Contacts of the helix formed by residues 263 - 285 (chain C) in PDB entry 1XV9
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 263 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253C ASN* 3.9 0.4 - - - -
255C GLY* 3.5 18.4 - - - +
257C ASN 3.7 0.2 - - - +
258C PRO* 3.1 28.4 - - - +
260C SER* 3.3 24.1 + - - +
262C ASN* 1.3 74.5 - - - +
264C PRO* 1.3 74.8 - - - +
265C VAL* 2.9 34.3 + - - +
266C THR* 3.1 27.9 + - - +
267C ASN* 2.9 25.7 + - - +
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Residues in contact with PRO 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C ALA* 4.6 3.1 - - + -
253C ASN 3.2 22.7 - - - +
255C GLY* 3.5 25.6 - - - +
262C ASN 3.4 4.2 - - - +
263C ASP* 1.3 87.8 - - - +
265C VAL* 1.3 57.5 + - + +
267C ASN* 3.6 2.9 - - - +
268C ILE* 3.1 32.2 + - + +
326C LEU* 4.7 1.9 - - - +
330C LEU* 4.7 7.9 - - + -
332C VAL* 4.5 11.2 - - + -
336C SER* 3.9 12.8 - - - +
337C ALA* 5.9 0.4 - - - -
340C ALA* 3.5 27.6 - - + -
342C VAL* 5.9 1.8 - - + -
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Residues in contact with VAL 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C ASP* 2.9 12.0 + - - +
264C PRO* 1.3 68.3 - - + +
266C THR* 1.3 62.6 + - - +
267C ASN 3.1 2.2 - - - -
268C ILE* 3.4 17.3 + - + +
269C CYS* 3.2 18.3 + - - -
340C ALA* 3.9 32.3 - - + +
342C VAL* 5.3 4.3 - - + -
439C PHE* 3.4 52.3 - - + -
445C THR* 4.3 11.2 - - - +
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Residues in contact with THR 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C PRO* 3.7 17.4 + - - +
260C SER 5.7 0.4 - - - -
263C ASP* 3.1 29.6 + - - +
265C VAL* 1.3 75.7 - - - +
267C ASN* 1.3 60.9 + - - +
269C CYS* 4.0 2.8 + - - +
270C GLN* 3.1 34.6 + - + +
445C THR* 3.8 23.8 + - + +
446C PRO* 4.7 18.1 - - + +
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Residues in contact with ASN 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C PRO 3.3 9.4 + - - +
262C ASN* 3.2 31.5 + - - +
263C ASP 2.9 23.5 + - - +
264C PRO 3.6 1.8 - - - +
266C THR* 1.3 79.1 - - - +
268C ILE* 1.3 59.3 + - - +
269C CYS 3.3 0.4 - - - -
270C GLN* 3.6 20.1 + - - +
271C ALA* 2.9 31.9 + - - +
326C LEU* 4.7 3.8 - - + +
328C THR* 3.8 18.8 + - - +
330C LEU* 3.3 26.9 - - + +
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Residues in contact with ILE 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C PRO* 3.1 19.9 + - + +
265C VAL* 3.4 22.6 + - + +
267C ASN* 1.3 78.1 - - - +
269C CYS* 1.3 58.3 + - - +
271C ALA* 3.9 4.3 - - - +
272C ALA* 3.0 29.5 + - + +
326C LEU* 4.3 20.4 - - + -
332C VAL* 6.2 0.2 - - + -
342C VAL* 5.0 12.1 - - + -
436C LEU* 5.3 5.6 - - + -
439C PHE* 5.3 4.5 - - + -
1002C F15 3.9 64.1 - - + +
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Residues in contact with CYS 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265C VAL* 3.2 18.2 - - - +
266C THR 4.1 5.2 - - - +
268C ILE* 1.3 81.2 - - - +
270C GLN* 1.3 60.3 + - + +
272C ALA* 4.8 0.7 - - - -
273C ASP* 3.2 15.9 + - - +
436C LEU* 5.9 3.8 - - - -
439C PHE* 4.4 24.2 - - - -
445C THR* 3.6 24.7 - - + -
446C PRO 4.7 8.3 - - - +
447C ILE* 4.6 10.3 - - + -
448C ASP* 4.9 3.0 - - - +
451C LEU* 3.1 35.8 - - + +
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Residues in contact with GLN 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C PRO 5.7 0.6 + - - -
266C THR* 3.1 28.7 + - + +
267C ASN* 3.4 25.3 + - - +
268C ILE 3.3 0.4 - - - -
