Contacts of the helix formed by residues 262 - 297 (chain O) in PDB entry 1KYO
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 GLU 262 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69N MET* 5.0 9.9 - - - +
76N TYR* 3.7 48.3 - - + +
80N TYR* 4.1 15.6 + - - -
182O LYS* 5.3 0.7 + - - -
259O ALA 4.7 0.7 - - - +
260O GLU* 3.4 20.7 - - - +
261O PRO* 1.3 81.2 - - - +
263O HIS* 1.3 68.4 + - - +
264O ASP 3.5 0.2 - - - -
265O GLU* 2.9 21.4 + - + +
266O ARG* 3.0 47.9 + - + +
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Residues in contact with HIS 263 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78O HIS* 3.7 12.5 + - + +
83O GLU 3.4 13.7 - - - -
85O PHE* 3.4 45.1 + + + -
256O ASN* 5.0 0.4 - - - -
260O GLU* 2.9 25.4 + - + +
261O PRO 4.7 1.3 - - - +
262O GLU* 1.3 77.1 - - - +
264O ASP* 1.3 84.2 + - - +
266O ARG* 3.1 25.7 + - - +
267O LYS* 3.0 62.6 + - + +
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Residues in contact with ASP 264 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84O THR* 3.5 22.3 - - + +
85O PHE* 2.9 29.4 + - - +
87O HIS* 2.7 33.8 + - - -
261O PRO 4.8 1.7 + - - +
262O GLU 3.1 2.6 + - - -
263O HIS* 1.3 88.2 + - - +
265O GLU* 1.3 57.2 - - - +
268O ARG 3.1 14.6 + - - -
40T TYR* 3.1 29.3 + - + -
48T LEU* 5.5 1.6 - - - +
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Residues in contact with GLU 265 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76N TYR* 4.2 6.7 - - + +
262O GLU* 2.9 11.0 + - + +
264O ASP* 1.3 76.2 - - - +
266O ARG* 1.3 66.4 + - - +
268O ARG* 2.5 40.6 + - - +
269O LEU* 2.9 54.7 + - + +
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Residues in contact with ARG 266 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76N TYR* 3.7 34.2 + - + -
80N TYR* 4.4 5.7 - - - -
244N VAL 4.1 13.2 - - - -
245N PHE* 2.7 56.7 + - + +
246N TYR* 4.4 5.1 + - - +
248N PRO* 3.6 20.3 - - - +
260O GLU* 3.1 29.3 + - - -
262O GLU* 3.0 39.9 + - + +
263O HIS* 3.5 26.5 - - - +
265O GLU* 1.3 76.5 - - - +
267O LYS* 1.3 67.1 + - - +
269O LEU* 3.3 0.6 + - - -
270O GLY* 2.9 23.6 + - - -
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Residues in contact with LYS 267 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245N PHE 4.8 5.2 - - - +
246N TYR* 3.4 31.2 + - + +
78O HIS 2.6 31.1 + - - -
80O GLY 2.9 30.5 + - - +
81O PRO* 4.2 11.6 - - - +
83O GLU 3.0 19.4 + - - +
263O HIS* 3.0 30.9 + - + +
264O ASP 3.5 3.1 - - - +
266O ARG* 1.3 84.3 - - - +
268O ARG* 1.3 61.9 + - - +
270O GLY 3.4 0.4 + - - +
271O LEU* 3.3 18.0 + - - +
40T TYR* 3.3 18.8 - - + +
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Residues in contact with ARG 268 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264O ASP 3.1 7.6 + - - +
265O GLU* 2.5 56.4 + - - +
267O LYS* 1.3 77.2 - - - +
269O LEU* 1.3 79.2 + - - +
271O LEU* 3.4 12.1 + - - +
272O LYS* 3.5 19.7 + - - +
33T ASP* 3.2 24.7 + - - -
36T ILE* 4.5 7.4 - - + -
37T THR* 3.2 37.7 + - - +
40T TYR* 3.8 41.5 + - + -
41T GLU* 6.3 0.2 - - - -
