
#######################################################
#                                                     #
#                        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    9 (   75),  selected    9 , name T0372TS249_4_2-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS249_4_2-D1.T0372_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    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    -       -      L      77           -
LGA    -       -      R      78           -
LGA    -       -      K      79           -
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    -       -      E      82           -
LGA    -       -      D      83           -
LGA    -       -      A      84           -
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    -       -      F      91           -
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    K     290      V      96          2.438
LGA    -       -      C      97           -
LGA    Y     291      S      98          3.895
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    M     292      R     101          1.658
LGA    A     293      A     102          1.289
LGA    C     294      D     103          0.929
LGA    L     295      L     104          1.167
LGA    K     296      E     105          0.579
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    D     297      P     109          2.441
LGA    -       -      E     110           -
LGA    H     298      R     111          2.111
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    9  126    5.0      9    2.07    22.22      6.404     0.415

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.334301 * X  +   0.885306 * Y  +  -0.323227 * Z  +  28.163626
  Y_new =   0.508144 * X  +  -0.458152 * Y  +  -0.729305 * Z  +  56.170341
  Z_new =  -0.793746 * X  +   0.079562 * Y  +  -0.603024 * Z  +  12.185726 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.010412   -0.131180  [ DEG:   172.4839     -7.5161 ]
  Theta =   0.916943    2.224650  [ DEG:    52.5369    127.4631 ]
  Phi   =   0.988897   -2.152696  [ DEG:    56.6596   -123.3404 ]
 
# 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: T0372TS249_4_2-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS249_4_2-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    9  126   5.0    9   2.07   22.22   6.404
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS249_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0372
PARENT N/A
ATOM   1035  N   LYS   290      25.212  49.746   3.838  1.00  0.00
ATOM   1036  CA  LYS   290      25.580  50.515   2.705  1.00  0.00
ATOM   1037  C   LYS   290      24.389  51.353   2.436  1.00  0.00
ATOM   1038  O   LYS   290      24.299  52.014   1.403  1.00  0.00
ATOM   1039  CB  LYS   290      25.918  49.665   1.495  1.00  0.00
ATOM   1040  CG  LYS   290      27.357  49.152   1.520  1.00  0.00
ATOM   1041  CD  LYS   290      27.692  48.314   2.750  1.00  0.00
ATOM   1042  CE  LYS   290      29.112  47.752   2.737  1.00  0.00
ATOM   1043  NZ  LYS   290      30.091  48.853   2.612  1.00  0.00
ATOM   1044  N   TYR   291      23.378  51.197   3.317  1.00  0.00
ATOM   1045  CA  TYR   291      22.204  51.988   3.229  1.00  0.00
ATOM   1046  C   TYR   291      22.712  53.310   3.660  1.00  0.00
ATOM   1047  O   TYR   291      22.736  53.677   4.835  1.00  0.00
ATOM   1048  CB  TYR   291      21.085  51.524   4.182  1.00  0.00
ATOM   1049  CG  TYR   291      19.829  52.244   3.817  1.00  0.00
ATOM   1050  CD1 TYR   291      19.151  51.909   2.666  1.00  0.00
ATOM   1051  CD2 TYR   291      19.310  53.229   4.625  1.00  0.00
ATOM   1052  CE1 TYR   291      17.988  52.555   2.315  1.00  0.00
ATOM   1053  CE2 TYR   291      18.148  53.880   4.280  1.00  0.00
