
#######################################################
#                                                     #
#                        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   17 (  137),  selected   17 , name T0349TS319_5-D1
# Molecule2: number of CA atoms   57 (  873),  selected   57 , name T0349_D1.pdb
# PARAMETERS: T0349TS319_5-D1.T0349_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    -       -      R       2           -
LGA    -       -      E       3           -
LGA    -       -      L       4           -
LGA    -       -      L       5           -
LGA    -       -      R       6           -
LGA    -       -      T       7           -
LGA    -       -      N       8           -
LGA    -       -      D       9           -
LGA    -       -      A      10           -
LGA    -       -      V      11           -
LGA    -       -      L      12           -
LGA    -       -      L      13           -
LGA    A      23      S      14          2.035
LGA    D      24      A      15          2.504
LGA    I      25      V      16          0.880
LGA    G      26      G      17          3.608
LGA    -       -      A      18           -
LGA    -       -      L      19           -
LGA    -       -      L      20           -
LGA    H      27      D      21          2.302
LGA    L      28      G      22          3.228
LGA    V      29      A      23          2.737
LGA    P      45      -       -           -
LGA    R      46      D      24           #
LGA    R      47      I      25          2.663
LGA    -       -      G      26           -
LGA    -       -      H      27           -
LGA    -       -      L      28           -
LGA    -       -      V      29           -
LGA    -       -      P      45           -
LGA    -       -      R      46           -
LGA    -       -      R      47           -
LGA    -       -      V      48           -
LGA    -       -      L      49           -
LGA    -       -      V      50           -
LGA    -       -      H      51           -
LGA    -       -      E      52           -
LGA    -       -      D      53           -
LGA    -       -      D      54           -
LGA    -       -      L      55           -
LGA    -       -      A      56           -
LGA    V      48      G      57          5.000
LGA    L      49      A      58          3.331
LGA    -       -      R      59           -
LGA    -       -      R      60           -
LGA    V      50      L      61          3.744
LGA    H      51      L      62          2.587
LGA    E      52      T      63           #
LGA    -       -      D      64           -
LGA    -       -      A      65           -
LGA    D      53      G      66          2.730
LGA    D      54      L      67          2.690
LGA    -       -      A      68           -
LGA    -       -      H      69           -
LGA    -       -      E      70           -
LGA    -       -      L      71           -
LGA    -       -      R      72           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   17   57    5.0     14    3.00     7.14     16.493     0.452

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.501029 * X  +   0.448534 * Y  +   0.740127 * Z  +  -1.479094
  Y_new =   0.723463 * X  +   0.252261 * Y  +  -0.642624 * Z  +   5.259209
  Z_new =  -0.474944 * X  +   0.857427 * Y  +  -0.198108 * Z  +   8.850276 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.797861   -1.343731  [ DEG:   103.0099    -76.9901 ]
  Theta =   0.494900    2.646693  [ DEG:    28.3557    151.6443 ]
  Phi   =   0.965093   -2.176499  [ DEG:    55.2958   -124.7042 ]
 
# 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: T0349TS319_5-D1                               
REMARK     2: T0349_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0349TS319_5-D1.T0349_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   17   57   5.0   14   3.00    7.14  16.493