269C CYS* 1.3 80.0 - - + +
271C ALA* 1.3 61.6 + - - +
273C ASP* 4.0 3.4 - - - +
274C LYS* 3.4 20.4 + - - +
328C THR* 4.2 10.0 - - + +
446C PRO 5.9 2.7 - - - +
448C ASP* 4.1 20.2 - - - +
686F ARG* 4.2 18.2 + - - -
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Residues in contact with ALA 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C ASN 2.9 18.2 + - - +
268C ILE* 3.9 4.5 - - - +
270C GLN* 1.3 74.7 - - - +
272C ALA* 1.3 61.0 + - - +
273C ASP 3.1 1.3 - - - -
274C LYS* 3.0 5.5 + - - +
275C GLN* 2.8 33.3 + - - +
326C LEU* 4.8 5.8 - - + -
327C ALA* 4.2 15.5 - - + +
328C THR* 3.3 22.0 - - + +
1002C F15 3.8 16.6 - - + +
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268C ILE* 3.0 15.4 + - + +
269C CYS* 4.4 2.9 - - - +
271C ALA* 1.3 75.9 - - - +
273C ASP* 1.3 63.0 + - - +
275C GLN 3.4 1.7 + - - -
276C LEU* 3.1 31.1 + - - +
305C TRP* 5.4 2.7 - - + -
309C LEU* 3.8 3.8 - - + +
436C LEU* 6.1 2.5 - - + -
451C LEU* 4.7 14.6 - - + -
1002C F15 3.3 44.3 - - + +
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Residues in contact with ASP 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C CYS 3.2 19.3 + - - +
270C GLN* 4.0 5.7 - - - +
271C ALA 3.1 0.4 - - - -
272C ALA* 1.3 80.6 - - - +
274C LYS* 1.3 58.7 + - - +
276C LEU* 3.6 9.4 - - - +
277C PHE* 3.0 35.2 - - - -
448C ASP* 3.4 27.5 - - + +
449C THR* 4.3 1.3 + - - -
450C PHE* 3.3 14.9 + - - +
451C LEU* 3.0 38.7 + - + +
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Residues in contact with LYS 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C PRO* 5.4 11.9 - - - +
270C GLN 3.4 13.7 + - - +
271C ALA* 3.0 9.1 + - - +
273C ASP* 1.3 78.4 + - - +
275C GLN* 1.3 79.5 + - - +
276C LEU 3.0 9.5 + - - -
277C PHE* 3.2 19.4 + - - +
278C THR* 3.6 22.2 + - + +
327C ALA 3.8 19.7 - - - +
328C THR* 5.5 3.4 - - + -
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Residues in contact with GLN 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C VAL* 5.9 1.9 - - - +
244C PRO* 5.7 5.2 - - - +
271C ALA 2.8 21.2 + - - +
272C ALA 3.4 3.6 + - - +
274C LYS* 1.3 102.7 - - - +
276C LEU* 1.3 57.8 + - - +
278C THR* 3.2 26.7 + - - +
279C LEU* 3.2 15.4 - - - +
309C LEU* 3.4 17.5 - - + +
312C SER* 5.6 2.4 + - - -
316C ARG* 3.6 13.3 + - - -
327C ALA* 3.2 32.8 - - + +
1002C F15 3.4 21.9 - - + +
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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
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272C ALA 3.1 12.4 + - - +
273C ASP* 3.6 4.3 - - - +
274C LYS 3.0 0.8 + - - -
275C GLN* 1.3 77.5 - - - +
277C PHE* 1.3 67.0 + - - +
279C LEU* 3.1 8.6 + - + +
280C VAL* 3.1 24.4 + - - +
305C TRP* 3.6 28.5 - - + -
309C LEU* 3.2 30.1 - - + -
450C PHE* 3.2 35.9 - - + -
451C LEU* 4.0 22.4 - - + -
454C MET* 3.6 25.8 - - + -
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Residues in contact with PHE 277 (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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273C ASP* 3.0 40.2 - - - -
274C LYS* 3.7 9.2 - - - +
276C LEU* 1.3 78.3 - - - +
278C THR* 1.3 64.4 + - + +
280C VAL* 3.0 27.1 + - - +
281C GLU* 3.3 9.2 + - - +
449C THR* 4.7 7.0 - - - -
450C PHE* 3.4 36.3 - + + -
632G ILE* 4.6 11.2 - - + -
635G ARG* 4.7 9.0 - - - -
636G LEU* 4.1 15.8 - - + +
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Residues in contact with THR 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C VAL* 4.2 26.6 - - + +
