Contacts of the helix formed by residues 261 - 282 (chain C) in PDB entry 3COG
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 THR 261 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B HIS* 3.7 23.5 + - - +
261B THR* 3.9 9.3 - - - +
265B ARG* 3.8 27.8 - - + -
344B PHE* 5.9 1.1 - - + -
380B LEU* 4.7 2.9 - - + -
217C HIS* 3.7 9.5 - - - -
257C ARG 4.2 0.7 + - - -
258C GLY* 3.1 7.0 + - - -
260C LYS* 1.3 80.0 - - - +
262C LEU* 1.3 65.6 + - - +
263C HIS* 3.3 2.9 - - - -
264C VAL* 3.3 15.5 + - + -
265C ARG* 2.9 47.6 + - - +
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Residues in contact with LEU 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C PHE* 3.7 29.4 - - + -
78C LEU* 4.3 4.5 - - + -
192C SER* 4.2 10.1 - - - +
193C PRO* 4.4 6.3 - - + -
194C TYR* 4.7 0.7 - - + -
213C TYR 3.6 25.8 - - - +
214C MET* 4.3 14.4 - - - +
258C GLY 3.6 1.6 + - - -
259C LEU* 3.0 36.5 + - + +
260C LYS 3.6 0.6 - - - -
261C THR* 1.3 76.3 - - - +
263C HIS* 1.3 58.9 + - - +
265C ARG* 3.5 14.8 - - - +
266C MET* 2.8 65.0 + - + +
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Residues in contact with HIS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B LYS* 4.7 8.5 - - - -
380B LEU* 2.8 33.2 + - + +
18C PHE* 4.4 9.4 - - + -
19C ALA* 3.3 28.0 - - + +
22C ALA* 5.2 3.0 - - + +
23C ILE* 4.5 4.5 - - + -
194C TYR* 3.6 34.2 - - + +
259C LEU 5.0 1.2 + - - -
260C LYS 3.4 26.6 + - - -
261C THR* 4.0 2.8 - - - -
262C LEU* 1.3 79.5 + - - +
264C VAL* 1.3 84.2 + - + +
266C MET* 3.9 1.0 - - - +
267C GLU* 3.1 34.7 + - - +
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Residues in contact with VAL 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B VAL* 3.7 38.3 - - + +
265B ARG* 4.6 3.8 - - + +
268B LYS* 3.8 36.3 - - + -
380B LEU* 5.1 2.9 - - + -
261C THR* 3.3 31.2 - - + +
263C HIS* 1.3 99.4 - - + +
265C ARG* 1.3 64.5 + - - +
267C GLU* 4.1 5.6 - - - +
268C LYS* 3.4 21.1 + - - +
271C LYS* 5.0 1.4 + - - -
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Residues in contact with ARG 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B THR* 3.9 18.4 - - + -
264B VAL* 4.6 2.5 - - + -
213C TYR* 3.0 20.0 + - - +
214C MET 3.1 21.6 + - - -
215C ASN 3.6 8.4 + - - -
216C GLY* 3.5 14.9 - - - -
217C HIS* 3.8 10.0 - - - -
258C GLY 3.0 21.6 + - - -
261C THR* 2.9 34.8 + - - +
262C LEU* 3.5 22.0 - - - +
264C VAL* 1.3 75.4 - - - +
266C MET* 1.3 64.1 + - - +
268C LYS 3.1 2.9 + - - -
269C HIS* 2.8 39.9 + - + -
342C GLY 4.5 4.6 + - - -
343C GLY 6.5 0.2 - - - -
344C PHE* 5.9 0.9 - - - -
380C LEU* 3.4 30.1 - - + +
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Residues in contact with MET 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C MET 3.8 16.6 - - - +
192C SER* 3.6 11.2 - - - +
194C TYR* 3.6 21.1 - - + -
195C PHE* 3.5 21.2 - - + -
213C TYR* 3.5 35.2 - - + -
262C LEU* 2.8 53.8 + - + +
265C ARG* 1.3 74.8 - - - +
267C GLU* 1.3 62.7 + - - +
269C HIS* 3.2 10.4 + - + +
270C PHE 3.0 19.1 + - - -
311C THR* 3.2 28.0 - - - +
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Residues in contact with GLU 267 (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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268B LYS* 6.1 2.5 - - - +
14C HIS* 3.0 24.6 + - - -
194C TYR* 2.5 35.8 + - - +
195C PHE* 4.8 0.9 - - - -
263C HIS 3.1 18.0 + - - +
264C VAL* 4.1 6.1 - - - +
266C MET* 1.3 75.7 - - - +
268C LYS* 1.3 58.3 + - - +
270C PHE* 3.3 20.6 + - - +
271C LYS* 3.1 44.1 + - + +
