
#######################################################
#                                                     #
#                        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   38 (   38),  selected   38 , name T0365TS464_5_2
# Molecule2: number of CA atoms  214 ( 1638),  selected  214 , name T0365.pdb
# PARAMETERS: T0365TS464_5_2.T0365.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      L       7           -
LGA    -       -      G       8           -
LGA    -       -      V       9           -
LGA    -       -      F      10           -
LGA    -       -      A      11           -
LGA    -       -      K      12           -
LGA    -       -      S      13           -
LGA    -       -      P      14           -
LGA    -       -      I      15           -
LGA    -       -      K      16           -
LGA    V      33      P      17          3.254
LGA    P      34      L      18          3.452
LGA    F      35      -       -           -
LGA    F      36      Q      19          1.700
LGA    E      37      E      20          2.519
LGA    A      38      H      21          1.919
LGA    T      39      M      22          2.450
LGA    I      40      D      23          3.050
LGA    T      41      K      24          2.788
LGA    G      42      V      25          4.290
LGA    N      43      -       -           -
LGA    W      44      Y      26          3.638
LGA    D      45      D      27          5.151
LGA    D      46      C      28           -
LGA    -       -      A      29           -
LGA    -       -      S      30           -
LGA    -       -      L      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      P      34           -
LGA    -       -      F      35           -
LGA    -       -      F      36           -
LGA    -       -      E      37           -
LGA    -       -      A      38           -
LGA    -       -      T      39           -
LGA    -       -      I      40           -
LGA    -       -      T      41           -
LGA    -       -      G      42           -
LGA    -       -      N      43           -
LGA    -       -      W      44           -
LGA    -       -      D      45           -
LGA    -       -      D      46           -
LGA    -       -      A      47           -
LGA    -       -      V      48           -
LGA    -       -      Q      49           -
LGA    -       -      I      50           -
LGA    -       -      R      51           -
LGA    -       -      K      52           -
LGA    -       -      Q      53           -
LGA    -       -      I      54           -
LGA    -       -      S      55           -
LGA    -       -      L      56           -
LGA    -       -      A      57           -
LGA    -       -      E      58           -
LGA    -       -      K      59           -
LGA    -       -      Q      60           -
LGA    -       -      G      61           -
LGA    -       -      D      62           -
LGA    -       -      S      63           -
LGA    -       -      L      64           -
LGA    -       -      K      65           -
LGA    -       -      R      66           -
LGA    -       -      E      67           -
LGA    -       -      I      68           -
LGA    -       -      R      69           -
LGA    -       -      L      70           -
LGA    -       -      T      71           -
LGA    -       -      L      72           -
LGA    -       -      F      77           -
LGA    -       -      M      78           -
LGA    -       -      P      79           -
LGA    -       -      V      80           -
LGA    -       -      E      81           -
LGA    D      62      R      82          2.651
LGA    S      63      T      83          2.234
LGA    L      64      D      84          2.189
LGA    K      65      L      85          1.833
LGA    R      66      L      86          1.312
LGA    E      67      E      87          1.250
LGA    I      68      L      88          1.527
LGA    R      69      L      89          1.044
LGA    L      70      T      90          1.504
LGA    -       -      Q      91           -
LGA    -       -      Q      92           -
LGA    -       -      D      93           -
LGA    -       -      K      94           -
LGA    -       -      I      95           -
LGA    -       -      A      96           -
LGA    -       -      N      97           -
LGA    -       -      K      98           -
LGA    -       -      A      99           -
LGA    -       -      K     100           -
LGA    -       -      D     101           -
LGA    -       -      I     102           -
