
#######################################################
#                                                     #
#                        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 (  114),  selected   23 , name T0386TS239_3_3-D1
# Molecule2: number of CA atoms  206 ( 1668),  selected  206 , name T0386_D1.pdb
# PARAMETERS: T0386TS239_3_3-D1.T0386_D1.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    -       -      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    I      13      L      36          4.315
LGA    I      14      N      37          2.299
LGA    S      15      A      38          2.705
LGA    P      16      F      39          3.178
LGA    H      17      L      40          3.196
LGA    -       -      E      41           -
LGA    -       -      K      42           -
LGA    -       -      C      43           -
LGA    H      18      S      44          1.359
LGA    Y      19      H      45           #
LGA    V      20      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    Y      21      R     167          2.519
LGA    P      22      T     168          2.659
LGA    -       -      Q     169           -
LGA    -       -      R     170           -
LGA    N      23      L     171          2.683
LGA    T      24      F     172          1.652
LGA    T      25      F     173          1.510
LGA    T      26      E     174          1.798
LGA    L      27      N     175          1.650
LGA    K      28      L     176          0.342
LGA    N      29      A     177          1.340
LGA    K      30      K     178          1.548
LGA    Y      31      A     179          1.213
LGA    G      32      A     180          2.064
LGA    I      33      G     181          1.787
LGA    -       -      H     182           -
LGA    K      34      Q     183           #
LGA    N      35      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           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   23  206    5.0     19    2.27     5.26      7.081     0.801

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.428057 * X  +   0.531805 * Y  +  -0.730719 * Z  +  41.900955
  Y_new =   0.219973 * X  +  -0.845533 * Y  +  -0.486504 * Z  +  96.351295
  Z_new =  -0.876572 * X  +   0.047513 * Y  +  -0.478919 * Z  +  92.958534 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.042708   -0.098884  [ DEG:   174.3343     -5.6657 ]
  Theta =   1.068693    2.072900  [ DEG:    61.2316    118.7684 ]
  Phi   =   0.474696   -2.666897  [ DEG:    27.1981   -152.8019 ]
 
# 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: T0386TS239_3_3-D1                             
REMARK     2: T0386_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0386TS239_3_3-D1.T0386_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   23  206   5.0   19   2.27    5.26   7.081
REMARK  ---------------------------------------------------------- 
MOLECULE T0386TS239_3_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0386
PARENT 1gz5_A
ATOM     61  N   ILE    13      32.923  72.648  49.608  1.00  9.99
ATOM     62  CA  ILE    13      31.685  73.100  48.973  1.00  9.99
ATOM     63  C   ILE    13      30.667  73.474  50.050  1.00  9.99
ATOM     64  O   ILE    13      30.662  72.890  51.139  1.00  9.99
ATOM     65  CB  ILE    13      31.138  71.990  48.070  1.00  9.99
ATOM     66  N   ILE    14      29.827  74.461  49.773  1.00  9.99
ATOM     67  CA  ILE    14      28.739  74.794  50.674  1.00  9.99
ATOM     68  C   ILE    14      27.426  74.685  49.942  1.00  9.99