274C LYS* 3.6 25.1 - - - +
275C GLN* 3.2 33.7 + - - +
277C PHE* 1.3 75.7 - - + +
279C LEU* 1.3 63.6 + - - +
281C GLU* 3.2 11.3 + - - +
282C TRP* 2.8 27.6 + - - +
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Residues in contact with LEU 279 (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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275C GLN 3.2 10.5 + - - +
276C LEU* 3.1 15.6 + - + +
278C THR* 1.3 82.7 + - - +
280C VAL* 1.3 56.7 + - - +
282C TRP* 3.1 9.9 + - + +
283C ALA* 2.9 29.4 + - + +
305C TRP* 3.9 24.2 - - + -
308C LEU* 3.4 27.4 - - + -
309C LEU* 3.9 20.9 - - + -
371C ARG* 3.3 41.3 - - - +
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Residues in contact with VAL 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU 3.1 16.1 + - - +
277C PHE 3.0 8.7 - - - +
279C LEU* 1.3 76.4 - - - +
281C GLU* 1.3 68.2 + - - +
283C ALA* 2.9 17.8 + - - +
284C LYS* 3.0 33.1 + - + +
301C LEU* 5.9 5.2 - - + -
450C PHE* 3.9 10.3 - - + -
633G LEU* 4.8 9.2 - - + -
636G LEU* 3.5 46.4 - - + -
637G LEU* 4.6 10.3 - - + +
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Residues in contact with GLU 281 (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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242C VAL* 5.2 4.7 - - + -
277C PHE 3.3 8.7 + - - +
278C THR* 3.2 12.7 + - - +
280C VAL* 1.3 83.9 - - - +
282C TRP* 1.3 63.3 + - - +
284C LYS* 3.3 33.7 + - - +
285C ARG* 3.0 49.6 + - - +
636G LEU* 5.0 1.0 - - - +
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Residues in contact with TRP 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C ILE* 5.1 0.8 + - + -
238C ALA* 3.5 26.0 + - - +
239C GLU* 2.9 28.4 + - - +
242C VAL* 4.0 17.9 - - + +
278C THR 2.8 14.0 + - - +
279C LEU* 3.1 24.5 - - + +
280C VAL 3.1 0.2 - - - -
281C GLU* 1.3 77.9 - - - +
283C ALA* 1.3 74.9 + - + +
285C ARG* 3.6 10.8 + - - +
286C ILE* 3.3 28.7 - - + +
308C LEU* 4.2 15.3 - - + -
368C GLY* 3.9 10.1 - - - -
371C ARG* 2.9 73.4 - - + +
372C ALA* 3.9 4.3 - - - -
375C LEU* 4.2 17.0 - - + -
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Residues in contact with ALA 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LEU 2.9 12.3 + - - +
280C VAL* 2.9 10.3 + - - +
282C TRP* 1.3 80.8 - - + +
284C LYS* 1.3 67.6 + - - +
286C ILE* 2.9 29.1 + - - +
289C PHE* 3.2 34.8 - - + +
301C LEU* 4.5 8.7 - - + -
375C LEU* 4.1 11.4 - - + -
637G LEU* 5.9 0.4 - - + -
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Residues in contact with LYS 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C VAL* 3.0 22.1 + - + +
281C GLU* 3.4 34.8 + - - +
283C ALA* 1.3 75.7 - - - +
285C ARG* 1.3 57.3 + - + +
286C ILE 2.7 19.6 + - - +
289C PHE* 3.9 4.0 - - - +
290C SER* 3.7 28.0 + - - +
636G LEU 2.7 29.6 + - - -
637G LEU* 3.8 22.9 - - + +
638G GLN 3.9 5.1 + - - +
639G GLU* 3.2 23.4 + - - +
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Residues in contact with ARG 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ARG* 3.7 11.1 - - - +
237C GLU 5.4 0.2 - - - -
238C ALA* 2.9 34.9 - - + +
241C ALA* 4.5 27.5 + - - +
242C VAL* 5.5 2.2 - - - -
281C GLU* 3.0 34.8 + - - +
282C TRP* 3.7 5.6 - - - +
283C ALA 3.2 0.2 - - - -
284C LYS* 1.3 77.7 - - + +
286C ILE* 1.3 57.8 + - - +
287C PRO* 4.0 1.3 - - - +
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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