
#######################################################
#                                                     #
#                        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   35 (   35),  selected   35 , name T0384TS464_2_2
# Molecule2: number of CA atoms  303 ( 2393),  selected  303 , name T0384.pdb
# PARAMETERS: T0384TS464_2_2.T0384.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      K       3           -
LGA    -       -      L       4           -
LGA    -       -      G       5           -
LGA    -       -      V       6           -
LGA    -       -      I       7           -
LGA    -       -      G       8           -
LGA    -       -      T       9           -
LGA    -       -      G      10           -
LGA    -       -      A      11           -
LGA    -       -      I      12           -
LGA    -       -      S      13           -
LGA    -       -      H      14           -
LGA    -       -      H      15           -
LGA    -       -      F      16           -
LGA    -       -      I      17           -
LGA    -       -      E      18           -
LGA    -       -      A      19           -
LGA    -       -      A      20           -
LGA    -       -      H      21           -
LGA    -       -      T      22           -
LGA    -       -      S      23           -
LGA    -       -      G      24           -
LGA    -       -      E      25           -
LGA    -       -      Y      26           -
LGA    -       -      Q      27           -
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      A      30           -
LGA    -       -      I      31           -
LGA    -       -      Y      32           -
LGA    -       -      S      33           -
LGA    -       -      R      34           -
LGA    -       -      K      35           -
LGA    -       -      L      36           -
LGA    -       -      E      37           -
LGA    -       -      T      38           -
LGA    -       -      A      39           -
LGA    -       -      A      40           -
LGA    -       -      T      41           -
LGA    -       -      F      42           -
LGA    -       -      A      43           -
LGA    -       -      S      44           -
LGA    -       -      R      45           -
LGA    -       -      Y      46           -
LGA    -       -      Q      47           -
LGA    -       -      N      48           -
LGA    -       -      I      49           -
LGA    -       -      Q      50           -
LGA    -       -      L      51           -
LGA    -       -      F      52           -
LGA    -       -      D      53           -
LGA    -       -      Q      54           -
LGA    -       -      L      55           -
LGA    -       -      E      56           -
LGA    -       -      V      57           -
LGA    -       -      F      58           -
LGA    -       -      F      59           -
LGA    -       -      K      60           -
LGA    -       -      S      61           -
LGA    -       -      S      62           -
LGA    -       -      F      63           -
LGA    -       -      D      64           -
LGA    -       -      L      65           -
LGA    -       -      V      66           -
LGA    -       -      Y      67           -
LGA    -       -      I      68           -
LGA    -       -      A      69           -
LGA    -       -      S      70           -
LGA    -       -      P      71           -
LGA    -       -      N      72           -
LGA    -       -      S      73           -
LGA    -       -      L      74           -
LGA    -       -      H      75           -
LGA    -       -      F      76           -
LGA    -       -      A      77           -
LGA    -       -      Q      78           -
LGA    -       -      A      79           -
LGA    -       -      K      80           -
LGA    -       -      A      81           -
LGA    -       -      A      82           -
LGA    -       -      L      83           -
LGA    -       -      S      84           -
LGA    -       -      A      85           -
LGA    -       -      G      86           -
LGA    -       -      K      87           -
LGA    -       -      H      88           -
LGA    -       -      V      89           -
LGA    -       -      I      90           -
LGA    -       -      L      91           -
LGA    -       -      E      92           -
LGA    -       -      K      93           -
LGA    -       -      P      94           -
LGA    -       -      A      95           -
LGA    -       -      V      96           -
LGA    -       -      S      97           -
LGA    -       -      Q      98           -
LGA    -       -      P      99           -
LGA    Q     267      Q     100          0.890
LGA    L     268      E     101          0.418
LGA    P     269      W     102          0.821
LGA    I     270      F     103          0.748
LGA    Q     271      D     104          0.604
LGA    Q     272      L     105          0.926
LGA    A     273      I     106          0.803
LGA    P     274      Q     107          0.262
LGA    H     275      T     108          1.099
LGA    T     276      A     109          1.691
LGA    M     277      E     110          0.728
LGA    T     278      K     111           -
LGA    E     279      N     112           -
LGA    E     280      N     113           -
LGA    V     281      C     114           -
LGA    A     282      -       -           -
LGA    A     283      -       -           -
LGA    F     284      F     115          6.317
LGA    A     285      I     116          4.540
LGA    H     286      F     117          3.151
LGA    M     287      E     118          2.036
LGA    I     288      A     119          2.903
LGA    Q     289      A     120          2.566
LGA    Q     290      R     121          4.815
