Contacts of the helix formed by residues 295 - 323 (chain E) 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 E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31E ARG* 3.8 9.4 - - - +
294E GLU* 1.3 76.5 + - - +
296E ILE* 1.3 59.4 + - + +
297E ASP* 2.9 26.9 + - - +
298E GLY* 2.7 30.0 + - - +
299E VAL* 3.0 9.9 + - - +
367G ALA 4.1 10.7 - - - +
368G ARG* 5.2 0.2 - - - -
369G GLY* 3.5 31.3 + - - +
371G ALA* 6.0 1.9 - - - -
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Residues in contact with ILE 296 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E VAL 5.5 0.9 - - - +
31E ARG* 3.9 8.1 - - - +
32E PRO* 6.3 4.5 - - + -
34E LEU* 4.4 17.5 - - + -
38E GLU* 6.2 0.4 - - + -
295E ASP* 1.3 77.6 - - + +
297E ASP* 1.3 79.0 + - - +
299E VAL* 3.2 31.7 + - + +
300E TRP* 3.3 41.2 - - + +
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Residues in contact with ASP 297 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295E ASP* 2.9 16.5 + - - +
296E ILE* 1.3 88.6 - - - +
298E GLY* 1.3 63.4 + - - +
299E VAL 3.4 0.2 + - - -
300E TRP* 3.5 13.4 + - - +
301E ALA 3.2 15.9 + - - -
374G ARG* 3.5 27.2 + - - +
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Residues in contact with GLY 298 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294E GLU* 3.7 29.6 - - - -
295E ASP* 2.7 19.0 + - - -
297E ASP* 1.3 70.7 - - - +
299E VAL* 1.3 59.7 + - - +
301E ALA* 3.3 7.7 + - - +
302E SER* 2.9 31.7 + - - -
371G ALA* 5.7 2.7 - - - -
373G GLU* 4.1 3.7 - - - +
374G ARG* 5.1 2.2 - - - -
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Residues in contact with VAL 299 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E VAL* 3.6 44.9 - - + +
31E ARG* 3.3 45.1 - - - +
290E PRO* 3.9 16.5 - - + +
294E GLU* 4.4 0.4 - - - +
295E ASP 3.0 7.9 + - - +
296E ILE* 3.2 15.5 - - + +
298E GLY* 1.3 74.9 - - - +
300E TRP* 1.3 73.6 + - + +
302E SER* 3.1 5.7 + - - -
303E ALA* 2.9 26.3 + - - +
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Residues in contact with TRP 300 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E VAL* 3.7 29.2 - - + -
34E LEU* 4.0 28.9 - - + -
38E GLU* 4.8 2.4 + - + -
39E ALA* 4.1 10.3 - - - -
42E ARG* 3.4 48.2 - - + +
43E LEU* 4.3 11.0 - - + -
46E LEU* 3.7 29.9 - - + +
296E ILE* 3.3 50.5 + - + +
297E ASP* 4.0 11.2 - - - +
299E VAL* 1.3 78.4 - - + +
301E ALA* 1.3 57.9 + - - +
303E ALA* 3.3 2.2 + - - +
304E ALA* 2.9 29.3 + - - +
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Residues in contact with ALA 301 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E ARG* 5.1 0.3 - - - -
297E ASP 3.2 13.9 + - - +
298E GLY* 3.5 11.2 - - - +
299E VAL 3.2 0.2 - - - -
300E TRP* 1.3 74.4 - - - +
302E SER* 1.3 62.2 + - - +
304E ALA* 3.3 7.5 + - - +
305E GLY* 2.9 24.6 + - - -
373G GLU* 5.0 2.9 - - - +
374G ARG* 3.7 49.6 - - + +
377G GLN* 5.6 3.6 - - - +
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Residues in contact with SER 302 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E ARG* 3.6 10.9 + - - +
288E PHE* 3.2 23.0 - - - -
290E PRO* 4.1 11.2 - - - +
291E PRO* 4.3 0.7 - - - +
298E GLY 2.9 17.1 + - - -
299E VAL 3.4 5.2 - - - -
