Contacts of the helix formed by residues 243 - 268 (chain C) in PDB entry 1D2V
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 MET 243 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A MET* 4.3 10.5 - - + -
88A GLN* 3.6 11.4 - - - +
91A GLN* 3.5 14.6 - - - +
605A HEM 1.6 70.9 - - + -
241C SER 3.9 1.8 - - - -
242C GLU* 1.3 79.9 - - - +
244C PRO* 1.4 65.8 - - + +
245C GLU* 3.0 32.3 - - - +
246C LEU* 2.9 29.4 + - + +
247C THR* 3.1 13.4 + - - -
339C ILE* 5.3 0.4 - - + -
361C LEU* 3.6 31.6 - - + -
364C VAL* 4.0 2.2 - - + -
365C PHE* 4.6 6.3 - - + -
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Residues in contact with PRO 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241C SER 4.7 0.4 - - - +
243C MET* 1.4 82.6 - - + +
245C GLU* 1.3 58.2 - - - +
247C THR* 3.1 12.5 + - - +
248C SER* 2.6 40.4 + - - -
343C MET* 3.5 25.8 - - + -
364C VAL* 3.1 32.3 - - + +
367C ALA* 3.9 22.0 - - + +
370C ARG* 4.7 3.6 - - + -
371C VAL* 4.1 9.3 - - + +
380C ILE* 3.8 14.3 - - + +
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Residues in contact with GLU 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 5.7 3.3 - - + +
87A MET* 5.5 1.1 - - + -
88A GLN* 3.1 20.9 - - - +
243C MET* 3.0 42.8 - - - +
244C PRO* 1.3 76.0 - - - +
246C LEU* 1.3 59.4 + - - +
248C SER* 3.3 3.8 + - - -
249C MET* 3.1 26.9 + - - +
342C PHE 4.6 1.2 - - - +
343C MET* 3.5 38.1 - - + +
344C PHE 5.9 0.4 - - - +
361C LEU* 3.9 4.6 - - - +
380C ILE* 3.6 20.6 - - + +
384C LEU* 3.9 26.8 - - + +
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Residues in contact with LEU 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLN* 3.2 24.6 + - - +
91A GLN* 3.5 17.5 - - - +
92A LEU* 3.9 26.5 - - + +
95A HIS* 3.6 25.8 - - + +
239C ARG 3.1 29.2 - - - +
240C SER* 3.7 5.8 - - - +
242C GLU* 4.2 4.7 - - + -
243C MET* 2.9 13.0 + - + +
245C GLU* 1.3 75.7 - - - +
247C THR* 1.3 67.3 + - - +
249C MET* 3.1 6.0 + - - +
250C HIS* 3.0 43.0 + - + +
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Residues in contact with THR 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211C LEU* 4.3 6.5 - - + -
233C PHE* 3.5 36.0 - - + -
240C SER 2.7 21.8 + - - +
241C SER* 3.3 13.7 - - - -
243C MET 3.1 8.4 + - - -
244C PRO* 3.3 16.0 - - - +
246C LEU* 1.3 74.6 - - - +
248C SER* 1.3 58.2 + - - +
250C HIS* 3.1 6.4 + - - +
251C THR* 2.8 40.8 + - - +
368C SER* 5.6 1.9 - - - -
371C VAL* 4.0 14.0 - - + +
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Residues in contact with SER 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C PRO 2.6 21.9 + - - -
245C GLU 3.5 7.2 - - - -
246C LEU 3.1 0.2 - - - -
247C THR* 1.3 73.2 - - - +
249C MET* 1.3 56.5 + - - +
251C THR* 3.3 3.3 + - - -
252C LEU* 2.9 27.7 + - - +
371C VAL* 5.1 0.5 - - - +
377C ILE* 3.4 35.6 - - - +
380C ILE* 3.1 31.9 - - - +
381C LEU* 3.9 15.1 - - - +
