Structural Bioinformatics Library
Template C++ / Python API for developping structural bioinformatics applications.
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Authors: S. Bereux and F. Cazals
Multiple Sequence Alignments are pivotal to understand commonalities and differences between protein sequences. Likewise, interface models are pivotal to mine to stability and the specificity of protein interactions. Combining MSA and interface models yields Multiple Interface String Alignment (MISA), namely alignments of strings coding properties of a.a. found at protein-protein interfaces.
Assume the interface of a complex has been found – we do so using the package Space_filling_model_interface . MISA are a visualization tool to display coherently various sequence and structure based statistics for the residues found at this interface, on a chain instance basis. That is, a MISA primarily consists of annotations for chain instances. Currently supported annotations for are:
The benefit of MISA are:
MISA id. A complex is specified by two sorted lists of chains ids i.e. for the two partners and defining the complex. For the sake of exposure, we also assume each partner is given a structure name (e.g. antibody or antigen or ...).
Likewise, an unbound structure is specified by a sorted list of chain ids . We consider a collection of complexes , and optionally a collection of unbound structures . The minimal setup is naturally that of a single complex without any unbound structure.
Our goal is two build one MISA for each so-called MISA id, which we formally define as:
Note that because of th sortedness, a given chain gets the same MISA id in a complex or unbound structure.
Interface strings (i-strings). In the sequel, we present MISA informally. We represent each instance with a so-called interface string encoding properties of amino acids found interfaces involving that chain. The interface string of a chain instance is a character string with one character per residue, and is actually defined from all instances with the same MISA id. To build this character string, we first define:
Using this consensus interface, the residues of a given chain instance (bound or unbound) are displayed as follows:
Finally, assembling i-strings yields MISA:
A colored MISA is a plain MISA whose 1-letter code of a.a. are colored using specific biological / biophysical properties:
coloring based on Secondary Structure Elements The type of SSE a given a.a. belongs to is especially useful when comparing bound and unbound structures, to assess perturbations in the hydrogen bonding network. Practically, we use the dictionary of SSE from ~[102] .
: coloring based on Buried Surface Area. Consider a chain instance in a complex. The BSA of this chain is defined as the accessible surface area (ASA) [149] of this chain in the partner alone minus the ASA of the chain in the complex. We report the BSA on a per residue basis, computed using the algorithm from [43].
: coloring based on the variation of accessible surface area.
A limitation of the BSA is that its calculation uses the geometry of the bound structure only. The calculation is thus oblivious to conformational changes which may be at play in case of induced fit or conformer selection. To mitigate the previous plot, we also provide a the so-called coloring scheme.
Consider an interface partner , in the complex, and consider the i-th residue of one of its chains. Let be the ASA of the i-th residue in the structure involving only those chains of partner . Also denote the average ASA of the i-th residue in unbound structures containing chains identical to those of partner . We compute for the i-th residue of a bound structure the quantity and display it with a color map.
: coloring based on B-factors.
The B-factors reflects the atomic thermal motions. Selected recent crystal structures report this information as a 3x3 ANISOU matrix (the anisotropic B-factor). In order to have a single quantity for all the crystals, the ANISOU matrix is converted into B-factor thanks to the formula [177] .
Optionally, one can choose to normalize the B-factor with respect to (i) all the residues in the chain, or (ii) all the displayed residues.
The package actually provides four complementary scripts:
The reader is referred to section Dependencies and Installation for installation related issues.
In the following, we briefly specify the entry of the scripts provided by this package, and refer the reader to the jupyter notebook of use cases.
This is the main script computing (colored) MISA.
Specification file. The link between Voronoi interfaces and interface strings is done by providing a list of so-called Interface string specifications:
We note that the tag ie string providing extra information is a placeholder to accommodate any relevant information. It should contain only alphanumerical characters, without blank spaces or special characters. For example, the tag may specify a feature (eg open or close) qualifying the crystallized conformation of the chain X.
Such interface string specifications are possibly enriched by specifying windows, ie a list of ranges of amino acids of interest – to be use to restrict the display.
