
#######################################################
#                                                     #
#                        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   35 (  140),  selected   35 , name T0312AL381_3-D1
# Molecule2: number of CA atoms  132 ( 1043),  selected  132 , name T0312_D1.pdb
# PARAMETERS: T0312AL381_3-D1.T0312_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      G       9           -
LGA    -       -      K      10           -
LGA    -       -      G      11           -
LGA    -       -      F      12           -
LGA    -       -      L      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      L      16           -
LGA    -       -      D      17           -
LGA    -       -      Y      18           -
LGA    -       -      G      19           -
LGA    -       -      K      20           -
LGA    -       -      D      21           -
LGA    V      62      L      22          1.156
LGA    K      63      V      23          3.928
LGA    -       -      R      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      E      27           -
LGA    -       -      E      28           -
LGA    -       -      F      29           -
LGA    -       -      L      30           -
LGA    -       -      E      31           -
LGA    -       -      E      32           -
LGA    -       -      K      33           -
LGA    -       -      G      34           -
LGA    -       -      I      35           -
LGA    -       -      H      36           -
LGA    -       -      A      37           -
LGA    -       -      A      38           -
LGA    -       -      H      39           -
LGA    -       -      I      40           -
LGA    -       -      S      41           -
LGA    -       -      A      42           -
LGA    -       -      I      43           -
LGA    -       -      G      44           -
LGA    -       -      A      45           -
LGA    -       -      V      46           -
LGA    -       -      R      47           -
LGA    -       -      S      48           -
LGA    K      64      A      49          3.417
LGA    E      65      V      50          1.976
LGA    L      66      I      51          4.279
LGA    -       -      G      52           -
LGA    -       -      Y      53           -
LGA    -       -      Y      54           -
LGA    -       -      D      55           -
LGA    -       -      Q      56           -
LGA    -       -      E      57           -
LGA    -       -      K      58           -
LGA    -       -      K      59           -
LGA    -       -      E      60           -
LGA    -       -      Y      61           -
LGA    -       -      V      62           -
LGA    M      67      K      63          5.114
LGA    E      68      K      64          2.839
LGA    P      69      E      65          2.676
LGA    L      70      L      66          3.606
LGA    E      71      M      67          3.422
LGA    I      72      E      68          1.637
LGA    -       -      P      69           -
LGA    L      73      L      70          4.027
LGA    S      74      E      71           -
LGA    L      75      I      72           #
LGA    S      76      L      73           -
LGA    -       -      S      74           -
LGA    G      77      L      75           #
LGA    N      78      S      76           -
LGA    V      79      G      77           #
LGA    S      80      N      78           #
LGA    M      81      V      79          4.294
LGA    K      82      S      80           #
LGA    -       -      M      81           -
LGA    -       -      K      82           -
LGA    -       -      D      83           -
LGA    -       -      S      84           -
LGA    -       -      K      85           -
LGA    D      83      P      86          2.378
LGA    S      84      F      87          2.227
LGA    K      85      C      88          1.623
LGA    -       -      H      89           -
LGA    P      86      I      90          2.366
LGA    F      87      H      91          2.922
LGA    C      88      V      92          2.044
LGA    H      89      L      93          3.396
LGA    I      90      L      94          2.244
LGA    H      91      G      95          2.841
LGA    V      92      K      96          3.427
LGA    L      93      D      97          2.658
LGA    -       -      G      98           -
LGA    L      94      E      99          5.001
LGA    G      95      V     100           -
LGA    K      96      Y     101           -
LGA    -       -      G     102           -
LGA    -       -      G     103           -
LGA    -       -      H     104           -
LGA    -       -      L     105           -
LGA    -       -      F     106           -
