
#######################################################
#                                                     #
#                        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 T0299AL586_1-D1
# Molecule2: number of CA atoms   91 (  726),  selected   91 , name T0299_D1.pdb
# PARAMETERS: T0299AL586_1-D1.T0299_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    T       2      M       1           -
LGA    L       6      T       2          2.863
LGA    L       7      R       3          2.558
LGA    V       8      Y       4          2.519
LGA    R       9      A       5          1.322
LGA    G      10      L       6          1.913
LGA    I      11      L       7          1.409
LGA    N      12      V       8          1.876
LGA    V      13      R       9          3.875
LGA    -       -      G      10           -
LGA    M      21      I      11           #
LGA    L      24      N      12           -
LGA    -       -      V      13           -
LGA    -       -      G      14           -
LGA    -       -      G      15           -
LGA    -       -      K      16           -
LGA    -       -      N      17           -
LGA    -       -      K      18           -
LGA    -       -      V      19           -
LGA    -       -      V      20           -
LGA    -       -      M      21           -
LGA    -       -      A      22           -
LGA    -       -      E      23           -
LGA    -       -      L      24           -
LGA    -       -      R      25           -
LGA    -       -      Q      26           -
LGA    L      28      E      27          3.144
LGA    T      29      L      28          1.673
LGA    -       -      T      29           -
LGA    -       -      N      30           -
LGA    L      31      L      31          2.358
LGA    -       -      G      32           -
LGA    G      43      L      33          1.910
LGA    T      48      E      34          3.097
LGA    -       -      K      35           -
LGA    -       -      V      36           -
LGA    F      74      E      37          3.880
LGA    S      75      S      38          3.767
LGA    -       -      Y      39           -
LGA    -       -      I      40           -
LGA    -       -      N      41           -
LGA    L      77      S      42          4.996
LGA    S      78      G      43          4.209
LGA    -       -      N      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      F      47           -
LGA    -       -      T      48           -
LGA    -       -      S      49           -
LGA    -       -      I      50           -
LGA    -       -      D      51           -
LGA    -       -      S      52           -
LGA    -       -      K      53           -
LGA    -       -      A      54           -
LGA    -       -      Q      55           -
LGA    -       -      L      56           -
LGA    -       -      V      57           -
LGA    -       -      E      58           -
LGA    K     169      K      59          3.185
LGA    F     171      L      60          4.451
LGA    D     172      E      61           -
LGA    I     174      T      62           -
LGA    G     175      F      63           -
LGA    -       -      F      64           -
LGA    -       -      A      65           -
LGA    -       -      V      66           -
LGA    -       -      H      67           -
LGA    -       -      Y      68           -
LGA    -       -      P      69           -
LGA    -       -      F      70           -
LGA    -       -      I      71           -
LGA    -       -      Q      72           -
LGA    -       -      S      73           -
LGA    -       -      F      74           -
LGA    -       -      S      75           -
LGA    -       -      L      76           -
LGA    L     178      L      77           #
LGA    K     180      S      78          4.349
LGA    -       -      A     168           -
LGA    -       -      K     169           -
LGA    -       -      T     170           -
LGA    -       -      F     171           -
LGA    -       -      D     172           -
LGA    -       -      K     173           -
LGA    -       -      I     174           -
LGA    -       -      G     175           -
LGA    -       -      Q     176           -
LGA    -       -      M     177           -
LGA    -       -      L     178           -
LGA    -       -      K     179           -
LGA    -       -      K     180           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   27   91    5.0     20    3.16    15.00     13.871     0.614

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.516058 * X  +   0.829392 * Y  +   0.213991 * Z  + -41.357559
  Y_new =   0.261915 * X  +  -0.390658 * Y  +   0.882489 * Z  +  26.619001
