Contacts of the helix formed by residues 260 - 284 (chain C) in PDB entry 2R7D
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 PRO 260 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C TYR* 4.0 26.9 - - + +
203C GLN* 3.3 28.0 - - - +
206C GLN* 3.6 25.4 - - + +
258C PRO* 3.0 12.3 - - + +
259C LYS* 1.3 99.7 - - - +
261C GLU* 1.3 65.7 + - - +
262C MSE 4.2 0.7 - - - +
263C ARG* 3.0 23.6 + - + +
264C THR* 3.7 4.0 + - - -
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Residues in contact with GLU 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206C GLN* 3.2 16.8 + - - +
209C LEU* 4.0 14.1 - - + +
220C ALA* 4.9 1.6 - - + -
224C ARG* 2.7 51.3 + - - +
227C ARG* 4.7 5.8 + - - +
259C LYS 3.7 0.8 + - - -
260C PRO* 1.3 71.2 - - - +
262C MSE 1.3 58.3 + - - +
264C THR* 2.9 13.3 + - - -
265C VAL* 2.9 35.2 + - + +
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Residues in contact with MSE 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ILE* 3.9 26.7 - - + -
202C TYR* 4.0 11.2 - - + +
205C ALA* 3.6 25.4 - - + +
206C GLN* 2.9 29.4 + - + +
209C LEU* 3.9 24.0 - - + -
216C PHE* 4.0 23.8 - - + +
219C LEU* 4.5 9.0 - - + -
220C ALA* 4.8 0.4 - - - -
260C PRO 3.2 0.4 - - - -
261C GLU* 1.3 76.4 - - - +
263C ARG* 1.3 61.3 + - - +
265C VAL* 3.6 30.4 - - + +
266C VAL* 3.0 31.5 + - + +
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Residues in contact with ARG 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C ASP* 2.5 37.8 + - - +
202C TYR* 3.4 44.7 + - + +
242C GLU* 5.1 9.2 + - - -
257C LEU* 4.0 24.0 - - - +
258C PRO* 2.9 32.3 + - - +
259C LYS* 4.2 21.3 - - - +
260C PRO* 3.0 19.8 + - + +
262C MSE 1.3 78.2 - - - +
264C THR* 1.3 60.7 + - - +
266C VAL* 3.5 2.8 + - - +
267C GLN* 3.1 27.2 + - + +
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Residues in contact with THR 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C ARG* 3.2 39.6 + - - +
259C LYS* 5.0 4.7 + - - +
260C PRO 4.1 6.6 + - - -
261C GLU* 2.9 13.8 + - - -
263C ARG* 1.3 79.1 - - - +
265C VAL* 1.3 64.6 + - - +
267C GLN* 3.4 17.4 + - - +
268C GLU* 3.1 16.8 + - - +
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Residues in contact with VAL 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C LEU* 3.6 40.4 - - + +
220C ALA* 3.8 21.8 - - + +
223C ALA* 3.7 13.8 - - + +
227C ARG* 4.3 4.9 - - - +
261C GLU* 2.9 34.3 + - + +
262C MSE 3.6 23.1 - - + +
263C ARG 3.2 0.2 - - - -
264C THR* 1.3 73.5 - - - +
266C VAL* 1.3 66.0 + - + +
268C GLU* 3.1 6.1 + - - +
269C CYS* 3.0 24.5 + - - -
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Residues in contact with VAL 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C ILE* 3.8 37.9 - - + +
102C ASP* 4.5 6.3 - - - +
104C VAL* 5.1 7.2 - - + -
202C TYR* 3.7 33.4 - - + +
262C MSE 3.0 23.7 + - + +
263C ARG 3.8 0.2 - - - +
265C VAL* 1.3 75.7 - - + +
267C GLN* 1.3 64.5 + - - +
269C CYS* 3.1 18.3 + - - +
270C MSE 3.1 31.8 + - + +
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Residues in contact with GLN 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C TYR* 5.5 0.4 + - - -
227C ARG* 5.8 1.4 - - - -
239C ASP* 4.1 20.8 + - - +
263C ARG* 3.1 15.4 + - + +
264C THR* 3.5 22.1 - - - +
265C VAL 3.2 0.4 - - - -
266C VAL* 1.3 76.6 - - - +
268C GLU* 1.3 66.3 + - - +
270C MSE 3.2 12.2 + - + +
271C THR* 3.1 28.1 + - - +