LGA    -       -      S     107           -
LGA    -       -      A     108           -
LGA    -       -      E     109           -
LGA    -       -      V     110           -
LGA    -       -      F     111           -
LGA    -       -      A     112           -
LGA    -       -      C     113           -
LGA    -       -      E     114           -
LGA    -       -      V     115           -
LGA    -       -      F     116           -
LGA    -       -      V     117           -
LGA    -       -      L     118           -
LGA    -       -      P     119           -
LGA    -       -      L     120           -
LGA    -       -      S     121           -
LGA    -       -      G     122           -
LGA    -       -      E     123           -
LGA    -       -      A     124           -
LGA    -       -      P     125           -
LGA    -       -      E     126           -
LGA    -       -      R     127           -
LGA    -       -      A     128           -
LGA    -       -      F     129           -
LGA    -       -      D     130           -
LGA    -       -      E     131           -
LGA    -       -      Q     132           -
LGA    -       -      T     133           -
LGA    -       -      G     134           -
LGA    -       -      L     135           -
LGA    -       -      F     136           -
LGA    -       -      L     137           -
LGA    -       -      W     138           -
LGA    -       -      L     139           -
LGA    -       -      E     140           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35  132    5.0     25    3.19     8.00     11.705     0.760

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.858803 * X  +   0.396106 * Y  +  -0.324895 * Z  +  59.236870
  Y_new =  -0.147350 * X  +  -0.798369 * Y  +  -0.583862 * Z  +  15.496015
  Z_new =  -0.490658 * X  +  -0.453549 * Y  +   0.744008 * Z  +  16.887863 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.547450    2.594143  [ DEG:   -31.3666    148.6335 ]
  Theta =   0.512844    2.628748  [ DEG:    29.3838    150.6162 ]
  Phi   =  -2.971671    0.169922  [ DEG:  -170.2642      9.7358 ]
 
# 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: T0312AL381_3-D1                               
REMARK     2: T0312_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0312AL381_3-D1.T0312_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35  132   5.0   25   3.19    8.00  11.705
REMARK  ---------------------------------------------------------- 
MOLECULE T0312AL381_3-D1
REMARK Aligment from pdb entry: 1fxtA
ATOM      1  N   VAL    62      58.867   9.866  10.541  1.00  0.00              
ATOM      2  CA  VAL    62      57.582   9.143  10.803  1.00  0.00              
ATOM      3  C   VAL    62      57.449   7.891   9.866  1.00  0.00              
ATOM      4  O   VAL    62      57.680   7.984   8.657  1.00  0.00              
ATOM      5  N   LYS    63      56.976   6.749  10.391  1.00  0.00              
ATOM      6  CA  LYS    63      56.276   5.717   9.558  1.00  0.00              
ATOM      7  C   LYS    63      54.740   5.756   9.852  1.00  0.00              
ATOM      8  O   LYS    63      54.316   5.663  11.009  1.00  0.00              
ATOM      9  N   LYS    64      53.899   5.870   8.812  1.00  0.00              
ATOM     10  CA  LYS    64      52.439   5.577   8.933  1.00  0.00              
ATOM     11  C   LYS    64      52.148   4.145   8.365  1.00  0.00              
ATOM     12  O   LYS    64      51.717   3.978   7.219  1.00  0.00              
ATOM     13  N   GLU    65      52.423   3.110   9.177  1.00  0.00              
ATOM     14  CA  GLU    65      52.387   1.685   8.743  1.00  0.00              
ATOM     15  C   GLU    65      51.048   0.988   9.180  1.00  0.00              
ATOM     16  O   GLU    65      50.700   0.936  10.364  1.00  0.00              
ATOM     17  N   LEU    66      50.262   0.497   8.207  1.00  0.00              
ATOM     18  CA  LEU    66      48.863   0.029   8.438  1.00  0.00              
ATOM     19  C   LEU    66      48.699  -1.258   9.314  1.00  0.00              
ATOM     20  O   LEU    66      49.478  -2.212   9.238  1.00  0.00              
ATOM     21  N   MET    67      47.619  -1.287  10.109  1.00  0.00              
ATOM     22  CA  MET    67      47.229  -2.485  10.921  1.00  0.00              
ATOM     23  C   MET    67      46.495  -3.610  10.095  1.00  0.00              
ATOM     24  O   MET    67      46.698  -4.788  10.409  1.00  0.00              
ATOM     25  N   GLU    68      45.665  -3.293   9.076  1.00  0.00              
ATOM     26  CA  GLU    68      45.124  -4.310   8.126  1.00  0.00              
