Contacts of the helix formed by residues 276 - 299 (chain C) in PDB entry 3P3W
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 LYS 276 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASN* 4.9 16.0 + - - +
17C VAL 6.0 0.8 - - - +
18C GLN* 4.2 23.1 - - + +
19C GLU* 4.2 9.6 + - - +
196C GLU* 6.0 0.2 + - - -
225C THR* 5.2 0.7 - - - -
226C ASP* 3.3 37.5 - - - +
245C VAL* 5.2 0.2 - - - -
269C GLU* 5.1 4.8 + - - -
273C ALA* 5.0 7.9 - - - -
274C PRO 3.0 7.6 + - - +
275C LEU* 1.3 77.0 - - - +
277C TYR* 1.3 63.5 + - + +
278C THR* 3.3 18.6 - - - +
279C SER* 2.8 23.2 + - - +
280C ALA* 2.9 17.3 + - - +
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Residues in contact with TYR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C ARG* 3.0 45.9 + - - -
194C GLU* 4.3 6.5 + - - -
195C VAL* 6.3 0.7 - - + -
221C ASN* 3.6 16.2 + - - -
222C LEU* 3.8 34.1 - - + +
223C GLY* 3.4 33.9 - - - -
225C THR* 5.8 0.4 + - - -
244C ILE* 3.8 19.1 - - + -
245C VAL* 4.1 8.9 - - + +
275C LEU 4.0 0.2 + - - -
276C LYS* 1.3 73.7 - - + +
278C THR* 1.3 75.0 + - + +
280C ALA* 3.4 8.5 - - - +
281C LEU* 2.8 56.3 + - + +
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Residues in contact with THR 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLU* 3.1 32.8 + - - +
76C PHE* 4.7 9.2 - - + -
99C PRO* 4.1 12.7 - - - +
114C ARG* 4.3 10.5 - - - +
276C LYS* 3.7 14.2 - - - +
277C TYR* 1.3 107.5 - - + +
279C SER* 1.3 58.3 + - - +
281C LEU* 3.5 2.9 + - - +
282C THR* 3.2 31.5 + - - +
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Residues in contact with SER 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLN* 3.1 42.9 + - - -
19C GLU* 3.6 7.4 - - - +
22C ALA* 3.4 11.9 - - - +
255C PHE* 5.2 0.9 - - - -
275C LEU* 3.8 9.2 - - - +
276C LYS* 2.8 37.6 + - - +
278C THR* 1.3 74.7 + - - +
280C ALA* 1.3 60.7 + - - +
282C THR* 2.6 22.2 + - - -
283C HIS* 3.9 5.5 + - - +
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C VAL* 3.8 24.9 - - + -
275C LEU* 4.6 15.9 - - + -
276C LYS 2.9 16.2 + - - +
277C TYR 3.2 6.0 + - - +
279C SER* 1.3 76.9 - - - +
281C LEU* 1.3 63.2 + - - +
282C THR 3.2 0.2 - - - -
283C HIS* 3.3 10.6 + - - +
284C ASP* 3.0 23.0 + - - +
338C MET* 4.5 17.5 - - + +
339C THR* 5.0 4.3 - - + -
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Residues in contact with LEU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C PRO* 3.7 31.4 - - + +
113C MET* 3.4 39.7 - - + +
114C ARG* 4.0 19.3 - - + -
115C PRO* 4.4 4.3 - - + -
244C ILE* 4.6 4.7 - - + -
277C TYR* 2.8 45.2 + - + +
278C THR 3.5 0.4 + - - +
280C ALA* 1.3 72.2 - - - +
282C THR* 1.3 57.6 + - - +
283C HIS 3.3 0.2 - - - -
284C ASP* 3.4 6.5 + - - +
285C ALA* 2.9 27.4 + - - +
339C THR* 3.6 24.0 - - + -
350C ARG* 4.3 5.6 - - - +
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Residues in contact with THR 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLU* 3.9 28.3 - - + +
22C ALA* 3.3 13.8 - - - +
23C PHE* 4.4 8.2 - - - -
74C PHE* 3.5 27.6 - - + -
76C PHE* 4.0 1.1 - - + -
99C PRO* 3.9 6.3 - - + -
278C THR 3.2 14.7 + - - +
279C SER* 2.6 27.0 + - - -
281C LEU* 1.3 76.9 - - - +
283C HIS* 1.3 61.9 + - - +
285C ALA* 3.4 14.7 + - - +
286C ILE* 3.4 22.5 - - - +
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Residues in contact with HIS 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ALA 4.6 2.4 + - - +
26C ALA* 3.6 27.6 - - + +
29C LEU* 4.4 18.8 - - + -
251C MET* 6.2 2.4 - - - +
255C PHE* 3.7 35.1 - + + +
279C SER 4.5 3.8 - - - +
280C ALA 3.3 9.7 + - - +
