
#######################################################
#                                                     #
#                        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_3-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356AL044_3-D1.T0356_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N       7           -
LGA    -       -      D       8           -
LGA    D     314      L       9          4.163
LGA    A     315      R      10          2.454
LGA    I     316      D      11          3.410
LGA    Y     317      F      12          2.192
LGA    -       -      L      13           -
LGA    H     318      T      14          0.806
LGA    S     319      L      15          0.873
LGA    T     320      L      16          0.620
LGA    Y     321      E      17          1.158
LGA    T     322      Q      18          1.986
LGA    G     323      Q      19          1.896
LGA    R     324      G      20          1.541
LGA    D     327      E      21          0.639
LGA    E     328      L      22          3.762
LGA    -       -      K      23           -
LGA    -       -      R      24           -
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    P     329      A      49          1.770
LGA    -       -      L      50           -
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    -       -      L      63           -
LGA    -       -      C      64           -
LGA    -       -      N      65           -
LGA    A     330      L      66          2.501
LGA    V     331      F      67          0.842
LGA    G     333      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    -       -      R      72           -
LGA    A     335      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    L     336      A      84          5.420
LGA    N     337      L      85          2.175
LGA    E     338      R      86           #
LGA    P     342      E      87           -
LGA    I     343      V      88          2.429
LGA    L     344      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    -       -      A     330           -
LGA    -       -      V     331           -
LGA    -       -      L     332           -
LGA    -       -      G     333           -
LGA    -       -      V     334           -
LGA    -       -      A     335           -
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     19    2.49     0.00     12.416     0.734

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.561430 * X  +   0.815302 * Y  +   0.141697 * Z  +  28.511103
  Y_new =   0.639764 * X  +  -0.319028 * Y  +  -0.699230 * Z  +  94.877914
  Z_new =  -0.524879 * X  +   0.483221 * Y  +  -0.700713 * Z  +  68.011238 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.537872   -0.603721  [ DEG:   145.4093    -34.5907 ]
  Theta =   0.552573    2.589020  [ DEG:    31.6601    148.3399 ]
  Phi   =   0.850520   -2.291073  [ DEG:    48.7312   -131.2688 ]
 
# 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_3-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL044_3-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   19   2.49    0.00  12.416
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL044_3-D1
REMARK Aligment from pdb entry: 2bco_A
ATOM     29  N   ASP   314      73.304  77.299  79.917  1.00  0.00              
ATOM     30  CA  ASP   314      72.496  77.266  81.125  1.00  0.00              
ATOM     31  C   ASP   314      73.316  77.860  82.258  1.00  0.00              
ATOM     32  O   ASP   314      73.650  77.179  83.219  1.00  0.00              
ATOM     33  N   ALA   315      74.692  80.860  85.252  1.00  0.00              
ATOM     34  CA  ALA   315      74.332  81.360  86.563  1.00  0.00              
ATOM     35  C   ALA   315      73.434  82.587  86.382  1.00  0.00              
ATOM     36  O   ALA   315      72.433  82.742  87.068  1.00  0.00              
ATOM     37  N   ILE   316      71.530  83.376  83.761  1.00  0.00              
ATOM     38  CA  ILE   316      70.233  82.980  83.217  1.00  0.00              
ATOM     39  C   ILE   316      69.310  82.444  84.303  1.00  0.00              
ATOM     40  O   ILE   316      68.138  82.806  84.349  1.00  0.00              
ATOM     41  N   TYR   317      69.841  81.575  85.162  1.00  0.00              
ATOM     42  CA  TYR   317      69.072  80.987  86.258  1.00  0.00              
ATOM     43  C   TYR   317      68.668  82.060  87.259  1.00  0.00              
ATOM     44  O   TYR   317      67.539  82.067  87.741  1.00  0.00              
ATOM     45  N   HIS   318      69.587  82.967  87.575  1.00  0.00              
ATOM     46  CA  HIS   318      69.263  84.056  88.491  1.00  0.00              
ATOM     47  C   HIS   318      68.113  84.869  87.898  1.00  0.00              
ATOM     48  O   HIS   318      67.262  85.375  88.632  1.00  0.00              
ATOM     49  N   SER   319      68.107  85.003  86.570  1.00  0.00              
ATOM     50  CA  SER   319      67.061  85.757  85.882  1.00  0.00              
ATOM     51  C   SER   319      65.727  85.073  86.086  1.00  0.00              
ATOM     52  O   SER   319      64.740  85.728  86.414  1.00  0.00              
ATOM     53  N   THR   320      65.703  83.754  85.889  1.00  0.00              
ATOM     54  CA  THR   320      64.486  82.968  86.066  1.00  0.00              
ATOM     55  C   THR   320      63.916  83.199  87.461  1.00  0.00              
ATOM     56  O   THR   320      62.721  83.448  87.616  1.00  0.00              