ATOM     69  O   ILE    14      27.412  74.807  48.723  1.00  9.99
ATOM     70  CB  ILE    14      28.872  76.198  51.270  1.00  9.99
ATOM     71  N   SER    15      26.339  74.420  50.685  1.00  9.99
ATOM     72  CA  SER    15      25.009  74.202  50.100  1.00  9.99
ATOM     73  C   SER    15      23.908  74.233  51.146  1.00  9.99
ATOM     74  O   SER    15      24.168  74.135  52.355  1.00  9.99
ATOM     75  CB  SER    15      24.984  72.893  49.290  1.00  9.99
ATOM     76  N   PRO    16      22.676  74.407  50.703  1.00  9.99
ATOM     77  CA  PRO    16      21.546  74.562  51.614  1.00  9.99
ATOM     78  C   PRO    16      20.637  73.365  51.473  1.00  9.99
ATOM     79  O   PRO    16      20.254  73.017  50.379  1.00  9.99
ATOM     80  CB  PRO    16      20.733  75.861  51.309  1.00  9.99
ATOM     81  N   HIS    17      20.307  72.704  52.586  1.00  9.99
ATOM     82  CA  HIS    17      19.383  71.557  52.555  1.00  9.99
ATOM     83  C   HIS    17      18.421  71.673  53.717  1.00  9.99
ATOM     84  O   HIS    17      18.685  71.128  54.759  1.00  9.99
ATOM     85  CB  HIS    17      20.148  70.228  52.708  1.00  9.99
ATOM     86  N   HIS    18      17.307  72.361  53.563  1.00  9.99
ATOM     87  CA  HIS    18      16.370  72.455  54.701  1.00  9.99
ATOM     88  C   HIS    18      15.832  71.058  55.079  1.00  9.99
ATOM     89  O   HIS    18      15.314  70.395  54.238  1.00  9.99
ATOM     90  CB  HIS    18      15.302  73.489  54.244  1.00  9.99
ATOM     91  N   TYR    19      16.059  70.604  56.310  1.00  9.99
ATOM     92  CA  TYR    19      15.673  69.280  56.801  1.00  9.99
ATOM     93  C   TYR    19      14.146  69.160  56.907  1.00  9.99
ATOM     94  O   TYR    19      13.454  70.146  57.197  1.00  9.99
ATOM     95  CB  TYR    19      16.353  68.987  58.150  1.00  9.99
ATOM     96  N   VAL    20      13.630  67.955  56.592  1.00  9.99
ATOM     97  CA  VAL    20      12.203  67.736  56.486  1.00  9.99
ATOM     98  C   VAL    20      11.777  66.558  57.311  1.00  9.99
ATOM     99  O   VAL    20      12.516  66.084  58.176  1.00  9.99
ATOM    100  CB  VAL    20      11.823  67.541  55.008  1.00  9.99
ATOM    101  N   TYR    21      10.613  66.044  56.953  1.00  9.99
ATOM    102  CA  TYR    21       9.808  65.168  57.742  1.00  9.99
ATOM    103  C   TYR    21       9.286  64.056  56.756  1.00  9.99
ATOM    104  O   TYR    21       9.449  64.183  55.542  1.00  9.99
ATOM    105  CB  TYR    21       8.703  66.137  58.342  1.00  9.99
ATOM    106  N   PRO    22       8.723  62.963  57.274  1.00  9.99
ATOM    107  CA  PRO    22       8.098  61.904  56.435  1.00  9.99
ATOM    108  C   PRO    22       6.585  62.091  56.405  1.00  9.99
ATOM    109  O   PRO    22       5.919  61.582  57.287  1.00  9.99
ATOM    110  CB  PRO    22       8.385  60.461  56.945  1.00  9.99
ATOM    111  N   ASN    23       6.041  62.801  55.413  1.00  9.99
ATOM    112  CA  ASN    23       4.646  63.291  55.491  1.00  9.99
ATOM    113  C   ASN    23       3.679  62.140  55.471  1.00  9.99
ATOM    114  O   ASN    23       2.630  62.223  56.126  1.00  9.99
ATOM    115  CB  ASN    23       4.479  64.172  54.238  1.00  9.99
ATOM    116  N   THR    24       4.034  61.091  54.744  1.00  9.99
ATOM    117  CA  THR    24       3.186  59.923  54.617  1.00  9.99
ATOM    118  C   THR    24       3.105  59.193  55.953  1.00  9.99
ATOM    119  O   THR    24       2.015  58.793  56.357  1.00  9.99
ATOM    120  CB  THR    24       3.690  58.953  53.506  1.00  9.99
ATOM    121  N   THR    25       4.244  58.994  56.622  1.00  9.99
