PROTEIN-PROTEIN SALT BRIDGES IN 1ZMS.
REPORTED BY FirstGlance in Jmol.
LIGAND-PROTEIN AND NUCLEIC-PROTEIN SALT BRIDGES ARE NOT LISTED.
ONLY PROTEIN-PROTEIN SALT BRIDGES ARE LISTED.
Salt bridges involving ligands+ or nucleic acids can be visualized using Contacts & Non-Covalent Interactions.. or Ends.. (Tools tab).
Salt bridges are defined here as oppositely charged atoms ≤4.0 Å apart
(Jeffrey, George A., An introduction to hydrogen bonding. Oxford Univ. Press, 1997. Page 192.)
This tab-delimited list is spreadsheet-ready for sorting and averaging (see procedure at bottom below).
To save this page so it can be viewed in a web browser, File, Save As, Web Page, Complete.
Count = Number of nitrogen atoms engaged in salt bridges, including those with alternate locations.
(The atom count in the lower left panel in FirstGlance excludes atoms with alternate locations.)
SeqNo = Sequence Number.
Ins = Insertion Code for sequence number (usually blank).
Chain: Oxygen anion chain is Bold* for between-chain bridges.
Atom:
SIDECHAINS: OD = Oxygen Delta; NE, OE = Nitrogen or Oxygen Epsilon; NH = Nitrogen Eta; NZ = Nitrogen Zeta.
CHAIN TERMINI: N, O, OXT are main chain atoms. (C for C-termini lacking 1 oxygen: more information.)
AltLoc = Alternate Location ID (usually blank).
ConSrf = ConSurf amino acid conservation level. 1 = most variable. 9 = most conserved. 0 = insufficient data. Blank = not processed by ConSurf.
DIST = Distance in Å between salt-bridged atoms.
When the C-terminus lacks one oxygen: distance between the cationic nitrogen and the terminal carboxy carbon.
NITROGEN CATIONS OXYGEN ANIONS
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Count Group1 SeqNo1 Ins1 Chain1 Atom1 AltLoc1 ConSrf1 DIST Group2 SeqNo2 Ins2 Chain2 Atom2 AltLoc2 ConSrf2 NOTES
1 ARG 323 A NH1 4 3.6 ASP 325 A1* OD2 4 Between chains.*
2 ARG 323 A NH2 4 2.7 ASP 325 A1* OD2 4 Between chains.*
3 ARG 334 A NH1 2 3.7 ASP 339 A1* OD1 4 Between chains.*
3 ARG 334 A NH1 2 2.8 ASP 339 A1* OD2 4 Between chains.*
4 ARG 334 A NH2 2 3.8 ASP 339 A1* OD2 4 Between chains.*
5 ARG 341 A NE 4 2.9 GLU 346 A1* OE2 4 Between chains.*
6 ARG 341 A NH1 4 3.7 ASP 339 A1* OD1 4 Between chains.*
7 ARG 341 A NH2 4 3.1 GLU 346 A1* OE1 4 Between chains.*
7 ARG 341 A NH2 4 3.5 GLU 346 A1* OE2 4 Between chains.*
8 LYS 357 A NZ 8 2.9 GLU 417 A2* OE2 3 Between chains.*
9 ARG 363 A NE 2 3.9 ASP 360 A OD1 6
9 ARG 363 A NE 2 3.4 GLU 367 A OE1 5
10 ARG 363 A NH2 2 3.3 ASP 360 A OD1 6
