
#######################################################
#                                                     #
#                        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    9 (  153),  selected    9 , name T0372TS304_1-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS304_1-D1.T0372_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    -       -      M       1           -
LGA    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    P     109      D      11          1.246
LGA    E     110      R      12          1.976
LGA    R     111      D      13          1.733
LGA    F     112      T      14          2.117
LGA    I     113      I      15          1.050
LGA    F     114      T      16          1.340
LGA    T     115      A      17          1.683
LGA    E     116      F      18          3.227
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    D     117      E     110          3.884
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9  126    5.0      9    2.22    11.11      6.271     0.389

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.892616 * X  +  -0.443726 * Y  +   0.079649 * Z  +  -4.628396
  Y_new =  -0.128183 * X  +  -0.080424 * Y  +   0.988484 * Z  +  47.979347
  Z_new =  -0.432211 * X  +  -0.892546 * Y  +  -0.128666 * Z  +  63.327477 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.713966    1.427627  [ DEG:   -98.2030     81.7970 ]
  Theta =   0.446943    2.694650  [ DEG:    25.6079    154.3921 ]
  Phi   =  -0.142629    2.998964  [ DEG:    -8.1720    171.8280 ]
 
# 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: T0372TS304_1-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS304_1-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9  126   5.0    9   2.22   11.11   6.271
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS304_1-D1
PFRMAT TS
TARGET T0372
MODEL 1 REFINED
PARENT 1P62_B
ATOM      1  N   PRO   109      50.974  57.086  10.313  1.00 10.00
ATOM      2  CA  PRO   109      49.623  56.447  10.289  1.00 10.00
ATOM      3  C   PRO   109      49.047  56.174  11.691  1.00 10.00
ATOM      4  O   PRO   109      47.843  56.164  11.878  1.00 10.00
ATOM      5  CB  PRO   109      49.869  55.119   9.554  1.00 10.00
ATOM      6  CG  PRO   109      51.446  54.889   9.632  1.00 10.00
ATOM      7  CD  PRO   109      52.018  56.254   9.651  1.00 10.00
ATOM      8 HA   PRO   109      48.917  57.077   9.704  1.00 10.00
ATOM      9 HB1  PRO   109      49.541  55.198   8.494  1.00 10.00
ATOM     10 HB2  PRO   109      49.332  54.290  10.065  1.00 10.00
ATOM     11 HG1  PRO   109      51.802  54.331   8.737  1.00 10.00
ATOM     12 HG2  PRO   109      51.714  54.343  10.565  1.00 10.00
ATOM     13 HD1  PRO   109      52.199  56.614   8.614  1.00 10.00
ATOM     14 HD2  PRO   109      52.960  56.273  10.243  1.00 10.00
ATOM     15  N   GLU   110      49.904  55.866  12.664  1.00 10.00
ATOM     16  CA  GLU   110      49.451  55.728  14.053  1.00 10.00
ATOM     17  C   GLU   110      48.885  56.999  14.705  1.00 10.00
ATOM     18  O   GLU   110      48.080  56.894  15.667  1.00 10.00
ATOM     19  CB  GLU   110      50.478  54.953  14.938  1.00 10.00
ATOM     20  CG  GLU   110      51.582  55.830  15.491  1.00 10.00
ATOM     21  CD  GLU   110      52.738  56.057  14.508  1.00 10.00
ATOM     22  OE1 GLU   110      52.601  55.836  13.257  1.00 10.00
ATOM     23  OE2 GLU   110      53.793  56.536  14.992  1.00 10.00
ATOM     24 HN   GLU   110      50.794  55.503  12.415  1.00 10.00
ATOM     25 HA   GLU   110      48.571  55.049  14.000  1.00 10.00
ATOM     26 HB1  GLU   110      50.937  54.146  14.325  1.00 10.00
ATOM     27 HB2  GLU   110      49.934  54.488  15.789  1.00 10.00
ATOM     28 HG1  GLU   110      51.150  56.818  15.764  1.00 10.00
ATOM     29 HG2  GLU   110      51.989  55.353  16.411  1.00 10.00
ATOM     30  N   ARG   111      49.235  58.171  14.181  1.00 10.00
ATOM     31  CA  ARG   111      48.726  59.444  14.630  1.00 10.00
ATOM     32  C   ARG   111      47.421  59.837  13.900  1.00 10.00