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Residues in contact with GLU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C ALA* 3.4 25.4 - - + +
226C SER* 2.7 30.4 + - - -
227C ARG* 3.0 40.0 + - - +
230C ARG* 2.8 39.7 + - - -
264C THR 3.1 4.4 + - - -
265C VAL 3.1 7.2 + - - +
267C GLN* 1.3 77.1 - - - +
269C CYS* 1.3 61.5 + - - +
271C THR* 3.2 8.1 + - - +
272C LEU* 2.9 30.2 + - + +
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Residues in contact with CYS 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C VAL* 3.9 24.9 - - + -
116C LEU* 4.1 13.7 - - + -
118C VAL* 3.6 8.9 - - + +
219C LEU* 4.0 30.1 - - - -
222C LEU* 6.3 1.3 - - - -
223C ALA* 5.3 2.7 - - - -
265C VAL* 3.0 27.6 + - - -
266C VAL* 3.1 9.6 + - - +
268C GLU* 1.3 73.8 - - - +
270C MSE 1.3 62.7 + - + +
272C LEU* 3.3 12.7 + - - +
273C ALA* 2.9 28.6 + - - +
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Residues in contact with MSE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ASP* 3.4 38.8 - - - +
104C VAL* 3.7 27.4 - - + -
118C VAL* 3.8 12.3 - - + -
266C VAL* 3.1 26.9 + - + +
267C GLN* 3.2 10.5 + - + +
269C CYS* 1.3 77.6 - - + +
271C THR* 1.3 58.4 + - - +
273C ALA* 3.2 6.2 + - - +
274C GLY* 2.9 25.3 + - - -
335C TYR* 4.3 6.2 + - - +
339C THR* 3.6 35.6 + - - +
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Residues in contact with THR 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C ARG* 3.9 30.7 + - - +
267C GLN* 3.1 18.8 + - - +
268C GLU* 3.5 16.7 + - - +
270C MSE 1.3 74.3 - - - +
272C LEU* 1.3 61.2 + - + +
274C GLY 3.2 0.9 + - - -
275C TRP* 2.9 28.3 + - + +
330C MSE 3.5 30.5 - - + +
332C LEU* 4.1 9.9 - - + -
335C TYR* 3.5 11.7 + - - -
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C LEU* 3.4 31.6 - - + -
177C LEU* 3.5 19.2 - - + +
179C LEU* 4.3 18.2 - - + -
183C GLY 5.9 0.9 - - - +
222C LEU* 4.9 8.3 - - + +
223C ALA* 5.3 1.1 - - - +
226C SER* 3.2 35.4 - - - +
230C ARG* 6.3 0.2 - - - -
268C GLU* 2.9 23.2 + - + +
269C CYS* 3.6 8.7 - - - +
271C THR* 1.3 76.5 - - + +
273C ALA* 1.3 53.6 + - - +
275C TRP* 3.3 30.1 + - + +
276C GLY 2.8 30.0 + - - -
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Residues in contact with ALA 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C VAL* 3.5 34.3 - - + +
175C ILE* 3.8 19.9 - - + +
177C LEU* 4.6 1.1 - - - +
269C CYS 2.9 13.1 + - - +
270C MSE 3.2 8.9 + - - +
272C LEU* 1.3 79.1 - - - +
274C GLY* 1.3 53.2 + - - +
276C GLY* 3.4 1.0 + - - -
277C THR* 2.7 37.9 + - - -
338C ALA* 5.7 0.4 - - - -
339C THR* 3.9 10.8 - - + -
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Residues in contact with GLY 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C MSE 2.9 12.4 + - - -
273C ALA* 1.3 73.4 - - - +
275C TRP* 1.3 64.4 + - - +
277C THR* 3.3 4.6 + - - -
278C ALA* 3.0 18.4 + - - +
335C TYR* 3.6 14.6 - - - -
336C ALA 2.9 35.1 + - - +
337C GLN* 5.1 0.2 - - - -
338C ALA* 4.8 5.2 - - - -
339C THR* 5.3 0.4 - - - +
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Residues in contact with TRP 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C LEU* 3.9 21.1 - - + -
179C LEU* 4.8 4.0 - - + -
183C GLY 5.0 6.5 - - - -
184C ASN* 5.7 0.7 - - - -
185C ALA* 3.9 34.3 - - + -
271C THR* 2.9 16.7 + - + +
272C LEU* 3.4 20.9 - - + +
274C GLY* 1.3 76.4 - - - +
276C GLY* 1.3 61.9 + - - +
278C ALA* 3.2 4.3 + - - +
279C ILE* 3.0 40.4 + - + +
332C LEU* 3.9 24.9 - - + +
333C ASP 5.3 1.2 - - - +
334C LEU* 3.5 38.6 - - + +
335C TYR* 3.6 6.4 - - - -
