Contacts of the helix formed by residues 295 - 323 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ARG* 4.2 7.6 - - - +
294B GLU* 1.3 76.0 - - - +
296B ILE* 1.3 62.9 + - + +
297B ASP* 2.9 22.3 + - - +
298B GLY* 2.8 35.5 + - - -
299B VAL* 2.9 14.6 + - - +
367D ALA 4.3 8.5 - - - +
369D GLY* 3.7 31.3 + - - +
371D ALA* 5.6 1.8 - - - +
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Residues in contact with ILE 296 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL 5.3 1.1 - - - +
31B ARG* 4.5 7.4 - - + +
32B PRO* 6.5 1.8 - - + -
34B LEU* 4.3 16.8 - - + -
295B ASP* 1.3 79.1 - - + +
297B ASP* 1.3 77.4 + - - +
299B VAL* 3.3 24.7 + - + +
300B TRP* 3.0 57.2 + - + +
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Residues in contact with ASP 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ASP* 2.9 18.1 + - - +
296B ILE* 1.3 88.4 - - - +
298B GLY* 1.3 61.5 + - - +
300B TRP* 3.4 11.4 + - - +
301B ALA 3.1 17.0 + - - -
374D ARG* 3.5 22.0 + - - +
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Residues in contact with GLY 298 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B GLU* 3.7 28.5 - - - -
295B ASP* 2.8 16.7 + - - -
297B ASP* 1.3 75.4 - - - +
299B VAL* 1.3 58.1 + - - +
301B ALA* 3.5 8.4 - - - +
302B SER* 2.8 32.4 + - - -
371D ALA* 5.9 1.6 - - - -
373D GLU* 4.2 2.6 - - - +
374D ARG* 5.2 1.3 - - - -
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Residues in contact with VAL 299 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 3.5 44.4 - - + +
31B ARG* 3.7 36.6 - - - +
290B PRO* 4.0 14.3 - - + +
294B GLU* 5.2 0.2 - - + -
295B ASP 2.9 18.5 + - - +
296B ILE* 3.3 23.1 - - + +
298B GLY* 1.3 77.6 - - - +
300B TRP* 1.3 67.8 + - + +
302B SER* 3.2 3.1 + - - -
303B ALA* 3.0 26.0 + - - +
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Residues in contact with TRP 300 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL* 3.8 30.5 - - + -
34B LEU* 3.8 29.4 - - + -
38B GLU* 5.1 0.2 - - + -
39B ALA* 4.4 4.3 - - - -
42B ARG* 3.5 53.1 - - + +
43B LEU* 4.2 9.9 - - + -
46B LEU* 4.0 26.2 - - + +
296B ILE* 3.0 52.4 + - + +
297B ASP* 3.9 10.8 - - - +
298B GLY 3.3 0.4 - - - -
299B VAL* 1.3 77.1 - - + +
301B ALA* 1.3 60.4 + - - +
303B ALA* 3.8 2.7 - - + +
304B ALA* 2.9 29.8 + - - +
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Residues in contact with ALA 301 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ARG* 5.3 0.2 - - - -
297B ASP 3.1 14.1 + - - +
298B GLY* 3.5 11.7 - - - +
300B TRP* 1.3 75.7 - - - +
302B SER* 1.3 57.8 + - - +
304B ALA* 3.4 7.7 + - - +
305B GLY* 3.0 23.9 + - - -
373D GLU* 5.1 2.1 - - - +
374D ARG* 3.6 47.1 - - + +
377D GLN* 5.7 3.8 - - - +
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Residues in contact with SER 302 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ARG* 3.7 12.6 + - - +
288B PHE* 3.5 22.0 - - - -
290B PRO* 4.0 13.6 - - - +
291B PRO* 4.5 0.3 - - - +
298B GLY 2.8 16.4 + - - -
299B VAL 3.5 3.8 - - - -
301B ALA* 1.3 75.3 - - - +
