
#######################################################
#                                                     #
#                        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   58 (   58),  selected   58 , name T0320TS464_5_1-D1
# Molecule2: number of CA atoms  214 ( 1760),  selected  214 , name T0320_D1.pdb
# PARAMETERS: T0320TS464_5_1-D1.T0320_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      Q       2           -
LGA    -       -      L       3           -
LGA    -       -      S       4           -
LGA    -       -      K       5           -
LGA    -       -      A       6           -
LGA    -       -      A       7           -
LGA    -       -      E       8           -
LGA    -       -      M       9           -
LGA    -       -      C      10           -
LGA    -       -      Y      11           -
LGA    -       -      E      12           -
LGA    -       -      I      13           -
LGA    -       -      T      14           -
LGA    -       -      N      15           -
LGA    -       -      S      16           -
LGA    -       -      Y      17           -
LGA    -       -      L      18           -
LGA    -       -      H      19           -
LGA    -       -      I      20           -
LGA    -       -      D      21           -
LGA    -       -      Q      22           -
LGA    -       -      K      23           -
LGA    -       -      S      24           -
LGA    -       -      Q      25           -
LGA    -       -      I      26           -
LGA    -       -      I      27           -
LGA    -       -      A      28           -
LGA    -       -      S      29           -
LGA    -       -      T      30           -
LGA    -       -      Q      31           -
LGA    -       -      E      32           -
LGA    -       -      A      33           -
LGA    -       -      I      34           -
LGA    -       -      R      35           -
LGA    -       -      L      36           -
LGA    -       -      T      37           -
LGA    -       -      R      38           -
LGA    -       -      K      39           -
LGA    -       -      Y      40           -
LGA    -       -      L      41           -
LGA    -       -      L      42           -
LGA    -       -      S      43           -
LGA    -       -      E      44           -
LGA    -       -      I      45           -
LGA    -       -      F      46           -
LGA    -       -      V      47           -
LGA    -       -      R      48           -
LGA    -       -      W      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    -       -      L      52           -
LGA    -       -      N      53           -
LGA    -       -      G      54           -
LGA    -       -      E      55           -
LGA    -       -      I      56           -
LGA    -       -      S      57           -
LGA    I      34      F      58          1.990
LGA    R      35      S      59          2.518
LGA    L      36      Y      60          1.516
LGA    T      37      N      61          4.834
LGA    R      38      G      62           -
LGA    F      58      -       -           -
LGA    S      59      G      63          3.216
LGA    Y      60      K      64          2.252
LGA    N      61      -       -           -
LGA    G      62      -       -           -
LGA    G      63      -       -           -
LGA    K      64      -       -           -
LGA    D      65      D      65           #
LGA    C      66      C      66           #
LGA    Q      67      Q      67          3.979
LGA    V      68      V      68          4.345
LGA    L      69      L      69          4.009
LGA    L      70      L      70          1.706
LGA    L      71      L      71          1.420
LGA    L      72      L      72          2.273
LGA    Y      73      Y      73          3.739
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      C      76           -
LGA    -       -      L      77           -
LGA    -       -      W      78           -
LGA    -       -      E      79           -
LGA    -       -      Y      80           -
LGA    -       -      F      81           -
LGA    -       -      F      82           -
LGA    -       -      I      83           -
LGA    -       -      K      84           -
LGA    -       -      A      85           -
LGA    -       -      Q      86           -
LGA    -       -      N      87           -
LGA    -       -      S      88           -
LGA    -       -      F      97           -
LGA    -       -      P      98           -
LGA    P     103      M      99           #
LGA    -       -      Q     100           -
LGA    T     104      R     101           #
LGA    V     105      L     102          4.570
LGA    F     106      P     103          4.111
LGA    I     107      T     104          3.858
LGA    D     108      V     105          4.983
LGA    Q     109      F     106          4.688
LGA    -       -      I     107           -
LGA    -       -      D     108           -
LGA    -       -      Q     109           -
LGA    -       -      E     110           -
LGA    -       -      E     111           -