Here is an illustration for the first example provided in the jupyter notebook:
Main options. The main arguments of the script are:
The script also requires some additional input data, which can either be re-computed, or directly provided by the user:
Specification file. The MISA id and coloring as well as the location of the individual files must be provided. These three pieces of information are provided thanks to a specification file, organized in three lines. Each line begins by a tag which indicates the information type provided on the line :
Here is an illustration for the first example provided in the jupyter notebook:
Main options. Summarizing, here are the main input arguments of the script :
The script displays the BSA of all (or selected user defined) residues.
Specification file. By default, all residues are processed. A specification file can also be provided to to specify selected residues.
The specification file then consists of a list of residue identifiers:
By default, in the absence of such a specification file, the BSA of every residue (with a BSA greater than or equal to 0.01) is displayed.
Here is an illustration for the first example provided in the jupyter notebook:
Main options. The main options are:
The script compares the i-strings and associated properties (in particular BSA) of two interfaces.
needs a specification file with two lines. Each of them contains the specification of one interface. There are two possible ways to specify an interface in this .
Automatic interface specification file. The first consists of extracting it from the output. One must then specify the following 3-tuple: which gives :
Here is an illustration for the first example provided in the jupyter notebook, which uses both specifications:
Manual interface specification. The second consists of enumerating the interface in a (def def-interface-file ) whose format is detailed in the following paragraph). One must then indicate in the : .
Using this compact residue specification, one can manually specify an interface in an :
Here is an illustration for the corresponding to the first example in the jupyter-notebook:
Main options. Summarizing, here are the main input arguments of the script :
The analysis provided by the previous scripts involve the following seven steps:
Step 1 : Parsing the input : Parse the specification file and gather the structural data processed
Step 2 : Constructing the MISA: Initializing the MISA by gathering the chains with the same MISA id and aligning them
Step 3 : Coloring the MISA: Collecting the coloring values and attributing the coloring to each chain of the MISA
Step 4 : Recording the cMISA: recording the colored MISA into an HTML file presenting simultaneously the four colorings
Step 5 : Construction of the PDB interface files: storing the interface residues shared by each pair of chain into PDB files
Step 6 : Computation of the i-RMSD for each pair of chain: computing the iRMSD for each pair of PDB interface files
Step 7 : Analysis of the interface RMSD (i-RMSD): clustering the chains according to the iRMSD and recording statistics on the iRMSD
Overview of sbl-misa.py |
Dictionary of Secondary Structures (DSSP). DSSP [102] : DSSP . The package DSSP is used to infer the type of secondary structure element a given aa belong to. The program mkdssp used is described here; one may also consult directly the source code. executable:
DSSP is provided by package managers. For example, it is easily installed as follows under Fedora
dnf install dssp.x86_64
Multi Sequence Alignment. We compute Multi Sequence Alignment with ClustalOmega [161] To install ClustalOmega, proceed as indicated on the web site ClustalOmega .
Python packages. The following python packages are used:
All of them are easily installed as follows:
pip3 install biopython numpy scipy pandas matplotlib weasyprint seaborn
We first list the required packages from the SBL, and then detail the two options supported to install these packages.
List of SBL packages. The computation of MISAs uses the following packages from the SBL:
Installation using package managers. One can install the executables and python scripts available within packages using package managers , (dnf or rpm under Linux Fedora). In short:
> dnf install sbl-VERSIONNUMBER-Linux-apps.rpm > dnf install sbl-VERSIONNUMBER-Linux-scripts.rpm
Installation upon git cloning the SBL. As explained in the installation guide, one can git clone the SBL, and compile the whole library, or more specifically the packages required, namely Space_filling_model_interface, Buried_surface_area and Space_filling_model_surface_volume.
To clone the SBL, proceed as indicated here. To compile the SBL or the required packages, follow the Compilation and installation .
Remark. Whatever the installation method used, make sure all executables and python scripts are visible from one's PATH environment variable.
See the following jupyter notebook:
The following notebook uses a number of files provided in the following directories: ```pdb misa-RBD-ACE2-cmp misa-RBD-IG'''
This first example provides a step by step comparison on the RBD.
First, the MISA is calculated for each of the chains specified in ifile-misa.txt
.