301E ALA* 1.3 75.4 - - - +
303E ALA* 1.3 62.7 + - - +
305E GLY* 3.2 2.6 + - - -
306E CYS* 3.1 23.2 + - - -
373G GLU* 2.8 38.3 + - - +
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Residues in contact with ALA 303 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E PHE* 3.4 26.0 - - + -
18E VAL* 4.0 18.2 - - + -
43E LEU* 4.7 1.6 - - + -
46E LEU* 3.9 15.0 - - + -
288E PHE* 3.6 10.7 - - - -
299E VAL 2.9 12.6 + - - +
300E TRP* 3.5 10.1 - - + +
301E ALA 3.2 0.2 - - - -
302E SER* 1.3 77.6 - - - +
304E ALA* 1.3 61.1 + - - +
306E CYS* 3.1 19.1 + - - +
307E MET* 3.6 4.4 + - - +
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Residues in contact with ALA 304 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E PRO* 5.7 2.0 - - - +
46E LEU* 4.3 17.6 - - + +
300E TRP 2.9 17.2 + - - +
301E ALA* 3.7 7.9 - - - +
303E ALA* 1.3 74.7 - - - +
305E GLY* 1.3 60.8 + - - +
306E CYS 3.2 0.2 + - - -
307E MET* 3.3 13.4 + - - +
308E ARG* 2.9 31.5 + - + +
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Residues in contact with GLY 305 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E ARG* 4.1 6.3 - - - -
301E ALA 2.9 14.9 + - - -
302E SER 3.2 5.3 + - - -
304E ALA* 1.3 78.3 - - - +
306E CYS* 1.3 61.4 + - - +
308E ARG* 4.2 2.9 - - - -
309E ASN* 2.9 33.4 + - - -
377G GLN* 3.9 26.5 - - - -
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Residues in contact with CYS 306 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E PHE* 4.1 3.8 - - + -
259E ARG* 3.6 20.2 - - - -
260E PHE* 3.7 18.1 - - - +
286E PHE* 3.6 39.4 - - + -
288E PHE* 3.9 25.6 - - - -
302E SER 3.1 18.1 + - - -
303E ALA 3.1 11.4 + - - +
305E GLY* 1.3 78.5 - - - +
307E MET* 1.3 63.2 + - - +
309E ASN* 3.5 2.8 + - - +
310E TYR* 3.2 15.6 + - - +
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Residues in contact with MET 307 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E PRO* 3.9 19.7 - - + -
11E PHE* 3.5 49.8 - - + -
13E PHE* 3.5 27.4 - - + -
43E LEU* 5.2 0.2 - - + -
46E LEU* 3.8 35.0 - - + +
47E GLY 4.2 9.4 - - - +
48E ALA* 4.3 3.6 - - + +
286E PHE* 3.9 13.9 - - + -
303E ALA 3.8 9.0 - - - +
304E ALA* 3.3 10.4 + - - +
306E CYS* 1.3 77.5 - - - +
308E ARG* 1.3 68.1 + - - +
310E TYR* 3.1 3.6 + - - +
311E LEU* 2.9 27.1 + - - +
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Residues in contact with ARG 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ASN 2.8 32.9 + - - +
3E TYR* 3.7 35.7 + - + +
5E PRO* 5.4 2.4 - - + +
304E ALA 2.9 18.4 + - - +
305E GLY* 3.9 4.7 - - - +
307E MET* 1.3 76.3 - - - +
309E ASN* 1.3 59.1 + - - +
311E LEU* 3.0 4.1 + - - +
312E ILE* 2.8 40.6 + - + +
377G GLN* 3.7 21.5 - - - +
381G ASP* 3.0 23.0 + - - -
386G ALA* 2.8 28.5 + - - +
387G ARG* 4.9 1.0 - - - +
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Residues in contact with ASN 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E ARG* 3.8 4.7 + - - -
260E PHE* 2.9 30.4 - - + +
261E GLY* 4.1 11.2 - - - -
305E GLY 2.9 15.2 + - - +
306E CYS 3.9 0.2 - - - +
308E ARG* 1.3 76.6 - - - +
310E TYR* 1.3 62.6 + - - +
312E ILE* 3.9 10.5 - - - +
313E LEU* 2.9 35.5 + - + +
377G GLN* 2.6 40.7 + - - -