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Residues in contact with MET 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 3.6 35.2 - - + +
88A GLN* 3.7 18.4 - - + +
89A TRP* 3.7 34.3 - - + -
92A LEU* 3.7 23.3 - - + -
245C GLU 3.1 13.6 + - - +
246C LEU* 3.1 7.5 + - - +
248C SER* 1.3 72.5 - - - +
250C HIS* 1.3 65.6 + - - +
252C LEU* 3.3 12.6 + - + +
253C LEU* 3.1 28.2 + - + +
381C LEU* 3.7 21.1 - - - -
384C LEU* 4.5 1.1 - - - -
533C LEU* 4.1 12.1 - - + -
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Residues in contact with HIS 250 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A LEU* 4.0 7.7 - - + +
95A HIS* 4.8 4.0 + - - +
175C MET* 3.1 48.3 + - + +
176C VAL* 5.1 6.5 - - - +
211C LEU* 3.8 20.4 - - + +
235C ALA* 3.9 10.4 - - + +
237C ASP* 4.3 8.5 - - + +
240C SER* 3.6 34.6 + - - -
246C LEU* 3.0 40.3 + - + +
247C THR* 3.4 7.9 - - - +
249C MET* 1.3 77.0 - - - +
251C THR* 1.3 62.7 + - - +
253C LEU* 3.4 5.5 + - - +
254C LEU* 3.1 22.0 + - - +
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Residues in contact with THR 251 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C ALA 3.2 27.6 - - - +
210C LEU* 4.1 14.4 - - + +
211C LEU* 3.7 21.5 + - - +
247C THR* 2.8 23.1 + - - +
248C SER 3.5 5.6 - - - -
250C HIS* 1.3 76.8 - - - +
252C LEU* 1.3 62.7 + - - +
254C LEU* 3.2 4.2 + - + +
255C ARG* 3.0 40.3 + - + +
377C ILE* 4.0 14.9 - - + +
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Residues in contact with LEU 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C SER 2.9 13.6 + - - +
249C MET* 3.4 23.3 - - + +
251C THR* 1.3 76.3 - - - +
253C LEU* 1.3 64.8 + - + +
255C ARG* 3.2 8.4 + - - +
256C GLU* 2.9 25.3 + - - +
377C ILE* 4.4 5.1 - - - +
381C LEU* 4.7 6.5 - - + -
533C LEU* 3.9 17.5 - - + -
536C ILE* 3.7 42.2 - - + +
537C ILE* 3.8 29.2 - - + -
540C ASN* 3.9 11.3 - - + -
541C THR* 4.2 10.1 - - + -
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Residues in contact with LEU 253 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TRP* 5.2 9.9 - - + -
92A LEU* 4.2 25.8 - - + -
175C MET* 4.5 4.3 - - + -
176C VAL* 4.0 32.3 - - + +
249C MET* 3.1 14.7 + - + +
250C HIS* 4.1 1.8 - - - +
252C LEU* 1.3 91.8 - - + +
254C LEU* 1.3 61.1 + - - +
256C GLU* 3.2 8.6 + - + +
257C HIS* 2.9 28.9 + - - +
284C VAL* 4.7 15.5 - - + +
287C MET* 6.2 2.7 - - + -
288C VAL* 4.2 23.6 - - + -
291C ILE* 6.3 0.2 - - + -
533C LEU* 5.8 0.7 - - + -
536C ILE* 4.7 17.3 - - + -
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Residues in contact with LEU 254 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C VAL* 5.0 4.4 - - + +
187C LEU* 6.5 0.4 - - + -
197C LEU* 3.6 33.0 - - + -
198C ALA 3.5 21.3 - - - +
199C VAL* 3.9 23.1 - - + -
209C ALA* 3.9 16.4 - - + -
210C LEU 4.3 13.7 - - - +
211C LEU* 4.1 20.0 - - + -
212C PRO* 5.0 2.5 - - + -
250C HIS 3.1 14.2 + - - +
251C THR 3.2 9.8 + - - +
253C LEU* 1.3 76.4 - - - +
255C ARG* 1.3 66.7 + - + +
257C HIS* 3.3 3.1 + - - +
258C ASN* 3.2 23.0 + - - +
