
#######################################################
#                                                     #
#                        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   20 (  150),  selected   20 , name T0343TS319_1
# Molecule2: number of CA atoms   94 (  282),  selected   94 , name T0343.pdb
# PARAMETERS: T0343TS319_1.T0343.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    V      78      T       2           -
LGA    -       -      W       3           -
LGA    -       -      R       4           -
LGA    -       -      E       5           -
LGA    -       -      I       6           -
LGA    -       -      L       7           -
LGA    -       -      R       8           -
LGA    -       -      K       9           -
LGA    -       -      E      10           -
LGA    -       -      G      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      D      14           -
LGA    -       -      L      15           -
LGA    -       -      G      16           -
LGA    -       -      E      17           -
LGA    -       -      F      18           -
LGA    -       -      I      19           -
LGA    -       -      V      20           -
LGA    -       -      E      21           -
LGA    -       -      L      22           -
LGA    -       -      V      23           -
LGA    -       -      Y      24           -
LGA    -       -      I      25           -
LGA    -       -      D      26           -
LGA    K      79      C      27          4.213
LGA    L      80      P      28          2.524
LGA    -       -      C      29           -
LGA    -       -      E      30           -
LGA    V      81      P      31          3.819
LGA    S      82      I      32          0.961
LGA    L      83      P      33          0.443
LGA    D      84      P      34          0.963
LGA    G      85      T      35          0.590
LGA    P      86      L      36          2.347
LGA    -       -      A      37           -
LGA    -       -      I      38           -
LGA    -       -      Y      39           -
LGA    -       -      D      40           -
LGA    -       -      K      41           -
LGA    -       -      K      42           -
LGA    -       -      G      43           -
LGA    -       -      D      44           -
LGA    -       -      E      45           -
LGA    -       -      W      46           -
LGA    -       -      Y      47           -
LGA    -       -      K      48           -
LGA    -       -      V      49           -
LGA    -       -      E      50           -
LGA    -       -      E      51           -
LGA    -       -      A      52           -
LGA    -       -      P      53           -
LGA    -       -      N      54           -
LGA    -       -      V      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      63           -
LGA    -       -      W      64           -
LGA    -       -      A      65           -
LGA    -       -      I      66           -
LGA    A      87      E      67          3.945
LGA    P      88      V      68          1.249
LGA    P      89      L      69          4.089
LGA    K      90      E      70          0.785
LGA    -       -      R      71           -
LGA    -       -      I      72           -
LGA    V      91      R      73          1.093
LGA    M      92      D      74          1.742
LGA    K      93      G      75          3.901
LGA    -       -      E      76           -
LGA    R      94      N      77          2.565
LGA    L      95      V      78           -
LGA    S      96      K      79           -
