
#######################################################
#                                                     #
#                        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 T0372TS349_4-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS349_4-D1.T0372_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    K     290      L      77          1.911
LGA    Y     291      R      78          1.321
LGA    M     292      K      79          3.265
LGA    -       -      L      80           -
LGA    A     293      I      81          1.535
LGA    C     294      E      82          2.822
LGA    -       -      D      83           -
LGA    L     295      A      84          1.654
LGA    -       -      D      85           -
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    K     296      K      88          2.972
LGA    D     297      H      89          3.765
LGA    -       -      N      90           -
LGA    H     298      F      91          2.252
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     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    2.52    11.11      5.469     0.343

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.159170 * X  +  -0.673583 * Y  +   0.721769 * Z  +  35.391785
  Y_new =  -0.694289 * X  +  -0.596132 * Y  +  -0.403223 * Z  + 127.831467
  Z_new =   0.701874 * X  +  -0.436936 * Y  +  -0.562548 * Z  +  31.539436 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.481216    0.660376  [ DEG:  -142.1632     37.8368 ]
  Theta =  -0.778025   -2.363567  [ DEG:   -44.5776   -135.4224 ]
  Phi   =  -1.345434    1.796158  [ DEG:   -77.0877    102.9123 ]
 
# 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: T0372TS349_4-D1                               
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS349_4-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   2.52   11.11   5.469
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS349_4-D1
PFRMAT TS
TARGET T0372
MODEL  4  REFINED
PARENT 1YR0_D
ATOM   1090  N   LYS   290      34.174  57.229  -4.002  1.00  0.00
ATOM   1091  CA  LYS   290      34.254  56.545  -5.311  1.00  0.00
ATOM   1092  C   LYS   290      34.226  57.671  -6.424  1.00  0.00
ATOM   1093  O   LYS   290      35.295  58.195  -6.755  1.00  0.00
ATOM   1094  CB  LYS   290      32.854  55.842  -5.371  1.00  0.00
ATOM   1095  CG  LYS   290      32.731  54.930  -4.134  1.00  0.00
ATOM   1096  CD  LYS   290      31.253  54.512  -4.226  1.00  0.00
ATOM   1097  CE  LYS   290      30.894  53.432  -3.237  1.00  0.00
ATOM   1098  NZ  LYS   290      31.954  52.387  -3.276  1.00  0.00
ATOM   1099  N   TYR   291      33.097  57.726  -7.203  1.00  0.00
ATOM   1100  CA  TYR   291      32.819  58.599  -8.345  1.00  0.00
ATOM   1101  C   TYR   291      33.457  58.015  -9.653  1.00  0.00
ATOM   1102  O   TYR   291      32.678  57.785 -10.584  1.00  0.00
ATOM   1103  CB  TYR   291      33.248  60.083  -8.105  1.00  0.00
ATOM   1104  CG  TYR   291      33.137  60.949  -9.370  1.00  0.00
ATOM   1105  CD1 TYR   291      31.891  61.414  -9.765  1.00  0.00
ATOM   1106  CD2 TYR   291      34.310  61.196 -10.083  1.00  0.00
ATOM   1107  CE1 TYR   291      31.815  62.146 -10.963  1.00  0.00
ATOM   1108  CE2 TYR   291      34.270  61.911 -11.275  1.00  0.00
ATOM   1109  CZ  TYR   291      33.006  62.370 -11.630  1.00  0.00
ATOM   1110  OH  TYR   291      32.950  63.084 -12.844  1.00  0.00
ATOM   1111  N   MET   292      34.771  57.831  -9.765  1.00  0.00
ATOM   1112  CA  MET   292      35.298  57.193 -10.940  1.00  0.00