380G MET* 3.3 26.5 - - - +
384G LEU* 4.9 2.3 - - + +
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Residues in contact with TYR 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E PHE* 3.8 24.2 - + + -
246E LEU* 4.0 17.7 - - + -
260E PHE* 3.6 28.6 - + + -
271E LEU* 6.0 0.2 - - + -
272E VAL* 3.7 28.3 - - + +
275E LEU* 4.0 15.9 - - + +
276E GLU* 2.8 28.8 + - - -
284E ARG* 2.9 38.1 + - + -
286E PHE* 4.4 1.1 - - + -
306E CYS 3.2 12.4 + - - +
307E MET 3.1 9.2 + - - +
309E ASN* 1.3 77.9 - - - +
311E LEU* 1.3 61.6 + - + +
313E LEU* 3.2 2.9 + - - +
314E LYS* 2.7 37.3 + - + -
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Residues in contact with LEU 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E TYR* 3.3 43.3 - - + +
4E GLN 3.7 3.8 - - - +
5E PRO* 3.7 28.9 - - + -
9E ASP* 3.9 24.5 - - - +
11E PHE* 4.0 10.5 - - + -
307E MET 2.9 15.9 + - - +
308E ARG 3.5 5.8 - - - +
310E TYR* 1.3 77.6 - - + +
312E ILE* 1.3 64.0 + - - +
314E LYS* 3.1 19.6 + - + +
315E GLU* 3.0 22.5 + - - +
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Residues in contact with ILE 312 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E TYR* 3.6 28.0 - - + -
308E ARG* 2.8 41.0 + - + +
309E ASN* 3.9 13.2 - - - +
311E LEU* 1.3 71.6 - - - +
313E LEU* 1.3 64.7 + - + +
315E GLU* 3.0 13.3 + - - +
316E ARG* 3.1 41.7 + - + +
381G ASP* 3.9 9.6 - - - +
384G LEU* 4.1 27.1 - - + -
386G ALA* 3.4 24.0 - - + -
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Residues in contact with LEU 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260E PHE* 4.1 11.7 - - + -
261E GLY* 4.6 7.9 - - - -
265E LEU* 4.2 14.6 - - + -
268E ALA* 3.7 31.9 - - + +
269E PHE* 4.0 18.0 - - + +
272E VAL* 4.0 14.1 - - + +
309E ASN* 2.9 28.0 + - + +
310E TYR 3.6 2.7 - - - +
312E ILE* 1.3 77.0 - - + +
314E LYS* 1.3 56.4 + - - +
316E ARG* 3.9 4.9 - - - +
317E ALA* 2.9 31.4 + - - +
383E LEU* 3.5 28.9 - - + -
384G LEU* 4.8 7.4 - - + -
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Residues in contact with LYS 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E ASP* 4.7 13.1 + - - -
272E VAL* 3.6 13.2 - - + +
276E GLU* 3.4 41.0 + - + +
310E TYR* 2.7 22.9 + - + +
311E LEU* 3.4 21.0 - - + +
313E LEU* 1.3 78.5 - - - +
315E GLU* 1.3 62.9 + - - +
317E ALA* 3.9 2.5 - - - +
318E ALA* 3.1 25.6 + - + +
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Residues in contact with GLU 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2E ASN* 4.9 4.0 - - - +
3E TYR* 2.7 39.2 + - + -
311E LEU 3.0 12.4 + - - +
312E ILE 3.5 6.3 - - - +
314E LYS* 1.3 79.4 - - - +
316E ARG* 1.3 80.0 + - - +
318E ALA* 3.8 4.8 - - - +
319E ALA* 3.1 24.4 + - + +
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Residues in contact with ARG 316 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3E TYR* 3.4 20.6 + - - -
269E PHE* 3.9 16.7 - - + -
312E ILE* 3.1 25.2 + - + +
313E LEU 4.0 2.2 - - - +
315E GLU* 1.3 93.6 + - - +
317E ALA* 1.3 58.9 + - - +
319E ALA* 3.8 7.0 - - - +
320E PHE* 2.9 30.0 + - - +
382E HIS* 3.2 24.6 - - - +
383E LEU* 2.9 30.9 + - + +
385E GLY* 3.5 17.1 - - - +
384G LEU* 2.7 33.7 + - - +