282C THR* 1.3 80.4 + - - +
284C ASP* 1.3 63.0 + - - +
286C ILE* 3.4 13.6 + - + +
287C LEU* 3.4 35.1 + - + +
338C MET* 3.6 34.6 - - + +
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Residues in contact with ASP 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C MET* 3.6 14.6 - - + -
280C ALA 3.0 14.6 - - - +
281C LEU* 3.4 10.5 + - - +
282C THR 3.3 0.4 - - - -
283C HIS* 1.3 76.2 - - - +
285C ALA* 1.3 58.9 + - - +
286C ILE 3.3 0.2 - - - -
287C LEU* 3.2 11.2 + - - +
288C VAL* 3.1 31.4 + - - +
337C GLY* 3.9 3.8 - - - -
338C MET* 2.8 39.1 + - - +
339C THR* 2.7 31.7 + - + +
342C ILE* 3.4 10.4 - - + +
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Residues in contact with ALA 285 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C PHE* 3.5 30.1 - - + -
97C VAL* 3.8 14.6 - - + +
113C MET* 4.0 13.5 - - + -
281C LEU 2.9 14.8 + - - +
282C THR 3.4 12.1 - - - +
283C HIS 3.2 0.4 - - - -
284C ASP* 1.3 75.9 - - - +
286C ILE* 1.3 62.4 + - + +
288C VAL* 3.6 3.2 + - - +
289C ILE* 3.3 29.7 + - - +
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Residues in contact with ILE 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 6.2 1.1 - - + -
23C PHE* 3.6 37.5 - - + +
26C ALA* 3.9 37.0 - - + +
27C VAL* 4.3 14.1 - - + +
30C TYR* 4.9 11.0 - - + -
43C LEU* 4.9 10.8 - - + -
282C THR 3.4 16.4 - - - +
283C HIS* 3.4 10.0 + - + +
284C ASP 3.3 0.6 - - - -
285C ALA* 1.3 79.1 - - + +
287C LEU* 1.3 58.2 + - + +
288C VAL 3.2 0.2 - - - -
289C ILE* 3.3 12.2 + - + +
290C ALA* 2.8 38.3 + - + +
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C MET* 5.5 3.8 - - - -
283C HIS* 3.4 41.9 + - + +
284C ASP* 3.2 12.0 + - + +
286C ILE* 1.3 82.0 - - + +
288C VAL* 1.3 59.4 + - - +
290C ALA* 4.1 7.6 - - + +
291C GLU* 3.7 17.8 + - - +
294C ARG* 5.4 2.6 + - - +
335C VAL* 3.9 25.3 - - + +
336C GLN 4.3 7.6 - - - +
337C GLY* 3.8 26.5 - - - -
342C ILE* 5.3 1.6 - - + -
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C VAL* 5.8 2.5 - - + -
111C ILE* 4.6 6.3 - - + -
113C MET* 3.8 24.9 - - + -
284C ASP 3.1 14.6 + - - +
285C ALA 3.8 7.6 - - - +
286C ILE 3.2 0.4 - - - -
287C LEU* 1.3 77.7 - - - +
289C ILE* 1.3 65.0 + - + +
292C ALA* 3.2 23.0 + - - +
330C LEU* 3.7 25.8 - - + +
333C VAL* 3.8 21.5 - - + +
335C VAL* 4.6 9.6 - - + -
342C ILE* 3.9 18.8 - - + -
344C PHE* 4.2 8.3 - - + -
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Residues in contact with ILE 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 6.0 0.2 - - + -
8C ILE* 4.2 36.3 - - + -
23C PHE* 5.7 0.2 - - + -
41C PHE* 6.4 0.2 - - + -
43C LEU* 4.6 17.3 - - + -
72C ALA* 5.1 6.7 - - + -
74C PHE* 5.3 6.5 - - + -
97C VAL* 4.4 20.9 - - + -
285C ALA* 3.3 20.6 + - + +
286C ILE* 3.3 15.8 + - + +
288C VAL* 1.3 77.2 - - + +
290C ALA* 1.3 61.7 - - - +
292C ALA* 3.4 0.3 + - - +
293C PHE* 3.1 50.7 + - + +
330C LEU* 4.2 17.9 - - + -
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR* 4.3 16.4 - - + -
41C PHE* 4.4 7.8 - - - -
43C LEU* 6.2 1.8 - - - -
286C ILE* 2.8 25.5 + - + +
287C LEU* 4.3 8.7 - - + +
288C VAL 3.4 0.2 - - - -
289C ILE* 1.3 74.6 - - - +
291C GLU* 1.3 57.4 + - - +
293C PHE* 4.0 1.7 - - - +
294C ARG* 3.2 58.1 + - - +
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Residues in contact with GLU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287C LEU 3.7 8.4 + - - +
289C ILE 3.4 0.2 - - - -
290C ALA* 1.3 77.8 - - - +
292C ALA* 1.3 60.3 + - - +
293C PHE 3.4 0.2 - - - -
294C ARG* 3.1 34.1 + - - +
295C TYR* 3.0 29.5 + - + +
333C VAL* 4.3 14.7 - - + +
