
#######################################################
#                                                     #
#                        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   30 (  120),  selected   30 , name T0356AL333_1-D1
# Molecule2: number of CA atoms  124 (  963),  selected  124 , name T0356_D1.pdb
# PARAMETERS: T0356AL333_1-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    -       -      L       9           -
LGA    -       -      R      10           -
LGA    -       -      D      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      T      14           -
LGA    -       -      L      15           -
LGA    -       -      L      16           -
LGA    -       -      E      17           -
LGA    -       -      Q      18           -
LGA    -       -      Q      19           -
LGA    -       -      G      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
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    L      13      I      35          0.711
LGA    -       -      T      36           -
LGA    -       -      E      37           -
LGA    T      14      I      38          3.533
LGA    L      15      A      39          3.317
LGA    L      16      D      40           -
LGA    -       -      R      41           -
LGA    E      17      T      42          3.969
LGA    Q      18      L      43          3.179
LGA    -       -      R      44           -
LGA    Q      19      A      45          3.610
LGA    G      20      G      46          3.559
LGA    E      21      -       -           -
LGA    L      22      G      47          5.430
LGA    I      38      P      48          4.388
LGA    A      39      A      49          2.113
LGA    D      40      L      50          2.593
LGA    R      41      L      51          3.713
LGA    T      42      F      52          4.506
LGA    -       -      E      53           -
LGA    L      43      N      54          5.172
LGA    R      44      P      55          2.812
LGA    A      45      K      56          3.142
LGA    -       -      G      57           -
LGA    G      46      Y      58          2.671
LGA    G      47      S      59          2.787
LGA    -       -      M      60           -
LGA    P      48      P      61          2.134
LGA    A      49      V      62          2.924
LGA    L      50      L      63          3.392
LGA    L      51      C      64          3.247
LGA    -       -      N      65           -
LGA    F      52      L      66          2.402
LGA    E      53      F      67          1.925
LGA    -       -      G      68           -
LGA    -       -      T      69           -
LGA    -       -      P      70           -
LGA    -       -      K      71           -
LGA    N      54      R      72          2.355
LGA    P      55      V      73          3.935
LGA    -       -      A      74           -
LGA    -       -      M      75           -
LGA    -       -      G      76           -
LGA    -       -      M      77           -
LGA    -       -      G      78           -
LGA    -       -      Q      79           -
LGA    -       -      E      80           -
LGA    K      56      D      81           #
LGA    G      57      V      82          2.129
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    -       -      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)   30  124    5.0     27    3.33    14.81     12.912     0.787

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.957065 * X  +   0.287729 * Y  +  -0.035188 * Z  + 151.948196
  Y_new =   0.250372 * X  +   0.759357 * Y  +  -0.600576 * Z  + -12.793522
  Z_new =  -0.146082 * X  +  -0.583600 * Y  +  -0.798793 * Z  + 241.060989 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.510622    0.630970  [ DEG:  -143.8481     36.1519 ]
  Theta =   0.146607    2.994986  [ DEG:     8.4000    171.6000 ]
  Phi   =   2.885723   -0.255870  [ DEG:   165.3398    -14.6602 ]
 
# 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: T0356AL333_1-D1                               
REMARK     2: T0356_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356AL333_1-D1.T0356_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   30  124   5.0   27   3.33   14.81  12.912
REMARK  ---------------------------------------------------------- 
MOLECULE T0356AL333_1-D1
REMARK Aligment from pdb entry: 1lwh_A
ATOM      9  N   LEU    13      60.729  65.161  95.545  1.00  0.00              
ATOM     10  CA  LEU    13      60.293  66.166  94.573  1.00  0.00              
ATOM     11  C   LEU    13      59.091  66.927  95.123  1.00  0.00              
ATOM     12  O   LEU    13      58.136  66.313  95.604  1.00  0.00              
ATOM     13  N   THR    14      59.150  68.257  95.051  1.00  0.00              
