Contacts of the helix formed by residues 2295 - 2320 (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 VAL2295 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2200C PHE* 3.4 26.0 - - + -
2203C GLN* 4.2 8.7 - - - +
2291C VAL 5.7 0.4 - - - +
2292C PHE 3.7 1.8 + - - -
2293C GLY 3.1 3.8 + - - -
2294C LEU* 1.3 91.3 - - + +
2296C PRO* 1.3 58.7 - - + +
2297C GLY 2.6 15.0 + - - +
2298C LEU* 2.6 58.6 + - + +
2299C MET 2.9 10.6 + - - -
2407C PHE* 5.4 3.6 - - + -
2408C LEU* 4.7 10.3 - - + -
2411C ASN* 4.0 2.2 - - - -
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Residues in contact with PRO2296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2294C LEU 4.0 2.5 - - - +
2295C VAL* 1.3 84.6 - - + +
2297C GLY* 1.3 61.1 + - - +
2299C MET* 4.0 5.6 - - + -
2300C MET* 3.0 24.4 + - - +
2407C PHE* 3.4 47.8 - - + +
2410C ASN 3.1 28.9 - - - +
2411C ASN* 3.3 23.8 - - - +
2413C ILE* 4.3 0.2 - - + -
2414C LEU* 3.8 8.3 - - + +
2422C PHE* 3.9 17.4 - - + -
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Residues in contact with GLY2297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2200C PHE* 3.6 42.0 - - - -
2295C VAL* 2.6 9.5 + - - +
2296C PRO* 1.3 75.6 - - - +
2298C LEU* 1.3 61.2 + - - +
2300C MET* 3.3 19.8 - - - +
2301C TYR* 3.4 9.7 + - - -
2407C PHE* 4.5 2.6 - - - -
2426C PHE* 4.2 8.3 - - - -
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Residues in contact with LEU2298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2200C PHE* 3.9 7.9 - - + +
2203C GLN* 3.1 40.6 - - + +
2204C HIS* 3.7 22.0 - - + +
2207C HIS* 5.1 4.7 - - + +
2291C VAL* 5.4 2.5 - - + +
2292C PHE* 3.6 46.7 - - + +
2295C VAL* 2.6 39.7 + - + +
2297C GLY* 1.3 68.0 - - - -
2299C MET* 1.3 69.4 - - - +
2301C TYR* 2.7 18.8 + - - +
2302C ALA* 3.0 10.2 + - - -
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Residues in contact with MET2299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2263C PRO* 4.2 4.0 - - - -
2273C MET* 5.1 1.1 - - + -
2275C TYR* 3.9 7.2 - - - +
2285C PHE* 3.4 36.6 - - + -
2287C VAL* 4.1 18.4 - - + -
2292C PHE* 2.9 29.9 + - + +
2293C GLY* 3.2 20.4 - - - -
2295C VAL 2.9 10.1 + - - +
2296C PRO* 3.9 3.8 - - + +
2298C LEU* 1.3 77.8 - - - +
2300C MET* 1.3 57.8 + - - +
2302C ALA* 3.2 6.7 - - - +
2303C THR* 2.6 35.0 + - - +
2411C ASN* 3.4 16.8 - - - +
2414C LEU* 3.6 20.2 - - + -
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Residues in contact with MET2300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2197C MET* 3.2 40.8 - - + +
2200C PHE* 5.6 0.9 - - - -
2296C PRO 3.0 19.8 + - - +
2297C GLY 3.3 11.0 - - - +
2298C LEU 2.8 4.4 + - - -
2299C MET* 1.3 73.9 - - - +
2301C TYR* 1.3 72.2 + - - +
2303C THR* 3.3 4.9 - - - -
2304C ILE* 2.9 32.0 + - + +
2414C LEU* 3.5 18.1 - - + +
2419C LEU* 3.4 21.1 - - + +
2422C PHE* 3.8 12.6 - - + +
2423C VAL* 3.5 30.7 - - + +
2426C PHE* 4.1 15.3 - - + -
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Residues in contact with TYR2301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2197C MET* 3.2 30.4 + - + +
2200C PHE* 3.3 29.2 - - + -
2201C PHE* 2.9 59.4 - + + +
