Contacts of the helix formed by residues 2309 - 2335 (chain B) in PDB entry 5WBY
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 SER2309 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391B ARG* 3.7 20.4 - - - -
2304B TRP* 5.5 1.1 - - - -
2307B SER* 3.2 8.0 - - - -
2308B PRO* 1.3 83.3 - - - +
2310B SER* 1.3 61.3 + - - +
2311B GLU* 2.9 32.1 + - - -
2312B VAL* 3.2 15.2 - - - +
2313B TRP* 3.0 27.6 + - - +
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Residues in contact with SER2310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1391B ARG* 2.8 34.4 + - - +
1394B ALA* 3.6 5.3 - - - +
1395B LYS* 3.4 34.9 - - - +
2304B TRP* 4.5 13.2 - - - -
2309B SER* 1.3 73.7 - - - +
2311B GLU* 1.3 61.4 + - - +
2313B TRP* 3.4 11.6 + - - +
2314B PHE* 3.0 28.2 + - - +
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Residues in contact with GLU2311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1387B ALA 5.5 2.9 - - - +
1390B CYS* 4.5 22.9 - - - -
1391B ARG* 3.3 41.0 + - - +
1394B ALA* 4.3 7.4 - - + -
2309B SER* 2.9 25.8 + - - -
2310B SER* 1.3 78.2 + - - +
2312B VAL* 1.3 73.2 + - + +
2314B PHE* 3.6 2.6 + - - +
2315B ASP* 3.2 36.4 + - - +
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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 PRO* 4.0 17.0 - - + -
2309B SER* 3.2 23.7 + - - +
2310B SER 3.3 0.2 - - - -
2311B GLU* 1.3 85.6 - - + +
2313B TRP* 1.3 65.4 + - - +
2315B ASP* 3.7 4.1 + - - +
2316B ARG* 3.2 58.7 + - + +
2349B LEU 5.1 0.9 - - - +
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Residues in contact with TRP2313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394B ALA 3.9 19.5 - - - -
1397B LEU* 4.9 2.2 - - + -
1398B HIS* 3.8 31.0 - + + -
1401B GLU* 4.0 7.2 - - - -
2300B ALA 5.0 3.6 + - - -
2303B LEU* 3.6 27.5 - - + +
2304B TRP* 3.6 36.4 - + + +
2307B SER* 3.6 15.8 - - - +
2309B SER 3.0 18.3 + - - +
2310B SER* 3.5 12.6 - - - +
2311B GLU 3.3 0.2 - - - -
2312B VAL* 1.3 77.9 - - - +
2314B PHE* 1.3 86.5 + + + +
2316B ARG* 3.5 5.9 + - + +
2317B ARG* 3.1 66.6 + - + +
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Residues in contact with PHE2314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1394B ALA* 4.6 5.6 - - + -
1397B LEU* 3.5 33.4 - - + -
1420B ASN* 4.1 5.8 - - - -
1423B LEU* 4.1 21.8 - - + -
1425B GLN* 3.6 39.9 - - + -
1428B ALA* 5.4 2.2 - - + -
2310B SER 3.0 16.6 + - - +
2311B GLU* 3.9 6.7 - - - +
2312B VAL 3.4 0.2 - - - -
2313B TRP* 1.3 89.3 - + + +
2315B ASP* 1.3 65.3 + - - +
2317B ARG* 3.2 25.5 + - - +
2318B THR* 2.8 49.7 + - - -
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Residues in contact with ASP2315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2311B GLU* 3.2 23.0 + - - +
2312B VAL* 4.2 4.5 - - - +
2314B PHE* 1.3 86.4 - - - +
2316B ARG* 1.3 61.3 + - - +
2318B THR* 3.2 7.5 + - - -
2319B ASN* 2.9 40.7 + - - +
2350B SER 4.9 0.2 - - - -
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Residues in contact with ARG2316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2303B LEU* 5.5 8.9 + - + -
2306B LYS* 4.1 9.7 + - - +
2307B SER* 3.6 30.0 - - - +
2308B PRO* 3.8 9.7 - - - +
2312B VAL* 3.2 38.0 + - + +
2313B TRP* 3.6 8.3 - - + +
