
#######################################################
#                                                     #
#                        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   64 (   64),  selected   64 , name T0372TS464_4_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372TS464_4_1-D2.T0372_D2.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    R     142      R     118           -
LGA    -       -      A     119           -
LGA    -       -      Y     120           -
LGA    -       -      A     121           -
LGA    -       -      D     122           -
LGA    -       -      Y     123           -
LGA    -       -      I     124           -
LGA    -       -      Y     125           -
LGA    -       -      L     126           -
LGA    -       -      R     127           -
LGA    N     143      S     128           #
LGA    H     144      D     129          4.755
LGA    I     145      L     130          3.475
LGA    N     146      A     131          3.161
LGA    R     147      T     132          2.657
LGA    F     148      L     133          2.431
LGA    R     149      K     134          0.652
LGA    N     150      G     135          4.466
LGA    T     151      -       -           -
LGA    Y     152      K     136          4.225
LGA    P     153      K     137          3.536
LGA    D     154      F     138          2.984
LGA    -       -      Q     139           -
LGA    -       -      A     140           -
LGA    -       -      K     141           -
LGA    -       -      R     142           -
LGA    -       -      N     143           -
LGA    -       -      H     144           -
LGA    -       -      I     145           -
LGA    -       -      N     146           -
LGA    -       -      R     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      N     150           -
LGA    -       -      T     151           -
LGA    -       -      Y     152           -
LGA    -       -      P     153           -
LGA    -       -      D     154           -
LGA    -       -      Y     155           -
LGA    -       -      E     156           -
LGA    -       -      Y     157           -
LGA    -       -      T     158           -
LGA    -       -      P     159           -
LGA    -       -      I     160           -
LGA    -       -      T     161           -
LGA    -       -      P     162           -
LGA    -       -      D     163           -
LGA    -       -      R     164           -
LGA    -       -      I     165           -
LGA    -       -      Q     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      L     169           -
LGA    A     173      D     170          4.453
LGA    E     174      L     171          3.705
LGA    W     175      E     172          2.535
LGA    C     176      A     173          3.212
LGA    K     177      E     174          3.388
LGA    -       -      W     175           -
LGA    V     178      C     176          2.802
LGA    N     179      K     177           -
LGA    N     180      V     178           -
LGA    -       -      N     179           -
LGA    -       -      N     180           -
LGA    C     181      C     181          4.381
LGA    D     182      D     182          2.987
LGA    Q     183      Q     183           -
LGA    -       -      Q     184           -
LGA    -       -      E     185           -
LGA    -       -      G     186           -
LGA    -       -      T     187           -
LGA    -       -      G     188           -
LGA    Q     184      N     189           #
LGA    -       -      E     190           -
LGA    -       -      R     191           -
LGA    E     185      R     192          4.119
LGA    -       -      A     193           -
LGA    -       -      L     194           -
LGA    G     186      I     195          1.848
LGA    T     187      Y     196          1.355
LGA    G     188      A     197          2.747
LGA    -       -      L     198           -
LGA    -       -      H     199           -
LGA    -       -      N     200           -
LGA    N     189      F     201          4.371
LGA    E     190      E     202           -
LGA    R     191      A     203           -
LGA    -       -      L     204           -
LGA    -       -      G     205           -
LGA    R     192      L     206          4.981
LGA    A     193      T     207           -
LGA    L     194      G     208           -
LGA    -       -      G     209           -
LGA    -       -      I     210           -
LGA    -       -      L     211           -
LGA    -       -      H     212           -
