Contacts of the helix formed by residues 213 - 241 (chain A) in PDB entry 3F9C
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 GLU 213 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 2.7 33.9 + - - -
208A THR 4.4 3.1 - - - +
209A LEU* 3.6 12.1 - - + -
210A LYS* 2.7 53.6 + - + +
212A GLU* 1.3 80.3 - - + +
214A GLU* 1.3 62.2 + - - +
215A THR 3.1 3.3 + - - -
216A HIS* 3.3 5.5 + - - +
217A ILE* 3.0 35.6 + - + +
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Residues in contact with GLU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A LEU* 3.8 20.8 - - + +
210A LYS 3.8 8.5 - - - +
211A GLN* 3.1 37.1 + - - +
213A GLU* 1.3 76.9 - - - +
215A THR* 1.3 62.8 + - - +
218A ARG* 2.9 72.5 + - - +
298A TRP* 4.3 6.8 - - - -
300A PHE* 3.5 15.6 - - + -
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Residues in contact with THR 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A GLN* 4.7 3.4 + - - -
212A GLU 5.2 1.2 + - - -
213A GLU 3.1 1.2 + - - -
214A GLU* 1.3 77.3 - - - +
216A HIS* 1.3 64.0 + - + +
218A ARG* 4.4 0.5 - - - +
219A ASN* 3.3 24.4 + - + +
300A PHE* 3.3 27.2 - - + +
301A PRO* 5.2 0.7 - - - +
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Residues in contact with HIS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A GLU 5.7 1.5 + - - +
213A GLU* 3.3 7.0 + - - +
215A THR* 1.3 80.8 - - - +
217A ILE* 1.3 77.4 + - + +
219A ASN* 3.5 4.5 + - - +
220A GLU* 3.1 58.9 + - + +
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 3.8 34.3 - - - +
209A LEU* 3.7 30.3 - - + -
213A GLU* 3.0 31.8 + - + +
216A HIS* 1.3 88.8 - - + +
218A ARG* 1.3 64.9 + - - +
220A GLU* 3.2 23.0 + - - +
221A GLN* 2.9 45.2 + - + +
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Residues in contact with ARG 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 3.5 46.5 - - - +
182A ARG 5.7 0.2 + - - -
207A ARG 4.9 6.7 + - - -
208A THR* 6.1 0.2 - - - +
209A LEU* 3.7 22.2 - - + +
214A GLU* 2.9 57.3 + - - +
215A THR 4.4 0.2 - - - +
217A ILE* 1.3 75.9 - - - +
219A ASN* 1.3 57.2 + - - +
221A GLN* 2.9 30.6 + - - +
222A VAL 3.0 23.4 + - - -
274A PHE* 3.7 7.3 - - - -
298A TRP* 3.6 20.5 - - + -
300A PHE* 4.0 6.3 - - + -
301A PRO* 3.5 30.2 - - + +
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Residues in contact with ASN 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A THR* 3.3 18.7 + - + +
216A HIS* 3.8 5.8 - - - +
217A ILE 3.2 0.6 - - - -
218A ARG* 1.3 79.6 - - - +
220A GLU* 1.3 61.7 + - - +
222A VAL* 3.2 8.2 - - - +
223A ARG* 2.7 59.2 + - - +
281A GLN* 5.2 0.8 + - - -
301A PRO 2.7 27.5 + - - +
302A LEU* 3.8 1.2 - - - +
303A GLY* 3.2 24.4 - - - +
305A GLU* 4.9 0.2 + - - -
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Residues in contact with GLU 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ARG* 5.5 0.7 + - - -
216A HIS* 3.1 48.2 + - + +
217A ILE* 3.2 28.1 + - - +
219A ASN* 1.3 74.9 + - - +
221A GLN* 1.3 59.2 + - + +
223A ARG* 3.6 12.6 + - - +
224A GLN* 3.1 26.3 + - - +