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Residues in contact with GLY 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ILE* 4.4 3.1 - - - -
177C LEU* 4.2 4.7 - - - -
188C VAL* 3.4 36.2 - - - +
272C LEU 2.8 16.3 + - - -
273C ALA 3.8 1.6 - - - -
275C TRP* 1.3 79.0 - - - +
277C THR* 1.3 55.6 + - - +
279C ILE* 3.2 7.1 + - - +
280C PHE* 2.9 26.9 + - - +
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Residues in contact with THR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175C ILE* 3.5 17.2 - - - +
190C VAL* 4.8 4.9 - - - -
273C ALA 2.7 25.2 + - - -
274C GLY* 3.4 9.2 - - - -
276C GLY* 1.3 79.0 - - - +
278C ALA* 1.3 56.9 + - - +
280C PHE* 3.5 7.3 + - - +
281C ALA* 3.0 27.0 + - - +
288C LEU* 4.0 9.9 - - + -
336C ALA* 4.4 4.0 - - + -
338C ALA* 3.7 13.0 - - + +
350C VAL* 3.7 30.3 - - + -
354C LEU* 4.2 14.1 - - + +
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C GLY 3.0 12.0 + - - +
275C TRP 3.2 7.4 + - - +
277C THR* 1.3 73.6 - - - +
279C ILE* 1.3 56.7 + - - +
281C ALA* 3.6 2.4 - - - +
282C ASP* 2.7 37.6 + - - +
290C PHE* 3.6 26.6 - - + -
334C LEU* 3.7 10.3 - - + +
335C TYR* 3.7 28.9 - - - +
336C ALA* 4.0 2.9 - - + +
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Residues in contact with ILE 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C VAL* 4.7 17.9 - - + -
275C TRP* 3.0 38.0 + - + +
276C GLY* 3.2 10.3 + - - +
278C ALA* 1.3 76.8 - - - +
280C PHE* 1.3 64.3 + - - +
282C ASP* 3.8 0.6 - - - +
283C ASP* 2.9 45.3 + - - +
334C LEU* 3.5 36.1 - - + -
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Residues in contact with PHE 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C VAL* 4.2 17.0 - - + +
189C ASP* 4.8 3.6 - - - -
190C VAL* 3.5 56.5 - - + -
276C GLY 2.9 16.2 + - - +
277C THR 3.7 4.3 - - - +
279C ILE* 1.3 77.9 - - - +
281C ALA* 1.3 62.7 + - - +
283C ASP* 3.5 3.0 + - - +
284C ASN* 2.7 50.8 + - - +
286C ILE* 4.3 6.7 - - + -
354C LEU* 4.0 16.2 - - + -
357C PHE* 3.9 29.2 - + - -
358C LEU* 4.5 8.3 - - + -
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Residues in contact with ALA 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C THR 3.0 10.4 + - - +
278C ALA 3.6 3.4 - - - +
279C ILE 3.2 0.2 - - - -
280C PHE* 1.3 76.6 - - - +
282C ASP* 1.3 56.0 + - - +
284C ASN 3.2 1.0 + - - -
285C GLU 2.7 30.7 + - - -
286C ILE* 2.8 36.8 + - + +
288C LEU* 3.2 36.1 - - + -
290C PHE* 3.9 4.9 - - + -
354C LEU* 5.1 1.8 - - + -
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Residues in contact with ASP 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C ALA 2.7 21.0 + - - +
279C ILE 3.8 2.9 - - - +
281C ALA* 1.3 73.6 - - - +
283C ASP* 1.3 69.1 + - - +
285C GLU* 3.3 18.3 + - - +
290C PHE* 4.4 1.5 - - - -
324C PRO* 3.4 33.7 - - + +
334C LEU* 4.0 13.6 - - + +
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Residues in contact with ASP 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE* 2.9 31.8 + - - +
280C PHE* 3.8 6.7 - - - +
282C ASP* 1.3 86.8 - - - +
284C ASN* 1.3 64.2 + - - +
285C GLU* 3.4 12.1 + - - +
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Residues in contact with ASN 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C PHE* 2.7 56.2 + - - +
283C ASP* 1.3 80.9 - - - +
285C GLU* 1.3 74.0 + - - +
286C ILE* 3.2 14.0 + - + +
357C PHE* 3.2 39.8 - - + -
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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