Contacts of the helix formed by residues 261 - 283 (chain O) in PDB entry 6NRB
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 261 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280M TYR* 3.1 42.0 + - + +
259O THR 4.8 0.2 - - - +
260O VAL* 1.3 79.7 - - + +
262O ASP* 1.3 62.2 + - - +
263O TYR 2.8 12.2 + - - -
264O GLN 3.6 4.5 + - - -
265O ALA* 3.6 15.8 + - + +
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Residues in contact with ASP 262 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256O ARG* 4.1 7.2 - - - +
257O VAL* 3.2 30.3 - - + +
258O HIS* 3.2 40.9 + - + +
259O THR 4.0 13.6 + - - +
260O VAL 3.3 2.8 - - - +
261O GLU* 1.3 80.2 + - - +
263O TYR* 1.3 63.8 + - - +
264O GLN 3.5 0.4 - - - -
265O ALA* 3.6 17.6 + - - +
266O ILE* 3.7 8.3 + - + +
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Residues in contact with TYR 263 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254M PRO* 5.0 0.2 - - + -
255M PHE 4.3 0.2 + - - -
256M GLU* 3.1 11.7 + - - -
257M PRO* 3.0 49.6 - - + +
258M PRO* 5.0 4.8 - - + +
260M PRO* 6.1 1.6 - - + -
277M LEU* 5.7 10.3 - - + -
280M TYR* 4.8 6.7 - - + -
281M GLU* 3.4 36.6 + - + -
285M PHE* 3.3 19.0 - + - -
307M ASP* 5.3 1.2 + - - +
257O VAL* 4.9 4.2 - - - +
258O HIS* 5.5 10.8 - + + +
260O VAL 4.3 8.2 + - - +
261O GLU 2.8 5.0 + - - +
262O ASP* 1.3 79.4 - - - +
264O GLN* 1.3 87.4 + - + +
266O ILE* 4.3 3.3 - - - +
267O VAL* 3.4 19.8 - - - +
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Residues in contact with GLN 264 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254M PRO* 3.2 27.3 - - - +
280M TYR* 4.5 6.0 - - + +
284M LYS* 3.7 42.2 - - + +
285M PHE* 3.3 15.4 - - - -
288M MET* 3.3 31.7 - - - +
261O GLU 3.6 2.8 + - - -
263O TYR* 1.3 107.4 - - + +
265O ALA* 1.3 64.1 + - - +
266O ILE 3.6 0.2 - - - -
267O VAL* 3.7 5.0 - - - +
268O ASP* 3.5 30.7 + - - +
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Residues in contact with ALA 265 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280M TYR* 5.5 0.4 + - - -
261O GLU* 3.6 27.1 + - + +
262O ASP* 3.6 14.1 + - - +
263O TYR 3.4 1.8 - - - -
264O GLN* 1.3 77.2 - - - +
266O ILE* 1.3 68.6 + - + +
267O VAL 3.3 0.5 + - - -
268O ASP* 3.8 1.4 + - - +
269O ALA* 3.4 21.0 + - - +
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Residues in contact with ILE 266 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260M PRO* 3.8 33.2 - - + -
261M LYS 4.5 1.8 - - - +
262M THR* 3.6 28.5 - - + +
250O LYS* 3.5 17.4 + - - +
255O ILE* 5.7 2.2 - - + +
256O ARG 4.2 7.6 - - - +
257O VAL* 3.6 44.0 - - + -
262O ASP* 3.7 7.2 + - + +
263O TYR 4.3 3.4 - - - +
265O ALA* 1.3 80.0 - - + +
267O VAL* 1.3 79.7 + - + +
269O ALA* 4.5 0.2 - - - -
270O GLU* 3.2 27.0 + - - +
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Residues in contact with VAL 267 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254M PRO* 3.5 33.4 - - + -
258M PRO* 3.5 24.7 - - + -
304M TRP* 3.7 7.9 - - + -
247O LYS* 5.4 1.1 - - + -
263O TYR 3.4 22.7 - - - +
264O GLN* 3.7 8.1 - - - +
265O ALA 3.2 0.4 - - - -
266O ILE* 1.3 87.4 - - + +
268O ASP* 1.3 62.3 + - - +
270O GLU* 2.9 25.7 + - - +
271O TRP* 3.0 36.1 - - + +
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Residues in contact with ASP 268 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254M PRO* 4.9 1.4 - - - +
284M LYS* 5.8 2.3 + - - -
288M MET* 4.8 10.3 - - - +
