
#######################################################
#                                                     #
#                        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   14 (   56),  selected   14 , name T0335AL333_1-D1
# Molecule2: number of CA atoms   36 (  584),  selected   36 , name T0335_D1.pdb
# PARAMETERS: T0335AL333_1-D1.T0335_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    -       -      A       5           -
LGA    A       5      K       6          1.646
LGA    K       6      I       7          1.613
LGA    -       -      A       8           -
LGA    -       -      R       9           -
LGA    I       7      I      10          0.896
LGA    A       8      N      11          1.662
LGA    R       9      E      12          3.147
LGA    -       -      L      13           -
LGA    -       -      A      14           -
LGA    I      10      A      15          3.092
LGA    N      11      K      16          3.208
LGA    -       -      A      17           -
LGA    -       -      K      18           -
LGA    -       -      A      19           -
LGA    -       -      G      20           -
LGA    E      12      V      21          2.234
LGA    K      18      I      22          2.092
LGA    A      19      T      23          3.946
LGA    -       -      E      24           -
LGA    -       -      E      25           -
LGA    G      20      E      26          2.496
LGA    -       -      K      27           -
LGA    -       -      A      28           -
LGA    -       -      E      29           -
LGA    V      21      Q      30          4.390
LGA    I      22      Q      31           -
LGA    -       -      K      32           -
LGA    T      23      L      33           #
LGA    -       -      R      34           -
LGA    -       -      Q      35           -
LGA    -       -      E      36           -
LGA    -       -      Y      37           -
LGA    -       -      L      38           -
LGA    -       -      K      39           -
LGA    -       -      G      40           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   14   36    5.0     12    2.72     8.33     23.311     0.425

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.544846 * X  +   0.102343 * Y  +   0.832267 * Z  +  -4.547263
  Y_new =   0.294161 * X  +   0.952776 * Y  +   0.075412 * Z  +   7.912266
  Z_new =  -0.785246 * X  +   0.285909 * Y  +  -0.549222 * Z  +  29.100216 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.661624   -0.479968  [ DEG:   152.4998    -27.5002 ]
  Theta =   0.903094    2.238499  [ DEG:    51.7435    128.2565 ]
  Phi   =   2.646539   -0.495054  [ DEG:   151.6355    -28.3645 ]
 
# 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: T0335AL333_1-D1                               
REMARK     2: T0335_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0335AL333_1-D1.T0335_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   14   36   5.0   12   2.72    8.33  23.311
REMARK  ---------------------------------------------------------- 
MOLECULE T0335AL333_1-D1
REMARK Aligment from pdb entry: 1uwv_A
ATOM     17  N   ALA     5       3.962  -6.866  -5.211  1.00  0.00              
ATOM     18  CA  ALA     5       2.578  -6.870  -4.727  1.00  0.00              
ATOM     19  C   ALA     5       1.710  -5.687  -5.136  1.00  0.00              
ATOM     20  O   ALA     5       2.201  -4.604  -5.467  1.00  0.00              
ATOM     21  N   LYS     6       0.402  -5.907  -5.020  1.00  0.00              
ATOM     22  CA  LYS     6      -0.616  -4.895  -5.237  1.00  0.00              
ATOM     23  C   LYS     6      -1.450  -4.708  -3.992  1.00  0.00              
ATOM     24  O   LYS     6      -1.974  -5.680  -3.433  1.00  0.00              
ATOM     25  N   ILE     7      -1.642  -3.454  -3.604  1.00  0.00              
