
#######################################################
#                                                     #
#                        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   14 (  115),  selected   14 , name T0319TS468_1
# Molecule2: number of CA atoms  135 ( 1055),  selected  135 , name T0319.pdb
# PARAMETERS: T0319TS468_1.T0319.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    -       -      K       2           -
LGA    -       -      F       3           -
LGA    -       -      L       4           -
LGA    -       -      T       5           -
LGA    -       -      T       6           -
LGA    G     108      N       7          0.987
LGA    E     109      F       8          2.842
LGA    M     110      L       9          2.247
LGA    K     111      K      10          1.234
LGA    C     112      C      11          1.352
LGA    R     113      S      12          1.193
LGA    N     114      V      13          1.051
LGA    -       -      K      14           -
LGA    -       -      A      15           -
LGA    C     115      C      16          1.723
LGA    G     116      D      17          1.888
LGA    -       -      T      18           -
LGA    H     117      S      19          3.989
LGA    -       -      N      20           -
LGA    -       -      D      21           -
LGA    I     118      N      22          2.927
LGA    Y     119      F      23          1.422
LGA    Y     120      P      24          2.428
LGA    -       -      L      25           -
LGA    -       -      Q      26           -
LGA    -       -      Y      27           -
LGA    -       -      D      28           -
LGA    -       -      G      29           -
LGA    -       -      S      30           -
LGA    -       -      K      31           -
LGA    -       -      C      32           -
LGA    -       -      Q      33           -
LGA    -       -      L      34           -
LGA    -       -      V      35           -
LGA    -       -      Q      36           -
LGA    -       -      D      37           -
LGA    -       -      E      38           -
LGA    -       -      S      39           -
LGA    -       -      I      40           -
LGA    -       -      E      41           -
LGA    -       -      F      42           -
LGA    -       -      N      43           -
LGA    -       -      P      44           -
LGA    -       -      E      45           -
LGA    -       -      F      46           -
LGA    -       -      L      47           -
LGA    -       -      L      48           -
LGA    -       -      N      49           -
LGA    -       -      I      50           -
LGA    -       -      V      51           -
LGA    -       -      D      52           -
LGA    -       -      R      53           -
LGA    -       -      V      54           -
LGA    -       -      D      55           -
LGA    -       -      W      56           -
LGA    -       -      P      57           -
LGA    -       -      A      58           -
LGA    -       -      V      59           -
LGA    -       -      L      60           -
LGA    -       -      T      61           -
LGA    I     121      V      62          3.314
LGA    -       -      A      63           -
LGA    -       -      A      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      G      67           -
LGA    -       -      N      68           -
LGA    -       -      N      69           -
LGA    -       -      A      70           -
LGA    -       -      L      71           -
LGA    -       -      P      72           -
LGA    -       -      P      73           -
LGA    -       -      T      74           -
LGA    -       -      K      75           -
LGA    -       -      P      76           -
LGA    -       -      S      77           -
LGA    -       -      F      78           -