ATOM     33  O   ARG   111      46.522  60.393  14.513  1.00 10.00
ATOM     34  CB  ARG   111      49.767  60.567  14.477  1.00 10.00
ATOM     35  CG  ARG   111      49.311  62.000  14.876  1.00 10.00
ATOM     36  CD  ARG   111      48.787  62.126  16.291  1.00 10.00
ATOM     37  NE  ARG   111      48.282  63.452  16.616  1.00 10.00
ATOM     38  CZ  ARG   111      47.035  63.887  16.402  1.00 10.00
ATOM     39 HN   ARG   111      49.797  58.162  13.363  1.00 10.00
ATOM     40 HA   ARG   111      48.487  59.352  15.714  1.00 10.00
ATOM     41 HB1  ARG   111      50.651  60.303  15.099  1.00 10.00
ATOM     42 HB2  ARG   111      50.090  60.594  13.413  1.00 10.00
ATOM     43 HG1  ARG   111      48.509  62.321  14.175  1.00 10.00
ATOM     44 HG2  ARG   111      50.177  62.689  14.760  1.00 10.00
ATOM     45 HD1  ARG   111      49.610  61.876  16.996  1.00 10.00
ATOM     46 HD2  ARG   111      47.966  61.388  16.431  1.00 10.00
ATOM     47 HE   ARG   111      48.936  64.112  16.967  1.00 10.00
ATOM     48  NH1 ARG   111      46.100  63.620  17.257  1.00 10.00
ATOM     49  NH2 ARG   111      46.762  64.569  15.336  1.00 10.00
ATOM     50 HH11 ARG   111      46.003  62.681  17.563  1.00 10.00
ATOM     51 HH12 ARG   111      45.290  64.196  17.256  1.00 10.00
ATOM     52 HH21 ARG   111      46.488  64.073  14.521  1.00 10.00
ATOM     53 HH22 ARG   111      47.212  65.447  15.217  1.00 10.00
ATOM     54  N   PHE   112      47.377  59.588  12.591  1.00 10.00
ATOM     55  CA  PHE   112      46.417  60.224  11.684  1.00 10.00
ATOM     56  C   PHE   112      45.396  59.280  10.993  1.00 10.00
ATOM     57  O   PHE   112      44.510  59.800  10.322  1.00 10.00
ATOM     58  CB  PHE   112      47.143  61.092  10.614  1.00 10.00
ATOM     59  CG  PHE   112      47.891  62.297  11.198  1.00 10.00
ATOM     60 HN   PHE   112      48.114  59.054  12.192  1.00 10.00
ATOM     61 HA   PHE   112      45.813  60.927  12.302  1.00 10.00
ATOM     62 HB1  PHE   112      47.871  60.450  10.073  1.00 10.00
ATOM     63 HB2  PHE   112      46.387  61.462   9.887  1.00 10.00
ATOM     64  CD1 PHE   112      49.153  62.509  10.676  1.00 10.00
ATOM     65  CD2 PHE   112      47.324  63.282  11.992  1.00 10.00
ATOM     66  CE1 PHE   112      49.564  63.809  10.477  1.00 10.00
ATOM     67  CE2 PHE   112      47.936  64.532  12.054  1.00 10.00
ATOM     68  CZ  PHE   112      49.138  64.749  11.393  1.00 10.00
ATOM     69 HD1  PHE   112      49.774  61.673  10.365  1.00 10.00
ATOM     70 HD2  PHE   112      46.426  63.082  12.571  1.00 10.00
ATOM     71 HE1  PHE   112      50.105  64.095   9.576  1.00 10.00
ATOM     72 HE2  PHE   112      47.476  65.343  12.612  1.00 10.00
ATOM     73 HZ   PHE   112      49.767  65.603  11.636  1.00 10.00
ATOM     74  N   ILE   113      45.473  57.962  11.153  1.00 10.00
ATOM     75  CA  ILE   113      44.586  57.038  10.420  1.00 10.00
ATOM     76  C   ILE   113      43.139  57.266  10.833  1.00 10.00
ATOM     77  O   ILE   113      42.310  57.297   9.973  1.00 10.00
ATOM     78  CB  ILE   113      44.952  55.577  10.666  1.00 10.00
ATOM     79 HN   ILE   113      46.264  57.587  11.621  1.00 10.00
ATOM     80 HA   ILE   113      44.677  57.246   9.331  1.00 10.00
ATOM     81 HB   ILE   113      45.531  55.211   9.790  1.00 10.00
ATOM     82  CG1 ILE   113      43.716  54.712  10.817  1.00 10.00
ATOM     83 HG11 ILE   113      43.929  53.705  10.390  1.00 10.00
ATOM     84 HG12 ILE   113      42.866  55.172  10.267  1.00 10.00
ATOM     85  CG2 ILE   113      45.826  55.470  11.898  1.00 10.00
ATOM     86 HG21 ILE   113      45.840  54.416  12.253  1.00 10.00
ATOM     87 HG22 ILE   113      45.430  56.131  12.699  1.00 10.00
ATOM     88 HG23 ILE   113      46.862  55.784  11.637  1.00 10.00
ATOM     89  CD1 ILE   113      43.356  54.560  12.279  1.00 10.00
ATOM     90 HD1  ILE   113      44.269  54.681  12.903  1.00 10.00
ATOM     91 HD2  ILE   113      42.924  53.549  12.448  1.00 10.00
ATOM     92 HD3  ILE   113      42.607  55.333  12.558  1.00 10.00
ATOM     93  N   PHE   114      42.849  57.385  12.141  1.00 10.00