ATOM     57  N   TYR   321      64.781  83.103  88.470  1.00  0.00              
ATOM     58  CA  TYR   321      64.366  83.265  89.854  1.00  0.00              
ATOM     59  C   TYR   321      63.862  84.676  90.131  1.00  0.00              
ATOM     60  O   TYR   321      62.818  84.859  90.752  1.00  0.00              
ATOM     61  N   THR   322      64.592  85.674  89.655  1.00  0.00              
ATOM     62  CA  THR   322      64.172  87.051  89.870  1.00  0.00              
ATOM     63  C   THR   322      62.847  87.332  89.174  1.00  0.00              
ATOM     64  O   THR   322      62.036  88.104  89.682  1.00  0.00              
ATOM     65  N   GLY   323      62.631  86.696  88.020  1.00  0.00              
ATOM     66  CA  GLY   323      61.405  86.886  87.245  1.00  0.00              
ATOM     67  C   GLY   323      60.235  86.141  87.847  1.00  0.00              
ATOM     68  O   GLY   323      59.099  86.356  87.448  1.00  0.00              
ATOM     69  N   ARG   324      60.518  85.263  88.802  1.00  0.00              
ATOM     70  CA  ARG   324      59.480  84.484  89.464  1.00  0.00              
ATOM     71  C   ARG   324      58.868  83.420  88.559  1.00  0.00              
ATOM     72  O   ARG   324      57.707  83.042  88.735  1.00  0.00              
ATOM     73  N   ASP   327      59.650  82.941  87.592  1.00  0.00              
ATOM     74  CA  ASP   327      59.187  81.893  86.688  1.00  0.00              
ATOM     75  C   ASP   327      59.152  80.643  87.562  1.00  0.00              
ATOM     76  O   ASP   327      60.170  80.212  88.102  1.00  0.00              
ATOM     77  N   GLU   328      57.964  80.080  87.716  1.00  0.00              
ATOM     78  CA  GLU   328      57.763  78.928  88.579  1.00  0.00              
ATOM     79  C   GLU   328      58.572  77.676  88.294  1.00  0.00              
ATOM     80  O   GLU   328      58.926  76.954  89.222  1.00  0.00              
ATOM     81  N   PRO   329      58.872  77.412  87.028  1.00  0.00              
ATOM     82  CA  PRO   329      59.635  76.221  86.699  1.00  0.00              
ATOM     83  C   PRO   329      60.378  76.327  85.377  1.00  0.00              
ATOM     84  O   PRO   329      59.983  77.089  84.487  1.00  0.00              
ATOM     85  N   ALA   330      61.470  75.569  85.269  1.00  0.00              
ATOM     86  CA  ALA   330      62.255  75.528  84.042  1.00  0.00              
ATOM     87  C   ALA   330      62.468  74.074  83.643  1.00  0.00              
ATOM     88  O   ALA   330      62.896  73.256  84.451  1.00  0.00              
ATOM     89  N   VAL   331      62.143  73.756  82.399  1.00  0.00              
ATOM     90  CA  VAL   331      62.304  72.403  81.880  1.00  0.00              
ATOM     91  C   VAL   331      63.621  72.392  81.079  1.00  0.00              
ATOM     92  O   VAL   331      63.810  73.195  80.164  1.00  0.00              
ATOM     93  N   GLY   333      64.537  71.504  81.448  1.00  0.00              
ATOM     94  CA  GLY   333      65.812  71.392  80.758  1.00  0.00              
ATOM     95  C   GLY   333      65.656  70.341  79.658  1.00  0.00              
ATOM     96  O   GLY   333      65.541  69.158  79.954  1.00  0.00              
ATOM     97  N   ALA   335      65.634  70.760  78.398  1.00  0.00              
ATOM     98  CA  ALA   335      65.482  69.798  77.306  1.00  0.00              
ATOM     99  C   ALA   335      66.640  68.803  77.270  1.00  0.00              
ATOM    100  O   ALA   335      67.760  69.142  77.644  1.00  0.00              
ATOM    101  N   LEU   336      63.046  74.887  67.536  1.00  0.00              
ATOM    102  CA  LEU   336      62.514  76.192  67.911  1.00  0.00              
ATOM    103  C   LEU   336      63.488  77.327  67.670  1.00  0.00              
ATOM    104  O   LEU   336      64.668  77.116  67.409  1.00  0.00              
ATOM    105  N   ASN   337      62.967  78.540  67.770  1.00  0.00              
ATOM    106  CA  ASN   337      63.750  79.744  67.562  1.00  0.00              
ATOM    107  C   ASN   337      64.802  79.873  68.669  1.00  0.00              
ATOM    108  O   ASN   337      65.944  80.272  68.415  1.00  0.00              
ATOM    109  N   GLU   338      64.403  79.530  69.893  1.00  0.00              
ATOM    110  CA  GLU   338      65.283  79.574  71.055  1.00  0.00              
ATOM    111  C   GLU   338      66.429  78.571  70.896  1.00  0.00              
ATOM    112  O   GLU   338      67.595  78.896  71.130  1.00  0.00              
ATOM    113  N   PRO   342      66.087  77.347  70.506  1.00  0.00              
ATOM    114  CA  PRO   342      67.089  76.307  70.303  1.00  0.00              
ATOM    115  C   PRO   342      68.088  76.733  69.229  1.00  0.00              
ATOM    116  O   PRO   342      69.280  76.479  69.355  1.00  0.00              
ATOM    117  N   ILE   343      67.602  77.382  68.174  1.00  0.00              
ATOM    118  CA  ILE   343      68.481  77.817  67.091  1.00  0.00              
ATOM    119  C   ILE   343      69.589  78.766  67.562  1.00  0.00              
ATOM    120  O   ILE   343      70.728  78.676  67.105  1.00  0.00              
ATOM    121  N   LEU   344      69.243  79.688  68.454  1.00  0.00              
ATOM    122  CA  LEU   344      70.214  80.637  68.976  1.00  0.00              
ATOM    123  C   LEU   344      71.208  79.945  69.895  1.00  0.00              
ATOM    124  O   LEU   344      72.390  80.246  69.866  1.00  0.00              
END
