Contacts of the helix formed by residues 207 - 230 (chain F) in PDB entry 1NU9
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 ASN 207 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49F HIS* 3.1 32.3 + - + -
52F GLU* 5.6 0.4 + - - -
145F ASP 3.3 11.7 - - - +
146F LEU* 3.4 18.3 + - - +
147F LYS 3.3 21.3 - - - +
149F PHE* 3.2 20.1 - - - -
205F ILE 4.6 0.2 - - - -
206F SER* 1.3 78.9 + - - +
208F GLU* 1.3 62.7 + - - +
209F ARG* 3.0 4.6 + - - +
210F ILE* 2.7 47.3 + - - +
211F GLU* 3.1 15.9 + - - +
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Residues in contact with GLU 208 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144F HIS* 4.3 6.8 - - - +
145F ASP* 3.4 27.0 + - + +
147F LYS 4.7 1.2 + - - +
149F PHE* 3.3 27.6 - - + -
207F ASN* 1.3 73.2 - - - +
209F ARG* 1.3 59.9 + - - +
211F GLU* 3.4 7.3 + - - +
212F LYS* 3.0 30.8 + - - +
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Residues in contact with ARG 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F GLU* 2.9 40.8 + - - +
53F LYS* 4.5 3.0 - - - +
54F GLU* 2.3 49.7 + - - -
143F HIS* 5.0 2.2 + - - -
145F ASP* 2.9 51.3 + - - +
146F LEU* 3.6 13.0 - - + +
207F ASN* 3.0 4.8 + - - +
208F GLU* 1.3 75.6 - - - +
210F ILE* 1.3 62.2 + - + +
212F LYS* 3.3 3.7 + - - -
213F GLU* 2.9 42.7 + - + +
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Residues in contact with ILE 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ARG* 3.9 26.9 - - - +
48F TYR* 3.8 29.2 - - + +
49F HIS* 4.0 8.7 - - - +
52F GLU* 4.1 7.6 - - - +
204F ARG 3.8 15.5 - - - +
205F ILE* 4.0 15.3 - - + -
206F SER* 3.7 23.1 - - - +
207F ASN* 2.7 35.6 + - - +
209F ARG* 1.3 73.3 - - - +
211F GLU* 1.3 55.2 + - - +
213F GLU* 4.7 3.8 - - - -
214F MET* 2.8 39.2 + - + +
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Residues in contact with GLU 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149F PHE* 3.7 15.8 - - - -
157F ALA* 3.5 28.2 - - + +
160F ARG* 2.7 42.8 + - - +
161F VAL* 4.9 0.7 - - + -
205F ILE* 3.6 16.5 - - + +
207F ASN 3.1 17.0 + - - +
208F GLU* 3.6 7.5 - - - +
210F ILE* 1.3 77.5 - - - +
212F LYS* 1.3 63.7 + - - +
214F MET* 4.0 1.6 - - - +
215F ILE* 3.0 36.6 + - + +
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Residues in contact with LYS 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F GLU 3.0 17.5 + - - +
209F ARG* 3.9 4.0 - - - +
211F GLU* 1.3 79.5 - - - +
213F GLU* 1.3 67.9 + - - +
215F ILE* 3.6 5.0 + - - +
216F LYS* 3.1 60.5 + - + +
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Residues in contact with GLU 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ARG* 6.4 1.3 - - - +
77D ARG* 3.0 37.5 + - + -
52F GLU* 5.4 3.8 - - - +
209F ARG* 2.9 38.2 + - + +
210F ILE* 4.3 3.6 - - - +
212F LYS* 1.3 86.4 - - + +
214F MET* 1.3 60.8 + - - +
215F ILE 3.2 0.2 - - - -
216F LYS* 3.7 6.2 + - - +
217F ASP* 2.8 40.2 + - - +
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Residues in contact with MET 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F TYR* 3.9 22.7 - - + +
161F VAL* 3.7 29.8 - - + -
195F VAL* 3.2 44.4 - - - +
196F LEU* 4.3 12.8 - - + -
203F HIS* 4.5 9.0 - - + +
205F ILE* 3.9 18.4 - - + -
210F ILE* 2.8 23.9 + - + +
211F GLU 4.0 2.2 - - - +
213F GLU* 1.3 77.1 - - - +
215F ILE* 1.3 56.6 + - - +
217F ASP* 3.6 7.8 - - - +
218F LEU* 2.9 38.3 + - + +
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Residues in contact with ILE 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F ARG* 3.8 38.6 - - + +