2204C HIS* 3.5 23.6 - + + +
2297C GLY 3.4 6.7 + - - -
2298C LEU 2.7 13.1 + - - +
2300C MET* 1.3 75.8 - - - +
2302C ALA* 1.3 73.5 + - - +
2304C ILE* 2.7 32.2 + - + +
2305C TRP* 2.9 22.2 + - - -
2564C ILE* 4.1 12.6 - - + +
2567C LEU* 5.4 1.3 - - + -
2568C ILE* 4.9 4.7 - - + -
2580C PHE* 3.6 6.4 - - - -
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Residues in contact with ALA2302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2204C HIS* 3.6 14.6 + - - +
2232C HIS 6.1 0.4 - - - +
2233C ILE* 6.1 2.5 - - - -
2263C PRO* 4.8 0.7 - - + -
2287C VAL* 4.4 29.2 - - + -
2292C PHE* 4.9 5.2 - - + -
2298C LEU 3.0 7.9 + - - +
2299C MET* 3.2 17.5 - - - +
2301C TYR* 1.3 83.5 - - - +
2303C THR* 1.3 56.4 + - - +
2304C ILE 2.5 9.4 + - - -
2305C TRP* 2.6 15.0 + - - -
2306C LEU* 2.8 13.9 + - + +
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Residues in contact with THR2303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2261C VAL 3.1 28.0 - - - +
2262C TYR* 3.6 15.1 - - + -
2263C PRO* 3.2 34.0 - - + +
2299C MET* 2.6 24.6 + - - +
2300C MET* 3.3 10.0 - - - -
2302C ALA* 1.3 73.6 - - - +
2304C ILE* 1.3 66.0 + - - +
2306C LEU* 3.6 5.0 - - + +
2307C ARG* 2.8 38.2 + - + +
2414C LEU* 4.5 1.2 - - - +
2419C LEU* 4.6 5.2 - - + -
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Residues in contact with ILE2304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2300C MET* 2.9 25.8 + - + +
2301C TYR* 2.7 50.1 + - + +
2302C ALA 2.5 3.8 + - - -
2303C THR* 1.3 71.0 - - - +
2305C TRP* 1.3 53.8 + - + +
2307C ARG* 2.6 33.4 + - - +
2419C LEU* 3.6 16.4 - - + -
2567C LEU* 3.4 26.2 - - + +
2568C ILE* 4.8 9.9 - - + -
2571C ASN* 2.7 40.7 + - + +
2572C VAL* 4.7 8.3 - - + -
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Residues in contact with TRP2305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2201C PHE* 4.8 16.0 - + - -
2204C HIS* 3.5 34.1 + + - -
2232C HIS* 5.2 2.3 - + - -
2233C ILE* 4.3 25.4 - - + -
2301C TYR* 2.9 20.6 + + + -
2302C ALA* 2.6 11.7 + - - +
2304C ILE* 1.3 75.5 - - - +
2306C LEU* 1.3 55.0 + - - +
2308C GLU* 2.6 39.5 + - + +
2309C HIS* 2.7 14.8 + - - +
2336C LEU* 4.1 17.0 - - + +
2339C GLU* 3.7 22.4 - - + -
2340C THR* 3.0 44.6 - - + -
2343C ILE* 4.3 10.1 - - + -
2567C LEU* 3.5 31.7 - - + +
2571C ASN* 4.1 0.2 - - - +
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Residues in contact with LEU2306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2233C ILE* 4.9 11.9 - - + +
2252C LEU* 4.7 15.9 - - + -
2253C LYS 3.9 17.7 - - - +
2254C TYR* 4.3 9.0 - - + -
2261C VAL* 3.9 15.7 - - + -
2262C TYR 5.0 2.5 - - - +
2263C PRO* 3.6 35.0 - - + -
2264C PRO* 4.5 1.8 - - + -
2287C VAL* 6.1 0.4 - - + -
2302C ALA* 2.8 14.7 + - + +
2303C THR* 3.6 11.0 - - - +
2305C TRP* 1.3 73.5 - - - +
2307C ARG* 1.3 82.6 + - + +
2309C HIS* 3.1 21.1 + - - +
2310C ASN* 3.3 12.6 + - + +
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Residues in contact with ARG2307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2260C GLU* 3.4 27.8 + - - +
2261C VAL* 2.5 75.2 + - + +
2262C TYR* 4.6 5.3 - - - -
