Contacts of the helix formed by residues 213 - 233 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146C LYS* 5.1 4.6 - - - +
149C GLN 5.4 4.6 + - - -
152C PRO 5.8 0.7 - - - +
285C ARG* 3.5 44.0 - - - +
372C PRO* 6.1 4.6 - - - +
208D SER* 3.6 18.8 + - - +
209D GLN* 3.4 31.8 + - - +
210D PRO* 3.7 29.0 + - - +
212D MET* 1.3 74.5 - - - +
214D TRP* 1.3 68.6 + - + +
215D ARG* 3.4 3.6 - - + +
216D ASP* 3.3 25.2 + - - +
217D ARG* 3.2 19.3 + - - +
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Residues in contact with TRP 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C ARG* 6.2 2.0 - - - +
286C ASP* 5.0 13.4 + - - -
207D ASN 3.5 15.7 - - - +
208D SER* 3.2 27.8 + - - -
212D MET 3.9 0.8 + - - -
213D ARG* 1.3 72.3 - - + +
215D ARG* 1.3 92.2 + - + +
217D ARG* 3.2 18.6 + - - +
218D PHE* 2.9 48.4 + + + -
241D ASN 5.6 0.2 - - - +
252D LYS* 3.9 30.5 - - + -
253D ARG* 3.5 61.7 - - + +
256D PHE* 3.8 29.6 - + + -
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Residues in contact with ARG 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161C LYS* 5.7 0.6 - - - +
258C ARG* 3.5 22.8 - - - +
285C ARG* 3.5 26.9 - - + +
286C ASP* 3.0 19.3 + - - +
287C ASN* 3.5 17.6 + - - +
288C GLY* 3.6 19.2 - - - +
213D ARG* 3.4 3.1 - - + +
214D TRP* 1.3 106.0 - - + +
216D ASP* 1.3 64.3 + - - +
218D PHE* 3.5 2.6 + - - +
219D LEU* 3.0 40.7 + - - +
256D PHE* 3.3 48.3 - - + -
58U SER* 4.9 6.9 + - - -
59U PRO 4.5 2.8 + - - -
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Residues in contact with ASP 216 (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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152C PRO 5.2 1.4 - - - +
153C HIS* 3.6 13.5 + - - -
157C VAL* 3.5 30.9 - - + +
161C LYS* 2.9 30.4 + - - +
182D ALA* 3.7 17.9 - - + -
213D ARG* 3.3 25.6 + - - +
215D ARG* 1.3 79.5 - - - +
217D ARG* 1.3 62.9 + - - +
219D LEU* 3.4 5.2 + - - +
220D PHE* 3.0 29.8 + - + -
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Residues in contact with ARG 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D ALA* 3.9 10.4 - - - +
185D TYR* 3.8 11.9 - - + -
202D ASP* 2.8 39.0 + - - +
206D VAL* 3.4 23.5 + - - +
207D ASN 2.8 30.9 + - - -
209D GLN* 5.5 0.2 + - - -
212D MET* 3.7 37.9 + - - +
213D ARG 3.2 5.8 + - - +
214D TRP* 3.2 14.0 + - - +
216D ASP* 1.3 78.9 - - - +
218D PHE* 1.3 86.0 + - + +
219D LEU 3.3 0.2 + - - -
220D PHE* 3.3 1.6 + - - +
221D CYS* 2.9 41.4 + - - +
240D LEU* 5.2 0.9 - - + +
241D ASN 3.9 6.9 + - - -
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Residues in contact with PHE 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214D TRP* 2.9 46.5 + + + +
215D ARG 3.7 4.7 - - - +
217D ARG* 1.3 102.4 - - - +
219D LEU* 1.3 63.0 + - - +
221D CYS* 3.9 1.0 - - - +
222D ALA* 3.0 25.3 + - - +
240D LEU* 3.7 51.2 - - + +
241D ASN 3.5 20.0 - - - -
242D ALA* 4.9 1.1 - - + -
253D ARG* 3.4 30.1 - - + -
256D PHE* 3.8 22.2 - + + -
257D ALA* 4.4 8.1 - - + -
260D LEU* 3.7 7.9 - - + +
265D VAL* 5.7 0.4 - - + -
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Residues in contact with LEU 219 (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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161C LYS* 4.1 23.8 - - - +
215D ARG* 3.0 33.0 + - - +
216D ASP* 3.6 5.2 - - - +
218D PHE* 1.3 78.0 - - - +
220D PHE* 1.3 68.2 + - + +
222D ALA* 3.4 7.1 + - - +
223D GLU* 3.3 15.9 + - - +
256D PHE* 4.3 7.8 - - + -
260D LEU* 4.7 6.7 - - + -
58U SER* 5.3 2.0 - - - +
59U PRO 3.9 20.9 - - - +
60U GLY 3.8 14.4 - - - +
61U TYR* 3.9 21.2 - - + +
65U ARG* 3.4 29.4 - - - +