LGA    -       -      T     112           -
LGA    -       -      F     113           -
LGA    S     138      P     114          1.235
LGA    G     139      T     115          1.628
LGA    A     140      L     116          1.803
LGA    S     141      E     117          0.903
LGA    V     142      N     118          1.461
LGA    N     143      F     119          2.235
LGA    M     144      V     120          2.249
LGA    A     145      L     121          2.269
LGA    D     146      E     122          1.656
LGA    A     147      T     123          1.803
LGA    F     148      S     124          1.792
LGA    R     149      E     125          1.854
LGA    D     150      R     126          2.116
LGA    F     151      Y     127          2.245
LGA    I     152      C     128          2.454
LGA    K     153      -       -           -
LGA    I     154      -       -           -
LGA    Y     155      -       -           -
LGA    P     156      -       -           -
LGA    E     157      -       -           -
LGA    T     158      -       -           -
LGA    E     159      L     129           #
LGA    A     160      S     130          2.915
LGA    I     161      L     131          5.588
LGA    V     162      Y     132          5.336
LGA    -       -      E     133           -
LGA    -       -      S     134           -
LGA    -       -      Q     135           -
LGA    -       -      R     136           -
LGA    -       -      V     142           -
LGA    -       -      N     143           -
LGA    -       -      M     144           -
LGA    -       -      A     145           -
LGA    -       -      D     146           -
LGA    -       -      A     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      D     150           -
LGA    -       -      F     151           -
LGA    -       -      I     152           -
LGA    -       -      K     153           -
LGA    -       -      I     154           -
LGA    -       -      Y     155           -
LGA    -       -      P     156           -
LGA    -       -      E     157           -
LGA    -       -      T     158           -
LGA    -       -      E     159           -
LGA    -       -      A     160           -
LGA    -       -      I     161           -
LGA    -       -      V     162           -
LGA    -       -      I     163           -
LGA    -       -      G     164           -
LGA    -       -      I     165           -
LGA    -       -      R     166           -
LGA    -       -      H     167           -
LGA    -       -      T     168           -
LGA    -       -      D     169           -
LGA    -       -      P     170           -
LGA    -       -      F     171           -
LGA    -       -      G     172           -
LGA    -       -      E     173           -
LGA    -       -      A     174           -
LGA    -       -      L     175           -
LGA    -       -      K     176           -
LGA    -       -      P     177           -
LGA    -       -      I     178           -
LGA    -       -      Q     179           -
LGA    -       -      R     180           -
LGA    -       -      T     181           -
LGA    -       -      D     182           -
LGA    -       -      S     183           -
LGA    -       -      N     184           -
LGA    -       -      W     185           -
LGA    -       -      P     186           -
LGA    -       -      D     187           -
LGA    -       -      F     188           -
LGA    -       -      M     189           -
LGA    -       -      R     190           -
LGA    -       -      L     191           -
LGA    -       -      Q     192           -
LGA    -       -      P     193           -
LGA    -       -      L     194           -
LGA    -       -      L     195           -
LGA    -       -      H     196           -
LGA    -       -      W     197           -
LGA    -       -      D     198           -
LGA    -       -      L     199           -
LGA    -       -      T     200           -
LGA    S     223      N     201          1.686
LGA    I     224      I     202          2.440
LGA    G     225      W     203          2.351
LGA    -       -      S     204           -
LGA    -       -      F     205           -
LGA    -       -      L     206           -
LGA    -       -      L     207           -
LGA    -       -      Y     208           -
LGA    -       -      S     209           -
LGA    -       -      N     210           -
LGA    -       -      E     211           -
LGA    -       -      P     212           -
LGA    -       -      I     213           -
LGA    -       -      C     214           -
LGA    -       -      G     215           -
LGA    -       -      L     216           -
LGA    -       -      Y     217           -
LGA    -       -      G     218           -
LGA    -       -      K     219           -
LGA    -       -      G     220           -
LGA    -       -      F     221           -
LGA    G     226      T     222          4.513
LGA    I     227      S     223          4.535
LGA    -       -      I     224           -
