
#######################################################
#                                                     #
#                        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    5 (   76),  selected    5 , name T0301TS069_1-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS069_1-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    F     178      R      15          0.310
LGA    L     179      G      16          0.563
LGA    D     180      G      17          0.770
LGA    P     181      T      18          0.624
LGA    S     182      S      19          0.236
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    -       -      D     129           -
LGA    -       -      G     130           -
LGA    -       -      I     131           -
LGA    -       -      C     132           -
LGA    -       -      E     133           -
LGA    -       -      V     134           -
LGA    -       -      R     135           -
LGA    -       -      I     136           -
LGA    -       -      W     137           -
LGA    -       -      Q     138           -
LGA    -       -      A     139           -
LGA    -       -      N     140           -
LGA    -       -      I     141           -
LGA    -       -      G     142           -
LGA    -       -      K     143           -
LGA    -       -      T     144           -
LGA    -       -      I     145           -
LGA    -       -      I     146           -
LGA    -       -      A     147           -
LGA    -       -      H     148           -
LGA    -       -      V     149           -
LGA    -       -      P     150           -
LGA    -       -      V     151           -
LGA    -       -      S     152           -
LGA    -       -      G     153           -
LGA    -       -      G     154           -
LGA    -       -      Q     155           -
LGA    -       -      V     156           -
LGA    -       -      Q     157           -
LGA    -       -      E     158           -
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    -       -      E     173           -
LGA    -       -      I     174           -
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    -       -      R     378           -
LGA    -       -      S     379           -
LGA    -       -      A     380           -
LGA    -       -      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)    5  200    5.0      5    0.54    20.00      2.500     0.783

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.707649 * X  +   0.268802 * Y  +   0.653436 * Z  +  75.578140
  Y_new =  -0.676355 * X  +  -0.525234 * Y  +  -0.516405 * Z  +  23.495911
  Z_new =   0.204396 * X  +  -0.807388 * Y  +   0.553486 * Z  +  36.949253 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.969850    2.171743  [ DEG:   -55.5683    124.4317 ]
  Theta =  -0.205846   -2.935746  [ DEG:   -11.7941   -168.2059 ]
  Phi   =  -2.378802    0.762791  [ DEG:  -136.2953     43.7047 ]
 
# 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: T0301TS069_1-D1                               
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS069_1-D1.T0301_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  200   5.0    5   0.54   20.00   2.500
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS069_1-D1
PFRMAT TS
TARGET T0301
MODEL 1
PARENT 1O9J_D
ATOM      1  N   PHE   178      75.684  27.665  17.386  1.00 10.00
ATOM      2  CA  PHE   178      76.943  27.107  17.686  1.00 10.00
ATOM      3  C   PHE   178      76.922  25.584  17.595  1.00 10.00
ATOM      4  O   PHE   178      76.145  24.902  18.364  1.00 10.00
ATOM      5  CB  PHE   178      77.348  27.614  19.076  1.00 10.00
ATOM      6  CG  PHE   178      78.699  27.106  19.509  1.00 10.00
ATOM      7  CD1 PHE   178      79.860  27.831  19.181  1.00 10.00
ATOM      8  CD2 PHE   178      78.798  26.004  20.380  1.00 10.00
ATOM      9  CE1 PHE   178      81.108  27.434  19.685  1.00 10.00
ATOM     10  CE2 PHE   178      80.046  25.609  20.887  1.00 10.00
ATOM     11  CZ  PHE   178      81.200  26.330  20.544  1.00 10.00
ATOM     12 HN   PHE   178      75.594  28.654  17.375  1.00 10.00
ATOM     13 HA   PHE   178      77.670  27.493  16.935  1.00 10.00
