Contacts of the helix formed by residues 215 - 247 (chain A) in PDB entry 5EP6
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 SER 215 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A SER* 1.3 86.6 + - - +
217A ASP* 3.1 24.3 + - - +
218A ASN* 3.5 24.0 + - - +
219A MET* 3.6 11.3 + - - +
687B THR* 5.1 2.1 + - - -
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Residues in contact with SER 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A SER* 1.3 92.0 + - - -
217A ASP* 1.3 63.2 + - - +
219A MET* 3.4 9.2 + - - +
220A GLN* 3.3 22.2 + - - +
679D SER 5.2 11.9 - - - -
682D THR* 5.2 6.4 - - - +
686D MET* 5.1 0.3 - - - +
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Residues in contact with ASP 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A SER* 3.1 21.4 + - - -
216A SER* 1.3 84.8 + - - +
218A ASN* 1.3 85.3 + - - +
220A GLN* 3.0 11.5 + - - +
221A HIS* 2.9 48.9 + - + +
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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
----------------------------------------------------------
215A SER 3.5 18.3 + - - +
216A SER 3.4 0.8 - - - -
217A ASP* 1.3 103.7 + - - +
219A MET* 1.3 57.6 + - - +
221A HIS* 3.6 14.9 - - - +
222A ALA* 3.0 27.4 + - - +
687B THR* 3.9 12.9 - - + +
691B LYS* 5.7 2.0 - - - -
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Residues in contact with MET 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A SER 3.6 8.8 + - - +
216A SER* 3.4 12.5 + - - +
217A ASP 3.2 0.6 - - - -
218A ASN* 1.3 76.2 - - - +
220A GLN* 1.3 59.7 + - - +
222A ALA 3.2 0.7 + - - -
223A TYR* 2.9 28.8 + - - +
683B LEU* 3.0 59.2 - - + +
686B MET* 4.0 5.8 - - + -
687B THR* 3.2 17.6 + - - +
690B MET* 3.4 12.9 - - + +
219C MET* 3.5 24.0 - - - +
682D THR* 5.8 1.8 - - + -
683D LEU* 4.6 7.0 - - - -
686D MET* 3.5 19.7 - - + +
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Residues in contact with GLN 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A SER 3.3 8.4 + - - +
217A ASP* 3.0 12.7 + - - +
219A MET* 1.3 77.4 - - - +
221A HIS* 1.3 62.6 + - + +
223A TYR* 3.5 16.6 + - - +
224A TRP* 2.9 28.6 + - - +
682D THR* 3.8 19.1 - - + +
685D GLU* 3.8 20.0 + - - +
686D MET* 3.3 28.0 - - + +
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Residues in contact with HIS 221 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASP* 2.9 52.5 + - + +
218A ASN* 3.6 15.7 - - - +
219A MET 3.2 0.2 - - - -
220A GLN* 1.3 79.0 - - + +
222A ALA* 1.3 64.4 + - - +
224A TRP* 3.3 7.4 + - - +
225A GLU* 3.0 31.8 + - + +
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Residues in contact with ALA 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ASN 3.0 17.6 + - - +
219A MET 3.7 4.0 - - - +
221A HIS* 1.3 75.5 - - - +
223A TYR* 1.3 57.8 + - - +
225A GLU* 3.4 5.9 + - - +
226A LEU* 3.0 29.6 + - - +
687B THR* 3.9 22.2 - - + +
690B MET* 3.8 21.9 - - + +
691B LYS* 4.2 16.2 - - + +
694B LYS* 5.6 0.5 - - - +
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Residues in contact with TYR 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A MET 2.9 17.3 + - - +
220A GLN* 3.6 24.2 - - - +
222A ALA* 1.3 75.3 - - - +
