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Clarification regarding Feature Group 3

Posted by lcarpp on 06 Jun 2019 at 14:47 GMT

The description of Feature Group 3 (S1 Text) should be updated as follows (edits are shown in bold, where "exposed surface area" has been changed to "antibody-contact surface area"):

"Feature Group 3: Sites with sufficient antibody-contact surface area
The Dictionary of Protein Secondary Structure was used to calculate the antibody-contact surface area of each of the 35 amino acids identified in [2] as a contact site between VRC01 and HIV-1 Env using Protein Data Bank IDs 3NGB, 4LSS, 4LST, 5FYJ, and 5FYK [3, 4]. The Env protein sequences were aligned to reference strain HXB2 using HIVAlign [5]. Env residues were sorted by maximum antibody-contact surface area across the five structures and then divided into three groups based on manually selected cutoffs based on breaks observed in the average surface area. Amino acid sites in the first two groups (i.e. with the most and next-to-most antibody-contact surface areas) were included in the analysis as input genotypic features.
Amino acid sites: 97, 198, 276, 278, 279, 280, 281, 282, 365, 366, 367, 368, 371, 415, 428, 429, 430, 455, 457, 458, 459, 460, 461, 467, 469, 473, 474 and 476."

The reference to Feature Group 3 in the main text should also be updated accordingly.

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