LGA    -       -      P      79           -
LGA    -       -      S      80           -
LGA    -       -      S      81           -
LGA    -       -      I      82           -
LGA    -       -      Q      83           -
LGA    -       -      E      84           -
LGA    -       -      L      85           -
LGA    -       -      T      86           -
LGA    -       -      D      87           -
LGA    -       -      D      88           -
LGA    -       -      D      89           -
LGA    -       -      M      90           -
LGA    -       -      A      91           -
LGA    -       -      I      92           -
LGA    -       -      L      93           -
LGA    -       -      N      94           -
LGA    -       -      D      95           -
LGA    -       -      L      96           -
LGA    -       -      H      97           -
LGA    -       -      T      98           -
LGA    -       -      L      99           -
LGA    -       -      L     100           -
LGA    -       -      L     101           -
LGA    -       -      Q     102           -
LGA    -       -      T     103           -
LGA    -       -      S     104           -
LGA    -       -      I     105           -
LGA    -       -      A     106           -
LGA    -       -      E     107           -
LGA    -       -      G     108           -
LGA    -       -      E     109           -
LGA    -       -      M     110           -
LGA    -       -      K     111           -
LGA    -       -      C     112           -
LGA    -       -      R     113           -
LGA    -       -      N     114           -
LGA    -       -      C     115           -
LGA    -       -      G     116           -
LGA    -       -      H     117           -
LGA    -       -      I     118           -
LGA    -       -      Y     119           -
LGA    -       -      Y     120           -
LGA    -       -      I     121           -
LGA    -       -      K     122           -
LGA    -       -      N     123           -
LGA    -       -      G     124           -
LGA    -       -      I     125           -
LGA    -       -      P     126           -
LGA    -       -      N     127           -
LGA    -       -      L     128           -
LGA    -       -      L     129           -
LGA    -       -      L     130           -
LGA    -       -      P     131           -
LGA    -       -      P     132           -
LGA    -       -      H     133           -
LGA    -       -      L     134           -
LGA    -       -      V     135           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   14  135    5.0     14    2.23    21.43      8.089     0.600

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.219338 * X  +   0.928735 * Y  +  -0.298902 * Z  +   0.512673
  Y_new =  -0.649352 * X  +   0.367615 * Y  +   0.665734 * Z  +  -3.702130
  Z_new =   0.728171 * X  +   0.048072 * Y  +   0.683708 * Z  + -10.624705 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.070195   -3.071398  [ DEG:     4.0219   -175.9781 ]
  Theta =  -0.815649   -2.325943  [ DEG:   -46.7332   -133.2668 ]
  Phi   =  -1.245049    1.896544  [ DEG:   -71.3361    108.6639 ]
 
# 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: T0319TS468_1                                  
REMARK     2: T0319.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0319TS468_1.T0319.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   14  135   5.0   14   2.23   21.43   8.089
REMARK  ---------------------------------------------------------- 
MOLECULE T0319TS468_1
PFRMAT TS
TARGET T0319    
MODEL  1
PARENT n/a
ATOM      1  N   GLY   108      17.205  -2.698  13.526  1.00  0.00
ATOM      2  CA  GLY   108      16.738  -1.784  12.493  1.00  0.00
ATOM      3  C   GLY   108      15.263  -1.930  12.155  1.00  0.00
