
#######################################################
#                                                     #
#                        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   67 (   67),  selected   67 , name T0379TS677_2-D2
# Molecule2: number of CA atoms   64 (  528),  selected   64 , name T0379_D2.pdb
# PARAMETERS: T0379TS677_2-D2.T0379_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N      17           -
LGA    -       -      R      18           -
LGA    N      17      E      19          2.554
LGA    R      18      E      20          2.334
LGA    E      19      S      21          1.754
LGA    E      20      I      22          1.479
LGA    S      21      R      23          0.852
LGA    I      22      R      24          1.015
LGA    R      23      F      25          1.008
LGA    R      24      K      26          1.597
LGA    F      25      A      27          1.826
LGA    K      26      I      28          2.129
LGA    A      27      G      29          2.473
LGA    I      28      V      30           -
LGA    G      29      -       -           -
LGA    V      30      -       -           -
LGA    A      31      -       -           -
LGA    D      32      A      31          3.576
LGA    I      33      D      32          1.173
LGA    E      34      I      33          3.434
LGA    E      35      E      34          4.223
LGA    M      36      E      35          2.693
LGA    L      37      M      36          2.985
LGA    D      38      L      37           #
LGA    P      39      D      38           #
LGA    -       -      P      39           -
LGA    Y      40      K      43          5.225
LGA    L      41      G      44          1.932
LGA    Q      42      L      45          4.619
LGA    K      43      F      46           #
LGA    G      44      L      47          4.479
LGA    L      45      D      48          2.462
LGA    F      46      -       -           -
LGA    L      47      -       -           -
LGA    D      48      -       -           -
LGA    L      49      -       -           -
LGA    E      50      -       -           -
LGA    S      51      -       -           -
LGA    G      52      -       -           -
LGA    R      53      L      49          5.123
LGA    K      54      E      50          3.315
LGA    S      55      S      51           -
LGA    E      56      G      52           -
LGA    -       -      R      53           -
LGA    -       -      K      54           -
LGA    E      57      S      55          4.785
LGA    -       -      E      56           -
LGA    -       -      E      57           -
LGA    -       -      E      58           -
LGA    E      58      F      59          3.972
LGA    F      59      R      60          4.571
LGA    R      60      T      61          3.871
LGA    T      61      E      62          1.815
LGA    E      62      L      63          2.221
LGA    L      63      S      64          2.275
LGA    S      64      R      65          1.659
LGA    R      65      Y      66          1.966
LGA    Y      66      I      67          2.101
LGA    I      67      G      68          1.068
LGA    G      68      K      69          1.344
LGA    K      69      E      70          0.650
LGA    E      70      L      71          0.559
LGA    L      71      T      72          1.275
LGA    T      72      Y      73          2.001
LGA    Y      73      Q      74          1.615
LGA    Q      74      Q      75          0.532
LGA    Q      75      V      76          1.884
LGA    V      76      Y      77          1.261
LGA    Y      77      D      78          0.446
LGA    D      78      A      79          1.467
LGA    A      79      L      80          2.023
LGA    L      80      L      81          1.120
LGA    L      81      G      82          1.876
LGA    G      82      F      83          2.258
LGA    F      83      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   67   64    5.0     50    2.63     6.00     53.379     1.834

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.669863 * X  +   0.665140 * Y  +  -0.329957 * Z  +  64.890152
  Y_new =  -0.737294 * X  +  -0.543433 * Y  +   0.401345 * Z  +  22.973648
  Z_new =   0.087641 * X  +   0.512122 * Y  +   0.854430 * Z  + -10.420587 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.539958   -2.601635  [ DEG:    30.9373   -149.0627 ]
  Theta =  -0.087753   -3.053839  [ DEG:    -5.0279   -174.9721 ]
  Phi   =  -2.308311    0.833282  [ DEG:  -132.2565     47.7435 ]
 
# 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: T0379TS677_2-D2                               
REMARK     2: T0379_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0379TS677_2-D2.T0379_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   67   64   5.0   50   2.63    6.00  53.379