224A TRP* 1.3 66.5 + - - +
226A LEU* 3.2 5.3 + - + +
227A LYS* 3.0 63.2 + - + +
690B MET* 3.7 21.7 - - - +
685D GLU* 3.8 23.4 + - - +
686D MET* 3.8 28.5 - - + -
689D GLY* 3.1 38.8 - - - -
690D MET* 4.4 2.9 - - + -
693D LEU* 4.6 8.5 - - + -
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Residues in contact with TRP 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A GLN 2.9 19.3 + - - +
221A HIS* 3.3 7.2 + - - +
223A TYR* 1.3 75.0 - - + +
225A GLU* 1.3 72.2 + - + +
227A LYS* 3.3 25.8 + - + +
228A ARG* 2.9 64.0 + - + +
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Residues in contact with GLU 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A HIS* 3.0 24.4 + - + +
222A ALA* 3.8 6.7 - - - +
223A TYR 3.3 0.2 - - - -
224A TRP* 1.3 88.9 - - + +
226A LEU* 1.3 57.6 + - - +
228A ARG* 3.3 31.1 + - - +
229A GLU* 3.0 28.2 + - - +
694B LYS* 3.7 18.6 - - + +
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ALA 3.0 17.2 + - - +
223A TYR* 3.5 5.8 - - + +
225A GLU* 1.3 73.6 - - - +
227A LYS* 1.3 64.0 + - - +
229A GLU* 3.2 2.1 + - - +
230A MET* 3.0 21.7 + - - +
690B MET* 3.9 37.5 - - + +
693B LEU* 4.0 7.2 - - + -
694B LYS* 3.8 25.3 - - - +
697B MET* 3.4 32.1 - - - -
226C LEU* 4.1 15.9 - - + -
690D MET* 5.1 1.3 - - + -
693D LEU* 3.8 25.8 - - + -
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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
----------------------------------------------------------
223A TYR* 3.0 61.3 + - + +
224A TRP* 3.6 26.9 - - + +
226A LEU* 1.3 75.6 - - - +
228A ARG* 1.3 62.5 + - - +
230A MET* 3.2 12.3 + - - +
231A SER* 3.2 16.1 + - - -
685D GLU* 5.0 5.1 + - - -
689D GLY* 5.8 0.4 - - - +
692D LYS* 6.5 0.7 - - - -
693D LEU* 4.3 21.5 - - + -
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Residues in contact with ARG 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A TRP* 2.9 58.6 + - + +
225A GLU* 3.4 30.9 + - - +
227A LYS* 1.3 76.5 - - - +
229A GLU* 1.3 67.2 + - - +
231A SER* 3.2 13.9 + - - -
232A ASN 3.3 1.6 + - - -
301A GOL 3.0 73.2 + - - +
694B LYS* 5.0 9.9 - - - +
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Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A GLU 3.0 16.5 + - - +
226A LEU 3.2 4.9 + - - +
228A ARG* 1.3 79.0 + - - +
230A MET* 1.3 66.1 + - - +
232A ASN* 3.0 36.5 + - - +
233A LEU* 3.0 20.4 + - - +
301A GOL 4.8 3.6 - - - -
694B LYS* 3.8 20.4 - - + +
697B MET* 3.6 30.3 - - + +
698B GLU* 3.5 35.0 - - + +
701B VAL* 3.8 10.2 - - - +
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Residues in contact with MET 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU 3.0 9.7 + - - +
227A LYS 3.2 10.1 + - - +
229A GLU* 1.3 77.2 - - - +
231A SER* 1.3 56.8 + - - +
233A LEU* 3.1 18.4 + - + +
234A HIS* 2.9 55.2 + - + +
697B MET* 3.4 20.5 - - + +
693D LEU* 3.6 33.2 - - + +
696D GLU* 3.9 25.4 - - + +
697D MET* 4.0 14.4 - - - +
700D VAL* 3.7 26.2 - - + -
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Residues in contact with SER 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A LYS 3.2 12.7 + - - -
228A ARG* 3.4 12.6 - - - -
229A GLU 3.2 0.6 - - - -
230A MET* 1.3 75.3 - - - +
