Contacts of the helix formed by residues 267 - 288 (chain D) in PDB entry 6F0X
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 GLY 267 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C ALA* 4.1 24.8 - - - +
264C CYS* 4.6 3.2 - - - +
304C LYS* 3.7 12.6 + - - -
265D ARG 3.7 1.1 + - - -
266D ALA* 1.3 73.4 - - - +
268D THR* 1.3 54.4 + - - +
270D PRO* 3.0 11.5 - - - +
271D SER* 2.2 41.0 + - - -
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Residues in contact with THR 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C ALA* 4.9 1.6 - - - +
266C ALA* 3.2 31.4 - - - -
267C GLY* 3.6 23.3 - - - +
268C THR* 4.4 4.7 - - - -
266D ALA* 3.7 2.7 - - - +
267D GLY* 1.3 72.3 - - - +
269D GLU* 1.3 61.0 + - - +
270D PRO 2.9 0.7 - - - -
271D SER* 2.8 25.9 + - - +
272D ASP* 3.0 14.2 + - - +
222E PHE* 5.6 6.5 - - - -
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Residues in contact with GLU 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D PHE* 6.5 0.4 - - - -
265D ARG* 6.4 0.4 - - + -
266D ALA* 4.9 2.8 + - + +
268D THR* 1.3 77.7 - - - +
270D PRO* 1.3 56.9 - - - +
272D ASP* 3.5 6.5 + - - +
273D ALA* 2.9 29.3 + - - +
222E PHE* 5.4 14.5 - - + -
267E GLY 4.0 20.6 - - - +
268E THR 4.7 7.0 - - - +
269E GLU* 6.1 0.7 - - - -
271E SER* 4.0 23.9 - - - -
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Residues in contact with PRO 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304C LYS* 2.9 28.3 - - - +
260D ALA* 5.4 8.5 - - + +
265D ARG* 5.1 10.3 - - - +
266D ALA 3.2 19.6 - - - +
267D GLY 3.1 6.6 - - - +
268D THR 2.9 0.4 - - - -
269D GLU* 1.3 77.4 - - - +
271D SER* 1.3 64.2 + - - +
273D ALA* 4.0 7.6 - - + -
274D ILE* 2.8 31.4 + - + +
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Residues in contact with SER 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C ALA* 4.5 11.4 - - - -
267C GLY* 5.3 4.5 - - - -
273C ALA* 6.0 2.5 - - - -
304C LYS* 4.9 1.3 - - - +
222D PHE* 5.6 1.6 - - - -
267D GLY 2.2 26.6 + - - -
268D THR* 2.8 16.2 + - - -
270D PRO* 1.3 66.6 - - - +
272D ASP* 1.3 59.5 - - - -
274D ILE* 3.8 6.9 - - - +
275D ARG* 2.6 56.1 + - - +
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Residues in contact with ASP 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218D PHE* 4.9 19.7 - - + -
222D PHE* 5.7 9.0 - - + -
225D SER* 4.2 7.5 + - - +
268D THR 3.0 9.6 + - - +
269D GLU* 3.8 8.3 - - - +
271D SER* 1.3 74.4 - - - +
273D ALA* 1.3 57.8 + - - +
275D ARG* 3.0 16.3 + - - +
276D VAL* 2.9 35.2 + - + +
222E PHE* 6.0 4.3 - - + -
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Residues in contact with ALA 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D LEU 4.7 10.5 - - - +
259D ALA* 5.4 4.9 - - + -
260D ALA* 5.3 13.2 - - + +
261D ARG* 5.7 2.5 - - - +
269D GLU 2.9 19.9 + - - +
270D PRO* 3.2 8.0 + - + +
272D ASP* 1.3 72.4 - - - +
274D ILE* 1.3 68.0 + - + +
276D VAL* 3.0 8.6 + - - +
277D VAL* 2.9 29.4 + - + +
271E SER* 5.8 6.1 - - - -
275E ARG* 6.0 4.5 - - - +
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Residues in contact with ILE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C GLU* 3.8 33.2 - - + +
256C SER* 4.9 2.7 - - - +
259C ALA* 6.1 2.9 - - - -
301C ILE* 5.7 2.5 - - + -
304C LYS* 3.4 42.6 - - + +
260D ALA 5.1 1.1 - - - +
261D ARG* 4.2 43.0 - - + +
270D PRO* 2.8 25.2 + - + +
271D SER* 3.8 4.7 - - - +
