Contacts of the helix formed by residues 295 - 323 (chain A) in PDB entry 6YBO
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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 4.2 8.7 - - - +
293A THR 4.1 0.8 + - - -
294A GLU* 1.3 76.4 - - - +
296A PHE* 1.3 66.0 + - - +
297A ASP* 3.1 24.6 + - - +
298A GLY* 3.0 17.8 + - - -
299A VAL* 3.0 12.3 + - - +
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Residues in contact with PHE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL 5.0 1.8 - - - -
31A ARG* 4.1 18.1 - - + +
32A ARG* 3.3 66.4 - - + -
34A LEU* 3.7 36.8 - - + -
295A ASP* 1.3 76.9 - - + +
297A ASP* 1.3 65.3 + - - +
299A VAL* 3.1 24.9 + - + +
300A TRP* 3.0 33.8 + - + +
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Residues in contact with ASP 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 5.4 3.8 + - - -
295A ASP* 3.1 15.2 + - - +
296A PHE* 1.3 78.0 - - - +
298A GLY* 1.3 58.2 + - - +
300A TRP* 3.4 10.6 + - - +
301A ALA* 3.0 26.5 + - - +
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Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A GLU* 3.8 29.2 - - - +
295A ASP* 3.0 16.2 + - - -
297A ASP* 1.3 75.7 - - - +
299A VAL* 1.3 62.9 + - - +
301A ALA* 3.7 7.4 - - - +
302A SER* 2.9 26.7 + - - -
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.6 38.6 - - + +
31A ARG* 3.5 39.0 - - - +
290A PRO* 3.9 20.9 - - + +
294A GLU* 4.3 0.4 - - - +
295A ASP 3.0 17.1 + - - +
296A PHE* 3.1 18.3 + - + +
298A GLY* 1.3 77.6 - - - +
300A TRP* 1.3 70.7 + - + +
302A SER* 3.3 2.4 + - - -
303A ALA* 3.0 26.2 + - - +
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Residues in contact with TRP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A VAL* 3.8 40.8 - - + -
34A LEU* 4.0 26.7 - - + -
38A GLU* 5.3 2.8 + - + -
39A SER* 4.2 9.2 - - - -
42A ARG* 3.4 69.1 - - + +
43A LEU* 4.1 12.6 - - + -
46A LEU* 3.9 27.6 - - + +
296A PHE* 3.0 37.2 + + + +
297A ASP* 4.1 8.1 - - - +
298A GLY 3.3 0.2 - - - -
299A VAL* 1.3 82.2 - - + +
301A ALA* 1.3 60.1 + - - +
303A ALA* 3.4 2.3 + - + +
304A ALA* 2.9 31.1 + - - +
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Residues in contact with ALA 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG* 5.2 0.2 - - - -
297A ASP 3.0 17.8 + - - +
298A GLY* 3.7 8.3 - - - +
299A VAL 3.3 0.2 - - - -
300A TRP* 1.3 77.5 - - - +
302A SER* 1.3 56.4 + - - +
304A ALA* 3.4 6.5 + - - +
305A GLY* 2.9 25.3 + - - -
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Residues in contact with SER 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG* 3.7 26.4 + - - +
288A PHE* 3.3 22.1 - - - -
290A PRO* 4.2 14.2 - - - +
291A PRO* 4.4 8.3 - - - +
294A GLU* 6.0 0.9 - - - -
298A GLY 2.9 18.8 + - - -
299A VAL 3.6 4.3 - - - -
301A ALA* 1.3 76.8 - - - +
303A ALA* 1.3 62.0 + - - +
305A GLY* 3.2 2.4 + - - -
306A CYS* 3.1 22.2 + - - -
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 3.6 29.4 - - + -
18A VAL* 4.0 12.8 - - + -
43A LEU* 4.6 2.5 - - + -
46A LEU* 4.2 12.8 - - + -
288A PHE* 3.7 15.4 - - + -
299A VAL 3.0 16.9 + - - +
300A TRP* 3.8 6.1 - - + +
302A SER* 1.3 76.5 - - - +
304A ALA* 1.3 62.6 + - - +
306A CYS* 3.2 19.0 + - - +
307A MET* 3.6 4.3 + - - +
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 5.7 0.9 - - - +
46A LEU* 4.3 16.9 - - + +
300A TRP 2.9 18.2 + - - +
301A ALA* 3.7 6.7 - - - +
303A ALA* 1.3 76.5 - - - +
305A GLY* 1.3 57.4 + - - +
307A MET* 3.2 17.9 + - + +
308A ARG* 3.0 28.1 + - - +
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Residues in contact with GLY 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG* 4.4 12.3 - - - -
301A ALA 2.9 15.5 + - - -