ATOM     27  C   GLU    68      46.145  -4.687   6.987  1.00  0.00              
ATOM     28  O   GLU    68      46.989  -5.562   7.194  1.00  0.00              
ATOM     29  N   PRO    69      46.086  -4.026   5.819  1.00  0.00              
ATOM     30  CA  PRO    69      47.063  -4.198   4.702  1.00  0.00              
ATOM     31  C   PRO    69      47.434  -2.789   4.119  1.00  0.00              
ATOM     32  O   PRO    69      48.528  -2.273   4.368  1.00  0.00              
ATOM     33  N   LEU    70      46.521  -2.145   3.365  1.00  0.00              
ATOM     34  CA  LEU    70      46.631  -0.711   2.979  1.00  0.00              
ATOM     35  C   LEU    70      45.216  -0.046   2.897  1.00  0.00              
ATOM     36  O   LEU    70      44.703   0.215   1.802  1.00  0.00              
ATOM     37  N   GLU    71      44.595   0.246   4.054  1.00  0.00              
ATOM     38  CA  GLU    71      43.232   0.847   4.119  1.00  0.00              
ATOM     39  C   GLU    71      43.216   2.421   3.971  1.00  0.00              
ATOM     40  O   GLU    71      43.950   3.001   3.165  1.00  0.00              
ATOM     41  N   ILE    72      42.339   3.113   4.712  1.00  0.00              
ATOM     42  CA  ILE    72      42.294   4.618   4.766  1.00  0.00              
ATOM     43  C   ILE    72      42.154   5.219   6.219  1.00  0.00              
ATOM     44  O   ILE    72      41.676   6.348   6.383  1.00  0.00              
ATOM     45  N   LEU    73      42.559   4.505   7.289  1.00  0.00              
ATOM     46  CA  LEU    73      42.262   4.893   8.696  1.00  0.00              
ATOM     47  C   LEU    73      43.202   4.270   9.777  1.00  0.00              
ATOM     48  O   LEU    73      43.765   5.034  10.569  1.00  0.00              
ATOM     49  N   SER    74      43.324   2.930   9.890  1.00  0.00              
ATOM     50  CA  SER    74      43.853   2.287  11.128  1.00  0.00              
ATOM     51  C   SER    74      45.397   2.038  11.062  1.00  0.00              
ATOM     52  O   SER    74      45.904   1.164  10.346  1.00  0.00              
ATOM     53  N   LEU    75      46.143   2.874  11.794  1.00  0.00              
ATOM     54  CA  LEU    75      47.594   3.084  11.556  1.00  0.00              
ATOM     55  C   LEU    75      48.440   2.867  12.842  1.00  0.00              
ATOM     56  O   LEU    75      48.137   3.407  13.908  1.00  0.00              
ATOM     57  N   SER    76      49.595   2.202  12.704  1.00  0.00              
ATOM     58  CA  SER    76      50.739   2.418  13.627  1.00  0.00              
ATOM     59  C   SER    76      51.522   3.707  13.193  1.00  0.00              
ATOM     60  O   SER    76      52.347   3.681  12.272  1.00  0.00              
ATOM     61  N   GLY    77      51.246   4.844  13.847  1.00  0.00              
ATOM     62  CA  GLY    77      52.025   6.095  13.642  1.00  0.00              
ATOM     63  C   GLY    77      53.278   6.154  14.526  1.00  0.00              
ATOM     64  O   GLY    77      53.164   6.314  15.742  1.00  0.00              
ATOM     65  N   ASN    78      54.461   5.958  13.935  1.00  0.00              
ATOM     66  CA  ASN    78      55.695   5.653  14.722  1.00  0.00              
ATOM     67  C   ASN    78      56.786   6.746  14.497  1.00  0.00              
ATOM     68  O   ASN    78      57.246   6.943  13.370  1.00  0.00              
ATOM     69  N   VAL    79      57.207   7.450  15.559  1.00  0.00              
ATOM     70  CA  VAL    79      58.299   8.469  15.488  1.00  0.00              
ATOM     71  C   VAL    79      59.682   7.955  16.023  1.00  0.00              
ATOM     72  O   VAL    79      59.766   6.984  16.784  1.00  0.00              
ATOM     73  N   SER    80      60.775   8.637  15.643  1.00  0.00              
ATOM     74  CA  SER    80      62.133   8.355  16.195  1.00  0.00              
ATOM     75  C   SER    80      62.435   9.165  17.507  1.00  0.00              
ATOM     76  O   SER    80      62.089  10.343  17.637  1.00  0.00              
ATOM     77  N   MET    81      64.371   9.787  26.461  1.00  0.00              
ATOM     78  CA  MET    81      63.599   9.238  25.295  1.00  0.00              
ATOM     79  C   MET    81      64.376   9.170  23.921  1.00  0.00              
ATOM     80  O   MET    81      63.767   8.913  22.883  1.00  0.00              
ATOM     81  N   LYS    82      65.713   9.293  23.930  1.00  0.00              
ATOM     82  CA  LYS    82      66.608   9.210  22.743  1.00  0.00              
ATOM     83  C   LYS    82      66.587   7.866  21.939  1.00  0.00              