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Residues in contact with PHE 220 (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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157C VAL* 5.3 3.4 - - + -
160C ASP* 3.6 42.0 - - + -
161C LYS* 3.9 26.5 - - + -
182D ALA* 3.7 27.6 - - + +
183D LYS* 3.8 21.3 - - + -
186D GLY* 4.5 1.6 - - - -
216D ASP* 3.0 25.4 + - + +
217D ARG 4.1 1.1 - - - +
219D LEU* 1.3 75.4 - - + +
221D CYS* 1.3 62.2 + - - +
223D GLU* 3.4 6.3 + - - +
224D ALA* 3.0 27.5 + - - +
65U ARG* 3.8 28.7 - - + -
66U TYR* 3.5 33.7 - + - +
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Residues in contact with CYS 221 (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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185D TYR* 3.9 14.4 - - - -
186D GLY* 4.6 7.0 - - - -
189D VAL* 4.1 13.0 - - + +
217D ARG* 2.9 37.7 + - - +
218D PHE 3.9 3.1 - - - +
220D PHE* 1.3 74.0 - - - +
222D ALA* 1.3 60.8 + - - +
224D ALA* 3.3 7.4 + - - +
225D LEU* 2.8 35.2 + - + +
238D HIS* 3.8 30.7 - - + -
240D LEU* 4.1 13.5 - - + -
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Residues in contact with ALA 222 (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 PHE 3.0 18.6 + - - +
219D LEU 3.5 6.1 - - - +
221D CYS* 1.3 75.7 - - - +
223D GLU* 1.3 65.9 + - - +
225D LEU* 3.6 11.2 - - - +
226D TYR* 3.1 39.5 + - + -
240D LEU* 6.1 0.4 - - - +
260D LEU* 4.1 20.4 - - + -
262D VAL* 4.4 11.4 - - + -
61U TYR* 4.3 9.9 - - + -
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Residues in contact with GLU 223 (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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219D LEU 3.3 7.1 + - - +
220D PHE* 3.6 11.5 - - - +
222D ALA* 1.3 78.6 - - - +
224D ALA* 1.3 62.0 + - - +
226D TYR* 4.0 1.6 - - - +
227D LYS* 3.1 25.6 + - + +
61U TYR* 3.4 19.9 - - + +
62U TYR 3.2 19.2 - - - +
63U ASP* 3.9 14.7 - - - +
64U GLY 3.6 4.0 + - - +
65U ARG* 2.9 55.8 + - - +
66U TYR* 3.2 28.7 + - + +
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Residues in contact with ALA 224 (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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186D GLY* 3.2 29.8 - - - +
189D VAL* 4.1 5.4 - - + -
190D TYR* 3.8 21.7 - - + +
220D PHE 3.0 17.3 + - - +
221D CYS 3.6 4.9 - - - +
223D GLU* 1.3 77.1 - - - +
225D LEU* 1.3 62.3 + - - +
227D LYS* 3.3 6.0 + - - +
228D ALA* 3.1 22.9 + - - +
66U TYR* 4.2 9.1 - - + -
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Residues in contact with LEU 225 (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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189D VAL* 4.6 1.8 - - + +
193D LEU* 3.7 25.1 - - + +
221D CYS* 2.8 22.5 + - + +
222D ALA* 3.6 9.9 - - - +
224D ALA* 1.3 72.9 - - - +
226D TYR* 1.3 84.9 + - + +
228D ALA* 3.4 2.4 + - - +
229D GLN* 3.0 32.3 + - - +
236D LYS* 4.0 23.4 - - + +
237D GLY* 4.6 2.2 - - - -
238D HIS* 4.1 28.3 - - + +
240D LEU* 5.9 2.0 - - + -
262D VAL* 3.8 27.6 - - + -
263D PRO* 4.9 3.8 - - + -
62V TYR* 6.2 0.2 - - - +
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Residues in contact with TYR 226 (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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222D ALA* 3.1 36.4 + - + +
223D GLU 4.0 3.1 - - - +
225D LEU* 1.3 93.0 - - + +
227D LYS* 1.3 64.8 + - - +
229D GLN* 3.9 17.4 - - - +
230D ALA* 3.1 24.4 + - - +
260D LEU* 2.8 28.0 + - + -
261D GLY 3.3 9.9 + - - -
262D VAL* 3.6 6.2 + - + -
263D PRO* 6.0 0.4 - - + -
55U HIS* 3.6 61.1 + + + +
56U HIS* 6.1 0.9 - - + -
61U TYR* 4.0 5.8 - + - +
