Contacts of the helix formed by residues 249 - 271 (chain D) in PDB entry 4LQL
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 TYR 249 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D GLY* 2.5 29.3 + - - +
243D ASP* 4.4 1.4 - - - -
248D LYS* 1.3 78.6 - - + +
250D VAL* 1.3 63.2 + - - +
251D HIS 3.7 1.6 - - - -
252D ASN* 3.0 33.6 + - + +
253D VAL* 4.2 6.6 + - - +
364D GLU* 3.6 32.1 - - + -
365D VAL* 4.7 6.5 - - + -
375D ASP* 4.8 11.9 - - + -
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Residues in contact with VAL 250 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D ASP 6.2 0.2 - - - -
244D ASN 4.8 10.9 - - - +
245D ASP* 4.4 1.7 - - - +
246D HIS* 3.6 30.5 - - - +
247D GLU 3.3 25.8 - - - +
248D LYS 2.6 9.0 + - - +
249D TYR* 1.3 72.5 - - - +
251D HIS* 1.3 65.5 + - + +
252D ASN* 3.5 0.7 + - - -
253D VAL* 4.1 6.6 + - - +
254D ARG* 4.3 10.6 + - - +
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Residues in contact with HIS 251 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D VAL* 1.3 78.2 - - + +
252D ASN* 1.3 62.7 + - - +
253D VAL 3.4 0.7 - - - -
254D ARG* 3.0 27.5 - - + -
255D TYR* 2.9 24.3 - + - -
374D ASP* 6.2 0.4 - - - -
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Residues in contact with ASN 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D TYR* 3.0 42.0 - - + +
250D VAL 3.2 1.0 + - - -
251D HIS* 1.3 81.9 - - - +
253D VAL* 1.3 58.9 + - - +
255D TYR* 3.1 13.2 - - - +
256D GLN* 3.5 0.7 + - - +
287D GLN* 2.5 42.1 + - - +
364D GLU* 4.6 4.5 - - + -
374D ASP* 4.0 19.8 + - - +
375D ASP* 3.6 22.7 + - - +
377D ALA* 4.8 1.3 - - - +
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Residues in contact with VAL 253 (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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230D TYR* 6.4 2.0 - - + -
233D LEU* 5.4 15.3 - - + -
239D LEU* 6.3 2.0 - - + -
243D ASP* 3.4 42.4 - - + +
244D ASN 5.7 0.2 - - - +
249D TYR 4.4 5.2 - - - +
250D VAL 4.1 4.9 + - - +
251D HIS 3.4 0.4 - - - -
252D ASN* 1.3 71.7 - - - +
254D ARG* 1.3 60.3 + - + +
255D TYR 2.9 9.6 + - - -
256D GLN* 3.1 12.7 + - - +
257D LEU* 3.1 14.0 + - + +
291D LEU* 4.5 17.7 - - + -
362D ARG* 4.9 7.9 - - + -
364D GLU* 4.6 2.0 - - + -
377D ALA* 3.6 24.0 - - + -
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Residues in contact with ARG 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ILE* 5.8 12.1 - - + +
227D ASP* 6.2 4.3 - - - -
230D TYR* 5.0 17.0 - - + -
250D VAL 4.3 8.2 + - - +
251D HIS* 3.0 21.8 + - + +
253D VAL* 1.3 75.0 - - + +
255D TYR* 1.3 58.2 + - - +
257D LEU* 4.4 9.9 - - + +
258D ARG* 4.4 13.7 + - - +
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Residues in contact with TYR 255 (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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251D HIS* 2.9 36.3 + + - -
252D ASN* 3.1 21.8 - - - +
253D VAL 2.9 0.6 - - - -
254D ARG* 1.3 77.8 - - - +
256D GLN* 1.3 61.2 + - - +
257D LEU 3.2 1.6 - - - -
258D ARG* 3.2 11.4 + - - +
259D GLU* 3.0 30.2 + - - +
286D GLU* 4.5 16.3 - - + +
287D GLN* 3.2 22.4 - - + +
374D ASP* 5.3 2.5 - - - -
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Residues in contact with GLN 256 (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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252D ASN 3.5 1.5 + - - +
253D VAL* 3.1 8.6 + - - +
255D TYR* 1.3 77.9 - - - +
257D LEU* 1.3 60.9 + - - +
258D ARG 3.2 0.4 - - - -
259D GLU* 3.8 9.2 - - - -
260D TYR* 3.4 16.5 + - - +
287D GLN* 4.0 15.3 - - + +
290D GLY 6.0 0.9 - - - +
291D LEU* 3.9 33.3 - - + +