LGA    -       -      V     213           -
LGA    -       -      N     214           -
LGA    -       -      G     215           -
LGA    -       -      K     216           -
LGA    -       -      I     217           -
LGA    -       -      V     218           -
LGA    -       -      A     219           -
LGA    -       -      F     220           -
LGA    -       -      T     221           -
LGA    I     195      F     222          2.399
LGA    Y     196      G     223          4.124
LGA    -       -      M     224           -
LGA    -       -      P     225           -
LGA    -       -      I     226           -
LGA    -       -      N     227           -
LGA    -       -      H     228           -
LGA    -       -      E     229           -
LGA    -       -      T     230           -
LGA    -       -      F     231           -
LGA    -       -      G     232           -
LGA    A     197      V     233          3.345
LGA    L     198      H     234           -
LGA    H     199      V     235           -
LGA    N     200      E     236           -
LGA    F     201      -       -           -
LGA    E     202      -       -           -
LGA    A     203      -       -           -
LGA    L     204      -       -           -
LGA    G     205      -       -           -
LGA    L     206      -       -           -
LGA    T     207      -       -           -
LGA    G     208      -       -           -
LGA    I     242      -       -           -
LGA    D     243      -       -           -
LGA    G     244      -       -           -
LGA    A     245      -       -           -
LGA    Y     246      -       -           -
LGA    E     268      K     237          3.826
LGA    D     269      A     238          0.525
LGA    -       -      D     239           -
LGA    L     270      T     240           #
LGA    G     271      S     241           -
LGA    I     272      I     242           -
LGA    E     273      D     243           -
LGA    -       -      G     244           -
LGA    -       -      A     245           -
LGA    -       -      Y     246           -
LGA    -       -      A     247           -
LGA    -       -      M     248           -
LGA    -       -      I     249           -
LGA    -       -      N     250           -
LGA    -       -      Y     251           -
LGA    -       -      E     252           -
LGA    -       -      F     253           -
LGA    -       -      A     254           -
LGA    -       -      N     255           -
LGA    -       -      R     256           -
LGA    -       -      I     257           -
LGA    -       -      P     258           -
LGA    -       -      E     259           -
LGA    -       -      Q     260           -
LGA    -       -      Y     261           -
LGA    -       -      I     262           -
LGA    -       -      Y     263           -
LGA    -       -      I     264           -
LGA    -       -      N     265           -
LGA    -       -      R     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      D     269           -
LGA    G     274      L     270           #
LGA    I     287      G     271           -
LGA    L     288      I     272           -
LGA    E     289      E     273           -
LGA    -       -      G     274           -
LGA    -       -      L     275           -
LGA    -       -      R     276           -
LGA    -       -      K     277           -
LGA    -       -      A     278           -
LGA    -       -      K     279           -
LGA    -       -      L     280           -
LGA    -       -      S     281           -
LGA    -       -      Y     282           -
LGA    -       -      Q     283           -
LGA    -       -      P     284           -
LGA    -       -      V     285           -
LGA    -       -      T     286           -
LGA    -       -      I     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   64  172    5.0     29    3.41     6.90      9.215     0.826

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.403177 * X  +  -0.693597 * Y  +  -0.596969 * Z  +  26.408533
  Y_new =   0.115748 * X  +  -0.608448 * Y  +   0.785107 * Z  +  37.356243
  Z_new =  -0.907772 * X  +  -0.385635 * Y  +  -0.165030 * Z  + 140.311996 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.975157    1.166435  [ DEG:  -113.1682     66.8318 ]
  Theta =   1.137943    2.003650  [ DEG:    65.1993    114.8007 ]
  Phi   =   0.279570   -2.862022  [ DEG:    16.0182   -163.9818 ]
 