2315B ASP* 1.3 77.5 - - - +
2317B ARG* 1.3 57.6 + - - +
2319B ASN* 3.6 0.5 + - - +
2320B TYR* 2.9 29.0 + - - +
2348B ARG 3.2 23.8 + - - -
2349B LEU* 2.7 47.7 + - - +
2350B SER 3.6 15.7 - - - +
2351B GLY* 3.5 13.3 - - - +
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Residues in contact with ARG2317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1397B LEU* 4.3 2.2 - - - +
1401B GLU* 2.7 41.8 + - - -
1420B ASN* 5.6 0.6 - - - +
2303B LEU* 6.1 4.0 - - + -
2313B TRP* 3.1 52.5 + - + +
2314B PHE* 3.5 32.8 - - - +
2315B ASP 3.2 0.2 - - - -
2316B ARG* 1.3 75.0 - - - +
2318B THR* 1.3 60.4 + - - +
2320B TYR* 3.4 8.2 - - + +
2321B THR* 2.9 35.5 + - - +
2386B ALA 3.2 27.1 - - - +
2387B MET* 4.0 9.6 + - - -
2388B GLU* 3.3 28.6 + - - +
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Residues in contact with THR2318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1425B GLN* 4.1 15.8 + - - +
2314B PHE* 2.8 36.6 + - - -
2315B ASP* 3.2 9.4 + - - -
2317B ARG* 1.3 77.9 - - - +
2319B ASN* 1.3 65.1 + - - +
2321B THR* 3.9 4.6 - - - -
2322B ARG* 3.2 62.4 + - - +
2388B GLU* 6.2 0.2 - - - -
2395B ASN* 4.6 10.7 - - - +
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Residues in contact with ASN2319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2219B ASN* 6.1 1.7 - - - +
2315B ASP* 2.9 23.2 + - - +
2316B ARG 3.7 0.2 - - - +
2318B THR* 1.3 77.5 - - - +
2320B TYR* 1.3 56.9 + - - +
2322B ARG* 3.9 6.9 + - - +
2323B SER* 2.9 35.3 + - - -
2350B SER* 3.4 29.3 + - - +
2351B GLY 4.3 0.7 - - - -
2352B LYS* 3.2 35.9 - - + +
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Residues in contact with TYR2320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2299B LEU* 3.9 4.4 - - + +
2303B LEU* 5.2 10.3 - - + -
2316B ARG 2.9 19.7 + - - +
2317B ARG* 3.4 8.7 - - + +
2318B THR 3.2 0.2 - - - -
2319B ASN* 1.3 73.2 - - - +
2321B THR* 1.3 82.7 + - - +
2323B SER* 3.1 4.0 + - - -
2324B LEU* 3.0 34.6 + - + +
2346B LEU* 3.5 33.0 - - + -
2351B GLY 3.3 13.4 + - - +
2353B ILE* 4.1 15.5 - - + -
2383B LEU* 2.9 54.7 + - + +
2386B ALA* 3.8 25.5 - - + +
2387B MET* 3.9 13.5 - - + -
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Residues in contact with THR2321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2317B ARG* 2.9 20.8 + - - +
2318B THR* 3.9 4.7 - - - -
2320B TYR* 1.3 80.4 - - - +
2322B ARG* 1.3 60.4 - - - +
2324B LEU* 3.9 3.8 - - - +
2325B ALA* 3.2 21.8 + - - +
2387B MET* 3.3 37.2 - - + +
2388B GLU* 4.1 9.5 + - - +
2391B GLY 5.0 0.4 - - - +
2395B ASN* 3.6 15.7 - - + -
2396B TYR* 3.5 34.6 - - + +
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Residues in contact with ARG2322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1425B GLN* 3.2 25.9 + - - +
1427B GLU* 3.3 25.5 + - - -
2218B LYS* 3.6 42.0 + - - +
2220B LEU* 3.8 17.7 - - + -
2318B THR* 3.2 33.6 + - - +
2319B ASN* 3.9 6.1 + - - +
2321B THR* 1.3 79.4 - - - +
2323B SER* 1.3 59.2 + - - +
2325B ALA* 3.0 5.7 + - - +
2326B VAL* 2.9 31.9 + - - +
2395B ASN* 3.5 14.3 + - + +
2399B THR* 3.5 22.6 - - - +
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Residues in contact with SER2323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2221B SER 4.7 11.4 - - - +