292D ALA* 3.7 15.7 + - + +
377D ALA* 4.4 6.5 - - + +
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Residues in contact with LEU 257 (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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226D ILE* 4.6 25.9 - - + +
229D ALA* 4.8 10.5 - - + -
230D TYR* 6.0 1.3 - - + -
233D LEU* 4.8 13.7 - - + -
253D VAL* 3.1 14.0 + - + +
254D ARG* 4.6 8.1 - - + -
255D TYR 3.2 0.2 - - - -
256D GLN* 1.3 77.1 - - - +
258D ARG* 1.3 61.1 - - - +
260D TYR* 4.0 2.7 - - - +
261D LEU* 3.2 32.0 + - + +
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Residues in contact with ARG 258 (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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218D VAL* 3.2 36.5 + - + +
219D ASN* 2.4 52.6 + - - +
221D ILE* 3.5 13.6 + - + +
223D GLU* 4.1 25.9 - - - +
226D ILE* 4.6 16.9 - - + +
254D ARG 4.4 9.1 + - - +
255D TYR* 3.2 19.5 + - - +
257D LEU* 1.3 77.9 - - - +
259D GLU* 1.3 62.2 + - - +
260D TYR 3.3 0.7 - - - -
261D LEU* 3.7 2.3 + - - +
262D GLY 3.5 14.6 + - - -
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Residues in contact with GLU 259 (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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218D VAL* 4.1 8.6 - - + +
255D TYR 3.0 17.3 + - - +
256D GLN* 3.7 5.1 + - - +
257D LEU 3.4 0.2 - - - -
258D ARG* 1.3 78.5 - - - +
260D TYR* 1.3 58.7 + - - +
262D GLY* 4.3 0.3 - - - -
263D ILE* 3.1 32.2 + - + +
285D LEU* 3.7 30.7 - - + -
286D GLU* 5.7 2.0 - - + +
287D GLN* 4.2 18.8 - - + +
289D PRO* 4.5 11.9 - - + -
292D ALA* 3.6 19.7 - - + -
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Residues in contact with TYR 260 (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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256D GLN 3.4 9.7 + - - +
257D LEU* 4.4 4.5 - - - +
258D ARG 3.3 0.6 - - - -
259D GLU* 1.3 76.4 - - - +
261D LEU* 1.3 67.9 + - + +
262D GLY 3.0 4.9 + - - -
263D ILE* 3.3 3.2 + - - +
264D LYS* 3.0 35.9 + - + +
292D ALA* 3.6 34.0 - - - +
295D LEU* 4.2 21.1 - - + -
296D LEU* 4.2 11.9 - - + -
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Residues in contact with LEU 261 (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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221D ILE* 3.8 27.0 - - + +
225D GLU* 4.1 35.4 - - + +
226D ILE* 5.6 1.8 - - + -
229D ALA* 3.9 24.0 - - + -
257D LEU* 3.2 27.7 + - - +
258D ARG 3.7 2.6 + - - +
260D TYR* 1.3 88.7 - - + +
262D GLY* 1.3 57.3 + - - +
264D LYS* 4.8 17.7 - - - +
265D LYS* 3.1 21.2 + - - +
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Residues in contact with GLY 262 (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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214D LEU* 4.3 1.1 - - - +
217D VAL* 3.8 10.6 - - - +
218D VAL* 4.0 31.0 - - - -
221D ILE* 4.6 0.2 - - - -
258D ARG 3.5 7.7 + - - -
259D GLU 4.3 0.2 - - - -
260D TYR 3.0 0.6 - - - -
261D LEU* 1.3 81.3 - - - +
263D ILE* 1.3 60.0 + - - +
265D LYS* 3.6 4.7 - - - +
266D PHE* 2.8 30.3 + - - +
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Residues in contact with ILE 263 (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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181D PHE* 5.0 3.6 - - + -
214D LEU* 4.3 24.4 - - + +
218D VAL* 4.8 1.2 - - + +
259D GLU* 3.1 24.9 + - + +
260D TYR* 3.7 0.9 - - - +
262D GLY* 1.3 74.1 - - - +
264D LYS* 1.3 55.9 + - - +
266D PHE* 2.7 24.4 + - - +
267D LEU* 2.8 23.0 + - + +
275D PHE* 4.5 18.8 - - + -
289D PRO* 5.6 8.1 - - + -
292D ALA* 5.5 2.9 - - + -
293D VAL* 6.4 0.2 - - + -
