
#######################################################
#                                                     #
#                        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   18 (  145),  selected   18 , name T0378TS021_1-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS021_1-D1.T0378_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    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      K       8           -
LGA    -       -      F       9           -
LGA    -       -      L      10           -
LGA    -       -      R      11           -
LGA    -       -      S      12           -
LGA    -       -      L      13           -
LGA    -       -      R      14           -
LGA    -       -      E      15           -
LGA    -       -      R      16           -
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    -       -      R      41           -
LGA    -       -      C      42           -
LGA    F      72      R      43          1.614
LGA    K      73      M      44          2.320
LGA    -       -      L      45           -
LGA    -       -      V      46           -
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    R      74      E      62          1.631
LGA    I      75      V      63          1.467
LGA    S      76      V      64          1.275
LGA    T      77      E      65          1.541
LGA    Q      78      L      66          1.990
LGA    T      79      P      67          1.841
LGA    T      80      E      68          1.152
LGA    P      81      S      69          3.308
LGA    Q      82      F      70          3.875
LGA    P      83      D      71          3.988
LGA    L      84      F      72          2.237
LGA    M      85      K      73          2.545
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    A      86      T      77          3.264
LGA    V      87      Q      78          5.053
LGA    F      88      T      79          0.522
LGA    D      89      T      80          2.142
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   18   89    5.0     18    2.58     0.00     14.639     0.672

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.211134 * X  +   0.661268 * Y  +   0.719824 * Z  + -17.712196
  Y_new =  -0.732027 * X  +  -0.594980 * Y  +   0.331866 * Z  +  18.142401
  Z_new =   0.647734 * X  +  -0.456863 * Y  +   0.609686 * Z  +  34.143734 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.643079    2.498514  [ DEG:   -36.8457    143.1543 ]
  Theta =  -0.704606   -2.436986  [ DEG:   -40.3710   -139.6290 ]
  Phi   =  -1.851599    1.289993  [ DEG:  -106.0888     73.9112 ]
 
# 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: T0378TS021_1-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS021_1-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   18   89   5.0   18   2.58    0.00  14.639
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS021_1-D1
PFRMAT TS
TARGET T0378
MODEL 1
PARENT N/A
ATOM      1  N   PHE    72       7.417  21.460  57.508  1.00 31.84       1SG   2
ATOM      2  CA  PHE    72       6.144  22.120  57.885  1.00 31.84       1SG   3
ATOM      3  CB  PHE    72       6.377  23.612  58.187  1.00 31.84       1SG   4
ATOM      4  CG  PHE    72       7.232  23.731  59.404  1.00 31.84       1SG   5
ATOM      5  CD1 PHE    72       8.604  23.675  59.304  1.00 31.84       1SG   6
ATOM      6  CD2 PHE    72       6.659  23.904  60.642  1.00 31.84       1SG   7
ATOM      7  CE1 PHE    72       9.389  23.789  60.429  1.00 31.84       1SG   8
ATOM      8  CE2 PHE    72       7.438  24.019  61.768  1.00 31.84       1SG   9
ATOM      9  CZ  PHE    72       8.807  23.960  61.661  1.00 31.84       1SG  10