303B ALA* 1.3 65.9 + - - +
305B GLY* 3.1 9.9 + - - -
306B CYS* 3.2 15.8 + - - -
373D GLU* 2.7 33.8 + - - +
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Residues in contact with ALA 303 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 3.5 26.6 - - + -
18B VAL* 3.9 20.0 - - + -
43B LEU* 4.6 2.9 - - + -
46B LEU* 4.1 15.0 - - + -
288B PHE* 3.6 11.3 - - - -
299B VAL 3.0 16.2 + - - +
300B TRP* 3.8 6.1 - - + +
302B SER* 1.3 74.0 - - - +
304B ALA* 1.3 63.1 + - - +
306B CYS* 3.1 19.3 + - - +
307B MET* 3.7 3.2 + - - +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 5.6 1.9 - - - +
46B LEU* 4.3 15.4 - - + +
300B TRP 2.9 18.4 + - - +
301B ALA* 3.5 7.9 - - - +
302B SER 3.2 0.2 - - - -
303B ALA* 1.3 78.1 - - - +
305B GLY* 1.3 61.9 + - - +
306B CYS 3.4 0.3 + - - -
307B MET* 3.5 14.6 + - - +
308B ARG* 3.0 23.7 + - - +
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Residues in contact with GLY 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ARG* 4.3 5.2 - - - -
301B ALA 3.0 14.9 + - - -
302B SER 3.1 5.3 + - - -
304B ALA* 1.3 74.7 - - - +
306B CYS* 1.3 55.7 + - - +
308B ARG* 4.0 5.8 - - - -
309B ASN* 2.7 42.4 + - - -
377D GLN* 3.9 23.8 - - - -
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Residues in contact with CYS 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 4.1 1.3 - - + -
259B ARG* 3.9 5.9 - - - +
260B PHE* 3.6 34.2 - - - -
286B PHE* 3.5 43.4 - - + -
288B PHE* 3.8 31.0 - - - -
302B SER 3.2 14.6 + - - -
303B ALA 3.1 10.6 + - - +
305B GLY* 1.3 77.0 - - - +
307B MET* 1.3 61.5 + - - +
309B ASN* 3.9 0.3 - - - +
310B TYR* 3.2 15.1 + - - +
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Residues in contact with MET 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B PRO* 4.0 17.5 - - + -
11B PHE* 3.5 49.8 - - + -
13B PHE* 3.8 33.2 - - + -
46B LEU* 3.5 46.4 - - + +
48B ALA* 4.2 11.7 - - + +
286B PHE* 3.8 7.6 - - + -
303B ALA 4.1 6.1 - - - +
304B ALA* 3.5 6.8 + - - +
305B GLY 3.3 0.4 - - - -
306B CYS* 1.3 72.2 - - - +
308B ARG* 1.3 67.2 + - - +
310B TYR* 3.2 1.9 + - - +
311B LEU* 2.9 29.9 + - - +
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Residues in contact with ARG 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASN* 3.2 27.3 + - - +
3B TYR* 3.5 32.6 + - + +
5B PRO* 5.3 1.9 - - + +
304B ALA 3.0 19.7 + - - +
305B GLY* 3.6 5.4 - - - +
307B MET* 1.3 75.9 - - - +
309B ASN* 1.3 64.5 + - - +
311B LEU* 3.0 8.1 + - - +
312B ILE* 2.9 33.0 + - + +
377D GLN* 3.9 16.4 - - - -
381D ASP* 2.8 28.9 + - - -
386D ALA* 3.0 27.7 + - - +
387D ARG* 5.1 2.0 - - - +
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Residues in contact with ASN 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ARG* 3.8 5.2 + - - -
260B PHE* 2.7 30.2 - - + +
261B GLY* 3.8 15.4 - - - -
265B LEU* 6.5 0.2 - - + -
305B GLY 2.7 18.8 + - - +
306B CYS 3.9 1.1 - - - +
308B ARG* 1.3 74.1 - - - +
310B TYR* 1.3 61.3 + - - +
312B ILE* 3.3 11.2 + - - +
313B LEU* 3.0 33.6 + - + +
