
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0350TS383_2
# Molecule2: number of CA atoms  109 ( 1798),  selected  109 , name T0350.pdb
# PARAMETERS: T0350TS383_2.T0350.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    -       -      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      Q      10           -
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    -       -      W      13           -
LGA    -       -      D      14           -
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      Q      19           -
LGA    -       -      I      20           -
LGA    -       -      H      21           -
LGA    -       -      N      22           -
LGA    -       -      Q      23           -
LGA    -       -      K      24           -
LGA    -       -      D      25           -
LGA    -       -      N      26           -
LGA    -       -      D      27           -
LGA    -       -      N      28           -
LGA    -       -      E      29           -
LGA    -       -      V      30           -
LGA    -       -      P      31           -
LGA    -       -      V      32           -
LGA    -       -      H      33           -
LGA    -       -      Q      34           -
LGA    -       -      V      35           -
LGA    -       -      S      36           -
LGA    -       -      Y      37           -
LGA    -       -      T      38           -
LGA    -       -      N      39           -
LGA    -       -      L      40           -
LGA    -       -      A      41           -
LGA    -       -      E      42           -
LGA    -       -      M      43           -
LGA    -       -      V      44           -
LGA    -       -      G      45           -
LGA    -       -      E      46           -
LGA    -       -      M      47           -
LGA    -       -      N      48           -
LGA    -       -      K      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      E      52           -
LGA    -       -      P      53           -
LGA    -       -      S      54           -
LGA    -       -      Q      55           -
LGA    -       -      V      56           -
LGA    -       -      H      57           -
LGA    -       -      L      58           -
LGA    -       -      K      59           -
LGA    -       -      F      60           -
LGA    E      61      E      61          2.247
LGA    L      62      L      62          1.191
LGA    H      63      H      63          2.904
LGA    D      64      D      64          4.552
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    K      65      N      67          3.623
LGA    L      66      E      68          1.419
LGA    N      67      Y      69          3.174
LGA    E      68      Y      70          1.221
LGA    Y      69      V      71          1.819
LGA    Y      70      K      72          1.478
LGA    V      71      V      73          0.881
LGA    K      72      I      74          1.430
LGA    V      73      E      75          1.799
LGA    I      74      D      76          4.087
LGA    E      75      S      77          3.156
LGA    D      76      T      78          1.916
LGA    S      77      N      79          4.468
LGA    T      78      E      80          2.736
LGA    -       -      V      81           -
LGA    -       -      I      82           -
LGA    N      79      R      83          3.748
LGA    E      80      E      84          2.547
LGA    V      81      I      85          2.348
LGA    -       -      P      86           -
LGA    -       -      P      87           -
LGA    -       -      K      88           -
LGA    -       -      R      89           -
LGA    -       -      W      90           -
LGA    -       -      L      91           -
LGA    -       -      D      92           -
LGA    I      82      F      93          3.333
LGA    R      83      Y      94          3.367
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    E      84      T      98          3.570
LGA    -       -      E      99           -
LGA    I      85      F     100           #
LGA    P      86      L     101          2.370
LGA    -       -      G     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -
