Contacts of the helix formed by residues 260 - 284 (chain C) in PDB entry 2GPV
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 SER 260 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C PRO* 2.9 17.0 + - - +
259C ASP* 1.3 75.4 - - - +
261C ASP* 1.3 73.6 + - - +
262C ILE 4.2 2.7 - - - -
263C LYS* 3.2 16.7 + - - +
264C ALA* 3.3 13.2 + - - +
339C LEU* 4.5 11.4 - - - +
447C HIS* 3.5 24.0 - - - -
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Residues in contact with ASP 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C SER* 1.3 77.2 - - - +
262C ILE* 1.3 89.4 + - - +
264C ALA* 3.4 3.1 + - - +
265C LEU* 3.1 32.0 + - + +
339C LEU 3.3 26.1 + - - +
340C ALA* 3.9 17.2 - - - +
443C LYS* 5.5 2.6 - - - +
447C HIS* 5.7 0.2 + - - -
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Residues in contact with ILE 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C SER* 3.3 1.0 - - - -
261C ASP* 1.3 98.2 + - - +
263C LYS* 1.3 51.8 + - - +
265C LEU* 3.7 9.5 - - + +
266C THR* 2.5 53.4 + - - +
443C LYS* 3.6 25.6 - - + +
444C VAL* 3.8 32.1 - - + +
447C HIS* 3.4 53.8 - - + +
448C LYS* 6.0 0.2 - - - -
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Residues in contact with LYS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C PRO* 4.6 11.7 - - + +
254C ASP* 3.0 33.0 + - - +
255C PRO* 4.1 7.3 + - - +
257C VAL* 2.7 43.6 + - + +
258C PRO 3.9 8.1 - - - +
259C ASP* 3.8 23.8 + - - +
260C SER* 3.2 22.6 + - - +
262C ILE* 1.3 74.1 - - - +
264C ALA* 1.3 70.1 + - - +
265C LEU 2.8 1.2 + - - -
266C THR* 2.8 7.1 + - - -
267C THR* 2.6 34.6 + - - +
330C TYR* 5.4 3.8 - - + +
447C HIS* 4.6 2.6 - - - -
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Residues in contact with ALA 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C SER 3.3 7.7 + - - +
261C ASP 3.6 3.8 - - - +
263C LYS* 1.3 77.5 - - - +
265C LEU* 1.3 57.0 + - + +
267C THR* 3.4 2.1 + - - -
268C LEU* 2.9 39.4 + - + +
330C TYR* 2.9 26.0 - - - +
332C MET* 4.5 7.0 - - + -
336C GLN 5.4 0.2 - - - +
340C ALA* 3.5 31.6 - - + -
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Residues in contact with LEU 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C ASP* 3.1 28.7 + - + +
262C ILE* 3.7 13.9 - - + +
263C LYS 2.8 3.4 + - - -
264C ALA* 1.3 72.0 - - + +
266C THR* 1.3 66.8 + - - +
267C THR 3.1 0.2 + - - -
268C LEU* 3.2 4.6 + - - +
269C CYS* 2.8 29.0 + - - +
340C ALA 3.7 16.6 - - - +
342C LEU* 3.9 21.1 - - + -
434C HIS* 5.4 3.1 - - - +
438C ILE* 5.2 20.9 - - + -
444C VAL* 5.2 9.2 - - + -
502C OHT 3.8 29.6 - - + -
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Residues in contact with THR 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ILE* 2.5 43.3 + - - +
263C LYS* 2.8 6.0 + - - -
265C LEU* 1.3 72.6 - - - +
267C THR* 1.3 63.0 + - - +
269C CYS* 3.3 8.3 - - + +
270C ASP* 3.2 22.7 + - + +
444C VAL* 4.2 10.9 - - + +
447C HIS* 5.3 1.2 - - - -
448C LYS* 5.0 14.8 - - - +
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Residues in contact with THR 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C ALA* 4.1 35.3 - - + +
253C PRO* 4.1 18.1 - - + +
254C ASP 5.0 1.2 + - - -
263C LYS* 2.6 31.9 + - - +
264C ALA* 3.6 6.1 - - - -
266C THR* 1.3 72.3 - - - +
268C LEU* 1.3 68.7 + - + +
269C CYS 3.2 0.2 + - - -
270C ASP* 3.3 6.4 + - - +
271C LEU* 3.0 21.0 + - + +
330C TYR* 4.1 23.3 - - + -
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Residues in contact with LEU 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C ALA 2.9 24.9 + - - +
