Contacts of the helix formed by residues 200 - 223 (chain A) in PDB entry 5I1U
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 HIS 200 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A HIS 3.4 18.2 + - - +
197A VAL* 3.1 11.0 + - - +
199A HIS* 1.3 77.6 - - - +
201A PRO* 1.3 80.9 - - + +
202A LEU* 2.9 43.0 + - + +
203A PHE* 3.0 14.4 + + + -
204A ARG* 2.9 19.1 + - - +
275A ALA* 3.9 23.5 + - + +
278A SER* 4.7 4.6 + - - -
279A MET* 3.6 27.3 - - + +
148B ALA 5.7 0.2 - - - -
152B ALA* 3.6 24.4 + - + +
155B ALA* 5.9 0.8 - - - +
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Residues in contact with PRO 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A HIS 4.0 4.0 - - - +
200A HIS* 1.3 100.4 - - + +
202A LEU* 1.3 62.1 + - - +
205A GLN* 3.1 32.4 + - - +
152B ALA* 3.6 18.2 - - + -
167B GLY* 3.5 30.1 - - - +
170B THR* 3.7 20.1 - - + +
171B LEU* 4.0 20.2 - - + +
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Residues in contact with LEU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A HIS* 2.9 22.1 + - + +
201A PRO* 1.3 80.8 - - - +
203A PHE* 1.3 75.0 + - + +
205A GLN* 3.6 9.8 - - - +
206A LEU* 3.0 46.9 + - + +
268A LEU* 3.4 40.5 - - + +
271A GLN* 3.7 33.0 - - + +
272A LEU* 3.9 8.5 - - + +
275A ALA* 3.9 9.6 - - + -
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Residues in contact with PHE 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A VAL* 3.2 46.9 - - + +
198A MET 4.0 5.6 - - - +
200A HIS* 3.0 19.1 + + + +
202A LEU* 1.3 88.8 - - + +
204A ARG* 1.3 66.0 + - - +
206A LEU* 3.3 14.2 + - + +
207A ARG* 3.0 24.6 + - - +
272A LEU* 3.5 31.6 - - + -
275A ALA* 4.9 6.3 - - + -
276A CYS* 4.1 10.1 - - - -
279A MET* 5.5 2.5 - - + -
289A ALA* 3.6 30.5 - - + -
292A TYR* 3.8 26.2 + + + -
293A ALA* 4.2 3.4 - - + -
296A MET* 4.5 3.0 - - + +
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Residues in contact with ARG 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A MET* 3.4 19.0 + - - +
199A HIS* 2.9 50.8 + - - +
200A HIS 2.9 13.1 + - - +
202A LEU 3.4 0.2 - - - -
203A PHE* 1.3 75.7 - - - +
205A GLN* 1.3 57.9 + - - +
207A ARG* 3.4 7.6 + - - +
208A GLN* 3.0 28.9 + - - +
145B TYR* 3.5 37.4 + - - -
149B CYS* 5.1 0.4 - - - -
170B THR* 3.7 29.5 + - + +
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Residues in contact with GLN 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A PRO* 3.1 27.8 + - - +
202A LEU* 3.6 6.0 - - - +
204A ARG* 1.3 73.7 - - - +
206A LEU* 1.3 65.5 + - - +
208A GLN* 3.9 4.7 - - - +
209A LEU* 3.0 34.4 + - + +
264A ARG* 2.9 32.0 + - - +
268A LEU* 3.6 21.6 - - + +
166B GLU* 3.3 12.9 - - - +
167B GLY* 3.5 23.7 - - - +
170B THR* 3.7 20.4 - - - +
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Residues in contact with LEU 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A LEU* 3.0 38.0 + - + +
203A PHE* 3.3 16.3 + - + +
205A GLN* 1.3 74.6 - - - +
207A ARG* 1.3 63.9 + - - +
209A LEU* 4.7 1.1 - - - -
210A ALA* 3.0 27.4 + - - +
265A PHE* 3.3 56.1 - - + +
268A LEU* 3.7 14.8 - - + +
269A ARG* 3.9 11.2 - - + +
272A LEU* 4.9 2.0 - - + -
293A ALA* 4.0 27.4 - - + -
296A MET* 3.9 10.1 - - + -
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Residues in contact with ARG 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A ARG* 4.4 4.8 - - - +
142A ASN* 4.3 2.2 - - - +
179A GLU* 2.8 47.9 + - - +
182A PHE* 3.6 31.0 + - + +
183A ASP* 2.9 32.3 + - - +
186A GLU* 5.4 0.2 + - - -
198A MET* 3.8 19.7 - - - +
203A PHE 3.0 17.0 + - - +
204A ARG* 3.7 7.2 - - - +
206A LEU* 1.3 77.9 - - - +
208A GLN* 1.3 57.1 + - - +
211A ALA* 2.9 31.2 + - - +
292A TYR* 2.9 33.9 + - - +
296A MET* 3.5 15.7 - - - -
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Residues in contact with GLN 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ARG* 3.3 41.2 + - - +
