CONTACTS & NON-COVALENT INTERACTIONS IN 1CRL
TO TARGET Halos: ~GLYCOPROTEINSUGARS
REPORTED BY FirstGlance in Jmol.
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 the target atom interacting with another atom, including target atoms with alternate locations.
Group = Residue code.
SeqNo = Sequence Number.
Ins = Insertion Code for sequence number (usually blank).
Atom: See Identifying Atoms.
AltLoc = Alternate Location ID (usually blank). See Conformations in FirstGlance.
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 the interacting target and contacting atoms.
BOND = Probable type of interaction or bond. See Definitions.
Cov.: Covalent, when DIST ≤ 1.75 Å (or ≤ 2.1 Å when one atom is not C, N, or O, e.g. S).
Hbond may be a salt bridge when involving non-standard amino acids, nucleotides, or ligands+.
CatPi: CAUTION: Detection of cation-pi interactions is approximate.
MetMisc: Metal and Miscellaneous. See Definitions.
DpClash: Deep Clash, DIST ≤ 0.5 Å between atoms. Atoms occupying the same space. When you target chain A, including ligands+,
in 1hho, this happens for PO4 due to symmetry operations constructing biological unit 1. Find.. PO4 finds 10 atoms, not 5.
CAUTION: Steric Clash Errors in the model may be reported as covalent or non-covalent bonds.
Also, clashes between alternate locations may be listed under "Cov.". See Conformations in FirstGlance.
CAUTION: Salt bridges and cation-pi interactions are listed only for standard amino acids.
FirstGlance cannot detect such interactions involving ligands+, non-standard amino acids, or nucleotides.
PLEASE NOTE the EXCLUSIONS below. §
TARGET ATOMS CONTACTING ATOMS
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Count Group1 SeqNo1 Ins1 Chain1 Atom1 AltLoc1 ConSrf1 DIST BOND Group2 SeqNo2 Ins2 Chain2 Atom2 AltLoc2 ConSrf2 NOTES