385G GLY 3.4 11.5 + - - -
386G ALA* 4.5 0.2 - - - +
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Residues in contact with ALA 317 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269E PHE* 3.6 18.3 - - + +
272E VAL* 4.7 0.9 - - + -
273E ASP* 3.8 39.6 - - + +
276E GLU* 6.0 2.9 - - + -
313E LEU 2.9 19.0 + - - +
314E LYS* 3.9 4.9 - - - +
316E ARG* 1.3 76.5 - - - +
318E ALA* 1.3 57.8 + - - +
320E PHE* 3.4 2.4 + - - +
321E ARG* 3.0 33.4 + - - +
----------------------------------------------------------
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Residues in contact with ALA 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314E LYS* 3.1 19.0 + - + +
315E GLU* 3.8 4.9 - - - +
317E ALA* 1.3 76.4 - - - +
319E ALA* 1.3 60.3 + - - +
321E ARG* 3.3 6.7 + - - +
322E ALA* 2.9 30.7 + - - +
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Residues in contact with ALA 319 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315E GLU* 3.1 20.9 + - + +
316E ARG* 3.8 9.4 - - - +
318E ALA* 1.3 73.4 - - - +
320E PHE* 1.3 66.6 + - - +
322E ALA* 3.3 5.8 + - - +
323E ASP* 3.0 26.2 + - - +
382E HIS* 3.4 17.1 - - + +
----------------------------------------------------------
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Residues in contact with PHE 320 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269E PHE* 4.5 10.3 - + + -
270E TRP* 4.2 7.2 - + - -
273E ASP* 4.7 3.4 - - - -
316E ARG 2.9 17.7 + - - +
317E ALA* 3.5 6.1 - - - +
319E ALA* 1.3 80.6 - - - +
321E ARG* 1.3 98.0 + - + +
322E ALA 3.3 0.2 + - - -
323E ASP* 3.4 5.5 + - - +
326E VAL* 3.3 51.4 - - + +
330E LEU* 5.2 0.7 - - + -
375E LEU* 4.0 10.3 - - + -
379E ALA* 3.6 37.2 - - + -
382E HIS* 3.5 25.9 + + + -
147F ALA* 3.7 25.8 - - + -
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Residues in contact with ARG 321 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270E TRP* 4.2 8.7 - - - -
273E ASP* 2.9 37.7 + - - +
277E SER* 5.5 11.5 - - - -
317E ALA 3.0 21.7 + - - +
318E ALA* 3.3 6.7 + - - +
320E PHE* 1.3 96.3 - - + +
322E ALA* 1.3 58.0 + - - +
323E ASP 3.4 0.4 + - - -
326E VAL* 5.1 2.0 - - - -
327E GLN* 3.3 21.3 - - - +
330E LEU* 4.0 33.9 - - - +
146F GLY 5.0 1.8 + - - -
147F ALA* 4.4 11.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 322 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318E ALA 2.9 17.8 + - - +
319E ALA* 4.0 5.6 - - - +
320E PHE 3.2 0.2 - - - -
321E ARG* 1.3 75.1 - - - +
323E ASP* 1.3 62.0 + - - +
324E PRO* 3.2 10.4 - - - +
327E GLN* 3.0 16.1 - - - +
----------------------------------------------------------
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Residues in contact with ASP 323 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319E ALA 3.0 16.1 + - - +
320E PHE 3.4 1.0 + - - +
322E ALA* 1.3 74.2 - - - +
324E PRO* 1.3 66.0 - - - +
325E GLU* 2.7 22.3 + - - +
326E VAL* 2.9 25.6 + - + +
327E GLN* 2.9 27.5 + - - +
382E HIS* 2.8 22.5 + - + +
387E ARG* 2.9 25.3 + - - -
----------------------------------------------------------
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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