273D ALA* 1.3 71.3 - - + +
275D ARG* 1.3 54.8 + - - +
276D VAL 2.7 12.3 + - - -
277D VAL* 2.8 14.9 + - - +
278D ASN* 2.9 19.9 + - - +
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Residues in contact with ARG 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215C HIS* 4.1 17.0 - - + +
218C PHE* 3.2 41.0 - - + -
255C GLU 5.5 0.8 + - - -
256C SER* 4.3 16.2 + - - +
259C ALA* 3.5 22.0 - - - +
273C ALA* 5.3 3.6 - - - +
222D PHE* 3.2 32.6 - - - -
223D SER* 4.9 7.6 - - - +
225D SER* 4.7 5.8 - - - +
226D GLY* 4.3 9.0 - - - +
271D SER* 2.6 65.4 + - - +
272D ASP* 3.0 15.0 - - - +
274D ILE* 1.3 78.3 - - - +
276D VAL* 1.3 54.3 + - - +
278D ASN* 2.7 23.9 + - - +
279D ALA* 4.3 1.0 - - - +
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Residues in contact with VAL 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D LEU* 3.5 24.9 - - + -
218D PHE* 6.2 2.2 - - + -
225D SER* 3.1 34.8 - - - +
226D GLY* 5.5 0.4 - - - -
229D VAL* 4.4 5.5 - - + +
257D LEU* 4.1 14.1 - - + +
272D ASP* 2.9 16.5 + - + +
273D ALA* 3.2 9.9 - - - +
274D ILE 2.7 4.6 + - - -
275D ARG* 1.3 71.8 - - - +
277D VAL* 1.3 72.1 + - + +
278D ASN* 2.9 9.4 - - - +
279D ALA* 3.0 10.4 + - - +
280D VAL* 3.0 25.4 + - + +
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Residues in contact with VAL 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257D LEU* 3.0 36.3 - - + +
258D THR* 3.5 24.5 - - - +
261D ARG* 3.0 29.4 - - + +
273D ALA* 3.1 15.5 - - + +
274D ILE* 2.8 5.6 + - - -
276D VAL* 1.3 75.5 - - + +
278D ASN* 1.3 62.6 + - - +
280D VAL* 3.2 6.6 + - + +
281D LEU* 2.9 43.2 + - + +
306D ASP* 5.2 0.9 - - - +
309D PHE* 4.4 9.0 - - + -
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Residues in contact with ASN 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214C SER* 5.0 2.7 - - - +
215C HIS* 4.8 2.0 - - - +
253C GLN* 3.0 28.1 - - + +
255C GLU* 4.8 1.6 - - - +
256C SER* 3.1 32.8 + - - +
261D ARG* 2.5 23.8 - - - +
274D ILE* 2.9 9.8 + - + +
275D ARG* 2.7 40.5 + - - +
276D VAL 2.9 1.6 - - - +
277D VAL* 1.3 73.1 - - - +
279D ALA* 1.3 84.4 + - - +
281D LEU* 3.2 2.3 + - - +
282D THR* 3.0 26.9 + - - +
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Residues in contact with ALA 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213C ASN* 5.4 2.7 - - - +
215C HIS* 3.6 25.4 - - + -
226D GLY* 5.0 5.6 - - - +
229D VAL* 4.9 6.3 - - + -
230D THR* 4.8 14.6 - - + -
275D ARG 4.3 2.0 - - - +
276D VAL 3.0 4.9 + - - +
278D ASN* 1.3 90.0 + - - +
280D VAL* 1.3 65.9 + - - +
282D THR* 2.5 24.5 + - - +
283D GLN* 2.9 17.5 + - + +
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Residues in contact with VAL 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D LEU* 4.9 0.2 - - + -
229D VAL* 3.6 26.0 - - + +
233D PHE* 4.4 8.4 - - + -
257D LEU* 4.0 23.1 - - + -
276D VAL* 3.0 32.4 + - + +
277D VAL* 3.3 10.5 - - - +
279D ALA* 1.3 77.8 - - - +
281D LEU* 1.3 64.4 + - - +
283D GLN* 3.1 4.3 + - - +
284D ILE* 3.0 28.5 + - + +
309D PHE* 3.5 31.9 - - + -
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Residues in contact with LEU 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C GLN* 4.3 9.6 - - - +
300C ASN* 5.9 2.2 - - - +
301C ILE* 5.7 0.2 - - + -
261D ARG* 3.5 29.2 - - - +
277D VAL* 2.9 24.0 + - + +
278D ASN 3.5 5.2 - - - +
280D VAL* 1.3 74.8 - - - +
282D THR* 1.3 62.9 + - - +