LGA    -       -      N     122           -
LGA    -       -      Y     123           -
LGA    -       -      H     124           -
LGA    -       -      E     125           -
LGA    -       -      K     126           -
LGA    -       -      A     127           -
LGA    -       -      F     128           -
LGA    -       -      T     129           -
LGA    -       -      T     130           -
LGA    -       -      I     131           -
LGA    -       -      K     132           -
LGA    -       -      N     133           -
LGA    -       -      F     134           -
LGA    -       -      L     135           -
LGA    -       -      A     136           -
LGA    -       -      D     137           -
LGA    -       -      Q     139           -
LGA    -       -      V     140           -
LGA    -       -      L     141           -
LGA    -       -      G     142           -
LGA    -       -      A     143           -
LGA    -       -      D     144           -
LGA    -       -      F     145           -
LGA    -       -      N     146           -
LGA    -       -      Y     147           -
LGA    -       -      A     148           -
LGA    -       -      K     149           -
LGA    -       -      Y     150           -
LGA    -       -      S     151           -
LGA    -       -      S     152           -
LGA    -       -      R     169           -
LGA    -       -      F     170           -
LGA    -       -      A     171           -
LGA    -       -      G     172           -
LGA    -       -      G     173           -
LGA    -       -      A     174           -
LGA    -       -      L     175           -
LGA    -       -      M     176           -
LGA    -       -      D     177           -
LGA    -       -      L     178           -
LGA    -       -      G     179           -
LGA    -       -      I     180           -
LGA    -       -      Y     181           -
LGA    -       -      P     182           -
LGA    -       -      L     183           -
LGA    -       -      Y     184           -
LGA    -       -      A     185           -
LGA    -       -      A     186           -
LGA    -       -      V     187           -
LGA    -       -      R     188           -
LGA    -       -      L     189           -
LGA    -       -      F     190           -
LGA    -       -      G     191           -
LGA    -       -      K     192           -
LGA    -       -      A     193           -
LGA    -       -      N     194           -
LGA    -       -      D     195           -
LGA    -       -      A     196           -
LGA    -       -      T     197           -
LGA    -       -      Y     198           -
LGA    -       -      H     199           -
LGA    -       -      A     200           -
LGA    -       -      Q     201           -
LGA    -       -      Q     202           -
LGA    -       -      L     203           -
LGA    -       -      D     204           -
LGA    -       -      N     205           -
LGA    -       -      S     206           -
LGA    -       -      I     207           -
LGA    -       -      D     208           -
LGA    -       -      L     209           -
LGA    -       -      N     210           -
LGA    -       -      G     211           -
LGA    -       -      D     212           -
LGA    -       -      G     213           -
LGA    -       -      I     214           -
LGA    -       -      L     215           -
LGA    -       -      F     216           -
LGA    -       -      Y     217           -
LGA    -       -      P     218           -
LGA    -       -      D     219           -
LGA    -       -      Y     220           -
LGA    -       -      Q     221           -
LGA    -       -      V     222           -
LGA    -       -      H     223           -
LGA    -       -      I     224           -
LGA    -       -      K     225           -
LGA    -       -      A     226           -
LGA    -       -      G     227           -
LGA    -       -      K     228           -
LGA    -       -      N     229           -
LGA    -       -      I     230           -
LGA    -       -      T     231           -
LGA    -       -      S     232           -
LGA    -       -      N     233           -
LGA    -       -      L     234           -
LGA    -       -      P     235           -
LGA    -       -      C     236           -
LGA    -       -      E     237           -
LGA    -       -      I     238           -
LGA    -       -      Y     239           -
LGA    -       -      T     240           -
LGA    -       -      T     241           -
LGA    -       -      D     242           -
LGA    -       -      G     243           -
LGA    -       -      T     244           -
LGA    -       -      L     245           -
LGA    -       -      T     246           -
LGA    -       -      L     247           -
LGA    -       -      N     248           -
LGA    -       -      T     249           -
LGA    -       -      I     250           -
LGA    -       -      E     251           -
LGA    -       -      H     252           -
LGA    -       -      I     253           -
LGA    -       -      R     254           -
LGA    -       -      S     255           -
LGA    -       -      A     256           -
LGA    -       -      I     257           -
LGA    -       -      F     258           -
LGA    -       -      T     259           -
LGA    -       -      D     260           -
LGA    -       -      H     261           -
LGA    -       -      Q     262           -
LGA    -       -      G     263           -
LGA    -       -      N     264           -
LGA    -       -      Q     265           -
LGA    -       -      V     266           -
LGA    -       -      Q     267           -
