Contacts of the helix formed by residues 295 - 323 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B ALA 4.4 9.9 - - - +
369B GLY* 3.6 31.1 + - - +
371B ALA* 5.6 2.6 - - - +
31D ARG* 3.9 8.5 - - - +
293D THR 4.1 0.6 + - - -
294D GLU* 1.3 75.9 + - - +
296D ILE* 1.3 68.3 + - + +
297D ASP* 2.6 41.0 + - - +
298D GLY* 2.8 17.9 + - - +
299D VAL* 3.1 12.3 + - - +
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Residues in contact with ILE 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D VAL 5.5 0.2 - - - +
31D ARG* 4.2 7.2 - - - +
32D PRO* 6.3 4.7 - - + -
34D LEU* 4.7 16.6 - - + -
38D GLU* 6.2 0.9 - - + -
295D ASP* 1.3 78.2 - - + +
297D ASP* 1.3 76.8 + - - +
299D VAL* 3.3 21.4 + - + -
300D TRP* 3.3 48.5 + - + +
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Residues in contact with ASP 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295D ASP* 2.6 23.2 + - - +
296D ILE* 1.3 86.3 - - - +
298D GLY* 1.3 54.6 + - - -
300D TRP* 3.5 11.5 + - - +
301D ALA* 3.1 25.1 + - - +
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Residues in contact with GLY 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B ALA* 5.7 2.2 - - - -
373B GLU* 4.0 3.5 - - - +
374B ARG 5.9 0.4 - - - -
294D GLU* 3.8 28.3 - - - -
295D ASP* 2.8 14.8 + - - -
297D ASP* 1.3 75.9 - - - +
299D VAL* 1.3 54.4 + - - +
301D ALA* 3.1 8.9 + - - +
302D SER* 2.7 36.3 + - - -
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Residues in contact with VAL 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D VAL* 3.5 37.7 - - + +
31D ARG* 3.3 43.7 - - - +
290D PRO* 3.7 24.0 - - + +
294D GLU* 4.3 0.4 - - - +
295D ASP 3.1 11.8 + - - +
296D ILE* 3.3 16.8 - - + +
298D GLY* 1.3 75.2 - - - +
300D TRP* 1.3 64.0 - - + +
302D SER* 3.1 3.8 + - - -
303D ALA* 2.9 27.2 + - - +
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Residues in contact with TRP 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D VAL* 3.4 31.4 - - + -
34D LEU* 3.9 33.0 - - + -
38D GLU* 4.9 1.5 - - + +
39D ALA* 4.0 11.9 - - - -
42D ARG* 3.3 49.3 - - + +
43D LEU* 3.8 13.9 - - + -
46D LEU* 4.0 29.6 - - + +
296D ILE* 3.3 42.7 + - + +
297D ASP* 3.9 13.0 - - - +
298D GLY 3.3 0.2 - - - -
299D VAL* 1.3 77.4 - - + +
301D ALA* 1.3 63.0 + - - +
303D ALA* 3.9 1.9 - - + +
304D ALA* 3.0 24.3 + - - +
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Residues in contact with ALA 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B GLU* 4.9 2.0 - - - -
374B ARG* 4.5 30.7 - - + +
377B GLN* 5.7 2.9 - - - +
259D ARG* 5.3 0.2 - - - -
297D ASP 3.1 15.5 + - - +
298D GLY* 3.1 12.5 + - - +
300D TRP* 1.3 76.8 - - - +
302D SER* 1.3 56.5 + - - +
304D ALA* 3.2 7.9 + - - +
305D GLY* 2.9 25.6 + - - -
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Residues in contact with SER 302 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B GLU* 2.7 38.3 + - - +
259D ARG* 3.6 16.8 + - - +
288D PHE* 3.4 21.7 - - - -
290D PRO* 4.0 12.6 - - - +
291D PRO* 4.4 0.5 - - - +
298D GLY 2.7 19.7 + - - -
299D VAL 3.5 4.7 - - - -
301D ALA* 1.3 73.6 - - - +
303D ALA* 1.3 61.2 + - - +
305D GLY* 3.1 10.6 + - - -
