Contacts of the helix formed by residues 281 - 305 (chain C) in PDB entry 1EQB
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 GLU 281 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277C LYS* 3.7 13.5 + - - +
278C GLU* 3.1 19.6 + - + +
279C ALA 4.3 0.7 - - - +
280C MET* 1.3 83.4 - - - +
282C PRO* 1.3 74.8 - - - +
283C GLU* 3.2 24.8 - - + +
284C PHE* 3.0 21.9 + - + +
285C LYS* 3.5 4.3 + - - +
11D TYR* 2.7 36.7 + - + +
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Residues in contact with PRO 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C MET 4.1 4.0 - - - +
281C GLU* 1.3 85.6 - - + +
283C GLU* 1.3 79.0 + - - +
284C PHE 3.0 4.9 - - - -
285C LYS* 3.0 20.2 + - + +
286C THR* 3.2 16.3 + - - +
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Residues in contact with GLU 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281C GLU* 3.2 29.4 - - + +
282C PRO* 1.3 96.3 - - - +
284C PHE* 1.3 56.9 + - - +
286C THR* 3.1 11.4 + - - +
287C TYR* 3.0 27.4 + - - +
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Residues in contact with PHE 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C GLY 3.8 15.5 - - - -
209C ALA* 3.9 8.3 - - + -
210C ALA* 4.5 5.6 - - + -
230C THR 4.0 8.7 - - - -
231C LEU* 4.1 23.1 - - + -
232C ALA* 4.8 4.5 - - + -
278C GLU* 3.6 15.9 - - + +
279C ALA* 3.0 44.4 - - + +
281C GLU* 3.0 17.2 + - + +
282C PRO 3.0 0.8 - - - -
283C GLU* 1.3 79.1 - - - +
285C LYS* 1.3 62.3 + - - +
287C TYR* 3.4 15.4 + + - +
288C GLN* 3.0 50.7 + - + +
371C ARG* 5.1 8.7 - - - -
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Residues in contact with LYS 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210C ALA* 3.1 40.8 - - + +
211C GLY* 5.3 0.9 - - - -
212C VAL* 6.2 0.4 - - - +
281C GLU 3.5 3.9 + - - +
282C PRO* 3.0 14.9 + - + +
284C PHE* 1.3 78.6 - - + +
286C THR* 1.3 64.0 + - + +
288C GLN* 3.5 3.8 + - - +
289C GLN* 3.1 45.5 + - + +
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Residues in contact with THR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C PRO 3.2 9.8 + - - +
283C GLU* 3.1 21.0 + - - +
285C LYS* 1.3 76.4 - - + +
287C TYR* 1.3 63.1 + - - +
289C GLN* 3.4 24.5 + - - +
290C GLN* 3.1 24.9 + - - +
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Residues in contact with TYR 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASN* 3.2 21.2 + - - -
230C THR* 4.5 4.9 - - - -
232C ALA* 5.1 1.8 - - + -
283C GLU 3.0 18.7 + - - +
284C PHE* 3.4 19.7 - + - +
285C LYS 3.1 0.2 - - - -
286C THR* 1.3 75.9 + - - +
288C GLN* 1.3 98.3 + - - +
290C GLN* 3.1 8.3 + - - +
291C VAL* 3.0 36.5 + - + +
367C PRO* 2.8 23.7 + - - +
370C THR* 3.8 8.3 - - + -
371C ARG* 3.3 49.5 - - + +
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Residues in contact with GLN 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C GLY 3.5 15.2 - - - +
207C LEU* 3.1 31.4 + - + +
210C ALA* 3.4 27.8 - - + -
212C VAL* 4.2 6.5 - - + +
230C THR* 3.3 14.0 + - - +
284C PHE* 3.0 41.2 + - + +
286C THR 3.4 0.2 - - - -
287C TYR* 1.3 105.2 - - - +
289C GLN* 1.3 61.6 + - - +
291C VAL* 3.1 10.8 + - - +
292C ALA* 3.0 23.7 + - - +
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Residues in contact with GLN 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212C VAL* 4.0 18.7 - - + +
285C LYS* 3.1 38.8 + - - +
286C THR* 3.5 28.0 + - - +
287C TYR 3.2 0.2 - - - -
288C GLN* 1.3 78.1 - - - +
290C GLN* 1.3 55.8 + - - +