377D GLN* 2.9 40.1 + - - +
380D MET* 3.4 21.4 - - - +
384D LEU* 5.0 2.8 - - + +
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Residues in contact with TYR 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.8 25.4 - + + -
246B LEU* 4.0 25.4 - - + -
260B PHE* 3.5 28.8 - + + -
272B VAL* 3.6 28.1 - - + +
275B LEU* 4.0 18.1 - - + +
276B GLU* 2.8 29.2 + - - -
284B ARG* 2.9 29.3 + - + -
286B PHE* 4.5 0.9 - - + -
306B CYS 3.2 11.9 + - - +
307B MET 3.2 8.6 + - - +
309B ASN* 1.3 78.6 - - - +
311B LEU* 1.3 60.4 + - + +
313B LEU* 3.9 3.0 - - - +
314B LYS* 2.9 32.7 + - + +
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Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.2 43.2 - - + +
4B GLN 4.1 1.6 - - - +
5B PRO* 3.7 30.5 - - + -
9B ASP* 4.0 14.8 - - - +
11B PHE* 3.8 21.5 - - + -
307B MET 2.9 16.9 + - - +
308B ARG 3.4 6.5 - - - +
310B TYR* 1.3 76.5 - - + +
312B ILE* 1.3 64.0 + - - +
314B LYS* 3.4 18.7 + - + +
315B GLU* 3.1 22.3 + - - +
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Residues in contact with ILE 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.8 28.0 - - + -
308B ARG* 2.9 30.7 + - + +
309B ASN* 3.7 17.3 - - - +
311B LEU* 1.3 76.3 - - - +
313B LEU* 1.3 59.9 + - - +
315B GLU* 3.2 4.2 + - - +
316B ARG* 2.9 60.1 + - + +
380D MET* 5.5 0.2 - - + -
381D ASP* 4.0 10.8 - - - +
384D LEU* 3.8 28.3 - - + -
386D ALA* 4.0 19.1 - - + -
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B PHE* 4.4 6.3 - - + -
261B GLY* 5.0 4.3 - - - -
265B LEU* 4.4 10.3 - - + +
268B ALA* 3.7 32.8 - - + +
269B PHE* 3.8 18.7 - - + +
272B VAL* 3.9 22.0 - - + -
309B ASN* 3.0 18.5 + - + +
310B TYR 3.9 0.9 - - - +
312B ILE* 1.3 73.6 - - + +
314B LYS* 1.3 61.6 + - - +
316B ARG* 3.7 2.9 - - - +
317B ALA* 2.8 34.0 + - - +
383B LEU* 3.5 31.6 - - + -
384D LEU* 4.2 16.8 - - + -
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Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ASP* 4.6 13.5 + - - +
272B VAL* 3.6 15.0 - - + +
276B GLU* 3.5 38.2 + - + +
310B TYR* 2.9 24.4 + - + +
311B LEU* 3.6 18.0 - - + +
313B LEU* 1.3 76.9 - - - +
315B GLU* 1.3 62.1 + - - +
317B ALA* 3.4 3.0 + - - +
318B ALA* 3.0 29.2 + - + +
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Residues in contact with GLU 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B ASN* 5.2 3.1 + - - -
3B TYR* 3.2 34.0 + - + -
311B LEU 3.1 10.4 + - - +
312B ILE 3.2 7.4 + - - +
314B LYS* 1.3 81.7 - - - +
316B ARG* 1.3 71.1 + - - +
318B ALA* 3.6 4.8 + - - +
319B ALA* 3.0 29.6 + - + +
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Residues in contact with ARG 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B TYR* 3.6 17.2 + - - -
269B PHE* 3.9 7.9 - - + -
312B ILE* 2.9 30.9 + - + +
313B LEU* 3.8 6.5 - - - +
315B GLU* 1.3 93.4 + - - +
317B ALA* 1.3 59.6 + - - +
319B ALA* 3.4 7.1 + - - +
320B PHE* 2.9 28.2 + - - +
382B HIS* 3.6 21.3 - - - +
383B LEU* 3.0 37.5 + - + +
385B GLY* 3.5 17.1 - - - +
384D LEU* 2.6 31.5 + - - +
385D GLY 3.3 16.2 + - - -
