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Moreover, two of these interactions are created by pairs of cooperative hot spots that interact across the interface: Gly-53 and Thr-55 of TCR that interact with the hot spots Gln-210 and Asn-23 of SAG respectively (1jck numbering).
Notably, all of these shared interactions are created by experimentally verified hot spots.
Four shared interactions (two hydrogen bonds and two aromatic interactions) are created by the conserved YY motif (Tyr-54, Tyr-55, 1bxi numbering) [ 60].
Moreover, as these spatially conserved interactions are created by amino acids with different identities, the similarities described above can not be recognized by residue based computational methods.
However, this is not simply because interactions are created equally, i.e., each node has the same probability of being linked to any other protein and old proteins have had more time to accumulate interactions.
Similar(55)
In the previous paper, a model considering multi-phase reactions and ionic interactions was created to describe the diffusion behavior of chloride ions in concrete immersed in NaCl and CaCl2 solutions.
Following a similar idea, three additional types of ecosystem interactions were created, including parasitism, third party-inducible parasitism, and predator-prey interaction (not shown in Figure 5).
Using VDAC1 and the six associated SDE genes as seeds together with their interactions found in the Human Protein Reference Database (HPRD) [48], a parent PPI network (including recursive interactions) was created using an in-house Java-based program.
For each species, a single file with non-redundant experiments supporting the interactions was created.
The circular plots illustrating the epistatic interactions were created with Circos (Krzywinski et al. 2009).
The circular plots illustrating the epistatic interactions were created with Circos [ 34].
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