179A GLU* 4.3 12.2 + - - +
204A ARG 3.0 16.3 + - - +
205A GLN* 3.2 5.4 + - - +
207A ARG* 1.3 74.5 - - - +
209A LEU* 1.3 60.1 + - + +
211A ALA* 3.3 12.2 + - - +
212A ASP* 2.9 54.3 + - - +
401B SO4 5.3 2.6 + - - +
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Residues in contact with LEU 209 (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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205A GLN* 3.0 23.8 + - + +
206A LEU 3.9 2.9 - - - +
208A GLN* 1.3 77.2 - - + +
210A ALA* 1.3 57.9 + - - +
212A ASP* 3.2 5.0 + - - +
213A ILE* 3.0 37.6 + - + +
261A MET* 3.8 42.2 - - + +
264A ARG* 3.6 29.8 - - + +
265A PHE* 3.7 21.8 - - + +
268A LEU* 3.8 14.8 - - + -
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Residues in contact with ALA 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A MET* 4.2 0.3 - - - +
182A PHE* 3.7 25.8 - - + -
206A LEU 3.0 19.1 + - - +
209A LEU* 1.3 77.4 - - - +
211A ALA* 1.3 57.0 + - - +
214A PRO* 3.0 24.8 - - - +
265A PHE* 3.8 8.9 - - + -
296A MET* 4.5 6.5 - - + -
300A LEU* 3.4 38.6 - - + +
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Residues in contact with ALA 211 (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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173A ARG* 6.3 0.4 - - + -
176A ALA* 5.5 1.0 - - - +
178A MET* 3.6 36.5 - - + +
179A GLU* 4.5 9.6 - - - +
182A PHE* 3.6 9.4 - - + -
207A ARG 2.9 19.2 + - - +
208A GLN* 3.6 18.4 - - - +
209A LEU 3.2 0.2 - - - -
210A ALA* 1.3 79.5 - - - +
212A ASP* 1.3 61.9 + - - +
214A PRO* 3.5 8.0 - - - +
215A SER* 4.4 6.9 + - - -
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Residues in contact with ASP 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ARG* 2.8 52.7 + - - +
208A GLN* 2.9 29.3 + - - +
209A LEU* 3.2 1.2 + - - +
211A ALA* 1.3 78.4 - - - +
213A ILE* 1.3 66.0 + - - +
215A SER* 2.4 31.0 + - - +
216A PHE* 3.3 15.0 + - + -
261A MET* 3.9 24.0 - - + +
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Residues in contact with ILE 213 (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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7A LEU* 3.5 27.8 - - + -
209A LEU* 3.0 26.5 + - + +
212A ASP* 1.3 76.9 - - - +
214A PRO* 1.3 70.7 - - + +
216A PHE* 3.0 14.8 + - - +
217A THR* 3.0 16.5 + - + +
258A ALA* 3.9 6.3 - - + +
261A MET* 3.6 30.7 - - + +
262A ALA* 3.5 31.4 - - + +
265A PHE* 4.8 1.3 - - + -
300A LEU* 4.0 28.9 - - + -
304A LEU* 4.6 6.5 - - + -
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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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178A MET* 4.7 8.5 - - + -
210A ALA 3.0 28.0 - - - +
211A ALA 3.5 10.8 - - - +
213A ILE* 1.3 87.6 - - + +
215A SER* 1.3 56.7 + - - +
217A THR* 3.3 9.9 + - - +
218A ASN* 2.9 31.9 + - - +
299A TRP* 4.0 22.2 - - + -
300A LEU* 4.0 7.0 - - + -
303A TYR* 3.6 28.8 + - + -
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Residues in contact with SER 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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169A LEU* 5.0 3.8 - - - +
172A ARG* 3.8 38.4 + - - +
173A ARG* 6.2 0.4 - - - +
176A ALA* 5.3 6.5 - - - -
211A ALA 4.4 4.8 + - - -
212A ASP* 2.4 31.8 + - - +
214A PRO* 1.3 80.1 - - - +
216A PHE* 1.3 72.2 + - - +
218A ASN* 3.9 4.6 - - - +
219A ASP* 3.2 29.1 + - - +
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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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165A ARG* 3.9 13.7 - - - -
169A LEU* 4.0 26.0 - - + -
212A ASP* 3.3 22.9 - - + +
213A ILE 3.0 7.9 + - - +
215A SER* 1.3 85.6 + - - +
217A THR* 1.3 66.5 + - - +
219A ASP* 3.2 11.8 + - - +
220A VAL* 3.2 17.7 + - - +
235A LEU* 3.5 29.2 - - + -
254A VAL* 3.6 28.4 - - + +
255A TRP* 6.2 0.2 - - - -