ATOM     14  CA  THR    14      58.066  69.133  95.508  1.00  0.00              
ATOM     15  C   THR    14      57.728  70.108  94.386  1.00  0.00              
ATOM     16  O   THR    14      58.573  70.906  93.986  1.00  0.00              
ATOM     17  N   LEU    15      56.501  70.055  93.880  1.00  0.00              
ATOM     18  CA  LEU    15      56.109  70.953  92.793  1.00  0.00              
ATOM     19  C   LEU    15      55.840  72.355  93.294  1.00  0.00              
ATOM     20  O   LEU    15      55.248  72.545  94.350  1.00  0.00              
ATOM     21  N   LEU    16      56.290  73.342  92.533  1.00  0.00              
ATOM     22  CA  LEU    16      56.079  74.730  92.910  1.00  0.00              
ATOM     23  C   LEU    16      55.344  75.479  91.805  1.00  0.00              
ATOM     24  O   LEU    16      54.772  76.534  92.048  1.00  0.00              
ATOM     25  N   GLU    17      55.357  74.932  90.594  1.00  0.00              
ATOM     26  CA  GLU    17      54.700  75.576  89.467  1.00  0.00              
ATOM     27  C   GLU    17      54.415  74.590  88.351  1.00  0.00              
ATOM     28  O   GLU    17      55.335  74.095  87.707  1.00  0.00              
ATOM     29  N   GLN    18      53.135  74.314  88.127  1.00  0.00              
ATOM     30  CA  GLN    18      52.711  73.385  87.084  1.00  0.00              
ATOM     31  C   GLN    18      51.888  74.114  86.015  1.00  0.00              
ATOM     32  O   GLN    18      50.665  73.972  85.960  1.00  0.00              
ATOM     33  N   GLN    19      52.552  74.890  85.170  1.00  0.00              
ATOM     34  CA  GLN    19      51.861  75.618  84.106  1.00  0.00              
ATOM     35  C   GLN    19      52.019  74.841  82.810  1.00  0.00              
ATOM     36  O   GLN    19      52.977  74.097  82.636  1.00  0.00              
ATOM     37  N   GLY    20      51.095  75.034  81.882  1.00  0.00              
ATOM     38  CA  GLY    20      51.155  74.354  80.590  1.00  0.00              
ATOM     39  C   GLY    20      52.515  74.535  79.908  1.00  0.00              
ATOM     40  O   GLY    20      53.179  73.562  79.567  1.00  0.00              
ATOM     41  N   GLU    21      52.936  75.781  79.727  1.00  0.00              
ATOM     42  CA  GLU    21      54.205  76.059  79.062  1.00  0.00              
ATOM     43  C   GLU    21      55.461  75.804  79.908  1.00  0.00              
ATOM     44  O   GLU    21      56.531  75.520  79.358  1.00  0.00              
ATOM     45  N   LEU    22      55.349  75.916  81.232  1.00  0.00              
ATOM     46  CA  LEU    22      56.508  75.691  82.092  1.00  0.00              
ATOM     47  C   LEU    22      56.257  75.033  83.449  1.00  0.00              
ATOM     48  O   LEU    22      55.164  75.056  84.004  1.00  0.00              
ATOM     49  N   ILE    38      57.324  74.458  83.982  1.00  0.00              
ATOM     50  CA  ILE    38      57.274  73.712  85.222  1.00  0.00              
ATOM     51  C   ILE    38      58.447  74.108  86.105  1.00  0.00              
ATOM     52  O   ILE    38      59.513  74.509  85.618  1.00  0.00              
ATOM     53  N   ALA    39      58.228  73.995  87.410  1.00  0.00              
ATOM     54  CA  ALA    39      59.235  74.319  88.409  1.00  0.00              
ATOM     55  C   ALA    39      58.987  73.401  89.594  1.00  0.00              
ATOM     56  O   ALA    39      57.840  73.224  90.004  1.00  0.00              
ATOM     57  N   ASP    40      60.055  72.792  90.113  1.00  0.00              
ATOM     58  CA  ASP    40      59.959  71.910  91.285  1.00  0.00              
ATOM     59  C   ASP    40      61.209  72.012  92.148  1.00  0.00              
ATOM     60  O   ASP    40      62.191  72.643  91.769  1.00  0.00              
ATOM     61  N   ARG    41      61.161  71.381  93.310  1.00  0.00              
ATOM     62  CA  ARG    41      62.265  71.421  94.253  1.00  0.00              
ATOM     63  C   ARG    41      62.722  70.029  94.706  1.00  0.00              
ATOM     64  O   ARG    41      61.918  69.192  95.120  1.00  0.00              
ATOM     65  N   THR    42      64.024  69.794  94.605  1.00  0.00              
ATOM     66  CA  THR    42      64.619  68.526  95.000  1.00  0.00              
ATOM     67  C   THR    42      65.225  68.746  96.362  1.00  0.00              
ATOM     68  O   THR    42      65.823  69.791  96.616  1.00  0.00              
ATOM     69  N   LEU    43      65.094  67.762  97.237  1.00  0.00              
ATOM     70  CA  LEU    43      65.647  67.924  98.560  1.00  0.00              
