Contacts of the helix formed by residues 2295 - 2320 (chain B) in PDB entry 1DCX
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2200B PHE* 3.5 26.2 - - + -
2203B GLN* 5.9 1.6 - - - +
2291B VAL 5.2 0.7 - - - +
2292B PHE 3.2 6.6 + - - +
2294B LEU* 1.3 82.9 - - + +
2296B PRO* 1.3 66.2 - - + +
2297B GLY 3.4 13.5 - - - +
2298B LEU* 3.0 28.6 + - + +
2299B MET* 2.9 27.6 + - - +
2407B PHE* 4.6 1.8 - - + +
2408B LEU* 3.7 28.0 - - + -
2409B TYR 4.6 0.9 - - - +
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Residues in contact with PRO2296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2294B LEU 3.4 7.4 - - - +
2295B VAL* 1.3 84.9 - - + +
2297B GLY* 1.3 57.6 + - - +
2299B MET* 3.6 7.4 + - + +
2300B MET* 3.1 26.9 + - - +
2407B PHE* 3.5 31.0 - - + +
2410B ASN 3.0 29.6 - - - +
2411B ASN* 4.9 3.4 - - - -
2413B ILE* 4.5 11.0 - - + -
2414B LEU* 3.9 15.9 - - + +
2422B PHE* 3.8 28.1 - - + -
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Residues in contact with GLY2297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2200B PHE* 3.7 27.7 - - - +
2295B VAL* 3.1 5.1 - - - +
2296B PRO* 1.3 80.6 - - - +
2298B LEU* 1.3 60.3 + - - +
2300B MET* 3.4 15.8 - - - +
2301B TYR* 3.7 17.0 + - - -
2407B PHE* 4.8 1.6 - - - -
2422B PHE* 4.3 1.2 - - - -
2426B PHE* 3.9 19.3 - - - -
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Residues in contact with LEU2298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2200B PHE* 3.8 26.9 - - + +
2203B GLN* 3.4 40.6 - - + +
2204B HIS* 3.9 13.4 - - + +
2291B VAL* 4.9 5.4 - - + +
2292B PHE* 3.6 42.4 - - + +
2295B VAL* 3.0 36.0 + - + +
2297B GLY* 1.3 72.4 - - - +
2299B MET* 1.3 61.1 + - - +
2300B MET 3.0 1.8 - - - -
2301B TYR* 3.1 6.5 + - - +
2302B ALA* 2.9 26.3 + - - +
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Residues in contact with MET2299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2262B TYR* 6.3 0.2 - - + -
2263B PRO* 4.4 3.6 - - - -
2285B PHE* 3.5 47.6 - - + -
2287B VAL* 4.0 19.7 - - + -
2292B PHE* 3.1 19.5 - - + +
2293B GLY* 3.1 37.2 - - - +
2295B VAL 2.9 14.8 + - - +
2296B PRO* 3.9 7.6 - - + +
2298B LEU* 1.3 76.8 - - - +
2300B MET* 1.3 57.8 + - - +
2302B ALA* 3.6 4.1 - - + +
2303B THR* 2.8 37.0 + - - +
2411B ASN* 4.7 5.4 - - + +
2414B LEU* 4.0 12.1 - - + -
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Residues in contact with MET2300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2197B MET* 4.2 10.1 - - - +
2296B PRO 3.1 17.8 + - - +
2297B GLY* 3.4 8.7 - - - +
2298B LEU 3.0 0.2 - - - -
2299B MET* 1.3 75.7 - - - +
2301B TYR* 1.3 72.3 + - - +
2303B THR 3.4 0.9 + - - -
2304B ILE* 3.0 35.2 + - + +
2414B LEU* 4.1 16.6 - - + -
2419B LEU* 3.6 21.2 - - + +
2422B PHE* 3.2 35.2 - - + +
2423B VAL* 3.3 35.0 - - + +
2426B PHE* 4.1 20.6 - - + -
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Residues in contact with TYR2301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2197B MET* 2.7 50.5 + - + +
2200B PHE* 3.6 21.3 - - + -
2201B PHE* 3.4 44.7 - + + +
2204B HIS* 3.6 28.5 - + + +
2297B GLY 3.7 14.9 + - - -