232A ASN* 1.3 57.9 + - - +
234A HIS* 3.4 12.4 + - - +
235A LEU* 3.0 28.2 + - - +
301A GOL 4.1 7.6 - - - -
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Residues in contact with ASN 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A ARG 3.3 1.4 + - - -
229A GLU* 3.0 37.5 + - - +
231A SER* 1.3 77.3 - - - +
233A LEU* 1.3 57.9 + - - +
235A LEU* 3.3 10.4 + - - +
236A VAL* 3.0 30.0 + - - +
301A GOL 2.8 59.1 + - - -
701B VAL* 4.1 11.8 - - + +
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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
----------------------------------------------------------
229A GLU 3.0 11.1 + - - +
230A MET* 3.1 34.5 + - + +
232A ASN* 1.3 75.3 - - - +
234A HIS* 1.3 66.0 + - - +
236A VAL* 3.4 3.3 - - + +
237A THR* 2.9 27.7 + - - -
697B MET* 4.1 10.3 - - + +
700B VAL* 4.1 11.0 - - + -
701B VAL* 3.8 19.9 - - + +
704B LEU* 4.0 26.0 - - + -
233C LEU* 3.6 25.4 - - + -
697D MET* 4.5 4.0 - - + -
700D VAL* 4.0 21.3 - - + -
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Residues in contact with HIS 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A MET* 2.9 43.8 + - + +
231A SER* 3.6 11.7 - - - +
233A LEU* 1.3 75.2 - - - +
235A LEU* 1.3 57.7 + - - +
237A THR* 3.4 6.0 + - - -
238A GLN* 2.9 35.1 + - + +
696D GLU* 2.9 40.9 + - + -
700D VAL* 3.7 16.2 - - + +
801D GOL 5.3 3.8 - - - -
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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
----------------------------------------------------------
231A SER 3.0 17.9 + - - +
232A ASN* 3.7 11.2 - - - +
233A LEU 3.2 0.2 - - - -
234A HIS* 1.3 77.9 - - - +
236A VAL* 1.3 58.3 + - - +
238A GLN* 3.0 10.5 + - + -
239A VAL* 2.8 47.5 + - + +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A ASN 3.0 16.5 + - - +
233A LEU* 3.4 15.7 - - - +
235A LEU* 1.3 76.9 - - - +
237A THR* 1.3 59.6 + - - +
239A VAL* 3.4 6.8 + - + +
240A GLN* 3.0 23.7 + - - +
701B VAL* 4.0 19.3 - - + +
704B LEU* 4.0 28.6 - - + +
705B ALA* 3.8 28.0 - - + +
708B ASN* 3.4 21.8 + - - +
801B GOL 6.1 0.7 - - - +
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Residues in contact with THR 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 2.9 21.8 + - - +
234A HIS* 3.6 6.1 - - - -
235A LEU 3.1 0.4 - - - -
236A VAL* 1.3 79.1 - - - +
238A GLN* 1.3 61.9 + - - +
240A GLN* 3.3 7.9 + - - +
241A ALA* 3.0 25.6 + - - +
704B LEU* 4.5 0.7 - - - +
700D VAL* 3.5 26.5 - - + +
703D GLU* 3.9 35.4 - - + +
704D LEU* 4.1 22.6 - - + +
707D ASN* 4.8 1.5 + - - +
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Residues in contact with GLN 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A HIS* 2.9 20.6 + - + +
235A LEU* 3.0 11.9 + - + +
237A THR* 1.3 76.5 - - - +
239A VAL* 1.3 64.5 + - - +
241A ALA* 3.3 12.0 + - - +
242A GLU* 3.0 23.4 + - - +
245A ARG* 5.0 7.6 + - - -
703D GLU* 2.8 38.4 + - - -
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Residues in contact with VAL 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LEU* 2.8 35.2 + - + +
236A VAL* 3.6 10.5 - - + +
238A GLN* 1.3 77.0 - - - +
240A GLN* 1.3 57.6 + - - +
242A GLU* 3.2 8.5 + - + +
243A LEU* 2.8 32.0 + - + +
