Contacts of the helix formed by residues 213 - 233 (chain C) in PDB entry 1IR1
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 ARG 213 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LYS* 5.1 4.4 - - - +
149B GLN 5.5 3.6 + - - -
152B PRO 5.7 0.7 - - - +
285B ARG* 3.8 45.8 - - - +
372B PRO* 6.1 3.8 - - - +
208C SER* 3.6 17.0 + - - +
209C GLN* 3.4 32.6 + - - +
210C PRO* 3.6 30.6 + - - +
212C MET* 1.3 75.0 - - - +
214C TRP* 1.3 68.2 + - + +
215C ARG* 3.4 4.0 - - + +
216C ASP* 3.3 24.6 + - - +
217C ARG* 3.2 19.7 + - - +
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Residues in contact with TRP 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B ASP* 4.8 16.0 + - + -
207C ASN 3.5 15.9 - - - +
208C SER* 3.2 29.0 + - - +
212C MET 3.9 0.4 + - - -
213C ARG* 1.3 73.1 - - + +
215C ARG* 1.3 93.2 + - + +
217C ARG* 3.2 13.1 + - - +
218C PHE* 2.9 46.9 + + + -
252C LYS* 3.7 30.5 - - + -
253C ARG* 3.6 57.4 - - + +
256C PHE* 3.9 28.5 - + + -
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Residues in contact with ARG 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 5.6 0.6 - - - +
258B ARG* 3.5 22.8 - - - +
285B ARG* 3.7 21.1 - - - +
286B ASP* 3.0 25.3 + - - +
287B ASN* 3.5 17.6 + - - +
288B GLY* 3.5 20.2 - - - +
213C ARG* 3.4 2.9 - - + +
214C TRP* 1.3 105.8 - - + +
216C ASP* 1.3 66.2 + - - +
218C PHE* 3.5 2.7 + - - +
219C LEU* 3.1 41.0 + - - +
256C PHE* 3.3 48.7 - - + -
58T SER* 4.8 7.5 - - - -
59T PRO* 4.6 2.6 + - - +
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Residues in contact with ASP 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B PRO 5.1 1.6 - - - +
153B HIS* 3.6 13.4 + - - -
157B VAL* 3.6 30.4 - - + +
161B LYS* 2.8 32.4 + - - +
285B ARG* 6.0 1.3 - - - -
182C ALA* 3.7 16.8 - - + -
213C ARG* 3.3 25.9 + - - +
214C TRP 3.2 0.2 - - - -
215C ARG* 1.3 79.3 - - - +
217C ARG* 1.3 63.7 + - - +
219C LEU* 3.4 5.1 + - - +
220C PHE* 3.1 30.5 + - + -
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Residues in contact with ARG 217 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C ALA* 3.8 10.9 - - - +
185C TYR* 3.7 13.0 - - + -
202C ASP* 2.8 40.6 + - - +
206C VAL* 3.5 22.5 + - - +
207C ASN 2.9 29.5 + - - -
212C MET* 3.6 38.6 + - - +
213C ARG 3.2 6.2 + - - +
214C TRP* 3.2 11.0 + - - +
216C ASP* 1.3 80.2 - - - +
218C PHE* 1.3 84.6 + - + +
220C PHE* 3.9 0.3 - - - +
221C CYS* 2.9 38.5 + - - +
240C LEU* 5.2 1.3 - - + +
241C ASN 4.0 5.9 + - - -
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Residues in contact with PHE 218 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214C TRP* 2.9 45.8 + + + +
215C ARG 3.7 4.9 - - - +
217C ARG* 1.3 101.0 - - - +
219C LEU* 1.3 62.7 + - - +
221C CYS* 3.5 1.6 + - - +
222C ALA* 3.0 24.4 + - - +
240C LEU* 3.7 49.2 - - + +
241C ASN 3.6 18.8 - - - -
242C ALA* 5.0 0.9 - - + -
253C ARG* 3.3 31.4 - - + -
256C PHE* 3.8 26.9 - + + -
257C ALA* 4.4 9.2 - - + -
260C LEU* 3.9 8.9 - - + +
265C VAL* 5.8 1.1 - - + -
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Residues in contact with LEU 219 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 4.2 21.1 - - - +
215C ARG* 3.1 30.2 + - - +
216C ASP* 3.6 5.6 - - - +
217C ARG 3.2 0.2 - - - -
218C PHE* 1.3 79.9 - - - +
220C PHE* 1.3 68.0 + - + +
222C ALA* 3.3 7.5 + - - +
223C GLU* 3.2 16.8 + - - +
256C PHE* 4.3 10.3 - - + -
260C LEU* 4.9 3.4 - - + -
