Contacts of the helix formed by residues 2324 - 2347 (chain C) in PDB entry 1DDX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY2324 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2322C GLU 4.3 0.2 + - - -
2323C TRP* 1.3 76.8 - - - +
2325C ASP* 1.3 70.5 + - - +
2326C GLU 3.3 2.5 - - - -
2327C GLN* 2.9 12.9 + - - +
2328C LEU* 2.8 24.3 + - - +
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Residues in contact with ASP2325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2245C ARG* 2.7 24.0 + - - -
2247C PHE* 3.0 25.4 + - - +
2248C LYS* 2.6 33.0 + - - +
2249C ASP 4.1 6.7 - - - +
2250C GLY* 2.6 34.3 + - - +
2324C GLY* 1.3 73.9 - - - +
2326C GLU* 1.3 60.1 + - - +
2328C LEU* 3.0 1.0 + - - +
2329C PHE* 2.9 25.5 + - - +
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Residues in contact with GLU2326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2238C LEU* 5.4 1.9 - - - +
2241C GLN* 4.9 0.2 - - - +
2242C HIS* 4.3 9.3 - - + -
2245C ARG* 3.0 39.3 + - - +
2247C PHE* 5.1 2.7 - - + -
2324C GLY 3.3 0.4 - - - -
2325C ASP* 1.3 79.0 + - - +
2327C GLN* 1.3 56.6 + - - +
2329C PHE 4.2 1.3 - - - -
2330C GLN* 3.0 26.6 + - - +
3134D TYR* 3.0 39.7 + - - -
3136D TYR* 3.2 5.0 + - - +
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Residues in contact with GLN2327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2323C TRP* 3.2 63.5 + - + +
2324C GLY* 2.9 19.6 + - - +
2326C GLU* 1.3 72.7 - - - +
2328C LEU* 1.3 56.2 + - - +
2330C GLN* 3.2 1.7 + - - +
2331C THR* 2.5 42.1 + - - +
3049D SER* 5.1 1.1 + - - -
3136D TYR* 2.7 53.1 + - + +
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Residues in contact with LEU2328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2249C ASP* 3.3 42.0 - - + +
2313C CYS* 4.0 5.8 - - - +
2316C LEU* 3.4 33.8 - - + +
2317C LYS* 3.5 25.4 - - + +
2320C HIS 5.8 0.2 - - - +
2323C TRP* 4.2 26.2 - - + +
2324C GLY 2.8 21.3 + - - +
2325C ASP 3.5 3.8 - - - +
2327C GLN* 1.3 76.7 - - - +
2329C PHE* 1.3 65.1 + - - +
2331C THR* 2.8 6.5 + - - -
2332C SER* 2.8 29.8 + - - -
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Residues in contact with PHE2329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2234C TYR* 4.0 29.2 - + + -
2241C GLN* 2.7 39.7 - - - -
2245C ARG* 3.2 48.5 - - + +
2250C GLY* 3.3 35.9 - - - -
2251C LYS 5.3 0.2 - - - -
2252C LEU* 4.9 3.4 - - + -
2309C HIS* 3.6 12.5 - + - -
2325C ASP 2.9 11.3 + - - +
2326C GLU 4.3 0.2 - - - +
2328C LEU* 1.3 77.4 - - - +
2330C GLN* 1.3 87.3 + - + +
2332C SER* 4.5 0.2 - - - -
2333C ARG* 3.3 26.5 + - - +
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Residues in contact with GLN2330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2238C LEU* 5.9 1.2 - - - +
2241C GLN* 4.7 4.2 + - - +
2245C ARG* 4.6 0.4 - - - +
2326C GLU* 3.0 37.9 + - - +
2327C GLN* 3.2 4.6 + - - +
2328C LEU 3.0 1.2 - - - -
2329C PHE* 1.3 95.9 - - + +