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Residues in contact with LEU 269 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74N ASN* 4.9 7.4 - - - +
76N TYR* 3.4 22.9 - - - +
77N ILE* 4.2 15.3 - - + -
245N PHE* 3.9 11.9 - - + -
265O GLU* 2.9 40.3 + - + +
266O ARG 3.8 3.6 - - - +
268O ARG* 1.3 93.1 - - - +
270O GLY* 1.3 58.4 + - - +
272O LYS* 3.4 15.5 + - + +
273O THR* 2.7 33.6 + - - -
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Residues in contact with GLY 270 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245N PHE* 3.6 31.4 - - - -
246N TYR* 3.1 13.2 - - - -
266O ARG 2.9 11.5 + - - -
267O LYS 3.4 1.3 + - - -
268O ARG 3.2 0.8 - - - -
269O LEU* 1.3 75.6 - - - +
271O LEU* 1.3 63.7 + - - +
273O THR* 3.2 1.9 + - - -
274O VAL* 2.9 30.0 + - - +
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Residues in contact with LEU 271 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246N TYR* 2.9 16.7 + - - +
81O PRO 5.9 0.2 - - - +
82O PHE* 3.4 30.5 - - + -
267O LYS 3.3 6.5 + - - +
268O ARG* 3.6 9.4 - - - +
269O LEU 3.3 0.4 - - - -
270O GLY* 1.3 77.4 - - - +
272O LYS* 1.3 62.8 + - - +
274O VAL* 4.1 3.0 - - + +
275O ILE* 3.1 45.9 + - + +
36T ILE* 3.4 28.9 - - + -
39T TRP* 3.9 29.8 - - + -
40T TYR* 4.7 8.5 - - + -
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Residues in contact with LYS 272 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268O ARG* 3.6 26.4 - - - +
269O LEU* 3.4 17.1 + - + +
270O GLY 3.4 0.4 - - - -
271O LEU* 1.3 76.4 - - - +
273O THR* 1.3 61.5 + - - +
275O ILE 3.9 0.2 + - - -
276O ILE* 3.2 35.7 + - + +
73P SER* 5.9 0.6 + - - -
29T GLN* 4.9 6.4 + - - +
32T PHE* 3.8 35.7 - - + -
33T ASP* 2.8 40.3 + - - +
36T ILE* 3.9 18.6 - - + -
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Residues in contact with THR 273 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241N ALA* 3.7 15.7 - - + -
245N PHE* 3.7 24.5 - - + -
269O LEU 2.7 22.3 + - - -
270O GLY* 3.6 4.9 - - - -
271O LEU 3.1 0.2 - - - -
272O LYS* 1.3 75.7 - - - +
274O VAL* 1.3 62.2 + - - +
276O ILE* 3.4 3.1 + - - +
277O LEU* 2.8 57.3 + - + +
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Residues in contact with VAL 274 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238N LEU* 3.8 16.8 - - + +
241N ALA* 5.0 9.9 - - + +
242N LEU* 3.6 33.0 - - + -
245N PHE* 6.2 0.2 - - + -
246N TYR* 3.8 13.7 - - + +
270O GLY* 2.9 16.9 + - - +
271O LEU* 4.2 4.9 - - + +
273O THR* 1.3 73.5 - - - +
275O ILE* 1.3 55.3 + - + +
278O SER* 2.6 51.8 + - - +
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Residues in contact with ILE 275 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271O LEU* 3.1 34.0 + - + +
274O VAL* 1.3 79.6 - - + +
276O ILE* 1.3 53.7 + - - +
278O SER* 3.6 5.5 - - - -
279O SER* 2.6 43.7 + - - +
32T PHE* 4.1 21.5 - - + -
36T ILE* 3.6 30.3 - - + -
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Residues in contact with ILE 276 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272O LYS* 3.2 23.1 + - + +
273O THR* 3.4 3.4 + - - +
275O ILE* 1.3 75.0 - - + +
277O LEU* 1.3 61.4 + - + +
279O SER* 3.3 5.8 + - - -