306D CYS 3.1 10.2 + - - -
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Residues in contact with ALA 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D PHE* 3.3 33.3 - - + -
18D VAL* 3.9 15.3 - - + -
43D LEU* 4.6 1.6 - - + -
46D LEU* 4.2 12.8 - - + -
288D PHE* 3.5 21.0 - - + -
299D VAL 2.9 15.4 + - - +
300D TRP* 3.9 5.2 - - + +
302D SER* 1.3 73.7 - - - +
304D ALA* 1.3 66.1 + - - +
306D CYS* 3.2 10.6 + - - +
307D MET* 3.6 4.7 + - - +
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Residues in contact with ALA 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PRO* 5.7 1.4 - - - +
46D LEU* 4.4 16.1 - - + +
300D TRP 3.0 18.9 + - - +
301D ALA* 3.2 6.5 + - - +
303D ALA* 1.3 76.0 - - - +
305D GLY* 1.3 63.0 + - - +
307D MET* 3.6 15.0 + - - +
308D ARG* 3.1 24.8 + - - +
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Residues in contact with GLY 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLN* 3.5 28.7 - - - -
259D ARG* 4.2 6.3 - - - -
301D ALA 2.9 13.3 + - - -
302D SER 3.1 6.1 + - - -
304D ALA* 1.3 76.6 - - - +
306D CYS* 1.3 66.8 + - - +
308D ARG* 4.3 2.7 - - - -
309D ASN* 3.0 29.1 + - - +
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Residues in contact with CYS 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D PHE* 4.1 0.4 - - + -
259D ARG* 3.7 15.2 - - - +
260D PHE* 3.4 36.5 - - - -
286D PHE* 3.8 38.5 - - + -
288D PHE* 4.0 24.0 - - - -
302D SER 3.1 9.6 + - - -
303D ALA 3.2 9.8 + - - +
305D GLY* 1.3 77.3 - - - +
307D MET* 1.3 63.8 + - - +
309D ASN* 3.5 0.7 + - - +
310D TYR* 3.3 19.1 + - - +
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Residues in contact with MET 307 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D PRO* 3.7 18.8 - - + -
11D PHE* 3.4 49.7 - - + -
13D PHE* 3.9 23.8 - - + -
46D LEU* 3.7 42.0 - - + +
48D ALA* 4.1 13.0 - - + +
286D PHE* 3.8 16.4 - - + -
303D ALA 3.6 6.7 + - - +
304D ALA* 3.6 10.0 + - - +
305D GLY 3.4 0.2 - - - -
306D CYS* 1.3 78.7 - - - +
308D ARG* 1.3 64.5 + - - +
310D TYR* 3.3 3.5 + - - +
311D LEU* 3.1 28.3 + - - +
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Residues in contact with ARG 308 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLN* 3.9 14.8 - - - +
381B ASP* 2.7 31.5 + - - -
386B ALA 2.8 28.1 + - - -
387B ARG* 4.9 2.8 - - - +
2D ASN 3.2 27.3 + - - +
3D TYR* 3.6 31.7 + - + +
5D PRO* 5.4 2.1 - - + +
304D ALA 3.1 18.8 + - - +
305D GLY* 3.8 5.4 - - - +
306D CYS 3.4 0.2 - - - -
307D MET* 1.3 76.7 - - - +
309D ASN* 1.3 57.4 + - - +
311D LEU* 3.2 4.4 + - - +
312D ILE* 2.9 39.6 + - + +
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Residues in contact with ASN 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B GLN* 2.9 39.9 + - - -
380B MET* 3.2 24.4 - - - +
384B LEU* 4.5 3.7 - - + +
259D ARG* 3.9 3.6 + - - -
260D PHE* 3.1 26.7 - - + +
261D GLY* 3.9 14.6 - - - -
265D LEU* 6.3 0.7 - - + -
305D GLY 3.0 14.6 + - - +
306D CYS 4.0 0.4 - - - +
308D ARG* 1.3 76.2 - - - +
310D TYR* 1.3 58.7 + - - +
312D ILE* 3.3 14.3 + - - +
313D LEU* 2.9 38.0 + - + +