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Residues in contact with LYS 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B ALA* 5.8 0.6 - - - +
263B HIS* 5.1 7.0 - - + +
264B VAL* 3.9 18.6 - - + -
264C VAL 3.4 11.4 + - - +
265C ARG 3.1 7.9 + - - +
267C GLU* 1.3 74.7 - - - +
269C HIS* 1.3 60.6 + - - +
271C LYS* 3.3 31.2 + - - +
272C ASN* 2.9 66.7 + - - +
380C LEU* 3.6 25.6 + - + +
381C GLU 4.2 8.3 + - - -
382C ASP* 5.0 4.8 + - - +
383C GLU* 4.7 7.5 - - - +
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Residues in contact with HIS 269 (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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213C TYR* 3.4 34.1 - + + -
265C ARG* 2.8 40.2 + - + +
266C MET* 3.5 15.3 - - + +
268C LYS* 1.3 72.1 - - - +
270C PHE* 1.3 53.2 + - - +
272C ASN* 4.2 0.4 - - - +
273C GLY* 2.8 32.2 + - - -
311C THR 4.4 0.9 - - - -
312C GLY* 3.6 22.6 - - - +
342C GLY 4.0 3.8 + - - -
343C GLY 3.3 27.5 + - - -
377C SER* 5.7 0.9 - - - -
378C VAL 2.8 27.4 + - - +
379C GLY* 3.7 4.5 - - - -
380C LEU* 3.5 23.9 - - + +
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Residues in contact with PHE 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C PHE* 4.2 21.5 - + - -
14C HIS* 6.1 1.1 - - - -
195C PHE* 3.9 9.0 - + + -
266C MET 3.0 10.8 + - - +
267C GLU* 3.4 20.0 - - - +
269C HIS* 1.3 73.8 - - - +
271C LYS* 1.3 62.2 + - - +
274C MET* 2.9 45.7 + - + +
291C TYR* 3.6 7.6 - - - -
293C GLY* 5.3 0.4 - - - -
308C THR 4.7 2.5 - - - -
309C GLY* 3.6 20.9 - - - -
310C CYS* 2.9 49.5 + - + +
311C THR 4.2 1.8 - - - -
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Residues in contact with LYS 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B VAL* 5.4 2.8 - - - +
264C VAL 5.0 1.0 + - - -
267C GLU* 3.1 27.1 + - + +
268C LYS* 3.3 51.1 + - + +
270C PHE* 1.3 80.7 - - - +
272C ASN* 1.3 62.1 + - - +
274C MET* 3.6 4.0 + - - +
275C ALA* 3.1 23.7 + - - +
383C GLU* 4.4 5.9 - - - +
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Residues in contact with ASN 272 (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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268C LYS* 2.9 39.4 + - - +
269C HIS 4.2 1.1 - - - +
271C LYS* 1.3 74.8 - - - +
273C GLY* 1.3 60.0 + - - +
275C ALA* 3.3 6.7 + - - +
276C VAL* 2.9 32.7 + - - +
378C VAL* 3.5 17.7 - - + -
379C GLY 2.9 21.2 + - - +
380C LEU* 3.8 2.4 - - - +
381C GLU 2.8 25.7 + - - -
383C GLU* 3.5 24.5 - - - +
386C LEU* 3.7 9.7 - - + +
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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
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269C HIS 2.8 23.1 + - - -
270C PHE 3.9 0.2 - - - -
272C ASN* 1.3 73.8 - - - +
274C MET* 1.3 54.8 - - - +
276C VAL* 3.3 0.9 + - - +
277C ALA* 2.8 30.0 + - - +
291C TYR* 3.9 12.6 - - - -
311C THR 4.2 3.4 - - - -
312C GLY* 4.4 0.2 - - - -
314C VAL* 3.6 18.3 - - - +
378C VAL* 4.0 10.9 - - - +
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Residues in contact with MET 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270C PHE* 2.9 31.6 + - + +
271C LYS* 3.9 5.2 - - - +
273C GLY* 1.3 72.3 - - - +
275C ALA* 1.3 67.0 + - - +
277C ALA* 3.3 1.6 + - - +
278C GLN* 3.0 62.4 + - + +
291C TYR* 3.7 23.9 + - + +
293C GLY* 3.3 31.0 - - - +
294C LEU* 4.5 4.3 - - + -
295C PRO* 5.4 3.4 - - + -
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Residues in contact with ALA 275 (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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271C LYS 3.1 14.1 + - - +