280O LEU* 2.9 52.9 + - + +
66P LEU* 4.4 20.0 - - + +
69P ALA* 5.7 3.6 - - + -
70P GLY* 5.2 11.9 - - - +
28T PHE* 4.0 22.2 - - + -
32T PHE* 3.5 28.0 - - + -
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Residues in contact with LEU 277 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234N PHE* 4.4 21.5 - - + +
237N MET* 3.7 50.0 - - + +
238N LEU* 3.7 20.0 - - + +
241N ALA* 3.8 6.1 - - + -
273O THR* 2.8 40.6 + - + +
276O ILE* 1.3 79.8 - - + +
278O SER* 1.3 62.4 + - - +
280O LEU* 3.5 6.7 + - + +
281O TYR* 3.1 24.1 + - - +
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Residues in contact with SER 278 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238N LEU* 3.4 18.8 - - - +
274O VAL* 2.6 35.9 + - - +
275O ILE* 3.6 6.3 - - - -
277O LEU* 1.3 74.4 - - - +
279O SER* 1.3 61.1 + - - +
281O TYR* 3.6 7.8 + - - +
282O LEU* 3.3 31.6 + - - +
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Residues in contact with SER 279 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275O ILE* 2.6 29.1 + - - +
276O ILE* 3.6 5.1 - - - -
278O SER* 1.3 74.3 - - - +
280O LEU* 1.3 67.0 + - - +
281O TYR 3.0 1.9 + - - -
282O LEU* 3.1 7.2 + - - +
283O LEU* 2.8 30.4 + - - +
66P LEU* 3.6 21.9 - - - +
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Residues in contact with LEU 280 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234N PHE* 3.7 35.1 - - + -
276O ILE* 2.9 48.3 + - + +
277O LEU* 3.8 8.7 - - + +
279O SER* 1.3 73.8 - - - +
281O TYR* 1.3 58.2 + - - +
283O LEU* 3.7 4.1 - - + +
284O SER* 2.9 31.7 + - - -
63P MET* 3.7 28.8 - - + +
66P LEU* 3.6 24.4 - - + +
67P SER* 3.3 25.1 - - - +
70P GLY* 6.3 0.4 - - - -
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Residues in contact with TYR 281 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231N VAL* 3.7 32.6 - - + +
234N PHE* 4.0 9.6 - - + +
235N LEU* 3.6 51.7 - - + +
238N LEU* 5.4 7.0 - - + -
277O LEU 3.1 17.8 + - - +
278O SER* 3.7 9.4 - - - +
279O SER 3.0 0.8 - - - -
280O LEU* 1.3 75.5 - - - +
282O LEU* 1.3 75.9 + - + +
284O SER* 2.6 22.9 + - - -
285O ILE* 3.4 26.3 + - + +
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Residues in contact with LEU 282 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278O SER* 3.3 16.3 + - - +
279O SER* 3.1 8.7 + - - +
281O TYR* 1.3 89.7 - - + +
283O LEU* 1.3 67.0 + - + +
285O ILE* 3.2 24.9 + - + +
286O TRP* 3.4 10.7 + - - +
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Residues in contact with LEU 283 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279O SER* 2.8 19.4 + - - +
280O LEU* 3.7 5.6 - - - +
282O LEU* 1.3 79.0 - - + +
284O SER* 1.3 63.2 + - - +
286O TRP* 3.1 15.7 + - - +
287O VAL* 3.2 17.2 + - - +
58P PHE* 5.6 1.1 - - + -
59P MET* 3.9 39.2 - - + +
62P ALA* 3.5 18.2 - - + +
63P MET* 3.3 38.1 - - + +
66P LEU* 4.6 12.6 - - + -
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Residues in contact with SER 284 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227N PHE* 5.1 3.3 - - - +
230N LEU* 4.7 3.6 - - - -
231N VAL* 3.7 27.3 - - - +
234N PHE* 3.7 21.6 - - - -
