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Table 4 Hydrogen bond occurrences during the molecular dynamics simulations

From: Knottin cyclization: impact on structure and dynamics

Local structure Residues MCoTI-II lin-MCoTI EETI-II
3-stranded β -sheet N33-O13 68.7 3.03 97.6 2.98 99.7 2.95
  N15-O31 98.7 2.94 98.9 2.93 98.8 2.97
  N26-O34 99.9 2.88 99.9 2.90 100.0 2.74
  N34-O26 99.5 2.91 99.6 2.89 97.2 2.98
  N28-O32 95.9 2.98 91.7 3.02 93.5 3.01
β -turns N25-O22 88.8 3.06 92.3 3.05 89.6 3.13
  N25-O23 7.5 3.20 5.1 3.21 21.6 3.22
  N31-O28 97.0 3.03 96.4 3.04 96.7 3.06
3-10 helix N20-O17 83.8 3.15 87.2 3.13 97.7 3.05
  N21-O18 81.9 3.17 67.8 3.19 70.6 3.19
  N21-O19 - - 5.6 3.15 0.2 3.35
C to N linker N6-O3 36.5 3.15 - - - -
  N6-O4 15.7 3.18 - - - -
Others N10-08 8.6 2.99     
  N11-O9 51.2 2.93 73.4 2.94 29.2 3.03
  N13-O11 13.5 3.12 22.1 3.19 9.2 3.06
Side chains N16-Asp20 76.1 2.90 81.6 2.94 98.7 2.88
  N17-Asp20 71.7 3.01 50.5 3.02 88.3 3.04
  N27-Asp18 93.7 2.90 90.9 2.92 22.0 2.97
  Arg16-Asp20 - - 21.5 3.00 5.8 2.99
  Arg17-Asp20 23.2 2.97 5.3 2.95 (Gln17)
  Lys13-Asp20 10.1 2.96 - - (Met13)
  N32-Asn30 68.8 3.16 70.1 3.16 79.6 3.15
  Lys13-O20 32.1 2.89 44.2 2.89 (Met13)
  Lys13-O14 15.8 2.93 30.8 2.94 (Met13)
  Lys14-O30 - - - - 7.3 3.02
  Lys14-O31 - - - - 7.4 3.09
  Lys10-O8 - - - - 6.6 2.96
  Arg16-O15 10.3 2.95 - - - -
  Arg28-O1 50.5 3.01 - - (Gly28)
  Arg28-O32    22.7 3.14 (Gly28)
  Arg28-O33 12.2 3.03 55.9 3.05 (Gly28)
  1. For each hydrogen bond, the percentage of occurrence is followed by the average distance between heavy atoms (in Å). Only hydrogen bonds that occur more than 5% of the time are reported using 3.5 Å and 120° as distance and angle cut-offs, respectively. Bold numbers indicate the highest percentages in each row. Nx and Ox refer to the amide and carbonyl groups of residue x, respectively. When side-chains are involved, the residue is indicated using the three letter code.