LGA    L      97      L      80           -
LGA    -       -      V      81           -
LGA    -       -      S      82           -
LGA    -       -      L      83           -
LGA    -       -      D      84           -
LGA    -       -      G      85           -
LGA    -       -      P      86           -
LGA    -       -      A      87           -
LGA    -       -      P      88           -
LGA    -       -      P      89           -
LGA    -       -      K      90           -
LGA    -       -      V      91           -
LGA    -       -      M      92           -
LGA    -       -      K      93           -
LGA    -       -      R      94           -
LGA    -       -      L      95           -
LGA    -       -      S      96           -
LGA    -       -      L      97           -
LGA    -       -      A      98           -
LGA    -       -      L      99           -
LGA    -       -      Q     100           -
LGA    -       -      K     101           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   20   94    5.0     16    2.59     0.00     12.731     0.595

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.956006 * X  +   0.205862 * Y  +  -0.208981 * Z  + -37.406807
  Y_new =  -0.043359 * X  +  -0.605414 * Y  +  -0.794729 * Z  + 113.889427
  Z_new =  -0.290125 * X  +   0.768827 * Y  +  -0.569853 * Z  +  -0.849072 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.208640   -0.932953  [ DEG:   126.5458    -53.4542 ]
  Theta =   0.294357    2.847235  [ DEG:    16.8654    163.1346 ]
  Phi   =  -0.045324    3.096269  [ DEG:    -2.5969    177.4032 ]
 
# 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: T0343TS319_1                                  
REMARK     2: T0343.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0343TS319_1.T0343.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20   94   5.0   16   2.59    0.00  12.731
REMARK  ---------------------------------------------------------- 
MOLECULE T0343TS319_1
PFRMAT TS
TARGET T0343
MODEL 1
PARENT N/A
ATOM      1  N   VAL    78      23.388  47.070  10.657  1.00 14.93       1SG   2
ATOM      2  CA  VAL    78      24.719  46.476  10.900  1.00 14.93       1SG   3
ATOM      3  CB  VAL    78      24.802  45.968  12.313  1.00 14.93       1SG   4
ATOM      4  CG1 VAL    78      26.190  45.356  12.554  1.00 14.93       1SG   5
ATOM      5  CG2 VAL    78      24.465  47.135  13.254  1.00 14.93       1SG   6
ATOM      6  C   VAL    78      24.886  45.349   9.932  1.00 14.93       1SG   7
ATOM      7  O   VAL    78      25.049  45.573   8.734  1.00 14.93       1SG   8
ATOM      8  N   LYS    79      24.851  44.098  10.427  1.00 77.34       1SG   9
ATOM      9  CA  LYS    79      24.962  42.971   9.552  1.00 77.34       1SG  10
ATOM     10  CB  LYS    79      26.044  41.960   9.950  1.00 77.34       1SG  11
ATOM     11  CG  LYS    79      26.104  40.769   8.995  1.00 77.34       1SG  12
ATOM     12  CD  LYS    79      27.278  39.817   9.250  1.00 77.34       1SG  13
ATOM     13  CE  LYS    79      28.644  40.400   8.881  1.00 77.34       1SG  14
ATOM     14  NZ  LYS    79      29.307  40.945  10.089  1.00 77.34       1SG  15
ATOM     15  C   LYS    79      23.663  42.246   9.639  1.00 77.34       1SG  16
ATOM     16  O   LYS    79      22.910  42.417  10.591  1.00 77.34       1SG  17
ATOM     17  N   LEU    80      23.353  41.427   8.617  1.00132.52       1SG  18
ATOM     18  CA  LEU    80      22.126  40.694   8.671  1.00132.52       1SG  19
ATOM     19  CB  LEU    80      21.320  40.723   7.363  1.00132.52       1SG  20
