Contacts of the helix formed by residues 295 - 323 (chain F) in PDB entry 4HHM
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 ASP 295 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31F ARG* 3.9 9.0 - - - +
294F GLU* 1.3 76.0 + - - +
296F ILE* 1.3 57.8 + - + +
297F ASP* 2.8 32.6 + - - +
298F GLY* 2.7 30.3 + - - -
299F VAL* 3.1 9.9 + - - +
367H ALA 4.4 8.9 - - - +
369H GLY* 3.7 30.9 + - - +
371H ALA* 5.5 2.3 - - - +
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Residues in contact with ILE 296 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F VAL 5.5 0.4 - - - +
31F ARG* 4.0 7.3 - - - +
32F PRO* 6.0 8.0 - - + +
34F LEU* 4.5 15.3 - - + -
38F GLU* 6.0 0.7 - - + -
295F ASP* 1.3 74.8 - - + +
297F ASP* 1.3 77.1 + - - +
299F VAL* 3.3 23.7 + - + +
300F TRP* 3.1 50.0 - - + +
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Residues in contact with ASP 297 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295F ASP* 2.8 27.8 + - - +
296F ILE* 1.3 80.5 - - - +
298F GLY* 1.3 63.5 + - - +
300F TRP* 3.6 9.4 + - - +
301F ALA* 3.1 22.0 + - - +
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Residues in contact with GLY 298 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294F GLU* 3.8 30.7 - - - -
295F ASP* 2.7 22.2 + - - -
297F ASP* 1.3 72.2 - - - +
299F VAL* 1.3 51.0 + - - -
301F ALA* 3.1 7.6 + - - +
302F SER* 2.7 38.3 + - - -
371H ALA* 5.7 1.8 - - - -
373H GLU* 4.3 2.0 - - - +
374H ARG 6.0 0.2 - - - -
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Residues in contact with VAL 299 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F VAL* 3.4 45.1 - - + +
31F ARG* 3.2 48.5 - - - +
290F PRO* 4.0 14.2 - - + +
294F GLU* 4.3 0.2 - - - +
295F ASP 3.1 6.0 + - - +
296F ILE* 3.4 18.6 - - + +
298F GLY* 1.3 75.8 - - - +
300F TRP* 1.3 65.1 + - + +
302F SER* 3.4 2.3 + - - -
303F ALA* 2.8 26.5 + - - +
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Residues in contact with TRP 300 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18F VAL* 3.8 18.2 - - + -
34F LEU* 3.9 22.0 - - + -
38F GLU* 4.5 1.5 - - + +
39F ALA* 3.9 17.7 - - - -
42F ARG* 3.3 51.0 - - + +
43F LEU* 3.6 32.5 - - + -
46F LEU* 3.7 19.2 - - + +
296F ILE* 3.1 51.9 + - + +
297F ASP* 4.2 9.2 - - - +
298F GLY 3.3 0.4 - - - -
299F VAL* 1.3 74.9 - - + +
301F ALA* 1.3 60.8 + - - +
303F ALA* 3.6 1.9 - - + +
304F ALA* 2.8 30.7 + - - +
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Residues in contact with ALA 301 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F ARG* 5.3 0.2 - - - -
297F ASP 3.1 16.0 + - - +
298F GLY* 3.1 12.7 + - - +
300F TRP* 1.3 74.5 - - - +
302F SER* 1.3 65.3 + - - +
304F ALA* 3.2 6.8 + - - +
305F GLY* 3.0 19.1 + - - -
373H GLU* 4.9 2.0 - - - -
374H ARG* 4.6 32.8 - - + +
377H GLN* 5.7 4.0 - - - +
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Residues in contact with SER 302 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F ARG* 3.6 17.3 + - - +
288F PHE* 3.5 19.8 - - - -
290F PRO* 4.2 11.3 - - - +
291F PRO* 4.7 0.2 - - - +
298F GLY 2.7 19.7 + - - -
299F VAL 3.9 3.6 - - - -
301F ALA* 1.3 72.4 - - - +
303F ALA* 1.3 64.1 + - - +
305F GLY* 3.0 11.6 + - - -
306F CYS* 3.2 12.5 + - - -
373H GLU* 2.9 36.6 + - - +