161F VAL* 3.7 37.2 - - + +
164F LEU* 3.6 19.1 - - + +
211F GLU* 3.0 24.9 + - + +
212F LYS* 3.8 6.3 - - - +
214F MET* 1.3 76.0 - - - +
216F LYS* 1.3 62.2 + - + +
218F LEU* 3.4 1.0 + - + -
219F GLU* 2.9 50.0 + - - +
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Residues in contact with LYS 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D ARG* 3.7 33.7 + - + +
212F LYS* 3.1 54.8 + - + +
213F GLU* 3.8 8.7 + - - +
215F ILE* 1.3 77.6 - - + +
217F ASP* 1.3 57.3 + - - +
219F GLU* 3.4 15.5 + - - +
220F SER* 2.8 31.0 + - - -
277F VAL* 3.8 16.2 - - + +
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Residues in contact with ASP 217 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ARG* 6.1 0.7 - - - -
76D TYR* 3.6 42.6 + - + +
77D ARG* 2.5 36.3 - - - -
195F VAL* 4.8 9.3 - - + +
213F GLU* 2.8 25.8 + - - +
214F MET* 3.6 9.3 - - - +
216F LYS* 1.3 75.7 - - - +
218F LEU* 1.3 52.7 + - - +
220F SER* 2.7 23.9 + - - -
221F ILE* 2.7 29.0 + - + +
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Residues in contact with LEU 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161F VAL* 3.5 39.3 - - + +
164F LEU* 3.5 21.8 - - + -
165F ALA* 3.8 18.2 - - + +
168F ALA* 5.5 1.1 - - + -
192F VAL* 4.1 29.3 - - + +
195F VAL* 3.7 27.8 - - + -
196F LEU* 4.4 3.8 - - + -
214F MET* 2.9 23.3 + - + +
215F ILE* 5.0 0.7 - - - -
217F ASP* 1.3 77.1 - - - +
219F GLU* 1.3 62.0 + - - +
221F ILE* 3.2 6.1 + - + +
222F ILE* 3.1 27.8 + - + +
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Residues in contact with GLU 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F LEU* 3.7 18.2 - - + +
215F ILE* 2.9 36.9 + - - +
216F LYS* 3.7 15.4 - - - +
218F LEU* 1.3 74.6 - - - +
220F SER* 1.3 64.3 + - - +
222F ILE* 3.2 8.6 + - - +
223F GLU* 2.9 33.9 + - - +
277F VAL* 3.8 17.2 - - + +
2004F IMD 5.3 8.1 - - + -
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Residues in contact with SER 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TYR* 4.3 1.9 + - - -
77D ARG* 3.8 19.1 + - - -
216F LYS 2.8 15.4 + - - -
217F ASP* 2.7 20.6 + - - -
219F GLU* 1.3 76.4 - - - +
221F ILE* 1.3 61.3 + - - +
223F GLU* 3.4 10.7 + - - -
224F ASP* 2.9 34.3 + - - +
277F VAL* 4.0 5.8 - - - +
278F LYS* 3.6 27.8 - - - +
280F TYR* 3.3 3.1 + - - -
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Residues in contact with ILE 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TYR* 3.8 27.6 - - + +
188F LEU* 3.6 26.0 - - + +
191F LYS* 3.7 45.0 + - + +
192F VAL* 3.9 12.8 - - + +
195F VAL* 3.8 26.0 - - + -
217F ASP 2.7 24.7 + - - +
218F LEU* 3.6 8.1 - - + +
219F GLU 3.2 0.2 - - - -
220F SER* 1.3 73.3 + - - +
222F ILE* 1.3 63.3 + - - +
224F ASP* 3.4 9.9 + - - +
225F PHE* 3.3 15.2 + - - +
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Residues in contact with ILE 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164F LEU* 3.5 32.1 - - + -
167F LYS* 5.0 1.6 - - + -
168F ALA* 3.8 35.4 - - + +
171F VAL* 5.1 4.7 - - + -
188F LEU* 4.2 8.3 - - + -
218F LEU* 3.1 15.3 + - + +
219F GLU* 3.6 7.9 - - - +
221F ILE* 1.3 73.9 - - + +
223F GLU* 1.3 67.6 + - - +
225F PHE* 3.1 11.3 + - - +
226F PHE* 3.1 40.7 - - + -
233F LYS* 4.0 15.9 - - + -
237F ILE* 5.0 7.2 - - + -
2004F IMD 4.3 13.2 - - + -
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Residues in contact with GLU 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219F GLU* 2.9 23.1 + - + +
220F SER* 3.7 2.9 - - - +
