
#######################################################
#                                                     #
#                        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   31 (   31),  selected   31 , name T0301TS464_4_2-D1
# Molecule2: number of CA atoms  200 ( 1505),  selected  200 , name T0301_D1.pdb
# PARAMETERS: T0301TS464_4_2-D1.T0301_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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    F      24      R       8           #
LGA    R      25      I       9          3.880
LGA    L      26      P      10          3.376
LGA    E      27      A      11          1.761
LGA    D      28      T      12          4.743
LGA    L      29      Y      13          2.964
LGA    P      30      -       -           -
LGA    E      31      L      14          4.279
LGA    S      32      R      15           #
LGA    C      33      G      16           #
LGA    -       -      G      17           -
LGA    -       -      T      18           -
LGA    -       -      S      19           -
LGA    -       -      K      20           -
LGA    -       -      G      21           -
LGA    -       -      V      22           -
LGA    -       -      F      23           -
LGA    G     110      F      24          4.302
LGA    A     111      R      25          2.602
LGA    G     112      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    A     113      G     110           #
LGA    -       -      A     111           -
LGA    -       -      G     112           -
LGA    F     114      A     113          2.318
LGA    A     115      F     114          4.911
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    V     134      P     127           #
LGA    -       -      E     128           -
LGA    -       -      D     129           -
LGA    R     135      G     130          3.586
LGA    I     136      I     131          1.360
LGA    W     137      C     132          2.361
LGA    Q     138      E     133          1.258
LGA    A     139      V     134          4.379
LGA    N     140      R     135          1.501
LGA    I     141      I     136          3.151
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    G     142      A     147          2.297
LGA    K     143      H     148           #
LGA    T     144      V     149          3.420
LGA    I     145      P     150           #
LGA    I     146      V     151          3.064
LGA    A     147      -       -           -
LGA    H     148      S     152          3.672
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)   31  200    5.0     21    3.29     9.52      6.323     0.620

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.185794 * X  +   0.863231 * Y  +   0.469375 * Z  +  27.735374
  Y_new =   0.762796 * X  +  -0.174398 * Y  +   0.622677 * Z  +  19.022514
  Z_new =   0.619373 * X  +   0.473727 * Y  +  -0.626067 * Z  +  -3.743392 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.493836   -0.647757  [ DEG:   142.8863    -37.1137 ]
  Theta =  -0.667943   -2.473649  [ DEG:   -38.2703   -141.7297 ]
  Phi   =   1.809713   -1.331879  [ DEG:   103.6889    -76.3111 ]
 
# 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: T0301TS464_4_2-D1                             
REMARK     2: T0301_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0301TS464_4_2-D1.T0301_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   31  200   5.0   21   3.29    9.52   6.323
REMARK  ---------------------------------------------------------- 
MOLECULE T0301TS464_4_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0301
PARENT N/A
ATOM      1  CA  PHE    24      66.342  36.467   8.085  1.00  0.00
ATOM      2  CA  ARG    25      66.830  37.648  11.666  1.00  0.00
ATOM      3  CA  LEU    26      66.066  34.116  12.850  1.00  0.00
ATOM      4  CA  GLU    27      68.756  32.667  10.576  1.00  0.00
ATOM      5  CA  ASP    28      71.342  35.085  12.025  1.00  0.00
ATOM      6  CA  LEU    29      70.407  33.928  15.536  1.00  0.00
ATOM      7  CA  PRO    30      70.345  30.215  14.677  1.00  0.00
ATOM      8  CA  GLU    31      73.648  30.465  12.781  1.00  0.00
ATOM      9  CA  SER    32      75.343  32.421  15.555  1.00  0.00
ATOM     10  CA  CYS    33      73.642  30.185  18.123  1.00  0.00
ATOM     11  CA  GLY   110      68.086  26.987   5.222  1.00  0.00
ATOM     12  CA  ALA   111      67.151  29.257   8.129  1.00  0.00
ATOM     13  CA  GLY   112      69.279  27.356  10.643  1.00  0.00
ATOM     14  CA  ALA   113      66.558  25.348  12.354  1.00  0.00
ATOM     15  CA  PHE   114      68.222  22.432  14.150  1.00  0.00
ATOM     16  CA  ALA   115      65.253  21.208  16.139  1.00  0.00
ATOM     17  CA  VAL   134      66.133  10.333  24.886  1.00  0.00
ATOM     18  CA  ARG   135      66.463  12.065  21.577  1.00  0.00
ATOM     19  CA  ILE   136      64.743  11.070  18.333  1.00  0.00
ATOM     20  CA  TRP   137      67.383  11.636  15.686  1.00  0.00
ATOM     21  CA  GLN   138      66.907  11.775  11.906  1.00  0.00
ATOM     22  CA  ALA   139      70.058  10.170  10.603  1.00  0.00
ATOM     23  CA  ASN   140      69.505  11.618   7.121  1.00  0.00
ATOM     24  CA  ILE   141      69.073  15.255   8.096  1.00  0.00
ATOM     25  CA  GLY   142      71.432  15.039  11.106  1.00  0.00
ATOM     26  CA  LYS   143      68.443  16.849  12.859  1.00  0.00
ATOM     27  CA  THR   144      66.975  16.825  16.372  1.00  0.00
ATOM     28  CA  ILE   145      63.290  16.072  15.710  1.00  0.00
ATOM     29  CA  ILE   146      61.923  15.378  19.343  1.00  0.00
ATOM     30  CA  ALA   147      63.027  14.931  22.957  1.00  0.00
ATOM     31  CA  HIS   148      61.145  12.346  24.998  1.00  0.00
TER
END
