
#######################################################
#                                                     #
#                        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   23 (  115),  selected   23 , name T0378TS239_3_2
# Molecule2: number of CA atoms  250 ( 1924),  selected  250 , name T0378.pdb
# PARAMETERS: T0378TS239_3_2.T0378.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    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      K       8           -
LGA    -       -      F       9           -
LGA    -       -      L      10           -
LGA    -       -      R      11           -
LGA    -       -      S      12           -
LGA    -       -      L      13           -
LGA    -       -      R      14           -
LGA    -       -      E      15           -
LGA    -       -      R      16           -
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    -       -      R      41           -
LGA    -       -      C      42           -
LGA    -       -      R      43           -
LGA    -       -      M      44           -
LGA    -       -      L      45           -
LGA    -       -      V      46           -
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    -       -      A      86           -
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -
LGA    -       -      L      90           -
LGA    -       -      P      91           -
LGA    -       -      A      92           -
LGA    -       -      E      93           -
LGA    -       -      P      94           -
LGA    -       -      E      95           -
LGA    M       1      P      96          3.822
LGA    L       2      V      97          2.986
LGA    S       3      V      98          1.680
LGA    A       4      E      99          1.787
LGA    N       5      G     100          1.550
LGA    Q       6      L     101          2.213
LGA    I       7      T     102          0.732
LGA    K       8      -       -           -
LGA    F       9      -       -           -
LGA    L      10      L     103          3.139
LGA    R      11      L     104          4.379
LGA    -       -      L     105           -
LGA    -       -      D     106           -
LGA    -       -      G     107           -
LGA    -       -      V     108           -
LGA    -       -      Q     109           -
LGA    -       -      D     110           -
LGA    -       -      P     111           -
LGA    -       -      G     112           -
LGA    -       -      N     113           -
LGA    -       -      V     114           -
LGA    -       -      G     115           -
LGA    -       -      T     116           -
LGA    -       -      I     117           -
LGA    -       -      L     118           -
LGA    -       -      R     119           -
LGA    -       -      T     120           -
LGA    -       -      A     121           -
LGA    -       -      D     122           -
LGA    -       -      W     123           -
LGA    -       -      F     124           -
LGA    -       -      G     125           -
LGA    -       -      I     126           -
LGA    -       -      R     127           -
LGA    -       -      H     128           -
LGA    -       -      V     129           -
LGA    -       -      W     130           -
LGA    -       -      L     131           -
LGA    -       -      G     132           -
LGA    -       -      T     133           -
LGA    -       -      G     134           -
LGA    -       -      S     135           -
LGA    -       -      A     136           -
LGA    -       -      D     137           -
LGA    -       -      V     138           -
LGA    -       -      F     139           -
LGA    -       -      S     140           -
LGA    -       -      P     141           -
LGA    -       -      K     142           -
LGA    -       -      V     143           -
LGA    -       -      V     144           -
LGA    -       -      Q     145           -
LGA    -       -      A     146           -
LGA    -       -      S     147           -
LGA    -       -      M     148           -
LGA    -       -      G     149           -
LGA    -       -      A     150           -
LGA    -       -      L     151           -
LGA    -       -      A     152           -
LGA    -       -      R     153           -
LGA    -       -      V     154           -
LGA    -       -      Q     155           -