280O LEU 2.9 16.1 + - - -
281O TYR* 2.6 25.8 + - - -
283O LEU* 1.3 75.5 - - - +
285O ILE* 1.3 56.9 + - - +
287O VAL* 3.3 3.3 + - - +
288O LYS* 2.9 29.8 + - - +
63P MET* 3.9 14.1 - - - -
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Residues in contact with ILE 285 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N TYR* 6.2 0.4 - - - +
231N VAL* 4.1 17.0 - - + -
281O TYR* 3.4 47.8 - - + +
282O LEU* 3.4 18.2 - - + +
283O LEU 3.1 0.8 + - - -
284O SER* 1.3 78.9 + - - +
286O TRP* 1.3 65.3 + - - +
288O LYS* 3.1 4.5 + - + +
289O LYS* 2.9 45.8 + - + +
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Residues in contact with TRP 286 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282O LEU 3.4 6.5 + - - +
283O LEU* 3.1 9.9 + - - +
285O ILE* 1.3 79.3 - - - +
287O VAL* 1.3 59.6 + - + +
289O LYS* 4.6 2.7 - - - -
290O PHE* 2.9 50.2 + + + -
52P GLY* 4.4 2.2 - - - -
55P TYR* 3.8 23.8 - + + -
56P ALA* 3.4 37.7 - - + -
59P MET* 3.3 40.0 - - + -
60P VAL* 6.4 0.2 - - + -
36S PRO* 4.1 17.6 + - + -
37S LEU* 3.0 46.3 + - + +
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Residues in contact with VAL 287 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227N PHE* 3.8 29.8 - - + -
283O LEU 3.2 15.5 + - - +
284O SER 3.6 6.1 - - - +
285O ILE 3.2 0.4 - - - -
286O TRP* 1.3 75.3 - - + +
288O LYS* 1.3 65.7 + - - +
290O PHE* 3.2 7.7 + - + +
291O LYS* 2.9 36.7 + - - +
59P MET* 4.0 24.2 - - + -
60P VAL* 4.2 20.0 - - + +
63P MET* 4.1 22.0 - - + -
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Residues in contact with LYS 288 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N TYR* 3.8 23.2 + - - +
227N PHE* 4.3 13.2 - - - +
228N LYS* 4.0 35.0 - - - +
231N VAL* 4.0 11.7 - - + -
284O SER 2.9 13.8 + - - +
285O ILE* 3.5 8.3 - - + +
287O VAL* 1.3 74.2 - - - +
289O LYS* 1.3 70.6 + - + +
291O LYS* 3.2 2.8 + - - -
292O TRP* 2.8 67.5 + - + +
296O LYS* 3.7 30.7 - - - +
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Residues in contact with LYS 289 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285O ILE* 2.9 34.9 + - + +
286O TRP* 3.6 3.1 - - - +
288O LYS* 1.3 85.7 - - + +
290O PHE* 1.3 55.8 + - - +
292O TRP* 3.5 3.9 - - - +
293O ALA* 2.7 37.2 + - - +
37S LEU* 3.4 31.0 - - + +
40S ILE* 3.0 40.8 - - + +
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Residues in contact with PHE 290 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445L MET* 3.8 19.5 - - + -
286O TRP* 2.9 38.7 + + + +
287O VAL* 3.2 9.8 + - + +
289O LYS* 1.3 78.6 - - - +
291O LYS* 1.3 76.7 + - + +
293O ALA* 3.4 3.2 + - + +
52P GLY* 4.0 8.7 - - - -
56P ALA* 3.5 31.2 - - + -
57P TYR* 5.5 1.8 - + - -
60P VAL* 5.8 6.1 - - + -
31S PRO* 3.2 52.6 - - + +
32S TYR* 4.0 35.2 - + - -
37S LEU* 3.3 11.0 - - + +
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Residues in contact with LYS 291 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445L MET* 4.1 29.9 - - + +
449L SER* 5.9 0.8 + - - -
223N SER* 4.4 20.0 + - - +
224N TYR* 3.4 21.1 + - + -
227N PHE* 3.6 52.3 - - + -
287O VAL* 2.9 28.0 + - - +