ATOM    122  CA  THR    25       4.229  58.301  57.902  1.00  9.99
ATOM    123  C   THR    25       3.481  59.087  58.999  1.00  9.99
ATOM    124  O   THR    25       2.718  58.474  59.784  1.00  9.99
ATOM    125  CB  THR    25       5.637  57.942  58.374  1.00  9.99
ATOM    126  N   THR    26       3.651  60.418  59.060  1.00  9.99
ATOM    127  CA  THR    26       2.895  61.144  60.062  1.00  9.99
ATOM    128  C   THR    26       1.406  61.154  59.795  1.00  9.99
ATOM    129  O   THR    26       0.627  61.049  60.750  1.00  9.99
ATOM    130  CB  THR    26       3.461  62.522  60.505  1.00  9.99
ATOM    131  N   LEU    27       1.020  61.195  58.511  1.00  9.99
ATOM    132  CA  LEU    27      -0.381  61.023  58.133  1.00  9.99
ATOM    133  C   LEU    27      -0.890  59.777  58.827  1.00  9.99
ATOM    134  O   LEU    27      -1.844  59.861  59.594  1.00  9.99
ATOM    135  CB  LEU    27      -0.559  60.909  56.607  1.00  9.99
ATOM    136  N   LYS    28      -0.205  58.650  58.609  1.00  9.99
ATOM    137  CA  LYS    28      -0.595  57.336  59.167  1.00  9.99
ATOM    138  C   LYS    28      -0.682  57.424  60.674  1.00  9.99
ATOM    139  O   LYS    28      -1.705  57.033  61.254  1.00  9.99
ATOM    140  CB  LYS    28       0.372  56.213  58.776  1.00  9.99
ATOM    141  N   ASN    29       0.347  57.972  61.326  1.00  9.99
ATOM    142  CA  ASN    29       0.299  57.919  62.783  1.00  9.99
ATOM    143  C   ASN    29      -0.763  58.866  63.342  1.00  9.99
ATOM    144  O   ASN    29      -1.427  58.507  64.320  1.00  9.99
ATOM    145  CB  ASN    29       1.685  57.987  63.467  1.00  9.99
ATOM    146  N   LYS    30      -0.955  60.020  62.688  1.00  9.99
ATOM    147  CA  LYS    30      -1.938  61.028  63.111  1.00  9.99
ATOM    148  C   LYS    30      -3.399  60.507  63.016  1.00  9.99
ATOM    149  O   LYS    30      -4.268  60.983  63.733  1.00  9.99
ATOM    150  CB  LYS    30      -1.776  62.299  62.300  1.00  9.99
ATOM    151  N   TYR    31      -3.644  59.520  62.160  1.00  9.99
ATOM    152  CA  TYR    31      -5.001  59.021  61.928  1.00  9.99
ATOM    153  C   TYR    31      -5.319  57.770  62.774  1.00  9.99
ATOM    154  O   TYR    31      -6.440  57.270  62.761  1.00  9.99
ATOM    155  CB  TYR    31      -5.204  58.701  60.413  1.00  9.99
ATOM    156  N   GLY    32      -4.330  57.267  63.506  1.00  9.99
ATOM    157  CA  GLY    32      -4.518  56.120  64.379  1.00  9.99
ATOM    158  C   GLY    32      -5.392  56.490  65.563  1.00  9.99
ATOM    159  O   GLY    32      -5.537  57.673  65.890  1.00  9.99
ATOM    160  N   ILE    33      -5.982  55.505  66.230  1.00  9.99
ATOM    161  CA  ILE    33      -6.948  55.805  67.298  1.00  9.99
ATOM    162  C   ILE    33      -6.287  56.557  68.466  1.00  9.99
ATOM    163  O   ILE    33      -5.076  56.383  68.708  1.00  9.99
ATOM    164  CB  ILE    33      -7.409  54.436  67.734  1.00  9.99
ATOM    165  N   LYS    34      -7.050  57.414  69.161  1.00  9.99
ATOM    166  CA  LYS    34      -6.485  58.094  70.330  1.00  9.99
ATOM    167  C   LYS    34      -6.490  57.161  71.539  1.00  9.99
ATOM    168  O   LYS    34      -7.400  56.337  71.667  1.00  9.99
ATOM    169  CB  LYS    34      -7.290  59.348  70.654  1.00  9.99
ATOM    170  N   ASN    35      -5.516  57.296  72.436  1.00  9.99
ATOM    171  CA  ASN    35      -5.580  56.618  73.746  1.00  9.99
ATOM    172  C   ASN    35      -6.917  56.966  74.437  1.00  9.99
ATOM    173  O   ASN    35      -7.367  58.136  74.306  1.00  9.99
ATOM    174  CB  ASN    35      -4.440  57.249  74.558  1.00  9.99
TER
END