LGA    -       -      P     156           -
LGA    -       -      T     157           -
LGA    -       -      P     158           -
LGA    -       -      L     159           -
LGA    -       -      K     160           -
LGA    -       -      N     161           -
LGA    -       -      T     162           -
LGA    -       -      V     163           -
LGA    -       -      D     164           -
LGA    -       -      T     165           -
LGA    -       -      L     166           -
LGA    -       -      A     167           -
LGA    -       -      Y     168           -
LGA    -       -      F     169           -
LGA    -       -      R     170           -
LGA    -       -      R     171           -
LGA    -       -      Q     172           -
LGA    -       -      G     173           -
LGA    -       -      I     174           -
LGA    -       -      P     175           -
LGA    S      12      V     176          4.342
LGA    L      13      Y     177          4.952
LGA    R      14      G     178          2.993
LGA    E      15      A     179          4.213
LGA    R      16      F     180          2.112
LGA    -       -      L     181           -
LGA    -       -      D     182           -
LGA    -       -      G     183           -
LGA    -       -      Q     184           -
LGA    -       -      S     185           -
LGA    -       -      L     186           -
LGA    -       -      Y     187           -
LGA    -       -      E     188           -
LGA    -       -      A     189           -
LGA    -       -      P     190           -
LGA    -       -      L     191           -
LGA    -       -      P     192           -
LGA    -       -      N     193           -
LGA    -       -      F     194           -
LGA    -       -      T     195           -
LGA    -       -      E     196           -
LGA    -       -      P     197           -
LGA    -       -      A     198           -
LGA    -       -      I     199           -
LGA    -       -      L     200           -
LGA    -       -      V     201           -
LGA    -       -      L     202           -
LGA    -       -      G     203           -
LGA    -       -      S     204           -
LGA    -       -      E     205           -
LGA    -       -      G     206           -
LGA    -       -      R     207           -
LGA    -       -      G     208           -
LGA    -       -      I     209           -
LGA    -       -      S     210           -
LGA    -       -      P     211           -
LGA    -       -      E     212           -
LGA    -       -      V     213           -
LGA    -       -      A     214           -
LGA    -       -      A     215           -
LGA    -       -      E     216           -
LGA    -       -      I     217           -
LGA    -       -      T     218           -
LGA    -       -      D     219           -
LGA    K      17      R     220          2.871
LGA    Y      18      L     221          1.731
LGA    R      19      T     222          3.643
LGA    L      20      I     223          2.899
LGA    R      21      P     224           #
LGA    E      22      A     225           -
LGA    Q      23      S     226           -
LGA    -       -      G     227           -
LGA    -       -      L     228           -
LGA    -       -      S     229           -
LGA    -       -      V     230           -
LGA    -       -      E     235           -
LGA    -       -      S     236           -
LGA    -       -      L     237           -
LGA    -       -      N     238           -
LGA    -       -      V     239           -
LGA    -       -      A     240           -
LGA    -       -      I     241           -
LGA    -       -      A     242           -
LGA    -       -      T     243           -
LGA    -       -      A     244           -
LGA    -       -      I     245           -
LGA    -       -      L     246           -
LGA    -       -      C     247           -
LGA    -       -      S     248           -
LGA    -       -      E     249           -
LGA    -       -      W     250           -
LGA    -       -      R     251           -
LGA    -       -      R     252           -
LGA    -       -      R     253           -
LGA    -       -      S     254           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23  250    5.0     18    3.11     5.56      4.396     0.561

