Contacts of the helix formed by residues 253 - 275 (chain F) in PDB entry 1PZN
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 ALA 253 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E ALA* 4.9 7.9 - - + -
248F TYR* 4.1 16.8 - - + -
249F ILE 3.3 26.9 - - - +
250F GLY 3.0 17.9 - - - +
251F ARG 2.7 2.6 - - - +
252F GLY* 1.3 79.5 - - - +
254F LEU* 1.3 63.2 + - - +
255F ALA 2.9 3.8 + - - -
256F GLU* 2.9 16.6 + - - +
257F ARG* 2.9 12.9 + - - +
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Residues in contact with LEU 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248F TYR 5.3 2.7 - - - +
250F GLY* 3.2 27.6 - - - +
251F ARG* 4.0 23.3 - - + +
252F GLY 4.2 1.3 - - - +
253F ALA* 1.3 75.1 - - + +
255F ALA* 1.3 65.8 + - - +
257F ARG* 3.8 36.1 - - - +
258F GLN* 3.1 29.1 + - + +
302F GLY* 5.9 6.1 - - - -
247G GLU 4.9 0.2 - - - +
249G ILE* 4.1 40.1 - - + +
250G GLY* 5.4 1.6 - - - +
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Residues in contact with ALA 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F GLY* 4.4 16.2 - - - +
253F ALA 2.9 1.4 + - - +
254F LEU* 1.3 82.8 - - - +
256F GLU* 1.3 57.6 + - - +
259F GLN* 2.9 33.8 + - - +
247G GLU 3.9 7.1 - - - +
249G ILE 4.2 9.9 + - - +
250G GLY 6.0 0.2 - - - +
252G GLY 5.9 2.2 - - - +
253G ALA* 4.8 17.0 - - + -
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Residues in contact with GLU 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259E GLN* 4.7 4.6 - - - +
248F TYR* 2.9 35.5 + - + -
252F GLY 5.6 1.6 - - - +
253F ALA* 2.9 10.6 + - - +
255F ALA* 1.3 75.9 - - + +
257F ARG* 1.3 57.1 + - - +
259F GLN* 3.2 7.3 - - - +
260F LYS* 2.7 50.2 + - + +
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Residues in contact with ARG 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244F PHE* 4.1 22.1 - - + +
245F ARG* 4.7 4.6 - - - +
248F TYR* 4.0 47.4 + - + -
253F ALA 2.9 12.0 + - - +
254F LEU* 3.3 30.4 + - - +
256F GLU* 1.3 71.3 - - - +
258F GLN* 1.3 83.2 + - - +
260F LYS* 3.0 4.1 + - - +
261F LEU* 2.5 40.2 + - + +
302F GLY* 2.7 37.3 + - - -
303F HIS 3.3 15.4 + - - -
304F ILE* 3.5 23.2 - - - +
305F LEU* 5.4 0.2 - - - +
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Residues in contact with GLN 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254F LEU* 3.1 19.8 + - + +
257F ARG* 1.3 108.6 + - - +
259F GLN* 1.3 57.5 + - - +
261F LEU* 3.6 20.1 - - - +
262F ALA* 2.6 36.2 + - - +
304F ILE* 4.5 2.9 - - - +
305F LEU* 4.6 5.6 - - - +
307F HIS* 3.6 22.1 + - - +
246G SER 3.5 21.3 - - - +
247G GLU* 3.8 11.0 - - - +
249G ILE* 3.6 27.4 - - + +
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Residues in contact with GLN 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255F ALA* 2.9 26.6 + - - +
256F GLU* 3.2 11.7 - - - +
258F GLN* 1.3 82.2 - - - +
260F LYS* 1.3 74.2 + - - +
262F ALA* 3.7 4.4 - - - +
263F LYS* 3.3 17.3 + - - +
209G ASN* 5.1 9.1 - - - +
247G GLU* 3.8 25.8 + - - +
248G TYR* 3.9 33.5 + - - -
253G ALA* 6.0 0.3 - - - +
256G GLU* 5.3 1.9 - - - +
260G LYS* 5.0 4.8 - - - +
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Residues in contact with LYS 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F MSE 3.9 33.7 - - + +
244F PHE* 4.4 4.3 - - + -
248F TYR* 4.6 3.1 - - - +
256F GLU* 2.7 42.2 + - + +
257F ARG 3.7 1.6 - - - +