2223B GLN* 5.7 0.4 - - - -
2319B ASN 2.9 21.4 + - - -
2320B TYR* 3.1 5.7 + - - -
2322B ARG* 1.3 76.2 - - - +
2324B LEU* 1.3 62.9 + - - +
2326B VAL* 3.5 10.6 + - - +
2327B MET* 3.4 19.8 + - - +
2352B LYS* 3.5 14.3 - - - -
2353B ILE* 3.0 43.9 + - - +
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Residues in contact with LEU2324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2320B TYR* 3.0 42.0 + - + +
2321B THR 3.9 2.0 - - - +
2323B SER* 1.3 79.0 + - - +
2325B ALA* 1.3 52.7 + - - +
2327B MET* 3.4 4.4 + - - +
2328B SER* 2.7 36.5 + - - +
2344B LEU* 5.2 5.8 - - + -
2353B ILE* 3.4 32.8 - - + -
2355B HIS* 5.2 5.8 + - + +
2378B ARG 4.5 7.2 - - - +
2379B LEU* 4.7 5.6 - - + -
2383B LEU* 4.0 27.6 - - + -
2387B MET* 4.4 13.0 - - + -
2396B TYR* 4.1 18.4 - - + -
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Residues in contact with ALA2325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2321B THR 3.2 11.7 + - - +
2322B ARG 3.0 8.6 + - - +
2324B LEU* 1.3 77.2 - - - +
2326B VAL* 1.3 67.3 + - - +
2328B SER* 3.3 4.4 + - - -
2329B MET* 3.2 27.4 + - - +
2396B TYR* 3.6 42.4 - - + +
2399B THR* 3.9 13.0 - - + -
2400B CYS* 3.7 5.6 - - - +
2403B VAL* 5.2 0.7 - - - -
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Residues in contact with VAL2326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2209B LEU* 4.2 16.8 - - + -
2220B LEU* 4.1 20.6 - - + -
2221B SER 4.2 11.0 - - - +
2222B ILE* 3.8 27.1 - - + -
2322B ARG 2.9 21.9 + - - +
2323B SER* 3.6 11.4 - - - +
2325B ALA* 1.3 78.2 - - - +
2327B MET* 1.3 58.9 + - + +
2329B MET* 3.4 1.9 + - - +
2330B VAL* 3.0 36.5 + - + +
2399B THR* 4.2 3.8 - - + +
2403B VAL* 3.8 25.9 - - + +
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Residues in contact with MET2327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2202B PHE* 3.6 25.8 - - + -
2222B ILE* 3.7 37.9 - - + -
2323B SER 3.4 11.1 + - - +
2324B LEU 3.4 3.6 + - - +
2325B ALA 3.3 0.4 - - - -
2326B VAL* 1.3 76.8 - - + +
2328B SER* 1.3 60.0 + - - +
2329B MET 3.4 0.2 - - - -
2330B VAL* 3.9 17.5 - - - -
2331B GLY* 3.0 32.8 + - - +
2336B LEU* 3.9 22.2 - - + -
2353B ILE* 5.1 2.7 - - + -
2355B HIS* 3.5 43.7 + - + +
2377B PHE* 5.0 1.9 - - - +
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Residues in contact with SER2328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2324B LEU* 2.7 27.2 + - - +
2325B ALA* 3.4 9.2 - - - -
2327B MET* 1.3 77.0 - - - +
2329B MET* 1.3 65.6 + - - +
2332B TYR* 3.1 21.8 + - - +
2377B PHE* 3.3 38.1 - - - +
2378B ARG 5.1 1.7 + - - -
2396B TYR* 2.8 29.9 + - - -
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Residues in contact with MET2329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2325B ALA 3.2 14.6 + - - +
2326B VAL 3.9 2.5 - - - +
2328B SER* 1.3 78.3 - - - +
2330B VAL* 1.3 65.4 + - - +
2332B TYR* 3.3 4.9 + - - +
2333B ILE* 3.3 28.0 + - - +
2377B PHE* 3.6 34.3 - - + -
2400B CYS* 3.6 50.9 - - + +
2403B VAL* 4.0 15.3 - - + -
2404B MET* 3.6 28.6 - - + +
2407B LEU* 4.6 2.0 - - + -
2525B VAL* 4.0 13.5 - - + -
2528B LEU* 4.2 10.1 - - + -
2529B ILE* 5.7 0.4 - - + -
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Residues in contact with VAL2330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2201B LEU* 5.3 5.9 - - + +