ATOM     26  CA  ILE     7      -2.453  -3.112  -2.445  1.00  0.00              
ATOM     27  C   ILE     7      -3.937  -3.089  -2.785  1.00  0.00              
ATOM     28  O   ILE     7      -4.351  -2.475  -3.739  1.00  0.00              
ATOM     29  N   ALA     8      -4.724  -3.784  -1.978  1.00  0.00              
ATOM     30  CA  ALA     8      -6.152  -3.940  -2.241  1.00  0.00              
ATOM     31  C   ALA     8      -6.923  -2.815  -1.554  1.00  0.00              
ATOM     32  O   ALA     8      -7.893  -2.277  -2.096  1.00  0.00              
ATOM     33  N   ARG     9      -6.468  -2.475  -0.352  1.00  0.00              
ATOM     34  CA  ARG     9      -7.246  -1.699   0.601  1.00  0.00              
ATOM     35  C   ARG     9      -6.357  -0.803   1.439  1.00  0.00              
ATOM     36  O   ARG     9      -5.195  -1.076   1.647  1.00  0.00              
ATOM     37  N   ILE    10      -6.944   0.261   1.957  1.00  0.00              
ATOM     38  CA  ILE    10      -6.284   1.153   2.889  1.00  0.00              
ATOM     39  C   ILE    10      -6.975   0.973   4.187  1.00  0.00              
ATOM     40  O   ILE    10      -8.173   1.239   4.263  1.00  0.00              
ATOM     41  N   ASN    11      -6.261   0.504   5.207  1.00  0.00              
ATOM     42  CA  ASN    11      -6.913   0.147   6.456  1.00  0.00              
ATOM     43  C   ASN    11      -7.203   1.410   7.324  1.00  0.00              
ATOM     44  O   ASN    11      -6.761   2.532   6.989  1.00  0.00              
ATOM     45  N   GLU    12      -7.981   1.254   8.391  1.00  0.00              
ATOM     46  CA  GLU    12      -8.219   2.384   9.300  1.00  0.00              
ATOM     47  C   GLU    12      -6.904   3.134   9.614  1.00  0.00              
ATOM     48  O   GLU    12      -6.874   4.365   9.562  1.00  0.00              
ATOM     49  N   LYS    18      -5.831   2.364   9.867  1.00  0.00              
ATOM     50  CA  LYS    18      -4.551   2.843  10.437  1.00  0.00              
ATOM     51  C   LYS    18      -3.502   3.314   9.386  1.00  0.00              
ATOM     52  O   LYS    18      -2.363   3.682   9.713  1.00  0.00              
ATOM     53  N   ALA    19      -3.887   3.301   8.123  1.00  0.00              
ATOM     54  CA  ALA    19      -3.120   3.998   7.115  1.00  0.00              
ATOM     55  C   ALA    19      -2.044   3.205   6.378  1.00  0.00              
ATOM     56  O   ALA    19      -1.354   3.781   5.544  1.00  0.00              
ATOM     57  N   GLY    20      -1.874   1.935   6.729  1.00  0.00              
ATOM     58  CA  GLY    20      -1.031   0.999   6.005  1.00  0.00              
ATOM     59  C   GLY    20      -1.881   0.392   4.907  1.00  0.00              
ATOM     60  O   GLY    20      -3.063   0.115   5.099  1.00  0.00              
ATOM     61  N   VAL    21      -1.264   0.160   3.770  1.00  0.00              
ATOM     62  CA  VAL    21      -1.915  -0.534   2.667  1.00  0.00              
ATOM     63  C   VAL    21      -2.040  -2.012   3.009  1.00  0.00              
ATOM     64  O   VAL    21      -1.197  -2.564   3.710  1.00  0.00              
ATOM     65  N   ILE    22      -3.116  -2.635   2.549  1.00  0.00              
ATOM     66  CA  ILE    22      -3.426  -4.034   2.849  1.00  0.00              
ATOM     67  C   ILE    22      -3.354  -4.747   1.523  1.00  0.00              
ATOM     68  O   ILE    22      -4.003  -4.340   0.590  1.00  0.00              
ATOM     69  N   THR    23      -2.474  -5.730   1.428  1.00  0.00              
ATOM     70  CA  THR    23      -2.260  -6.506   0.212  1.00  0.00              
ATOM     71  C   THR    23      -2.260  -7.974   0.580  1.00  0.00              
ATOM     72  O   THR    23      -2.295  -8.320   1.748  1.00  0.00              
END