ATOM   1113  C   MET   292      35.157  55.669 -10.682  1.00  0.00
ATOM   1114  O   MET   292      35.441  55.262  -9.517  1.00  0.00
ATOM   1115  CB  MET   292      36.772  57.568 -11.207  1.00  0.00
ATOM   1116  CG  MET   292      37.289  56.870 -12.488  1.00  0.00
ATOM   1117  SD  MET   292      38.914  57.404 -12.891  1.00  0.00
ATOM   1118  CE  MET   292      38.535  58.951 -13.721  1.00  0.00
ATOM   1119  N   ALA   293      34.551  54.882 -11.612  1.00  0.00
ATOM   1120  CA  ALA   293      34.517  53.452 -11.272  1.00  0.00
ATOM   1121  C   ALA   293      36.008  53.131 -11.173  1.00  0.00
ATOM   1122  O   ALA   293      36.603  52.973 -12.259  1.00  0.00
ATOM   1123  CB  ALA   293      33.766  52.632 -12.322  1.00  0.00
ATOM   1124  N   CYS   294      36.568  52.763 -10.004  1.00  0.00
ATOM   1125  CA  CYS   294      38.050  52.600 -10.056  1.00  0.00
ATOM   1126  C   CYS   294      38.637  51.288  -9.489  1.00  0.00
ATOM   1127  O   CYS   294      39.598  51.416  -8.741  1.00  0.00
ATOM   1128  CB  CYS   294      38.620  53.865  -9.491  1.00  0.00
ATOM   1129  SG  CYS   294      38.311  54.147  -7.714  1.00  0.00
ATOM   1130  N   LEU   295      38.494  50.187 -10.185  1.00  0.00
ATOM   1131  CA  LEU   295      39.120  48.884  -9.867  1.00  0.00
ATOM   1132  C   LEU   295      38.208  47.816 -10.427  1.00  0.00
ATOM   1133  O   LEU   295      37.077  47.859 -10.050  1.00  0.00
ATOM   1134  CB  LEU   295      39.304  48.804  -8.341  1.00  0.00
ATOM   1135  CG  LEU   295      40.214  47.894  -7.603  1.00  0.00
ATOM   1136  CD1 LEU   295      40.344  46.492  -8.222  1.00  0.00
ATOM   1137  CD2 LEU   295      41.674  48.417  -7.473  1.00  0.00
ATOM   1138  N   LYS   296      38.700  46.692 -10.925  1.00  0.00
ATOM   1139  CA  LYS   296      37.785  45.607 -11.395  1.00  0.00
ATOM   1140  C   LYS   296      36.333  46.130 -11.703  1.00  0.00
ATOM   1141  O   LYS   296      35.417  45.377 -11.398  1.00  0.00
ATOM   1142  CB  LYS   296      37.799  44.465 -10.357  1.00  0.00
ATOM   1143  CG  LYS   296      39.167  43.949 -10.040  1.00  0.00
ATOM   1144  CD  LYS   296      39.054  42.913  -8.944  1.00  0.00
ATOM   1145  CE  LYS   296      40.388  42.188  -8.829  1.00  0.00
ATOM   1146  NZ  LYS   296      39.988  40.726  -8.627  1.00  0.00
ATOM   1147  N   ASP   297      36.126  47.201 -12.514  1.00  0.00
ATOM   1148  CA  ASP   297      34.856  47.821 -12.786  1.00  0.00
ATOM   1149  C   ASP   297      34.112  48.415 -11.483  1.00  0.00
ATOM   1150  O   ASP   297      32.867  48.503 -11.588  1.00  0.00
ATOM   1151  CB  ASP   297      33.993  46.825 -13.495  1.00  0.00
ATOM   1152  CG  ASP   297      34.339  46.236 -14.800  1.00  0.00
ATOM   1153  OD1 ASP   297      33.659  45.270 -15.242  1.00  0.00
ATOM   1154  OD2 ASP   297      35.291  46.749 -15.423  1.00  0.00
ATOM   1155  N   HIS   298      34.797  49.117 -10.521  1.00  0.00
ATOM   1156  CA  HIS   298      34.154  49.665  -9.282  1.00  0.00
ATOM   1157  C   HIS   298      34.907  50.867  -8.497  1.00  0.00
ATOM   1158  O   HIS   298      36.137  50.721  -8.450  1.00  0.00
ATOM   1159  CB  HIS   298      33.844  48.510  -8.298  1.00  0.00
ATOM   1160  CG  HIS   298      35.007  47.624  -7.958  1.00  0.00
ATOM   1161  ND1 HIS   298      35.243  46.551  -8.782  1.00  0.00
ATOM   1162  CD2 HIS   298      35.955  47.625  -7.017  1.00  0.00
ATOM   1163  CE1 HIS   298      36.296  45.901  -8.301  1.00  0.00
ATOM   1164  NE2 HIS   298      36.726  46.524  -7.225  1.00  0.00
TER
END