LGA    -       -      S     103           -
LGA    -       -      G     104           -
LGA    -       -      R     105           -
LGA    -       -      V     106           -
LGA    -       -      I     107           -
LGA    -       -      G     108           -
LGA    -       -      R     109           -
LGA    -       -      Q     110           -
LGA    -       -      L     111           -
LGA    -       -      L     112           -
LGA    -       -      I     113           -
LGA    -       -      P     114           -
LGA    -       -      Q     115           -
LGA    -       -      A     116           -
LGA    -       -      L     117           -
LGA    -       -      Q     118           -
LGA    -       -      V     119           -
LGA    -       -      P     120           -
LGA    -       -      F     121           -
LGA    -       -      I     122           -
LGA    -       -      A     123           -
LGA    -       -      Y     124           -
LGA    -       -      L     125           -
LGA    -       -      Q     126           -
LGA    -       -      R     127           -
LGA    -       -      C     128           -
LGA    -       -      I     129           -
LGA    -       -      D     130           -
LGA    -       -      A     131           -
LGA    D     173      V     132          2.539
LGA    D     174      G     133          5.040
LGA    L     175      L     134           #
LGA    Q     176      A     135          1.355
LGA    -       -      Q     136           -
LGA    -       -      Q     137           -
LGA    -       -      V     138           -
LGA    -       -      I     139           -
LGA    -       -      N     140           -
LGA    -       -      E     141           -
LGA    -       -      L     142           -
LGA    -       -      D     143           -
LGA    -       -      D     144           -
LGA    -       -      L     145           -
LGA    -       -      L     146           -
LGA    -       -      E     147           -
LGA    -       -      A     148           -
LGA    -       -      R     151           -
LGA    -       -      G     152           -
LGA    -       -      R     153           -
LGA    -       -      E     154           -
LGA    -       -      V     155           -
LGA    -       -      D     156           -
LGA    -       -      F     157           -
LGA    -       -      V     158           -
LGA    -       -      A     159           -
LGA    -       -      K     160           -
LGA    -       -      M     161           -
LGA    -       -      I     162           -
LGA    -       -      N     163           -
LGA    -       -      E     164           -
LGA    -       -      L     165           -
LGA    -       -      D     166           -
LGA    -       -      I     167           -
LGA    -       -      I     168           -
LGA    -       -      E     169           -
LGA    -       -      E     170           -
LGA    -       -      D     171           -
LGA    -       -      T     172           -
LGA    -       -      D     173           -
LGA    -       -      D     174           -
LGA    -       -      L     175           -
LGA    -       -      Q     176           -
LGA    -       -      I     177           -
LGA    -       -      Q     178           -
LGA    -       -      L     179           -
LGA    -       -      R     180           -
LGA    -       -      R     181           -
LGA    -       -      Q     182           -
LGA    -       -      L     183           -
LGA    -       -      F     184           -
LGA    -       -      A     185           -
LGA    -       -      L     186           -
LGA    -       -      E     187           -
LGA    -       -      S     188           -
LGA    -       -      E     189           -
LGA    -       -      L     190           -
LGA    -       -      N     191           -
LGA    -       -      P     192           -
LGA    -       -      V     193           -
LGA    -       -      D     194           -
LGA    -       -      V     195           -
LGA    -       -      M     196           -
LGA    -       -      F     197           -
LGA    -       -      L     198           -
LGA    -       -      Y     199           -
LGA    -       -      K     200           -
LGA    -       -      T     201           -
LGA    -       -      I     202           -
LGA    -       -      E     203           -
LGA    -       -      W     204           -
LGA    -       -      V     205           -
LGA    -       -      G     206           -