2303C THR* 2.8 37.6 + - - +
2304C ILE* 2.6 18.5 + - - +
2306C LEU* 1.3 78.2 - - + +
2308C GLU* 1.3 60.5 + - - +
2310C ASN* 3.6 4.0 + - - +
2311C ARG* 2.8 24.1 + - - +
2419C LEU* 4.2 17.5 - - - +
2571C ASN* 3.3 35.7 + - + +
2572C VAL* 5.9 0.9 - - - -
2573C LYS 6.1 0.6 - - - +
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Residues in contact with GLU2308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2304C ILE 2.7 5.9 + - - -
2305C TRP* 2.6 32.0 + - + +
2307C ARG* 1.3 70.7 - - - +
2309C HIS* 1.3 63.9 + - - +
2311C ARG* 2.8 39.2 + - - +
2312C VAL* 2.8 18.3 + - - +
2336C LEU* 3.2 23.3 - - + +
2339C GLU* 2.5 38.5 - - - +
2567C LEU* 4.2 8.5 - - + +
2570C ASN* 5.1 0.9 - - - +
2571C ASN* 2.8 23.4 + - - +
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Residues in contact with HIS2309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2233C ILE* 5.5 0.4 - - + -
2234C TYR* 2.8 37.8 + + - -
2250C GLY 2.9 22.7 + - - -
2252C LEU* 3.4 21.6 + - + +
2305C TRP 2.7 10.1 + - - +
2306C LEU* 3.3 10.8 - - - +
2308C GLU* 1.3 70.5 - - - +
2310C ASN* 1.3 79.8 + - - +
2312C VAL* 2.6 28.8 + - - +
2313C CYS* 2.9 19.8 + - - -
2329C PHE* 3.6 17.3 - + - -
2332C SER* 3.3 23.3 - - - -
2336C LEU* 3.5 20.4 - - + +
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Residues in contact with ASN2310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2251C LYS* 3.7 20.0 - - + +
2252C LEU* 2.9 40.4 + - - +
2254C TYR* 3.4 27.6 - - + +
2306C LEU* 3.3 12.9 + - - +
2307C ARG* 4.1 6.5 - - - +
2309C HIS* 1.3 93.8 - - - +
2311C ARG* 1.3 63.4 + - - +
2313C CYS* 3.2 8.9 + - - +
2314C ASP* 3.1 25.6 + - - +
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Residues in contact with ARG2311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2307C ARG 2.8 15.8 + - - +
2308C GLU* 2.8 55.1 + - - +
2310C ASN* 1.3 79.2 - - - +
2312C VAL* 1.3 61.1 + - - +
2314C ASP* 3.2 14.3 + - - +
2315C ILE* 3.2 40.7 + - + +
2339C GLU* 3.9 6.1 + - - -
2558C ILE* 4.1 13.1 - - - +
2570C ASN* 3.8 44.4 + - - +
2571C ASN* 4.0 5.2 - - - +
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Residues in contact with VAL2312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2308C GLU* 2.8 16.7 + - - +
2309C HIS 2.6 15.7 + - - +
2311C ARG* 1.3 70.1 - - - +
2313C CYS* 1.3 68.0 + - - +
2315C ILE* 2.8 22.6 + - + +
2316C LEU* 2.9 22.5 + - + +
2332C SER* 3.2 33.4 - - - +
2335C ILE* 3.9 15.3 - - + -
2336C LEU* 3.9 20.6 - - + -
2558C ILE* 3.8 26.0 - - + -
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Residues in contact with CYS2313 (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 20.6 - - + +
2250C GLY* 3.1 30.5 - - - -
2251C LYS* 3.8 9.6 - - + -
2309C HIS* 2.9 25.8 + - - -
2310C ASN* 3.2 11.8 + - - +
2312C VAL* 1.3 76.8 - - - +
2314C ASP* 1.3 58.7 + - - +
2316C LEU* 3.0 5.8 + - - +
2317C LYS* 2.8 31.1 + - - +
2328C LEU* 4.0 3.8 - - - +
2329C PHE* 4.9 1.3 - - - -
2332C SER* 3.1 23.1 - - - -
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Residues in contact with ASP2314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2249C ASP* 5.4 1.4 - - - +