386D ALA* 4.2 4.4 - - - +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B PHE* 3.4 22.1 - - + -
272B VAL 4.8 0.2 - - - -
273B ASP* 3.7 37.4 - - + +
276B GLU* 6.0 2.5 - - + -
313B LEU 2.8 21.7 + - - +
314B LYS* 3.9 4.3 - - - +
316B ARG* 1.3 70.5 - - - +
318B ALA* 1.3 61.3 + - - +
320B PHE* 3.3 3.1 + - - +
321B ARG* 3.0 33.0 + - - +
----------------------------------------------------------
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B LYS* 3.0 20.7 + - + +
315B GLU* 3.9 5.6 - - - +
317B ALA* 1.3 73.6 - - - +
319B ALA* 1.3 60.6 + - - +
321B ARG* 3.5 5.4 + - - +
322B ALA* 3.0 32.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B GLU* 3.0 20.8 + - + +
316B ARG* 3.7 9.0 - - - +
317B ALA 3.3 0.2 - - - -
318B ALA* 1.3 76.9 - - - +
320B PHE* 1.3 62.7 + - - +
322B ALA* 3.4 4.9 + - - +
323B ASP* 3.1 24.4 + - - +
382B HIS* 3.6 15.3 - - + +
----------------------------------------------------------
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Residues in contact with PHE 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A ALA* 3.9 15.9 - - + -
269B PHE* 4.5 11.0 - + + -
270B TRP* 3.9 13.7 - + - -
273B ASP* 4.4 4.3 - - - -
316B ARG 2.9 17.8 + - - +
317B ALA* 3.4 7.4 - - - +
318B ALA 3.2 0.2 - - - -
319B ALA* 1.3 78.9 - - - +
321B ARG* 1.3 94.1 + - - +
323B ASP 3.3 3.1 + - - -
326B VAL* 3.2 53.9 - - + +
330B LEU* 5.6 0.2 - - + -
375B LEU* 4.1 8.1 - - + -
378B LEU* 4.1 0.4 - - + -
379B ALA* 3.3 43.5 - - + -
382B HIS* 3.6 26.6 + + + -
----------------------------------------------------------
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A GLY 5.0 1.6 + - - -
147A ALA* 4.4 10.7 + - - +
270B TRP* 4.0 15.6 - - - -
273B ASP* 2.9 37.6 + - - +
277B SER* 5.6 11.4 - - - -
317B ALA 3.0 19.7 + - - +
318B ALA* 4.0 6.3 - - - +
320B PHE* 1.3 91.1 - - + +
322B ALA* 1.3 57.7 + - - +
323B ASP 3.2 0.9 + - - -
326B VAL* 4.8 2.8 - - - +
327B GLN* 3.2 26.7 + - - +
330B LEU* 4.0 35.2 - - - +
335B LEU* 6.0 0.2 - - - +
----------------------------------------------------------
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Residues in contact with ALA 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ALA 3.0 19.6 + - - +
319B ALA* 3.8 5.4 - - - +
320B PHE 3.3 0.2 - - - -
321B ARG* 1.3 76.2 - - - +
323B ASP* 1.3 62.1 + - - +
324B PRO* 3.3 10.6 - - - +
327B GLN* 4.0 10.3 + - - +
----------------------------------------------------------
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Residues in contact with ASP 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ALA 3.1 11.7 + - - +
320B PHE 3.4 13.2 - - - +
321B ARG 3.2 2.0 - - - -
322B ALA* 1.3 76.2 - - - +
324B PRO* 1.3 73.8 - - - +
325B GLU* 2.7 20.4 + - - +
326B VAL* 2.9 21.7 + - + +
327B GLN* 2.9 14.4 + - - +
382B HIS* 2.8 23.1 + - + +
387B ARG* 2.8 27.6 + - - -
----------------------------------------------------------
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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