345M PHE* 5.1 3.5 - - - -
346M SER* 4.0 12.6 + - - +
264O GLN* 3.5 22.0 + - - +
265O ALA 4.7 1.1 - - - +
267O VAL* 1.3 81.0 - - - +
269O ALA* 1.3 61.2 + - - +
270O GLU 3.3 0.2 - - - -
271O TRP* 3.1 59.1 + - - +
272O ASN* 3.3 17.2 + - - +
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Residues in contact with ALA 269 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250O LYS* 4.0 20.2 - - + +
265O ALA 3.4 17.3 + - - +
266O ILE 3.9 3.8 - - - +
267O VAL 3.1 0.6 - - - -
268O ASP* 1.3 75.3 - - - +
270O GLU* 1.3 60.9 + - - +
271O TRP 3.0 5.4 + - - -
272O ASN* 3.4 4.3 + - - +
273O ILE* 3.3 32.0 + - + +
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Residues in contact with GLU 270 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261M LYS* 3.1 20.3 + - - +
262M THR* 2.2 41.3 + - - -
344M ARG* 4.5 0.2 + - - -
247O LYS* 3.1 35.4 - - + +
248O ALA* 2.8 56.5 + - - +
250O LYS* 3.7 13.3 - - - -
266O ILE* 3.2 17.3 + - - +
267O VAL* 2.9 10.5 + - - +
269O ALA* 1.3 75.4 - - - +
271O TRP* 1.3 62.8 + - - +
274O LEU* 3.8 2.4 - - - +
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Residues in contact with TRP 271 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252M THR 3.1 22.7 - - - -
253M CYS* 3.4 27.6 - - + -
254M PRO* 3.7 6.1 - - + -
288M MET* 5.4 0.4 - - + -
304M TRP* 3.0 30.0 - + - -
344M ARG* 2.9 40.2 + - + +
345M PHE* 3.5 9.2 - + + -
346M SER* 3.2 46.9 - - - -
247O LYS* 4.7 2.5 - - + -
267O VAL* 3.0 17.4 + - - +
268O ASP* 3.2 33.2 - - - +
269O ALA 3.0 0.4 - - - -
270O GLU* 1.3 81.4 - - - +
272O ASN* 1.3 65.1 + - - +
274O LEU* 3.1 22.3 - - - +
275O TYR* 3.2 18.3 + - + -
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Residues in contact with ASN 272 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346M SER* 4.6 12.9 + - - -
268O ASP* 3.3 18.1 + - - +
269O ALA* 3.4 4.7 + - - +
271O TRP* 1.3 75.4 - - - +
273O ILE* 1.3 56.8 + - + +
274O LEU 3.1 1.3 - - - -
275O TYR* 3.1 32.0 + - + +
276O ASP* 2.6 33.7 + - - +
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Residues in contact with ILE 273 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248O ALA* 3.6 11.7 - - + -
249O GLU 3.7 18.6 - - - +
250O LYS* 3.6 32.5 - - + -
251O ASP 5.7 0.4 - - - +
269O ALA* 3.3 14.1 + - + +
272O ASN* 1.3 72.9 - - + +
274O LEU* 1.3 55.1 + - - +
276O ASP* 3.3 14.2 - - + +
277O LYS* 2.7 42.8 + - + +
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Residues in contact with LEU 274 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344M ARG* 4.4 8.3 - - - +
244O LEU* 4.1 9.4 - - + -
245O GLU* 3.1 42.6 - - - +
246O LEU 3.4 12.6 - - - +
248O ALA* 3.2 14.8 - - + +
270O GLU 3.8 9.0 - - - +
271O TRP 3.1 12.2 + - - +
273O ILE* 1.3 73.0 - - - +
275O TYR* 1.3 57.7 + - + +
277O LYS* 2.9 6.6 + - - +
278O LEU* 2.3 61.0 + - + +
298O VAL* 4.4 3.1 - - + -
299O ALA* 3.7 26.7 - - + +
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Residues in contact with TYR 275 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343M PRO* 4.2 1.7 - - - +
344M ARG* 3.2 29.2 - - + +
346M SER* 5.2 4.9 - - - -
347M GLU* 3.3 33.8 - - + +
271O TRP* 3.2 18.1 + - + -
272O ASN* 3.1 35.6 + - + +
274O LEU* 1.3 78.5 - - + +
276O ASP* 1.3 52.7 + - - +
278O LEU* 3.5 19.3 - - + -
279O GLU* 2.4 43.2 + - + +
298O VAL* 5.0 6.3 - - + -
302O TYR* 3.3 43.5 - + + +
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Residues in contact with ASP 276 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272O ASN 2.6 16.5 + - - +