ATOM     10  C   PHE    72       5.171  22.024  56.760  1.00 31.84       1SG  11
ATOM     11  O   PHE    72       5.556  22.060  55.591  1.00 31.84       1SG  12
ATOM     12  N   LYS    73       3.875  21.873  57.087  1.00 75.57       1SG  13
ATOM     13  CA  LYS    73       2.912  21.778  56.035  1.00 75.57       1SG  14
ATOM     14  CB  LYS    73       2.279  20.381  55.931  1.00 75.57       1SG  15
ATOM     15  CG  LYS    73       1.532  20.133  54.621  1.00 75.57       1SG  16
ATOM     16  CD  LYS    73       1.274  18.649  54.359  1.00 75.57       1SG  17
ATOM     17  CE  LYS    73       0.701  18.351  52.972  1.00 75.57       1SG  18
ATOM     18  NZ  LYS    73       0.685  16.891  52.738  1.00 75.57       1SG  19
ATOM     19  C   LYS    73       1.825  22.756  56.331  1.00 75.57       1SG  20
ATOM     20  O   LYS    73       1.158  22.674  57.361  1.00 75.57       1SG  21
ATOM     21  N   ARG    74       1.633  23.730  55.423  1.00125.75       1SG  22
ATOM     22  CA  ARG    74       0.607  24.704  55.624  1.00125.75       1SG  23
ATOM     23  CB  ARG    74       1.169  26.034  56.157  1.00125.75       1SG  24
ATOM     24  CG  ARG    74       1.817  25.888  57.539  1.00125.75       1SG  25
ATOM     25  CD  ARG    74       2.709  27.065  57.941  1.00125.75       1SG  26
ATOM     26  NE  ARG    74       1.840  28.262  58.103  1.00125.75       1SG  27
ATOM     27  CZ  ARG    74       2.400  29.457  58.450  1.00125.75       1SG  28
ATOM     28  NH1 ARG    74       3.746  29.539  58.665  1.00125.75       1SG  29
ATOM     29  NH2 ARG    74       1.615  30.567  58.580  1.00125.75       1SG  30
ATOM     30  C   ARG    74       0.030  24.962  54.273  1.00125.75       1SG  31
ATOM     31  O   ARG    74       0.760  24.990  53.283  1.00125.75       1SG  32
ATOM     32  N   ILE    75      -1.302  25.130  54.180  1.00 97.38       1SG  33
ATOM     33  CA  ILE    75      -1.840  25.399  52.883  1.00 97.38       1SG  34
ATOM     34  CB  ILE    75      -2.709  24.299  52.344  1.00 97.38       1SG  35
ATOM     35  CG2 ILE    75      -3.998  24.235  53.179  1.00 97.38       1SG  36
ATOM     36  CG1 ILE    75      -2.948  24.509  50.840  1.00 97.38       1SG  37
ATOM     37  CD1 ILE    75      -3.528  23.278  50.149  1.00 97.38       1SG  38
ATOM     38  C   ILE    75      -2.661  26.644  52.948  1.00 97.38       1SG  39
ATOM     39  O   ILE    75      -3.453  26.836  53.869  1.00 97.38       1SG  40
ATOM     40  N   SER    76      -2.464  27.549  51.969  1.00 41.84       1SG  41
ATOM     41  CA  SER    76      -3.256  28.740  51.940  1.00 41.84       1SG  42
ATOM     42  CB  SER    76      -2.493  29.999  52.394  1.00 41.84       1SG  43
ATOM     43  OG  SER    76      -2.065  29.860  53.741  1.00 41.84       1SG  44
ATOM     44  C   SER    76      -3.654  28.960  50.516  1.00 41.84       1SG  45
ATOM     45  O   SER    76      -2.823  28.891  49.611  1.00 41.84       1SG  46
ATOM     46  N   THR    77      -4.952  29.234  50.286  1.00128.71       1SG  47
ATOM     47  CA  THR    77      -5.423  29.487  48.959  1.00128.71       1SG  48
ATOM     48  CB  THR    77      -6.913  29.398  48.824  1.00128.71       1SG  49
ATOM     49  OG1 THR    77      -7.537  30.382  49.636  1.00128.71       1SG  50
ATOM     50  CG2 THR    77      -7.367  27.993  49.257  1.00128.71       1SG  51
ATOM     51  C   THR    77      -5.042  30.894  48.649  1.00128.71       1SG  52
ATOM     52  O   THR    77      -4.897  31.724  49.542  1.00128.71       1SG  53
ATOM     53  N   GLN    78      -4.852  31.200  47.360  1.00124.42       1SG  54
ATOM     54  CA  GLN    78      -4.482  32.528  46.995  1.00124.42       1SG  55