Content of ./misa-RBD-ACE2-cmp/ifile-misa.txt
:
# Windows for ACE2-bound-to-SARS-CoV-1
[ACE2-bound-to-SARS-CoV-1_0 (19, 83) (321,393)]
./pdb/2ajf.pdb (A, E, SARS-CoV-1-RBD, bound) (B, A, ACE2-bound-to-SARS-CoV-1, bound)
./pdb/2ajf.pdb (A, F, SARS-CoV-1-RBD, bound) (B, B, ACE2-bound-to-SARS-CoV-1, bound)
./pdb/5x58.pdb (A, A, SARS-CoV-1-RBD, unbound-closed)
./pdb/6crz.pdb (A, C, SARS-CoV-1-RBD, unbound-closed)
# Specification for SARS-CoV-2
./pdb/6m0j.pdb (C, E, SARS-CoV-2-RBD, bound) (D, A, ACE2-bound-to-SARS-CoV-2, bound)
./pdb/6lzg.pdb (C, B, SARS-CoV-2-RBD, bound) (D, A, ACE2-bound-to-SARS-CoV-2, bound)
./pdb/6vxx.pdb (C, A, SARS-CoV-2-RBD, unbound-closed)
./pdb/6vyb.pdb (C, A, SARS-CoV-2-RBD, unbound-closed)
Each line corresponds to a complex, or to an unbound structure if the structure is alone on its line. For each complex, we provided one or two examples of bound complexes, as well as two examples of unbound complexes, in order to be able to calculate the $\Delta\_ASA$ induced by the conformational change. Otherwise, the $\Delta\_ASA$ won't be computed.
The first line of the file is used to restrict the displayed portion of the interface for the SARS-CoV-1 RBD, in order to compact the output.
The details of the specification are developed in the paper.
#!/usr/bin/python3
import os
import subprocess
import re
import shutil
from IPython.core.display import display, HTML
from collections import defaultdict
from IPython.display import IFrame
from SBL import SBL_pytools
from SBL_pytools import SBL_pytools as sblpyt
exe = shutil.which('sbl-misa.py')
if not exe: # if exe == None
print('sbl-misa.py not in your PATH')
ifile = './misa-RBD-ACE2-cmp/ifile-misa.txt'
prefix_dir = './misa-RBD-ACE2-cmp' # To append at the beginning of every input and output directories
# It allows to compacify the possible specification of the sub-output directories.
prefix = 'demo-misa-1' # To append at the beginning of the output files
verbose = '0'
normalize_b_factor = '2' # Normalization with only respect to the displayed residues
cmd = [exe, "-ifile", ifile, "-prefix_dir", prefix_dir, '-prefix', prefix, '--verbose', verbose, '-normalize_b_factor', normalize_b_factor]
print('Running %s -ifile %s -prefix_dir %s -prefix %s --verbose %s -normalize_b_factor %s' % (exe, ifile, prefix_dir, prefix, verbose, normalize_b_factor))
s = subprocess.check_output(cmd, encoding='UTF-8')
print('\nDone')
#print(s)
Running /user/fcazals/home/projects/proj-soft/sbl-install/lib/python3.8/site-packages/SBL/sbl-misa.py -ifile ./misa-RBD-ACE2-cmp/ifile-misa.txt -prefix_dir ./misa-RBD-ACE2-cmp -prefix demo-misa-1 --verbose 0 -normalize_b_factor 2 Done
sbl-misa.py
displays the MISA, with several colorings showing complementary data.