273O ILE* 3.3 19.6 - - + +
275O TYR* 1.3 71.6 - - - +
277O LYS* 1.3 51.8 + - - +
279O GLU* 3.1 7.5 + - - +
280O LYS* 2.5 68.8 + - - +
283O HIS* 5.1 1.4 - - - -
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Residues in contact with LYS 277 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243O GLU 5.0 6.8 + - - +
244O LEU* 3.6 11.4 - - + -
245O GLU* 2.9 31.4 + - - -
248O ALA* 4.1 13.9 - - - +
249O GLU* 3.7 26.7 + - - +
273O ILE* 2.7 30.8 + - + +
274O LEU* 3.6 7.0 - - - +
276O ASP* 1.3 73.8 - - - +
278O LEU* 1.3 60.9 + - - +
280O LYS* 3.2 32.9 - - + +
281O ILE* 3.0 22.7 - - - +
334O VAL* 4.8 9.0 - - + +
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Residues in contact with LEU 278 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244O LEU* 3.4 18.8 - - + +
274O LEU* 2.3 50.1 + - + +
275O TYR* 3.2 23.3 - - + +
277O LYS* 1.3 66.7 - - - +
279O GLU* 1.3 57.9 + - - +
281O ILE* 2.8 20.8 + - - +
282O HIS* 3.0 28.2 + - + -
299O ALA* 3.5 17.0 - - + -
302O TYR* 3.3 33.2 - - + -
303O PHE* 3.4 32.5 - - + -
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Residues in contact with GLU 279 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275O TYR* 2.4 32.9 + - + +
276O ASP* 3.6 5.4 - - - +
278O LEU* 1.3 72.6 - - - +
280O LYS* 1.3 50.3 + - - +
281O ILE 3.1 0.2 - - - -
282O HIS* 2.7 32.1 + - - +
283O HIS* 2.3 53.6 + - + +
302O TYR* 2.9 20.7 + - + +
306O ARG* 2.5 33.1 + - - -
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Residues in contact with LYS 280 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276O ASP* 2.5 50.0 + - - +
277O LYS* 3.2 33.0 - - + +
278O LEU 3.0 0.2 - - - -
279O GLU* 1.3 72.9 - - - +
281O ILE* 1.3 57.4 + - - +
283O HIS* 3.3 15.3 - - + -
284O SER* 3.7 0.7 + - - -
334O VAL* 2.9 41.1 - - + +
335O ASN* 2.2 34.0 + - - +
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Residues in contact with ILE 281 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238O ALA* 4.4 8.0 - - + +
240O LEU* 3.4 34.3 - - + -
242O VAL* 4.1 14.8 - - + -
244O LEU* 3.7 29.4 - - + -
277O LYS 3.0 26.7 - - - +
278O LEU 2.8 8.1 + - - +
280O LYS* 1.3 77.0 - - - +
282O HIS* 1.3 66.0 + - + +
284O SER* 3.7 5.5 + - - -
285O GLY 3.5 18.5 - - - +
286O ALA* 4.4 2.5 - - + +
289O VAL* 3.6 32.3 - - + -
291O SER* 5.0 0.2 - - - +
334O VAL* 3.2 18.4 - - + +
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Residues in contact with HIS 282 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278O LEU* 3.0 40.7 + - + -
279O GLU* 2.7 44.4 + - - +
281O ILE* 1.3 85.1 - - + +
283O HIS* 1.3 63.3 + - - +
284O SER 3.4 1.0 + - - -
285O GLY* 3.7 14.5 - - - -
286O ALA* 4.0 4.8 + - - +
289O VAL* 4.2 0.9 - - + -
302O TYR* 3.9 4.5 - + - -
303O PHE* 3.0 33.8 - + - -
306O ARG* 3.2 34.2 + - - +
308O MET* 3.6 21.7 - - + +
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Residues in contact with HIS 283 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276O ASP* 5.1 1.6 - - - -
279O GLU* 2.3 48.4 + - + +
280O LYS* 3.3 18.8 - - + -
282O HIS* 1.3 70.5 - - - +
284O SER* 1.3 68.1 + - - +
335O ASN* 3.1 31.1 + - - -
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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) + - + + + + + -
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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