284D ILE* 3.1 6.6 + - + +
285D ASP* 2.9 29.2 + - - +
308D ALA* 3.5 29.2 - - + -
309D PHE* 3.5 36.1 - - + +
312D ARG* 3.1 26.4 + - - +
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Residues in contact with THR 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C GLU* 5.5 7.2 - - - +
213C ASN* 5.3 4.2 + - - -
252C ASP* 3.7 26.5 - - + +
253C GLN* 3.8 13.0 - - - +
278D ASN 3.0 13.4 + - - +
279D ALA* 2.5 28.6 + - - +
281D LEU* 1.3 74.8 - - - +
283D GLN* 1.3 63.6 + - - +
285D ASP* 3.2 10.3 + - - +
286D GLN* 2.9 34.4 + - - +
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Residues in contact with GLN 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ILE* 6.3 0.8 - - - +
213C ASN* 4.7 12.3 + - - +
229D VAL* 5.1 4.0 - - + +
230D THR* 4.2 31.8 - - + +
233D PHE* 3.3 38.4 - - + +
279D ALA* 2.9 23.8 + - - +
280D VAL* 3.1 3.1 + - - +
282D THR* 1.3 83.6 + - - +
284D ILE* 1.3 63.3 + - - +
286D GLN* 2.8 39.3 + - - +
287D ILE* 2.9 27.8 + - - +
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Residues in contact with ILE 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D ASN* 4.8 3.8 - - + +
174D VAL* 3.5 27.6 - - + -
233D PHE* 4.0 14.8 - - + -
280D VAL* 3.0 20.2 + - + +
281D LEU* 3.1 9.4 + - + +
283D GLN* 1.3 76.1 - - - +
285D ASP* 1.3 65.9 + - - +
287D ILE* 3.0 11.4 + - + +
288D LYS* 3.0 23.3 + - + +
295D ILE* 3.9 24.2 - - + -
309D PHE* 3.3 40.2 - - + -
312D ARG* 4.3 14.8 - - - +
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Residues in contact with ASP 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386C ARG* 4.3 6.9 + - - -
901C AGS 4.4 11.8 + - - +
172D ASN* 5.0 0.2 - - - -
281D LEU* 2.9 17.4 + - - +
282D THR* 3.6 11.4 - - - +
284D ILE* 1.3 74.8 - - - +
286D GLN* 1.3 58.6 + - - +
288D LYS* 3.0 44.3 + - - +
289D ARG* 4.6 4.5 + - - -
312D ARG* 3.1 49.5 + - - -
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Residues in contact with GLN 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C ASN* 4.1 20.6 - - - +
211C GLU* 5.4 5.9 + - - -
213C ASN* 5.9 1.4 - - - +
237D GLN* 5.6 2.9 - - - +
282D THR* 2.9 19.1 + - - +
283D GLN* 2.8 43.8 + - - +
285D ASP* 1.3 76.0 - - - +
287D ILE* 1.3 62.6 + - + +
288D LYS 2.8 11.3 + - - -
289D ARG* 3.0 29.1 + - - +
290D HIS* 5.5 0.7 - - - -
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Residues in contact with ILE 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D ASN 6.2 0.4 - - - +
173D ARG* 4.0 8.3 + - - -
233D PHE* 4.7 23.8 - - + +
236D ILE* 5.6 3.8 - - + -
237D GLN* 4.3 17.0 - - - +
240D ILE* 4.4 17.7 - - + -
249D VAL* 5.5 4.0 - - + -
283D GLN* 2.9 16.5 + - + +
284D ILE* 3.1 21.1 - - + +
286D GLN* 1.3 74.9 - - + +
288D LYS* 1.3 57.1 + - - +
289D ARG 2.8 11.2 + - - +
290D HIS* 3.7 19.2 + - - +
293D VAL* 4.6 16.6 - - + +
295D ILE* 3.5 34.1 - - + -
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Residues in contact with LYS 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C SER* 5.4 0.6 + - - -
386C ARG* 4.9 3.2 - - - +
901C AGS 3.8 29.7 + - - -
170D THR* 4.2 15.9 + - + +
172D ASN* 3.3 39.9 + - + +
173D ARG* 2.2 38.1 + - - +
284D ILE* 3.0 10.3 + - + +
285D ASP* 3.0 40.5 + - - +
286D GLN 2.8 2.2 + - - +
287D ILE* 1.3 76.1 - - - +
289D ARG* 1.3 71.9 + - + +
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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