
#######################################################
#                                                     #
#                        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   24 (   96),  selected   24 , name T0301AL333_3-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301AL333_3-D1.T0301_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    -       -      M       1           -
LGA    -       -      A       2           -
LGA    -       -      H       3           -
LGA    -       -      P       4           -
LGA    -       -      P       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      R       8           -
LGA    -       -      I       9           -
LGA    -       -      P      10           -
LGA    -       -      A      11           -
LGA    -       -      T      12           -
LGA    -       -      Y      13           -
LGA    -       -      L      14           -
LGA    -       -      R      15           -
LGA    -       -      G      16           -
LGA    -       -      G      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      K      20           -
LGA    -       -      G      21           -
LGA    -       -      V      22           -
LGA    -       -      F      23           -
LGA    -       -      F      24           -
LGA    -       -      R      25           -
LGA    -       -      L      26           -
LGA    -       -      E      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      P      30           -
LGA    -       -      E      31           -
LGA    -       -      S      32           -
LGA    -       -      C      33           -
LGA    -       -      R      34           -
LGA    -       -      V      35           -
LGA    -       -      P      36           -
LGA    -       -      G      37           -
LGA    -       -      E      38           -
LGA    -       -      A      39           -
LGA    -       -      R      40           -
LGA    -       -      D      41           -
LGA    -       -      R      42           -
LGA    -       -      L      43           -
LGA    -       -      F      44           -
LGA    -       -      M      45           -
LGA    -       -      R      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      G      49           -
LGA    -       -      S      50           -
LGA    -       -      P      51           -
LGA    -       -      D      52           -
LGA    -       -      P      53           -
LGA    -       -      Y      54           -
LGA    -       -      A      55           -
LGA    -       -      A      56           -
LGA    -       -      H      57           -
LGA    -       -      I      58           -
LGA    -       -      D      59           -
LGA    -       -      G      60           -
LGA    -       -      M      61           -
LGA    -       -      G      62           -
LGA    -       -      G      63           -
LGA    -       -      A      64           -
LGA    -       -      T      65           -
LGA    -       -      S      66           -
LGA    -       -      S      67           -
LGA    -       -      T      68           -
LGA    -       -      S      69           -
LGA    -       -      K      70           -
LGA    -       -      C      71           -
LGA    -       -      V      72           -
LGA    -       -      I      73           -
LGA    -       -      L      74           -
LGA    -       -      S      75           -
LGA    -       -      K      76           -
LGA    -       -      S      77           -
LGA    -       -      S      78           -
LGA    -       -      Q      79           -
LGA    -       -      P      80           -
LGA    -       -      G      81           -
LGA    -       -      H      82           -
LGA    -       -      D      83           -
LGA    -       -      V      84           -
LGA    -       -      D      85           -
LGA    -       -      Y      86           -
LGA    -       -      L      87           -
LGA    -       -      Y      88           -
LGA    -       -      G      89           -
LGA    -       -      Q      90           -
LGA    -       -      V      91           -
LGA    -       -      S      92           -
LGA    -       -      I      93           -
LGA    -       -      D      94           -
LGA    -       -      K      95           -
LGA    -       -      P      96           -
LGA    -       -      F      97           -
LGA    -       -      V      98           -
LGA    -       -      D      99           -