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Residues in contact with ARG 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205C ASP* 3.0 38.0 + - - +
208C ARG* 3.6 22.8 - - - +
209C ALA* 2.7 45.1 + - + +
210C LEU* 4.4 1.0 - - - +
251C THR* 3.0 23.1 + - - +
252C LEU* 3.5 7.0 - - - +
254C LEU* 1.3 79.1 - - + +
256C GLU* 1.4 52.0 + - - +
258C ASN* 3.1 7.8 + - - +
259C ARG* 2.7 35.3 + - - +
377C ILE* 3.2 28.9 - - - +
378C ASP* 4.7 1.4 + - - -
540C ASN* 2.9 41.5 + - + +
541C THR* 4.2 4.0 - - - +
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Residues in contact with GLU 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C LEU 2.9 13.6 + - - +
253C LEU* 3.2 15.2 + - + +
255C ARG* 1.4 76.9 - - - +
257C HIS* 1.4 57.8 + - - +
259C ARG* 2.6 46.4 + - - -
260C LEU* 2.9 45.5 + - + +
284C VAL* 4.6 4.5 - - + -
287C MET* 3.3 37.7 - - - +
536C ILE* 4.2 15.9 - - + +
539C ASP* 4.3 1.7 - - - +
540C ASN* 2.8 25.1 + - - +
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Residues in contact with HIS 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176C VAL* 5.4 0.2 - - + -
177C TYR* 2.8 30.3 + + - +
195C GLY 2.9 25.2 + - - -
197C LEU* 3.5 30.2 - - + +
253C LEU 2.9 11.7 + - - +
254C LEU 3.6 1.8 - - - +
255C ARG 3.2 0.2 - - - -
256C GLU* 1.4 76.4 - - - +
258C ASN* 1.3 73.4 + - - +
260C LEU* 3.3 4.2 + - - +
261C ALA* 2.9 27.2 + - + +
277C TYR* 3.3 43.9 - + - -
280C ALA* 3.4 15.2 - - + +
281C ARG 3.7 1.6 - - - -
284C VAL* 4.0 8.2 - - + +
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Residues in contact with ASN 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C LEU* 3.3 28.3 - - + +
197C LEU* 2.8 45.4 + - - +
199C VAL* 3.5 19.8 - - - +
209C ALA* 5.3 2.0 - - - +
254C LEU* 3.2 12.6 + - - +
255C ARG* 3.1 9.4 + - - +
257C HIS* 1.3 83.0 - - - +
259C ARG* 1.3 56.9 + - - +
261C ALA* 3.5 1.9 + - - +
262C THR* 2.8 35.2 + - - -
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Residues in contact with ARG 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C ARG 2.7 20.1 + - - +
256C GLU* 2.6 43.4 + - - +
258C ASN* 1.3 72.9 - - - +
260C LEU* 1.3 72.3 + - - +
262C THR* 3.2 7.1 + - - -
263C GLU* 2.9 74.0 + - + +
287C MET* 4.9 0.6 - - - +
539C ASP* 3.5 43.4 + - - +
540C ASN* 3.6 13.9 - - - +
569C ALA* 5.6 6.3 - - - +
570C LEU* 4.6 15.8 + - - +
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Residues in contact with LEU 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C GLU* 2.9 46.1 + - + +
257C HIS 3.7 2.7 - - - +
259C ARG* 1.3 80.8 - - - +
261C ALA* 1.3 67.5 + - - +
263C GLU* 3.4 5.0 + - - +
264C LEU* 2.9 33.0 + - + +
280C ALA* 4.0 11.0 - - + +
283C ILE* 3.4 41.7 - - + -
284C VAL* 3.8 20.6 - - + -
287C MET* 4.5 0.4 - - - -
570C LEU* 3.9 12.1 - - + -
572C LEU* 4.1 17.9 - - + -
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C LEU 3.6 22.7 - - - +
195C GLY 4.0 11.2 - - - +
196C LEU* 3.7 13.5 - - + -