LGA    -       -      D     106           -
LGA    -       -      E     107           -
LGA    -       -      K     108           -
LGA    -       -      K     109           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   26  109    5.0     25    2.82    24.00     15.671     0.857

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.254749 * X  +  -0.708397 * Y  +   0.658238 * Z  +  10.188872
  Y_new =  -0.931843 * X  +   0.361729 * Y  +   0.028655 * Z  +   2.936845
  Z_new =  -0.258403 * X  +  -0.606075 * Y  +  -0.752264 * Z  + -22.026165 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.463406    0.678187  [ DEG:  -141.1427     38.8573 ]
  Theta =   0.261369    2.880224  [ DEG:    14.9753    165.0247 ]
  Phi   =  -1.837657    1.303935  [ DEG:  -105.2900     74.7100 ]
 
# 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: T0350TS383_2                                  
REMARK     2: T0350.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS383_2.T0350.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   26  109   5.0   25   2.82   24.00  15.671
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS383_2
PFRMAT TS
TARGET T0350
MODEL 2
PARENT 1g5vA
ATOM      1  N   GLU    61      14.164   8.082 -25.427  1.00  0.00
ATOM      2  CA  GLU    61      13.996   8.284 -26.863  1.00  0.00
ATOM      3  C   GLU    61      12.906   7.377 -27.417  1.00  0.00
ATOM      4  O   GLU    61      12.598   6.336 -26.841  1.00  0.00
ATOM      5  N   LEU    62      12.316   7.784 -28.537  1.00  0.00
ATOM      6  CA  LEU    62      11.253   7.009 -29.167  1.00  0.00
ATOM      7  C   LEU    62      11.376   7.030 -30.686  1.00  0.00
ATOM      8  O   LEU    62      11.796   8.028 -31.271  1.00  0.00
ATOM      9  N   HIS    63      10.998   5.923 -31.319  1.00  0.00
ATOM     10  CA  HIS    63      11.057   5.815 -32.770  1.00  0.00
ATOM     11  C   HIS    63       9.712   5.357 -33.330  1.00  0.00
ATOM     12  O   HIS    63       9.451   4.160 -33.446  1.00  0.00
ATOM     13  N   ASP    64       8.861   6.322 -33.664  1.00  0.00
ATOM     14  CA  ASP    64       7.534   6.031 -34.201  1.00  0.00
ATOM     15  C   ASP    64       7.607   5.127 -35.430  1.00  0.00
ATOM     16  O   ASP    64       6.631   4.460 -35.777  1.00  0.00
ATOM     17  N   LYS    65       8.763   5.110 -36.089  1.00  0.00
ATOM     18  CA  LYS    65       8.952   4.287 -37.281  1.00  0.00
ATOM     19  C   LYS    65       8.597   2.828 -37.002  1.00  0.00
ATOM     20  O   LYS    65       7.626   2.302 -37.543  1.00  0.00
ATOM     21  N   LEU    66       9.393   2.181 -36.154  1.00  0.00
ATOM     22  CA  LEU    66       9.163   0.784 -35.804  1.00  0.00
ATOM     23  C   LEU    66       8.379   0.666 -34.500  1.00  0.00
ATOM     24  O   LEU    66       8.441  -0.359 -33.819  1.00  0.00
ATOM     25  N   ASN    67       7.635   1.720 -34.168  1.00  0.00
ATOM     26  CA  ASN    67       6.824   1.748 -32.952  1.00  0.00
ATOM     27  C   ASN    67       7.593   1.182 -31.758  1.00  0.00
ATOM     28  O   ASN    67       7.182   0.188 -31.156  1.00  0.00
ATOM     29  N   GLU    68       8.709   1.820 -31.420  1.00  0.00
ATOM     30  CA  GLU    68       9.532   1.378 -30.301  1.00  0.00
ATOM     31  C   GLU    68      10.017   2.566 -29.476  1.00  0.00
ATOM     32  O   GLU    68       9.687   3.714 -29.771  1.00  0.00
ATOM     33  N   TYR    69      10.805   2.282 -28.444  1.00  0.00
ATOM     34  CA  TYR    69      11.338   3.326 -27.578  1.00  0.00
ATOM     35  C   TYR    69      12.466   2.790 -26.702  1.00  0.00
ATOM     36  O   TYR    69      12.707   1.584 -26.653  1.00  0.00
ATOM     37  N   TYR    70      13.149   3.695 -26.011  1.00  0.00
ATOM     38  CA  TYR    70      14.251   3.325 -25.132  1.00  0.00
ATOM     39  C   TYR    70      13.980   3.796 -23.707  1.00  0.00
ATOM     40  O   TYR    70      13.681   4.969 -23.481  1.00  0.00
ATOM     41  N   VAL    71      14.079   2.879 -22.750  1.00  0.00
ATOM     42  CA  VAL    71      13.834   3.213 -21.353  1.00  0.00
ATOM     43  C   VAL    71      15.116   3.164 -20.531  1.00  0.00