302A SER 3.2 4.7 + - - -
303A ALA 3.2 0.4 - - - -
304A ALA* 1.3 73.9 - - - +
306A CYS* 1.3 64.5 + - - +
308A ARG* 4.2 9.6 - - - -
309A ASN* 2.9 35.5 + - - -
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Residues in contact with CYS 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 4.3 0.4 - - + -
259A ARG* 3.8 10.2 - - - +
260A PHE* 3.6 33.0 - - - -
286A PHE* 3.6 45.2 - - + -
288A PHE* 4.0 23.3 - - - -
302A SER 3.1 19.4 + - - -
303A ALA 3.2 9.6 + - - +
305A GLY* 1.3 78.5 - - - +
307A MET* 1.3 61.3 + - - +
309A ASN* 4.1 0.2 - - - +
310A TYR* 3.3 15.2 + - - +
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Residues in contact with MET 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PRO* 3.8 23.1 - - + -
11A PHE* 3.6 43.4 - - + -
13A PHE* 3.9 20.2 - - + -
46A LEU* 3.6 38.1 - - + +
48A ALA* 4.3 11.4 - - + +
286A PHE* 3.9 14.6 - - + -
303A ALA 4.0 12.8 - - - +
304A ALA* 3.2 12.4 + - - +
306A CYS* 1.3 74.1 - - - +
308A ARG* 1.3 65.9 + - - +
310A TYR* 3.3 3.5 + - - +
311A LEU* 3.0 28.7 + - - +
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Residues in contact with ARG 308 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 4.0 52.7 + - + +
5A PRO* 5.4 1.2 - - + +
304A ALA 3.0 16.8 + - - +
305A GLY* 3.4 8.7 + - - +
307A MET* 1.3 76.9 - - - +
309A ASN* 1.3 60.8 + - - +
311A LEU* 3.2 3.7 + - - +
312A ILE* 2.9 50.7 + - + +
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Residues in contact with ASN 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ARG* 4.0 21.8 - - - +
260A PHE* 2.9 28.7 + - + +
261A GLY* 4.0 18.1 - - - -
265A LEU* 6.4 0.9 - - + -
305A GLY* 2.9 19.2 + - - +
306A CYS 4.1 1.1 - - - +
308A ARG* 1.3 77.7 - - - +
310A TYR* 1.3 65.6 + - - +
312A ILE* 3.4 14.3 + - - +
313A LEU* 3.0 35.0 + - + +
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Residues in contact with TYR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE* 3.7 28.0 - + + -
246A LEU* 4.1 17.9 - - + -
260A PHE* 3.8 24.9 - + + -
272A VAL* 3.8 24.2 - - + +
275A LEU* 4.0 18.2 - - + +
276A GLU* 2.6 30.7 + - - +
284A ARG* 3.2 33.1 + - + +
286A PHE* 4.6 0.9 - - + -
306A CYS 3.3 10.7 + - - +
307A MET 3.3 8.6 + - - +
309A ASN* 1.3 78.6 - - - +
311A LEU* 1.3 61.3 + - + +
313A LEU* 3.3 3.3 + - - +
314A LYS* 2.8 36.4 + - + +
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 3.5 42.5 - - + +
4A GLN 3.8 3.4 - - - +
5A PRO* 3.7 29.6 - - + -
9A ASP* 4.0 18.8 - - - +
11A PHE* 4.0 17.3 - - + -
307A MET 3.0 18.3 + - - +
308A ARG 3.7 6.1 - - - +
310A TYR* 1.3 75.5 - - + +
312A ILE* 1.3 64.9 + - - +
314A LYS* 3.4 19.3 + - + +
315A GLU* 3.1 22.5 + - - +
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Residues in contact with ILE 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 3.8 33.7 - - + -
308A ARG* 2.9 46.2 + - + +
309A ASN* 3.9 15.3 - - - +
311A LEU* 1.3 74.8 - - - +
313A LEU* 1.3 69.1 + - + +
315A GLU* 3.1 4.9 + - - +
316A ARG* 3.0 52.0 + - + +
383A LEU* 5.9 0.4 - - + +
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Residues in contact with LEU 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PHE* 4.1 13.7 - - + -
261A GLY* 5.1 1.1 - - - -
265A LEU* 4.3 16.6 - - + -
268A ALA* 3.7 35.7 - - + +
269A PHE* 4.1 14.8 - - + -
272A VAL* 4.0 14.5 - - + +
309A ASN* 3.0 26.6 + - + +
310A TYR 3.8 2.7 - - - +
312A ILE* 1.3 81.1 - - + +
314A LYS* 1.3 57.8 + - - +
316A ARG* 3.3 4.0 + - + +
317A ALA* 2.9 32.7 + - - +
383A LEU* 3.5 31.6 - - + -
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASP* 4.6 13.1 + - - -
272A VAL* 3.6 15.1 - - + +
276A GLU* 3.8 37.7 + - + +
310A TYR* 2.8 26.2 + - + +