58T SER* 5.0 3.8 - - - +
59T PRO 3.8 21.8 - - - +
60T GLY 3.7 13.7 - - - +
61T TYR* 3.9 22.4 - - + +
65T ARG* 3.4 29.6 - - - +
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Residues in contact with PHE 220 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B VAL* 5.3 2.9 - - + -
160B ASP* 3.6 42.0 - - + -
161B LYS* 3.9 29.2 - - + -
182C ALA* 3.7 27.6 - - + +
183C LYS* 3.9 17.7 - - + -
186C GLY* 4.4 2.2 - - - -
216C ASP* 3.1 26.9 + - + +
217C ARG 4.1 1.6 - - - +
219C LEU* 1.3 74.1 - - + +
221C CYS* 1.3 60.7 + - - +
223C GLU* 3.3 5.4 + - - +
224C ALA* 3.0 27.4 + - - +
65T ARG* 3.8 29.6 - - + -
66T TYR* 3.5 34.1 - + - +
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Residues in contact with CYS 221 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C ALA 5.5 0.2 - - - -
185C TYR* 3.9 13.7 - - - -
186C GLY* 4.4 7.2 - - - -
189C VAL* 4.1 13.0 - - + +
217C ARG* 2.9 37.5 + - - +
218C PHE 3.9 2.9 - - - +
220C PHE* 1.3 77.8 - - - +
222C ALA* 1.3 57.9 + - - +
224C ALA* 3.4 6.4 + - - +
225C LEU* 2.9 34.9 + - + +
238C HIS* 3.8 37.5 - - + -
240C LEU* 4.2 6.5 - - + -
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Residues in contact with ALA 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218C PHE 3.0 17.9 + - - +
219C LEU 3.5 6.3 - - - +
220C PHE 3.2 0.2 - - - -
221C CYS* 1.3 74.7 - - - +
223C GLU* 1.3 66.1 + - - +
225C LEU* 3.4 12.1 + - - +
226C TYR* 3.0 44.2 + - + -
240C LEU* 6.1 0.8 - - - +
260C LEU* 4.3 24.2 - - + -
262C VAL* 4.5 6.7 - - + -
61T TYR* 4.3 6.3 - - + -
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Residues in contact with GLU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219C LEU 3.2 10.2 + - - +
220C PHE* 3.3 11.0 + - - +
222C ALA* 1.3 78.7 - - - +
224C ALA* 1.3 62.6 + - - +
226C TYR* 3.5 1.7 + - - +
227C LYS* 3.1 24.3 + - + +
61T TYR* 3.5 17.4 - - + +
62T TYR 3.2 18.2 - - - +
63T ASP* 4.0 13.3 - - - +
64T GLY 3.6 3.7 + - - +
65T ARG* 2.9 56.9 + - - +
66T TYR* 3.1 29.4 + - + +
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Residues in contact with ALA 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C GLY* 3.1 32.5 - - - +
189C VAL* 4.2 4.3 - - + -
190C TYR* 3.9 21.5 - - + +
220C PHE 3.0 16.8 + - - +
221C CYS 3.6 5.2 - - - +
222C ALA 3.2 0.2 - - - -
223C GLU* 1.3 77.8 - - - +
225C LEU* 1.3 62.5 + - - +
227C LYS* 3.2 6.1 + - - +
228C ALA* 3.1 22.3 + - - +
66T TYR* 4.1 8.0 - - + -
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Residues in contact with LEU 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C VAL* 4.9 1.6 - - + -
193C LEU* 3.8 26.9 - - + +
221C CYS* 2.9 24.8 + - + +
222C ALA* 3.7 7.6 - - - +
224C ALA* 1.3 74.1 - - - +
226C TYR* 1.3 84.4 + - + +
228C ALA* 3.4 1.9 + - - +
229C GLN* 3.0 32.5 + - - +
236C LYS* 4.0 23.7 - - + +
237C GLY* 4.6 2.0 - - - +
238C HIS* 4.1 27.4 - - + +
240C LEU* 5.6 2.5 - - + -
262C VAL* 4.0 26.2 - - + -
263C PRO* 5.0 3.6 - - + -
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Residues in contact with TYR 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C ALA* 3.0 38.5 + - + +
223C GLU 4.0 2.7 - - - +
225C LEU* 1.3 88.4 - - + +
227C LYS* 1.3 65.5 + - - +
229C GLN* 3.8 18.1 - - - +
230C ALA* 3.1 24.1 + - - +
260C LEU* 2.7 28.3 + - + -
261C GLY 3.3 10.6 - - - -
262C VAL* 3.6 9.1 + - + +
263C PRO* 6.0 0.9 - - + -
55T HIS* 3.6 61.4 + + + +