ATOM     71  C   LEU    43      65.676  66.616  99.331  1.00  0.00              
ATOM     72  O   LEU    43      64.979  65.664  98.990  1.00  0.00              
ATOM     73  N   ARG    44      66.530  66.581 100.349  1.00  0.00              
ATOM     74  CA  ARG    44      66.652  65.451 101.262  1.00  0.00              
ATOM     75  C   ARG    44      67.060  66.116 102.573  1.00  0.00              
ATOM     76  O   ARG    44      66.860  67.325 102.723  1.00  0.00              
ATOM     77  N   ALA    45      67.618  65.381 103.523  1.00  0.00              
ATOM     78  CA  ALA    45      67.969  66.025 104.785  1.00  0.00              
ATOM     79  C   ALA    45      69.025  67.143 104.762  1.00  0.00              
ATOM     80  O   ALA    45      68.939  68.089 105.545  1.00  0.00              
ATOM     81  N   GLY    46      70.006  67.060 103.871  1.00  0.00              
ATOM     82  CA  GLY    46      71.040  68.074 103.844  1.00  0.00              
ATOM     83  C   GLY    46      71.194  68.893 102.548  1.00  0.00              
ATOM     84  O   GLY    46      72.240  69.524 102.333  1.00  0.00              
ATOM     85  N   GLY    47      70.163  68.899 101.695  1.00  0.00              
ATOM     86  CA  GLY    47      70.191  69.675 100.441  1.00  0.00              
ATOM     87  C   GLY    47      68.801  70.087  99.985  1.00  0.00              
ATOM     88  O   GLY    47      67.788  69.647 100.530  1.00  0.00              
ATOM     89  N   PRO    48      68.783  70.915  98.944  1.00  0.00              
ATOM     90  CA  PRO    48      67.561  71.397  98.318  1.00  0.00              
ATOM     91  C   PRO    48      67.984  72.190  97.094  1.00  0.00              
ATOM     92  O   PRO    48      68.848  73.052  97.189  1.00  0.00              
ATOM     93  N   ALA    49      67.390  71.885  95.945  1.00  0.00              
ATOM     94  CA  ALA    49      67.719  72.573  94.705  1.00  0.00              
ATOM     95  C   ALA    49      66.401  72.836  93.998  1.00  0.00              
ATOM     96  O   ALA    49      65.489  72.003  94.045  1.00  0.00              
ATOM     97  N   LEU    50      66.294  74.002  93.367  1.00  0.00              
ATOM     98  CA  LEU    50      65.092  74.365  92.635  1.00  0.00              
ATOM     99  C   LEU    50      65.411  74.274  91.149  1.00  0.00              
ATOM    100  O   LEU    50      66.413  74.825  90.678  1.00  0.00              
ATOM    101  N   LEU    51      64.551  73.558  90.428  1.00  0.00              
ATOM    102  CA  LEU    51      64.706  73.311  89.001  1.00  0.00              
ATOM    103  C   LEU    51      63.621  73.992  88.190  1.00  0.00              
ATOM    104  O   LEU    51      62.433  73.897  88.512  1.00  0.00              
ATOM    105  N   PHE    52      64.035  74.632  87.103  1.00  0.00              
ATOM    106  CA  PHE    52      63.103  75.362  86.245  1.00  0.00              
ATOM    107  C   PHE    52      63.152  74.906  84.785  1.00  0.00              
ATOM    108  O   PHE    52      64.187  75.045  84.116  1.00  0.00              
ATOM    109  N   GLU    53      62.021  74.398  84.295  1.00  0.00              
ATOM    110  CA  GLU    53      61.920  73.906  82.918  1.00  0.00              
ATOM    111  C   GLU    53      60.952  74.717  82.073  1.00  0.00              
ATOM    112  O   GLU    53      59.766  74.805  82.405  1.00  0.00              
ATOM    113  N   ASN    54      61.457  75.293  80.978  1.00  0.00              
ATOM    114  CA  ASN    54      60.625  76.077  80.068  1.00  0.00              
ATOM    115  C   ASN    54      60.506  75.391  78.712  1.00  0.00              
ATOM    116  O   ASN    54      61.382  75.507  77.845  1.00  0.00              
ATOM    117  N   PRO    55      59.401  74.681  78.539  1.00  0.00              
ATOM    118  CA  PRO    55      59.152  73.960  77.308  1.00  0.00              
ATOM    119  C   PRO    55      58.707  74.817  76.130  1.00  0.00              
ATOM    120  O   PRO    55      58.480  74.285  75.042  1.00  0.00              
ATOM    121  N   LYS    56      58.591  76.130  76.331  1.00  0.00              
ATOM    122  CA  LYS    56      58.155  77.024  75.253  1.00  0.00              
ATOM    123  C   LYS    56      59.207  78.036  74.829  1.00  0.00              
ATOM    124  O   LYS    56      60.311  78.065  75.366  1.00  0.00              
ATOM    125  N   GLY    57      58.848  78.877  73.863  1.00  0.00              
ATOM    126  CA  GLY    57      59.780  79.872  73.364  1.00  0.00              
ATOM    127  C   GLY    57      59.490  81.327  73.700  1.00  0.00              
ATOM    128  O   GLY    57      58.862  82.031  72.913  1.00  0.00              
END