ATOM     20  CG  LEU    80      20.001  39.928   7.428  1.00132.52       1SG  21
ATOM     21  CD2 LEU    80      19.402  39.740   6.025  1.00132.52       1SG  22
ATOM     22  CD1 LEU    80      19.010  40.551   8.423  1.00132.52       1SG  23
ATOM     23  C   LEU    80      22.467  39.265   8.906  1.00132.52       1SG  24
ATOM     24  O   LEU    80      23.447  38.757   8.367  1.00132.52       1SG  25
ATOM     25  N   VAL    81      21.668  38.584   9.749  1.00 32.48       1SG  26
ATOM     26  CA  VAL    81      21.881  37.182   9.948  1.00 32.48       1SG  27
ATOM     27  CB  VAL    81      21.824  36.767  11.390  1.00 32.48       1SG  28
ATOM     28  CG1 VAL    81      21.903  35.232  11.469  1.00 32.48       1SG  29
ATOM     29  CG2 VAL    81      22.949  37.488  12.152  1.00 32.48       1SG  30
ATOM     30  C   VAL    81      20.748  36.502   9.253  1.00 32.48       1SG  31
ATOM     31  O   VAL    81      19.584  36.732   9.578  1.00 32.48       1SG  32
ATOM     32  N   SER    82      21.063  35.643   8.267  1.00 62.35       1SG  33
ATOM     33  CA  SER    82      20.022  34.971   7.542  1.00 62.35       1SG  34
ATOM     34  CB  SER    82      20.484  34.391   6.192  1.00 62.35       1SG  35
ATOM     35  OG  SER    82      19.401  33.745   5.537  1.00 62.35       1SG  36
ATOM     36  C   SER    82      19.540  33.841   8.389  1.00 62.35       1SG  37
ATOM     37  O   SER    82      20.207  33.430   9.338  1.00 62.35       1SG  38
ATOM     38  N   LEU    83      18.340  33.318   8.072  1.00 87.34       1SG  39
ATOM     39  CA  LEU    83      17.849  32.223   8.845  1.00 87.34       1SG  40
ATOM     40  CB  LEU    83      16.379  31.870   8.556  1.00 87.34       1SG  41
ATOM     41  CG  LEU    83      15.849  30.687   9.390  1.00 87.34       1SG  42
ATOM     42  CD2 LEU    83      14.475  30.226   8.877  1.00 87.34       1SG  43
ATOM     43  CD1 LEU    83      15.838  31.014  10.891  1.00 87.34       1SG  44
ATOM     44  C   LEU    83      18.694  31.062   8.473  1.00 87.34       1SG  45
ATOM     45  O   LEU    83      18.846  30.729   7.300  1.00 87.34       1SG  46
ATOM     46  N   ASP    84      19.277  30.417   9.491  1.00 61.15       1SG  47
ATOM     47  CA  ASP    84      20.175  29.334   9.245  1.00 61.15       1SG  48
ATOM     48  CB  ASP    84      21.225  29.158  10.351  1.00 61.15       1SG  49
ATOM     49  CG  ASP    84      22.214  30.312  10.253  1.00 61.15       1SG  50
ATOM     50  OD1 ASP    84      22.232  30.980   9.184  1.00 61.15       1SG  51
ATOM     51  OD2 ASP    84      22.966  30.539  11.238  1.00 61.15       1SG  52
ATOM     52  C   ASP    84      19.383  28.075   9.168  1.00 61.15       1SG  53
ATOM     53  O   ASP    84      18.194  28.078   8.852  1.00 61.15       1SG  54
ATOM     54  N   GLY    85      20.071  26.953   9.439  1.00 65.70       1SG  55
ATOM     55  CA  GLY    85      19.486  25.651   9.402  1.00 65.70       1SG  56
ATOM     56  C   GLY    85      19.001  25.355  10.784  1.00 65.70       1SG  57
ATOM     57  O   GLY    85      18.201  26.102  11.347  1.00 65.70       1SG  58
ATOM     58  N   PRO    86      19.461  24.258  11.324  1.00155.01       1SG  59
ATOM     59  CA  PRO    86      19.042  23.845  12.636  1.00155.01       1SG  60
ATOM     60  CD  PRO    86      19.827  23.126  10.488  1.00155.01       1SG  61
ATOM     61  CB  PRO    86      19.517  22.404  12.791  1.00155.01       1SG  62
ATOM     62  CG  PRO    86      19.547  21.878  11.343  1.00155.01       1SG  63
ATOM     63  C   PRO    86      19.508  24.752  13.731  1.00155.01       1SG  64