LGA    -       -      W     100           -
LGA    -       -      S     101           -
LGA    -       -      G     102           -
LGA    -       -      N     103           -
LGA    -       -      C     104           -
LGA    -       -      G     105           -
LGA    -       -      N     106           -
LGA    -       -      L     107           -
LGA    -       -      S     108           -
LGA    -       -      T     109           -
LGA    -       -      G     110           -
LGA    -       -      A     111           -
LGA    -       -      G     112           -
LGA    -       -      A     113           -
LGA    -       -      F     114           -
LGA    -       -      A     115           -
LGA    -       -      L     116           -
LGA    -       -      H     117           -
LGA    -       -      A     118           -
LGA    -       -      G     119           -
LGA    -       -      L     120           -
LGA    -       -      V     121           -
LGA    -       -      D     122           -
LGA    -       -      P     123           -
LGA    -       -      A     124           -
LGA    -       -      R     125           -
LGA    -       -      I     126           -
LGA    -       -      P     127           -
LGA    -       -      E     128           -
LGA    P       4      D     129          2.764
LGA    P       5      G     130          1.763
LGA    Q       6      I     131          0.858
LGA    I       7      C     132          0.566
LGA    R       8      E     133          1.761
LGA    I       9      V     134          1.059
LGA    P      10      R     135          1.570
LGA    A      11      I     136          1.866
LGA    G     102      W     137          1.280
LGA    N     103      Q     138          0.644
LGA    -       -      A     139           -
LGA    -       -      N     140           -
LGA    -       -      I     141           -
LGA    -       -      G     142           -
LGA    C     104      K     143          1.844
LGA    G     105      T     144          0.729
LGA    A     124      I     145          1.727
LGA    R     125      I     146          1.115
LGA    I     126      A     147          0.768
LGA    P     127      H     148          1.076
LGA    E     128      V     149          1.451
LGA    D     129      P     150          3.205
LGA    -       -      V     151           -
LGA    -       -      S     152           -
LGA    -       -      G     153           -
LGA    -       -      G     154           -
LGA    -       -      Q     155           -
LGA    -       -      V     156           -
LGA    -       -      Q     157           -
LGA    G     130      E     158          3.823
LGA    -       -      T     159           -
LGA    -       -      G     160           -
LGA    -       -      D     161           -
LGA    -       -      F     162           -
LGA    -       -      E     163           -
LGA    -       -      L     164           -
LGA    -       -      D     165           -
LGA    -       -      G     166           -
LGA    -       -      V     167           -
LGA    -       -      T     168           -
LGA    -       -      F     169           -
LGA    -       -      P     170           -
LGA    -       -      A     171           -
LGA    -       -      A     172           -
LGA    I     131      E     173          2.481
LGA    C     132      I     174          1.518
LGA    -       -      V     175           -
LGA    -       -      L     176           -
LGA    -       -      E     177           -
LGA    -       -      F     178           -
LGA    -       -      L     179           -
LGA    -       -      D     180           -
LGA    -       -      P     181           -
LGA    -       -      S     182           -
LGA    E     133      R     378          2.781
LGA    -       -      S     379           -
LGA    V     134      A     380          5.058
LGA    R     135      R     381           -
LGA    -       -      I     382           -
LGA    -       -      L     383           -
LGA    -       -      M     384           -
LGA    -       -      E     385           -
LGA    -       -      G     386           -
LGA    -       -      W     387           -
LGA    -       -      V     388           -
LGA    -       -      R     389           -
LGA    -       -      V     390           -
LGA    -       -      P     391           -
LGA    -       -      G     392           -
LGA    -       -      D     393           -