ATOM   1054  CZ  TYR   291      17.486  53.543   3.123  1.00  0.00
ATOM   1055  OH  TYR   291      16.294  54.207   2.767  1.00  0.00
ATOM   1056  N   MET   292      23.226  54.020   2.648  1.00  0.00
ATOM   1057  CA  MET   292      23.738  55.325   2.803  1.00  0.00
ATOM   1058  C   MET   292      22.504  56.117   2.670  1.00  0.00
ATOM   1059  O   MET   292      21.935  56.226   1.583  1.00  0.00
ATOM   1060  CB  MET   292      24.681  55.735   1.662  1.00  0.00
ATOM   1061  CG  MET   292      26.003  54.967   1.647  1.00  0.00
ATOM   1062  SD  MET   292      26.988  55.271   0.155  1.00  0.00
ATOM   1063  CE  MET   292      25.913  54.234  -0.874  1.00  0.00
ATOM   1064  N   ALA   293      22.032  56.646   3.803  1.00  0.00
ATOM   1065  CA  ALA   293      20.827  57.395   3.744  1.00  0.00
ATOM   1066  C   ALA   293      21.139  58.532   2.844  1.00  0.00
ATOM   1067  O   ALA   293      20.315  58.968   2.045  1.00  0.00
ATOM   1068  CB  ALA   293      20.405  57.966   5.109  1.00  0.00
ATOM   1069  N   CYS   294      22.376  59.038   2.966  1.00  0.00
ATOM   1070  CA  CYS   294      22.840  60.103   2.138  1.00  0.00
ATOM   1071  C   CYS   294      22.833  59.662   0.708  1.00  0.00
ATOM   1072  O   CYS   294      22.432  60.434  -0.159  1.00  0.00
ATOM   1073  CB  CYS   294      24.273  60.569   2.451  1.00  0.00
ATOM   1074  SG  CYS   294      24.371  61.611   3.934  1.00  0.00
ATOM   1075  N   LEU   295      23.265  58.417   0.407  1.00  0.00
ATOM   1076  CA  LEU   295      23.328  58.044  -0.987  1.00  0.00
ATOM   1077  C   LEU   295      22.230  57.070  -1.324  1.00  0.00
ATOM   1078  O   LEU   295      22.286  55.894  -0.967  1.00  0.00
ATOM   1079  CB  LEU   295      24.673  57.401  -1.373  1.00  0.00
ATOM   1080  CG  LEU   295      24.786  57.044  -2.865  1.00  0.00
ATOM   1081  CD1 LEU   295      24.718  58.304  -3.743  1.00  0.00
ATOM   1082  CD2 LEU   295      26.040  56.199  -3.140  1.00  0.00
ATOM   1083  N   LYS   296      21.178  57.575  -2.008  1.00  0.00
ATOM   1084  CA  LYS   296      19.997  56.853  -2.413  1.00  0.00
ATOM   1085  C   LYS   296      20.156  55.928  -3.603  1.00  0.00
ATOM   1086  O   LYS   296      19.595  54.834  -3.597  1.00  0.00
ATOM   1087  CB  LYS   296      18.825  57.798  -2.728  1.00  0.00
ATOM   1088  CG  LYS   296      18.403  58.649  -1.528  1.00  0.00
ATOM   1089  CD  LYS   296      17.982  57.834  -0.302  1.00  0.00
ATOM   1090  CE  LYS   296      17.682  58.695   0.927  1.00  0.00
ATOM   1091  NZ  LYS   296      17.295  57.834   2.067  1.00  0.00
ATOM   1092  N   ASP   297      20.884  56.334  -4.671  1.00  0.00
ATOM   1093  CA  ASP   297      20.854  55.562  -5.898  1.00  0.00
ATOM   1094  C   ASP   297      21.971  54.567  -6.053  1.00  0.00
ATOM   1095  O   ASP   297      23.024  54.657  -5.429  1.00  0.00
ATOM   1096  CB  ASP   297      20.836  56.442  -7.160  1.00  0.00
ATOM   1097  CG  ASP   297      22.106  57.279  -7.182  1.00  0.00
ATOM   1098  OD1 ASP   297      22.927  57.136  -6.238  1.00  0.00
ATOM   1099  OD2 ASP   297      22.265  58.081  -8.141  1.00  0.00
ATOM   1100  N   HIS   298      21.758  53.585  -6.958  1.00  0.00
ATOM   1101  CA  HIS   298      22.717  52.555  -7.255  1.00  0.00
ATOM   1102  C   HIS   298      22.780  51.600  -6.099  1.00  0.00
ATOM   1103  O   HIS   298      22.282  51.879  -5.008  1.00  0.00
ATOM   1104  CB  HIS   298      24.135  53.065  -7.583  1.00  0.00
ATOM   1105  CG  HIS   298      24.218  53.743  -8.921  1.00  0.00
ATOM   1106  ND1 HIS   298      24.230  53.066 -10.122  1.00  0.00
ATOM   1107  CD2 HIS   298      24.300  55.064  -9.240  1.00  0.00
ATOM   1108  CE1 HIS   298      24.317  54.003 -11.099  1.00  0.00
ATOM   1109  NE2 HIS   298      24.362  55.230 -10.612  1.00  0.00
TER
END