2331C THR* 1.3 66.4 + - - +
2333C ARG* 3.6 6.2 + - - +
2334C LEU* 3.2 26.3 + - - +
3134D TYR* 3.6 14.6 + - + -
3136D TYR* 4.6 3.8 - - + -
3137D LYS 5.5 1.1 - - - +
3138D SER* 3.0 34.5 + - - -
3139D TRP* 3.4 7.3 + - - +
3140D GLU* 3.1 34.2 + - - +
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Residues in contact with THR2331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2316C LEU* 3.3 13.9 - - + -
2323C TRP* 2.9 25.6 - - + -
2327C GLN* 2.5 29.2 + - - +
2328C LEU 2.8 0.4 + - - -
2330C GLN* 1.3 69.4 - - - +
2332C SER* 1.3 71.6 + - - +
2334C LEU* 2.8 15.7 + - - +
2335C ILE* 2.9 20.5 + - + +
2549C THR 4.2 4.9 - - - +
2550C PHE* 3.4 39.3 - - - +
2551C GLY 3.6 4.0 - - - +
3136D TYR* 5.6 0.7 - - - -
3137D LYS 5.9 1.3 - - - -
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Residues in contact with SER2332 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2234C TYR* 4.4 1.1 - - - -
2309C HIS* 3.3 27.4 - - - -
2312C VAL* 3.2 30.3 - - - +
2313C CYS* 3.1 26.8 + - - -
2316C LEU* 3.8 2.4 - - - +
2328C LEU 2.8 14.5 + - - -
2331C THR* 1.3 74.4 - - - +
2333C ARG* 1.3 55.5 + - - -
2334C LEU 2.6 1.9 + - - -
2335C ILE* 2.6 27.2 + - - +
2336C LEU* 2.8 13.2 + - - -
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Residues in contact with ARG2333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2229C ASP* 2.7 31.2 + - - +
2230C LEU* 4.2 0.5 - - - +
2231C ASN* 4.2 11.1 - - - +
2234C TYR* 3.1 66.9 + - + +
2235C GLY 4.6 5.9 + - - -
2241C GLN* 3.7 15.0 - - - +
2329C PHE* 3.3 22.6 + - + +
2330C GLN* 3.7 7.9 - - - +
2332C SER* 1.3 78.4 - - - +
2334C LEU* 1.3 60.2 + - - +
2336C LEU* 4.0 1.1 - - - -
2337C ILE* 3.1 30.6 + - + +
3139D TRP* 3.4 47.1 - - + +
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Residues in contact with LEU2334 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2330C GLN 3.2 15.4 + - - +
2331C THR* 2.8 12.6 + - - +
2332C SER 2.6 4.6 + - - -
2333C ARG* 1.3 74.3 - - - +
2335C ILE* 1.3 63.4 + - - +
2337C ILE* 3.4 6.6 + - + +
2338C GLY* 3.0 18.4 + - - -
2539C ILE* 4.9 11.4 - - + +
2544C TYR* 4.9 7.6 - - + -
2549C THR* 3.5 37.0 - - + +
2550C PHE* 4.0 18.4 - - + -
2559C ILE* 4.0 2.6 - - - +
3137D LYS* 3.9 21.8 - - + +
3138D SER* 4.5 0.9 - - - -
3139D TRP* 3.8 44.2 - - + +
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Residues in contact with ILE2335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2312C VAL* 3.9 17.3 - - + -
2316C LEU* 3.9 17.3 - - + -
2331C THR* 2.9 37.8 + - + +
2332C SER* 2.6 12.7 + - - +
2334C LEU* 1.3 68.2 - - - +
2336C LEU* 1.3 66.5 + - - +
2338C GLY 2.8 10.7 + - - -
2339C GLU* 2.9 13.5 + - - +
2550C PHE* 3.6 28.9 - - + +
2555C GLY* 3.3 20.0 - - - +
2558C ILE* 3.4 34.1 - - + -
2559C ILE* 3.0 16.2 - - + +
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Residues in contact with LEU2336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2230C LEU* 3.7 14.4 - - + -