# 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: T0372TS464_4_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS464_4_1-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   64  172   5.0   29   3.41    6.90   9.215
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS464_4_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM     48  CA  ARG   142      34.116  45.154  32.558  1.00  0.00
ATOM     49  CA  ASN   143      32.681  48.605  33.009  1.00  0.00
ATOM     50  CA  HIS   144      29.648  47.644  30.928  1.00  0.00
ATOM     51  CA  ILE   145      28.857  44.975  33.541  1.00  0.00
ATOM     52  CA  ASN   146      28.749  47.790  36.127  1.00  0.00
ATOM     53  CA  ARG   147      26.448  49.931  33.972  1.00  0.00
ATOM     54  CA  PHE   148      24.187  46.989  33.143  1.00  0.00
ATOM     55  CA  ARG   149      22.677  47.039  36.632  1.00  0.00
ATOM     56  CA  ASN   150      20.908  50.160  35.378  1.00  0.00
ATOM     57  CA  THR   151      20.093  48.701  31.978  1.00  0.00
ATOM     58  CA  TYR   152      18.566  45.346  32.745  1.00  0.00
ATOM     59  CA  PRO   153      17.678  43.063  35.698  1.00  0.00
ATOM     60  CA  ASP   154      18.908  40.030  33.779  1.00  0.00
ATOM     61  CA  ALA   173      45.939  32.681  26.719  1.00  0.00
ATOM     62  CA  GLU   174      43.047  31.544  24.619  1.00  0.00
ATOM     63  CA  TRP   175      44.175  33.667  21.718  1.00  0.00
ATOM     64  CA  CYS   176      47.629  32.010  22.069  1.00  0.00
ATOM     65  CA  LYS   177      46.137  28.541  21.524  1.00  0.00
ATOM     66  CA  VAL   178      44.165  29.751  18.475  1.00  0.00
ATOM     67  CA  ASN   179      47.325  31.102  16.982  1.00  0.00
ATOM     68  CA  ASN   180      49.168  27.873  17.800  1.00  0.00
ATOM     69  CA  CYS   181      46.488  25.620  16.319  1.00  0.00
ATOM     70  CA  ASP   182      45.928  27.678  13.254  1.00  0.00
ATOM     71  CA  GLN   183      49.659  28.344  12.759  1.00  0.00
ATOM     72  CA  GLN   184      48.871  32.000  12.094  1.00  0.00
ATOM     73  CA  GLU   185      50.195  34.599  14.483  1.00  0.00
ATOM     74  CA  GLY   186      48.790  37.980  15.428  1.00  0.00
ATOM     75  CA  THR   187      49.915  41.556  15.984  1.00  0.00
ATOM     76  CA  GLY   188      49.701  43.325  19.255  1.00  0.00
ATOM     77  CA  ASN   189      47.013  45.414  17.792  1.00  0.00
ATOM     78  CA  GLU   190      44.534  42.741  16.757  1.00  0.00
ATOM     79  CA  ARG   191      44.710  40.798  20.035  1.00  0.00
ATOM     80  CA  ARG   192      44.072  44.119  21.695  1.00  0.00
ATOM     81  CA  ALA   193      41.149  44.683  19.322  1.00  0.00
ATOM     82  CA  LEU   194      39.802  41.210  20.115  1.00  0.00
ATOM     83  CA  ILE   195      40.529  41.743  23.799  1.00  0.00
ATOM     84  CA  TYR   196      37.638  44.182  24.044  1.00  0.00
ATOM     85  CA  ALA   197      35.222  41.986  22.086  1.00  0.00
ATOM     86  CA  LEU   198      35.886  38.894  24.215  1.00  0.00
ATOM     87  CA  HIS   199      35.254  41.055  27.286  1.00  0.00
ATOM     88  CA  ASN   200      31.886  42.255  25.993  1.00  0.00
ATOM     89  CA  PHE   201      28.565  41.142  27.207  1.00  0.00
ATOM     90  CA  GLU   202      29.600  37.889  28.946  1.00  0.00
ATOM     91  CA  ALA   203      28.604  39.369  32.292  1.00  0.00
ATOM     92  CA  LEU   204      25.151  39.777  30.802  1.00  0.00
ATOM     93  CA  GLY   205      24.293  36.368  29.406  1.00  0.00
ATOM     94  CA  LEU   206      25.268  37.249  25.840  1.00  0.00
ATOM     95  CA  THR   207      27.438  34.647  24.099  1.00  0.00
ATOM     96  CA  GLY   208      30.231  36.630  22.482  1.00  0.00
ATOM     97  CA  ILE   242      15.027  45.652  28.916  1.00  0.00
ATOM     98  CA  ASP   243      16.697  42.464  30.260  1.00  0.00
ATOM     99  CA  GLY   244      20.299  43.232  28.986  1.00  0.00
ATOM    100  CA  ALA   245      20.182  40.264  26.602  1.00  0.00
ATOM    101  CA  TYR   246      19.704  40.804  22.847  1.00  0.00
ATOM    102  CA  GLU   268      39.014  30.765  24.745  1.00  0.00
ATOM    103  CA  ASP   269      39.096  32.797  27.926  1.00  0.00
ATOM    104  CA  LEU   270      35.446  33.886  27.773  1.00  0.00
ATOM    105  CA  GLY   271      33.828  30.808  26.229  1.00  0.00
ATOM    106  CA  ILE   272      32.579  32.959  23.371  1.00  0.00
ATOM    107  CA  GLU   273      31.997  31.112  20.097  1.00  0.00
ATOM    108  CA  GLY   274      32.261  32.036  16.402  1.00  0.00
ATOM    109  CA  ILE   287      32.367  54.118  14.327  1.00  0.00
ATOM    110  CA  LEU   288      35.111  56.012  12.519  1.00  0.00
ATOM    111  CA  GLU   289      38.724  54.976  13.300  1.00  0.00
TER
END