311A LEU* 3.6 19.3 - - + +
312A ILE 3.2 0.2 - - - -
313A LEU* 1.3 77.4 - - - +
315A GLU* 1.3 61.4 + - - +
317A ALA* 4.0 1.9 - - - +
318A ALA* 3.0 26.0 + - + +
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 2.6 39.0 + - + -
311A LEU 3.1 13.8 + - - +
312A ILE 3.1 5.7 + - - +
314A LYS* 1.3 77.8 - - - +
316A ARG* 1.3 79.9 + - - +
318A ALA* 3.4 5.1 + - - +
319A ALA* 3.0 29.6 + - + +
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Residues in contact with ARG 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A TYR* 3.8 16.8 + - - -
269A PHE* 3.9 14.4 - - + -
312A ILE* 3.0 31.6 + - + +
313A LEU* 3.9 4.7 - - - +
315A GLU* 1.3 94.3 + - - +
317A ALA* 1.3 58.7 + - - +
319A ALA* 3.4 7.8 + - - +
320A PHE* 3.0 28.1 + - - +
382A HIS* 3.4 23.7 - - - +
383A LEU* 2.9 31.9 + - + +
384A LEU 3.7 3.8 + - - -
385A GLY* 3.5 19.7 - - - +
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A PHE* 3.7 20.1 - - + +
272A VAL* 4.8 0.4 - - + -
273A ASP* 3.8 40.1 - - + +
276A GLU* 6.2 1.6 - - + -
313A LEU 2.9 17.5 + - - +
314A LYS* 4.0 4.9 - - - +
316A ARG* 1.3 75.8 - - - +
318A ALA* 1.3 62.7 + - - +
320A PHE* 3.3 3.1 + - - +
321A ARG* 3.1 28.6 + - - +
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Residues in contact with ALA 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A LYS* 3.0 20.4 + - + +
315A GLU* 3.7 5.8 - - - +
317A ALA* 1.3 78.1 - - - +
319A ALA* 1.3 62.1 + - - +
321A ARG* 3.3 5.3 + - - +
322A ALA* 3.0 26.0 + - - +
----------------------------------------------------------
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLU* 3.0 19.8 + - + +
316A ARG* 3.7 10.1 - - - +
318A ALA* 1.3 76.1 - - - +
320A PHE* 1.3 63.5 + - - +
322A ALA* 3.4 5.3 + - - +
323A ASP* 3.1 24.8 + - - +
382A HIS* 3.5 17.9 - - + +
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Residues in contact with PHE 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A PHE* 4.3 12.8 - + + -
270A TRP* 4.0 17.5 - + - -
273A ASP* 4.7 2.5 - - - -
316A ARG 3.0 17.5 + - - +
317A ALA* 3.4 7.0 - - - +
319A ALA* 1.3 79.0 - - - +
321A ARG* 1.3 98.7 - - + +
322A ALA 3.3 0.2 + - - -
323A ASP 3.4 2.3 + - - -
326A VAL* 3.2 62.2 - - + +
330A LEU* 5.3 1.1 - - + -
375A LEU* 4.2 17.3 - - + -
378A LEU 4.2 0.2 - - - -
379A ALA* 3.6 42.6 - - + -
382A HIS* 3.7 20.8 + + + -
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Residues in contact with ARG 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A TRP* 4.0 14.1 - - - -
273A ASP* 2.7 44.0 + - - +
277A SER* 4.6 10.6 + - - +
317A ALA 3.1 15.4 + - - +
318A ALA* 4.0 5.2 - - - +
320A PHE* 1.3 91.7 - - + +
322A ALA* 1.3 57.8 + - - +
323A ASP 3.4 0.6 + - - -
326A VAL* 4.9 2.6 - - - +
327A GLN* 3.0 26.3 + - - +
330A LEU* 3.8 36.0 - - - +
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Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ALA 3.0 17.2 + - - +
319A ALA* 4.0 5.8 - - - +
320A PHE 3.2 0.2 - - - -
321A ARG* 1.3 76.2 - - - +
323A ASP* 1.3 63.3 + - - +
324A PRO* 3.3 9.7 - - - +
327A GLN* 3.7 11.4 + - - +
----------------------------------------------------------
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Residues in contact with ASP 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ALA 3.1 15.4 + - - +
320A PHE 3.4 9.1 + - - +
322A ALA* 1.3 76.0 - - - +
324A PRO* 1.3 73.3 - - - +
325A GLU* 2.9 19.9 + - - +
326A VAL* 3.0 19.4 + - + +
327A GLN* 3.0 13.4 + - - +
382A HIS* 2.7 27.4 + - + +
387A ARG* 2.8 25.2 + - - -
----------------------------------------------------------
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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