2233C ILE* 4.8 5.8 - - + -
2234C TYR* 3.3 24.0 - - + +
2305C TRP* 4.1 17.2 - - + +
2308C GLU* 3.2 34.3 - - + +
2309C HIS* 3.5 35.0 - - + +
2312C VAL* 3.9 15.3 - - + -
2332C SER 2.8 17.0 + - - +
2333C ARG 4.2 0.2 - - - +
2335C ILE* 1.3 69.5 - - - +
2337C ILE* 1.3 68.2 + - - +
2339C GLU* 2.8 23.0 + - - +
2340C THR* 2.9 14.1 + - - -
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Residues in contact with ILE2337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2228C VAL* 3.7 11.6 - - + +
2229C ASP* 3.7 28.3 - - - +
2230C LEU* 3.3 28.3 - - + +
2333C ARG* 3.1 27.9 + - + +
2334C LEU* 3.6 5.8 - - + +
2336C LEU* 1.3 76.9 - - - +
2338C GLY* 1.3 68.4 + - - +
2340C THR* 3.4 3.5 + - - -
2341C ILE* 2.9 29.3 + - + +
2537C ASN* 4.2 9.2 - - - +
2539C ILE* 3.9 28.5 - - + -
3139D TRP* 3.9 23.1 - - + -
----------------------------------------------------------
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Residues in contact with GLY2338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2334C LEU 3.0 8.4 + - - -
2335C ILE 2.8 10.5 + - - -
2337C ILE* 1.3 82.7 - - - +
2339C GLU* 1.3 63.3 + - - -
2341C ILE* 3.0 6.0 + - - +
2342C LYS* 2.8 20.4 + - - +
2361C PHE* 4.1 1.7 - - - -
2539C ILE* 4.2 11.2 - - - -
2559C ILE* 3.3 26.7 - - - +
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Residues in contact with GLU2339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2305C TRP* 3.7 9.7 - - + -
2308C GLU* 2.5 38.3 - - - +
2311C ARG* 3.9 2.1 + - - -
2335C ILE* 2.9 9.7 + - - +
2336C LEU* 2.8 28.8 + - - +
2338C GLY* 1.3 67.8 - - - -
2340C THR* 1.3 51.1 + - - +
2342C LYS* 2.6 26.6 + - - +
2343C ILE* 2.6 25.8 + - + +
2558C ILE* 2.7 35.2 - - + +
2559C ILE* 3.5 6.4 - - - +
2562C ALA* 3.5 28.3 - - + -
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Residues in contact with THR2340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2201C PHE* 5.5 1.6 - - + -
2205C PHE* 3.8 22.7 - - + -
2208C GLN* 4.7 0.2 - - - +
2228C VAL* 3.7 24.0 - - + -
2230C LEU* 3.6 22.0 - - + +
2305C TRP* 3.0 33.9 - - + -
2336C LEU 2.9 13.0 + - - -
2337C ILE 3.4 8.3 - - - -
2339C GLU* 1.3 72.9 - - - +
2341C ILE* 1.3 66.3 + - - +
2342C LYS 2.8 0.3 + - - -
2343C ILE* 3.7 3.3 - - - +
2344C VAL* 2.8 27.5 + - + +
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Residues in contact with ILE2341 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2228C VAL* 3.5 28.9 - - + -
2337C ILE* 2.9 31.0 + - + +
2338C GLY* 3.4 8.1 - - - +
2340C THR* 1.3 74.3 - - - +
2342C LYS* 1.3 61.0 + - - +
2344C VAL* 4.0 0.7 - - - +
2345C ILE* 3.1 38.5 + - + +
2361C PHE* 3.4 29.2 - - + -
2534C LEU* 3.0 45.8 - - + +
2537C ASN* 4.2 11.9 - - + -
2539C ILE* 5.5 0.9 - - + -
2540C CYS* 4.4 2.7 - - - -
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Residues in contact with LYS2342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2338C GLY 2.8 10.1 + - - +