ATOM      4  O   GLY   108      14.745  -1.201  11.310  1.00  0.00
ATOM      5  N   GLU   109      14.572  -2.854  12.823  1.00  0.00
ATOM      6  CA  GLU   109      13.152  -3.061  12.562  1.00  0.00
ATOM      7  C   GLU   109      12.344  -1.884  13.090  1.00  0.00
ATOM      8  O   GLU   109      12.637  -1.392  14.177  1.00  0.00
ATOM      9  CB  GLU   109      12.661  -4.337  13.249  1.00  0.00
ATOM     10  CG  GLU   109      11.210  -4.680  12.957  1.00  0.00
ATOM     11  CD  GLU   109      10.776  -5.978  13.609  1.00  0.00
ATOM     12  OE1 GLU   109      11.608  -6.603  14.300  1.00  0.00
ATOM     13  OE2 GLU   109       9.603  -6.371  13.429  1.00  0.00
ATOM     14  N   MET   110      11.382  -1.405  12.295  1.00  0.00
ATOM     15  CA  MET   110      10.469  -0.321  12.705  1.00  0.00
ATOM     16  C   MET   110       9.051  -0.793  12.369  1.00  0.00
ATOM     17  O   MET   110       8.820  -1.363  11.305  1.00  0.00
ATOM     18  CB  MET   110      10.795   0.969  11.949  1.00  0.00
ATOM     19  CG  MET   110       9.859   2.125  12.263  1.00  0.00
ATOM     20  SD  MET   110      10.367   3.665  11.474  1.00  0.00
ATOM     21  CE  MET   110       9.985   3.311   9.761  1.00  0.00
ATOM     22  N   LYS   111       8.115  -0.585  13.289  1.00  0.00
ATOM     23  CA  LYS   111       6.741  -1.051  13.093  1.00  0.00
ATOM     24  C   LYS   111       5.780   0.130  13.159  1.00  0.00
ATOM     25  O   LYS   111       6.028   1.074  13.900  1.00  0.00
ATOM     26  CB  LYS   111       6.356  -2.058  14.178  1.00  0.00
ATOM     27  CG  LYS   111       7.146  -3.357  14.127  1.00  0.00
ATOM     28  CD  LYS   111       6.680  -4.328  15.200  1.00  0.00
ATOM     29  CE  LYS   111       7.451  -5.637  15.130  1.00  0.00
ATOM     30  NZ  LYS   111       6.987  -6.610  16.157  1.00  0.00
ATOM     31  N   CYS   112       4.701   0.084  12.372  1.00  0.00
ATOM     32  CA  CYS   112       3.719   1.167  12.389  1.00  0.00
ATOM     33  C   CYS   112       2.819   1.050  13.637  1.00  0.00
ATOM     34  O   CYS   112       2.215  -0.003  13.894  1.00  0.00
ATOM     35  CB  CYS   112       2.835   1.108  11.142  1.00  0.00
ATOM     36  SG  CYS   112       1.565   2.393  11.064  1.00  0.00
ATOM     37  N   ARG   113       2.750   2.132  14.413  1.00  0.00
ATOM     38  CA  ARG   113       1.935   2.127  15.626  1.00  0.00
ATOM     39  C   ARG   113       0.445   2.038  15.308  1.00  0.00
ATOM     40  O   ARG   113      -0.337   1.544  16.115  1.00  0.00
ATOM     41  CB  ARG   113       2.165   3.407  16.431  1.00  0.00
ATOM     42  CG  ARG   113       3.535   3.493  17.083  1.00  0.00
ATOM     43  CD  ARG   113       3.713   4.808  17.824  1.00  0.00
ATOM     44  NE  ARG   113       5.047   4.933  18.406  1.00  0.00
ATOM     45  CZ  ARG   113       5.537   6.059  18.915  1.00  0.00
ATOM     46  NH1 ARG   113       6.763   6.077  19.423  1.00  0.00
ATOM     47  NH2 ARG   113       4.803   7.162  18.916  1.00  0.00
ATOM     48  N   ASN   114       0.070   2.478  14.109  1.00  0.00
ATOM     49  CA  ASN   114      -1.325   2.446  13.692  1.00  0.00
ATOM     50  C   ASN   114      -1.820   1.147  13.106  1.00  0.00
ATOM     51  O   ASN   114      -2.811   0.602  13.574  1.00  0.00
ATOM     52  CB  ASN   114      -1.587   3.501  12.614  1.00  0.00
ATOM     53  CG  ASN   114      -1.517   4.915  13.155  1.00  0.00
ATOM     54  OD1 ASN   114      -1.618   5.134  14.362  1.00  0.00
ATOM     55  ND2 ASN   114      -1.343   5.881  12.260  1.00  0.00
ATOM     56  N   CYS   115      -1.140   0.659  12.063  1.00  0.00
ATOM     57  CA  CYS   115      -1.583  -0.548  11.368  1.00  0.00
ATOM     58  C   CYS   115      -0.712  -1.788  11.551  1.00  0.00
ATOM     59  O   CYS   115      -1.035  -2.863  11.015  1.00  0.00