259F GLN* 1.3 87.0 + - - +
261F LEU* 1.3 68.0 + - - +
263F LYS* 2.9 16.9 + - + +
264F HIS* 2.7 21.3 + - - +
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Residues in contact with LEU 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240F LEU* 5.0 7.9 - - + -
241F THR* 5.4 3.1 - - + -
244F PHE* 4.2 23.4 - - + -
257F ARG* 2.5 23.9 + - + +
258F GLN* 3.6 19.3 - - - +
260F LYS* 1.3 71.1 - - - +
262F ALA* 1.3 56.6 + - - +
264F HIS* 2.6 35.6 + - + +
265F LEU* 2.8 44.2 + - + -
304F ILE* 3.2 37.7 - - + -
305F LEU 4.0 9.6 - - - +
307F HIS* 4.9 2.0 - - + +
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Residues in contact with ALA 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258F GLN 2.6 22.0 + - - +
259F GLN 3.7 4.7 - - - +
261F LEU* 1.3 73.0 - - - +
263F LYS* 1.3 56.5 + - - +
265F LEU* 3.9 7.2 - - - +
266F ALA* 2.9 30.9 + - - +
307F HIS* 4.6 14.1 - - + -
308F SER* 5.4 2.6 + - - +
206G PHE 4.7 1.6 - - - +
207G ASN* 4.1 7.9 + - + +
247G GLU* 3.8 36.3 - - + +
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Residues in contact with LYS 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F MSE 5.7 2.0 - - - -
216F GLN* 4.0 12.9 - - - +
259F GLN 3.3 11.6 + - - +
260F LYS* 2.9 26.8 + - + +
262F ALA* 1.3 81.5 - - - +
264F HIS* 1.3 54.7 + - - +
266F ALA* 3.5 7.9 + - + +
267F ASP* 2.8 60.2 + - - +
207G ASN* 4.3 10.5 - - - +
209G ASN* 6.2 2.2 - - - +
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Residues in contact with HIS 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F GLN* 3.1 36.3 + - + -
212F MSE 3.7 32.9 - - + -
215F VAL* 2.9 37.7 - - + +
237F VAL* 4.6 4.0 - - + -
240F LEU* 3.6 23.7 - - + +
244F PHE* 4.0 7.2 - + + -
260F LYS 2.7 11.0 + - - +
261F LEU* 2.6 20.4 + - + +
263F LYS* 1.3 67.8 - - - +
265F LEU* 1.3 57.5 + - - +
267F ASP* 2.6 32.2 + - - +
268F LEU* 3.0 17.8 + - + +
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Residues in contact with LEU 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F ILE* 5.1 7.6 - - + +
240F LEU* 3.7 30.3 - - + -
261F LEU* 2.8 38.6 + - + +
262F ALA* 3.9 4.7 - - - +
264F HIS* 1.3 72.5 - - - +
266F ALA* 1.3 56.8 + - - +
268F LEU* 3.0 15.7 + - + +
269F HIS* 2.8 35.4 + - + +
281F VAL* 5.9 0.2 - - + -
306F ALA* 3.6 35.9 - - + -
307F HIS* 4.2 17.7 - - + +
308F SER* 4.2 19.7 - - - +
309F ALA 5.3 1.8 - - - +
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Residues in contact with ALA 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262F ALA 2.9 19.6 + - - +
263F LYS* 3.6 7.0 - - + +
265F LEU* 1.3 76.1 - - - +
267F ASP* 1.3 62.4 + - - +
269F HIS* 3.7 3.4 - - - +
270F ARG* 3.1 23.9 + - - +
206G PHE* 3.8 30.9 + - + +
207G ASN* 3.3 24.2 - - - +
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Residues in contact with ASP 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212F MSE 5.1 3.6 - - - +
215F VAL* 4.2 17.9 - - + -
216F GLN* 4.0 21.0 + - + +
263F LYS* 2.8 55.5 + - - +
264F HIS* 2.6 23.6 + - + +
266F ALA* 1.3 73.4 - - - +
268F LEU* 1.3 58.5 + - - +
270F ARG* 3.5 8.3 + - - +
271F LEU* 3.3 26.0 + - - +
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Residues in contact with LEU 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F ILE* 4.1 9.2 - - + -
215F VAL* 3.4 33.2 - - + -
235F LEU* 4.2 26.2 - - + -
237F VAL* 4.2 5.2 - - + -
240F LEU* 4.2 15.9 - - + -