ATOM     64  O   PRO    86      20.576  25.347  13.605  1.00155.01       1SG  65
ATOM     65  N   ALA    87      18.682  24.894  14.792  1.00 56.69       1SG  66
ATOM     66  CA  ALA    87      18.934  25.738  15.931  1.00 56.69       1SG  67
ATOM     67  CB  ALA    87      17.701  25.877  16.835  1.00 56.69       1SG  68
ATOM     68  C   ALA    87      20.083  25.256  16.773  1.00 56.69       1SG  69
ATOM     69  O   ALA    87      20.931  26.070  17.139  1.00 56.69       1SG  70
ATOM     70  N   PRO    88      20.185  24.003  17.144  1.00 78.06       1SG  71
ATOM     71  CA  PRO    88      19.199  22.993  16.874  1.00 78.06       1SG  72
ATOM     72  CD  PRO    88      21.495  23.432  17.408  1.00 78.06       1SG  73
ATOM     73  CB  PRO    88      19.916  21.651  17.007  1.00 78.06       1SG  74
ATOM     74  CG  PRO    88      21.203  21.971  17.783  1.00 78.06       1SG  75
ATOM     75  C   PRO    88      18.030  23.116  17.795  1.00 78.06       1SG  76
ATOM     76  O   PRO    88      18.163  23.683  18.880  1.00 78.06       1SG  77
ATOM     77  N   PRO    89      16.914  22.617  17.356  1.00 72.56       1SG  78
ATOM     78  CA  PRO    89      15.711  22.668  18.141  1.00 72.56       1SG  79
ATOM     79  CD  PRO    89      16.635  22.581  15.932  1.00 72.56       1SG  80
ATOM     80  CB  PRO    89      14.549  22.590  17.145  1.00 72.56       1SG  81
ATOM     81  CG  PRO    89      15.185  22.083  15.843  1.00 72.56       1SG  82
ATOM     82  C   PRO    89      15.707  21.586  19.171  1.00 72.56       1SG  83
ATOM     83  O   PRO    89      16.564  20.702  19.119  1.00 72.56       1SG  84
ATOM     84  N   LYS    90      14.750  21.644  20.117  1.00122.66       1SG  85
ATOM     85  CA  LYS    90      14.652  20.661  21.153  1.00122.66       1SG  86
ATOM     86  CB  LYS    90      13.479  20.891  22.120  1.00122.66       1SG  87
ATOM     87  CG  LYS    90      13.752  21.948  23.191  1.00122.66       1SG  88
ATOM     88  CD  LYS    90      14.871  21.549  24.155  1.00122.66       1SG  89
ATOM     89  CE  LYS    90      14.973  22.464  25.371  1.00122.66       1SG  90
ATOM     90  NZ  LYS    90      13.696  22.436  26.120  1.00122.66       1SG  91
ATOM     91  C   LYS    90      14.449  19.329  20.518  1.00122.66       1SG  92
ATOM     92  O   LYS    90      14.048  19.221  19.361  1.00122.66       1SG  93
ATOM     93  N   VAL    91      14.771  18.270  21.282  1.00 31.49       1SG  94
ATOM     94  CA  VAL    91      14.640  16.939  20.781  1.00 31.49       1SG  95
ATOM     95  CB  VAL    91      15.228  15.901  21.689  1.00 31.49       1SG  96
ATOM     96  CG1 VAL    91      14.935  14.513  21.093  1.00 31.49       1SG  97
ATOM     97  CG2 VAL    91      16.722  16.202  21.890  1.00 31.49       1SG  98
ATOM     98  C   VAL    91      13.190  16.625  20.663  1.00 31.49       1SG  99
ATOM     99  O   VAL    91      12.402  16.880  21.574  1.00 31.49       1SG 100
ATOM    100  N   MET    92      12.801  16.083  19.500  1.00106.28       1SG 101
ATOM    101  CA  MET    92      11.452  15.660  19.283  1.00106.28       1SG 102
ATOM    102  CB  MET    92      11.186  15.257  17.820  1.00106.28       1SG 103
ATOM    103  CG  MET    92      11.029  16.461  16.881  1.00106.28       1SG 104
ATOM    104  SD  MET    92      12.523  17.459  16.606  1.00106.28       1SG 105
ATOM    105  CE  MET    92      11.623  18.820  15.803  1.00106.28       1SG 106
ATOM    106  C   MET    92      11.189  14.486  20.175  1.00106.28       1SG 107