334C GLN 5.6 1.6 - - - +
335C VAL* 3.8 32.4 - - + +
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Residues in contact with ALA 292 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288C VAL 3.2 19.8 + - - +
289C ILE 3.8 2.5 - - - +
291C GLU* 1.3 78.3 - - - +
293C PHE* 1.3 60.9 + - + +
295C TYR* 3.4 6.4 + - - +
296C LEU* 3.1 31.2 + - + +
329C ALA* 3.8 28.5 - - + +
330C LEU* 3.8 22.9 - - + -
333C VAL* 4.0 7.8 - - + +
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Residues in contact with PHE 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 3.6 39.2 - - + +
41C PHE* 3.5 23.9 - + + -
43C LEU* 6.3 0.2 - - + -
71C TYR* 3.8 25.8 - + + -
72C ALA* 4.6 13.5 - - + -
289C ILE* 3.1 48.2 + - + +
292C ALA* 1.3 80.5 - - + +
294C ARG* 1.3 58.4 + - - +
295C TYR 3.3 0.2 - - - -
296C LEU* 3.6 18.2 - - + +
297C ARG* 3.1 26.2 + - - +
303C VAL* 4.9 5.8 - - + -
326C ILE* 3.5 31.6 - - + -
330C LEU* 5.4 4.5 - - + -
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Residues in contact with ARG 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C TYR* 3.3 33.1 - - - -
40C PRO* 3.9 26.3 - - + +
41C PHE* 3.7 16.2 - - + -
287C LEU* 5.4 2.8 + - - +
290C ALA* 3.2 40.0 + - - +
291C GLU* 3.1 38.6 + - - +
292C ALA 3.3 0.4 - - - -
293C PHE* 1.3 74.4 - - - +
295C TYR* 1.3 59.7 + - - +
296C LEU 3.3 0.4 - - - -
297C ARG* 3.4 12.3 + - + +
298C ARG* 3.2 21.3 + - - +
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Residues in contact with TYR 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLN* 4.3 9.1 + - - -
346B THR* 5.1 3.0 + - - -
347B TYR* 4.0 22.5 + - - -
291C GLU* 3.0 19.9 + - + +
292C ALA* 3.5 8.5 - - - +
293C PHE 3.3 0.2 - - - -
294C ARG* 1.3 75.2 - - - +
296C LEU* 1.3 65.4 + - + +
297C ARG 3.1 0.4 - - - -
298C ARG* 3.2 22.1 + - + +
299C GLN* 3.4 34.9 + - + +
329C ALA* 4.5 12.1 - - + +
332C MET* 3.8 38.2 - - + +
333C VAL* 5.9 1.6 - - + -
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Residues in contact with LEU 296 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292C ALA* 3.1 21.4 + - + +
293C PHE* 3.6 29.6 - - + +
294C ARG 3.3 0.4 - - - -
295C TYR* 1.3 77.2 - - + +
297C ARG* 1.3 56.3 + - - +
299C GLN* 3.6 1.3 + - - -
300C ARG* 3.0 22.3 + - - -
301C VAL* 3.0 50.7 + - + +
303C VAL* 4.7 9.9 - - + -
325C ASP 3.9 20.6 - - - +
326C ILE* 3.7 26.9 - - + -
329C ALA* 4.3 11.4 - - + -
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Residues in contact with ARG 297 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PRO 4.5 15.4 + - - -
4C ASN* 3.7 22.4 + - - +
40C PRO* 4.1 29.2 + - - +
41C PHE* 4.3 20.1 - - + +
293C PHE 3.1 18.0 + - - +
294C ARG* 3.4 14.6 - - - +
295C TYR 3.1 0.4 - - - -
296C LEU* 1.3 75.8 - - - +
298C ARG* 1.3 62.8 + - - +
299C GLN 3.3 0.2 - - - -
300C ARG* 3.3 14.2 + - - +
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Residues in contact with ARG 298 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294C ARG 3.2 12.1 + - - +
295C TYR* 3.2 18.6 + - + +
297C ARG* 1.3 77.4 - - - +
299C GLN* 1.3 75.4 + - - +
300C ARG 3.8 0.2 + - - -
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Residues in contact with GLN 299 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLN* 4.4 25.7 + - - +
324B ILE* 4.3 18.1 - - + +
295C TYR* 3.4 41.7 + - + +
296C LEU* 3.6 1.1 + - - +
298C ARG* 1.3 92.3 - - - +
300C ARG* 1.3 60.2 + - - +
301C VAL* 3.1 29.9 + - + +
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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