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Residues in contact with ALA 303 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F PHE* 3.3 28.1 - - + -
18F VAL* 3.8 24.0 - - + -
43F LEU* 4.3 3.1 - - + -
46F LEU* 4.1 11.9 - - + -
288F PHE* 3.5 14.5 - - + -
299F VAL 2.8 18.1 + - - +
300F TRP* 3.6 8.5 - - - +
302F SER* 1.3 76.8 - - - +
304F ALA* 1.3 62.3 + - - +
306F CYS* 3.3 8.8 + - - +
307F MET* 3.7 3.3 + - - +
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Residues in contact with ALA 304 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F PRO* 5.8 0.9 - - - +
46F LEU* 4.2 17.4 - - + +
300F TRP 2.8 17.7 + - - +
301F ALA* 3.5 8.1 - - - +
303F ALA* 1.3 74.0 - - - +
305F GLY* 1.3 60.5 + - - +
307F MET* 3.5 15.4 + - + +
308F ARG* 3.0 29.5 + - - +
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Residues in contact with GLY 305 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F ARG* 4.2 5.4 - - - -
301F ALA 3.0 10.4 + - - -
302F SER 3.0 8.6 + - - -
304F ALA* 1.3 76.4 - - - +
306F CYS* 1.3 64.0 + - - +
308F ARG* 4.3 4.7 - - - -
309F ASN* 2.9 33.4 + - - +
377H GLN* 3.9 24.2 - - - -
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Residues in contact with CYS 306 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F PHE* 4.1 0.7 - - + -
259F ARG* 3.6 24.2 - - - +
260F PHE* 3.7 17.7 - - - -
286F PHE* 3.5 41.0 - - + -
288F PHE* 3.7 34.1 - - - -
302F SER 3.2 11.1 + - - -
303F ALA 3.5 7.2 - - - +
304F ALA 3.3 0.2 - - - -
305F GLY* 1.3 77.9 - - - +
307F MET* 1.3 63.8 + - - +
309F ASN* 4.0 2.1 - - - +
310F TYR* 3.2 15.8 + - - +
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Residues in contact with MET 307 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5F PRO* 3.9 18.6 - - + -
11F PHE* 3.7 44.6 - - + -
13F PHE* 3.9 26.0 - - + -
43F LEU* 6.1 0.2 - - + -
46F LEU* 3.6 40.4 - - + +
48F ALA* 4.1 13.5 - - + +
286F PHE* 3.9 7.6 - - + -
303F ALA 3.7 13.0 + - - +
304F ALA* 3.5 10.9 + - + +
306F CYS* 1.3 81.4 - - - +
308F ARG* 1.3 62.8 + - - +
310F TYR* 3.2 4.3 + - - +
311F LEU* 3.1 27.9 + - - +
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Residues in contact with ARG 308 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F ASN 3.1 26.5 + - - +
3F TYR* 3.5 33.4 + - + +
4F GLN* 5.4 3.0 + - - +
5F PRO* 5.3 1.7 - - + +
304F ALA 3.0 18.6 + - - +
305F GLY* 3.8 4.9 - - - +
307F MET* 1.3 75.4 - - - +
309F ASN* 1.3 65.9 + - - +
311F LEU* 3.0 5.1 + - - +
312F ILE* 2.9 33.3 + - + +
377H GLN* 3.5 21.3 - - - +
381H ASP* 2.9 24.7 + - - -
386H ALA 3.0 26.7 + - - -
387H ARG* 4.9 6.3 + - - +
----------------------------------------------------------
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Residues in contact with ASN 309 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F ARG* 3.9 5.9 + - - -
260F PHE* 2.9 28.8 - - + +
261F GLY* 3.8 15.0 - - - -
265F LEU* 6.5 0.2 - - + -
305F GLY 2.9 21.8 + - - +
306F CYS 4.0 0.7 - - - +
308F ARG* 1.3 72.7 - - - +
310F TYR* 1.3 63.7 + - - +
312F ILE* 3.3 12.2 + - - +
313F LEU* 3.0 33.2 + - + +
377H GLN* 3.2 34.6 + - - -
380H MET* 3.2 25.3 - - - +
384H LEU* 4.5 2.1 - - + +
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Residues in contact with TYR 310 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F PHE* 3.8 24.7 - + + -