2339C GLU 2.6 19.7 + - - +
2341C ILE* 1.3 68.1 - - - +
2343C ILE* 1.3 59.7 + - - +
2344C VAL 2.9 2.3 + - - -
2345C ILE 3.1 1.9 + - - -
2346C GLU* 2.7 73.9 + - + +
2360C LYS* 6.0 0.2 - - - +
2361C PHE* 3.5 21.3 + - + +
2559C ILE* 3.3 20.6 - - + +
2560C ASN* 3.0 34.0 + - - +
2561C THR* 4.4 0.2 - - - +
2562C ALA* 3.2 25.4 - - + +
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Residues in contact with ILE2343 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2201C PHE* 3.9 22.2 - - + -
2305C TRP* 4.3 11.4 - - + -
2339C GLU* 2.6 20.0 + - + +
2340C THR* 3.9 4.3 - - - +
2342C LYS* 1.3 73.8 - - - +
2344C VAL* 1.3 58.9 + - - +
2346C GLU* 5.2 0.2 - - - -
2347C ASP* 3.0 29.2 - - + +
2348C TYR* 3.3 2.8 + - - +
2562C ALA* 3.8 10.3 - - + -
2563C SER 3.6 18.4 - - - +
2564C ILE* 3.6 43.5 - - + +
2567C LEU* 3.6 31.0 - - + -
2580C PHE* 4.6 0.4 - - + -
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Residues in contact with VAL2344 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2201C PHE* 3.6 28.5 - - + -
2205C PHE* 3.5 35.2 - - + -
2340C THR* 2.8 23.4 + - + +
2341C ILE 4.0 3.1 - - - +
2342C LYS 2.9 0.4 + - - -
2343C ILE* 1.3 76.3 - - - +
2345C ILE* 1.3 69.5 + - - +
2346C GLU 3.2 0.2 + - - -
2348C TYR* 3.3 9.9 + - + -
2349C VAL* 2.9 39.6 + - + -
2534C LEU* 3.8 22.7 - - + -
2701C PGX 4.1 6.1 - - - +
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Residues in contact with ILE2345 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2113C MET* 5.2 6.3 - - + -
2341C ILE* 3.1 37.6 + - + +
2342C LYS 3.1 1.9 + - - +
2344C VAL* 1.3 83.6 - - - +
2346C GLU* 1.3 63.6 + - + +
2349C VAL* 3.3 12.2 - - + +
2350C GLN 3.3 15.1 + - - -
2359C LEU* 3.9 17.5 - - + +
2360C LYS 4.1 13.2 - - - +
2361C PHE* 3.6 31.6 - - + -
2531C LEU* 4.4 13.5 - - + -
2534C LEU* 3.5 26.5 - - + -
2535C MET* 4.0 11.4 - - + -
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Residues in contact with GLU2346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2109C ARG* 3.7 10.6 + - - -
2342C LYS* 2.7 63.6 + - + +
2343C ILE* 5.2 0.2 - - - -
2345C ILE* 1.3 72.8 - - - +
2347C ASP* 1.3 65.8 + - - +
2350C GLN* 2.9 22.5 + - - +
2358C LYS* 5.9 2.3 - - - +
2359C LEU 3.4 20.7 - - - +
2360C LYS* 4.0 5.5 - - - +
2361C PHE* 3.0 40.0 + - + +
----------------------------------------------------------
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Residues in contact with ASP2347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2343C ILE* 3.0 18.5 + - - +
2346C GLU* 1.3 82.8 - - - +
2348C TYR* 1.3 77.1 + - - +
2349C VAL 3.4 0.7 - - - -
2350C GLN* 2.5 21.8 + - - +
2351C HIS* 3.0 4.6 + - - -
2562C ALA 5.5 0.2 - - - -
2563C SER* 3.4 13.5 - - - -
2564C ILE* 2.6 42.1 + - - +
2580C PHE* 3.6 16.2 - - + -
----------------------------------------------------------
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il