REMARK  ---------------------------------------------------------- 
MOLECULE T0349TS319_5-D1
PFRMAT TS
TARGET T0349
MODEL 5
PARENT N/A
ATOM      1  N   ALA    23      -5.525  -0.437   6.944  1.00 12.98       1SG   2
ATOM      2  CA  ALA    23      -4.446  -1.241   7.559  1.00 12.98       1SG   3
ATOM      3  CB  ALA    23      -3.559  -1.878   6.478  1.00 12.98       1SG   4
ATOM      4  C   ALA    23      -3.581  -0.413   8.446  1.00 12.98       1SG   5
ATOM      5  O   ALA    23      -4.069   0.338   9.290  1.00 12.98       1SG   6
ATOM      6  N   ASP    24      -2.254  -0.558   8.280  1.00 48.31       1SG   7
ATOM      7  CA  ASP    24      -1.305   0.132   9.102  1.00 48.31       1SG   8
ATOM      8  CB  ASP    24       0.146  -0.327   8.859  1.00 48.31       1SG   9
ATOM      9  CG  ASP    24       0.286  -1.751   9.374  1.00 48.31       1SG  10
ATOM     10  OD1 ASP    24      -0.767  -2.389   9.637  1.00 48.31       1SG  11
ATOM     11  OD2 ASP    24       1.449  -2.217   9.516  1.00 48.31       1SG  12
ATOM     12  C   ASP    24      -1.343   1.611   8.851  1.00 48.31       1SG  13
ATOM     13  O   ASP    24      -1.299   2.400   9.791  1.00 48.31       1SG  14
ATOM     14  N   ILE    25      -1.462   2.025   7.576  1.00157.26       1SG  15
ATOM     15  CA  ILE    25      -1.329   3.410   7.212  1.00157.26       1SG  16
ATOM     16  CB  ILE    25      -1.130   3.597   5.728  1.00157.26       1SG  17
ATOM     17  CG2 ILE    25      -2.498   3.383   5.057  1.00157.26       1SG  18
ATOM     18  CG1 ILE    25      -0.475   4.945   5.364  1.00157.26       1SG  19
ATOM     19  CD1 ILE    25      -1.331   6.183   5.613  1.00157.26       1SG  20
ATOM     20  C   ILE    25      -2.537   4.185   7.635  1.00157.26       1SG  21
ATOM     21  O   ILE    25      -3.666   3.698   7.562  1.00157.26       1SG  22
ATOM     22  N   GLY    26      -2.300   5.417   8.141  1.00 35.79       1SG  23
ATOM     23  CA  GLY    26      -3.352   6.322   8.514  1.00 35.79       1SG  24
ATOM     24  C   GLY    26      -3.126   7.597   7.758  1.00 35.79       1SG  25
ATOM     25  O   GLY    26      -1.998   8.057   7.594  1.00 35.79       1SG  26
ATOM     26  N   HIS    27      -4.228   8.221   7.302  1.00107.43       1SG  27
ATOM     27  CA  HIS    27      -4.160   9.398   6.486  1.00107.43       1SG  28
ATOM     28  ND1 HIS    27      -5.590   6.834   5.123  1.00107.43       1SG  29
ATOM     29  CG  HIS    27      -5.211   8.061   4.617  1.00107.43       1SG  30
ATOM     30  CB  HIS    27      -5.255   9.338   5.409  1.00107.43       1SG  31
ATOM     31  NE2 HIS    27      -4.942   6.479   3.025  1.00107.43       1SG  32
ATOM     32  CD2 HIS    27      -4.822   7.822   3.332  1.00107.43       1SG  33
ATOM     33  CE1 HIS    27      -5.407   5.924   4.130  1.00107.43       1SG  34
ATOM     34  C   HIS    27      -4.472  10.563   7.371  1.00107.43       1SG  35
ATOM     35  O   HIS    27      -5.641  10.867   7.597  1.00107.43       1SG  36
ATOM     36  N   LEU    28      -3.445  11.260   7.905  1.00101.48       1SG  37
ATOM     37  CA  LEU    28      -3.803  12.355   8.761  1.00101.48       1SG  38
ATOM     38  CB  LEU    28      -3.729  12.061  10.272  1.00101.48       1SG  39
ATOM     39  CG  LEU    28      -4.610  10.884  10.739  1.00101.48       1SG  40
ATOM     40  CD2 LEU    28      -4.981  11.008  12.225  1.00101.48       1SG  41
ATOM     41  CD1 LEU    28      -3.994   9.521  10.370  1.00101.48       1SG  42
ATOM     42  C   LEU    28      -2.902  13.521   8.516  1.00101.48       1SG  43
ATOM     43  O   LEU    28      -1.820  13.400   7.943  1.00101.48       1SG  44
ATOM     44  N   VAL    29      -3.390  14.705   8.924  1.00 42.05       1SG  45