246F LEU* 3.9 19.1 - - + -
260F PHE* 3.4 30.4 - + + -
272F VAL* 3.7 28.6 - - + +
275F LEU* 4.1 14.9 - - + +
276F GLU* 2.6 29.4 + - - -
284F ARG* 2.9 35.5 + - + -
286F PHE* 4.3 1.1 - - + -
306F CYS 3.2 11.6 + - - +
307F MET 3.5 8.1 - - - +
308F ARG 3.2 0.8 - - - -
309F ASN* 1.3 79.6 - - - +
311F LEU* 1.3 61.1 + - + +
313F LEU* 3.7 2.2 - - - +
314F LYS* 2.8 35.5 + - + +
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Residues in contact with LEU 311 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F TYR* 3.4 40.9 - - + +
4F GLN 3.7 2.2 - - - +
5F PRO* 3.5 32.3 - - + -
9F ASP* 3.9 19.7 - - - +
11F PHE* 3.8 17.9 - - + -
307F MET 3.1 14.9 + - - +
308F ARG 3.0 6.5 + - - +
310F TYR* 1.3 73.7 - - + +
312F ILE* 1.3 65.8 + - - +
314F LYS* 3.5 19.1 - - + +
315F GLU* 3.0 23.4 + - - +
----------------------------------------------------------
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Residues in contact with ILE 312 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F TYR* 3.7 27.1 - - + -
308F ARG* 2.9 30.6 + - + +
309F ASN* 3.3 18.4 + - - +
311F LEU* 1.3 76.3 - - - +
313F LEU* 1.3 63.6 + - + +
315F GLU* 3.1 6.4 + - - +
316F ARG* 3.1 36.3 + - + +
381H ASP* 3.8 16.8 - - - +
384H LEU* 3.8 32.8 - - + -
386H ALA* 3.7 25.4 - - + -
----------------------------------------------------------
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Residues in contact with LEU 313 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F PHE* 4.1 11.7 - - + -
261F GLY* 5.0 4.0 - - - -
265F LEU* 4.6 15.3 - - + +
268F ALA* 3.5 42.2 - - + +
269F PHE* 3.7 10.0 - - + +
272F VAL* 3.9 13.0 - - + -
309F ASN* 3.0 23.1 + - + +
310F TYR 3.8 2.9 - - - +
312F ILE* 1.3 74.7 - - + +
314F LYS* 1.3 67.0 + - - +
316F ARG* 3.7 4.1 - - + +
317F ALA* 2.8 27.4 + - - +
383F LEU* 3.4 31.4 - - + -
384H LEU* 4.6 10.1 - - + -
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Residues in contact with LYS 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F ASP* 4.4 14.1 + - - -
272F VAL* 3.5 15.2 - - + +
276F GLU* 3.6 36.4 + - + +
310F TYR* 2.8 28.7 + - + +
311F LEU* 3.5 18.3 - - + +
312F ILE 3.2 0.2 - - - -
313F LEU* 1.3 76.5 - - - +
315F GLU* 1.3 59.6 + - - +
317F ALA* 3.4 2.5 + - - +
318F ALA* 3.0 30.8 + - + +
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Residues in contact with GLU 315 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F ASN* 5.3 1.2 + - - +
3F TYR* 2.5 40.0 + - + -
311F LEU 3.0 13.4 + - - +
312F ILE 3.3 6.7 - - - +
314F LYS* 1.3 78.4 - - - +
316F ARG* 1.3 75.9 + - - +
318F ALA* 3.2 7.2 + - - +
319F ALA* 3.0 28.9 + - + +
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Residues in contact with ARG 316 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3F TYR* 3.4 18.2 + - - -
269F PHE* 3.7 8.7 - - + -
312F ILE* 3.1 21.1 + - + +
313F LEU* 4.0 4.3 - - - +
315F GLU* 1.3 89.5 + - - +
317F ALA* 1.3 60.4 + - - +
319F ALA* 3.6 6.9 + - - +
320F PHE* 3.0 29.3 + - - +
382F HIS* 3.1 26.8 + - - +
383F LEU* 2.8 42.0 + - + +
385F GLY* 3.9 10.0 - - - +
384H LEU* 2.6 34.5 + - - +
385H GLY 3.2 16.0 + - - -
386H ALA* 4.0 5.1 - - - +
----------------------------------------------------------