2298B LEU 3.1 3.4 + - - +
2300B MET* 1.3 84.9 - - - +
2302B ALA* 1.3 68.0 + - - +
2304B ILE* 3.0 18.4 + - + -
2305B TRP* 2.9 40.9 + + - -
2426B PHE* 6.0 0.2 - + - -
2564B ILE* 4.4 10.2 - - + +
2567B LEU* 5.1 1.6 - - + -
2568B ILE* 4.7 2.0 - - + -
2580B PHE* 4.2 4.0 - - - -
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Residues in contact with ALA2302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2204B HIS* 3.8 8.6 + - - -
2232B HIS 5.8 1.1 - - - +
2233B ILE* 5.7 3.7 - - - +
2263B PRO* 4.7 2.5 - - - +
2287B VAL* 3.9 29.1 - - + +
2292B PHE* 4.6 11.9 - - + -
2298B LEU 2.9 13.9 + - - +
2299B MET* 3.6 16.4 - - - +
2301B TYR* 1.3 78.1 - - - +
2303B THR* 1.3 56.9 + - - +
2305B TRP* 3.6 3.1 + - - +
2306B LEU* 3.0 29.9 + - - +
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Residues in contact with THR2303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2261B VAL* 3.3 26.7 - - + +
2262B TYR* 3.8 19.3 - - + -
2263B PRO* 3.3 22.3 - - - +
2299B MET* 2.8 22.8 + - - +
2300B MET* 3.6 5.8 - - - -
2302B ALA* 1.3 75.6 - - - +
2304B ILE* 1.3 59.2 + - - +
2306B LEU* 3.5 2.8 + - + +
2307B ARG* 3.0 50.7 + - - +
2414B LEU* 4.5 2.6 - - - +
2419B LEU* 4.3 11.4 - - + -
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Residues in contact with ILE2304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2197B MET* 5.3 0.2 - - + -
2300B MET* 3.0 36.1 + - + +
2301B TYR* 3.0 16.1 + - + +
2303B THR* 1.3 77.2 - - - +
2305B TRP* 1.3 59.1 + - + +
2307B ARG* 3.3 10.4 + - - +
2308B GLU* 2.9 25.1 + - - +
2419B LEU* 3.7 19.1 - - + -
2423B VAL* 4.8 2.2 - - + -
2567B LEU* 3.7 44.9 - - + +
2568B ILE* 4.2 17.0 - - + -
2571B ASN* 3.9 7.0 - - + +
2572B VAL* 4.1 20.9 - - + -
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Residues in contact with TRP2305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2201B PHE* 4.5 15.0 - + - -
2204B HIS* 3.4 32.9 + + + -
2230B LEU* 5.9 0.2 - - + -
2232B HIS* 5.5 0.8 + - - -
2233B ILE* 3.4 29.8 - - + +
2301B TYR* 2.9 30.1 + + + +
2302B ALA 4.2 1.6 - - - +
2304B ILE* 1.3 75.3 - - + +
2306B LEU* 1.3 66.6 + - - +
2308B GLU* 3.5 5.1 - - + +
2309B HIS* 2.9 23.9 + - - +
2336B LEU* 3.8 37.3 - - + +
2339B GLU* 4.2 7.4 - - + -
2340B THR* 3.4 42.0 - - + -
2343B ILE* 4.1 13.7 - - + -
2567B LEU* 3.8 41.6 - - + +
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Residues in contact with LEU2306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2233B ILE* 5.1 4.4 - - + +
2252B LEU* 4.3 26.4 - - + +
2253B LYS 3.7 13.5 - - - +
2254B TYR* 4.0 14.1 - - + -
2261B VAL* 4.2 10.5 - - + -
2262B TYR 4.4 0.4 - - - -
2263B PRO* 3.4 44.0 - - + -
2264B PRO* 4.3 2.0 - - + -
2287B VAL* 5.7 1.3 - - + -
2302B ALA 3.0 18.7 + - - +
2303B THR 3.7 5.6 - - - +
2305B TRP* 1.3 74.7 - - - +
2307B ARG* 1.3 64.9 + - - +
2309B HIS* 3.1 12.8 + - - +
2310B ASN* 3.3 32.1 + - - +
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Residues in contact with ARG2307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2260B GLU* 3.4 25.1 + - - +
2261B VAL* 2.5 63.5 + - + +
2262B TYR* 4.8 1.8 - - - -