296D LEU* 3.6 26.0 - - + -
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Residues in contact with LYS 264 (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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260D TYR* 3.0 18.8 + - + +
261D LEU* 4.8 17.9 - - - +
263D ILE* 1.3 78.1 - - - +
265D LYS* 1.3 66.2 + - - +
267D LEU* 3.3 6.3 + - - +
268D ASP* 3.1 28.4 + - - +
296D LEU* 3.6 15.1 - - + +
299D ASP* 5.6 6.7 - - + -
301D TYR* 3.1 37.9 - - + +
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Residues in contact with LYS 265 (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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217D VAL* 4.2 11.9 - - + -
221D ILE* 4.9 7.9 - - + -
261D LEU 3.1 25.1 + - - +
262D GLY* 3.6 8.0 + - - +
264D LYS* 1.3 80.7 - - - +
266D PHE* 1.3 60.7 + - - +
268D ASP* 4.5 1.2 - - - +
269D ASP* 2.9 33.4 + - - -
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Residues in contact with PHE 266 (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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179D ALA* 5.3 3.6 - - + -
181D PHE* 3.8 28.0 - + + -
209D TYR* 4.1 22.9 - + + -
213D GLU* 3.7 27.1 - - + -
214D LEU* 4.0 19.1 - - + -
217D VAL* 3.6 27.8 - - + +
262D GLY 2.8 13.9 + - - +
263D ILE 2.7 14.7 + - - +
265D LYS* 1.3 71.1 - - - +
267D LEU* 1.3 72.9 + - + +
268D ASP 3.2 0.5 + - - -
269D ASP* 3.3 10.4 + - - +
270D ASN* 3.6 20.2 + - + +
272D TYR* 6.1 1.1 - + - -
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Residues in contact with LEU 267 (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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179D ALA* 4.2 7.9 - - + -
181D PHE* 4.4 9.9 - - + -
263D ILE* 2.8 27.7 + - + +
264D LYS* 3.7 7.4 - - - +
266D PHE* 1.3 77.3 - - + +
268D ASP* 1.3 59.0 + - - +
270D ASN* 3.4 1.6 + - - +
271D GLY 3.0 9.5 + - - -
272D TYR* 2.7 62.7 + - + +
274D ALA 3.7 14.1 - - - +
275D PHE* 3.5 40.8 - - + -
296D LEU* 5.0 2.2 - - + -
301D TYR* 4.6 19.7 - - + -
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Residues in contact with ASP 268 (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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264D LYS* 3.1 15.4 + - - +
265D LYS* 4.5 1.8 - - - +
267D LEU* 1.3 75.9 - - - +
269D ASP* 1.3 56.7 + - - +
270D ASN 2.7 16.0 + - - -
271D GLY* 3.0 12.4 + - - +
272D TYR 4.6 3.4 - - - +
301D TYR* 3.4 31.0 - - - -
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Residues in contact with ASP 269 (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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265D LYS* 2.9 24.2 - - - +
266D PHE* 3.3 4.9 + - - +
268D ASP* 1.3 73.7 - - - +
270D ASN* 1.3 58.6 + - + +
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Residues in contact with ASN 270 (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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177D LYS* 3.5 10.6 + - - +
266D PHE* 3.6 23.0 + - + +
267D LEU 3.4 3.2 + - - +
268D ASP 2.7 6.0 + - - -
269D ASP* 1.3 77.4 - - + +
271D GLY* 1.3 54.9 + - - +
272D TYR* 3.9 7.9 - - + -
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Residues in contact with GLY 271 (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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175D HIS 5.4 0.2 - - - +
177D LYS* 3.0 34.5 - - - +
267D LEU 3.0 2.2 + - - -
268D ASP* 3.0 10.2 + - - -
270D ASN* 1.3 80.1 - - - +
272D TYR* 1.3 63.4 + - - +
273D ASP* 3.8 8.3 + - - -
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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