LGA    -       -      A     394           -
LGA    -       -      F     395           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   24  200    5.0     23    2.11     0.00      9.946     1.039

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.369083 * X  +   0.724341 * Y  +  -0.582330 * Z  +  66.742599
  Y_new =  -0.114672 * X  +   0.657271 * Y  +   0.744879 * Z  +  26.462706
  Z_new =   0.922295 * X  +  -0.208145 * Y  +   0.325649 * Z  +   9.811708 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.568725    2.572868  [ DEG:   -32.5855    147.4145 ]
  Theta =  -1.173977   -1.967615  [ DEG:   -67.2639   -112.7361 ]
  Phi   =  -0.301239    2.840354  [ DEG:   -17.2597    162.7403 ]
 
# 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: T0301AL333_3-D1                               
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301AL333_3-D1.T0301_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   24  200   5.0   23   2.11    0.00   9.946
REMARK  ---------------------------------------------------------- 
MOLECULE T0301AL333_3-D1
REMARK Aligment from pdb entry: 1lv3_A
ATOM      1  N   PRO     4      60.733   8.987  24.622  1.00  0.00              
ATOM      2  CA  PRO     4      62.102   9.581  24.603  1.00  0.00              
ATOM      3  C   PRO     4      62.678   9.389  23.187  1.00  0.00              
ATOM      4  O   PRO     4      63.842   9.078  22.996  1.00  0.00              
ATOM      5  N   PRO     5      61.827   9.559  22.199  1.00  0.00              
ATOM      6  CA  PRO     5      62.215   9.382  20.771  1.00  0.00              
ATOM      7  C   PRO     5      63.320  10.352  20.365  1.00  0.00              
ATOM      8  O   PRO     5      63.164  11.560  20.420  1.00  0.00              
ATOM      9  N   GLN     6      64.416   9.815  19.912  1.00  0.00              
ATOM     10  CA  GLN     6      65.535  10.667  19.444  1.00  0.00              
ATOM     11  C   GLN     6      65.458  10.689  17.918  1.00  0.00              
ATOM     12  O   GLN     6      65.851   9.744  17.252  1.00  0.00              
ATOM     13  N   ILE     7      64.928  11.749  17.358  1.00  0.00              
ATOM     14  CA  ILE     7      64.800  11.818  15.872  1.00  0.00              
ATOM     15  C   ILE     7      66.170  12.146  15.279  1.00  0.00              
ATOM     16  O   ILE     7      66.986  12.789  15.910  1.00  0.00              
ATOM     17  N   ARG     8      66.440  11.673  14.090  1.00  0.00              
ATOM     18  CA  ARG     8      67.773  11.923  13.468  1.00  0.00              
ATOM     19  C   ARG     8      67.614  12.678  12.143  1.00  0.00              
ATOM     20  O   ARG     8      66.978  12.203  11.218  1.00  0.00              
ATOM     21  N   ILE     9      68.209  13.844  12.051  1.00  0.00              
ATOM     22  CA  ILE     9      68.128  14.646  10.790  1.00  0.00              
ATOM     23  C   ILE     9      69.236  14.171   9.839  1.00  0.00              
ATOM     24  O   ILE     9      70.375  14.002  10.236  1.00  0.00              
ATOM     25  N   PRO    10      68.907  13.938   8.594  1.00  0.00              
ATOM     26  CA  PRO    10      69.934  13.458   7.625  1.00  0.00              
ATOM     27  C   PRO    10      70.592  14.646   6.915  1.00  0.00              
ATOM     28  O   PRO    10      69.928  15.567   6.474  1.00  0.00              
ATOM     29  N   ALA    11      71.900  14.615   6.797  1.00  0.00              
ATOM     30  CA  ALA    11      72.644  15.716   6.112  1.00  0.00              
ATOM     31  C   ALA    11      72.273  15.710   4.621  1.00  0.00              
ATOM     32  O   ALA    11      72.515  14.735   3.938  1.00  0.00              
ATOM     33  N   GLY   102      71.686  16.793   4.162  1.00  0.00              
ATOM     34  CA  GLY   102      71.260  16.930   2.753  1.00  0.00              
ATOM     35  C   GLY   102      72.453  17.209   1.818  1.00  0.00              
ATOM     36  O   GLY   102      72.335  17.079   0.612  1.00  0.00              
ATOM     37  N   ASN   103      73.590  17.600   2.354  1.00  0.00              
ATOM     38  CA  ASN   103      74.772  17.896   1.483  1.00  0.00              
ATOM     39  C   ASN   103      75.496  16.602   1.092  1.00  0.00              
ATOM     40  O   ASN   103      75.773  16.376  -0.073  1.00  0.00              
ATOM     41  N   CYS   104      75.813  15.760   2.044  1.00  0.00              