REMARK  ---------------------------------------------------------- 
MOLECULE T0379TS677_2-D2
PFRMAT TS
TARGET T0379
MODEL  2  REFINED
PARENT 1qh9_A
ATOM     19  CA  ASN    17      67.248   1.056  17.336  1.00 99.00
ATOM     20  CA  ARG    18      69.087   4.278  18.168  1.00 99.00
ATOM     21  CA  GLU    19      66.211   5.388  20.418  1.00 99.00
ATOM     22  CA  GLU    20      66.460   2.155  22.417  1.00 91.00
ATOM     23  CA  SER    21      70.003   3.000  23.446  1.00 99.00
ATOM     24  CA  ILE    22      69.148   6.581  24.299  1.00 90.00
ATOM     25  CA  ARG    23      66.335   5.253  26.533  1.00 99.00
ATOM     26  CA  ARG    24      68.644   2.832  28.343  1.00 99.00
ATOM     27  CA  PHE    25      71.042   5.667  29.071  1.00 99.00
ATOM     28  CA  LYS    26      68.200   7.577  30.713  1.00 99.00
ATOM     29  CA  ALA    27      66.854   4.567  32.627  1.00 99.00
ATOM     30  CA  ILE    28      69.700   1.969  32.843  1.00 99.00
ATOM     31  CA  GLY    29      68.569  -1.600  32.222  1.00 94.00
ATOM     32  CA  VAL    30      65.046  -0.588  31.095  1.00 84.00
ATOM     33  CA  ALA    31      65.768   0.622  27.534  1.00 84.00
ATOM     34  CA  ASP    32      64.198  -2.281  25.610  1.00 99.00
ATOM     35  CA  ILE    33      61.057  -2.155  27.783  1.00 99.00
ATOM     36  CA  GLU    34      60.576   1.593  27.493  1.00 99.00
ATOM     37  CA  GLU    35      61.076   1.774  23.734  1.00 99.00
ATOM     38  CA  MET    36      58.908  -1.289  23.115  1.00 99.00
ATOM     39  CA  LEU    37      55.840   0.019  24.972  1.00 99.00
ATOM     40  CA  ASP    38      56.448   3.633  23.873  1.00 99.00
ATOM     41  CA  PRO    39      56.184   2.623  20.196  1.00 99.00
ATOM     42  CA  TYR    40      52.946   0.676  20.684  1.00 82.00
ATOM     43  CA  LEU    41      51.315   3.540  22.583  1.00 80.00
ATOM     44  CA  GLN    42      52.336   5.940  19.784  1.00 66.00
ATOM     45  CA  LYS    43      50.504   3.676  17.319  1.00 52.00
ATOM     46  CA  GLY    44      47.468   3.153  19.541  1.00 37.00
ATOM     47  CA  LEU    45      47.085   6.840  20.327  1.00 56.00
ATOM     48  CA  PHE    46      47.124   7.882  16.672  1.00 60.00
ATOM     49  CA  LEU    47      44.524   5.217  15.848  1.00 99.00
ATOM     50  CA  ASP    48      42.319   5.813  18.907  1.00 99.00
ATOM     51  CA  LEU    49      42.310   9.604  18.570  1.00 99.00
ATOM     52  CA  GLU    50      41.409   9.240  14.877  1.00 79.00
ATOM     60  CA  SER    51      52.417  13.598  16.488  1.00 92.00
ATOM     61  CA  GLY    52      54.784  15.489  18.778  1.00 99.00
ATOM     62  CA  ARG    53      52.116  15.682  21.480  1.00 99.00
ATOM     63  CA  LYS    54      51.123  12.071  20.789  1.00 99.00
ATOM     64  CA  SER    55      54.774  11.025  21.232  1.00 99.00
ATOM     65  CA  GLU    56      55.124  12.820  24.583  1.00 99.00
ATOM     66  CA  GLU    57      51.831  11.388  25.898  1.00 94.00
ATOM     67  CA  GLU    58      52.896   7.907  24.849  1.00 99.00
ATOM     68  CA  PHE    59      56.165   8.329  26.775  1.00 99.00
ATOM     69  CA  ARG    60      54.462   9.801  29.859  1.00 99.00
ATOM     70  CA  THR    61      52.132   6.775  30.048  1.00 99.00
ATOM     71  CA  GLU    62      55.048   4.387  29.433  1.00 99.00
ATOM     72  CA  LEU    63      57.087   5.690  32.360  1.00 99.00
ATOM     73  CA  SER    64      54.081   5.996  34.663  1.00 99.00
ATOM     74  CA  ARG    65      53.174   2.392  33.796  1.00 99.00
ATOM     75  CA  TYR    66      56.729   1.214  34.533  1.00 99.00
ATOM     76  CA  ILE    67      57.127   3.097  37.806  1.00 99.00
ATOM     77  CA  GLY    68      59.725   5.390  36.246  1.00 99.00
ATOM     78  CA  LYS    69      59.963   9.071  37.127  1.00 99.00
ATOM     79  CA  GLU    70      60.085  11.209  33.977  1.00 99.00
ATOM     80  CA  LEU    71      61.147  14.843  34.286  1.00 99.00
ATOM     81  CA  THR    72      60.774  17.420  31.489  1.00 99.00
ATOM     82  CA  TYR    73      64.477  17.501  30.668  1.00 99.00
ATOM     83  CA  GLN    74      64.737  13.742  30.115  1.00 99.00
ATOM     84  CA  GLN    75      61.442  13.724  28.206  1.00 99.00
ATOM     85  CA  VAL    76      62.726  16.175  25.612  1.00 99.00
ATOM     86  CA  TYR    77      66.009  14.274  25.157  1.00 99.00
ATOM     87  CA  ASP    78      64.301  10.963  24.379  1.00 99.00
ATOM     88  CA  ALA    79      61.942  12.741  22.007  1.00 99.00
ATOM     89  CA  LEU    80      64.836  14.476  20.221  1.00 99.00
ATOM     90  CA  LEU    81      66.318  11.017  19.630  1.00 53.00
ATOM     91  CA  GLY    82      63.948  10.534  16.675  1.00 78.00
ATOM     92  CA  PHE    83      65.457  13.506  14.823  1.00 87.00
TER
END