ATOM     60  CB  CYS   115      -1.638  -0.308   9.859  1.00  0.00
ATOM     61  SG  CYS   115      -2.770   1.008   9.352  1.00  0.00
ATOM     62  N   GLY   116       0.405  -1.635  12.256  1.00  0.00
ATOM     63  CA  GLY   116       1.295  -2.761  12.490  1.00  0.00
ATOM     64  C   GLY   116       2.193  -3.162  11.335  1.00  0.00
ATOM     65  O   GLY   116       2.879  -4.183  11.430  1.00  0.00
ATOM     66  N   HIS   117       2.201  -2.404  10.242  1.00  0.00
ATOM     67  CA  HIS   117       3.085  -2.741   9.106  1.00  0.00
ATOM     68  C   HIS   117       4.537  -2.709   9.584  1.00  0.00
ATOM     69  O   HIS   117       4.913  -1.879  10.414  1.00  0.00
ATOM     70  CB  HIS   117       2.905  -1.733   7.970  1.00  0.00
ATOM     71  CG  HIS   117       3.560  -2.145   6.688  1.00  0.00
ATOM     72  ND1 HIS   117       4.915  -2.020   6.470  1.00  0.00
ATOM     73  CD2 HIS   117       3.109  -2.722   5.429  1.00  0.00
ATOM     74  CE1 HIS   117       5.204  -2.470   5.236  1.00  0.00
ATOM     75  NE2 HIS   117       4.124  -2.892   4.606  1.00  0.00
ATOM     76  N   ILE   118       5.345  -3.618   9.051  1.00  0.00
ATOM     77  CA  ILE   118       6.746  -3.736   9.438  1.00  0.00
ATOM     78  C   ILE   118       7.710  -3.284   8.348  1.00  0.00
ATOM     79  O   ILE   118       7.536  -3.594   7.173  1.00  0.00
ATOM     80  CB  ILE   118       7.118  -5.193   9.772  1.00  0.00
ATOM     81  CG1 ILE   118       6.293  -5.695  10.958  1.00  0.00
ATOM     82  CG2 ILE   118       8.592  -5.297  10.132  1.00  0.00
ATOM     83  CD1 ILE   118       6.418  -7.183  11.203  1.00  0.00
ATOM     84  N   TYR   119       8.716  -2.526   8.763  1.00  0.00
ATOM     85  CA  TYR   119       9.742  -2.029   7.861  1.00  0.00
ATOM     86  C   TYR   119      11.096  -2.321   8.471  1.00  0.00
ATOM     87  O   TYR   119      11.217  -2.843   9.594  1.00  0.00
ATOM     88  CB  TYR   119       9.588  -0.521   7.654  1.00  0.00
ATOM     89  CG  TYR   119       8.265  -0.117   7.045  1.00  0.00
ATOM     90  CD1 TYR   119       7.186   0.228   7.850  1.00  0.00
ATOM     91  CD2 TYR   119       8.098  -0.082   5.667  1.00  0.00
ATOM     92  CE1 TYR   119       5.973   0.598   7.302  1.00  0.00
ATOM     93  CE2 TYR   119       6.892   0.286   5.100  1.00  0.00
ATOM     94  CZ  TYR   119       5.826   0.627   5.931  1.00  0.00
ATOM     95  OH  TYR   119       4.619   0.995   5.383  1.00  0.00
ATOM     96  N   TYR   120      12.124  -1.982   7.720  1.00  0.00
ATOM     97  CA  TYR   120      13.473  -2.156   8.196  1.00  0.00
ATOM     98  C   TYR   120      14.300  -1.011   7.630  1.00  0.00
ATOM     99  O   TYR   120      14.338  -0.799   6.412  1.00  0.00
ATOM    100  CB  TYR   120      14.039  -3.497   7.724  1.00  0.00
ATOM    101  CG  TYR   120      15.442  -3.776   8.213  1.00  0.00
ATOM    102  CD1 TYR   120      15.674  -4.156   9.528  1.00  0.00
ATOM    103  CD2 TYR   120      16.530  -3.659   7.357  1.00  0.00
ATOM    104  CE1 TYR   120      16.954  -4.413   9.985  1.00  0.00
ATOM    105  CE2 TYR   120      17.816  -3.912   7.796  1.00  0.00
ATOM    106  CZ  TYR   120      18.021  -4.291   9.121  1.00  0.00
ATOM    107  OH  TYR   120      19.296  -4.546   9.573  1.00  0.00
ATOM    108  N   ILE   121      14.945  -0.266   8.523  1.00  0.00
ATOM    109  CA  ILE   121      15.729   0.898   8.134  1.00  0.00
ATOM    110  C   ILE   121      16.847   0.630   7.135  1.00  0.00
ATOM    111  O   ILE   121      17.189   1.500   6.338  1.00  0.00
ATOM    112  CB  ILE   121      16.420   1.545   9.348  1.00  0.00
ATOM    113  CG1 ILE   121      15.378   2.030  10.358  1.00  0.00
ATOM    114  CG2 ILE   121      17.260   2.735   8.912  1.00  0.00
ATOM    115  CD1 ILE   121      15.970   2.490  11.673  1.00  0.00
TER
END
