Molecular Dynamics Simulations - Table I
TABLE I
SUMMARY OF H-BONDS BETWEEN GR DBD AMINO ACIDS AND GRE NUCLEOTIDES DURING
30 PICOSECONDS OF MOLECULAR DYNAMICS USING A GR DBD / 17 BP GRE MODEL
IN A 80 ANGSTROM DIAMETER WATER DROPLET
Column numbers represent the following:
(1) H-bonding Amino Acid (2) Amino Acid Number (3) Amino Acid H-bonding Atom
(4) H-Bonding Nucleotide (5) Nucleotide Number (6) Nucleotide H-bonding Atom
(7) First Occurrence of H-bond (in 0.1 picoseconds)
(8) Last Occurrence of H-bond (in 0.1 picoseconds)
(9) Frequency of H-bond Occurrence (10) Codon or Anticodon H-bond
* Denotes codon or anticodon reading 3' to 5'.
Direct H-bonds are in Boldface and water mediated H-bonds are in plain text.
LEFT PROTEIN MONOMER H-BONDS RIGHT PROTEIN MONOMER H-BONDS
1 2 3 4 5 6 7 8 9 10 1 2 3 4 5 6 7 8 9 10
--------------EXON 3-------------- --------------EXON 3--------------
K 461 HZ G 8 N7 7 203 49 K 461 HZ A 37 N7 1 8 8 C
K 461 HZ G 8 O6 10 300 99 K 461 HZ A 36 N7 9 11 6 C
K 461 HZ G 8 OP 1 1 1 K 461 HZ A 37 H61 98 24 10 C
K 461 HZ T 9 O4 5 13 13 K 461 HZ A 37 N7 13 34 24 C
K 465 HZ A 49 N7 1 195 101 F 464 O G 38 OP 15 101 51 AC
K 465 O A 49 H61 193 300 106
K 465 O A 49 H62 280 280 1 K 465 HZ T 20 O4 1 222 96 AC*
K 465 HZ G 8 H1 225 286 32 K 465 HZ A 37 N7 78 252 57 C
K 465 HZ G 8 N7 19 204 50 K 465 HZ G 38 N7 210 250 4 C
K 465 HZ G 8 O6 18 300 211 K 465 HZ G 38 O6 1 300 342 C
K 465 HZ T 9 O4 5 5 1 K 465 HZ C 21 H41 5 291 150 AC
K 465 HZ A 49 OP 25 31 7 K 465 HZ A 37 H61 18 296 227 C
K 465 HZ A 50 H61 1 298 292 K 465 HZ A 37 N7 109 300 134 C
K 465 HZ A 50 N7 18 299 167
K 465 HZ C 51 H42 255 265 11 R 466 HH1 A 39 N7 1 52 8 C
R 466 HH2 G 18 O6 25 300 221
R 466 HH2 T 10 O4 3 9 7 R 466 HH1 G 38 O3' 158 280 11 C
R 466 HH1 A 11 N7 47 134 13 R 466 HH1 A 39 OP 1 298 278 C
R 466 HE G 47 N7 279 286 8 R 466 HH2 A 39 OP 58 293 128 C
R 466 HE G 47 O6 18 300 168 R 466 HH2 A 40 H61 25 300 221
R 466 HH1 G 47 O6 54 300 241 R 466 HH2 A 40 N7 25 300 75
R 466 HH1 T 10 OP 12 12 1
R 466 HH1 C 12 H41 23 300 32 E 469 OE G 38 O5' 123 293 82 C
R 466 HH1 G 47 O6 119 121 3 E 469 OE G 38 OP 20 300 358 C
E 469 O A 39 OP 1 2 2 C
V 468 O T 9 OP 71 273 36 C E 469 OE A 39 OP 1 300 259 C
E 469 O T 9 OP 187 300 58 --------------EXON 4--------------
E 469 OE T 10 OP 5 292 158 Q 471 HE2 G 18 N7 9 223 144 AC
Q 471 HE2 G 18 O6 6 289 133 AC
--------------EXON 4-------------- Q 471 HE2 T 17 O4 98 299 27 AC
Q 471 HE2 G 47 N7 150 152 3 AC Q 471 OE T 17 O4 100 103 4 AC
Q 471 HE2 G 47 O6 80 80 1 AC Q 471 HE2 G 18 O6 98 299 15 AC
Q 471 HE2 C 12 H41 11 88 17 C Q 471 OE G 18 O6 37 186 86 AC
Q 471 OE C 12 H41 87 160 10 C Q 471 OE A 40 H61 35 186 52 C*
Q 471 HE2 T 46 O5' 150 150 1 AC Q 471 OE A 40 N7 80 80 1 C*
Q 471 HE2 T 46 OP 106 300 170 AC Q 471 HE2 C 41 H42 150 150 1 C
Q 471 O T 46 OP 18 77 47 AC Q 471 OE C 41 H41 4 79 27 C
Q 471 HE2 G 47 O6 119 119 1 AC Q 471 OE C 41 H42 150 150 1 C
H 472 O T 46 OP 134 145 12 H 472 O T 17 OP 10 13 4
N 473 HD2 T 46 O4' 19 36 18 AC* N 473 HD2 T 17 O4' 124 263 37
N 473 HD2 T 46 O5' 2 300 115 AC* N 473 HD2 T 17 O5' 23 263 97
N 473 HD2 T 46 OP 1 1 1 AC* N 473 HD2 T 17 OP 77 300 137
N 473 HD2 T 46 O5' 150 150 1 AC* N 473 HD2 G 18 OP 66 75 10 AC
N 473 HD2 T 46 OP 76 300 57 AC*
N 473 OD T 46 OP 5 5 1 AC* Y 474 H T 17 O5' 87 248 75
Y 474 H T 17 OP 108 133 8
Y 474 H T 46 O5' 23 202 32 Y 474 H G 18 OP 126 248 84
Y 474 H T 46 OP 47 300 218
Y 474 H T 46 OP 1 6 6 L 475 H T 17 O5' 87 132 24 C
Y 474 OH G 47 OP 1 12 12 AC L 475 H T 17 OP 108 289 138 C
L 475 H T 46 OP 258 284 27 N 506 OD A 36 H5T 169 169 1 C*
L 475 H T 46 OP 1 300 172 C N 506 OD A 36 O5T 269 295 8 C*
N 506 OD A 36 OP 270 272 3 C*
A 477 O G 47 OP 70 272 98 N 506 OD A 37 OP 1 3 3 C*
N 506 HD2 G 7 OP 297 300 4 AC* L 507 O A 37 OP 47 300 53 AC
N 506 HD2 G 7 H5T 279 283 5 AC*
N 506 HD2 G 7 OP 258 290 17 AC*
N 506 O G 7 H5T 209 211 3 AC*
N 506 O G 7 O5' 145 208 62 AC*
N 506 O G 7 OP 139 300 145 AC*
L 507 O G 8 OP 124 201 12 C
--------------EXON 5--------------
R 510 HH1 G 7 O5T 156 300 9