272C ASN 3.6 4.7 - - - +
274C MET* 1.3 79.0 - - - +
276C VAL* 1.3 56.1 + - - +
278C GLN* 3.6 10.0 + - - +
279C PHE* 3.0 29.1 + - - +
383C GLU* 3.5 38.8 - - + +
387C LEU* 3.8 9.4 - - + +
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Residues in contact with VAL 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C ASN* 2.9 21.1 + - - +
273C GLY 3.6 3.4 - - - +
275C ALA* 1.3 73.5 - - - +
277C ALA* 1.3 67.1 + - - +
279C PHE* 3.2 2.9 + - - +
280C LEU* 2.9 43.9 + - + +
314C VAL* 4.1 5.8 - - + -
335C PHE* 4.7 0.4 - - + -
376C LEU* 3.8 12.8 - - + -
378C VAL* 3.8 28.7 - - + -
383C GLU* 6.4 0.7 - - + -
386C LEU* 4.7 10.5 - - + -
387C LEU* 3.8 15.0 - - + -
390C LEU* 3.8 24.0 - - + -
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Residues in contact with ALA 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 GLY 2.8 20.6 + - - +
274C MET 3.7 3.4 - - - +
276C VAL* 1.3 73.8 - - - +
278C GLN* 1.3 57.8 + - - +
280C LEU* 3.3 2.9 + - - +
281C GLU* 2.9 30.3 + - - +
289C VAL* 3.9 2.2 - - - +
291C TYR* 3.5 41.1 - - + -
294C LEU* 3.8 12.8 - - + +
314C VAL* 4.0 14.6 - - + -
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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
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274C MET* 3.0 52.3 + - + +
275C ALA* 3.9 7.6 - - - +
277C ALA* 1.3 72.8 - - - +
279C PHE* 1.3 65.0 + - - +
281C GLU* 3.4 4.3 + - - +
282C SER* 3.3 24.3 + - - -
294C LEU* 3.6 21.9 - - + +
295C PRO* 6.1 1.0 - - - +
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Residues in contact with PHE 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 ALA 3.0 19.1 + - - +
276C VAL 3.5 3.1 - - - +
278C GLN* 1.3 76.6 - - - +
280C LEU* 1.3 72.6 + - + +
282C SER* 3.4 7.2 + - - -
283C ASN* 3.3 39.3 + - + +
387C LEU* 3.6 35.0 - - + -
390C LEU* 4.0 11.7 - - + -
391C ASP* 3.5 52.3 - - + -
394C LEU* 4.3 7.9 - - + -
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Residues in contact with LEU 280 (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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276C VAL* 2.9 39.2 + - + +
277C ALA 3.7 1.3 - - - +
279C PHE* 1.3 85.6 - - + +
281C GLU* 1.3 62.0 + - - +
283C ASN* 3.1 13.1 + - - +
286C VAL* 3.3 30.2 - - + +
289C VAL* 3.6 14.4 - - + -
314C VAL* 3.9 12.6 - - + -
316C PHE* 3.7 34.1 - - + -
376C LEU* 3.8 7.9 - - + -
390C LEU* 4.5 9.9 - - + -
394C LEU* 3.8 27.4 - - + -
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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
----------------------------------------------------------
277C ALA 2.9 16.9 + - - +
278C GLN* 4.1 5.4 - - - +
279C PHE 3.3 0.6 - - - -
280C LEU* 1.3 77.7 - - - +
282C SER* 1.3 59.0 + - - +
283C ASN 3.2 3.4 + - - +
286C VAL* 5.0 2.9 - - - +
288C LYS* 6.2 0.2 - - - -
289C VAL* 3.4 26.0 + - + +
294C LEU* 3.7 21.6 - - + +
295C PRO* 5.8 0.9 - - - +
296C SER* 2.6 36.3 + - - -
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Residues in contact with SER 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C GLN 3.3 14.7 + - - -
279C PHE* 3.7 7.1 + - - -
280C LEU 3.2 0.8 - - - -
281C GLU* 1.3 77.1 - - - +
283C ASN* 1.3 59.8 + - - +
284C PRO* 3.8 6.2 - - - +
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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
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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) + - + + + + + -
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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