ATOM     45  CA  VAL    29      -2.686  15.949   8.838  1.00 42.05       1SG  46
ATOM     46  CB  VAL    29      -3.561  17.085   9.271  1.00 42.05       1SG  47
ATOM     47  CG1 VAL    29      -2.735  18.382   9.302  1.00 42.05       1SG  48
ATOM     48  CG2 VAL    29      -4.787  17.121   8.342  1.00 42.05       1SG  49
ATOM     49  C   VAL    29      -1.516  15.910   9.772  1.00 42.05       1SG  50
ATOM     50  O   VAL    29      -0.405  16.298   9.415  1.00 42.05       1SG  51
ATOM    160  N   PRO    45      -0.812  16.785  -1.597  1.00183.50       1SG 161
ATOM    161  CA  PRO    45      -0.418  16.348  -0.283  1.00183.50       1SG 162
ATOM    162  CD  PRO    45       0.194  16.269  -2.529  1.00183.50       1SG 163
ATOM    163  CB  PRO    45       0.634  15.249  -0.435  1.00183.50       1SG 164
ATOM    164  CG  PRO    45       1.332  15.641  -1.725  1.00183.50       1SG 165
ATOM    165  C   PRO    45       0.055  17.327   0.702  1.00183.50       1SG 166
ATOM    166  O   PRO    45       1.247  17.426   0.968  1.00183.50       1SG 167
ATOM    167  N   ARG    46      -0.930  18.055   1.244  1.00184.08       1SG 168
ATOM    168  CA  ARG    46      -0.745  18.859   2.395  1.00184.08       1SG 169
ATOM    169  CB  ARG    46      -1.851  19.914   2.567  1.00184.08       1SG 170
ATOM    170  CG  ARG    46      -1.458  21.058   3.504  1.00184.08       1SG 171
ATOM    171  CD  ARG    46      -2.520  22.150   3.647  1.00184.08       1SG 172
ATOM    172  NE  ARG    46      -3.745  21.480   4.155  1.00184.08       1SG 173
ATOM    173  CZ  ARG    46      -3.840  21.172   5.481  1.00184.08       1SG 174
ATOM    174  NH1 ARG    46      -2.845  21.544   6.339  1.00184.08       1SG 175
ATOM    175  NH2 ARG    46      -4.920  20.474   5.935  1.00184.08       1SG 176
ATOM    176  C   ARG    46      -0.791  17.855   3.503  1.00184.08       1SG 177
ATOM    177  O   ARG    46      -0.167  18.012   4.552  1.00184.08       1SG 178
ATOM    178  N   ARG    47      -1.569  16.777   3.247  1.00129.96       1SG 179
ATOM    179  CA  ARG    47      -1.819  15.701   4.163  1.00129.96       1SG 180
ATOM    180  CB  ARG    47      -3.062  14.862   3.805  1.00129.96       1SG 181
ATOM    181  CG  ARG    47      -4.375  15.639   3.916  1.00129.96       1SG 182
ATOM    182  CD  ARG    47      -4.437  16.546   5.149  1.00129.96       1SG 183
ATOM    183  NE  ARG    47      -5.803  17.139   5.218  1.00129.96       1SG 184
ATOM    184  CZ  ARG    47      -6.804  16.473   5.869  1.00129.96       1SG 185
ATOM    185  NH1 ARG    47      -6.546  15.276   6.472  1.00129.96       1SG 186
ATOM    186  NH2 ARG    47      -8.063  16.996   5.920  1.00129.96       1SG 187
ATOM    187  C   ARG    47      -0.649  14.773   4.181  1.00129.96       1SG 188
ATOM    188  O   ARG    47       0.128  14.706   3.229  1.00129.96       1SG 189
ATOM    189  N   VAL    48      -0.489  14.031   5.297  1.00 42.53       1SG 190
ATOM    190  CA  VAL    48       0.620  13.134   5.432  1.00 42.53       1SG 191
ATOM    191  CB  VAL    48       1.437  13.381   6.670  1.00 42.53       1SG 192
ATOM    192  CG1 VAL    48       2.459  12.243   6.822  1.00 42.53       1SG 193
ATOM    193  CG2 VAL    48       2.075  14.773   6.576  1.00 42.53       1SG 194
ATOM    194  C   VAL    48       0.109  11.741   5.578  1.00 42.53       1SG 195
ATOM    195  O   VAL    48      -0.925  11.501   6.202  1.00 42.53       1SG 196
ATOM    196  N   LEU    49       0.834  10.779   4.979  1.00 65.67       1SG 197
ATOM    197  CA  LEU    49       0.507   9.403   5.179  1.00 65.67       1SG 198
ATOM    198  CB  LEU    49       1.019   8.465   4.070  1.00 65.67       1SG 199
ATOM    199  CG  LEU    49       0.270   8.540   2.729  1.00 65.67       1SG 200
