
#######################################################
#                                                     #
#                        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   12 (   48),  selected   12 , name T0386AL381_5
# Molecule2: number of CA atoms  291 ( 2337),  selected  291 , name T0386.pdb
# PARAMETERS: T0386AL381_5.T0386.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    -       -      K       9           -
LGA    -       -      N      10           -
LGA    -       -      T      11           -
LGA    -       -      E      12           -
LGA    -       -      I      13           -
LGA    -       -      I      14           -
LGA    -       -      S      15           -
LGA    -       -      P      16           -
LGA    -       -      H      17           -
LGA    -       -      H      18           -
LGA    -       -      Y      19           -
LGA    -       -      V      20           -
LGA    -       -      Y      21           -
LGA    -       -      P      22           -
LGA    -       -      N      23           -
LGA    -       -      T      24           -
LGA    -       -      T      25           -
LGA    -       -      T      26           -
LGA    -       -      L      27           -
LGA    -       -      K      28           -
LGA    -       -      N      29           -
LGA    -       -      K      30           -
LGA    -       -      Y      31           -
LGA    -       -      G      32           -
LGA    -       -      I      33           -
LGA    -       -      K      34           -
LGA    -       -      N      35           -
LGA    -       -      L      36           -
LGA    -       -      N      37           -
LGA    -       -      A      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      E      41           -
LGA    -       -      K      42           -
LGA    -       -      C      43           -
LGA    -       -      S      44           -
LGA    -       -      H      45           -
LGA    -       -      D      46           -
LGA    -       -      T      47           -
LGA    -       -      A      48           -
LGA    -       -      K      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      I      52           -
LGA    -       -      N      53           -
LGA    -       -      L      54           -
LGA    -       -      R      55           -
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    -       -      S      58           -
LGA    -       -      L      59           -
LGA    -       -      P      60           -
LGA    -       -      E      61           -
LGA    -       -      Y      62           -
LGA    -       -      F      63           -
LGA    -       -      D      64           -
LGA    -       -      T      65           -
LGA    -       -      A      66           -
LGA    -       -      Y      67           -
LGA    -       -      L      68           -
LGA    -       -      C      69           -
LGA    -       -      H      70           -
LGA    -       -      I      71           -
LGA    -       -      H      72           -
LGA    -       -      Q      73           -
LGA    -       -      Q      74           -
LGA    -       -      L      75           -
LGA    -       -      F      76           -
LGA    -       -      K      77           -
LGA    -       -      N      78           -
LGA    -       -      T      79           -
LGA    -       -      F      80           -
LGA    -       -      E      81           -
LGA    -       -      W      82           -
LGA    -       -      A      83           -
LGA    -       -      G      84           -
LGA    -       -      Y      85           -
LGA    -       -      L      86           -
LGA    -       -      R      87           -
LGA    -       -      H      88           -
LGA    -       -      I      89           -
LGA    -       -      P      90           -
LGA    -       -      F      91           -
LGA    -       -      T      92           -
LGA    -       -      F      93           -
LGA    -       -      A      94           -
LGA    -       -      D      95           -
LGA    -       -      G      96           -
LGA    -       -      T      97           -
LGA    -       -      T      98           -
LGA    -       -      A      99           -
LGA    -       -      A     100           -
LGA    -       -      M     101           -
LGA    -       -      P     102           -
LGA    -       -      E     103           -
LGA    -       -      M     104           -
LGA    -       -      K     105           -
LGA    -       -      R     106           -
LGA    -       -      T     107           -
LGA    -       -      G     108           -
LGA    -       -      W     109           -
LGA    -       -      K     110           -
LGA    -       -      N     111           -
LGA    -       -      A     112           -
LGA    -       -      F     113           -
LGA    -       -      A     114           -
LGA    -       -      I     115           -
LGA    -       -      G     116           -
LGA    -       -      D     117           -
LGA    -       -      E     118           -
LGA    -       -      I     119           -
LGA    -       -      Q     120           -
LGA    -       -      E     121           -
LGA    -       -      G     122           -
LGA    -       -      L     123           -
LGA    -       -      Q     124           -
LGA    -       -      R     125           -
LGA    -       -      L     126           -
LGA    -       -      D     127           -
LGA    -       -      Q     128           -
LGA    -       -      T     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      E     132           -
LGA    -       -      K     133           -
LGA    -       -      N     134           -
LGA    -       -      N     135           -
LGA    -       -      L     136           -
LGA    -       -      Q     137           -
LGA    -       -      G     138           -
LGA    -       -      L     139           -
