Contacts of the helix formed by residues 272 - 295 (chain C) in PDB entry 1D7W
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 ASP 272 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C GLN* 3.3 21.3 - - - +
270C ARG 3.4 5.4 + - - +
271C TRP* 1.3 75.5 - - - +
273C GLY* 1.4 59.1 + - - +
274C GLU* 3.9 10.6 - - - +
275C ARG* 2.9 37.4 + - - +
276C LEU* 2.9 27.6 + - - +
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Residues in contact with GLY 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ARG* 4.2 5.6 - - - -
192C ASN 5.3 0.7 - - - -
193C GLN* 2.7 45.3 + - - -
195C GLY* 3.3 15.6 - - - -
272C ASP* 1.4 66.3 - - - +
274C GLU* 1.3 54.0 + - - +
276C LEU* 3.2 1.9 + - - -
277C TYR* 2.8 33.6 + - - +
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Residues in contact with GLU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ARG* 2.7 38.0 + - - +
193C GLN* 4.5 1.2 + - - -
272C ASP* 3.5 11.5 + - - +
273C GLY* 1.3 72.9 - - - +
275C ARG* 1.3 58.8 + - - +
277C TYR* 3.8 0.3 - - - +
278C GLN* 2.8 67.3 + - + +
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Residues in contact with ARG 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LYS* 3.1 27.7 - - - +
7A TYR* 3.5 21.0 + - - -
271C TRP* 3.6 45.7 - - + +
272C ASP* 2.9 28.4 + - - +
274C GLU* 1.3 77.8 - - - +
276C LEU* 1.3 56.2 + - - +
278C GLN* 3.4 3.2 + - - +
279C GLU* 2.9 38.0 + - + +
577C GLU* 3.4 30.5 + - - -
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Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193C GLN 3.6 21.1 - - - +
194C LEU* 3.8 20.6 - - - +
195C GLY 4.5 2.0 - - - -
261C ALA* 3.6 10.9 - - + +
264C LEU* 3.7 15.0 - - + +
265C LYS* 3.5 47.1 - - + +
271C TRP* 3.6 30.3 - - + +
272C ASP 2.9 20.3 + - - +
273C GLY 3.2 3.8 + - - +
275C ARG* 1.3 72.8 - - - +
277C TYR* 1.3 66.0 + - - +
279C GLU* 3.9 3.6 - - - +
280C ALA* 3.0 27.7 + - - +
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Residues in contact with TYR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.6 24.5 - - + +
177C TYR* 3.6 33.9 + + - +
184C ALA* 4.8 2.4 + - - +
188C ARG* 3.4 65.3 - - + +
195C GLY* 3.6 17.8 + - - +
196C LEU 5.0 0.7 - - - -
197C LEU* 4.1 4.7 - - + -
257C HIS* 3.6 18.1 - + - -
273C GLY 2.8 20.7 + - - +
274C GLU 3.8 0.9 - - - +
276C LEU* 1.3 73.9 - - - +
278C GLN* 1.4 86.1 + - + +
281C ARG* 2.8 43.9 + - - +
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Residues in contact with GLN 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 3.5 50.1 - - + +
8A ARG 5.1 1.4 + - - -
10A ILE* 6.0 2.4 - - - +
188C ARG* 4.8 0.8 - - - +
274C GLU* 2.8 47.5 + - + +
275C ARG 3.9 1.1 - - - +
277C TYR* 1.4 92.0 - - + +
279C GLU* 1.4 58.3 + - - +
281C ARG* 3.2 34.4 + - - +
282C LYS* 2.9 28.9 + - - +
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Residues in contact with GLU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LYS* 4.5 3.5 + - - -
7A TYR* 2.4 30.8 + - - +
264C LEU* 3.7 20.0 - - + -
271C TRP* 3.4 29.4 - - + -
275C ARG* 2.9 27.7 + - + +
276C LEU 3.9 0.9 - - - +
278C GLN* 1.4 74.1 - - - +
280C ALA* 1.3 65.2 + - - +
282C LYS* 3.4 14.0 + - - +
283C ILE* 3.2 26.9 + - - +
524C GLN* 5.0 1.6 + - - -
575C TRP* 3.6 24.5 + - + -
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177C TYR* 4.1 2.9 - - - -
257C HIS* 3.6 35.7 - - + +
260C LEU* 3.9 9.6 - - + +
261C ALA* 3.8 14.6 - - - +
264C LEU* 3.8 7.3 - - + +
276C LEU 3.0 17.3 + - - +
279C GLU* 1.3 73.1 - - - +
281C ARG* 1.3 65.5 + - - +