2303B THR* 3.0 41.0 + - - +
2304B ILE* 3.3 6.8 - - - +
2306B LEU* 1.3 81.9 - - - +
2308B GLU* 1.3 61.4 + - - +
2309B HIS 3.3 0.5 + - - -
2310B ASN* 3.3 7.2 + - - +
2311B ARG* 3.0 21.3 + - - +
2419B LEU* 4.4 16.1 - - - +
2571B ASN* 3.0 42.5 + - + +
2572B VAL* 4.4 6.9 - - - +
2573B LYS* 4.5 4.4 - - - +
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Residues in contact with GLU2308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2304B ILE 2.9 13.7 + - - +
2305B TRP* 3.2 8.9 + - + +
2307B ARG* 1.3 76.1 - - - +
2309B HIS* 1.3 61.8 + - - +
2311B ARG* 2.5 38.7 + - - +
2312B VAL* 3.0 25.8 + - - +
2336B LEU* 4.0 12.3 - - + -
2339B GLU* 2.6 37.9 - - - +
2567B LEU* 3.9 19.7 - - + -
2570B ASN* 4.6 1.6 + - - +
2571B ASN* 3.0 29.3 + - - +
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Residues in contact with HIS2309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2233B ILE* 5.7 0.4 - - + -
2234B TYR* 2.8 36.9 + + + -
2250B GLY 2.8 23.2 + - - -
2251B LYS* 4.1 0.4 - - - -
2252B LEU* 3.8 24.8 - - + +
2305B TRP 2.9 12.9 + - - +
2306B LEU 3.1 9.8 + - - +
2308B GLU* 1.3 75.9 - - - +
2310B ASN* 1.3 67.9 + - - +
2312B VAL* 3.2 5.2 + - - +
2313B CYS* 2.9 38.3 + - - -
2329B PHE* 3.6 19.8 - + - -
2332B SER* 3.6 23.9 + - - -
2333B ARG 4.2 0.2 - - - -
2336B LEU* 3.9 13.6 - - + +
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Residues in contact with ASN2310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2251B LYS* 3.2 36.3 - - + +
2252B LEU* 3.2 12.4 + - - +
2254B TYR* 3.7 25.5 - - - -
2261B VAL* 5.0 4.0 - - - +
2306B LEU* 3.3 29.2 + - - +
2307B ARG* 3.6 8.8 - - - +
2309B HIS* 1.3 77.6 - - - +
2311B ARG* 1.3 66.1 + - - +
2313B CYS* 3.2 9.7 + - - +
2314B ASP* 2.9 29.2 + - - +
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Residues in contact with ARG2311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2307B ARG 3.0 14.5 + - - +
2308B GLU* 2.5 58.5 + - - +
2310B ASN* 1.3 75.6 - - - +
2312B VAL* 1.3 70.8 + - - +
2314B ASP* 3.0 12.6 + - - +
2315B ILE* 3.0 52.9 + - + +
2339B GLU* 4.6 0.8 + - - -
2558B ILE* 4.6 13.5 - - - +
2570B ASN* 3.7 43.6 + - - +
2571B ASN* 3.9 7.4 - - - +
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Residues in contact with VAL2312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2308B GLU* 3.0 35.0 + - - +
2309B HIS 3.6 4.3 - - - +
2311B ARG* 1.3 85.6 - - - +
2313B CYS* 1.3 57.6 + - - +
2315B ILE* 3.2 8.3 + - - +
2316B LEU* 2.9 31.4 + - + +
2332B SER* 3.6 22.0 - - - +
2335B ILE* 3.9 28.7 - - + -
2336B LEU* 3.8 13.9 - - + -
2339B GLU* 3.8 4.7 - - - +
2558B ILE* 4.2 13.5 - - + -
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Residues in contact with CYS2313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2249B ASP* 3.4 14.9 - - - +
2250B GLY* 3.2 36.8 - - - -
2251B LYS* 3.7 12.1 - - + -
2309B HIS* 2.9 27.1 + - - -
2310B ASN 3.3 9.2 - - - +
2311B ARG 3.1 0.4 - - - -
2312B VAL* 1.3 77.4 - - - +
2314B ASP* 1.3 56.5 + - - +
2316B LEU* 3.4 3.6 + - - +
2317B LYS* 2.9 31.2 + - - +
2328B LEU* 4.3 6.4 - - - +
2332B SER* 3.3 22.0 - - - -