708B ASN* 3.7 19.3 - - + +
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Residues in contact with GLN 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL 3.0 13.7 + - - +
237A THR* 3.3 10.3 + - - +
239A VAL* 1.3 76.8 - - - +
241A ALA* 1.3 62.2 + - - +
243A LEU* 3.2 4.0 + - - +
244A LEU* 3.0 28.4 + - + +
704B LEU* 4.3 12.9 + - - +
707B ASN* 4.4 2.6 - - - +
708B ASN* 3.0 32.1 + - - +
711B LEU* 4.6 13.1 - - + +
240C GLN* 2.9 43.5 + - - -
704D LEU* 3.5 9.4 - - - +
707D ASN* 2.9 28.3 + - - +
711D LEU* 5.8 1.1 - - - -
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Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A THR 3.0 8.6 + - - +
238A GLN* 3.5 15.9 - - - +
239A VAL 3.3 0.2 - - - -
240A GLN* 1.3 75.4 - - - +
242A GLU* 1.3 65.2 + - - +
244A LEU* 3.4 8.9 + - - +
245A ARG* 3.2 37.8 + - - +
703D GLU* 3.7 23.3 - - - +
707D ASN* 4.5 10.2 - - - +
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Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLN 3.0 13.2 + - - +
239A VAL* 3.5 11.2 - - + +
241A ALA* 1.3 75.6 - - - +
243A LEU* 1.3 65.2 + - - +
245A ARG* 3.0 45.7 + - - +
246A LYS* 3.1 44.4 + - + +
802D GOL 4.0 14.3 + - - +
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A VAL* 2.8 20.7 + - + +
240A GLN* 3.5 5.8 - - + +
242A GLU* 1.3 79.5 - - + +
244A LEU* 1.3 63.1 + - + +
246A LYS* 2.9 14.7 + - - +
247A LEU* 3.1 22.1 + - + +
708B ASN* 3.1 51.4 - - + +
711B LEU* 3.9 17.9 - - + -
712B GLU* 3.9 17.7 - - + -
723D LEU* 3.5 30.5 - - + -
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Residues in contact with LEU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLN* 3.0 22.1 + - + +
241A ALA* 3.7 9.0 - - - +
242A GLU 3.3 0.2 - - - -
243A LEU* 1.3 76.3 - - - +
245A ARG* 1.3 61.8 + - + +
246A LYS 3.4 0.5 + - - -
247A LEU* 3.7 22.5 + - + +
711B LEU* 4.5 11.4 - - + -
717B LEU* 3.6 31.2 - - + +
707D ASN* 3.5 46.0 - - + +
710D ILE* 4.5 15.0 - - + -
711D LEU* 4.0 27.8 - - + -
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Residues in contact with ARG 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A GLN* 5.0 6.5 + - - -
241A ALA* 3.2 30.0 + - - +
242A GLU* 3.0 48.1 + - - +
244A LEU* 1.3 78.7 - - + +
246A LYS* 1.3 57.8 + - + +
247A LEU 3.5 1.6 + - - +
724D ARG* 2.6 29.7 + - - +
----------------------------------------------------------
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLU* 3.1 39.9 - - + +
243A LEU* 2.9 6.7 + - - +
245A ARG* 1.3 82.7 - - + +
247A LEU* 1.3 63.4 + - - +
723D LEU* 3.8 10.7 - - + -
724D ARG* 3.0 57.5 + - - +
802D GOL 3.8 42.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.1 28.9 + - + +
244A LEU* 3.7 31.2 + - + +
245A ARG 3.5 3.1 - - - +
246A LYS* 1.3 82.2 - - - +
248A LYS* 1.3 71.5 + - - +
249A THR* 3.6 10.6 + - - +
711B LEU* 3.3 38.6 - - + +
715B GLY* 3.7 26.5 - - - +
716B SER* 4.0 6.1 - - - +
717B LEU* 4.4 14.7 - - + +
711D LEU* 5.3 0.9 - - + -
722D GLY 3.7 9.4 - - - +
723D LEU 4.5 0.4 - - - +
724D ARG* 4.0 9.6 + - - -
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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).
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