LGA    -       -      L     268           -
LGA    -       -      P     269           -
LGA    -       -      I     270           -
LGA    -       -      Q     271           -
LGA    -       -      Q     272           -
LGA    -       -      A     273           -
LGA    -       -      P     274           -
LGA    -       -      H     275           -
LGA    -       -      T     276           -
LGA    -       -      M     277           -
LGA    -       -      T     278           -
LGA    -       -      E     279           -
LGA    P     291      E     280          2.868
LGA    -       -      V     281           -
LGA    -       -      A     282           -
LGA    -       -      A     283           -
LGA    D     292      F     284          1.463
LGA    L     293      A     285          2.275
LGA    N     294      H     286          3.498
LGA    L     295      M     287          4.985
LGA    -       -      I     288           -
LGA    -       -      Q     289           -
LGA    -       -      Q     290           -
LGA    Y     296      P     291           #
LGA    Q     297      D     292          3.716
LGA    -       -      L     293           -
LGA    -       -      N     294           -
LGA    T     298      L     295          2.851
LGA    W     299      Y     296          0.492
LGA    L     300      Q     297           #
LGA    Y     301      T     298           #
LGA    -       -      W     299           -
LGA    -       -      L     300           -
LGA    -       -      Y     301           -
LGA    -       -      D     302           -
LGA    -       -      A     303           -
LGA    -       -      G     304           -
LGA    -       -      S     305           -
LGA    -       -      V     306           -
LGA    -       -      H     307           -
LGA    -       -      E     308           -
LGA    -       -      L     309           -
LGA    -       -      L     310           -
LGA    -       -      Y     311           -
LGA    -       -      T     312           -
LGA    -       -      M     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      T     316           -
LGA    -       -      A     317           -
LGA    -       -      G     318           -
LGA    -       -      I     319           -
LGA    -       -      R     320           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   35  303    5.0     26    2.75     7.69      5.971     0.913

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.051614 * X  +  -0.278062 * Y  +  -0.959175 * Z  +  14.269651
  Y_new =  -0.746638 * X  +   0.648593 * Y  +  -0.147848 * Z  +  55.220818
  Z_new =   0.663225 * X  +   0.708526 * Y  +  -0.241088 * Z  +  58.799419 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.898774   -1.242818  [ DEG:   108.7917    -71.2083 ]
  Theta =  -0.725120   -2.416473  [ DEG:   -41.5463   -138.4537 ]
  Phi   =  -1.639815    1.501778  [ DEG:   -93.9545     86.0455 ]
 
# 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: T0384TS464_2_2                                
REMARK     2: T0384.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0384TS464_2_2.T0384.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   35  303   5.0   26   2.75    7.69   5.971
REMARK  ---------------------------------------------------------- 
MOLECULE T0384TS464_2_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0384
PARENT N/A
ATOM      1  CA  GLN   267     -13.320  97.349  79.821  1.00  0.00
ATOM      2  CA  LEU   268     -15.684  95.385  82.051  1.00  0.00
ATOM      3  CA  PRO   269     -13.095  92.643  82.499  1.00  0.00
ATOM      4  CA  ILE   270     -10.296  95.153  83.025  1.00  0.00
ATOM      5  CA  GLN   271     -12.183  96.964  85.793  1.00  0.00
ATOM      6  CA  GLN   272     -13.152  93.735  87.554  1.00  0.00
ATOM      7  CA  ALA   273      -9.662  92.234  87.314  1.00  0.00
ATOM      8  CA  PRO   274      -8.027  95.434  88.557  1.00  0.00
ATOM      9  CA  HIS   275      -9.981  95.030  91.798  1.00  0.00
ATOM     10  CA  THR   276      -8.695  91.579  92.749  1.00  0.00
ATOM     11  CA  MET   277      -5.329  92.154  91.080  1.00  0.00
ATOM     12  CA  THR   278      -5.022  89.524  88.355  1.00  0.00
ATOM     13  CA  GLU   279      -4.460  90.028  84.630  1.00  0.00
ATOM     14  CA  GLU   280      -6.910  90.279  81.737  1.00  0.00
ATOM     15  CA  VAL   281      -5.252  87.494  79.730  1.00  0.00
ATOM     16  CA  ALA   282      -6.092  84.827  82.313  1.00  0.00
ATOM     17  CA  ALA   283      -9.717  85.902  82.011  1.00  0.00
ATOM     18  CA  PHE   284     -11.663  85.456  85.129  1.00  0.00
ATOM     19  CA  ALA   285     -10.209  82.023  85.631  1.00  0.00
ATOM     20  CA  HIS   286     -13.604  81.067  87.038  1.00  0.00
ATOM     21  CA  MET   287     -15.375  82.225  83.910  1.00  0.00
ATOM     22  CA  ILE   288     -13.191  80.497  81.294  1.00  0.00
ATOM     23  CA  GLN   289     -13.538  76.914  80.015  1.00  0.00
ATOM     24  CA  GLN   290     -11.509  74.400  81.971  1.00  0.00
ATOM     25  CA  PRO   291     -10.738  73.634  85.593  1.00  0.00
ATOM     26  CA  ASP   292     -10.738  76.915  87.438  1.00  0.00
ATOM     27  CA  LEU   293      -7.995  75.798  89.794  1.00  0.00
ATOM     28  CA  ASN   294      -5.459  75.163  87.061  1.00  0.00
ATOM     29  CA  LEU   295      -6.536  78.131  84.936  1.00  0.00
ATOM     30  CA  TYR   296      -6.222  80.483  87.867  1.00  0.00
ATOM     31  CA  GLN   297      -2.678  79.309  88.472  1.00  0.00
ATOM     32  CA  THR   298      -1.976  79.730  84.780  1.00  0.00
ATOM     33  CA  TRP   299      -3.066  83.363  84.762  1.00  0.00
ATOM     34  CA  LEU   300      -1.095  84.268  87.866  1.00  0.00
ATOM     35  CA  TYR   301       1.892  82.536  86.296  1.00  0.00
TER
END
