
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0356AL044_5-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356AL044_5-D1.T0356_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    -       -      N       7           -
LGA    -       -      D       8           -
LGA    D     314      L       9          3.757
LGA    A     315      R      10          1.998
LGA    -       -      D      11           -
LGA    I     316      F      12          1.756
LGA    Y     317      L      13          0.937
LGA    H     318      T      14          1.261
LGA    S     319      L      15          1.217
LGA    T     320      L      16          0.886
LGA    Y     321      E      17          0.838
LGA    T     322      Q      18          0.928
LGA    G     323      Q      19          1.354
LGA    R     324      G      20          1.834
LGA    D     327      E      21          3.268
LGA    -       -      L      22           -
LGA    E     328      K      23          2.516
LGA    P     329      R      24          3.382
LGA    -       -      I      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      P      28           -
LGA    -       -      V      29           -
LGA    -       -      D      30           -
LGA    -       -      P      31           -
LGA    -       -      H      32           -
LGA    -       -      L      33           -
LGA    -       -      E      34           -
LGA    -       -      I      35           -
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    -       -      I      38           -
LGA    -       -      A      39           -
LGA    -       -      D      40           -
LGA    -       -      R      41           -
LGA    -       -      T      42           -
LGA    -       -      L      43           -
LGA    -       -      R      44           -
LGA    -       -      A      45           -
LGA    -       -      G      46           -
LGA    -       -      G      47           -
LGA    -       -      P      48           -
LGA    A     330      A      49          3.041
LGA    V     331      L      50          2.873
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      E      53           -
LGA    -       -      N      54           -
LGA    -       -      P      55           -
LGA    -       -      K      56           -
LGA    -       -      G      57           -
LGA    -       -      Y      58           -
LGA    -       -      S      59           -
LGA    -       -      M      60           -
LGA    -       -      P      61           -
LGA    -       -      V      62           -
LGA    G     333      L      63          3.366
LGA    A     335      C      64          3.992
LGA    -       -      N      65           -
LGA    -       -      L      66           -
LGA    -       -      F      67           -
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    -       -      V      73           -
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    -       -      D      81           -
LGA    -       -      V      82           -
LGA    -       -      S      83           -
LGA    -       -      A      84           -
LGA    -       -      L      85           -
LGA    -       -      R      86           -
LGA    -       -      E      87           -
LGA    -       -      V      88           -
LGA    -       -      G      89           -
LGA    -       -      K      90           -
LGA    -       -      L      91           -
LGA    -       -      L      92           -
LGA    -       -      A      93           -
LGA    -       -      F      94           -
LGA    -       -      L      95           -
LGA    -       -      K      96           -
LGA    -       -      D     314           -
LGA    -       -      A     315           -
LGA    -       -      I     316           -
LGA    -       -      Y     317           -
LGA    -       -      H     318           -
LGA    -       -      S     319           -
LGA    -       -      T     320           -
LGA    -       -      Y     321           -
LGA    -       -      T     322           -
LGA    -       -      G     323           -
LGA    -       -      R     324           -
LGA    -       -      P     325           -
LGA    -       -      P     326           -
LGA    -       -      D     327           -
LGA    -       -      E     328           -
LGA    -       -      P     329           -
LGA    L     336      A     330          1.705
LGA    N     337      V     331          1.694
LGA    E     338      L     332          2.328
LGA    P     342      G     333          5.317
LGA    I     343      V     334           -
LGA    L     344      A     335          4.362