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Residues in contact with ASP2314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2249B ASP* 5.4 1.2 - - - +
2251B LYS* 2.6 38.0 + - - -
2310B ASN* 2.9 13.1 + - - +
2311B ARG* 3.3 11.3 - - - +
2313B CYS* 1.3 76.5 - - - +
2315B ILE* 1.3 63.3 + - + +
2317B LYS* 3.4 10.3 + - - +
2318B GLN* 3.1 23.3 + - - +
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Residues in contact with ILE2315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2311B ARG* 3.0 56.8 + - + +
2312B VAL* 3.5 8.1 - - - +
2314B ASP* 1.3 78.8 - - + +
2316B LEU* 1.3 64.0 + - + +
2318B GLN* 3.3 15.1 + - - +
2319B GLU* 3.2 20.0 + - + +
2554B VAL* 3.6 29.8 - - + -
2558B ILE* 4.1 20.4 - - + -
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Residues in contact with LEU2316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2312B VAL* 2.9 24.6 + - + +
2313B CYS 3.9 3.1 - - - +
2315B ILE* 1.3 77.8 - - + +
2317B LYS* 1.3 56.7 + - - +
2319B GLU* 3.0 7.3 + - + +
2320B HIS* 2.7 43.6 + - + +
2323B TRP* 4.4 13.9 - - + -
2328B LEU* 4.0 14.4 - - + +
2331B THR* 3.8 28.3 - - + -
2332B SER* 3.6 25.8 - - - +
2335B ILE* 4.1 6.7 - - + -
2550B PHE 3.9 19.1 - - - +
2551B GLY* 4.4 7.0 - - - +
2554B VAL* 5.7 0.4 - - + -
2555B GLY* 4.7 8.3 - - - +
2558B ILE* 5.8 0.2 - - + -
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Residues in contact with LYS2317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2249B ASP* 2.9 38.8 + - + +
2313B CYS 2.9 18.6 + - - +
2314B ASP* 3.7 11.0 - - - +
2315B ILE 3.3 0.2 - - - -
2316B LEU* 1.3 76.4 - - - +
2318B GLN* 1.3 63.2 + - - +
2320B HIS 3.2 3.5 + - - -
2321B PRO* 3.1 38.8 + - + +
2323B TRP 4.6 9.1 + - - -
2328B LEU* 3.8 22.9 - - + +
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Residues in contact with GLN2318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2314B ASP 3.1 10.5 + - - +
2315B ILE* 3.3 16.9 - - - +
2317B LYS* 1.3 82.6 - - - +
2319B GLU* 1.3 69.0 + - - +
2321B PRO* 3.8 8.7 - - - +
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Residues in contact with GLU2319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A THR* 3.9 10.4 - - - +
2315B ILE* 3.2 13.7 + - + +
2316B LEU* 3.0 10.8 + - + +
2318B GLN* 1.3 88.0 - - - +
2320B HIS* 1.3 81.5 + - + +
2321B PRO* 3.4 6.7 - - - +
2322B GLU* 3.8 2.6 - - - +
2551B GLY 5.1 2.2 - - - +
2554B VAL* 3.4 42.2 - - + +
----------------------------------------------------------
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Residues in contact with HIS2320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A MET* 3.8 12.1 - - + -
49A SER 2.9 29.3 + - - -
50A THR* 4.4 3.4 - - + -
2316B LEU* 2.7 23.7 + - + +
2317B LYS* 3.2 10.9 + - - +
2319B GLU* 1.3 88.9 + - + +
2321B PRO* 1.3 57.0 - - - +
2322B GLU* 2.8 18.3 + - - +
2323B TRP* 2.9 77.9 + + + +
2328B LEU* 4.8 0.3 - - - +
2551B GLY* 2.7 28.5 + - - -
----------------------------------------------------------
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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