2251C LYS* 2.9 36.7 + - - -
2310C ASN 3.1 10.4 + - - +
2311C ARG* 3.5 10.6 - - - +
2312C VAL 3.1 0.8 - - - -
2313C CYS* 1.3 77.0 - - - +
2315C ILE* 1.3 62.4 + - + +
2317C LYS* 3.3 10.5 + - - +
2318C GLN* 3.0 24.4 + - - +
----------------------------------------------------------
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Residues in contact with ILE2315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2311C ARG* 3.2 31.9 - - + +
2312C VAL* 2.8 33.5 + - - +
2314C ASP* 1.3 72.0 - - + +
2316C LEU* 1.3 64.2 + - + +
2318C GLN* 3.1 21.3 - - + +
2319C GLU* 3.1 11.3 + - - +
2554C VAL* 4.0 23.8 - - + -
2558C ILE* 3.4 27.1 - - + -
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Residues in contact with LEU2316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2312C VAL* 2.9 16.6 + - + +
2313C CYS 3.4 7.2 - - - +
2315C ILE* 1.3 75.3 - - + +
2317C LYS* 1.3 51.0 + - - +
2318C GLN 2.6 5.8 + - - -
2319C GLU* 2.5 32.5 + - + +
2320C HIS* 2.7 21.3 + - + +
2323C TRP* 4.4 4.0 - - + -
2328C LEU* 3.4 19.5 - - + +
2331C THR* 3.3 34.5 - - + +
2332C SER* 3.8 20.2 - - - +
2335C ILE* 3.9 9.2 - - + -
2550C PHE 4.0 19.3 - - - +
2551C GLY* 4.6 10.8 - - - +
2554C VAL* 5.6 0.9 - - + -
2555C GLY* 4.5 12.1 - - - +
2558C ILE* 6.3 0.7 - - + -
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Residues in contact with LYS2317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2249C ASP* 2.8 37.0 + - + +
2251C LYS* 5.7 2.8 - - - +
2313C CYS 2.8 19.0 + - - +
2314C ASP* 3.7 10.2 + - - +
2316C LEU* 1.3 70.5 - - - +
2318C GLN* 1.3 61.5 + - - +
2320C HIS 4.0 9.4 - - - +
2321C PRO* 3.5 23.3 - - + +
2328C LEU* 3.5 19.1 - - + +
----------------------------------------------------------
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Residues in contact with GLN2318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2314C ASP 3.0 11.5 + - - +
2315C ILE* 3.1 16.2 - - + +
2316C LEU 2.6 4.8 + - - -
2317C LYS* 1.3 78.0 - - - +
2319C GLU* 1.3 71.9 - - - +
2320C HIS 3.5 0.2 + - - -
2321C PRO* 3.7 9.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU2319 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2315C ILE* 3.1 9.4 + - - +
2316C LEU* 2.5 18.6 + - + +
2318C GLN* 1.3 83.3 - - - +
2320C HIS* 1.3 79.4 + - + +
2321C PRO* 3.3 8.1 - - - +
2322C GLU* 3.9 2.1 - - - +
2551C GLY 4.5 10.8 - - - +
2554C VAL* 3.2 43.0 - - + +
3048D MET* 5.7 1.6 - - + -
3050D THR* 4.8 3.3 - - - -
3051D GLY* 4.6 3.6 + - - -
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Residues in contact with HIS2320 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2316C LEU* 2.7 16.5 + - + +
2317C LYS* 3.7 12.3 - - - +
2319C GLU* 1.3 92.5 + - + +
2321C PRO* 1.3 59.7 - - - +
2322C GLU* 2.7 20.3 + - - +
2323C TRP* 3.0 73.1 + + + +
2328C LEU* 5.1 0.5 - - - +
2551C GLY* 3.3 21.5 + - - -
3048D MET* 3.2 31.9 - - + -
3049D SER 3.1 17.8 + - - -
3050D THR* 4.4 3.1 - - - -
----------------------------------------------------------
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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