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Residues in contact with TYR 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D PHE* 3.9 23.8 - + + -
246D LEU* 4.2 14.4 - - + -
260D PHE* 3.3 36.5 - + + -
272D VAL* 3.8 18.0 - - + +
275D LEU* 4.1 15.5 - - + +
276D GLU* 2.9 30.8 + - - +
284D ARG* 3.1 36.6 + - + -
286D PHE* 4.5 1.1 - - + -
306D CYS 3.3 6.6 + - - +
307D MET* 3.3 9.3 + - - +
308D ARG 3.2 0.6 - - - -
309D ASN* 1.3 79.6 - - - +
311D LEU* 1.3 57.9 + - + +
313D LEU* 3.2 4.4 + - - +
314D LYS* 2.7 44.7 + - + -
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Residues in contact with LEU 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D TYR* 3.6 41.0 - - + +
4D GLN 4.0 2.5 - - - +
5D PRO* 3.7 30.3 - - + -
9D ASP* 3.8 23.1 - - + +
11D PHE* 3.9 14.6 - - + -
307D MET 3.1 15.2 + - - +
308D ARG 3.7 6.3 - - - +
310D TYR* 1.3 78.9 - - + +
312D ILE* 1.3 63.1 + - - +
314D LYS* 3.3 22.5 + - + +
315D GLU* 3.0 23.0 + - - +
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Residues in contact with ILE 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ASP* 3.7 17.3 - - - +
384B LEU* 4.0 22.2 - - + -
386B ALA* 3.7 28.7 - - + -
3D TYR* 3.7 27.8 - - + -
308D ARG* 2.9 33.8 + - + +
309D ASN* 3.6 17.7 - - - +
311D LEU* 1.3 76.1 - - - +
313D LEU* 1.3 64.8 + - + +
315D GLU* 3.2 4.2 + - - +
316D ARG* 3.0 46.5 + - + +
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Residues in contact with LEU 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LEU* 4.5 9.2 - - + -
260D PHE* 4.1 7.4 - - + -
261D GLY* 5.0 3.8 - - - -
265D LEU* 4.3 15.9 - - + +
268D ALA* 3.6 40.6 - - + +
269D PHE* 4.2 12.0 - - + -
272D VAL* 3.8 18.8 - - + -
309D ASN* 2.9 24.3 + - + +
310D TYR 3.7 3.1 - - - +
312D ILE* 1.3 76.8 - - + +
314D LYS* 1.3 56.6 + - - +
316D ARG* 3.9 4.2 - - + +
317D ALA* 2.8 33.8 + - - +
383D LEU* 3.4 31.9 - - + -
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Residues in contact with LYS 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D ASP* 4.3 15.0 + - - +
272D VAL* 3.5 15.6 - - + +
276D GLU* 3.6 37.8 + - + +
310D TYR* 2.7 27.5 + - + +
311D LEU* 3.4 23.0 - - + +
312D ILE 3.2 0.2 - - - -
313D LEU* 1.3 74.0 - - - +
315D GLU* 1.3 56.4 + - - +
317D ALA* 3.8 1.9 - - - +
318D ALA* 3.0 30.3 + - + +
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Residues in contact with GLU 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D ASN* 5.3 4.2 + - - -
3D TYR* 2.9 37.3 + - + -
311D LEU 3.0 12.6 + - - +
312D ILE 3.2 6.9 + - - +
314D LYS* 1.3 77.9 - - - +
316D ARG* 1.3 78.4 + - - +
318D ALA* 3.2 7.9 + - - +
319D ALA* 3.0 23.8 + - + +
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Residues in contact with ARG 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384B LEU* 2.7 32.5 + - - +
385B GLY 3.1 19.0 + - - -
386B ALA* 4.0 4.6 - - - +
3D TYR* 3.6 15.2 + - - -
269D PHE* 3.9 13.7 - - + -
312D ILE* 3.0 24.2 + - + +
313D LEU* 3.9 5.6 - - - +
315D GLU* 1.3 96.6 + - - +
317D ALA* 1.3 57.0 + - - +
319D ALA* 3.4 7.8 + - - +
320D PHE* 3.0 28.6 + - - +
382D HIS* 3.5 22.0 - - - +
383D LEU* 2.9 30.1 + - + +
385D GLY* 3.6 15.8 - - - +