LGA    -       -      T     140           -
LGA    -       -      R     141           -
LGA    -       -      E     142           -
LGA    -       -      E     143           -
LGA    -       -      F     144           -
LGA    -       -      N     145           -
LGA    -       -      S     146           -
LGA    -       -      E     147           -
LGA    -       -      A     148           -
LGA    -       -      I     149           -
LGA    -       -      E     150           -
LGA    -       -      L     151           -
LGA    -       -      F     152           -
LGA    -       -      N     153           -
LGA    -       -      S     154           -
LGA    -       -      L     155           -
LGA    -       -      N     156           -
LGA    -       -      Q     157           -
LGA    -       -      L     158           -
LGA    -       -      H     159           -
LGA    -       -      P     160           -
LGA    -       -      F     161           -
LGA    -       -      R     162           -
LGA    -       -      E     163           -
LGA    -       -      G     164           -
LGA    -       -      N     165           -
LGA    -       -      G     166           -
LGA    -       -      R     167           -
LGA    -       -      T     168           -
LGA    -       -      Q     169           -
LGA    -       -      R     170           -
LGA    -       -      L     171           -
LGA    -       -      F     172           -
LGA    -       -      F     173           -
LGA    -       -      E     174           -
LGA    -       -      N     175           -
LGA    -       -      L     176           -
LGA    -       -      A     177           -
LGA    -       -      K     178           -
LGA    -       -      A     179           -
LGA    -       -      A     180           -
LGA    -       -      G     181           -
LGA    -       -      H     182           -
LGA    -       -      Q     183           -
LGA    -       -      L     184           -
LGA    -       -      N     185           -
LGA    -       -      F     186           -
LGA    -       -      S     187           -
LGA    -       -      L     188           -
LGA    -       -      I     189           -
LGA    -       -      T     190           -
LGA    -       -      K     191           -
LGA    -       -      E     192           -
LGA    -       -      R     193           -
LGA    -       -      M     194           -
LGA    -       -      M     195           -
LGA    -       -      V     196           -
LGA    -       -      A     197           -
LGA    -       -      S     198           -
LGA    -       -      V     199           -
LGA    -       -      A     200           -
LGA    -       -      V     201           -
LGA    -       -      A     202           -
LGA    -       -      E     203           -
LGA    -       -      N     204           -
LGA    -       -      G     205           -
LGA    -       -      D     206           -
LGA    -       -      L     207           -
LGA    -       -      E     208           -
LGA    -       -      P     209           -
LGA    -       -      M     210           -
LGA    -       -      Q     211           -
LGA    -       -      H     212           -
LGA    -       -      L     213           -
LGA    -       -      F     214           -
LGA    -       -      E     215           -
LGA    -       -      D     216           -
LGA    -       -      I     217           -
LGA    -       -      S     218           -
LGA    -       -      N     219           -
LGA    E      12      P     220          1.421
LGA    I      13      E     221          1.186
LGA    I      14      K     222          3.450
LGA    S      15      I     223           -
LGA    -       -      R     224           -
LGA    -       -      L     225           -
LGA    -       -      L     226           -
LGA    -       -      K     227           -
LGA    -       -      E     228           -
LGA    -       -      F     229           -
LGA    -       -      M     230           -
LGA    -       -      H     231           -
LGA    -       -      T     232           -
LGA    -       -      M     233           -
LGA    -       -      K     234           -
LGA    -       -      N     235           -
LGA    -       -      T     236           -
LGA    -       -      G     237           -
LGA    -       -      R     238           -
LGA    -       -      N     239           -
LGA    -       -      V     240           -
LGA    -       -      N     241           -
LGA    -       -      D     242           -
LGA    -       -      R     243           -
LGA    -       -      P     244           -
LGA    -       -      V     245           -
LGA    -       -      M     246           -
LGA    -       -      V     247           -
LGA    -       -      A     248           -
LGA    -       -      K     249           -
LGA    -       -      E     250           -
LGA    -       -      G     251           -
LGA    -       -      E     252           -
LGA    -       -      T     253           -
LGA    -       -      Y     254           -
LGA    -       -      T     255           -
LGA    -       -      G     256           -
LGA    -       -      T     257           -
LGA    -       -      Y     258           -
LGA    -       -      R     259           -
LGA    -       -      G     260           -
LGA    -       -      A     261           -
LGA    -       -      G     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    P      16      G     265          2.971
LGA    -       -      F     266           -
LGA    -       -      A     267           -
LGA    -       -      L     268           -
LGA    -       -      N     269           -
LGA    -       -      V     270           -
LGA    -       -      K     271           -
LGA    -       -      G     272           -
LGA    -       -      A     273           -
LGA    -       -      Y     274           -
LGA    -       -      I     275           -