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.459142 * X  +  -0.783275 * Y  +  -0.419129 * Z  +  45.390842
  Y_new =  -0.770551 * X  +  -0.116355 * Y  +  -0.626668 * Z  +  25.921013
  Z_new =   0.442086 * X  +   0.610689 * Y  +  -0.656977 * Z  +  30.505253 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.392692   -0.748900  [ DEG:   137.0912    -42.9088 ]
  Theta =  -0.457923   -2.683670  [ DEG:   -26.2370   -153.7630 ]
  Phi   =  -1.033426    2.108167  [ DEG:   -59.2109    120.7891 ]
 
# 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: T0378TS239_3_2                                
REMARK     2: T0378.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS239_3_2.T0378.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23  250   5.0   18   3.11    5.56   4.396
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS239_3_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0378
PARENT 1ipa_A
ATOM      1  N   MET     1      19.137   2.157  54.562  1.00  9.99
ATOM      2  CA  MET     1      20.197   1.271  55.017  1.00  9.99
ATOM      3  C   MET     1      21.144   0.873  53.898  1.00  9.99
ATOM      4  O   MET     1      20.714   0.428  52.834  1.00  9.99
ATOM      5  CB  MET     1      19.593   0.014  55.644  1.00  9.99
ATOM      6  N   LEU     2      22.437   1.028  54.152  1.00  9.99
ATOM      7  CA  LEU     2      23.451   0.679  53.169  1.00  9.99
ATOM      8  C   LEU     2      23.554  -0.842  53.051  1.00  9.99
ATOM      9  O   LEU     2      24.155  -1.365  52.113  1.00  9.99
ATOM     10  CB  LEU     2      24.829   1.271  53.560  1.00  9.99
ATOM     11  N   SER     3      22.946  -1.543  54.008  1.00  9.99
ATOM     12  CA  SER     3      22.956  -3.000  54.034  1.00  9.99
ATOM     13  C   SER     3      21.849  -3.562  53.153  1.00  9.99
ATOM     14  O   SER     3      21.836  -4.755  52.849  1.00  9.99
ATOM     15  CB  SER     3      22.786  -3.498  55.465  1.00  9.99
ATOM     16  N   ALA     4      20.920  -2.697  52.754  1.00  9.99
ATOM     17  CA  ALA     4      19.810  -3.085  51.894  1.00  9.99
ATOM     18  C   ALA     4      20.392  -3.803  50.672  1.00  9.99
ATOM     19  O   ALA     4      21.227  -3.252  49.959  1.00  9.99
ATOM     20  CB  ALA     4      19.033  -1.833  51.474  1.00  9.99
ATOM     21  N   ASN     5      19.951  -5.045  50.416  1.00  9.99
ATOM     22  CA  ASN     5      20.434  -5.849  49.283  1.00  9.99
ATOM     23  C   ASN     5      20.491  -5.125  47.938  1.00  9.99
ATOM     24  O   ASN     5      21.387  -5.378  47.131  1.00  9.99
ATOM     25  CB  ASN     5      19.482  -7.051  49.277  1.00  9.99
ATOM     26  N   GLN     6      19.541  -4.228  47.699  1.00  9.99
ATOM     27  CA  GLN     6      19.527  -3.482  46.454  1.00  9.99
ATOM     28  C   GLN     6      20.722  -2.543  46.406  1.00  9.99
ATOM     29  O   GLN     6      21.329  -2.347  45.356  1.00  9.99
ATOM     30  CB  GLN     6      18.237  -2.671  46.323  1.00  9.99
ATOM     31  N   ILE     7      21.055  -1.968  47.555  1.00  9.99
ATOM     32  CA  ILE     7      22.170  -1.049  47.653  1.00  9.99
ATOM     33  C   ILE     7      23.503  -1.792  47.616  1.00  9.99
ATOM     34  O   ILE     7      24.511  -1.257  47.157  1.00  9.99
ATOM     35  CB  ILE     7      22.085  -0.207  48.944  1.00  9.99
ATOM     36  N   LYS     8      23.514  -3.024  48.098  1.00  9.99
ATOM     37  CA  LYS     8      24.737  -3.811  48.073  1.00  9.99
ATOM     38  C   LYS     8      25.055  -4.195  46.627  1.00  9.99
ATOM     39  O   LYS     8      26.222  -4.294  46.242  1.00  9.99
ATOM     40  CB  LYS     8      24.572  -5.063  48.939  1.00  9.99
ATOM     41  N   PHE     9      24.013  -4.395  45.826  1.00  9.99
ATOM     42  CA  PHE     9      24.196  -4.758  44.427  1.00  9.99
ATOM     43  C   PHE     9      24.711  -3.567  43.623  1.00  9.99
ATOM     44  O   PHE     9      25.573  -3.715  42.770  1.00  9.99
ATOM     45  CB  PHE     9      22.882  -5.257  43.824  1.00  9.99
ATOM     46  N   LEU    10      24.189  -2.381  43.899  1.00  9.99
ATOM     47  CA  LEU    10      24.637  -1.197  43.182  1.00  9.99
ATOM     48  C   LEU    10      26.067  -0.788  43.570  1.00  9.99
ATOM     49  O   LEU    10      26.840  -0.335  42.725  1.00  9.99
ATOM     50  CB  LEU    10      23.661  -0.048  43.427  1.00  9.99
ATOM     51  N   ARG    11      26.425  -0.968  44.840  1.00  9.99
