
#######################################################
#                                                     #
#                        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   34 (   34),  selected   34 , name T0320TS464_1_2
# Molecule2: number of CA atoms  287 ( 2364),  selected  287 , name T0320.pdb
# PARAMETERS: T0320TS464_1_2.T0320.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    -       -      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    -       -      F      58           -
LGA    -       -      S      59           -
LGA    -       -      Y      60           -
LGA    -       -      N      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      K      64           -
LGA    -       -      D      65           -
LGA    -       -      C      66           -
LGA    -       -      Q      67           -
LGA    -       -      V      68           -
LGA    -       -      L      69           -
LGA    -       -      L      70           -
LGA    -       -      L      71           -
LGA    -       -      L      72           -
LGA    -       -      Y      73           -
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    -       -      M      99           -
LGA    -       -      Q     100           -
LGA    -       -      R     101           -
LGA    -       -      L     102           -
LGA    -       -      P     103           -
LGA    -       -      T     104           -
LGA    -       -      V     105           -
LGA    -       -      F     106           -
LGA    -       -      I     107           -
LGA    -       -      D     108           -
LGA    -       -      Q     109           -
LGA    -       -      E     110           -
LGA    -       -      E     111           -
LGA    -       -      T     112           -
LGA    -       -      F     113           -
LGA    -       -      P     114           -
LGA    -       -      T     115           -
LGA    -       -      L     116           -
LGA    -       -      E     117           -
LGA    -       -      N     118           -
LGA    -       -      F     119           -
LGA    -       -      V     120           -
LGA    -       -      L     121           -
LGA    -       -      E     122           -
LGA    -       -      T     123           -
LGA    -       -      S     124           -
LGA    -       -      E     125           -
LGA    -       -      R     126           -
LGA    -       -      Y     127           -
LGA    -       -      C     128           -
LGA    -       -      L     129           -
LGA    -       -      S     130           -
LGA    -       -      L     131           -
LGA    -       -      Y     132           -
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    -       -      N     201           -
LGA    -       -      I     202           -
LGA    -       -      W     203           -
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    -       -      T     222           -
LGA    F      58      S     223          3.064
LGA    S      59      I     224          2.390
LGA    Y      60      G     225          0.993
LGA    N      61      G     226          1.674
LGA    G      62      I     227          2.126
LGA    G      63      -       -           -
LGA    K      64      N     228          3.975
LGA    D      65      N     229          2.806
LGA    C      66      S     230          2.450
LGA    Q      67      L     231          2.315
LGA    V      68      -       -           -
LGA    L      69      P     232          4.430
LGA    L      70      N     233          2.144
LGA    L      71      P     234          1.742
LGA    L      72      H     235          4.232
LGA    Y      73      L     236          4.222
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    -       -      V     275           -
LGA    A     145      D     276          0.513
LGA    D     146      K     277          4.024
LGA    -       -      E     278           -
LGA    A     147      R     279          3.765
LGA    F     148      F     280          3.309
LGA    R     149      S     281          2.177
LGA    D     150      K     282          2.756
LGA    F     151      Y     283          2.876
LGA    I     152      H     284          1.256
LGA    K     153      D     285          1.414
LGA    I     154      N     286          2.542
LGA    Y     155      Y     287          1.423
LGA    P     156      Y     288          4.905
LGA    E     157      P     289          4.344
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    S     223      R     303          4.915
LGA    I     224      I     304          2.166
LGA    G     225      -       -           -
LGA    G     226      -       -           -
LGA    I     227      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   34  287    5.0     29    3.04    10.34      6.097     0.924

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.222433 * X  +   0.927888 * Y  +   0.299246 * Z  + -82.385071
  Y_new =  -0.710237 * X  +  -0.056051 * Y  +   0.701728 * Z  +  90.385361
  Z_new =   0.667897 * X  +  -0.368623 * Y  +   0.646553 * Z  +  20.037666 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.518171    2.623421  [ DEG:   -29.6890    150.3110 ]
  Theta =  -0.731380   -2.410213  [ DEG:   -41.9050   -138.0950 ]
  Phi   =  -1.267290    1.874302  [ DEG:   -72.6104    107.3896 ]
 
# 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_1_2                                
REMARK     2: T0320.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS464_1_2.T0320.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   34  287   5.0   29   3.04   10.34   6.097
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS464_1_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT N/A
ATOM      1  CA  PHE    58      19.319  20.843  13.711  1.00  0.00
ATOM      2  CA  SER    59      21.919  23.406  12.780  1.00  0.00
ATOM      3  CA  TYR    60      25.068  21.723  11.508  1.00  0.00
ATOM      4  CA  ASN    61      28.403  23.534  11.681  1.00  0.00
ATOM      5  CA  GLY    62      28.694  22.701   7.981  1.00  0.00
ATOM      6  CA  GLY    63      26.273  23.071   5.097  1.00  0.00
ATOM      7  CA  LYS    64      27.998  20.058   3.580  1.00  0.00
ATOM      8  CA  ASP    65      26.854  18.124   6.644  1.00  0.00
ATOM      9  CA  CYS    66      23.353  19.539   6.206  1.00  0.00
ATOM     10  CA  GLN    67      23.332  18.502   2.544  1.00  0.00
ATOM     11  CA  VAL    68      24.139  14.950   3.573  1.00  0.00
ATOM     12  CA  LEU    69      21.516  14.948   6.345  1.00  0.00
ATOM     13  CA  LEU    70      18.906  15.817   3.740  1.00  0.00
ATOM     14  CA  LEU    71      18.636  13.035   1.164  1.00  0.00
ATOM     15  CA  LEU    72      19.474  11.290   4.563  1.00  0.00
ATOM     16  CA  TYR    73      16.225  12.936   5.642  1.00  0.00
ATOM     17  CA  ALA   145      22.180  29.442   1.249  1.00  0.00
ATOM     18  CA  ASP   146      23.778  27.263  -1.371  1.00  0.00
ATOM     19  CA  ALA   147      22.217  24.175   0.210  1.00  0.00
ATOM     20  CA  PHE   148      18.789  25.693  -0.511  1.00  0.00
ATOM     21  CA  ARG   149      19.808  25.808  -4.194  1.00  0.00
ATOM     22  CA  ASP   150      20.975  22.180  -4.173  1.00  0.00
ATOM     23  CA  PHE   151      17.881  21.004  -2.302  1.00  0.00
ATOM     24  CA  ILE   152      15.735  21.382  -5.415  1.00  0.00
ATOM     25  CA  LYS   153      17.568  18.257  -6.560  1.00  0.00
ATOM     26  CA  ILE   154      17.364  16.534  -3.193  1.00  0.00
ATOM     27  CA  TYR   155      13.743  16.841  -2.203  1.00  0.00
ATOM     28  CA  PRO   156      10.417  18.303  -3.433  1.00  0.00
ATOM     29  CA  GLU   157       9.590  19.486   0.075  1.00  0.00
ATOM     30  CA  SER   223      26.384  11.086  12.539  1.00  0.00
ATOM     31  CA  ILE   224      26.463  13.556   9.641  1.00  0.00
ATOM     32  CA  GLY   225      28.800  15.935  11.456  1.00  0.00
ATOM     33  CA  GLY   226      29.029  18.517  14.225  1.00  0.00
ATOM     34  CA  ILE   227      25.665  20.030  15.035  1.00  0.00
TER
END