LGA    -       -      G     225           -
LGA    -       -      G     226           -
LGA    -       -      I     227           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   58  214    5.0     41    3.13    19.51     12.356     1.267

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.913841 * X  +  -0.387107 * Y  +  -0.122647 * Z  +  55.129284
  Y_new =   0.144337 * X  +   0.591962 * Y  +  -0.792936 * Z  +  12.933046
  Z_new =   0.379554 * X  +   0.706915 * Y  +   0.596833 * Z  + -29.110205 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.869634   -2.271959  [ DEG:    49.8263   -130.1737 ]
  Theta =  -0.389314   -2.752279  [ DEG:   -22.3060   -157.6940 ]
  Phi   =   0.156652   -2.984941  [ DEG:     8.9755   -171.0245 ]
 
# 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: T0320TS464_5_1-D1                             
REMARK     2: T0320_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_5_1-D1.T0320_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   58  214   5.0   41   3.13   19.51  12.356
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_5_1-D1
REMARK PARENT number 1
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  ILE    34      19.897  28.948  26.671  1.00  0.00
ATOM      2  CA  ARG    35      20.213  25.884  24.481  1.00  0.00
ATOM      3  CA  LEU    36      19.942  27.784  21.231  1.00  0.00
ATOM      4  CA  THR    37      22.362  30.432  22.485  1.00  0.00
ATOM      5  CA  ARG    38      24.856  27.667  23.491  1.00  0.00
ATOM      6  CA  PHE    58      18.006  20.366  20.376  1.00  0.00
ATOM      7  CA  SER    59      18.512  22.099  17.068  1.00  0.00
ATOM      8  CA  TYR    60      15.281  22.189  15.091  1.00  0.00
ATOM      9  CA  ASN    61      15.367  22.536  11.309  1.00  0.00
ATOM     10  CA  GLY    62      12.953  25.429  11.830  1.00  0.00
ATOM     11  CA  GLY    63      13.004  28.384  14.193  1.00  0.00
ATOM     12  CA  LYS    64       9.220  28.226  14.084  1.00  0.00
ATOM     13  CA  ASP    65       9.532  24.742  15.565  1.00  0.00
ATOM     14  CA  CYS    66      12.283  26.374  17.651  1.00  0.00
ATOM     15  CA  GLN    67       9.965  29.148  18.838  1.00  0.00
ATOM     16  CA  VAL    68       7.119  26.691  19.401  1.00  0.00
ATOM     17  CA  LEU    69       9.501  24.380  21.273  1.00  0.00
ATOM     18  CA  LEU    70      10.487  27.216  23.668  1.00  0.00
ATOM     19  CA  LEU    71       6.805  27.869  24.384  1.00  0.00
ATOM     20  CA  LEU    72       6.359  24.219  25.321  1.00  0.00
ATOM     21  CA  TYR    73       9.520  24.295  27.427  1.00  0.00
ATOM     22  CA  PRO   103      16.313  37.003  36.457  1.00  0.00
ATOM     23  CA  THR   104      18.675  38.471  33.874  1.00  0.00
ATOM     24  CA  VAL   105      19.488  36.538  30.699  1.00  0.00
ATOM     25  CA  PHE   106      22.488  37.664  28.656  1.00  0.00
ATOM     26  CA  ILE   107      22.223  36.564  25.067  1.00  0.00
ATOM     27  CA  ASP   108      25.512  36.294  23.182  1.00  0.00
ATOM     28  CA  GLN   109      24.837  35.689  19.466  1.00  0.00
ATOM     29  CA  SER   138      24.923  32.433   7.579  1.00  0.00
ATOM     30  CA  GLY   139      21.508  30.761   7.165  1.00  0.00
ATOM     31  CA  ALA   140      21.695  29.123  10.620  1.00  0.00
ATOM     32  CA  SER   141      22.496  32.323  12.561  1.00  0.00
ATOM     33  CA  VAL   142      19.555  33.907  10.735  1.00  0.00
ATOM     34  CA  ASN   143      17.253  31.122  11.959  1.00  0.00
ATOM     35  CA  MET   144      18.642  31.267  15.510  1.00  0.00
ATOM     36  CA  ALA   145      18.082  35.033  15.655  1.00  0.00
ATOM     37  CA  ASP   146      14.524  36.243  15.441  1.00  0.00
ATOM     38  CA  ALA   147      13.447  33.599  17.956  1.00  0.00
ATOM     39  CA  PHE   148      15.789  35.236  20.488  1.00  0.00
ATOM     40  CA  ARG   149      13.820  38.470  19.955  1.00  0.00
ATOM     41  CA  ASP   150      10.467  36.722  20.425  1.00  0.00
ATOM     42  CA  PHE   151      11.682  34.817  23.484  1.00  0.00
ATOM     43  CA  ILE   152      11.521  37.954  25.623  1.00  0.00
ATOM     44  CA  LYS   153       7.766  37.405  25.419  1.00  0.00
ATOM     45  CA  ILE   154       7.978  33.658  25.930  1.00  0.00
ATOM     46  CA  TYR   155      10.200  33.250  28.943  1.00  0.00
ATOM     47  CA  PRO   156      10.953  32.928  32.611  1.00  0.00
ATOM     48  CA  GLU   157      13.767  35.432  32.054  1.00  0.00
ATOM     49  CA  THR   158      12.681  38.790  33.543  1.00  0.00
ATOM     50  CA  GLU   159      15.040  40.673  31.188  1.00  0.00
ATOM     51  CA  ALA   160      17.050  39.647  28.158  1.00  0.00
ATOM     52  CA  ILE   161      20.006  41.774  27.033  1.00  0.00
ATOM     53  CA  VAL   162      21.451  40.737  23.697  1.00  0.00
ATOM     54  CA  SER   223       6.773  16.393  18.249  1.00  0.00
ATOM     55  CA  ILE   224       7.412  20.068  17.482  1.00  0.00
ATOM     56  CA  GLY   225       9.096  19.302  14.167  1.00  0.00
ATOM     57  CA  GLY   226      12.260  17.972  12.551  1.00  0.00
ATOM     58  CA  ILE   227      15.246  18.237  14.849  1.00  0.00
TER
END