257C HIS* 2.9 18.2 + - - +
258C ASN 3.7 0.2 - - - +
260C LEU* 1.3 77.0 - - - +
262C THR* 1.4 56.8 + - - +
264C LEU* 3.2 6.4 + - - +
265C LYS* 2.9 29.9 + - - +
276C LEU* 3.7 11.0 - - + +
280C ALA* 3.8 12.9 - - + +
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Residues in contact with THR 262 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196C LEU* 4.4 9.4 - - - +
258C ASN* 2.8 23.7 + - - +
259C ARG* 3.2 6.4 + - - -
261C ALA* 1.4 74.4 - - - +
263C GLU* 1.3 65.2 + - + +
265C LYS* 3.0 18.3 + - + +
266C SER* 3.2 17.2 + - - +
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Residues in contact with GLU 263 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259C ARG* 2.9 53.5 + - + +
260C LEU 3.9 1.3 - - - +
262C THR* 1.3 78.4 - - + +
264C LEU* 1.3 61.7 + - - +
266C SER* 3.3 7.7 + - - +
267C LEU* 3.2 31.6 + - + +
570C LEU 4.9 4.5 - - - +
572C LEU* 3.2 32.5 - - + +
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C LEU 2.9 26.2 + - - +
261C ALA* 3.6 4.0 - - - +
263C GLU* 1.3 75.7 - - - +
265C LYS* 1.3 53.8 + - - +
267C LEU* 3.3 5.1 + - + -
268C ASN* 2.8 41.8 + - - +
271C TRP* 4.3 9.9 - - + -
276C LEU* 3.7 14.8 - - + +
279C GLU* 3.8 29.8 - - + -
280C ALA* 3.9 13.0 - - - +
283C ILE* 4.1 11.9 - - + -
572C LEU* 4.5 16.6 - - + -
575C TRP* 3.6 36.6 - - + -
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Residues in contact with LYS 265 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C GLN* 5.1 5.7 + - - +
194C LEU* 4.5 25.4 - - + +
261C ALA 2.9 14.1 + - - +
262C THR* 3.0 13.7 + - + +
264C LEU* 1.3 78.3 - - - +
266C SER* 1.3 60.9 + - - +
268C ASN 3.3 2.3 - - - +
269C PRO* 3.2 50.6 + - - +
271C TRP 3.9 10.2 + - - +
276C LEU* 3.7 29.1 - - + +
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Residues in contact with SER 266 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C THR* 3.2 14.0 + - - +
263C GLU* 3.7 10.7 - - - -
264C LEU 3.3 0.2 - - - -
265C LYS* 1.3 77.6 - - - +
267C LEU* 1.3 68.8 + - - +
269C PRO* 3.7 13.7 - - - +
576C ARG* 5.0 2.9 + - - -
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C GLU* 3.2 22.5 + - + +
264C LEU* 3.8 7.4 - - + +
266C SER* 1.3 84.7 - - - +
268C ASN* 1.3 69.5 + - - +
269C PRO* 3.4 7.7 - - - +
572C LEU* 4.8 19.5 - - + +
573C ALA* 4.9 7.2 - - - -
576C ARG* 3.1 77.5 + - + +
----------------------------------------------------------
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Residues in contact with ASN 268 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C LEU* 2.8 20.2 + - - +
265C LYS* 3.3 10.6 - - - +
267C LEU* 1.3 81.7 - - - +
269C PRO* 1.4 64.1 - - - +
270C ARG 3.3 3.1 - - - -
271C TRP* 3.1 63.3 + - + +
575C TRP 3.0 24.2 + - - -
576C ARG* 3.6 2.6 - - - +
577C GLU* 2.7 34.9 + - - +
----------------------------------------------------------
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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