ATOM     14 HB1  PHE   178      77.371  28.730  19.054  1.00 10.00
ATOM     15 HB2  PHE   178      76.569  27.319  19.818  1.00 10.00
ATOM     16 HD1  PHE   178      79.803  28.701  18.523  1.00 10.00
ATOM     17 HD2  PHE   178      77.903  25.449  20.657  1.00 10.00
ATOM     18 HE1  PHE   178      82.000  27.994  19.405  1.00 10.00
ATOM     19 HE2  PHE   178      80.116  24.749  21.548  1.00 10.00
ATOM     20 HZ   PHE   178      82.171  26.033  20.937  1.00 10.00
ATOM     21  N   LEU   179      77.724  24.954  16.719  1.00 10.00
ATOM     22  CA  LEU   179      77.606  23.581  16.340  1.00 10.00
ATOM     23  C   LEU   179      78.946  22.971  15.947  1.00 10.00
ATOM     24  O   LEU   179      79.642  23.460  14.991  1.00 10.00
ATOM     25  CB  LEU   179      76.645  23.441  15.144  1.00 10.00
ATOM     26  CG  LEU   179      75.180  23.845  15.398  1.00 10.00
ATOM     27  CD1 LEU   179      74.461  24.009  14.067  1.00 10.00
ATOM     28 HN   LEU   179      78.609  25.394  16.604  1.00 10.00
ATOM     29 HA   LEU   179      77.229  22.974  17.195  1.00 10.00
ATOM     30 HB1  LEU   179      77.059  24.075  14.321  1.00 10.00
ATOM     31 HB2  LEU   179      76.655  22.387  14.776  1.00 10.00
ATOM     32  CD2 LEU   179      74.422  22.849  16.290  1.00 10.00
ATOM     33 HG   LEU   179      75.141  24.848  15.875  1.00 10.00
ATOM     34 HD11 LEU   179      75.016  24.678  13.380  1.00 10.00
ATOM     35 HD12 LEU   179      73.482  24.483  14.275  1.00 10.00
ATOM     36 HD13 LEU   179      74.331  23.028  13.556  1.00 10.00
ATOM     37 HD21 LEU   179      73.368  23.184  16.428  1.00 10.00
ATOM     38 HD22 LEU   179      74.890  22.783  17.296  1.00 10.00
ATOM     39 HD23 LEU   179      74.416  21.835  15.828  1.00 10.00
ATOM     40  N   ASP   180      79.389  21.905  16.631  1.00 10.00
ATOM     41  CA  ASP   180      80.665  21.298  16.499  1.00 10.00
ATOM     42  C   ASP   180      81.820  22.332  16.599  1.00 10.00
ATOM     43  O   ASP   180      82.690  22.451  15.659  1.00 10.00
ATOM     44  CB  ASP   180      80.662  20.383  15.246  1.00 10.00
ATOM     45  CG  ASP   180      81.595  19.206  15.334  1.00 10.00
ATOM     46  OD1 ASP   180      82.198  18.760  14.264  1.00 10.00
ATOM     47 HN   ASP   180      78.837  21.633  17.402  1.00 10.00
ATOM     48 HA   ASP   180      80.734  20.614  17.371  1.00 10.00
ATOM     49 HB1  ASP   180      80.915  20.976  14.338  1.00 10.00
ATOM     50 HB2  ASP   180      79.653  19.940  15.088  1.00 10.00
ATOM     51  OD2 ASP   180      81.914  18.698  16.502  1.00 10.00
ATOM     52  N   PRO   181      81.935  23.112  17.716  1.00 10.00
ATOM     53  CA  PRO   181      82.891  24.245  17.810  1.00 10.00
ATOM     54  C   PRO   181      83.100  25.213  16.656  1.00 10.00
ATOM     55  O   PRO   181      84.039  26.075  16.789  1.00 10.00
ATOM     56  CB  PRO   181      84.115  23.530  18.361  1.00 10.00
ATOM     57 HA   PRO   181      82.561  24.948  18.615  1.00 10.00
ATOM     58 HB1  PRO   181      84.544  22.827  17.607  1.00 10.00
ATOM     59 HB2  PRO   181      84.897  24.246  18.704  1.00 10.00
ATOM     60  CG  PRO   181      83.470  22.786  19.532  1.00 10.00
ATOM     61 HG1  PRO   181      84.071  21.890  19.811  1.00 10.00
ATOM     62 HG2  PRO   181      83.381  23.460  20.417  1.00 10.00
ATOM     63  CD  PRO   181      82.073  22.419  19.017  1.00 10.00
ATOM     64 HD1  PRO   181      81.248  22.713  19.706  1.00 10.00
ATOM     65 HD2  PRO   181      82.078  21.307  18.924  1.00 10.00
ATOM     66  N   SER   182      82.147  25.408  15.722  1.00 10.00
ATOM     67  CA  SER   182      82.122  26.568  14.870  1.00 10.00
ATOM     68  C   SER   182      80.780  27.295  14.804  1.00 10.00
ATOM     69  O   SER   182      79.772  26.827  15.450  1.00 10.00
ATOM     70  CB  SER   182      82.541  26.103  13.469  1.00 10.00
ATOM     71 HN   SER   182      81.258  25.135  16.069  1.00 10.00
ATOM     72 HA   SER   182      82.815  27.359  15.240  1.00 10.00
ATOM     73 HB1  SER   182      81.787  25.371  13.084  1.00 10.00
ATOM     74 HB2  SER   182      83.521  25.576  13.538  1.00 10.00
ATOM     75  OG  SER   182      82.665  27.209  12.548  1.00 10.00
ATOM     76 HG   SER   182      81.689  27.425  12.256  1.00 10.00
TER
END