An individual summary figure for each of the chains specified in ifile-misa.txt
is produced. For example, here are the figures generated for SARS-CoV-2-RBD and for SARS-CoV-1-ACE2 (for which the effect of the window specification, restricting the range of displayed residues, can be observed) :
#IFrame(src='./misa-RBD-ACE2-cmp/MISA/SARS-CoV-2-RBD_0-demo-misa-1.html', width="100%", height=600)
display(HTML('./misa-RBD-ACE2-cmp/MISA/SARS-CoV-2-RBD_0-demo-misa-1.html'))
Legend for the amino acids (aa) encoding : For aa not at the interface : _ if aa is missing - if aa is present For aa at the interface : * if aa is missing X if consensus aa (= most frequent among the bound structures, and in case of tie the first by alphabetical order) x otherwise (For bound structure files only) : x or X if the aa is part of the consensus interface but not part of the interface of this fileMISA SSE for MISA-ID SARS-CoV-2-RBD_03-turn helix - 4-turn helix - 5-turn helix - Isolated beta-bridge residue - Extended strand - Bend - Hydrogen bonded turn - Other - Missing Residue - Residue Index 403----410-------420-------430-------440-------450-------460-------470-------480-------490-------500---- | | | | | | | | | | | bound-6m0j-E, res :2.45 Å, 27 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQ bound-6lzg-B, res :2.5 Å, 39 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQ unbound-closed-6vxx-A, res :2.8 Å, 0 interf res R-DE----------KI--Y-----------------N-----**G-Y---Y-**_____-------____*_***______****_YF-LQSYGFQPTN*VGYQ unbound-closed-6vyb-A, res :3.2 Å, 0 interf res R-DE----------KI--Y-----------------N---__***-Y---Y-LF--------------__*_***______****_*F-LQSYGFQPTN*VGYQMISA BSA for MISA-ID SARS-CoV-2-RBD_0In dark grey, residues with missing data for coloring Buried Surface Area (BSA) (in Å2) | bound-6m0j-E : total bsa = 887.29 Å2 | bound-6lzg-B : total bsa = 1120.20 Å2 Residue Index 403----410-------420-------430-------440-------450-------460-------470-------480-------490-------500---- | | | | | | | | | | | bound-6m0j-E, res :2.45 Å, 27 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQ bound-6lzg-B, res :2.5 Å, 39 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQMISA Delta_ASA for MISA-ID SARS-CoV-2-RBD_0In dark grey, residues with missing data for coloring Bound structures : In light grey residues in bound structure for which miss corresponding ASA values in the unbound structures Per residue i, delta_ASA = ASA[i] - mean(ASA[i]) (mean is computed using the unbound structures) (in Å2) Unbound structures : Accessible Surface Area (ASA) (in Å2) Residue Index 403----410-------420-------430-------440-------450-------460-------470-------480-------490-------500---- | | | | | | | | | | | bound-6m0j-E, res :2.45 Å, 27 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQ bound-6lzg-B, res :2.5 Å, 39 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQ unbound-closed-6vxx-A, res :2.8 Å, 0 interf res R-DE----------KI--Y-----------------N-----**G-Y---Y-**_____-------____*_***______****_YF-LQSYGFQPTN*VGYQ unbound-closed-6vyb-A, res :3.2 Å, 0 interf res R-DE----------KI--Y-----------------N---__***-Y---Y-LF--------------__*_***______****_*F-LQSYGFQPTN*VGYQMISA B_factor for MISA-ID SARS-CoV-2-RBD_0In dark grey, residues with missing data for coloring B-Factor (in Å2) Residue Index 403----410-------420-------430-------440-------450-------460-------470-------480-------490-------500---- | | | | | | | | | | | bound-6m0j-E, res :2.45 Å, 27 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQ bound-6lzg-B, res :2.5 Å, 39 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQ unbound-closed-6vxx-A, res :2.8 Å, 0 interf res R-DE----------KI--Y-----------------N-----**G-Y---Y-**_____-------____*_***______****_YF-LQSYGFQPTN*VGYQ unbound-closed-6vyb-A, res :3.2 Å, 0 interf res R-DE----------KI--Y-----------------N---__***-Y---Y-LF--------------__*_***______****_*F-LQSYGFQPTN*VGYQ
#IFrame(src='./misa-RBD-ACE2-cmp/MISA/ACE2-bound-to-SARS-CoV-1_0-demo-misa-1.html', width="100%", height=600)