ATOM    107  O   MET    92      10.099  14.348  20.728  1.00106.28       1SG 108
ATOM    108  N   LYS    93      12.207  13.622  20.352  1.00120.22       1SG 109
ATOM    109  CA  LYS    93      12.107  12.402  21.113  1.00120.22       1SG 110
ATOM    110  CB  LYS    93      13.386  11.552  21.019  1.00120.22       1SG 111
ATOM    111  CG  LYS    93      13.710  11.034  19.617  1.00120.22       1SG 112
ATOM    112  CD  LYS    93      12.766   9.935  19.136  1.00120.22       1SG 113
ATOM    113  CE  LYS    93      13.215   8.534  19.555  1.00120.22       1SG 114
ATOM    114  NZ  LYS    93      12.239   7.526  19.086  1.00120.22       1SG 115
ATOM    115  C   LYS    93      11.927  12.717  22.568  1.00120.22       1SG 116
ATOM    116  O   LYS    93      12.358  13.762  23.056  1.00120.22       1SG 117
ATOM    117  N   ARG    94      11.246  11.804  23.295  1.00107.62       1SG 118
ATOM    118  CA  ARG    94      11.066  11.950  24.711  1.00107.62       1SG 119
ATOM    119  CB  ARG    94       9.944  12.916  25.109  1.00107.62       1SG 120
ATOM    120  CG  ARG    94       8.577  12.526  24.554  1.00107.62       1SG 121
ATOM    121  CD  ARG    94       7.475  13.491  24.982  1.00107.62       1SG 122
ATOM    122  NE  ARG    94       6.220  13.100  24.284  1.00107.62       1SG 123
ATOM    123  CZ  ARG    94       5.019  13.570  24.732  1.00107.62       1SG 124
ATOM    124  NH1 ARG    94       4.958  14.324  25.867  1.00107.62       1SG 125
ATOM    125  NH2 ARG    94       3.873  13.292  24.046  1.00107.62       1SG 126
ATOM    126  C   ARG    94      10.717  10.604  25.261  1.00107.62       1SG 127
ATOM    127  O   ARG    94      10.609   9.624  24.524  1.00107.62       1SG 128
ATOM    128  N   LEU    95      10.552  10.524  26.597  1.00 99.83       1SG 129
ATOM    129  CA  LEU    95      10.218   9.283  27.240  1.00 99.83       1SG 130
ATOM    130  CB  LEU    95      10.560   9.268  28.738  1.00 99.83       1SG 131
ATOM    131  CG  LEU    95      12.074   9.345  29.013  1.00 99.83       1SG 132
ATOM    132  CD2 LEU    95      12.397   9.106  30.498  1.00 99.83       1SG 133
ATOM    133  CD1 LEU    95      12.663  10.661  28.482  1.00 99.83       1SG 134
ATOM    134  C   LEU    95       8.746   9.058  27.096  1.00 99.83       1SG 135
ATOM    135  O   LEU    95       7.971   9.995  26.918  1.00 99.83       1SG 136
ATOM    136  N   SER    96       8.330   7.775  27.151  1.00 73.98       1SG 137
ATOM    137  CA  SER    96       6.938   7.453  27.022  1.00 73.98       1SG 138
ATOM    138  CB  SER    96       6.669   5.963  26.737  1.00 73.98       1SG 139
ATOM    139  OG  SER    96       5.275   5.733  26.599  1.00 73.98       1SG 140
ATOM    140  C   SER    96       6.266   7.816  28.306  1.00 73.98       1SG 141
ATOM    141  O   SER    96       6.910   7.925  29.350  1.00 73.98       1SG 142
ATOM    142  N   LEU    97       4.934   8.010  28.248  1.00 65.91       1SG 143
ATOM    143  CA  LEU    97       4.182   8.403  29.403  1.00 65.91       1SG 144
ATOM    144  CB  LEU    97       4.037   7.286  30.456  1.00 65.91       1SG 145
ATOM    145  CG  LEU    97       3.071   6.160  30.039  1.00 65.91       1SG 146
ATOM    146  CD2 LEU    97       3.514   5.471  28.740  1.00 65.91       1SG 147
ATOM    147  CD1 LEU    97       1.627   6.680  29.973  1.00 65.91       1SG 148
ATOM    148  C   LEU    97       4.867   9.598  30.056  1.00 65.91       1SG 149
ATOM    149  O   LEU    97       5.152   9.523  31.282  1.00 65.91       1SG 150
ATOM    150  OXT LEU    97       5.113  10.600  29.334  1.00 65.91       1SG 151
TER
END