265C LEU* 3.9 3.1 - - - +
267C THR* 1.3 74.6 - - - +
269C CYS* 1.3 58.2 + - - +
271C LEU* 3.2 9.5 + - + +
272C ALA* 2.9 31.5 + - - +
326C TYR* 3.5 44.4 - - + -
330C TYR* 4.0 11.9 - - + -
332C MET* 4.2 15.7 - - - -
342C LEU* 3.8 28.5 - - + -
502C OHT 3.7 38.9 - - + -
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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
----------------------------------------------------------
265C LEU 2.8 15.3 + - - +
266C THR* 3.3 14.1 - - - +
268C LEU* 1.3 77.6 - - - +
270C ASP* 1.3 64.7 + - - +
272C ALA* 3.1 1.7 + - - +
273C ASP* 2.9 32.0 + - - +
435C PHE* 3.8 21.8 - - - -
439C LYS* 5.4 3.6 - - - -
502C OHT 3.7 26.8 - - - -
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Residues in contact with ASP 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C ALA 5.9 0.9 - - - +
266C THR* 3.2 10.8 + - + +
267C THR* 3.8 8.1 - - - +
269C CYS* 1.3 78.5 - - - +
271C LEU* 1.3 61.9 + - - +
273C ASP* 3.5 8.5 + - - +
274C ARG* 2.9 61.4 + - - +
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Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ILE* 4.1 19.1 - - + +
250C TYR 3.8 24.5 - - - +
251C ALA* 4.2 18.8 - - + -
267C THR* 3.0 14.1 + - + +
268C LEU* 3.4 15.5 - - + +
270C ASP* 1.3 75.1 + - - +
272C ALA* 1.3 59.8 + - - +
274C ARG* 3.3 12.9 + - - +
275C GLU* 2.9 44.7 + - + +
326C TYR* 3.7 36.6 - - + +
327C ALA* 4.4 1.1 - - + -
502C OHT 4.3 7.0 - - + -
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C LEU 2.9 12.8 + - - +
269C CYS 3.4 7.9 - - - +
271C LEU* 1.3 76.2 - - - +
273C ASP* 1.3 63.8 + - - +
275C GLU* 2.9 10.3 + - - +
276C LEU* 2.8 28.7 + - + +
309C LEU* 3.8 11.3 - - + +
502C OHT 3.5 46.9 - - + -
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Residues in contact with ASP 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C CYS* 2.9 20.8 + - - +
270C ASP* 3.7 8.6 - - - +
272C ALA* 1.3 76.1 - - - +
274C ARG* 1.3 60.0 + - + +
276C LEU* 3.5 20.2 - - - +
277C VAL* 3.5 13.5 + - - +
502C OHT 2.8 40.8 + - - +
1323I ILE* 3.9 16.5 - - + +
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Residues in contact with ARG 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ILE* 3.6 24.6 - - + +
250C TYR 3.1 28.8 + - - +
251C ALA 3.4 18.0 + - - -
252C MET* 3.3 27.0 - - - +
270C ASP* 2.9 34.3 + - - +
271C LEU* 3.7 18.5 - - - +
272C ALA 3.2 0.8 - - - -
273C ASP* 1.3 78.0 - - + +
275C GLU* 1.3 64.8 + - - +
277C VAL* 3.3 18.7 + - + +
278C VAL* 3.5 15.8 + - - +
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Residues in contact with GLU 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C ILE* 3.9 24.2 - - + -
271C LEU* 2.9 40.6 + - + +
272C ALA 2.9 4.6 + - - +
274C ARG* 1.3 72.3 - - - +
276C LEU* 1.3 53.4 + - - +
278C VAL* 3.2 5.5 - - + +
279C ILE* 2.6 44.4 + - + +
309C LEU* 3.2 27.9 - - + +
312C GLY* 5.7 0.7 - - - -
316C ARG* 4.0 19.0 + - - -
326C TYR 4.3 0.5 - - - +
502C OHT 2.7 28.0 + - - -
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Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ALA 2.8 18.8 + - - +
273C ASP* 3.5 7.9 - - - +
275C GLU* 1.3 76.7 - - - +
277C VAL* 1.3 53.6 + - - +
279C ILE* 4.0 11.2 - - + +
280C ILE* 2.6 47.7 + - + +
305C TRP* 3.7 41.1 - - + -
309C LEU* 4.6 11.9 - - + -
502C OHT 3.7 31.0 - - - -
1320I LEU* 4.6 8.3 - - + -
1323I ILE* 3.8 26.2 - - + -
1324I ILE* 5.7 2.2 - - + -