ATOM     52  CA  ARG    11      27.767  -0.608  45.316  1.00  9.99
ATOM     53  C   ARG    11      28.878  -1.368  44.585  1.00  9.99
ATOM     54  O   ARG    11      29.985  -0.853  44.415  1.00  9.99
ATOM     55  CB  ARG    11      27.880  -0.842  46.834  1.00  9.99
ATOM     56  N   SER    12      28.587  -2.590  44.156  1.00  9.99
ATOM     57  CA  SER    12      29.566  -3.394  43.441  1.00  9.99
ATOM     58  C   SER    12      29.990  -2.711  42.143  1.00  9.99
ATOM     59  O   SER    12      31.081  -2.949  41.628  1.00  9.99
ATOM     60  CB  SER    12      28.977  -4.773  43.125  1.00  9.99
ATOM     61  N   LEU    13      29.121  -1.859  41.613  1.00  9.99
ATOM     62  CA  LEU    13      29.415  -1.167  40.369  1.00  9.99
ATOM     63  C   LEU    13      30.545  -0.149  40.521  1.00  9.99
ATOM     64  O   LEU    13      30.991   0.441  39.535  1.00  9.99
ATOM     65  CB  LEU    13      28.145  -0.496  39.828  1.00  9.99
ATOM     66  N   ARG    14      31.020   0.058  41.750  1.00  9.99
ATOM     67  CA  ARG    14      32.125   0.994  41.953  1.00  9.99
ATOM     68  C   ARG    14      33.427   0.371  41.460  1.00  9.99
ATOM     69  O   ARG    14      34.401   1.073  41.203  1.00  9.99
ATOM     70  CB  ARG    14      32.252   1.406  43.422  1.00  9.99
ATOM     71  N   GLU    15      33.424  -0.950  41.303  1.00  9.99
ATOM     72  CA  GLU    15      34.598  -1.659  40.815  1.00  9.99
ATOM     73  C   GLU    15      34.423  -2.017  39.334  1.00  9.99
ATOM     74  O   GLU    15      33.320  -2.346  38.894  1.00  9.99
ATOM     75  CB  GLU    15      34.829  -2.892  41.681  1.00  9.99
ATOM     76  N   ARG    16      35.508  -1.947  38.564  1.00  9.99
ATOM     77  CA  ARG    16      35.422  -2.211  37.130  1.00  9.99
ATOM     78  C   ARG    16      34.950  -3.584  36.675  1.00  9.99
ATOM     79  O   ARG    16      34.099  -3.670  35.800  1.00  9.99
ATOM     80  CB  ARG    16      36.753  -1.911  36.431  1.00  9.99
ATOM     81  N   LYS    17      35.503  -4.651  37.236  1.00  9.99
ATOM     82  CA  LYS    17      35.099  -5.993  36.823  1.00  9.99
ATOM     83  C   LYS    17      33.581  -6.195  36.899  1.00  9.99
ATOM     84  O   LYS    17      32.989  -6.821  36.024  1.00  9.99
ATOM     85  CB  LYS    17      35.802  -7.055  37.682  1.00  9.99
ATOM     86  N   TYR    18      32.964  -5.662  37.948  1.00  9.99
ATOM     87  CA  TYR    18      31.528  -5.784  38.144  1.00  9.99
ATOM     88  C   TYR    18      30.721  -4.992  37.129  1.00  9.99
ATOM     89  O   TYR    18      29.643  -5.417  36.729  1.00  9.99
ATOM     90  CB  TYR    18      31.172  -5.353  39.562  1.00  9.99
ATOM     91  N   ARG    19      31.238  -3.845  36.707  1.00  9.99
ATOM     92  CA  ARG    19      30.542  -3.041  35.717  1.00  9.99
ATOM     93  C   ARG    19      30.594  -3.752  34.376  1.00  9.99
ATOM     94  O   ARG    19      29.607  -3.806  33.647  1.00  9.99
ATOM     95  CB  ARG    19      31.204  -1.671  35.562  1.00  9.99
ATOM     96  N   LEU    20      31.758  -4.304  34.056  1.00  9.99
ATOM     97  CA  LEU    20      31.942  -4.982  32.783  1.00  9.99
ATOM     98  C   LEU    20      31.130  -6.257  32.626  1.00  9.99
ATOM     99  O   LEU    20      30.534  -6.489  31.577  1.00  9.99
ATOM    100  CB  LEU    20      33.425  -5.296  32.554  1.00  9.99
ATOM    101  N   ARG    21      31.090  -7.080  33.665  1.00  9.99
ATOM    102  CA  ARG    21      30.365  -8.329  33.558  1.00  9.99
ATOM    103  C   ARG    21      28.864  -8.105  33.519  1.00  9.99
ATOM    104  O   ARG    21      28.157  -8.806  32.806  1.00  9.99
ATOM    105  CB  ARG    21      30.737  -9.270  34.706  1.00  9.99
ATOM    106  N   GLU    22      28.378  -7.119  34.261  1.00  9.99
ATOM    107  CA  GLU    22      26.941  -6.840  34.288  1.00  9.99
ATOM    108  C   GLU    22      26.505  -5.787  33.279  1.00  9.99
ATOM    109  O   GLU    22      25.316  -5.529  33.129  1.00  9.99
ATOM    110  CB  GLU    22      26.512  -6.384  35.673  1.00  9.99
ATOM    111  N   GLN    23      27.466  -5.186  32.590  1.00  9.99
ATOM    112  CA  GLN    23      27.169  -4.154  31.607  1.00  9.99
ATOM    113  C   GLN    23      26.324  -3.024  32.181  1.00  9.99
ATOM    114  O   GLN    23      25.389  -2.544  31.538  1.00  9.99
ATOM    115  CB  GLN    23      26.477  -4.760  30.391  1.00  9.99
TER
END