264F HIS* 3.0 15.8 + - + +
265F LEU* 3.0 27.8 + - + +
267F ASP* 1.3 75.2 - - - +
269F HIS* 1.3 66.2 + - - +
271F LEU* 3.1 7.4 + - - +
272F ALA* 2.9 22.3 + - - +
279F VAL* 4.1 17.3 - - + +
281F VAL* 4.2 16.8 - - + -
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Residues in contact with HIS 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F GLN 5.9 0.2 + - - -
132F ALA* 5.6 0.6 - - - -
133F ILE* 3.3 29.0 - - + +
265F LEU* 2.8 30.8 + - + +
266F ALA* 3.7 4.3 - - - +
268F LEU* 1.3 72.4 - - - +
270F ARG* 1.3 67.5 + - - +
272F ALA* 3.1 3.1 + - - +
273F ASN* 3.0 26.8 + - - -
308F SER* 2.7 51.7 + - - -
310F THR* 3.8 14.2 + - - -
175G ASN* 6.3 0.2 - - + -
204G ARG* 4.3 13.2 + - - -
206G PHE* 3.4 40.9 - + + -
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Residues in contact with ARG 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F GLU* 2.1 46.9 + - - -
266F ALA 3.1 14.7 + - - +
267F ASP* 3.7 9.4 + - - +
268F LEU 3.2 0.2 - - - -
269F HIS* 1.3 79.6 - - - +
271F LEU* 1.3 64.3 + - - +
273F ASN* 3.1 1.7 + - - +
274F LEU* 2.6 62.7 + - + +
206G PHE* 4.0 17.4 - - + -
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Residues in contact with LEU 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215F VAL* 3.7 39.5 - - + +
218F ALA* 4.7 4.7 - - + -
219F GLU* 4.0 28.0 - - + +
222F ILE* 5.2 4.0 - - + -
235F LEU* 4.0 22.2 - - + -
267F ASP 3.3 9.3 + - - +
268F LEU* 3.1 8.8 + - - +
270F ARG* 1.3 85.5 - - - +
272F ALA* 1.3 64.0 + - - +
274F LEU* 4.4 0.2 - - - -
275F TYR* 3.0 54.4 + - + +
277F ILE* 4.1 9.8 - - + +
279F VAL* 5.4 2.0 - - + -
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Residues in contact with ALA 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F GLN* 3.1 11.1 - - - -
132F ALA 3.8 17.0 - - - +
133F ILE* 3.9 9.6 - - + -
268F LEU 2.9 12.5 + - - +
269F HIS 3.1 8.7 + - - +
271F LEU* 1.3 75.3 - - - +
273F ASN* 1.3 60.6 + - - +
276F ASP 3.1 5.9 + - - -
277F ILE* 2.9 43.4 + - - +
279F VAL* 3.8 14.7 - - + +
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Residues in contact with ASN 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103F TYR* 6.1 0.5 - - - -
106F LYS* 6.1 2.1 - - - +
131F GLN* 2.9 50.1 + - + +
269F HIS* 3.0 16.0 + - - +
270F ARG* 3.9 1.3 - - - +
272F ALA* 1.3 75.0 - - - +
274F LEU* 1.3 66.6 + - - +
275F TYR 2.9 3.2 + - - -
276F ASP* 3.5 7.3 + - - -
175G ASN* 5.5 0.7 - - - +
204G ARG* 4.6 12.5 + - - +
206G PHE* 3.4 27.4 - - + -
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Residues in contact with LEU 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270F ARG* 2.6 47.4 + - + +
273F ASN* 1.3 72.6 - - - +
275F TYR* 1.3 99.5 + - + +
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Residues in contact with TYR 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219F GLU* 2.6 32.2 + - + -
222F ILE* 3.4 27.8 - - + -
223F LYS* 3.8 23.5 - - + +
226F LEU* 4.0 29.0 - - + +
232F VAL 4.5 1.0 - - - +
233F LYS* 4.3 5.5 + - - -
271F LEU* 3.0 35.9 + - + +
273F ASN 3.0 0.6 - - - -
274F LEU* 1.3 111.9 - - + +
276F ASP* 1.3 72.6 + - - +
277F ILE* 3.1 20.9 + - + +
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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
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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