0.372226 * Z  + -29.805664
  Y_new =  -0.376626 * X  +  -0.012872 * Y  +   0.926276 * Z  +  27.458025
  Z_new =  -0.110767 * X  +  -0.992104 * Y  +  -0.058825 * Z  +  53.051071 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.630021    1.511572  [ DEG:   -93.3933     86.6067 ]
  Theta =   0.110995    3.030597  [ DEG:     6.3596    173.6404 ]
  Phi   =  -0.388670    2.752923  [ DEG:   -22.2691    157.7309 ]
 
# 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: T0378AL316_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378AL316_5-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   13   89   5.0   12   3.68    8.33   8.205
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL316_5-D1
REMARK Aligment from pdb entry: 1v2x_A
ATOM      1  N   SER    56       9.052  19.897  52.245  1.00  0.00              
ATOM      2  CA  SER    56       9.141  21.053  51.302  1.00  0.00              
ATOM      3  C   SER    56       7.933  21.158  50.377  1.00  0.00              
ATOM      4  O   SER    56       7.383  22.245  50.189  1.00  0.00              
ATOM      5  N   THR    57       7.527  20.038  49.784  1.00  0.00              
ATOM      6  CA  THR    57       6.383  20.067  48.887  1.00  0.00              
ATOM      7  C   THR    57       5.098  19.976  49.710  1.00  0.00              
ATOM      8  O   THR    57       4.016  20.320  49.241  1.00  0.00              
ATOM      9  N   PRO    58       5.217  19.516  50.946  1.00  0.00              
ATOM     10  CA  PRO    58       4.051  19.423  51.812  1.00  0.00              
ATOM     11  C   PRO    58       3.697  20.870  52.180  1.00  0.00              
ATOM     12  O   PRO    58       2.529  21.254  52.301  1.00  0.00              
ATOM     13  N   HIS    59       4.747  21.667  52.330  1.00  0.00              
ATOM     14  CA  HIS    59       4.658  23.077  52.675  1.00  0.00              
ATOM     15  C   HIS    59       4.196  23.917  51.483  1.00  0.00              
ATOM     16  O   HIS    59       3.453  24.889  51.633  1.00  0.00              
ATOM     17  N   ASP    60       4.621  23.522  50.292  1.00  0.00              
ATOM     18  CA  ASP    60       4.285  24.279  49.103  1.00  0.00              
ATOM     19  C   ASP    60       3.265  23.553  48.209  1.00  0.00              
ATOM     20  O   ASP    60       2.196  24.087  47.917  1.00  0.00              
ATOM     21  N   ALA    61       3.577  22.327  47.813  1.00  0.00              
ATOM     22  CA  ALA    61       2.688  21.560  46.946  1.00  0.00              
ATOM     23  C   ALA    61       1.295  21.413  47.534  1.00  0.00              
ATOM     24  O   ALA    61       0.327  21.268  46.799  1.00  0.00              
ATOM     25  N   GLU    62       1.182  21.470  48.853  1.00  0.00              
ATOM     26  CA  GLU    62      -0.126  21.306  49.469  1.00  0.00              
ATOM     27  C   GLU    62      -0.774  22.602  49.938  1.00  0.00              
ATOM     28  O   GLU    62      -1.549  23.220  49.211  1.00  0.00              
ATOM     29  N   VAL    63      -0.457  22.994  51.167  1.00  0.00              
ATOM     30  CA  VAL    63      -1.005  24.191  51.770  1.00  0.00              
ATOM     31  C   VAL    63      -0.989  25.349  50.778  1.00  0.00              
ATOM     32  O   VAL    63      -2.030  25.916  50.456  1.00  0.00              
ATOM     33  N   VAL    64       0.204  25.673  50.291  1.00  0.00              
ATOM     34  CA  VAL    64       0.415  26.759  49.349  1.00  0.00              
ATOM     35  C   VAL    64      -0.509  26.711  48.124  1.00  0.00              
ATOM     36  O   VAL    64      -1.203  27.682  47.835  1.00  0.00              
ATOM     37  N   GLU    65      -0.513  25.581  47.424  1.00  0.00              
ATOM     38  CA  GLU    65      -1.324  25.382  46.217  1.00  0.00              
ATOM     39  C   GLU    65      -2.835  25.376  46.463  1.00  0.00              
ATOM     40  O   GLU    65      -3.579  26.006  45.707  1.00  0.00              
ATOM     41  N   LEU    66      -3.304  24.680  47.499  1.00  0.00              
ATOM     42  CA  LEU    66      -4.743  24.660  47.754  1.00  0.00              
ATOM     43  C   LEU    66      -5.275  26.037  48.172  1.00  0.00              
ATOM     44  O   LEU    66      -6.368  26.429  47.779  1.00  0.00              
ATOM     45  N   PRO    67      -4.508  26.775  48.969  1.00  0.00              
ATOM     46  CA  PRO    67      -4.942  28.094  49.402  1.00  0.00              
ATOM     47  C   PRO    67      -5.065  29.077  48.224  1.00  0.00              
ATOM     48  O   PRO    67      -5.980  29.913  48.170  1.00  0.00              
ATOM     49  N   GLU    68      -4.134  28.997  47.283  1.00  0.00              
ATOM     50  CA  GLU    68      -4.179  29.923  46.168  1.00  0.00              
ATOM     51  C   GLU    68      -5.319  29.505  45.286  1.00  0.00              
ATOM     52  O   GLU    68      -6.002  30.351  44.724  1.00  0.00              
END
