tanu/LSHTM_analysis
1
0
Fork 0
Code Issues Pull requests Releases Wiki Activity

added hbond residues in config for all genes

Browse source
This commit is contained in:
Tanushree Tunstall 2022-02-09 15:59:18 +00:00
parent 7a14655ecb
commit 6ffb084546
9 changed files with 686 additions and 110 deletions
Download patch file Download diff file Expand all files Collapse all files

111
config/embb.R
View file

@ -1,7 +1,110 @@
gene = "embB"
drug = "ethambutol"
aa_plip = c(299, 302, 303, 327, 594, 988, 1028 )
aa_ligplus = c(299, 302, 303, 306, 334, 594, 988, 1028)
#active_aa_pos = c(299, 302, 303, 306, 327, 334, 594, 988, 1028 )
active_aa_pos = sort(unique(c(aa_plip, aa_ligplus)))
# interacting chain B
#==========
# LIGPLUS
#===========
aa_ligplus_emb = c(299, 302, 303, 306, 334, 594, 988, 1028)
aa_ligplus_emb_hbond = c(299, 594)
aa_ligplus_ca = c(952, 954, 959)
aa_ligplus_ca_hbond = c(952, 954, 959)
aa_ligplus_cdl = c(460, 665, 568, 601, 572, 579, 580, 583)
aa_ligplus_cdl_hbond = c(601, 568, 665)
aa_ligplus_dsl = c(435, 442, 489, 452, 330, 589, 509, 446, 445, 506, 592, 590, 514, 403, 515)
aa_ligplus_dsl_hbond = c(445, 590, 592, 403)
#==========
# PLIP
#===========
aa_plip_emb = c(299, 302, 303, 327, 594, 988, 1028)
aa_plip_emb_hbond = c(299, 327, 594)
aa_plip_ca = c(952, 954, 959)
aa_plip_cdl = c(456, 572, 579, 583, 568)
#aa_plip_cdl_sb = c(537, 568, 601, 665)
aa_plip_dsl = c(330, 435, 446, 452, 489, 506, 589, 590, 445, 403, 595)
aa_plip_dsl_hbond = c(445, 590)
#aa_plip_dsl_sb = c(403, 595)
#==========
# Arpeggio
#===========
# emb:1402, 1403
aa_arpeg_emb = c(298, 299, 302, 303, 306, 318, 327, 334, 403, 445, 592, 594, 988, 1028)
aa_arpeg_ca = c(847, 853, 854, 952, 954, 955, 956, 959, 960)
aa_arpeg_cdl = c(456, 457, 460, 461, 521, 525, 533, 537, 554, 558, 568
, 569, 572, 573, 575, 576, 579, 580, 582, 583, 586, 601, 605, 616, 658
, 661, 662, 665)
aa_arpeg_dsl = c(299, 322, 329, 330, 403, 435, 438, 439, 442, 445, 446
, 449, 452, 455, 486, 489, 490, 493, 506, 509, 510, 513, 514
, 515, 587, 589, 590, 592, 595)
##############################################################
active_aa_pos = sort(unique(c(aa_ligplus_emb
, aa_plip_emb
, aa_arpeg_emb
, aa_ligplus_ca
, aa_plip_ca
, aa_arpeg_ca
, aa_ligplus_cdl
, aa_plip_cdl
, aa_arpeg_cdl
, aa_ligplus_dsl
, aa_plip_dsl
, aa_arpeg_dsl)))
##############################################################
cat("\nNo. of active site residues for gene"
, gene, ":"
, length(active_aa_pos)
, "\nThese are:\n"
, active_aa_pos)
##############################################################
aa_pos_emb = sort(unique(c( aa_ligplus_emb
, aa_plip_emb
, aa_arpeg_emb)))
aa_pos_drug = aa_pos_emb
aa_pos_emb_hbond = sort(unique(c( aa_ligplus_emb_hbond
, aa_plip_emb_hbond)))
aa_pos_ca = sort(unique(c( aa_ligplus_ca
, aa_plip_ca
, aa_arpeg_ca)))
aa_pos_cdl = sort(unique(c( aa_ligplus_cdl
, aa_plip_cdl
, aa_arpeg_cdl )))
aa_pos_cdl_hbond = sort(unique(c( aa_ligplus_cdl_hbond )))
aa_pos_dsl = sort(unique(c( aa_ligplus_dsl
, aa_plip_dsl
, aa_arpeg_dsl)))
aa_pos_dsl_hbond = sort(unique(c( aa_ligplus_dsl_hbond
, aa_plip_dsl_hbond)))
cat("\n==================================================="
, "\nActive site residues for", gene, "comprise of..."
, "\n==================================================="
, "\nNo. of", drug, "binding residues:" , length(aa_pos_emb), "\n"
, aa_pos_emb
, "\nNo. of co-factor 'Ca' binding residues:", length(aa_pos_ca) , "\n"
, aa_pos_ca
, "\nNo. of ligand 'CDL' binding residues:" , length(aa_pos_cdl), "\n"
, aa_pos_cdl
, "\nNo. of ligand 'DSL' binding residues:" , length(aa_pos_dsl), "\n"
, aa_pos_dsl, "\n"
)
##############################################################