LGA    -       -      I     276           -
LGA    H      17      G     277          2.581
LGA    -       -      N     278           -
LGA    H      18      I     279          1.528
LGA    Y      19      D     280          2.026
LGA    V      20      H     281          0.857
LGA    Y      21      L     282          0.857
LGA    P      22      P     283          3.111
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      Q     286           -
LGA    N      23      L     287          1.135
LGA    -       -      K     288           -
LGA    -       -      I     289           -
LGA    -       -      L     290           -
LGA    -       -      K     291           -
LGA    -       -      P     292           -
LGA    -       -      G     293           -
LGA    -       -      D     294           -
LGA    -       -      K     295           -
LGA    -       -      I     296           -
LGA    -       -      T     297           -
LGA    -       -      F     298           -
LGA    -       -      T     299           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   12  291    5.0     11    2.13     9.09      2.988     0.494

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.241006 * X  +   0.684804 * Y  +   0.687720 * Z  +  -4.857689
  Y_new =  -0.417084 * X  +  -0.712916 * Y  +   0.563730 * Z  +  64.489388
  Z_new =   0.876332 * X  +  -0.150975 * Y  +   0.457438 * Z  +  28.720146 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.318787    2.822806  [ DEG:   -18.2652    161.7348 ]
  Theta =  -1.068193   -2.073399  [ DEG:   -61.2030   -118.7970 ]
  Phi   =  -2.094759    1.046833  [ DEG:  -120.0209     59.9791 ]
 
# 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: T0386AL381_5                                  
REMARK     2: T0386.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386AL381_5.T0386.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   12  291   5.0   11   2.13    9.09   2.988
REMARK  ---------------------------------------------------------- 
MOLECULE T0386AL381_5
REMARK Aligment from pdb entry: 1fdw
ATOM      1  N   GLU    12       0.012  57.464  75.120  1.00  0.00              
ATOM      2  CA  GLU    12       1.394  57.779  75.404  1.00  0.00              
ATOM      3  C   GLU    12       1.463  58.794  76.542  1.00  0.00              
ATOM      4  O   GLU    12       0.786  59.774  76.617  1.00  0.00              
ATOM      5  N   ILE    13       2.237  58.383  77.501  1.00  0.00              
ATOM      6  CA  ILE    13       2.383  59.119  78.737  1.00  0.00              
ATOM      7  C   ILE    13       3.855  59.450  78.945  1.00  0.00              
ATOM      8  O   ILE    13       4.792  58.655  78.796  1.00  0.00              
ATOM      9  N   ILE    14       4.092  60.721  79.253  1.00  0.00              
ATOM     10  CA  ILE    14       5.443  61.202  79.493  1.00  0.00              
ATOM     11  C   ILE    14       5.899  60.768  80.877  1.00  0.00              
ATOM     12  O   ILE    14       5.473  61.344  81.880  1.00  0.00              
ATOM     13  N   SER    15       6.807  59.786  80.934  1.00  0.00              
ATOM     14  CA  SER    15       7.277  59.372  82.263  1.00  0.00              
ATOM     15  C   SER    15       8.529  60.138  82.624  1.00  0.00              
ATOM     16  O   SER    15       8.870  61.080  81.924  1.00  0.00              
ATOM     17  N   PRO    16       9.215  59.727  83.695  1.00  0.00              
ATOM     18  CA  PRO    16      10.456  60.364  84.106  1.00  0.00              
ATOM     19  C   PRO    16      11.277  59.442  84.990  1.00  0.00              
ATOM     20  O   PRO    16      10.789  58.537  85.645  1.00  0.00              
ATOM     21  N   HIS    17      12.577  59.717  85.095  1.00  0.00              
ATOM     22  CA  HIS    17      13.401  58.925  86.003  1.00  0.00              
ATOM     23  C   HIS    17      12.931  59.228  87.419  1.00  0.00              
ATOM     24  O   HIS    17      12.996  58.375  88.317  1.00  0.00              
ATOM     25  N   HIS    18      12.376  60.411  87.675  1.00  0.00              
ATOM     26  CA  HIS    18      11.883  60.701  89.021  1.00  0.00              
ATOM     27  C   HIS    18      10.639  59.901  89.376  1.00  0.00              
ATOM     28  O   HIS    18      10.184  59.935  90.532  1.00  0.00              
ATOM     29  N   TYR    19      10.036  59.193  88.444  1.00  0.00              
ATOM     30  CA  TYR    19       8.864  58.388  88.666  1.00  0.00              
ATOM     31  C   TYR    19       9.237  56.929  88.909  1.00  0.00              
ATOM     32  O   TYR    19       8.337  56.101  89.053  1.00  0.00              
ATOM     33  N   VAL    20      10.523  56.616  88.921  1.00  0.00              
ATOM     34  CA  VAL    20      11.084  55.329  89.198  1.00  0.00              
ATOM     35  C   VAL    20      12.078  55.345  90.378  1.00  0.00              
ATOM     36  O   VAL    20      12.501  54.237  90.743  1.00  0.00              
ATOM     37  N   TYR    21      12.460  56.496  90.911  1.00  0.00              
ATOM     38  CA  TYR    21      13.368  56.473  92.076  1.00  0.00              
ATOM     39  C   TYR    21      13.296  57.853  92.724  1.00  0.00              
ATOM     40  O   TYR    21      13.224  58.815  91.941  1.00  0.00              
ATOM     41  N   PRO    22      13.295  57.971  94.043  1.00  0.00              
ATOM     42  CA  PRO    22      13.147  59.282  94.661  1.00  0.00              
ATOM     43  C   PRO    22      14.374  60.155  94.664  1.00  0.00              
ATOM     44  O   PRO    22      15.495  59.726  94.939  1.00  0.00              
ATOM     45  N   ASN    23      14.237  61.434  94.375  1.00  0.00              
ATOM     46  CA  ASN    23      15.256  62.469  94.340  1.00  0.00              
ATOM     47  C   ASN    23      14.984  63.487  95.447  1.00  0.00              
ATOM     48  O   ASN    23      13.919  64.109  95.550  1.00  0.00              
END