288O LYS* 3.8 4.9 - - - +
290O PHE* 1.3 88.3 - - + +
292O TRP* 1.3 64.4 + - + +
293O ALA 3.4 0.4 + - - -
294O GLY* 4.5 2.5 + - - -
60P VAL* 5.4 8.7 - - - +
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Residues in contact with TRP 292 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N SER 3.9 15.5 - - - -
219N ILE* 3.7 22.4 - - + -
224N TYR* 2.8 48.4 + + + -
225N PHE* 3.9 29.2 - + - -
227N PHE* 5.8 0.9 - - + -
228N LYS* 4.2 13.2 - - + +
288O LYS* 2.8 59.4 + - + +
289O LYS* 3.1 4.2 + - - +
291O LYS* 1.3 77.6 - - + +
293O ALA* 1.3 63.8 + - - +
294O GLY 3.1 3.6 - - - -
295O ILE* 3.0 33.7 + - + +
296O LYS* 3.0 37.0 + - + +
83R LEU* 4.7 7.6 - - + -
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Residues in contact with ALA 293 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289O LYS 2.7 15.1 + - - +
290O PHE* 3.4 17.4 + - + +
292O TRP* 1.3 72.4 - - - +
294O GLY* 1.3 62.4 + - - +
296O LYS* 4.7 5.2 - - - -
297O THR* 3.2 28.7 + - - +
31S PRO* 3.9 13.2 - - + +
34S GLN* 3.4 23.3 + - + +
37S LEU* 4.6 12.6 - - + -
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Residues in contact with GLY 294 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444L TYR* 6.2 3.6 - - - -
445L MET* 5.7 2.5 - - - -
224N TYR* 6.0 0.9 - - - -
291O LYS 4.5 2.3 + - - -
292O TRP 3.0 1.4 + - - -
293O ALA* 1.3 79.8 - - - +
295O ILE* 1.3 65.0 + - - +
297O THR* 3.8 9.0 + - - -
298O ARG* 3.8 5.9 + - - -
28S ALA* 4.0 17.2 - - - +
29S VAL 3.8 20.3 - - - +
31S PRO* 3.5 16.6 - - - +
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Residues in contact with ILE 295 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443L ASP* 4.9 7.2 - - + -
24N SER* 5.1 0.4 - - - -
219N ILE* 4.3 20.9 - - + -
224N TYR* 3.8 35.2 - - + +
291O LYS 5.4 0.2 + - - -
292O TRP* 3.0 21.5 + - + +
294O GLY* 1.3 76.3 - - - +
296O LYS* 1.3 65.4 + - - +
298O ARG* 3.0 58.3 - - - +
80R GLN* 3.2 6.8 + - - -
83R LEU* 3.9 24.5 - - + -
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Residues in contact with LYS 296 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288O LYS* 3.7 26.1 - - - +
292O TRP* 3.0 36.6 + - + +
293O ALA* 4.4 5.4 - - - +
294O GLY 3.5 0.2 - - - -
295O ILE* 1.3 75.3 - - - +
297O THR* 1.3 62.2 + - + +
298O ARG 3.4 1.4 - - - +
80R GLN* 3.8 1.7 + - - -
83R LEU* 3.1 40.6 + - + +
84R THR* 3.5 28.8 + - - +
85R HIS* 4.1 15.6 + - - -
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Residues in contact with THR 297 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293O ALA* 3.2 20.2 + - - +
294O GLY 3.8 4.3 + - - -
295O ILE 3.2 0.4 - - - -
296O LYS* 1.3 82.6 - - + +
298O ARG* 1.3 67.5 + - - +
299O LYS* 3.9 9.0 - - - +
39P PHE* 3.4 24.1 - - - -
41P ASP* 6.1 0.2 - - - -
42P VAL* 4.0 29.9 - - + +
28S ALA* 5.7 0.4 - - - -
29S VAL* 4.9 4.7 + - - +
34S GLN* 3.6 24.5 + - - +
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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) + - + + + + + -
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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