Contacts of the helix formed by residues 213 - 235 (chain A) in PDB entry 1C3Q
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 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-6A HIS 5.4 0.7 - - - +
-4A HIS* 4.9 6.5 + - - -
176A ASP* 5.2 2.7 + - - +
211A GLU* 2.8 26.5 + - - +
212A GLU* 1.3 76.6 - - + +
214A PRO* 1.3 63.4 - - - +
215A LEU* 2.9 26.1 + - - +
216A PHE* 3.0 36.2 + - + -
217A ALA 2.8 24.4 + - - -
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Residues in contact with PRO 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-10A ARG* 4.2 7.9 - - - +
118A ALA* 3.6 35.4 - - + +
119A ALA* 5.1 0.4 - - + -
164A VAL* 3.7 15.5 - - + +
208A CYS* 4.3 10.6 - - - -
212A GLU 3.1 12.3 - - - +
213A ASN* 1.3 86.7 - - - +
215A LEU* 1.3 57.0 + - - +
217A ALA* 3.7 8.6 - - + +
218A ALA* 2.9 32.6 + - - +
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Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-4A HIS* 3.9 16.4 - - + +
164A VAL* 3.6 14.0 - - + +
174A ILE* 3.8 26.7 - - + +
175A ALA* 4.3 19.1 - - - +
176A ASP* 3.6 28.9 - - + +
179A HIS* 3.8 20.9 - - + -
181A TYR* 4.1 8.5 - - + -
213A ASN* 2.9 16.7 + - - +
214A PRO* 1.3 76.2 - - - +
216A PHE* 1.3 66.7 + - + +
218A ALA* 3.6 1.4 - - - +
219A ILE* 3.1 41.3 + - + +
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Residues in contact with PHE 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-6A HIS* 3.1 52.0 - + + -
-5A HIS* 3.8 0.9 - - - -
-4A HIS* 3.3 57.0 - + - -
1A MET* 3.6 41.9 - - + +
211A GLU* 4.0 12.8 - - + +
213A ASN* 3.0 32.1 + - + +
215A LEU* 1.3 86.6 - - + +
217A ALA* 1.3 62.6 + - - +
219A ILE* 3.4 0.9 + - - +
220A ALA* 3.0 25.0 + - - +
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Residues in contact with ALA 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A VAL 5.2 0.2 - - - -
207A PHE* 3.5 11.2 - - - +
208A CYS* 3.7 40.4 - - - +
211A GLU* 3.6 18.5 - - + +
213A ASN 2.8 16.0 + - - +
214A PRO 3.7 4.7 - - - +
216A PHE* 1.3 77.9 - - - +
218A ALA* 1.3 57.1 + - - +
220A ALA* 3.3 3.6 + - - +
221A ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ALA* 5.3 2.9 - - + -
164A VAL* 4.4 7.9 - - + -
166A ALA* 5.1 3.6 - - + -
174A ILE* 4.1 21.1 - - + -
204A VAL* 4.3 26.8 - - + +
214A PRO 2.9 18.5 + - - +
215A LEU 3.6 4.0 - - - +
217A ALA* 1.3 77.0 - - - +
219A ILE* 1.3 56.8 + - - +
221A ALA* 3.7 1.6 - - - +
222A ILE* 2.9 38.5 + - + +
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Residues in contact with ILE 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.7 23.8 - - + -
174A ILE* 3.5 26.9 - - + -
181A TYR* 3.6 42.6 - - + -
183A LEU* 3.9 4.7 - - + +
215A LEU* 3.1 26.6 + - + +
216A PHE 3.8 4.3 - - - +
218A ALA* 1.3 75.1 - - - +
220A ALA* 1.3 59.5 + - - +
223A SER* 2.8 36.5 + - - +
266A ILE* 3.5 37.0 - - + -
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Residues in contact with ALA 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.9 3.4 - - + -
6A ALA* 3.7 34.0 - - - +
9A CYS* 3.8 12.1 - - + -
207A PHE* 3.7 17.0 - - + -
216A PHE 3.0 17.0 + - - +
217A ALA 3.7 3.8 - - - +