LGA    -       -      G     207           -
LGA    -       -      L     208           -
LGA    -       -      A     209           -
LGA    -       -      D     210           -
LGA    -       -      L     211           -
LGA    -       -      A     212           -
LGA    I     177      E     213          2.853
LGA    Q     178      R     214          2.472
LGA    L     179      V     215          2.611
LGA    R     180      G     216          1.877
LGA    R     181      S     217          0.854
LGA    Q     182      R     218          0.816
LGA    L     183      L     219          1.961
LGA    F     184      E     220          2.335
LGA    A     185      L     221          1.911
LGA    L     186      M     222          2.482
LGA    E     187      L     223          2.458
LGA    -       -      A     224           -
LGA    -       -      R     225           -
LGA    -       -      V     226           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   38  214    5.0     34    2.60    11.76     10.721     1.257

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.033349 * X  +  -0.590582 * Y  +   0.806288 * Z  +  20.575056
  Y_new =  -0.998088 * X  +   0.061692 * Y  +   0.003906 * Z  +  54.180157
  Z_new =  -0.052049 * X  +  -0.804616 * Y  +  -0.591510 * Z  +  41.546936 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.204722    0.936870  [ DEG:  -126.3213     53.6787 ]
  Theta =   0.052072    3.089520  [ DEG:     2.9835    177.0165 ]
  Phi   =  -1.604197    1.537396  [ DEG:   -91.9137     88.0863 ]
 
# 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: T0365TS464_5_2                                
REMARK     2: T0365.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0365TS464_5_2.T0365.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   38  214   5.0   34   2.60   11.76  10.721
REMARK  ---------------------------------------------------------- 
MOLECULE T0365TS464_5_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0365
PARENT N/A
ATOM      1  CA  VAL    33      35.897  17.313  27.787  1.00  0.00
ATOM      2  CA  PRO    34      37.769  16.527  31.001  1.00  0.00
ATOM      3  CA  PHE    35      35.916  19.206  32.956  1.00  0.00
ATOM      4  CA  PHE    36      32.636  18.070  31.445  1.00  0.00
ATOM      5  CA  GLU    37      33.304  14.490  32.462  1.00  0.00
ATOM      6  CA  ALA    38      34.257  15.519  36.016  1.00  0.00
ATOM      7  CA  THR    39      31.194  17.725  36.320  1.00  0.00
ATOM      8  CA  ILE    40      28.869  14.923  35.268  1.00  0.00
ATOM      9  CA  THR    41      30.435  12.435  37.675  1.00  0.00
ATOM     10  CA  GLY    42      30.386  14.961  40.522  1.00  0.00
ATOM     11  CA  ASN    43      34.198  14.868  40.708  1.00  0.00
ATOM     12  CA  TRP    44      34.220  18.668  40.607  1.00  0.00
ATOM     13  CA  ASP    45      31.400  21.055  41.445  1.00  0.00
ATOM     14  CA  ASP    46      30.428  23.114  38.411  1.00  0.00
ATOM     15  CA  ASP    62      41.193  20.193  23.046  1.00  0.00
ATOM     16  CA  SER    63      43.883  22.186  24.817  1.00  0.00
ATOM     17  CA  LEU    64      41.131  24.311  26.271  1.00  0.00
ATOM     18  CA  LYS    65      39.417  21.126  27.431  1.00  0.00
ATOM     19  CA  ARG    66      42.714  19.678  28.687  1.00  0.00
ATOM     20  CA  GLU    67      43.395  22.709  30.828  1.00  0.00
ATOM     21  CA  ILE    68      39.924  22.401  32.301  1.00  0.00
ATOM     22  CA  ARG    69      40.356  18.679  33.022  1.00  0.00
ATOM     23  CA  LEU    70      43.684  18.718  34.875  1.00  0.00
ATOM     24  CA  ASP   173      29.645  26.335  40.288  1.00  0.00
ATOM     25  CA  ASP   174      32.824  26.109  42.356  1.00  0.00
ATOM     26  CA  LEU   175      34.994  25.662  39.243  1.00  0.00
ATOM     27  CA  GLN   176      33.214  27.700  36.555  1.00  0.00
ATOM     28  CA  ILE   177      35.197  30.919  36.994  1.00  0.00
ATOM     29  CA  GLN   178      38.225  29.002  36.328  1.00  0.00
ATOM     30  CA  LEU   179      36.410  28.188  33.092  1.00  0.00
ATOM     31  CA  ARG   180      35.833  31.909  32.412  1.00  0.00
ATOM     32  CA  ARG   181      39.429  32.840  33.203  1.00  0.00
ATOM     33  CA  GLN   182      40.695  29.926  31.061  1.00  0.00
ATOM     34  CA  LEU   183      38.371  30.913  28.222  1.00  0.00
ATOM     35  CA  PHE   184      39.804  34.428  27.793  1.00  0.00
ATOM     36  CA  ALA   185      43.193  32.924  27.126  1.00  0.00
ATOM     37  CA  LEU   186      41.980  31.024  24.061  1.00  0.00
ATOM     38  CA  GLU   187      39.382  33.223  22.370  1.00  0.00
TER
END