LGA    -       -      L     336           -
LGA    -       -      N     337           -
LGA    -       -      E     338           -
LGA    -       -      V     339           -
LGA    -       -      F     340           -
LGA    -       -      V     341           -
LGA    -       -      P     342           -
LGA    -       -      I     343           -
LGA    -       -      L     344           -
LGA    -       -      Q     345           -
LGA    -       -      K     346           -
LGA    -       -      Q     347           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24  124    5.0     23    2.67     4.35     13.761     0.829

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.083579 * X  +  -0.725270 * Y  +  -0.683372 * Z  + 148.138809
  Y_new =  -0.861520 * X  +   0.397229 * Y  +  -0.316216 * Z  + 141.635803
  Z_new =   0.500798 * X  +   0.562310 * Y  +  -0.658035 * Z  + 128.247391 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.434475   -0.707117  [ DEG:   139.4852    -40.5148 ]
  Theta =  -0.524520   -2.617073  [ DEG:   -30.0528   -149.9472 ]
  Phi   =  -1.667507    1.474085  [ DEG:   -95.5411     84.4589 ]
 
# 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: T0356AL044_5-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_5-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24  124   5.0   23   2.67    4.35  13.761
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_5-D1
REMARK Aligment from pdb entry: 1yw4_A
ATOM     29  N   ASP   314      72.935  72.808  84.848  1.00  0.00              
ATOM     30  CA  ASP   314      71.855  73.786  84.795  1.00  0.00              
ATOM     31  C   ASP   314      72.407  75.205  84.682  1.00  0.00              
ATOM     32  O   ASP   314      73.250  75.620  85.477  1.00  0.00              
ATOM     33  N   ALA   315      72.566  78.884  85.309  1.00  0.00              
ATOM     34  CA  ALA   315      72.055  79.807  86.313  1.00  0.00              
ATOM     35  C   ALA   315      71.715  81.184  85.762  1.00  0.00              
ATOM     36  O   ALA   315      71.054  81.980  86.429  1.00  0.00              
ATOM     37  N   ILE   316      69.778  81.630  83.294  1.00  0.00              
ATOM     38  CA  ILE   316      68.344  81.536  83.044  1.00  0.00              
ATOM     39  C   ILE   316      67.580  81.488  84.362  1.00  0.00              
ATOM     40  O   ILE   316      66.470  82.010  84.466  1.00  0.00              
ATOM     41  N   TYR   317      68.172  80.855  85.366  1.00  0.00              
ATOM     42  CA  TYR   317      67.539  80.782  86.675  1.00  0.00              
ATOM     43  C   TYR   317      67.388  82.202  87.194  1.00  0.00              
ATOM     44  O   TYR   317      66.421  82.529  87.883  1.00  0.00              
ATOM     45  N   HIS   318      68.349  83.052  86.849  1.00  0.00              
ATOM     46  CA  HIS   318      68.320  84.442  87.278  1.00  0.00              
ATOM     47  C   HIS   318      67.148  85.154  86.615  1.00  0.00              
ATOM     48  O   HIS   318      66.352  85.816  87.283  1.00  0.00              
ATOM     49  N   SER   319      67.042  85.004  85.297  1.00  0.00              
ATOM     50  CA  SER   319      65.964  85.631  84.532  1.00  0.00              
ATOM     51  C   SER   319      64.609  85.184  85.068  1.00  0.00              
ATOM     52  O   SER   319      63.669  85.974  85.165  1.00  0.00              
ATOM     53  N   THR   320      64.512  83.899  85.388  1.00  0.00              
ATOM     54  CA  THR   320      63.281  83.343  85.923  1.00  0.00              
ATOM     55  C   THR   320      62.988  83.969  87.282  1.00  0.00              
ATOM     56  O   THR   320      61.858  84.385  87.558  1.00  0.00              
ATOM     57  N   TYR   321      64.016  84.045  88.122  1.00  0.00              
ATOM     58  CA  TYR   321      63.876  84.621  89.457  1.00  0.00              
ATOM     59  C   TYR   321      63.324  86.038  89.354  1.00  0.00              
ATOM     60  O   TYR   321      62.274  86.344  89.916  1.00  0.00              
ATOM     61  N   THR   322      64.040  86.902  88.644  1.00  0.00              
ATOM     62  CA  THR   322      63.588  88.275  88.470  1.00  0.00              
ATOM     63  C   THR   322      62.523  88.304  87.380  1.00  0.00              
ATOM     64  O   THR   322      62.624  89.050  86.408  1.00  0.00              
ATOM     65  N   GLY   323      61.507  87.469  87.554  1.00  0.00              
ATOM     66  CA  GLY   323      60.405  87.370  86.609  1.00  0.00              
ATOM     67  C   GLY   323      59.140  87.003  87.372  1.00  0.00              