219A ILE* 1.3 77.0 - - - +
221A ALA* 1.3 63.2 + - - +
223A SER* 3.9 0.3 - - - -
224A SER* 2.9 30.8 + - - -
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 4.6 1.1 - - - -
203A VAL* 3.8 8.2 - - + +
204A VAL* 3.6 34.5 - - + +
207A PHE* 3.6 25.7 - - + -
217A ALA 2.9 17.4 + - - +
218A ALA 3.7 4.0 - - - +
220A ALA* 1.3 77.3 - - - +
222A ILE* 1.3 57.9 + - - +
224A SER* 3.8 1.6 - - - -
225A TYR* 3.0 30.8 + - - +
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Residues in contact with ILE 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ARG* 5.0 1.1 - - + -
166A ALA* 4.0 19.1 - - + -
168A THR* 4.4 13.0 - - + -
172A ASP* 4.0 22.9 - - + +
174A ILE* 3.5 28.9 - - + -
183A LEU* 3.7 17.7 - - + -
185A ASN* 5.2 1.6 - - - +
200A LEU* 3.9 32.1 - - + -
204A VAL* 4.3 10.8 - - + -
218A ALA 2.9 17.8 + - - +
221A ALA* 1.3 75.5 - - - +
223A SER* 1.3 57.5 + - - +
225A TYR* 3.8 1.7 - - + +
226A GLY* 3.0 24.3 + - - -
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Residues in contact with SER 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA* 4.6 4.7 - - - -
183A LEU* 3.8 11.1 - - - +
185A ASN* 4.4 11.0 + - - +
219A ILE 2.8 23.1 + - - -
220A ALA* 3.9 4.3 - - - -
222A ILE* 1.3 75.2 - - - +
224A SER* 1.3 65.6 + - - +
226A GLY* 3.3 1.6 + - - -
227A VAL* 3.0 30.5 + - - +
264A ALA* 4.0 20.4 - - - -
266A ILE* 3.4 27.2 - - - +
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Residues in contact with SER 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ALA 4.3 2.8 + - - -
10A LEU* 4.0 16.8 - - - +
39A LEU* 5.7 3.1 - - - -
203A VAL* 6.1 0.2 - - - -
207A PHE* 3.8 20.4 - - - -
220A ALA 2.9 21.4 + - - -
221A ALA 3.8 2.5 - - - -
223A SER* 1.3 77.5 - - - +
225A TYR* 1.3 63.0 + - - +
227A VAL* 3.4 3.1 + - - +
228A ALA* 3.0 23.6 + - - +
252A LEU* 5.5 1.6 - - - -
255A VAL* 4.9 6.8 - - - +
260A VAL* 3.9 31.0 - - - +
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Residues in contact with TYR 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190A LEU* 4.4 25.8 - - + -
196A ALA* 2.8 36.2 + - + +
199A LEU* 3.6 35.8 - - + +
200A LEU* 3.8 32.8 - - + -
203A VAL* 4.2 15.2 - - + +
221A ALA 3.0 18.2 + - - +
222A ILE 3.8 4.5 - - - +
224A SER* 1.3 77.8 - - - +
226A GLY* 1.3 57.8 + - - +
228A ALA* 3.3 4.3 + - - +
229A ALA* 2.9 27.2 + - - +
248A LEU* 3.9 17.1 - - + +
252A LEU* 3.8 28.0 - - + -
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Residues in contact with GLY 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 3.9 7.6 - - - -
186A GLY* 3.3 25.1 + - - -
190A LEU* 5.7 1.1 - - - -
222A ILE 3.0 17.8 + - - -
223A SER 3.7 1.3 - - - -
225A TYR* 1.3 80.5 - - - +
227A VAL* 1.3 56.1 + - - +
229A ALA* 3.1 4.3 + - - +
230A GLN* 2.9 32.7 + - - +
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A ASN* 4.1 6.0 - - - +
223A SER 3.0 21.7 + - - +
224A SER* 3.7 6.3 - - - +
226A GLY* 1.3 75.3 - - - +
228A ALA* 1.3 64.7 + - - +
230A GLN* 3.2 9.6 + - + +
231A LEU* 3.0 28.2 + - + +
255A VAL* 4.0 19.5 - - + -
259A ASP 4.0 7.6 - - - +
260A VAL* 4.5 6.5 - - + +
263A TRP* 3.8 31.0 - - + -
264A ALA* 3.7 32.5 - - + +