1 NAG 1 B C1 1.5 Cov. ASN 351 A ND2 8 Between chains.
2 NAG 1 B O4 1.4 Cov. NAG 2 B C1
3 NAG 994 A C1 1.5 Cov. ASN 314 A ND2 5
4 NAG 1 B N2 3.3 Hbond TYR 299 A OH 5 Between chains.
5 NAG 1 B N2 2.9 Hbond ASN 351 A ND2 8 Between chains.
6 NAG 1 B O3 3.3 Hbond NAG 2 B O5
7 NAG 1 B O4 2.9 Hbond NAG 2 B N2
8 NAG 1 B O4 2.3 Hbond NAG 2 B O5
9 NAG 1 B O5 2.4 Hbond ASN 351 A ND2 8 Between chains.
10 NAG 1 B O6 2.7 Hbond GLU 70 A OE1 1 Between chains.
11 NAG 1 B O6 3.3 Hbond GLU 70 A OE2 1 Between chains.
12 NAG 1 B O6 3.4 Hbond HOH 716 A O Between chains.
13 NAG 1 B O6 2.9 Hbond HOH 891 A O Between chains.
14 NAG 994 A N2 2.9 Hbond ASN 314 A ND2 5
15 NAG 994 A O5 2.3 Hbond ASN 314 A ND2 5
16 NAG 994 A O7 3.0 Hbond TRP 221 A NE1 6
17 NAG 994 A O7 2.9 Hbond ASN 222 A ND2 8
18 NAG 994 A O7 3.1 Hbond HOH 679 A O
19 NAG 1 B C1 3.5 Apolar TYR 299 A CE1 5 Between chains.
20 NAG 1 B C1 3.9 Apolar TYR 299 A CZ 5 Between chains.
21 NAG 1 B C1 3.8 Apolar ASN 351 A CB 8 Between chains.
22 NAG 1 B C1 2.5 Apolar ASN 351 A CG 8 Between chains.
23 NAG 1 B C2 3.5 Apolar ASN 351 A CG 8 Between chains.
24 NAG 1 B C3 3.6 Apolar NAG 2 B C1
25 NAG 1 B C4 2.4 Apolar NAG 2 B C1
26 NAG 1 B C4 3.7 Apolar NAG 2 B C2
27 NAG 1 B C5 3.8 Apolar TYR 299 A CG 5 Between chains.
28 NAG 1 B C5 3.8 Apolar TYR 299 A CD1 5 Between chains.
29 NAG 1 B C5 3.9 Apolar TYR 299 A CD2 5 Between chains.
30 NAG 1 B C5 3.9 Apolar TYR 299 A CE1 5 Between chains.
31 NAG 1 B C5 4.0 Apolar TYR 299 A CZ 5 Between chains.
32 NAG 1 B C5 3.3 Apolar NAG 2 B C1
33 NAG 1 B C6 3.9 Apolar GLU 70 A CD 1 Between chains.
34 NAG 1 B C6 4.0 Apolar TYR 299 A CG 5 Between chains.
35 NAG 1 B C6 3.2 Apolar NAG 2 B C1
36 NAG 1 B C7 3.9 Apolar ASN 351 A CG 8 Between chains.
37 NAG 1 B C8 4.0 Apolar GLN 357 A CB 5 Between chains.
38 NAG 1 B C8 3.8 Apolar GLN 357 A CG 5 Between chains.
39 NAG 1 B C8 3.8 Apolar GLN 357 A CD 5 Between chains.
40 NAG 994 A C1 3.9 Apolar VAL 313 A CG2 2
41 NAG 994 A C1 3.8 Apolar ASN 314 A CB 5
42 NAG 994 A C1 2.5 Apolar ASN 314 A CG 5
43 NAG 994 A C2 3.5 Apolar ASN 314 A CG 5
44 NAG 994 A C5 3.8 Apolar VAL 313 A CG2 2
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AVERAGE CONSERVATION LEVELS PER ATOMS IN INTERACTING PAIRS (FOR PER RESIDUE, SEE BELOW)
Target Target Contacting Contacting
Atom ConSurf Average ConSurf Average
Bond Type Max Å Pairs Atoms ConSurf Atoms ConSurf
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Hydrogen bonds (putative) 3.5 15 0 9 5.2
Apolar interactions 4.0 26 0 21 5.1
Salt bridges 4.0 0 0 0
Cation pi interactions (possible†) 6.0 0 0 0
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†CAUTION: Detection of Cation-Pi interactions is approximate.
For Covalent bonds/deep clashes and Metal & miscellaneous: See the main per-atom-pair listing above.
Cation Cation Pi Ring Pi Ring
ConSurf Average ConSurf Average
Bond Type Max Å Atoms ConSurf Atoms ConSurf
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Cation pi interactions (possible†) 6.0 0 0
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†CAUTION: Detection of Cation-Pi interactions is approximate.
Cation Residues are Arg or Lys. Pi Ring Residues are Phe, Tyr or Trp.
"ConSurf Atoms" and Averages exclude blanks (not processed by ConSurf) and zeros (insufficient data).
Averages include atoms in all listed atom pairs (sometimes multiples/residue) that have ConSurf levels of 1-9.
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.
More ~terms are explained when you click the pink button [List Contacts Counts] in the Contacts Shown panel in FirstGlance.
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
• Cationic (+) amino acids in cation-pi interactions
• Cationic (+) amino acids NOT in cation-pi interactions
• Aromatic amino acids in cation-pi interactions
• Aromatic amino acids NOT in cation-pi interactions
• Amino acids in cation-pi interactions
• Aromatic amino acids
• 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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§ EXCLUSIONS:
- HYDROGEN atoms are always excluded from the above report. 83% of models in the Protein Data Bank
have no hydrogen atoms (July, 2025). The contacts and non-covalent interactions tool
in FirstGlance ignores hydrogen atoms when they are present (see Definitions).
- WATER is automatically excluded from the target unless you checked Target Water within Target Chains(s),
(or you checked Target All Water; or you target atoms with halos, and some water has halos from Find..).
Non-targeted water oxygens contacting target atoms are always reported.
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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.)
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