63U ASP* 5.1 0.2 - - - +
53V ARG* 3.1 30.4 + - - -
62V TYR* 5.6 4.3 - + - -
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Residues in contact with LYS 227 (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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190D TYR* 3.6 40.8 - - + -
223D GLU* 3.1 20.6 + - + +
224D ALA* 3.6 5.2 - - - +
225D LEU 3.2 0.2 - - - -
226D TYR* 1.3 77.6 - - - +
228D ALA* 1.3 56.8 + - - +
230D ALA* 3.4 6.3 + - - +
231D GLU* 3.0 30.0 + - + +
45U GLU* 2.9 32.6 + - - -
47U ASP* 5.2 0.6 + - - -
48U HIS* 5.8 4.8 - - - +
52U TYR* 6.1 0.9 - - - +
55U HIS* 5.8 1.8 - - - -
64U GLY* 5.5 5.8 - - - +
66U TYR* 3.0 37.1 + - + +
67U TRP* 4.4 2.7 - - - +
68U THR* 4.6 1.1 - - - -
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Residues in contact with ALA 228 (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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190D TYR* 3.9 15.9 - - + +
193D LEU* 3.5 32.8 - - + -
194D ARG* 3.9 12.3 - - - +
224D ALA 3.1 16.4 + - - +
225D LEU 3.7 4.3 - - - +
227D LYS* 1.3 78.6 - - - +
229D GLN* 1.3 57.5 + - - +
231D GLU* 3.4 3.1 + - - +
232D THR* 3.0 35.5 + - - +
236D LYS* 4.3 2.7 - - + -
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Residues in contact with GLN 229 (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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225D LEU* 3.0 21.7 + - - +
226D TYR* 3.9 16.5 - - - +
228D ALA* 1.3 73.8 - - - +
230D ALA* 1.3 61.7 + - - +
233D GLY* 2.8 30.7 + - - -
234D GLU 3.2 24.5 - - - +
235D ILE* 3.5 13.2 - - - +
236D LYS* 3.1 29.5 + - + +
51V VAL* 4.2 15.7 + - + +
52V TYR* 6.0 0.6 - - - +
53V ARG* 5.9 2.0 - - - +
62V TYR* 3.9 28.4 + - - -
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Residues in contact with ALA 230 (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 TYR 3.1 18.4 + - - +
227D LYS* 3.7 6.3 - - - +
228D ALA 3.3 0.2 - - - -
229D GLN* 1.3 78.1 - - - +
231D GLU* 1.3 62.2 + - - +
233D GLY* 4.1 0.3 + - - -
55U HIS* 5.4 8.1 - - + +
10V LYS* 3.3 21.8 + - - -
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Residues in contact with GLU 231 (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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190D TYR* 2.6 30.7 + - - -
194D ARG* 2.9 44.1 + - - +
227D LYS* 3.0 18.5 + - + +
228D ALA* 3.7 4.7 - - - +
230D ALA* 1.3 77.8 - - - +
232D THR* 1.3 61.2 + - + +
4V TRP* 5.2 0.2 - - - -
5V PRO 4.2 1.7 - - - +
6V THR* 3.9 32.2 - - - +
9V MET* 4.2 13.4 + - + +
10V LYS* 3.4 19.3 + - - +
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Residues in contact with THR 232 (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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193D LEU 4.3 0.2 - - - +
194D ARG* 3.6 33.9 - - + +
228D ALA 3.0 19.3 + - - +
231D GLU* 1.3 82.5 - - + +
233D GLY* 1.3 63.7 + - - +
234D GLU* 3.3 13.0 + - - -
236D LYS* 3.2 26.0 - - - +
9V MET 4.4 8.3 - - - +
10V LYS* 3.4 4.3 - - - -
11V ARG* 2.7 32.6 + - + +
17V TYR* 4.8 10.3 - - - +
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Residues in contact with GLY 233 (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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229D GLN* 2.8 19.3 + - - -
230D ALA 4.1 0.6 + - - -
231D GLU 3.7 1.2 - - - -
232D THR* 1.3 73.4 - - - +
234D GLU* 1.3 61.9 + - - +
235D ILE 4.4 0.2 + - - -
10V LYS* 4.0 7.7 - - - +
11V ARG 4.3 2.8 - - - +
50V PHE* 4.0 34.6 - - - +
51V VAL* 4.8 10.8 + - - +
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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