257A GLU* 3.5 25.1 - - + -
258A ALA* 3.9 14.4 - - + -
261A MET* 3.9 22.4 - - + -
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Residues in contact with THR 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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7A LEU* 4.0 17.5 - - + -
213A ILE 3.0 12.8 + - - +
214A PRO* 3.3 15.4 + - - +
216A PHE* 1.3 77.7 - - - +
218A ASN* 1.3 63.8 + - - +
220A VAL* 3.2 3.3 + - - +
221A ARG* 3.0 25.6 + - - +
255A TRP* 3.7 29.7 - - + -
258A ALA* 4.0 9.9 - - + -
303A TYR* 3.8 3.6 - - - -
304A LEU* 4.0 16.1 - - + +
307A GLU* 2.7 31.2 + - - -
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Residues in contact with ASN 218 (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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172A ARG* 4.4 12.8 + - - +
214A PRO 2.9 21.2 + - - +
215A SER* 3.9 4.9 - - - +
217A THR* 1.3 78.4 + - - +
219A ASP* 1.3 67.3 + - - +
221A ARG* 3.2 5.0 + - - +
222A SER* 2.9 41.6 + - - -
226A GLU* 5.4 1.4 - - - +
303A TYR* 3.8 13.8 + - - +
306A TRP* 6.2 1.2 - - - -
307A GLU* 3.5 8.7 + - - +
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Residues in contact with ASP 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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168A TYR* 2.7 35.2 + - - -
172A ARG* 5.0 4.4 - - - -
215A SER 3.2 18.8 + - - +
216A PHE 3.7 4.7 - - - +
217A THR 3.2 0.4 - - - -
218A ASN* 1.3 89.7 - - - +
220A VAL* 1.3 61.1 + - - +
222A SER* 3.7 2.2 + - - -
223A PHE* 3.1 13.3 + - - +
226A GLU* 4.6 3.5 - - - +
234A ASN* 3.0 38.8 + - - +
235A LEU* 2.8 29.0 + - + +
236A VAL* 4.3 3.4 - - + +
254A VAL* 5.1 0.9 - - + -
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Residues in contact with VAL 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* 3.7 39.9 + - + -
216A PHE 3.2 6.3 + - - +
217A THR 3.2 7.4 + - - +
219A ASP* 1.3 78.6 - - - +
221A ARG* 1.3 63.9 + - - +
222A SER 3.2 0.5 + - - -
223A PHE* 3.4 12.4 + - - +
224A ALA 4.9 0.3 + - - -
236A VAL* 3.8 14.1 - - + -
251A CYS* 3.9 21.9 - - + +
254A VAL* 3.5 32.5 - - + -
255A TRP* 3.9 25.1 - - + +
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Residues in contact with ARG 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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1A MET* 4.3 16.0 + - - +
2A SER 2.8 27.7 + - - -
3A ASP* 3.6 19.5 + - - +
5A THR 2.8 25.3 + - - -
6A SER* 4.6 2.4 - - - +
217A THR 3.0 20.5 + - - +
218A ASN* 3.2 9.4 + - - +
220A VAL* 1.3 78.2 - - - +
222A SER* 1.3 58.7 + - - +
223A PHE 3.7 0.3 + - - -
224A ALA* 4.7 6.6 + - - +
225A GLN* 5.4 3.5 - - - +
255A TRP* 3.6 22.1 - - + -
304A LEU 5.1 1.2 + - - -
307A GLU* 3.0 44.4 + - + +
308A SER* 3.5 22.6 - - - -
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Residues in contact with SER 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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218A ASN* 2.9 29.4 + - - -
219A ASP* 3.7 3.1 + - - -
221A ARG* 1.3 75.7 - - - +
223A PHE* 1.3 66.2 + - - +
224A ALA 3.2 3.4 + - - -
225A GLN* 3.2 19.6 + - - +
226A GLU* 3.0 48.6 + - - +
234A ASN* 3.5 6.1 + - - -
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Residues in contact with PHE 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASP 3.1 18.0 + - - +
220A VAL 3.7 9.2 - - - +
221A ARG 3.4 1.8 - - - -
222A SER* 1.3 76.9 - - - +
224A ALA* 1.3 72.0 + - + +
226A GLU* 3.2 19.9 + - + +
234A ASN* 3.7 12.1 - - - +
236A VAL* 3.8 24.9 - - + -
237A MET* 3.4 38.4 - - + -
240A ARG* 3.9 13.5 - - - -
247A THR* 3.3 34.5 - - + -
251A CYS* 4.5 9.4 - - - -
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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) + - + + + + + -
------------------------------------------------------------
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