292C ALA* 3.6 4.3 + - - +
293C LYS* 2.9 48.4 + - - +
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Residues in contact with GLN 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C THR 3.1 10.8 + - - +
287C TYR* 3.1 6.8 + - - +
289C GLN* 1.3 76.7 - - - +
291C VAL* 1.3 56.8 + - - +
293C LYS* 3.4 11.5 - - - +
294C ASN* 2.6 69.8 + - - +
370C THR* 3.4 19.7 - - + -
374C PHE 5.0 0.4 - - - +
375C LYS* 3.6 30.9 - - + +
376C GLU* 3.2 23.5 + - - +
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Residues in contact with VAL 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LEU* 4.6 6.1 - - + -
230C THR* 5.4 0.2 - - + -
287C TYR* 3.0 36.8 + - + +
288C GLN* 3.1 17.9 + - - +
290C GLN* 1.3 77.2 - - - +
292C ALA* 1.3 62.3 + - - +
294C ASN 3.3 0.2 + - - -
295C ALA* 3.0 12.1 + - - +
317C HIS* 3.6 25.4 - - + -
366C THR* 2.7 32.5 + - - +
367C PRO* 3.9 14.6 - - + -
370C THR* 3.5 25.6 - - + -
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Residues in contact with ALA 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207C LEU* 5.2 3.4 - - + -
212C VAL* 4.2 20.4 - - + -
288C GLN 3.0 11.5 + - - +
289C GLN* 4.0 3.6 - - - +
291C VAL* 1.3 79.5 - - - +
293C LYS* 1.3 63.5 + - - +
295C ALA* 3.1 5.2 + - - +
296C LYS* 3.1 32.1 + - - +
315C ASP 5.4 2.9 - - - +
316C ASN* 3.7 27.1 - - - +
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Residues in contact with LYS 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C GLN* 2.9 35.4 + - - +
290C GLN* 3.4 17.2 - - - +
292C ALA* 1.3 77.1 - - - +
294C ASN* 1.3 62.0 + - - +
296C LYS* 3.2 12.9 + - + +
297C ALA* 3.2 19.4 + - - +
376C GLU* 3.2 35.2 - - + +
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Residues in contact with ASN 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C GLN* 2.6 31.6 + - - +
291C VAL 3.7 3.4 - - - +
293C LYS* 1.3 68.8 - - - +
295C ALA* 1.3 66.2 + - - +
297C ALA* 3.2 8.2 + - - +
298C MET* 3.1 26.9 + - - +
366C THR* 3.8 11.4 - - + -
369C ILE* 5.0 2.8 - - + +
370C THR* 2.9 26.5 + - - +
374C PHE* 3.2 24.5 + - - +
375C LYS 3.0 5.1 - - - -
376C GLU* 3.0 29.8 + - - +
379C ALA* 4.1 9.8 - - + +
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Residues in contact with ALA 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C VAL 3.0 12.6 + - - +
292C ALA 3.1 5.6 + - - +
294C ASN* 1.3 78.2 - - - +
296C LYS* 1.3 62.4 + - - +
298C MET* 3.3 4.2 + - - +
299C VAL* 3.2 25.5 + - - +
314C THR* 3.9 10.1 - - + +
316C ASN 3.3 26.5 - - - +
317C HIS 3.9 9.0 - - - +
319C PHE* 3.9 6.5 - - + -
366C THR* 3.4 20.2 - - + +
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Residues in contact with LYS 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292C ALA* 3.1 18.2 + - - +
293C LYS* 3.6 12.8 - - + +
294C ASN 3.2 0.2 - - - -
295C ALA* 1.3 79.5 - - - +
297C ALA* 1.3 62.8 + - - +
299C VAL* 3.2 5.7 + - - +
300C GLU* 3.1 30.2 + - + +
314C THR* 2.7 40.1 + - + +
315C ASP* 3.8 16.9 + - - +
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Residues in contact with ALA 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293C LYS 3.2 9.1 + - - +
294C ASN 3.2 10.6 + - - +
296C LYS* 1.3 80.8 - - - +
298C MET* 1.3 60.7 + - - +
300C GLU* 3.6 13.6 + - - +
301C VAL* 3.5 24.8 + - - +
376C GLU* 4.2 21.5 - - + +
379C ALA* 4.6 2.5 - - + -
380C LYS* 3.8 30.2 - - + +
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Residues in contact with MET 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LEU* 4.1 15.3 - - + -