283C ILE* 3.1 5.4 + - - +
284C VAL* 2.9 26.0 + - - +
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Residues in contact with ARG 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A TYR* 4.7 1.0 - - - +
8A ARG* 2.8 43.5 + - - +
9A THR 2.9 26.7 + - - -
10A ILE* 3.8 25.5 + - - +
172C ASP* 4.9 12.4 + - - +
177C TYR* 3.2 45.0 + - + +
178C GLY 5.5 1.0 + - - -
257C HIS* 3.9 0.6 + - - -
277C TYR* 2.8 38.5 + - + +
278C GLN* 3.2 30.0 + - - +
280C ALA* 1.3 76.9 - - - +
282C LYS* 1.4 55.2 + - - +
284C VAL* 3.4 2.4 + - - +
285C GLY* 3.0 26.7 + - - -
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Residues in contact with LYS 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LYS* 3.9 16.8 + - - +
7A TYR* 4.3 23.1 - - + -
278C GLN 2.9 18.3 + - - +
279C GLU* 3.6 15.5 + - - +
280C ALA 3.2 0.2 - - - -
281C ARG* 1.4 73.8 - - - +
283C ILE* 1.3 61.6 + - - +
285C GLY* 3.5 1.5 + - - -
286C ALA* 3.0 26.7 + - - +
512C PHE* 6.3 0.2 - - - -
519C VAL* 2.6 48.0 + - + +
520C PHE* 3.5 28.5 - - + -
524C GLN* 5.7 0.2 + - - -
575C TRP* 6.1 0.2 - - - +
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Residues in contact with ILE 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C LEU* 3.4 26.2 - - + -
264C LEU* 4.3 13.2 - - + -
279C GLU 3.2 13.6 + - - +
280C ALA 3.1 7.9 + - - +
282C LYS* 1.3 76.9 - - - +
284C VAL* 1.3 54.2 + - - +
286C ALA* 3.2 8.2 + - - +
287C MET* 2.8 49.6 + - + +
520C PHE* 4.6 3.6 - - + -
528C LEU* 4.2 12.3 - - + -
570C LEU* 4.5 3.1 - - + -
572C LEU* 4.0 17.9 - - + -
575C TRP* 3.4 44.6 - - + +
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Residues in contact with VAL 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C ALA* 3.8 19.5 - - + -
176C VAL* 4.7 9.0 - - + -
177C TYR* 3.2 30.3 - - + +
253C LEU* 4.6 15.9 - - + +
256C GLU* 4.5 6.7 - - + -
257C HIS* 4.1 17.5 - - + +
260C LEU* 3.9 16.4 - - + -
280C ALA 2.9 14.9 + - - +
281C ARG 3.7 1.1 - - - +
282C LYS 3.4 0.2 - - - -
283C ILE* 1.3 74.1 - - - +
285C GLY* 1.3 58.7 + - - +
287C MET* 3.1 12.1 + - + +
288C VAL* 3.0 31.9 + - + +
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Residues in contact with GLY 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 5.9 2.2 - - - -
171C VAL 4.0 3.0 - - - +
172C ASP* 4.3 13.2 - - - -
173C ALA* 4.2 15.9 - - - +
281C ARG 3.0 16.1 + - - -
282C LYS* 3.9 2.5 - - - -
284C VAL* 1.3 76.1 - - - +
286C ALA* 1.3 60.9 + - - +
288C VAL* 3.4 4.0 + - - +
289C GLN* 3.2 30.5 + - - +
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C LYS 3.0 14.8 + - - +
283C ILE* 3.2 10.3 + - - +
285C GLY* 1.3 74.6 - - - +
287C MET* 1.3 59.8 + - - +
289C GLN* 3.3 4.5 + - - +
290C ILE* 2.9 37.5 + - + +
514C TRP* 4.1 15.7 - - + -
520C PHE* 3.8 25.8 - - + -
528C LEU* 4.3 14.4 - - + -
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Residues in contact with MET 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C LEU* 6.0 4.0 - - + -
256C GLU* 3.3 36.6 - - - +
260C LEU* 4.4 0.2 - - - -
283C ILE* 2.8 37.7 + - + +
284C VAL* 3.1 13.4 + - + +
286C ALA* 1.3 77.3 - - + +
288C VAL* 1.3 62.4 + - + +
291C ILE* 3.0 33.0 + - + +
528C LEU* 5.4 1.1 - - + -
531C ILE* 3.9 37.9 - - + +
536C ILE* 3.7 19.1 - - + -
570C LEU* 4.0 8.1 - - + -
1609C ACT 3.8 22.2 - - + -
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Residues in contact with VAL 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TRP* 3.8 25.2 - - + -
93A LEU* 4.6 4.9 - - + -
96A ASP* 3.7 14.6 - - - +