ATOM     55  CB  GLN    78      -3.080  32.649  46.365  1.00124.42       1SG  56
ATOM     56  CG  GLN    78      -2.566  34.092  46.307  1.00124.42       1SG  57
ATOM     57  CD  GLN    78      -1.257  34.113  45.536  1.00124.42       1SG  58
ATOM     58  OE1 GLN    78      -1.001  33.240  44.710  1.00124.42       1SG  59
ATOM     59  NE2 GLN    78      -0.407  35.138  45.814  1.00124.42       1SG  60
ATOM     60  C   GLN    78      -5.486  32.941  45.983  1.00124.42       1SG  61
ATOM     61  O   GLN    78      -6.632  32.494  46.006  1.00124.42       1SG  62
ATOM     62  N   THR    79      -5.067  33.797  45.041  1.00156.20       1SG  63
ATOM     63  CA  THR    79      -5.958  34.247  44.025  1.00156.20       1SG  64
ATOM     64  CB  THR    79      -5.456  35.497  43.352  1.00156.20       1SG  65
ATOM     65  OG1 THR    79      -5.184  36.484  44.337  1.00156.20       1SG  66
ATOM     66  CG2 THR    79      -6.532  36.054  42.402  1.00156.20       1SG  67
ATOM     67  C   THR    79      -5.982  33.103  43.062  1.00156.20       1SG  68
ATOM     68  O   THR    79      -5.650  31.979  43.429  1.00156.20       1SG  69
ATOM     69  N   THR    80      -6.430  33.308  41.820  1.00103.63       1SG  70
ATOM     70  CA  THR    80      -6.475  32.171  40.967  1.00103.63       1SG  71
ATOM     71  CB  THR    80      -7.116  32.463  39.635  1.00103.63       1SG  72
ATOM     72  OG1 THR    80      -8.442  32.927  39.831  1.00103.63       1SG  73
ATOM     73  CG2 THR    80      -7.124  31.182  38.783  1.00103.63       1SG  74
ATOM     74  C   THR    80      -5.083  31.634  40.765  1.00103.63       1SG  75
ATOM     75  O   THR    80      -4.910  30.433  40.938  1.00103.63       1SG  76
ATOM     76  N   PRO    81      -4.075  32.427  40.456  1.00166.04       1SG  77
ATOM     77  CA  PRO    81      -2.761  31.861  40.201  1.00166.04       1SG  78
ATOM     78  CD  PRO    81      -4.316  33.590  39.613  1.00166.04       1SG  79
ATOM     79  CB  PRO    81      -2.030  32.865  39.313  1.00166.04       1SG  80
ATOM     80  CG  PRO    81      -3.156  33.630  38.606  1.00166.04       1SG  81
ATOM     81  C   PRO    81      -1.953  31.525  41.424  1.00166.04       1SG  82
ATOM     82  O   PRO    81      -2.302  31.974  42.514  1.00166.04       1SG  83
ATOM     83  N   GLN    82      -0.862  30.733  41.265  1.00231.12       1SG  84
ATOM     84  CA  GLN    82      -0.007  30.442  42.383  1.00231.12       1SG  85
ATOM     85  CB  GLN    82       0.366  28.968  42.631  1.00231.12       1SG  86
ATOM     86  CG  GLN    82      -0.684  28.179  43.412  1.00231.12       1SG  87
ATOM     87  CD  GLN    82       0.015  26.955  43.998  1.00231.12       1SG  88
ATOM     88  OE1 GLN    82       0.879  26.347  43.367  1.00231.12       1SG  89
ATOM     89  NE2 GLN    82      -0.350  26.605  45.261  1.00231.12       1SG  90
ATOM     90  C   GLN    82       1.290  31.170  42.255  1.00231.12       1SG  91
ATOM     91  O   GLN    82       1.742  31.608  41.193  1.00231.12       1SG  92
ATOM     92  N   PRO    83       1.851  31.282  43.424  1.00154.01       1SG  93
ATOM     93  CA  PRO    83       3.090  31.968  43.668  1.00154.01       1SG  94
ATOM     94  CD  PRO    83       1.007  31.261  44.608  1.00154.01       1SG  95
ATOM     95  CB  PRO    83       3.159  32.192  45.178  1.00154.01       1SG  96
ATOM     96  CG  PRO    83       1.693  32.182  45.628  1.00154.01       1SG  97
ATOM     97  C   PRO    83       4.304  31.255  43.169  1.00154.01       1SG  98
ATOM     98  O   PRO    83       5.383  31.828  43.315  1.00154.01       1SG  99
ATOM     99  N   LEU    84       4.169  30.034  42.600  1.00246.98       1SG 100
ATOM    100  CA  LEU    84       5.324  29.252  42.235  1.00246.98       1SG 101