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Residues in contact with GLN 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A ASP* 3.0 46.7 + - + +
182A ARG* 4.0 5.7 + - - +
183A SER* 3.9 12.5 - - - +
207A ARG* 5.3 3.8 + - - +
209A LEU* 5.3 3.0 - - - +
217A ILE* 2.9 32.9 + - + +
218A ARG* 2.9 44.7 + - - +
220A GLU* 1.3 76.9 - - + +
222A VAL* 1.3 59.4 + - - +
224A GLN* 3.8 2.1 - - - +
225A ARG* 2.9 35.3 + - - +
274A PHE* 3.5 9.9 - - + -
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Residues in contact with VAL 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ARG 3.0 13.6 + - - +
219A ASN* 3.2 21.3 - - - +
221A GLN* 1.3 75.1 - - - +
223A ARG* 1.3 57.3 + - + +
225A ARG* 3.4 4.1 + - - +
226A ALA* 3.0 29.8 + - - +
274A PHE* 4.0 7.1 - - + -
277A ALA* 3.8 36.3 - - + +
278A THR* 3.9 17.0 - - - +
281A GLN* 3.7 22.5 - - + +
301A PRO* 3.5 27.1 - - + +
302A LEU* 4.4 2.5 - - + -
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Residues in contact with ARG 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ASN* 2.7 41.4 + - - +
220A GLU* 3.6 12.1 - - - +
222A VAL* 1.3 75.2 - - + +
224A GLN* 1.3 65.4 + - - +
226A ALA* 3.5 3.1 + - - +
227A LYS* 3.1 22.6 + - - +
281A GLN* 4.3 25.6 - - - +
285A GLU* 4.5 7.7 + - - +
303A GLY* 5.3 0.4 - - - -
305A GLU* 3.1 30.8 + - - -
309A ARG* 6.2 0.6 - - - +
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Residues in contact with GLN 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASN 5.4 1.8 + - - -
180A ARG* 3.0 28.9 + - - +
181A ASP* 3.8 18.5 - - + +
220A GLU 3.1 17.5 + - - +
221A GLN* 3.8 4.2 - - - +
223A ARG* 1.3 76.1 - - - +
225A ARG* 1.3 53.7 + - - +
227A LYS* 3.1 26.2 + - - +
228A GLU* 2.8 58.3 + - - +
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Residues in contact with ARG 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A SER* 3.1 19.0 + - - -
151A HIS* 2.7 41.6 + - - -
152A GLY 3.5 11.9 + - - -
179A HIS* 3.5 26.5 - - + +
181A ASP* 3.1 26.1 + - - +
183A SER* 2.7 20.2 + - - -
221A GLN 2.9 20.5 + - - +
222A VAL* 3.5 5.2 - - - +
224A GLN* 1.3 77.7 - - - +
226A ALA* 1.3 51.7 + - - +
228A GLU* 3.2 5.8 + - - +
229A CYS* 2.9 35.9 + - - -
274A PHE* 3.4 36.0 - - - +
278A THR* 3.2 27.8 + - + +
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Residues in contact with ALA 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A VAL 3.0 8.3 + - - +
223A ARG 3.6 4.7 - - - +
225A ARG* 1.3 72.8 - - - +
227A LYS* 1.3 58.9 + - - +
229A CYS* 3.2 3.8 + - - +
230A SER* 2.9 31.4 + - - -
278A THR* 3.9 2.2 - - - +
281A GLN* 3.4 32.3 - - + -
282A THR* 3.5 27.1 - - - +
285A GLU* 3.7 17.9 - - - +
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Residues in contact with LYS 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LYS* 5.7 8.7 + - - +
223A ARG 3.1 14.8 + - - +
224A GLN* 3.5 39.3 + - - +
226A ALA* 1.3 74.5 - - - +
228A GLU* 1.3 65.7 + - - +
230A SER* 3.4 7.5 + - - -
231A GLN* 2.9 44.2 + - + +
285A GLU* 4.4 5.5 + - - +
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Residues in contact with GLU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ASN 5.3 0.9 - - - +