ATOM     44  O   VAL    71      15.970   2.300 -20.740  1.00  0.00
ATOM     45  N   LYS    72      15.233   4.091 -19.586  1.00  0.00
ATOM     46  CA  LYS    72      16.399   4.160 -18.714  1.00  0.00
ATOM     47  C   LYS    72      16.053   3.647 -17.321  1.00  0.00
ATOM     48  O   LYS    72      15.065   4.071 -16.722  1.00  0.00
ATOM     49  N   VAL    73      16.867   2.729 -16.810  1.00  0.00
ATOM     50  CA  VAL    73      16.637   2.157 -15.489  1.00  0.00
ATOM     51  C   VAL    73      17.117   3.100 -14.392  1.00  0.00
ATOM     52  O   VAL    73      18.317   3.240 -14.159  1.00  0.00
ATOM     53  N   ILE    74      16.166   3.748 -13.728  1.00  0.00
ATOM     54  CA  ILE    74      16.478   4.688 -12.656  1.00  0.00
ATOM     55  C   ILE    74      17.291   4.021 -11.550  1.00  0.00
ATOM     56  O   ILE    74      16.762   3.235 -10.766  1.00  0.00
ATOM     57  N   GLU    75      18.581   4.344 -11.494  1.00  0.00
ATOM     58  CA  GLU    75      19.445   3.774 -10.476  1.00  0.00
ATOM     59  C   GLU    75      20.438   2.777 -11.040  1.00  0.00
ATOM     60  O   GLU    75      21.498   2.551 -10.454  1.00  0.00
ATOM     61  N   ASP    76      21.144   2.835 -14.596  1.00  0.00
ATOM     62  CA  ASP    76      21.789   3.510 -15.709  1.00  0.00
ATOM     63  C   ASP    76      21.591   2.793 -17.031  1.00  0.00
ATOM     64  O   ASP    76      21.503   3.431 -18.080  1.00  0.00
ATOM     65  N   SER    77      21.528   1.464 -16.983  1.00  0.00
ATOM     66  CA  SER    77      21.348   0.658 -18.187  1.00  0.00
ATOM     67  C   SER    77      20.131   1.114 -18.987  1.00  0.00
ATOM     68  O   SER    77      19.111   1.503 -18.418  1.00  0.00
ATOM     69  N   THR    78      20.246   1.055 -20.311  1.00  0.00
ATOM     70  CA  THR    78      19.160   1.451 -21.199  1.00  0.00
ATOM     71  C   THR    78      18.820   0.317 -22.159  1.00  0.00
ATOM     72  O   THR    78      19.693  -0.195 -22.859  1.00  0.00
ATOM     73  N   ASN    79      17.551  -0.078 -22.185  1.00  0.00
ATOM     74  CA  ASN    79      17.110  -1.163 -23.057  1.00  0.00
ATOM     75  C   ASN    79      15.920  -0.737 -23.912  1.00  0.00
ATOM     76  O   ASN    79      15.053   0.013 -23.459  1.00  0.00
ATOM     77  N   GLU    80      15.885  -1.222 -25.150  1.00  0.00
ATOM     78  CA  GLU    80      14.801  -0.898 -26.073  1.00  0.00
ATOM     79  C   GLU    80      13.580  -1.771 -25.801  1.00  0.00
ATOM     80  O   GLU    80      13.687  -2.993 -25.696  1.00  0.00
ATOM     81  N   VAL    81      12.417  -1.136 -25.690  1.00  0.00
ATOM     82  CA  VAL    81      11.173  -1.849 -25.427  1.00  0.00
ATOM     83  C   VAL    81      10.054  -1.343 -26.331  1.00  0.00
ATOM     84  O   VAL    81      10.236  -0.384 -27.084  1.00  0.00
ATOM     85  N   ILE    82       4.742  -0.552 -22.343  1.00  0.00
ATOM     86  CA  ILE    82       5.139   0.413 -21.325  1.00  0.00
ATOM     87  C   ILE    82       4.119   0.459 -20.189  1.00  0.00
ATOM     88  O   ILE    82       2.930   0.667 -20.423  1.00  0.00
ATOM     89  N   ARG    83       4.594   0.263 -18.964  1.00  0.00
ATOM     90  CA  ARG    83       3.722   0.282 -17.795  1.00  0.00
ATOM     91  C   ARG    83       3.655   1.681 -17.188  1.00  0.00
ATOM     92  O   ARG    83       4.593   2.466 -17.309  1.00  0.00
ATOM     93  N   GLU    84       2.536   1.984 -16.536  1.00  0.00
ATOM     94  CA  GLU    84       2.342   3.286 -15.909  1.00  0.00
ATOM     95  C   GLU    84       3.189   3.415 -14.643  1.00  0.00
ATOM     96  O   GLU    84       3.573   2.412 -14.042  1.00  0.00
ATOM     97  N   ILE    85       3.495   4.657 -14.219  1.00  0.00
ATOM     98  CA  ILE    85       4.302   4.905 -13.018  1.00  0.00
ATOM     99  C   ILE    85       3.613   4.426 -11.745  1.00  0.00
ATOM    100  O   ILE    85       2.505   3.890 -11.791  1.00  0.00
ATOM    101  N   PRO    86       4.277   4.622 -10.609  1.00  0.00
ATOM    102  CA  PRO    86       3.729   4.206  -9.322  1.00  0.00
ATOM    103  C   PRO    86       3.563   5.399  -8.385  1.00  0.00
ATOM    104  O   PRO    86       4.253   6.410  -8.521  1.00  0.00
TER
END