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Residues in contact with ALA 317 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269D PHE* 3.5 21.4 - - + -
272D VAL* 4.6 2.9 - - + -
273D ASP* 4.0 35.1 - - + +
276D GLU* 5.9 2.7 - - + -
313D LEU 2.8 20.1 + - - +
314D LYS 3.8 3.6 - - - +
316D ARG* 1.3 77.1 - - - +
318D ALA* 1.3 62.3 + - - +
320D PHE* 3.4 2.4 + - - +
321D ARG* 3.1 28.1 + - - +
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Residues in contact with ALA 318 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314D LYS* 3.0 19.7 + - + +
315D GLU* 3.2 8.0 + - - +
317D ALA* 1.3 77.5 - - - +
319D ALA* 1.3 56.1 + - - +
321D ARG* 3.4 4.9 + - - +
322D ALA* 2.9 31.7 + - - +
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Residues in contact with ALA 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D GLU* 3.0 17.0 + - + +
316D ARG* 3.8 10.5 - - - +
318D ALA* 1.3 72.7 - - - +
320D PHE* 1.3 65.8 + - - +
322D ALA* 3.7 5.2 - - - +
323D ASP* 3.0 25.6 + - - +
382D HIS* 3.5 16.8 - - + +
----------------------------------------------------------
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Residues in contact with PHE 320 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147C ALA* 3.9 20.2 - - + -
269D PHE* 4.4 10.3 - + + -
270D TRP* 4.3 6.3 - + - -
273D ASP* 4.6 3.6 - - - -
316D ARG 3.0 17.8 + - - +
317D ALA* 3.5 6.7 - - - +
318D ALA 3.2 0.2 - - - -
319D ALA* 1.3 80.4 - - - +
321D ARG* 1.3 99.0 + - + +
323D ASP 3.2 1.7 + - - -
326D VAL* 3.1 54.3 - - + +
330D LEU* 4.9 0.4 - - + -
375D LEU* 4.2 11.9 - - + -
378D LEU* 4.0 0.7 - - + -
379D ALA* 3.5 42.2 - - + -
382D HIS* 3.7 26.4 + + + -
----------------------------------------------------------
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Residues in contact with ARG 321 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146C GLY 5.1 1.6 + - - -
147C ALA* 4.2 21.4 + - - +
150C ASP* 6.0 0.2 + - - -
270D TRP* 4.3 3.8 - - - -
273D ASP* 2.9 43.4 + - - +
277D SER* 5.6 9.9 - - - -
317D ALA 3.1 11.3 + - - +
318D ALA* 4.0 4.3 - - - +
320D PHE* 1.3 96.0 - - + +
322D ALA* 1.3 57.6 + - - +
326D VAL* 4.7 2.6 - - - +
327D GLN* 3.0 26.7 - - - +
330D LEU* 4.0 34.6 - - - +
335D LEU* 6.2 0.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 322 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D ALA 2.9 19.1 + - - +
319D ALA* 4.1 4.5 - - - +
321D ARG* 1.3 75.4 - - - +
323D ASP* 1.3 64.4 + - - +
324D PRO* 3.3 10.7 - - - +
327D GLN* 3.6 12.6 - - - +
----------------------------------------------------------
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Residues in contact with ASP 323 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319D ALA 3.0 17.5 + - - +
320D PHE 3.2 1.8 + - - -
321D ARG 3.3 0.2 - - - -
322D ALA* 1.3 75.1 - - - +
324D PRO* 1.3 67.7 - - - +
325D GLU* 2.6 33.3 + - - +
326D VAL* 2.8 39.7 + - + +
327D GLN* 2.8 14.8 + - - +
382D HIS* 3.0 19.9 + - + +
387D ARG* 2.9 26.9 + - - -
----------------------------------------------------------
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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