11 LYS 365 A NZ 3 3.8 GLU 480 A OE1 3
11 LYS 365 A NZ 3 3.3 GLU 480 A OE2 3
12 ARG 393 A NH1 8 3.0 ASP 210 B* OXT C-terminus. Between chains.*
13 ARG 393 A NH2 8 3.7 ASP 210 B* O C-terminus. Between chains.*
13 ARG 393 A NH2 8 2.8 ASP 210 B* OD1 Between chains.*
13 ARG 393 A NH2 8 3.9 ASP 210 B* OD2 Between chains.*
13 ARG 393 A NH2 8 2.8 ASP 210 B* OXT C-terminus. Between chains.*
14 ARG 415 A NH2 5 3.6 GLU 463 A OE1 4
15 ARG 323 A1 NH1 4 3.6 ASP 325 A2* OD2 4 Between chains.*
16 ARG 323 A1 NH2 4 2.7 ASP 325 A2* OD2 4 Between chains.*
17 ARG 334 A1 NH1 2 3.7 ASP 339 A2* OD1 4 Between chains.*
17 ARG 334 A1 NH1 2 2.8 ASP 339 A2* OD2 4 Between chains.*
18 ARG 334 A1 NH2 2 3.8 ASP 339 A2* OD2 4 Between chains.*
19 ARG 341 A1 NE 4 2.9 GLU 346 A2* OE2 4 Between chains.*
20 ARG 341 A1 NH1 4 3.7 ASP 339 A2* OD1 4 Between chains.*
21 ARG 341 A1 NH2 4 3.1 GLU 346 A2* OE1 4 Between chains.*
21 ARG 341 A1 NH2 4 3.5 GLU 346 A2* OE2 4 Between chains.*
22 LYS 357 A1 NZ 8 2.9 GLU 417 A* OE2 3 Between chains.*
23 ARG 363 A1 NE 2 3.9 ASP 360 A1 OD1 6
23 ARG 363 A1 NE 2 3.4 GLU 367 A1 OE1 5
24 ARG 363 A1 NH2 2 3.3 ASP 360 A1 OD1 6
25 LYS 365 A1 NZ 3 3.8 GLU 480 A1 OE1 3
25 LYS 365 A1 NZ 3 3.3 GLU 480 A1 OE2 3
26 ARG 393 A1 NH2 8 2.8 ASP 210 B1* OD1 Between chains.*
26 ARG 393 A1 NH2 8 3.9 ASP 210 B1* OD2 Between chains.*
27 ARG 415 A1 NH2 5 3.6 GLU 463 A1 OE1 4
28 LYS 493 A1 NZ 7 3.3 PRO 504 A* O 8 C-terminus. Between chains.*
29 ARG 323 A2 NH1 4 3.6 ASP 325 A* OD2 4 Between chains.*
30 ARG 323 A2 NH2 4 2.7 ASP 325 A* OD2 4 Between chains.*
31 ARG 334 A2 NH1 2 3.7 ASP 339 A* OD1 4 Between chains.*
31 ARG 334 A2 NH1 2 2.8 ASP 339 A* OD2 4 Between chains.*
32 ARG 334 A2 NH2 2 3.8 ASP 339 A* OD2 4 Between chains.*
33 ARG 341 A2 NE 4 2.9 GLU 346 A* OE2 4 Between chains.*
34 ARG 341 A2 NH1 4 3.7 ASP 339 A* OD1 4 Between chains.*
35 ARG 341 A2 NH2 4 3.1 GLU 346 A* OE1 4 Between chains.*
35 ARG 341 A2 NH2 4 3.5 GLU 346 A* OE2 4 Between chains.*
36 LYS 357 A2 NZ 8 2.9 GLU 417 A1* OE2 3 Between chains.*
37 ARG 363 A2 NE 2 3.9 ASP 360 A2 OD1 6
37 ARG 363 A2 NE 2 3.4 GLU 367 A2 OE1 5
38 ARG 363 A2 NH2 2 3.3 ASP 360 A2 OD1 6
39 LYS 365 A2 NZ 3 3.8 GLU 480 A2 OE1 3
39 LYS 365 A2 NZ 3 3.3 GLU 480 A2 OE2 3
40 ARG 393 A2 NH2 8 2.8 ASP 210 B2* OD1 Between chains.*
40 ARG 393 A2 NH2 8 3.9 ASP 210 B2* OD2 Between chains.*
41 ARG 415 A2 NH2 5 3.6 GLU 463 A2 OE1 4
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Average distance between 58 salt-bridged atom pairs: 3.4 Å.