  Z_new =   0.815527 * X  +  -0.399368 * Y  +  -0.418832 * Z  +  18.135654 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.379979    0.761614  [ DEG:  -136.3627     43.6373 ]
  Theta =  -0.953639   -2.187953  [ DEG:   -54.6395   -125.3605 ]
  Phi   =   0.469653   -2.671939  [ DEG:    26.9092   -153.0909 ]
 
# 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: T0299AL586_1-D1                               
REMARK     2: T0299_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0299AL586_1-D1.T0299_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   27   91   5.0   20   3.16   15.00  13.871
REMARK  ---------------------------------------------------------- 
MOLECULE T0299AL586_1-D1
REMARK Aligment from pdb entry: 1k66_A
ATOM      1  N   THR     2     -22.876  42.758   0.436  1.00  0.00              
ATOM      2  CA  THR     2     -22.373  43.812   1.306  1.00  0.00              
ATOM      3  C   THR     2     -21.380  44.669   0.533  1.00  0.00              
ATOM      4  O   THR     2     -20.723  44.188  -0.389  1.00  0.00              
ATOM      5  N   LEU     6     -17.028  51.615  -4.939  1.00  0.00              
ATOM      6  CA  LEU     6     -15.889  51.946  -4.083  1.00  0.00              
ATOM      7  C   LEU     6     -14.820  50.850  -4.123  1.00  0.00              
ATOM      8  O   LEU     6     -14.884  49.874  -3.378  1.00  0.00              
ATOM      9  N   LEU     7     -13.812  51.008  -4.992  1.00  0.00              
ATOM     10  CA  LEU     7     -12.754  49.998  -5.096  1.00  0.00              
ATOM     11  C   LEU     7     -11.879  49.825  -3.861  1.00  0.00              
ATOM     12  O   LEU     7     -11.631  50.768  -3.109  1.00  0.00              
ATOM     13  N   VAL     8     -11.414  48.598  -3.671  1.00  0.00              
ATOM     14  CA  VAL     8     -10.511  48.266  -2.585  1.00  0.00              
ATOM     15  C   VAL     8      -9.209  47.883  -3.270  1.00  0.00              
ATOM     16  O   VAL     8      -9.185  46.960  -4.085  1.00  0.00              
ATOM     17  N   ARG     9      -8.141  48.610  -2.971  1.00  0.00              
ATOM     18  CA  ARG     9      -6.840  48.298  -3.544  1.00  0.00              
ATOM     19  C   ARG     9      -6.084  47.470  -2.510  1.00  0.00              
ATOM     20  O   ARG     9      -5.868  47.922  -1.384  1.00  0.00              
ATOM     21  N   GLY    10      -5.698  46.256  -2.889  1.00  0.00              
ATOM     22  CA  GLY    10      -4.967  45.376  -1.984  1.00  0.00              
ATOM     23  C   GLY    10      -3.535  45.221  -2.485  1.00  0.00              
ATOM     24  O   GLY    10      -3.313  44.717  -3.582  1.00  0.00              
ATOM     25  N   ILE    11      -2.567  45.668  -1.691  1.00  0.00              
ATOM     26  CA  ILE    11      -1.164  45.547  -2.076  1.00  0.00              
ATOM     27  C   ILE    11      -0.621  44.373  -1.276  1.00  0.00              
ATOM     28  O   ILE    11      -0.273  44.496  -0.099  1.00  0.00              
ATOM     29  N   ASN    12      -0.559  43.227  -1.943  1.00  0.00              
ATOM     30  CA  ASN    12      -0.131  41.982  -1.318  1.00  0.00              
ATOM     31  C   ASN    12       0.682  41.140  -2.295  1.00  0.00              
ATOM     32  O   ASN    12       0.202  40.819  -3.377  1.00  0.00              
ATOM     33  N   VAL    13       1.896  40.766  -1.907  1.00  0.00              
ATOM     34  CA  VAL    13       2.732  39.969  -2.799  1.00  0.00              
ATOM     35  C   VAL    13       2.584  38.459  -2.615  1.00  0.00              
ATOM     36  O   VAL    13       3.001  37.694  -3.481  1.00  0.00              
ATOM     37  N   MET    21      -3.289  36.530  -0.547  1.00  0.00              
ATOM     38  CA  MET    21      -4.296  37.238  -1.325  1.00  0.00              
ATOM     39  C   MET    21      -5.478  36.343  -1.669  1.00  0.00              
ATOM     40  O   MET    21      -6.630  36.759  -1.557  1.00  0.00              
ATOM     41  N   LEU    24      -7.647  35.634   1.359  1.00  0.00              
ATOM     42  CA  LEU    24      -8.384  36.863   1.653  1.00  0.00              
ATOM     43  C   LEU    24      -9.529  37.074   0.664  1.00  0.00              
ATOM     44  O   LEU    24     -10.668  37.338   1.054  1.00  0.00              
ATOM     45  N   LEU    28     -12.488  34.780   1.192  1.00  0.00              
ATOM     46  CA  LEU    28     -13.260  35.161   2.368  1.00  0.00              
ATOM     47  C   LEU    28     -14.207  36.313   2.036  1.00  0.00              
ATOM     48  O   LEU    28     -15.337  36.343   2.525  1.00  0.00              
ATOM     49  N   THR    29     -13.755  37.265   1.219  1.00  0.00              
ATOM     50  CA  THR    29     -14.623  38.380   0.838  1.00  0.00              