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Residues in contact with ALA 317 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F PHE* 3.4 21.7 - - + -
272F VAL 4.8 0.4 - - - -
273F ASP* 3.8 35.2 - - + +
276F GLU* 5.9 2.9 - - + -
313F LEU 2.8 18.5 + - - +
314F LYS* 3.8 5.4 - - - +
316F ARG* 1.3 76.1 - - - +
318F ALA* 1.3 65.7 + - - +
320F PHE* 3.5 1.4 + - - +
321F ARG* 3.2 29.6 + - - +
----------------------------------------------------------
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Residues in contact with ALA 318 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F LYS* 3.0 21.3 + - + +
315F GLU* 3.2 8.0 + - - +
317F ALA* 1.3 77.8 - - - +
319F ALA* 1.3 57.3 + - - +
321F ARG* 3.3 6.2 + - - +
322F ALA* 3.0 29.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 319 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315F GLU* 3.0 18.4 + - + +
316F ARG* 4.0 6.3 - - - +
317F ALA 3.3 0.2 - - - -
318F ALA* 1.3 75.4 - - - +
320F PHE* 1.3 64.1 + - - +
322F ALA* 3.7 5.6 - - - +
323F ASP* 3.0 25.6 + - - +
382F HIS* 3.4 19.4 - - + +
----------------------------------------------------------
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Residues in contact with PHE 320 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147E ALA* 3.7 24.7 - - + -
269F PHE* 4.3 13.5 - + + -
270F TRP* 4.2 7.9 - + - -
273F ASP* 4.6 1.3 - - - -
316F ARG 3.0 19.1 + - - +
317F ALA 3.8 4.3 - - - +
319F ALA* 1.3 76.6 - - - +
321F ARG* 1.3 97.1 + - + +
323F ASP 3.5 0.7 + - - -
326F VAL* 2.9 63.0 - - + +
330F LEU* 5.4 0.4 - - + -
375F LEU* 4.1 11.2 - - + -
378F LEU* 4.4 0.4 - - + -
379F ALA* 3.5 40.4 - - + -
382F HIS* 3.7 19.9 + + + -
----------------------------------------------------------
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Residues in contact with ARG 321 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146E GLY 5.2 1.4 + - - -
147E ALA* 4.5 10.1 + - - +
270F TRP* 4.1 12.9 - - - -
273F ASP* 2.6 38.3 + - - +
277F SER* 5.3 13.6 + - - -
317F ALA 3.2 18.0 + - - +
318F ALA* 3.3 5.1 + - - +
320F PHE* 1.3 96.4 - - + +
322F ALA* 1.3 57.6 + - - +
323F ASP 3.5 0.5 + - - -
326F VAL* 4.8 2.0 - - - +
327F GLN* 3.2 26.0 - - - +
330F LEU* 4.0 32.3 - - - +
----------------------------------------------------------
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Residues in contact with ALA 322 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318F ALA 3.0 18.2 + - - +
319F ALA* 3.4 5.8 + - - +
320F PHE 3.3 0.2 - - - -
321F ARG* 1.3 75.8 - - - +
323F ASP* 1.3 59.5 + - - +
324F PRO* 3.2 15.1 - - - +
327F GLN* 4.1 9.3 - - - +
----------------------------------------------------------
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Residues in contact with ASP 323 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319F ALA 3.0 16.3 + - - +
320F PHE 3.6 0.2 - - - +
321F ARG 3.3 1.0 - - - -
322F ALA* 1.3 76.8 - - - +
324F PRO* 1.3 65.8 - - - +
325F GLU* 2.9 19.8 + - - +
326F VAL* 2.8 27.3 + - + +
327F GLN* 2.8 29.1 + - - +
382F HIS* 2.7 24.6 + - + +
387F ARG* 2.8 26.4 + - - -
----------------------------------------------------------
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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).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il