79A THR* 4.8 1.8 + - - +
177A VAL* 4.3 9.6 - - + +
178A GLU 4.7 2.5 - - - -
179A HIS* 2.7 45.2 + - + +
180A ARG* 3.2 21.3 + - - +
224A GLN* 2.8 46.4 + - - +
225A ARG* 3.2 12.5 + - - +
227A LYS* 1.3 78.8 + - - +
229A CYS* 1.3 59.7 + - - +
231A GLN* 3.9 8.9 - - - +
232A ALA* 2.9 32.8 + - - +
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Residues in contact with CYS 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 3.9 27.0 - - + +
150A SER* 4.1 10.5 - - - -
177A VAL* 4.7 3.8 - - - -
179A HIS* 4.1 10.8 - - - -
225A ARG 2.9 17.6 + - - -
226A ALA 3.2 7.4 + - - +
228A GLU* 1.3 77.0 - - - +
230A SER* 1.3 58.2 + - - +
232A ALA* 3.8 3.0 - - - +
233A LEU* 2.9 28.9 + - - +
269A VAL* 4.4 5.2 - - + -
278A THR* 3.8 20.4 - - - -
282A THR* 3.8 20.0 - - + +
289A PHE* 3.7 6.0 - - + -
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ALA 2.9 16.7 + - - -
227A LYS* 3.6 7.6 - - - -
229A CYS* 1.3 78.4 - - - +
231A GLN* 1.3 55.7 + - - +
233A LEU* 3.3 1.2 + - - +
234A SER* 3.0 15.6 + - - -
282A THR* 4.2 3.5 - - - +
285A GLU* 4.9 6.0 + - - +
286A ASP* 2.8 37.4 + - - +
288A ARG* 2.8 23.0 + - - -
289A PHE* 4.2 3.8 - - - -
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Residues in contact with GLN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE 5.0 0.8 + - - -
77A LYS 2.9 28.9 + - - +
78A GLY* 3.4 12.9 + - - -
79A THR* 3.2 18.3 + - - +
227A LYS* 2.9 35.1 + - + +
228A GLU* 3.9 9.0 - - - +
230A SER* 1.3 74.3 - - - +
232A ALA* 1.3 59.9 + - - +
234A SER* 3.2 9.1 + - - -
235A LEU* 2.9 27.4 + - + +
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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
----------------------------------------------------------
79A THR* 3.6 30.2 + - + -
81A LEU* 4.1 8.1 - - + -
148A VAL* 4.9 3.4 - - + -
175A ALA* 5.4 0.2 - - + -
177A VAL* 3.6 23.8 - - + -
228A GLU 2.9 18.9 + - - +
229A CYS 3.8 2.7 - - - +
231A GLN* 1.3 75.4 - - - +
233A LEU* 1.3 64.5 + - - +
235A LEU* 3.3 2.8 + - - +
236A ILE* 3.0 29.7 + - + +
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 3.7 19.5 - - + -
148A VAL* 4.4 8.0 - - + +
229A CYS 2.9 15.2 + - - +
230A SER 3.4 9.0 - - - +
232A ALA* 1.3 77.8 - - - +
234A SER* 1.3 62.9 + - - +
236A ILE* 3.2 3.5 + - - -
237A LEU* 2.9 40.4 + - + +
267A ILE* 3.7 35.0 - - + -
288A ARG* 3.7 39.3 - - + +
289A PHE* 3.6 28.7 - - + -
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Residues in contact with SER 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A SER 3.0 7.6 + - - -
231A GLN* 3.2 13.3 + - - -
233A LEU* 1.3 74.8 - - - +
235A LEU* 1.3 54.4 + - - +
237A LEU* 3.7 2.9 - - - +
238A ASP* 2.8 48.9 + - - +
288A ARG* 2.8 34.7 + - - +
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Residues in contact with LEU 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.7 29.4 - - + -
72A PHE* 3.7 52.9 - - + +
79A THR* 3.8 21.3 - - + +
81A LEU* 4.7 1.6 - - + -
231A GLN* 2.9 13.1 + - + +
232A ALA* 3.5 9.4 - - - +
233A LEU 3.2 0.4 - - - -
234A SER* 1.3 76.4 - - - +
236A ILE* 1.3 57.2 + - + +