ATOM     42  CA  CYS   104      76.532  14.487   1.717  1.00  0.00              
ATOM     43  C   CYS   104      75.616  13.272   1.932  1.00  0.00              
ATOM     44  O   CYS   104      75.807  12.238   1.316  1.00  0.00              
ATOM     45  N   GLY   105      74.634  13.380   2.800  1.00  0.00              
ATOM     46  CA  GLY   105      73.722  12.225   3.058  1.00  0.00              
ATOM     47  C   GLY   105      74.258  11.429   4.247  1.00  0.00              
ATOM     48  O   GLY   105      74.818  10.361   4.086  1.00  0.00              
ATOM     49  N   ALA   124      74.098  11.959   5.435  1.00  0.00              
ATOM     50  CA  ALA   124      74.600  11.263   6.654  1.00  0.00              
ATOM     51  C   ALA   124      73.579  11.416   7.789  1.00  0.00              
ATOM     52  O   ALA   124      73.138  12.508   8.092  1.00  0.00              
ATOM     53  N   ARG   125      73.197  10.324   8.407  1.00  0.00              
ATOM     54  CA  ARG   125      72.196  10.385   9.518  1.00  0.00              
ATOM     55  C   ARG   125      72.830  11.039  10.750  1.00  0.00              
ATOM     56  O   ARG   125      73.761  10.512  11.334  1.00  0.00              
ATOM     57  N   ILE   126      72.324  12.180  11.148  1.00  0.00              
ATOM     58  CA  ILE   126      72.878  12.881  12.344  1.00  0.00              
ATOM     59  C   ILE   126      71.791  12.963  13.419  1.00  0.00              
ATOM     60  O   ILE   126      70.715  13.479  13.185  1.00  0.00              
ATOM     61  N   PRO   127      72.071  12.446  14.591  1.00  0.00              
ATOM     62  CA  PRO   127      71.068  12.471  15.701  1.00  0.00              
ATOM     63  C   PRO   127      70.559  13.906  15.929  1.00  0.00              
ATOM     64  O   PRO   127      71.321  14.857  15.924  1.00  0.00              
ATOM     65  N   GLU   128      69.266  14.060  16.119  1.00  0.00              
ATOM     66  CA  GLU   128      68.673  15.416  16.343  1.00  0.00              
ATOM     67  C   GLU   128      68.151  15.524  17.783  1.00  0.00              
ATOM     68  O   GLU   128      67.848  14.533  18.424  1.00  0.00              
ATOM     69  N   ASP   129      68.043  16.733  18.286  1.00  0.00              
ATOM     70  CA  ASP   129      67.545  16.945  19.675  1.00  0.00              
ATOM     71  C   ASP   129      68.656  17.580  20.507  1.00  0.00              
ATOM     72  O   ASP   129      68.898  18.772  20.424  1.00  0.00              
ATOM     73  N   GLY   130      69.338  16.790  21.298  1.00  0.00              
ATOM     74  CA  GLY   130      70.449  17.330  22.136  1.00  0.00              
ATOM     75  C   GLY   130      71.387  16.180  22.534  1.00  0.00              
ATOM     76  O   GLY   130      71.622  15.919  23.701  1.00  0.00              
ATOM     77  N   ILE   131      71.921  15.490  21.555  1.00  0.00              
ATOM     78  CA  ILE   131      72.844  14.352  21.838  1.00  0.00              
ATOM     79  C   ILE   131      74.207  14.630  21.196  1.00  0.00              
ATOM     80  O   ILE   131      75.234  14.566  21.848  1.00  0.00              
ATOM     81  N   CYS   132      74.216  14.943  19.924  1.00  0.00              
ATOM     82  CA  CYS   132      75.504  15.230  19.218  1.00  0.00              
ATOM     83  C   CYS   132      75.789  16.738  19.237  1.00  0.00              
ATOM     84  O   CYS   132      74.916  17.530  19.542  1.00  0.00              
ATOM     85  N   GLU   133      77.006  17.093  18.894  1.00  0.00              
ATOM     86  CA  GLU   133      77.435  18.502  18.844  1.00  0.00              
ATOM     87  C   GLU   133      76.914  19.158  17.557  1.00  0.00              
ATOM     88  O   GLU   133      76.603  20.334  17.535  1.00  0.00              
ATOM     89  N   VAL   134      76.818  18.392  16.491  1.00  0.00              
ATOM     90  CA  VAL   134      76.322  18.938  15.197  1.00  0.00              
ATOM     91  C   VAL   134      74.983  18.278  14.846  1.00  0.00              
ATOM     92  O   VAL   134      74.878  17.540  13.883  1.00  0.00              
ATOM     93  N   ARG   135      73.953  18.540  15.619  1.00  0.00              
ATOM     94  CA  ARG   135      72.611  17.934  15.333  1.00  0.00              
ATOM     95  C   ARG   135      72.235  18.200  13.864  1.00  0.00              
ATOM     96  O   ARG   135      71.986  17.265  13.127  1.00  0.00              
END