222F ILE* 1.3 75.2 - - + +
224F ASP* 1.3 58.8 + - - +
226F PHE* 3.2 5.6 + - - +
227F ILE* 2.8 32.4 + - - +
233F LYS* 3.8 30.9 - - + -
272F TRP* 4.0 13.9 - - + +
275F LYS 4.1 4.3 - - - +
276F THR* 3.3 25.7 - - + +
277F VAL* 2.8 36.9 + - - +
278F LYS 4.5 0.7 + - - -
280F TYR* 3.6 11.8 + - - +
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Residues in contact with ASP 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TYR* 4.0 6.2 + - - -
191F LYS* 2.6 30.6 + - - +
220F SER 2.9 20.4 + - - +
221F ILE* 3.4 12.2 - - - +
223F GLU* 1.3 75.8 - - - +
225F PHE* 1.3 64.7 + - - +
227F ILE* 4.3 4.3 - - - -
228F GLU* 2.9 44.6 + - - +
278F LYS* 2.9 28.8 + - - +
280F TYR* 2.6 29.4 + - - -
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Residues in contact with PHE 225 (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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171F VAL* 3.6 24.7 - - + -
175F PHE* 3.7 29.8 - + + -
181F HIS* 4.2 2.5 - - + -
184F GLU* 3.4 25.1 - - + +
185F ALA* 3.7 24.9 - - + -
188F LEU* 4.1 22.4 - - + -
221F ILE 3.3 6.9 + - - +
222F ILE 3.1 11.5 + - - +
224F ASP* 1.3 80.5 - - - +
226F PHE* 1.3 81.1 + + + +
228F GLU* 4.0 2.9 - - - +
229F THR* 2.9 58.6 + - + +
231F LEU* 4.2 5.8 - - + -
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Residues in contact with PHE 226 (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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171F VAL* 4.0 22.0 - - + -
222F ILE* 3.1 39.2 + - + -
223F GLU* 3.2 3.4 + - - +
225F PHE* 1.3 93.7 - + - +
227F ILE* 1.3 66.6 + - - +
229F THR* 3.7 2.7 - - - -
230F GLY* 3.0 19.4 + - - -
231F LEU* 3.1 37.0 + - + +
232F ASN 3.4 25.8 - - - -
233F LYS* 3.8 22.2 - - + -
234F PRO* 3.9 13.9 - - + -
237F ILE* 5.1 0.4 - - + -
265F VAL* 3.9 16.2 - - + -
272F TRP* 3.4 18.4 - - + -
273F LYS* 6.1 0.2 - - - -
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Residues in contact with ILE 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223F GLU 2.8 21.6 + - - +
224F ASP 3.6 3.6 - - - +
226F PHE* 1.3 77.9 - - - +
228F GLU* 1.3 69.2 + - + +
230F GLY* 3.6 8.1 + - - -
272F TRP* 3.7 20.9 - - + -
273F LYS* 4.8 15.7 - - + +
276F THR* 4.9 1.3 - - + -
280F TYR* 3.5 61.5 - - + -
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Residues in contact with GLU 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LYS* 3.6 28.0 + - - -
110D LYS* 3.2 29.5 + - - +
184F GLU* 4.2 14.5 - - + +
187F GLU* 4.2 6.6 - - - +
191F LYS* 4.8 3.8 + - - -
224F ASP* 2.9 38.4 + - - +
225F PHE* 4.1 3.3 - - - +
227F ILE* 1.3 82.0 - - + +
229F THR* 1.3 61.8 + - - +
230F GLY 3.2 1.6 - - - -
280F TYR* 5.7 1.7 - - - -
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Residues in contact with THR 229 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181F HIS* 3.2 45.1 - - + +
184F GLU* 3.4 32.1 - - + -
225F PHE* 2.9 34.9 + - + +
226F PHE* 3.5 2.6 + - - -
228F GLU* 1.3 75.8 - - - +
230F GLY* 1.3 62.6 + - - +
231F LEU* 3.2 22.9 + - - +
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Residues in contact with GLY 230 (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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226F PHE 3.0 9.2 + - - -
227F ILE 3.6 6.7 + - - -
228F GLU 3.2 3.6 + - - -
229F THR* 1.3 79.9 - - - +
231F LEU* 1.3 65.2 + - - +
232F ASN* 4.2 3.3 + - - -
273F LYS* 5.7 5.5 + - - -
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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