238A ASP* 3.6 5.0 - - - +
239A ILE* 3.0 45.7 + - + +
243A LYS* 5.4 3.8 - - + -
245A VAL* 4.1 7.4 - - + -
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 5.1 7.9 - - + -
81A LEU* 3.5 27.6 - - + -
83A LEU* 4.8 10.8 - - + -
146A LEU* 3.8 20.0 - - + -
148A VAL* 5.3 0.9 - - + -
173A ILE* 5.8 1.6 - - + -
175A ALA* 3.8 18.8 - - + -
232A ALA 3.0 25.9 + - - +
233A LEU* 3.2 7.9 + - - +
235A LEU* 1.3 79.2 - - - +
237A LEU* 1.3 54.2 + - - +
239A ILE* 3.3 8.1 + - - +
240A ASP* 2.7 33.3 + - - +
258A LEU* 5.5 13.1 - - + +
262A ILE* 3.6 32.3 - - + -
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Residues in contact with LEU 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A LEU* 5.2 0.4 - - + -
233A LEU* 2.9 44.0 + - + +
234A SER* 3.7 5.2 - - - +
236A ILE* 1.3 77.3 - - - +
238A ASP* 1.3 64.5 + - - +
240A ASP* 3.2 2.4 - - - +
241A HIS* 3.2 13.9 + - - +
262A ILE* 4.2 13.2 - - + -
264A ARG* 2.9 59.5 + - + +
267A ILE* 4.0 18.6 - - + -
288A ARG* 3.8 26.0 - - - +
285B GLU 5.9 0.7 - - - +
287B GLN* 4.2 14.8 - - + +
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Residues in contact with ASP 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A SER* 2.8 35.2 + - - +
235A LEU* 3.6 6.6 + - - +
236A ILE 3.3 0.2 - - - -
237A LEU* 1.3 71.5 - - - +
239A ILE* 1.3 63.0 + - - +
241A HIS* 3.1 12.4 + - - +
242A GLY 3.4 0.5 + - - -
243A LYS* 3.0 55.3 + - + +
264A ARG* 5.8 0.2 + - - -
285B GLU* 4.4 14.0 - - - +
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Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 3.7 30.5 - - + -
235A LEU* 3.0 27.1 + - + +
236A ILE* 3.8 6.3 - - - +
238A ASP* 1.3 66.3 - - - +
240A ASP* 1.3 68.3 + - - +
241A HIS 2.9 3.2 + - - -
242A GLY* 3.2 10.0 + - - -
243A LYS 4.1 11.0 - - - +
245A VAL* 3.9 38.1 - - + -
255A MET* 3.3 32.1 - - + +
256A GLU* 5.3 1.6 - - - -
258A LEU* 3.7 21.1 - - + -
259A LYS* 3.5 14.2 - - + +
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Residues in contact with ASP 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE 2.7 18.8 + - - +
237A LEU* 3.2 12.8 - - - +
238A ASP 3.3 0.2 - - - -
239A ILE* 1.3 72.9 - - - +
241A HIS* 1.3 64.4 + - - +
242A GLY 3.5 1.1 + - - -
258A LEU 3.5 9.8 + - - -
259A LYS* 3.6 1.6 - - - +
260A ASP* 2.7 34.7 + - - +
261A SER 2.9 30.1 + - - -
262A ILE* 3.1 27.4 + - + +
264A ARG* 2.8 37.0 + - - +
----------------------------------------------------------
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Residues in contact with HIS 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A LEU 3.2 8.6 + - - +
238A ASP* 3.1 6.3 + - - +
239A ILE 2.9 1.2 - - - -
240A ASP* 1.3 94.7 + - - +
242A GLY* 1.3 59.1 + - - +
243A LYS 3.5 3.4 + - - -
260A ASP* 4.5 2.5 - - - -
264A ARG* 3.4 36.2 + - - +
284B SER* 2.6 33.4 + - - +
285B GLU* 6.1 0.4 - - - -
305B GLU* 5.3 2.3 - - - +
309B ARG* 3.0 74.4 + - + +
311B PRO* 4.3 2.4 - - + +
----------------------------------------------------------
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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