display(HTML('misa-RBD-ACE2-cmp/MISA/ACE2-bound-to-SARS-CoV-1_0-demo-misa-1.html'))
Legend for the amino acids (aa) encoding : For aa not at the interface : _ if aa is missing - if aa is present For aa at the interface : * if aa is missing X if consensus aa (= most frequent among the bound structures, and in case of tie the first by alphabetical order) x otherwise (For bound structure files only) : x or X if the aa is part of the consensus interface but not part of the interface of this fileMISA SSE for MISA-ID ACE2-bound-to-SARS-CoV-1_03-turn helix - 4-turn helix - 5-turn helix - Isolated beta-bridge residue - Extended strand - Bend - Hydrogen bonded turn - Other - Missing Residue - Residue Index -20--------30--------40--------50--------60--------70--------80-- 321------330-------340-------350-------360-------370-------380-------390- | | | | | | | | | | | | | | | bound-2ajf-A, res :2.9 Å, 33 interf res S---EQ-KTF-DK--H--ED--YQ--L---------------------------------L--MY ---TQGF-EN----------------------KGDFR----------------------------AAQP---R bound-2ajf-B, res :2.9 Å, 27 interf res S---EQ-KTF-DK--H--ED--YQ--L---------------------------------L--MY ---TQGF-EN----------------------KGDFR----------------------------AAQP---RMISA BSA for MISA-ID ACE2-bound-to-SARS-CoV-1_0In dark grey, residues with missing data for coloring Buried Surface Area (BSA) (in Å2) | bound-2ajf-A : total bsa = 888.38 Å2 | bound-2ajf-B : total bsa = 817.21 Å2 Residue Index -20--------30--------40--------50--------60--------70--------80-- 321------330-------340-------350-------360-------370-------380-------390- | | | | | | | | | | | | | | | bound-2ajf-A, res :2.9 Å, 33 interf res S---EQ-KTF-DK--H--ED--YQ--L---------------------------------L--MY ---TQGF-EN----------------------KGDFR----------------------------AAQP---R bound-2ajf-B, res :2.9 Å, 27 interf res S---EQ-KTF-DK--H--ED--YQ--L---------------------------------L--MY ---TQGF-EN----------------------KGDFR----------------------------AAQP---RMISA Delta_ASA for MISA-ID ACE2-bound-to-SARS-CoV-1_0In dark grey, residues with missing data for coloring Bound structures : In light grey residues in bound structure for which miss corresponding ASA values in the unbound structures Per residue i, delta_ASA = ASA[i] - mean(ASA[i]) (mean is computed using the unbound structures) (in Å2) Unbound structures : Accessible Surface Area (ASA) (in Å2) Residue Index -20--------30--------40--------50--------60--------70--------80-- 321------330-------340-------350-------360-------370-------380-------390- | | | | | | | | | | | | | | | bound-2ajf-A, res :2.9 Å, 33 interf res S---EQ-KTF-DK--H--ED--YQ--L---------------------------------L--MY ---TQGF-EN----------------------KGDFR----------------------------AAQP---R bound-2ajf-B, res :2.9 Å, 27 interf res S---EQ-KTF-DK--H--ED--YQ--L---------------------------------L--MY ---TQGF-EN----------------------KGDFR----------------------------AAQP---RMISA B_factor for MISA-ID ACE2-bound-to-SARS-CoV-1_0In dark grey, residues with missing data for coloring B-Factor (in Å2) Residue Index -20--------30--------40--------50--------60--------70--------80-- 321------330-------340-------350-------360-------370-------380-------390- | | | | | | | | | | | | | | | bound-2ajf-A, res :2.9 Å, 33 interf res S---EQ-KTF-DK--H--ED--YQ--L---------------------------------L--MY ---TQGF-EN----------------------KGDFR----------------------------AAQP---R bound-2ajf-B, res :2.9 Å, 27 interf res S---EQ-KTF-DK--H--ED--YQ--L---------------------------------L--MY ---TQGF-EN----------------------KGDFR----------------------------AAQP---R
Once these individual figures have been generated, a call to sbl-misa-mix.py
allows to simultaneously compare different MISA_id in the same figure. In the sequel, we focus on the following three colored MISA: SSE, BSA, Delta_ASA,
sbl-misa-mix.py
parses the specification file ifile-misa-mix.txt
, from which it finds the location of the directory containing the input data, the MISA_id to be displayed, and the colorings to be displayed.