ATOM     94  CA  PHE   114      41.440  57.606  12.598  1.00 10.00
ATOM     95  C   PHE   114      40.836  58.876  11.942  1.00 10.00
ATOM     96  O   PHE   114      39.688  58.866  11.409  1.00 10.00
ATOM     97  CB  PHE   114      41.326  57.710  14.109  1.00 10.00
ATOM     98  CG  PHE   114      39.966  58.141  14.567  1.00 10.00
ATOM     99  CD1 PHE   114      38.965  57.209  14.770  1.00 10.00
ATOM    100  CD2 PHE   114      39.679  59.465  14.760  1.00 10.00
ATOM    101  CE1 PHE   114      37.618  57.638  15.159  1.00 10.00
ATOM    102  CE2 PHE   114      38.426  59.871  15.163  1.00 10.00
ATOM    103  CZ  PHE   114      37.415  58.965  15.366  1.00 10.00
ATOM    104 HN   PHE   114      43.589  57.565  12.778  1.00 10.00
ATOM    105 HA   PHE   114      40.831  56.734  12.270  1.00 10.00
ATOM    106 HB1  PHE   114      42.076  58.447  14.473  1.00 10.00
ATOM    107 HB2  PHE   114      41.556  56.717  14.553  1.00 10.00
ATOM    108 HD1  PHE   114      39.178  56.150  14.641  1.00 10.00
ATOM    109 HD2  PHE   114      40.454  60.209  14.591  1.00 10.00
ATOM    110 HE1  PHE   114      36.811  56.919  15.278  1.00 10.00
ATOM    111 HE2  PHE   114      38.235  60.929  15.324  1.00 10.00
ATOM    112 HZ   PHE   114      36.440  59.314  15.696  1.00 10.00
ATOM    113  N   THR   115      41.604  59.965  11.962  1.00 10.00
ATOM    114  CA  THR   115      41.100  61.245  11.457  1.00 10.00
ATOM    115  C   THR   115      40.850  61.151   9.935  1.00 10.00
ATOM    116  O   THR   115      39.829  61.609   9.422  1.00 10.00
ATOM    117  CB  THR   115      42.142  62.334  11.763  1.00 10.00
ATOM    118  OG1 THR   115      42.302  62.458  13.174  1.00 10.00
ATOM    119  CG2 THR   115      41.770  63.670  11.260  1.00 10.00
ATOM    120 HN   THR   115      42.420  59.963  12.528  1.00 10.00
ATOM    121 HA   THR   115      40.146  61.494  11.972  1.00 10.00
ATOM    122 HB   THR   115      43.116  62.037  11.311  1.00 10.00
ATOM    123 HG1  THR   115      42.693  63.406  13.307  1.00 10.00
ATOM    124 HG21 THR   115      41.961  64.429  12.051  1.00 10.00
ATOM    125 HG22 THR   115      42.379  63.911  10.360  1.00 10.00
ATOM    126 HG23 THR   115      40.691  63.678  10.991  1.00 10.00
ATOM    127  N   GLU   116      41.845  60.589   9.237  1.00 10.00
ATOM    128  CA  GLU   116      41.723  60.333   7.814  1.00 10.00
ATOM    129  C   GLU   116      40.510  59.466   7.457  1.00 10.00
ATOM    130  O   GLU   116      39.664  59.816   6.569  1.00 10.00
ATOM    131  CB  GLU   116      43.055  59.780   7.182  1.00 10.00
ATOM    132  CG  GLU   116      42.901  59.508   5.704  1.00 10.00
ATOM    133 HN   GLU   116      42.588  60.157   9.734  1.00 10.00
ATOM    134 HA   GLU   116      41.541  61.319   7.331  1.00 10.00
ATOM    135 HB1  GLU   116      43.336  58.835   7.698  1.00 10.00
ATOM    136 HB2  GLU   116      43.865  60.528   7.330  1.00 10.00
ATOM    137 HG1  GLU   116      43.816  59.838   5.164  1.00 10.00
ATOM    138 HG2  GLU   116      42.738  58.420   5.537  1.00 10.00
ATOM    139  CD  GLU   116      41.724  60.274   5.210  1.00 10.00
ATOM    140  OE1 GLU   116      41.884  61.230   4.334  1.00 10.00
ATOM    141  OE2 GLU   116      40.527  59.996   5.664  1.00 10.00
ATOM    142  N   ASP   117      15.408  53.224  -8.339  1.00 10.00
ATOM    143  CA  ASP   117      15.341  53.721  -9.769  1.00 10.00
ATOM    144  C   ASP   117      16.723  53.844 -10.426  1.00 10.00
ATOM    145  O   ASP   117      16.962  53.308 -11.500  1.00 10.00
ATOM    146  CB  ASP   117      14.650  55.096  -9.830  1.00 10.00
ATOM    147  CG  ASP   117      13.339  55.122 -10.631  1.00 10.00
ATOM    148 HN   ASP   117      14.666  52.696  -7.942  1.00 10.00
ATOM    149 HA   ASP   117      14.737  53.000 -10.363  1.00 10.00
ATOM    150 HB1  ASP   117      14.433  55.427  -8.791  1.00 10.00
ATOM    151 HB2  ASP   117      15.356  55.823 -10.290  1.00 10.00
ATOM    152  OD1 ASP   117      12.313  54.416 -10.228  1.00 10.00
ATOM    153  OD2 ASP   117      13.248  55.849 -11.714  1.00 10.00
TER
END