ATOM    200  CD2 LEU    49      -1.211   8.173   2.903  1.00 65.67       1SG 201
ATOM    201  CD1 LEU    49       0.943   7.640   1.677  1.00 65.67       1SG 202
ATOM    202  C   LEU    49       1.270   9.034   6.397  1.00 65.67       1SG 203
ATOM    203  O   LEU    49       2.484   8.823   6.341  1.00 65.67       1SG 204
ATOM    204  N   VAL    50       0.582   8.947   7.544  1.00 44.15       1SG 205
ATOM    205  CA  VAL    50       1.307   8.645   8.736  1.00 44.15       1SG 206
ATOM    206  CB  VAL    50       0.778   9.325   9.961  1.00 44.15       1SG 207
ATOM    207  CG1 VAL    50       1.549   8.798  11.182  1.00 44.15       1SG 208
ATOM    208  CG2 VAL    50       0.908  10.844   9.767  1.00 44.15       1SG 209
ATOM    209  C   VAL    50       1.195   7.180   8.950  1.00 44.15       1SG 210
ATOM    210  O   VAL    50       0.107   6.612   8.873  1.00 44.15       1SG 211
ATOM    211  N   HIS    51       2.339   6.533   9.231  1.00102.56       1SG 212
ATOM    212  CA  HIS    51       2.338   5.112   9.390  1.00102.56       1SG 213
ATOM    213  ND1 HIS    51       4.160   2.091   9.160  1.00102.56       1SG 214
ATOM    214  CG  HIS    51       3.351   2.965   8.469  1.00102.56       1SG 215
ATOM    215  CB  HIS    51       3.455   4.455   8.562  1.00102.56       1SG 216
ATOM    216  NE2 HIS    51       2.769   0.848   7.950  1.00102.56       1SG 217
ATOM    217  CD2 HIS    51       2.506   2.192   7.738  1.00102.56       1SG 218
ATOM    218  CE1 HIS    51       3.769   0.841   8.813  1.00102.56       1SG 219
ATOM    219  C   HIS    51       2.548   4.796  10.835  1.00102.56       1SG 220
ATOM    220  O   HIS    51       3.424   5.355  11.495  1.00102.56       1SG 221
ATOM    221  N   GLU    52       1.725   3.873  11.369  1.00 84.46       1SG 222
ATOM    222  CA  GLU    52       1.832   3.502  12.746  1.00 84.46       1SG 223
ATOM    223  CB  GLU    52       0.775   2.466  13.157  1.00 84.46       1SG 224
ATOM    224  CG  GLU    52       0.628   2.241  14.661  1.00 84.46       1SG 225
ATOM    225  CD  GLU    52      -0.696   1.518  14.841  1.00 84.46       1SG 226
ATOM    226  OE1 GLU    52      -1.710   2.025  14.294  1.00 84.46       1SG 227
ATOM    227  OE2 GLU    52      -0.714   0.450  15.510  1.00 84.46       1SG 228
ATOM    228  C   GLU    52       3.187   2.907  12.880  1.00 84.46       1SG 229
ATOM    229  O   GLU    52       3.640   2.184  11.998  1.00 84.46       1SG 230
ATOM    230  N   ASP    53       3.892   3.213  13.981  1.00 44.76       1SG 231
ATOM    231  CA  ASP    53       5.221   2.701  14.054  1.00 44.76       1SG 232
ATOM    232  CB  ASP    53       6.064   3.332  15.177  1.00 44.76       1SG 233
ATOM    233  CG  ASP    53       6.355   4.770  14.763  1.00 44.76       1SG 234
ATOM    234  OD1 ASP    53       6.436   5.022  13.531  1.00 44.76       1SG 235
ATOM    235  OD2 ASP    53       6.493   5.637  15.668  1.00 44.76       1SG 236
ATOM    236  C   ASP    53       5.134   1.229  14.243  1.00 44.76       1SG 237
ATOM    237  O   ASP    53       4.195   0.712  14.846  1.00 44.76       1SG 238
ATOM    238  N   ASP    54       6.125   0.508  13.694  1.00 24.27       1SG 239
ATOM    239  CA  ASP    54       6.113  -0.919  13.804  1.00 24.27       1SG 240
ATOM    240  CB  ASP    54       6.115  -1.414  15.255  1.00 24.27       1SG 241
ATOM    241  CG  ASP    54       7.467  -1.064  15.848  1.00 24.27       1SG 242
ATOM    242  OD1 ASP    54       8.351  -0.603  15.074  1.00 24.27       1SG 243
ATOM    243  OD2 ASP    54       7.631  -1.243  17.082  1.00 24.27       1SG 244
ATOM    244  C   ASP    54       4.842  -1.425  13.142  1.00 24.27       1SG 245
ATOM    245  O   ASP    54       4.262  -0.675  12.311  1.00 24.27       1SG 246
ATOM    246  OXT ASP    54       4.432  -2.573  13.458  1.00 24.27       1SG 247
TER
END