ATOM     84  O   LYS    82      66.626   6.780  22.523  1.00  0.00              
ATOM     85  N   ASP    83      66.661   7.941  20.599  1.00  0.00              
ATOM     86  CA  ASP    83      67.069   6.786  19.741  1.00  0.00              
ATOM     87  C   ASP    83      66.236   5.488  19.820  1.00  0.00              
ATOM     88  O   ASP    83      66.644   4.528  20.478  1.00  0.00              
ATOM     89  N   SER    84      65.080   5.471  19.155  1.00  0.00              
ATOM     90  CA  SER    84      64.115   4.345  19.282  1.00  0.00              
ATOM     91  C   SER    84      62.813   4.515  18.473  1.00  0.00              
ATOM     92  O   SER    84      62.374   5.637  18.220  1.00  0.00              
ATOM     93  N   LYS    85      62.168   3.404  18.085  1.00  0.00              
ATOM     94  CA  LYS    85      60.867   3.457  17.355  1.00  0.00              
ATOM     95  C   LYS    85      59.654   3.523  18.350  1.00  0.00              
ATOM     96  O   LYS    85      59.297   2.529  18.989  1.00  0.00              
ATOM     97  N   PRO    86      59.027   4.702  18.475  1.00  0.00              
ATOM     98  CA  PRO    86      57.912   4.947  19.434  1.00  0.00              
ATOM     99  C   PRO    86      56.520   4.660  18.782  1.00  0.00              
ATOM    100  O   PRO    86      55.964   5.506  18.078  1.00  0.00              
ATOM    101  N   PHE    87      55.982   3.449  18.999  1.00  0.00              
ATOM    102  CA  PHE    87      54.827   2.904  18.215  1.00  0.00              
ATOM    103  C   PHE    87      53.441   3.322  18.829  1.00  0.00              
ATOM    104  O   PHE    87      53.137   2.976  19.973  1.00  0.00              
ATOM    105  N   CYS    88      52.600   4.024  18.045  1.00  0.00              
ATOM    106  CA  CYS    88      51.259   4.516  18.504  1.00  0.00              
ATOM    107  C   CYS    88      50.132   3.901  17.605  1.00  0.00              
ATOM    108  O   CYS    88      50.063   4.209  16.413  1.00  0.00              
ATOM    109  N   HIS    89      49.211   3.102  18.168  1.00  0.00              
ATOM    110  CA  HIS    89      47.965   2.672  17.466  1.00  0.00              
ATOM    111  C   HIS    89      46.909   3.838  17.348  1.00  0.00              
ATOM    112  O   HIS    89      46.692   4.605  18.295  1.00  0.00              
ATOM    113  N   ILE    90      46.323   4.022  16.152  1.00  0.00              
ATOM    114  CA  ILE    90      45.532   5.244  15.801  1.00  0.00              
ATOM    115  C   ILE    90      44.213   4.832  15.049  1.00  0.00              
ATOM    116  O   ILE    90      44.246   4.473  13.866  1.00  0.00              
ATOM    117  N   HIS    91      43.056   5.032  15.700  1.00  0.00              
ATOM    118  CA  HIS    91      41.770   5.319  15.001  1.00  0.00              
ATOM    119  C   HIS    91      41.603   6.874  14.850  1.00  0.00              
ATOM    120  O   HIS    91      41.319   7.585  15.817  1.00  0.00              
ATOM    121  N   VAL    92      41.792   7.403  13.629  1.00  0.00              
ATOM    122  CA  VAL    92      41.370   8.791  13.242  1.00  0.00              
ATOM    123  C   VAL    92      39.826   8.796  12.941  1.00  0.00              
ATOM    124  O   VAL    92      39.483   8.429  11.815  1.00  0.00              
ATOM    125  N   LEU    93      38.851   9.123  13.845  1.00  0.00              
ATOM    126  CA  LEU    93      37.453   8.606  13.728  1.00  0.00              
ATOM    127  C   LEU    93      36.634   8.968  12.447  1.00  0.00              
ATOM    128  O   LEU    93      37.014   9.862  11.691  1.00  0.00              
ATOM    129  N   LEU    94      35.532   8.242  12.197  1.00  0.00              
ATOM    130  CA  LEU    94      34.735   8.313  10.923  1.00  0.00              
ATOM    131  C   LEU    94      34.561   9.686  10.176  1.00  0.00              
ATOM    132  O   LEU    94      34.783   9.754   8.964  1.00  0.00              
ATOM    133  N   GLY    95      34.236  10.764  10.901  1.00  0.00              
ATOM    134  CA  GLY    95      34.097  12.141  10.347  1.00  0.00              
ATOM    135  C   GLY    95      35.444  12.952  10.098  1.00  0.00              
ATOM    136  O   GLY    95      35.411  14.176   9.952  1.00  0.00              
ATOM    137  N   LYS    96      36.626  12.303  10.006  1.00  0.00              
ATOM    138  CA  LYS    96      37.927  12.942   9.627  1.00  0.00              
ATOM    139  C   LYS    96      37.902  13.536   8.166  1.00  0.00              
ATOM    140  O   LYS    96      37.607  12.766   7.246  1.00  0.00              
END