(Minimum 2.7, Maximum 3.9)
* 40 atom pairs in salt bridges between chains (inter-chain salt bridges).
58 total atom pairs in salt bridges.
4 atom pairs in salt bridges containing charged protein chain terminus atoms.
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SALT BRIDGES: AVERAGE CONSERVATION LEVELS FROM CONSURF PER ATOMS IN PAIRS
Maximum 4.0 Å between salt-bridged ions.
SaltBr Cation (+) SaltBr Anion (-)
Cation Average Anion Average SaltBr Average
N ConSurf N ConSurf N ConSurf
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58 4.2 49 4.2 107 4.2
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N is the number of pairs involving the ion type that have ConSurf levels 1-9.
Averages include all listed salt-bridged atom pairs, sometimes multiple pairs/atom,
that have ConSurf levels of 1-9.
Averages exclude blanks (not processed by ConSurf) and zeros (insufficient data).
To get the average ConSurf conservation level for any group of atoms or residues
that you specify, use Find.. (Focus Box), and then click List Found Atoms.
To obtain per-residue averages (rather than averages per interacting atom pair), include ~alphacarbons in Find..
Below are some examples. Click the links below to see the query used in Find...
You may use ~terms defined by FirstGlance in your Find.. query.
Links below work only when the FirstGlance session that generated this report remains active in a separate browser tab.
• Cationic (+) amino acids in salt bridges
• Cationic (+) amino acids NOT in salt bridges
• Anionic (-) amino acids in salt bridges
• Anionic (-) amino acids NOT in salt bridges
• Amino acids in salt bridges
• Cationic (+) amino acids
• Anionic (-) amino acids
• Charged amino acids that are NOT in salt bridges
• Charged amino acids
• Uncharged polar amino acids
• Apolar amino acids
• All amino acids
Verification:
The averages reported here can be verified by importing this report into a spreadsheet.
The ConSurf values can be verified against the "Per Residue Details" report at ConSurf.
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Spreadsheet Procedure:
- Copy only the above rows between the above rows beginning ⤋⤋⤋ and ⤊⤊⤊.
- MICROSOFT EXCEL:
-- Open a new, blank spreadsheet. Click cell A1.
-- Edit, Paste Special, Text.
-- Auto-set all column widths: Select entire sheet (Ctrl-A or Cmd-A), double click on any
column boundary in the row of column letters at the top.
-- Delete blank rows: Select the Group1 column (click on column B at the top).
In the Home tab, open Find & Select, click on Go to Special...,
check Blanks, OK. Right click on a selected cell, Delete..., Entire row.
-- Delete all asterisks (*): Edit menu at top, Find..., Replace....
Enter ~* (tilde asterisk) in the Find slot, and nothing in the Replace slot. Replace all.
- GOOGLE SHEETS:
-- Use the Chrome Browser.
-- Go to sheets.google.com.
-- Login (or create a login, recording your password safely).
-- Click the big + to open a new sheet.
-- Open the Sheet Edit menu, Paste Special, Values Only.
(If asked to install the free Chrome Extension Google Docs Offline, do that first.)
-- Auto-set all column widths: Click A above the first column to select the entire column. Holding down Shift,
click the letter above the last occupied column to select all columns. Double-click a column boundary.
-- Delete all asterisks (*): Open the Sheets Edit menu and click Find and Replace. The rest is straightforward.
-- Sort by multiple columns: Ctrl-A (macOS Cmd-A) twice to select all data. Open Data, Sort Range, Advanced Options.
Check "Data has header row". The rest is straightforward.
-- (Blank rows will gather at the end after sorting.)