294C ASN 3.1 12.6 + - - +
295C ALA 3.8 2.2 - - - +
297C ALA* 1.3 73.9 - - - +
299C VAL* 1.3 65.6 + - - +
301C VAL* 3.4 3.3 + - - +
302C PHE* 3.1 30.3 + - + -
319C PHE* 3.8 15.7 - - + -
364C VAL* 4.4 9.6 - - + -
366C THR* 4.0 21.3 - - - -
369C ILE* 4.3 7.9 - - - -
379C ALA* 3.5 17.5 - - + +
382C LEU* 3.8 23.1 - - + -
383C ALA* 3.7 37.0 - - + +
386C MET* 4.0 13.5 - - - -
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Residues in contact with VAL 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295C ALA 3.2 15.2 + - - +
296C LYS* 3.5 10.1 - - - +
298C MET* 1.3 74.0 - - - +
300C GLU* 1.3 67.9 + - + +
302C PHE* 3.2 7.1 + - - +
303C LEU* 3.0 39.3 + - + +
309C VAL* 4.3 10.3 - - + -
312C GLY 4.4 0.4 - - - +
313C GLY* 4.1 21.5 - - - -
314C THR* 3.6 16.8 - - + +
319C PHE* 3.4 33.9 - - + -
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Residues in contact with GLU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296C LYS* 3.1 20.9 + - + +
297C ALA* 3.7 15.7 - - - +
299C VAL* 1.3 79.6 - - + +
301C VAL* 1.3 66.2 + - + +
303C LEU* 3.0 9.9 + - - +
304C GLU* 2.9 40.0 + - + +
380C LYS* 4.0 21.4 + - - -
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Residues in contact with VAL 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297C ALA 3.5 15.5 - - - +
298C MET 3.4 6.5 + - - +
299C VAL 3.3 0.6 - - - -
300C GLU* 1.3 77.1 - - + +
302C PHE* 1.3 63.9 + - - +
304C GLU* 3.2 12.4 + - + +
305C ARG* 2.9 40.0 + - + +
380C LYS* 3.7 32.1 - - + +
383C ALA* 3.8 7.9 - - + +
384C GLY* 3.9 30.1 - - - +
387C CYS* 4.8 0.2 - - - -
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Residues in contact with PHE 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C MET* 3.1 29.6 + - + +
299C VAL* 3.2 8.7 + - - +
301C VAL* 1.3 75.1 - - - +
303C LEU* 1.3 60.2 + - - +
305C ARG 3.4 6.2 + - - -
306C GLY 3.4 0.2 + - - -
307C TYR* 2.9 43.7 + - + +
309C VAL* 4.0 14.1 - - + -
319C PHE* 4.2 15.9 - + - -
321C VAL* 3.7 30.5 - - + -
362C ILE* 5.0 2.0 - - + -
364C VAL* 5.1 1.3 - - + -
383C ALA* 3.8 26.2 - - + -
386C MET* 4.0 35.9 - - + -
387C CYS* 4.0 16.8 - - - -
390C LEU* 4.3 17.0 - - + -
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Residues in contact with LEU 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299C VAL* 3.0 26.2 + - + +
300C GLU* 3.5 8.7 - - - +
302C PHE* 1.3 71.4 - - - +
304C GLU* 1.3 60.3 + - + +
305C ARG 3.0 4.7 - - - -
306C GLY* 3.0 18.9 + - - -
307C TYR 3.3 20.1 - - - +
308C LYS* 5.0 0.9 - - - -
309C VAL* 3.8 22.9 - - + +
312C GLY* 3.8 23.3 - - - +
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Residues in contact with GLU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C GLU* 2.9 35.6 + - - +
301C VAL* 3.2 10.5 + - + +
303C LEU* 1.3 75.8 - - + +
305C ARG* 1.3 63.4 + - + +
306C GLY 3.3 1.4 + - - -
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Residues in contact with ARG 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C VAL* 2.9 27.3 + - + +
302C PHE 3.8 2.5 - - - +
303C LEU 3.0 0.6 - - - -
304C GLU* 1.3 83.6 - - + +
306C GLY* 1.3 59.1 + - - +
307C TYR* 3.6 13.0 - - + -
326C LYS* 4.7 3.1 + - - -
384C GLY* 3.5 24.2 + - - -
387C CYS* 3.3 26.7 - - - +
388C ASP* 2.7 36.3 + - - +
391C ASP* 2.8 31.8 + - - +
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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