ATOM     68  O   GLY   323      58.022  87.232  86.904  1.00  0.00              
ATOM     69  N   ARG   324      59.330  86.422  88.550  1.00  0.00              
ATOM     70  CA  ARG   324      58.206  86.024  89.371  1.00  0.00              
ATOM     71  C   ARG   324      58.324  84.597  89.869  1.00  0.00              
ATOM     72  O   ARG   324      57.733  84.247  90.887  1.00  0.00              
ATOM     73  N   ASP   327      59.077  83.765  89.152  1.00  0.00              
ATOM     74  CA  ASP   327      59.252  82.375  89.558  1.00  0.00              
ATOM     75  C   ASP   327      59.787  82.372  90.986  1.00  0.00              
ATOM     76  O   ASP   327      60.757  83.065  91.289  1.00  0.00              
ATOM     77  N   GLU   328      59.155  81.587  91.855  1.00  0.00              
ATOM     78  CA  GLU   328      59.546  81.523  93.255  1.00  0.00              
ATOM     79  C   GLU   328      60.224  80.210  93.626  1.00  0.00              
ATOM     80  O   GLU   328      60.683  80.044  94.755  1.00  0.00              
ATOM     81  N   PRO   329      60.284  79.280  92.677  1.00  0.00              
ATOM     82  CA  PRO   329      60.902  77.982  92.915  1.00  0.00              
ATOM     83  C   PRO   329      61.113  77.226  91.610  1.00  0.00              
ATOM     84  O   PRO   329      60.389  77.438  90.636  1.00  0.00              
ATOM     85  N   ALA   330      62.108  76.343  91.597  1.00  0.00              
ATOM     86  CA  ALA   330      62.406  75.554  90.408  1.00  0.00              
ATOM     87  C   ALA   330      62.568  74.074  90.744  1.00  0.00              
ATOM     88  O   ALA   330      63.281  73.710  91.678  1.00  0.00              
ATOM     89  N   VAL   331      61.871  73.226  89.996  1.00  0.00              
ATOM     90  CA  VAL   331      61.973  71.785  90.183  1.00  0.00              
ATOM     91  C   VAL   331      62.918  71.290  89.086  1.00  0.00              
ATOM     92  O   VAL   331      62.697  71.561  87.906  1.00  0.00              
ATOM     93  N   GLY   333      63.974  70.588  89.480  1.00  0.00              
ATOM     94  CA  GLY   333      64.946  70.055  88.528  1.00  0.00              
ATOM     95  C   GLY   333      64.633  68.579  88.298  1.00  0.00              
ATOM     96  O   GLY   333      64.707  67.770  89.228  1.00  0.00              
ATOM     97  N   ALA   335      64.273  68.233  87.065  1.00  0.00              
ATOM     98  CA  ALA   335      63.955  66.850  86.719  1.00  0.00              
ATOM     99  C   ALA   335      65.218  65.999  86.712  1.00  0.00              
ATOM    100  O   ALA   335      66.243  66.401  86.165  1.00  0.00              
ATOM    101  N   LEU   336      57.549  65.569  78.122  1.00  0.00              
ATOM    102  CA  LEU   336      57.061  66.942  78.075  1.00  0.00              
ATOM    103  C   LEU   336      57.686  67.722  76.926  1.00  0.00              
ATOM    104  O   LEU   336      58.739  67.361  76.406  1.00  0.00              
ATOM    105  N   ASN   337      57.030  68.801  76.533  1.00  0.00              
ATOM    106  CA  ASN   337      57.528  69.600  75.438  1.00  0.00              
ATOM    107  C   ASN   337      58.871  70.236  75.805  1.00  0.00              
ATOM    108  O   ASN   337      59.788  70.267  74.985  1.00  0.00              
ATOM    109  N   GLU   338      58.999  70.726  77.038  1.00  0.00              
ATOM    110  CA  GLU   338      60.251  71.358  77.452  1.00  0.00              
ATOM    111  C   GLU   338      61.421  70.364  77.496  1.00  0.00              
ATOM    112  O   GLU   338      62.576  70.744  77.299  1.00  0.00              
ATOM    113  N   PRO   342      61.135  69.095  77.768  1.00  0.00              
ATOM    114  CA  PRO   342      62.202  68.105  77.783  1.00  0.00              
ATOM    115  C   PRO   342      62.643  67.886  76.331  1.00  0.00              
ATOM    116  O   PRO   342      63.838  67.888  76.030  1.00  0.00              
ATOM    117  N   ILE   343      61.668  67.707  75.439  1.00  0.00              
ATOM    118  CA  ILE   343      61.958  67.485  74.021  1.00  0.00              
ATOM    119  C   ILE   343      62.866  68.560  73.438  1.00  0.00              
ATOM    120  O   ILE   343      63.882  68.246  72.814  1.00  0.00              
ATOM    121  N   LEU   344      62.518  69.830  73.635  1.00  0.00              
ATOM    122  CA  LEU   344      63.341  70.903  73.075  1.00  0.00              
ATOM    123  C   LEU   344      64.708  70.987  73.749  1.00  0.00              
ATOM    124  O   LEU   344      65.730  71.195  73.087  1.00  0.00              
END