ATOM     51  C   THR    29     -15.758  37.868  -0.040  1.00  0.00              
ATOM     52  O   THR    29     -16.892  38.344   0.046  1.00  0.00              
ATOM     53  N   LEU    31     -18.640  36.397   1.817  1.00  0.00              
ATOM     54  CA  LEU    31     -19.500  37.383   2.470  1.00  0.00              
ATOM     55  C   LEU    31     -20.312  38.180   1.455  1.00  0.00              
ATOM     56  O   LEU    31     -21.111  39.043   1.823  1.00  0.00              
ATOM     57  N   GLY    43     -19.166  40.355  -0.838  1.00  0.00              
ATOM     58  CA  GLY    43     -18.667  41.709  -1.061  1.00  0.00              
ATOM     59  C   GLY    43     -18.726  42.069  -2.544  1.00  0.00              
ATOM     60  O   GLY    43     -18.248  41.312  -3.389  1.00  0.00              
ATOM     61  N   THR    48     -17.627  45.225  -3.695  1.00  0.00              
ATOM     62  CA  THR    48     -16.599  46.207  -4.020  1.00  0.00              
ATOM     63  C   THR    48     -15.594  45.553  -4.962  1.00  0.00              
ATOM     64  O   THR    48     -15.161  44.425  -4.726  1.00  0.00              
ATOM     65  N   PHE    74     -12.199  44.480  -6.350  1.00  0.00              
ATOM     66  CA  PHE    74     -10.891  44.331  -5.731  1.00  0.00              
ATOM     67  C   PHE    74      -9.774  44.417  -6.769  1.00  0.00              
ATOM     68  O   PHE    74      -9.779  43.690  -7.759  1.00  0.00              
ATOM     69  N   SER    75      -8.828  45.321  -6.540  1.00  0.00              
ATOM     70  CA  SER    75      -7.687  45.488  -7.428  1.00  0.00              
ATOM     71  C   SER    75      -6.454  45.087  -6.644  1.00  0.00              
ATOM     72  O   SER    75      -6.292  45.489  -5.496  1.00  0.00              
ATOM     73  N   LEU    77      -2.159  44.744  -6.325  1.00  0.00              
ATOM     74  CA  LEU    77      -0.819  45.143  -6.738  1.00  0.00              
ATOM     75  C   LEU    77       0.105  44.239  -5.926  1.00  0.00              
ATOM     76  O   LEU    77      -0.162  43.961  -4.751  1.00  0.00              
ATOM     77  N   SER    78       1.178  43.771  -6.554  1.00  0.00              
ATOM     78  CA  SER    78       2.131  42.887  -5.895  1.00  0.00              
ATOM     79  C   SER    78       3.367  43.631  -5.411  1.00  0.00              
ATOM     80  O   SER    78       3.889  43.331  -4.342  1.00  0.00              
ATOM    281  N   LYS   169     -11.115  39.283   8.910  1.00  0.00              
ATOM    282  CA  LYS   169     -11.614  39.740   7.624  1.00  0.00              
ATOM    283  C   LYS   169     -13.094  40.103   7.671  1.00  0.00              
ATOM    284  O   LYS   169     -13.507  41.098   7.088  1.00  0.00              
ATOM    285  N   PHE   171     -13.314  43.464   9.269  1.00  0.00              
ATOM    286  CA  PHE   171     -12.771  44.474   8.363  1.00  0.00              
ATOM    287  C   PHE   171     -13.851  44.852   7.354  1.00  0.00              
ATOM    288  O   PHE   171     -14.064  46.026   7.053  1.00  0.00              
ATOM    289  N   ASP   172     -14.537  43.843   6.825  1.00  0.00              
ATOM    290  CA  ASP   172     -15.594  44.084   5.848  1.00  0.00              
ATOM    291  C   ASP   172     -16.735  44.930   6.413  1.00  0.00              
ATOM    292  O   ASP   172     -17.147  45.922   5.810  1.00  0.00              
ATOM    293  N   ILE   174     -15.188  48.740   7.336  1.00  0.00              
ATOM    294  CA  ILE   174     -14.828  49.586   6.203  1.00  0.00              
ATOM    295  C   ILE   174     -15.789  49.645   5.036  1.00  0.00              
ATOM    296  O   ILE   174     -15.973  50.703   4.436  1.00  0.00              
ATOM    297  N   GLY   175     -16.406  48.520   4.709  1.00  0.00              
ATOM    298  CA  GLY   175     -17.284  48.504   3.556  1.00  0.00              
ATOM    299  C   GLY   175     -18.756  48.749   3.827  1.00  0.00              
ATOM    300  O   GLY   175     -19.527  48.949   2.891  1.00  0.00              
ATOM    301  N   LEU   178     -16.668  56.702   3.763  1.00  0.00              
ATOM    302  CA  LEU   178     -15.369  56.934   3.140  1.00  0.00              
ATOM    303  C   LEU   178     -15.366  58.230   2.343  1.00  0.00              
ATOM    304  O   LEU   178     -16.400  58.654   1.842  1.00  0.00              
ATOM    305  N   LYS   180     -13.945  58.571  -2.623  1.00  0.00              
ATOM    306  CA  LYS   180     -12.832  57.857  -3.235  1.00  0.00              
ATOM    307  C   LYS   180     -11.479  58.289  -2.678  1.00  0.00              
ATOM    308  O   LYS   180     -10.469  57.633  -2.916  1.00  0.00              
END