56T HIS* 6.1 1.1 - - + -
61T TYR* 3.9 5.6 - + - +
63T ASP* 5.1 0.4 - - - +
53U ARG* 3.2 29.3 + - - -
62U TYR* 5.7 3.1 - + - -
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Residues in contact with LYS 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C TYR* 3.5 41.5 - - + -
223C GLU* 3.1 16.3 + - + +
224C ALA* 3.5 9.4 - - - +
226C TYR* 1.3 77.4 - - - +
228C ALA* 1.3 61.4 + - - +
230C ALA* 3.4 5.5 + - - +
231C GLU* 3.0 24.7 + - + +
45T GLU* 2.9 32.0 + - - -
48T HIS* 5.9 4.8 - - - +
52T TYR* 6.2 0.4 - - - +
55T HIS* 5.8 0.9 - - - -
64T GLY* 5.6 5.0 - - - +
66T TYR* 3.1 36.9 + - + +
67T TRP* 4.5 2.2 - - - +
68T THR* 4.6 0.9 - - - -
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Residues in contact with ALA 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C TYR* 3.9 15.4 - - + +
193C LEU* 3.6 32.5 - - + -
194C ARG* 4.0 12.1 - - - +
224C ALA 3.1 15.5 + - - +
225C LEU 3.7 4.7 - - - +
227C LYS* 1.3 79.9 - - - +
229C GLN* 1.3 61.9 + - - +
231C GLU* 3.3 2.7 + - - +
232C THR* 3.0 31.0 + - - +
236C LYS* 4.3 2.5 - - + -
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Residues in contact with GLN 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C LEU* 3.0 20.7 + - - +
226C TYR* 3.8 19.0 - - - +
227C LYS 3.3 0.2 - - - -
228C ALA* 1.3 77.6 - - - +
230C ALA* 1.3 57.2 + - - +
233C GLY* 2.8 30.1 + - - -
234C GLU 3.4 21.3 - - - +
235C ILE* 3.5 15.3 - - - +
236C LYS* 3.1 28.9 + - + +
51U VAL* 4.3 15.9 + - + +
52U TYR* 6.1 1.8 - - - +
53U ARG* 5.5 4.2 - - - +
62U TYR* 3.8 27.4 + - - -
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Residues in contact with ALA 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C TYR 3.1 17.9 + - - +
227C LYS* 3.7 5.4 - - - +
229C GLN* 1.3 78.2 - - - +
231C GLU* 1.3 62.7 + - - +
233C GLY* 4.1 0.5 + - - -
54T GLU* 6.2 0.2 - - - +
55T HIS* 5.4 9.4 - - + +
10U LYS* 3.6 21.1 + - - -
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Residues in contact with GLU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C TYR* 2.6 29.9 + - - -
194C ARG* 3.1 43.9 + - - +
227C LYS* 3.0 18.4 + - + +
228C ALA* 3.6 5.8 - - - +
229C GLN 3.2 0.2 - - - -
230C ALA* 1.3 80.7 - - - +
232C THR* 1.3 61.4 + - + +
4U TRP* 5.3 0.5 - - - -
5U PRO 4.2 1.2 - - - +
6U THR* 4.0 31.2 - - - +
9U MET* 4.3 15.8 + - + +
10U LYS* 3.7 14.2 + - - +
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Residues in contact with THR 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C LEU 4.3 0.2 - - - +
194C ARG* 3.6 35.4 - - + +
228C ALA 3.0 17.8 + - - +
231C GLU* 1.3 81.8 - - + +
233C GLY* 1.3 62.6 + - - +
234C GLU* 3.2 17.1 + - - +
236C LYS* 3.3 22.2 - - - +
9U MET 4.5 8.3 - - - +
10U LYS* 3.5 3.0 - - - -
11U ARG* 2.8 32.4 + - + +
17U TYR* 4.8 10.1 - - - +
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Residues in contact with GLY 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C GLN 2.8 18.1 + - - -
230C ALA* 4.1 0.8 + - - -
231C GLU 3.6 1.4 - - - -
232C THR* 1.3 73.7 - - - +
234C GLU* 1.3 61.9 + - - +
235C ILE 4.3 0.2 + - - -
10U LYS* 3.9 16.7 - - - +
11U ARG 4.4 3.4 - - - +
50U PHE* 4.1 24.8 - - - +
51U VAL* 4.5 15.5 + - - +
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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
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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