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Residues in contact with VAL 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C ASP 3.7 13.9 - - - +
274C ARG* 3.3 12.6 + - + +
276C LEU* 1.3 77.6 - - - +
278C VAL* 1.3 64.1 + - + +
280C ILE* 3.7 10.5 + - - +
281C GLY* 3.3 19.1 + - - -
1323I ILE* 4.2 14.4 - - + -
1327I ALA* 4.8 10.1 - - + +
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Residues in contact with VAL 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C PRO* 4.2 24.1 - - + +
249C ILE* 3.5 30.1 - - + -
274C ARG 3.5 6.9 + - - +
275C GLU* 3.2 14.6 - - + +
277C VAL* 1.3 80.6 - - + +
279C ILE* 1.3 68.1 + - + +
280C ILE 3.2 1.1 - - - -
281C GLY* 3.7 2.5 - - - +
282C TRP* 2.9 23.2 + - - +
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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
----------------------------------------------------------
246C PRO* 5.3 4.3 - - + -
275C GLU* 2.6 27.7 + - + +
276C LEU* 3.5 13.9 - - + +
278C VAL* 1.3 75.1 - - + +
280C ILE* 1.3 65.4 + - + +
282C TRP* 3.1 19.7 + - + +
283C ALA* 3.0 18.9 + - - +
301C LEU* 4.6 10.3 - - + -
305C TRP* 4.9 3.6 - - - +
308C ILE* 3.5 47.6 - - + +
309C LEU* 3.7 35.4 - - + +
370C LYS* 6.1 2.2 - - - +
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Residues in contact with ILE 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU* 2.6 29.5 + - + +
277C VAL* 3.8 4.5 - - - +
279C ILE* 1.3 74.8 - - + +
281C GLY* 1.3 63.4 + - - +
283C ALA* 3.1 21.8 + - - +
284C LYS* 3.6 12.0 + - - +
301C LEU* 4.2 20.4 - - + -
1323I ILE* 3.7 14.8 - - + +
1324I ILE* 3.7 36.6 - - + -
1327I ALA* 3.4 33.0 - - + +
1328I LEU* 4.2 23.8 - - + +
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Residues in contact with GLY 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C VAL 3.3 11.5 + - - -
278C VAL* 3.4 5.5 + - - -
279C ILE 3.3 0.2 - - - -
280C ILE* 1.3 80.7 - - - +
282C TRP* 1.3 59.8 + - - +
284C LYS* 3.9 24.9 - - - +
285C HIS* 3.3 19.3 + - - -
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Residues in contact with TRP 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C LEU* 4.6 14.8 + - + +
244C ALA* 3.3 32.1 - - + +
245C GLU* 4.8 2.4 + - - -
246C PRO* 3.8 21.8 - - + -
278C VAL 2.9 13.2 + - - +
279C ILE* 3.3 30.1 - - + +
280C ILE 3.1 0.2 - - - -
281C GLY* 1.3 77.0 - - - +
283C ALA* 1.3 67.0 + - + +
284C LYS 3.1 2.2 - - - -
285C HIS* 2.9 32.4 + - - +
286C ILE* 3.5 32.9 + - + +
308C ILE* 4.3 17.9 - - + -
367C VAL* 4.3 7.6 + - - +
370C LYS* 3.8 33.2 - - + +
371C ALA* 3.8 26.2 - - + -
374C LEU* 4.0 12.8 - - + -
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Residues in contact with ALA 283 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C ILE 3.0 10.8 + - - +
280C ILE* 3.1 11.8 + - - +
282C TRP* 1.3 86.4 - - + +
284C LYS* 1.3 61.9 + - - +
286C ILE* 3.2 17.6 + - - +
289C PHE* 3.1 44.0 - - + +
301C LEU* 4.3 10.5 - - + -
374C LEU* 3.9 16.2 - - + -
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Residues in contact with LYS 284 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C ILE* 3.8 15.0 - - - +
281C GLY* 3.9 18.4 - - - +
282C TRP 3.1 0.2 - - - -
283C ALA* 1.3 78.0 - - - +
285C HIS* 1.3 61.8 + - + +
286C ILE 3.4 8.3 + - - +
289C PHE* 4.1 5.8 - - + -
290C SER* 3.2 30.6 + - - +
297C GLN* 5.5 2.5 - - - +
1327I ALA* 3.2 13.9 + - - +
1328I LEU* 4.3 26.9 - - + +
1330I GLY 2.6 38.2 + - - +
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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