2202B PHE* 3.9 28.5 - - + -
2205B VAL* 3.8 31.9 - - + -
2222B ILE* 3.9 15.5 - - + -
2326B VAL* 3.0 23.3 + - + +
2327B MET* 3.9 7.0 - - - -
2329B MET* 1.3 75.2 - - - +
2331B GLY* 1.3 63.6 + - - +
2333B ILE* 3.2 7.8 + - - +
2334B LEU* 3.1 20.0 + - + +
2403B VAL* 4.1 5.6 - - + -
2407B LEU* 4.0 20.2 - - + -
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Residues in contact with GLY2331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2327B MET* 3.0 30.0 + - - +
2330B VAL* 1.3 78.7 - - - +
2332B TYR* 1.3 48.9 + - - +
2334B LEU* 3.3 4.2 + - - -
2335B GLY 2.7 30.5 + - - -
2336B LEU* 2.8 29.3 + - - -
2376B PRO 4.8 3.6 - - - -
2377B PHE* 5.9 1.1 - - - -
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Residues in contact with TYR2332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2328B SER 3.1 20.1 + - - +
2329B MET* 3.5 6.1 - - - +
2330B VAL 3.2 0.2 - - - -
2331B GLY* 1.3 75.8 - - - +
2333B ILE* 1.3 55.0 + - + +
2335B GLY* 3.1 6.3 + - - -
2363B GLU* 5.6 0.9 - - - -
2376B PRO* 3.6 30.9 + - + -
2377B PHE* 4.2 8.3 - - + -
2404B MET* 4.3 11.0 - - + -
2503B ARG* 3.9 10.4 + - - -
2507B LYS* 2.7 64.7 + - + +
2512B ASP* 2.6 43.0 + - - +
2513B PHE* 4.3 2.8 - - - -
2524B GLN* 4.1 3.6 - - - -
2528B LEU* 3.5 38.1 - - + +
2531B GLN* 5.3 2.9 - - - -
----------------------------------------------------------
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Residues in contact with ILE2333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2201B LEU* 6.4 1.1 - - + -
2329B MET 3.3 11.2 + - - +
2330B VAL* 3.2 7.2 + - - +
2332B TYR* 1.3 76.7 - - + +
2334B LEU* 1.3 61.2 - - - +
2335B GLY 3.2 0.9 + - - -
2362B PHE* 5.2 0.2 - - - -
2404B MET* 4.1 15.9 - - + -
2407B LEU* 3.5 39.0 - - + -
2414B VAL* 4.3 6.7 - - + -
2418B LEU* 4.2 11.2 - - + +
2504B VAL* 3.9 37.1 - - + +
2507B LYS* 3.7 26.4 + - + +
2508B LEU* 3.8 33.2 - - + -
----------------------------------------------------------
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Residues in contact with LEU2334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2198B VAL* 3.7 35.4 - - + -
2201B LEU* 4.0 15.0 - - + +
2202B PHE* 4.2 15.9 - - + -
2330B VAL 3.1 10.4 + - - +
2331B GLY* 3.6 8.3 - - - +
2333B ILE* 1.3 78.4 - - - +
2335B GLY* 1.3 49.7 + - - +
2336B LEU* 4.3 15.7 - - + +
2358B PHE* 4.7 0.2 - - + -
2361B CYS* 3.9 29.2 - - + -
2362B PHE* 2.7 38.1 + - + -
2418B LEU* 3.8 28.3 - - + -
2421B PHE* 4.5 5.8 - - + -
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Residues in contact with GLY2335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2331B GLY 2.7 8.5 + - - -
2332B TYR* 3.1 14.8 + - - -
2333B ILE 3.1 0.2 - - - -
2334B LEU* 1.3 75.7 - - - +
2336B LEU* 1.3 65.1 + - - +
2337B GLY* 3.0 5.0 + - - -
2360B ASP 3.8 0.2 - - - +
2362B PHE* 2.7 33.5 + - - +
2363B GLU* 4.0 5.3 - - - +
2365B ALA* 5.5 0.5 - - - +
2366B MET* 6.0 2.1 - - - +
2376B PRO 5.6 1.3 - - - -
2507B LYS* 3.9 9.4 - - - -
----------------------------------------------------------
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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).
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