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A SER 3.0 13.2 + - - +
225A TYR 3.5 8.3 - - - +
227A VAL* 1.3 78.0 - - - +
229A ALA* 1.3 56.7 + - - +
231A LEU* 3.4 3.2 + - - +
232A ALA* 2.9 29.3 + - - +
248A LEU* 4.3 3.8 - - + -
251A LYS* 3.5 31.1 - - + +
252A LEU* 3.9 24.5 - - + +
255A VAL* 4.5 10.0 - - + +
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Residues in contact with ALA 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A GLY* 4.1 5.6 - - - -
187A HIS* 4.5 2.5 - - - +
190A LEU* 3.9 38.4 - - + -
225A TYR* 2.9 13.9 + - + +
226A GLY 3.1 10.1 + - - +
228A ALA* 1.3 75.5 - - - +
230A GLN* 1.3 59.6 + - - +
232A ALA* 3.3 3.2 + - - -
233A ALA* 2.9 30.7 + - - +
244A PHE* 3.5 8.3 - - + -
248A LEU* 4.1 10.7 - - + +
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Residues in contact with GLN 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A HIS 4.2 0.9 - - - +
185A ASN* 2.6 49.9 + - - +
186A GLY 3.1 24.7 - - - +
187A HIS* 4.8 1.8 - - + -
226A GLY 2.9 15.9 + - - +
227A VAL* 3.7 8.0 - - + +
229A ALA* 1.3 75.1 - - - +
231A LEU* 1.3 66.2 + - + +
233A ALA* 3.3 6.6 + - - +
234A GLN* 3.0 26.4 + - - +
263A TRP* 4.9 15.0 + - - +
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A VAL* 3.0 31.2 + - + +
228A ALA* 3.6 5.4 - - - +
230A GLN* 1.3 82.3 - - + +
232A ALA* 1.3 61.9 + - - +
234A GLN* 3.7 27.1 + - - +
235A GLN* 3.7 6.8 + - - +
251A LYS* 4.0 26.9 - - + -
255A VAL* 4.3 12.3 - - + -
259A ASP* 4.1 27.8 - - + +
263A TRP* 4.3 20.4 - - + +
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Residues in contact with ALA 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ALA 2.9 17.4 + - - +
229A ALA* 3.6 5.6 - - - +
230A GLN 3.2 0.2 - - - -
231A LEU* 1.3 74.5 - - - +
233A ALA* 1.3 63.2 + - - +
235A GLN* 3.2 5.9 + - - +
236A THR* 3.0 26.9 + - - -
244A PHE* 3.8 11.0 - - + -
247A GLU* 3.6 37.1 - - + +
248A LEU* 3.7 8.7 - - - +
251A LYS* 3.8 6.9 - - + +
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A HIS* 3.3 43.7 - - + +
189A LEU* 4.5 1.1 - - + -
229A ALA 2.9 16.8 + - - +
230A GLN 3.3 4.0 + - - +
232A ALA* 1.3 72.4 - - - +
234A GLN* 1.3 54.1 + - - +
235A GLN 2.7 6.1 + - - -
236A THR 2.5 23.2 + - - +
237A ALA* 2.6 19.0 + - - +
244A PHE* 3.5 15.2 - - + -
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Residues in contact with GLN 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A GLN 3.0 16.2 + - - +
231A LEU* 3.7 22.5 - - - +
233A ALA* 1.3 75.8 - - - +
235A GLN* 1.3 62.5 + - + +
236A THR 3.9 0.2 + - - -
237A ALA* 5.1 3.5 + - - +
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Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU 3.7 7.4 + - - +
232A ALA 3.2 8.3 + - - +
233A ALA 2.7 4.4 + - - -
234A GLN* 1.3 81.5 + - + +
236A THR* 1.3 59.7 + - - +
239A LYS* 3.5 26.6 + - - +
247A GLU* 4.6 17.5 - - + +
251A LYS* 5.4 4.8 - - - +
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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
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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