171C VAL* 3.7 18.6 - - + -
173C ALA* 4.1 18.2 - - + +
175C MET* 4.3 8.5 - - + -
253C LEU* 4.3 22.9 - - + -
284C VAL* 3.0 14.9 + - + +
285C GLY 3.8 7.0 - - - +
286C ALA 3.3 0.2 - - - -
287C MET* 1.3 76.3 - - + +
289C GLN* 1.4 56.3 + - - +
292C THR* 2.7 41.1 + - - +
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Residues in contact with GLN 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 3.2 9.1 - - - +
171C VAL* 3.0 37.3 + - + +
285C GLY 3.2 18.6 + - - +
286C ALA 3.3 5.4 + - - +
288C VAL* 1.4 75.2 - - - +
290C ILE* 1.4 56.6 + - - +
292C THR* 3.3 1.5 + - - -
293C TYR* 2.9 36.8 + - - +
510C ASP* 3.1 24.7 + - - -
512C PHE 4.7 0.4 - - - -
513C TRP* 3.3 32.0 - - + +
514C TRP* 2.8 38.1 + - + +
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Residues in contact with ILE 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C ALA* 2.9 23.6 + - + +
287C MET 4.0 2.7 - - - +
289C GLN* 1.4 71.6 - - - +
291C ILE* 1.3 67.4 + - - +
293C TYR* 5.4 0.9 - - - -
294C ARG* 2.9 67.6 + - + +
514C TRP* 3.7 40.4 - - + +
528C LEU* 3.3 40.6 - - + +
529C ALA* 4.6 1.6 - - - +
531C ILE* 4.0 13.5 - - + -
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Residues in contact with ILE 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TRP* 3.7 33.7 - - + -
253C LEU* 6.2 0.9 - - + -
287C MET* 3.0 24.2 + - + +
290C ILE* 1.3 75.4 - - - +
292C THR* 1.3 56.4 + - - +
295C ASP* 3.0 25.9 + - - +
296C TYR* 3.0 23.0 + - - +
531C ILE* 3.8 13.5 - - + -
532C SER* 4.8 0.4 - - - -
533C LEU* 4.1 29.4 - - + +
536C ILE* 4.0 26.5 - - + -
551C ILE* 5.7 0.2 - - + -
552C PHE* 3.6 29.4 - - + -
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Residues in contact with THR 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A TRP* 2.9 19.3 + - - +
93A LEU* 3.5 36.2 - - + +
171C VAL* 5.0 1.3 - - + -
288C VAL* 2.7 24.3 + - - +
289C GLN* 3.6 4.3 - - - -
290C ILE 3.1 0.2 - - - -
291C ILE* 1.3 77.0 - - - +
293C TYR* 1.3 77.0 + - + +
296C TYR* 3.2 10.6 + - + +
297C LEU* 2.7 43.5 + - + +
503C PHE* 4.1 4.0 - - + -
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Residues in contact with TYR 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171C VAL* 4.3 10.2 - - + +
289C GLN* 2.9 19.4 + - - +
290C ILE* 5.4 0.7 - - - -
292C THR* 1.3 90.3 - - + +
294C ARG* 1.3 62.8 + - - +
297C LEU* 3.8 17.7 - - + -
298C PRO* 3.5 17.5 - - - +
306C MET* 4.1 14.6 - - + +
310C LEU* 4.0 18.8 - - + -
503C PHE* 2.7 48.0 + + - -
506C LEU* 3.7 6.8 - - - +
507C ARG* 3.5 24.6 + - + -
513C TRP* 3.3 40.6 - + + -
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Residues in contact with ARG 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ILE* 2.9 43.3 + - + +
291C ILE* 5.1 0.2 - - - +
293C TYR* 1.3 78.5 - - - +
295C ASP* 1.3 89.4 + - - +
298C PRO* 3.6 15.1 - - - +
529C ALA* 2.9 27.5 + - - +
531C ILE* 2.9 26.9 + - - +
532C SER* 4.0 12.1 - - - +
549C ASN* 5.7 1.6 - - - +
550C ASN* 4.8 1.7 + - - -
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Residues in contact with ASP 295 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291C ILE* 3.0 27.5 + - - +
294C ARG* 1.3 125.0 + - - +
296C TYR* 1.3 61.0 + - - +
298C PRO* 3.8 2.5 - - - -
299C LEU* 3.9 12.0 - - - +
532C SER* 5.7 0.2 - - - -
533C LEU* 5.4 2.3 + - - +
549C ASN* 6.4 0.2 - - - -
550C ASN* 3.0 38.2 + - - +
551C ILE* 5.6 3.3 - - + +
552C PHE* 3.5 18.5 - - + -
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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