Content of ./misa-RBD-ACE2-cmp/ifile-misa-mix.txt
:
# List of input directories
localisation (./misa-RBD-ACE2-cmp/MISA)
# List of MISA_chain_ids
misa_chain_id (SARS-CoV-1-RBD_0, SARS-CoV-2-RBD_0)
# List of colorings of interest
coloring (SSE, BSA, Delta_ASA)
exe = shutil.which('sbl-misa-mix.py')
if not exe: # if exe == None
print('sbl-misa-mix.py not in your PATH')
prefix = 'demo-mix-1' # To append at the beginning of the output files
mix_ifile = './misa-RBD-ACE2-cmp/ifile-misa-mix.txt' # Specification file
odir = './misa-RBD-ACE2-cmp' # Output directory
verbose = '0'
cmd = [exe, "-mix_ifile", mix_ifile, '-prefix', prefix, '-odir', odir, '--verbose', verbose]
print('Running %s -mix_ifile %s -prefix %s -odir %s --verbose %s' % (exe, mix_ifile, prefix, odir, verbose))
s = subprocess.check_output(cmd, encoding='UTF-8')
print('\nDone')
#print(s)
Running /user/fcazals/home/projects/proj-soft/sbl-install/lib/python3.8/site-packages/SBL/sbl-misa-mix.py -mix_ifile ./misa-RBD-ACE2-cmp/ifile-misa-mix.txt -prefix demo-mix-1 -odir ./misa-RBD-ACE2-cmp --verbose 0 Done
The first figure of the article corresponds to the output of sbl-misa-mix.py
, run with the ifile-misa-mix.txt
presented above :
#IFrame(src='./misa-RBD-ACE2-cmp/demo-mix-1_SSE_BSA_Delta_ASA_SARS-CoV-1-RBD_0_SARS-CoV-2-RBD_0_mixed_figure.html', width="100%", height=600)
display(HTML('./misa-RBD-ACE2-cmp/demo-mix-1_SSE_BSA_Delta_ASA_SARS-CoV-1-RBD_0_SARS-CoV-2-RBD_0_mixed_figure.html'))
Legend for the amino acids (aa) encoding : For aa not at the interface : _ if aa is missing - if aa is present For aa at the interface : * if aa is missing X if consensus aa (= most frequent among the bound structures, and in case of tie the first by alphabetical order) x otherwise (For bound structure files only) : x or X if the aa is part of the consensus interface but not part of the interface of this file )MISA SSE for MISA-ID SARS-CoV-1-RBD_03-turn helix - 4-turn helix - 5-turn helix - Isolated beta-bridge residue - Extended strand - Bend - Hydrogen bonded turn - Other - Missing Residue - Residue Index 390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490 | | | | | | | | | | | bound-2ajf-E, res :2.9 Å, 29 interf res K--D--Q-------VI--Y-----------------R-----S---Y---Y-YL----------------F-PD------P-LNCY---NDYG-YTTTGI-YQ bound-2ajf-F, res :2.9 Å, 29 interf res K--D--Q-------VI--Y-----------------R-----S---Y---Y-YL----------------F-PD------P-LNCY---NDYG-YTTTGI-YQ unbound-closed-5x58-A, res :3.2 Å, 0 interf res K--D--Q-------VI--Y-----------------R-----S---Y---Y-YL----------------F-PD------P-LNCY---NDYG-YTTTGI-YQ unbound-closed-6crz-C, res :3.3 Å, 0 interf res K--D--Q-------VI--Y-----------------R-----S---Y---Y-YL----------------F-PD------P-LNCY---NDYG-YTTTGI-YQMISA SSE for MISA-ID SARS-CoV-2-RBD_03-turn helix - 4-turn helix - 5-turn helix - Isolated beta-bridge residue - Extended strand - Bend - Hydrogen bonded turn - Other - Missing Residue - Residue Index 403----410-------420-------430-------440-------450-------460-------470-------480-------490-------500---- | | | | | | | | | | | bound-6m0j-E, res :2.45 Å, 27 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQ bound-6lzg-B, res :2.5 Å, 39 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQ unbound-closed-6vxx-A, res :2.8 Å, 0 interf res