ATOM    101  CB  LEU    84       4.997  27.974  41.444  1.00246.98       1SG 102
ATOM    102  CG  LEU    84       4.289  26.912  42.308  1.00246.98       1SG 103
ATOM    103  CD1 LEU    84       4.045  25.612  41.532  1.00246.98       1SG 104
ATOM    104  CD2 LEU    84       5.050  26.675  43.622  1.00246.98       1SG 105
ATOM    105  C   LEU    84       6.292  30.079  41.454  1.00246.98       1SG 106
ATOM    106  O   LEU    84       6.026  30.548  40.349  1.00246.98       1SG 107
ATOM    107  N   MET    85       7.454  30.277  42.100  1.00144.30       1SG 108
ATOM    108  CA  MET    85       8.543  31.113  41.696  1.00144.30       1SG 109
ATOM    109  CB  MET    85       9.600  31.200  42.806  1.00144.30       1SG 110
ATOM    110  CG  MET    85      10.745  32.174  42.542  1.00144.30       1SG 111
ATOM    111  SD  MET    85      11.960  32.244  43.894  1.00144.30       1SG 112
ATOM    112  CE  MET    85      12.947  33.574  43.153  1.00144.30       1SG 113
ATOM    113  C   MET    85       9.215  30.622  40.458  1.00144.30       1SG 114
ATOM    114  O   MET    85       9.515  31.428  39.579  1.00144.30       1SG 115
ATOM    115  N   ALA    86       9.446  29.298  40.343  1.00216.05       1SG 116
ATOM    116  CA  ALA    86      10.242  28.817  39.248  1.00216.05       1SG 117
ATOM    117  CB  ALA    86      10.410  27.287  39.232  1.00216.05       1SG 118
ATOM    118  C   ALA    86       9.636  29.259  37.957  1.00216.05       1SG 119
ATOM    119  O   ALA    86       8.509  28.910  37.613  1.00216.05       1SG 120
ATOM    120  N   VAL    87      10.422  30.055  37.211  1.00165.39       1SG 121
ATOM    121  CA  VAL    87      10.014  30.651  35.976  1.00165.39       1SG 122
ATOM    122  CB  VAL    87      11.069  31.529  35.370  1.00165.39       1SG 123
ATOM    123  CG1 VAL    87      11.358  32.684  36.341  1.00165.39       1SG 124
ATOM    124  CG2 VAL    87      12.298  30.664  35.038  1.00165.39       1SG 125
ATOM    125  C   VAL    87       9.764  29.543  35.026  1.00165.39       1SG 126
ATOM    126  O   VAL    87       8.892  29.636  34.164  1.00165.39       1SG 127
ATOM    127  N   PHE    88      10.531  28.454  35.214  1.00252.20       1SG 128
ATOM    128  CA  PHE    88      10.550  27.314  34.352  1.00252.20       1SG 129
ATOM    129  CB  PHE    88      11.247  26.089  34.971  1.00252.20       1SG 130
ATOM    130  CG  PHE    88      11.596  25.152  33.863  1.00252.20       1SG 131
ATOM    131  CD1 PHE    88      12.778  25.310  33.179  1.00252.20       1SG 132
ATOM    132  CD2 PHE    88      10.765  24.121  33.500  1.00252.20       1SG 133
ATOM    133  CE1 PHE    88      13.113  24.453  32.159  1.00252.20       1SG 134
ATOM    134  CE2 PHE    88      11.093  23.260  32.478  1.00252.20       1SG 135
ATOM    135  CZ  PHE    88      12.274  23.427  31.799  1.00252.20       1SG 136
ATOM    136  C   PHE    88       9.149  26.937  34.021  1.00252.20       1SG 137
ATOM    137  O   PHE    88       8.222  27.115  34.810  1.00252.20       1SG 138
ATOM    138  N   ASP    89       8.979  26.452  32.787  1.00102.71       1SG 139
ATOM    139  CA  ASP    89       7.708  26.091  32.247  1.00102.71       1SG 140
ATOM    140  CB  ASP    89       7.730  25.758  30.750  1.00102.71       1SG 141
ATOM    141  CG  ASP    89       7.697  27.093  30.017  1.00102.71       1SG 142
ATOM    142  OD1 ASP    89       7.514  28.137  30.702  1.00102.71       1SG 143
ATOM    143  OD2 ASP    89       7.847  27.091  28.767  1.00102.71       1SG 144
ATOM    144  C   ASP    89       7.135  24.938  33.001  1.00102.71       1SG 145
ATOM    145  O   ASP    89       5.942  24.661  32.894  1.00102.71       1SG 146
TER
END