R-DE----------KI--Y-----------------N-----**G-Y---Y-**_____-------____*_***______****_YF-LQSYGFQPTN*VGYQ unbound-closed-6vyb-A, res :3.2 Å, 0 interf res R-DE----------KI--Y-----------------N---__***-Y---Y-LF--------------__*_***______****_*F-LQSYGFQPTN*VGYQMISA BSA for MISA-ID SARS-CoV-1-RBD_0In dark grey, residues with missing data for coloring Buried Surface Area (BSA) (in Å2) | bound-2ajf-E : total bsa = 925.41 Å2 | bound-2ajf-F : total bsa = 864.87 Å2 Residue Index 390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490 | | | | | | | | | | | bound-2ajf-E, res :2.9 Å, 29 interf res K--D--Q-------VI--Y-----------------R-----S---Y---Y-YL----------------F-PD------P-LNCY---NDYG-YTTTGI-YQ bound-2ajf-F, res :2.9 Å, 29 interf res K--D--Q-------VI--Y-----------------R-----S---Y---Y-YL----------------F-PD------P-LNCY---NDYG-YTTTGI-YQMISA BSA for MISA-ID SARS-CoV-2-RBD_0In dark grey, residues with missing data for coloring Buried Surface Area (BSA) (in Å2) | bound-6m0j-E : total bsa = 887.29 Å2 | bound-6lzg-B : total bsa = 1120.20 Å2 Residue Index 403----410-------420-------430-------440-------450-------460-------470-------480-------490-------500---- | | | | | | | | | | | bound-6m0j-E, res :2.45 Å, 27 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQ bound-6lzg-B, res :2.5 Å, 39 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQMISA Delta_ASA for MISA-ID SARS-CoV-1-RBD_0In dark grey, residues with missing data for coloring Bound structures : In light grey residues in bound structure for which miss corresponding ASA values in the unbound structures Per residue i, delta_ASA = ASA[i] - mean(ASA[i]) (mean is computed using the unbound structures) (in Å2) Unbound structures : Accessible Surface Area (ASA) (in Å2) Residue Index 390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490 | | | | | | | | | | | bound-2ajf-E, res :2.9 Å, 29 interf res K--D--Q-------VI--Y-----------------R-----S---Y---Y-YL----------------F-PD------P-LNCY---NDYG-YTTTGI-YQ bound-2ajf-F, res :2.9 Å, 29 interf res K--D--Q-------VI--Y-----------------R-----S---Y---Y-YL----------------F-PD------P-LNCY---NDYG-YTTTGI-YQ unbound-closed-5x58-A, res :3.2 Å, 0 interf res K--D--Q-------VI--Y-----------------R-----S---Y---Y-YL----------------F-PD------P-LNCY---NDYG-YTTTGI-YQ unbound-closed-6crz-C, res :3.3 Å, 0 interf res K--D--Q-------VI--Y-----------------R-----S---Y---Y-YL----------------F-PD------P-LNCY---NDYG-YTTTGI-YQMISA Delta_ASA for MISA-ID SARS-CoV-2-RBD_0In dark grey, residues with missing data for coloring Bound structures : In light grey residues in bound structure for which miss corresponding ASA values in the unbound structures Per residue i, delta_ASA = ASA[i] - mean(ASA[i]) (mean is computed using the unbound structures) (in Å2) Unbound structures : Accessible Surface Area (ASA) (in Å2) Residue Index 403----410-------420-------430-------440-------450-------460-------470-------480-------490-------500---- | | | | | | | | | | | bound-6m0j-E, res :2.45 Å, 27 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQ bound-6lzg-B, res :2.5 Å, 39 interf res R-DE----------KI--Y-----------------N-----VGG-Y---Y-LF----------------Y-AGS------EGFN-YF-LQSYGFQPTNGVGYQ unbound-closed-6vxx-A, res :2.8 Å, 0 interf res R-DE----------KI--Y-----------------N-----**G-Y---Y-**_____-------____*_***______****_YF-LQSYGFQPTN*VGYQ unbound-closed-6vyb-A, res :3.2 Å, 0 interf res R-DE