Contacts of the helix formed by residues 267 - 289 (chain A) in PDB entry 1TQ6
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 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A CYS* 3.6 22.4 - - + +
241A PRO* 4.1 16.9 - - + +
266A ILE* 1.3 94.0 - - + +
268A ASP* 1.3 64.3 + - - +
269A SER* 3.5 9.6 + - - -
270A VAL* 3.0 27.3 + - - +
271A ILE* 3.1 26.3 + - - +
406A LEU* 3.7 10.3 - - - -
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Residues in contact with ASP 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A THR* 1.3 74.9 - - - +
269A SER* 1.3 53.8 + - - +
271A ILE* 3.3 6.8 + - - +
272A GLU* 2.7 37.2 + - - +
403A LYS* 3.5 40.6 - - - +
406A LEU* 3.5 17.1 - - - +
407A LYS* 6.1 0.7 - - - +
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Residues in contact with SER 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 5.8 4.9 + - - -
241A PRO* 6.4 1.6 - - - -
267A THR* 3.2 8.5 + - - -
268A ASP* 1.3 77.8 - - - +
270A VAL* 1.3 56.6 + - - +
272A GLU* 3.6 6.4 - - - +
273A LYS* 2.7 36.7 + - - +
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Residues in contact with VAL 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A PRO* 5.4 4.5 - - + -
244A MET* 3.4 28.5 - - + -
245A ASP* 6.2 0.2 - - - +
260A MET* 3.8 17.9 - - + +
263A LEU* 4.3 13.7 - - + +
264A PRO 3.5 21.5 - - - +
265A ASN* 4.6 2.5 - - - -
266A ILE* 3.9 6.5 - - + +
267A THR* 3.0 26.3 + - + +
269A SER* 1.3 76.0 - - - +
271A ILE* 1.3 65.2 + - - +
273A LYS* 3.1 8.5 + - - +
274A LYS* 2.9 26.7 + - - +
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Residues in contact with ILE 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A ASN* 3.9 30.7 - - + +
267A THR 3.1 15.4 + - - +
268A ASP* 3.5 7.4 - - - +
270A VAL* 1.3 76.3 - - - +
272A GLU* 1.3 62.4 + - - +
274A LYS* 3.1 17.4 + - - +
275A ARG* 3.1 11.8 + - - +
320A PHE* 3.5 24.6 - - + -
399A THR* 3.9 24.9 - - + +
402A ALA* 3.9 29.4 - - + +
403A LYS* 4.1 10.5 - - + +
406A LEU* 4.1 19.1 - - + -
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Residues in contact with GLU 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A ASP 2.7 21.7 + - - +
269A SER* 3.7 8.1 - - - +
271A ILE* 1.3 74.6 - - - +
273A LYS* 1.3 62.7 + - - +
275A ARG* 2.8 39.7 + - - +
276A GLN* 3.2 47.9 + - + +
399A THR* 4.2 0.9 - - - +
403A LYS* 2.9 24.6 + - - +
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Residues in contact with LYS 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 5.3 1.7 + - - -
31A ARG* 3.5 52.2 - - + +
245A ASP* 3.8 28.6 + - - +
248A ILE* 4.2 24.7 - - - +
260A MET* 3.6 28.7 - - + -
269A SER 2.7 20.9 + - - +
270A VAL* 3.4 6.5 - - - +
272A GLU* 1.3 74.1 - - - +
274A LYS* 1.3 62.4 + - - +
276A GLN* 3.4 6.6 + - - +
277A PHE* 3.2 40.1 + - + -
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Residues in contact with LYS 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A MET* 3.2 38.6 - - + +
261A VAL* 3.4 22.1 + - + +
262A SER 4.6 0.4 + - - -
263A LEU* 2.9 25.2 + - - +
265A ASN* 2.8 25.2 + - - +
270A VAL* 2.9 17.9 + - - +
271A ILE* 3.1 10.3 + - - +
273A LYS* 1.3 78.8 - - - +
275A ARG* 1.3 62.7 + - - +
277A PHE* 3.3 3.7 + - - +
278A LEU* 3.1 28.1 + - + +
319A VAL* 2.6 35.9 + - + +
320A PHE* 3.8 15.3 - - + -
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Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ILE 3.1 9.0 + - - +
272A GLU* 2.8 52.5 + - - +
273A LYS 3.3 0.4 - - - -
274A LYS* 1.3 76.8 - - - +
276A GLN* 1.3 68.3 + - - +
278A LEU* 3.3 1.4 + - - -
279A LYS* 2.9 52.2 + - + +
320A PHE* 3.9 7.5 - - - -
395A LEU* 3.7 13.7 - - + +
396A ASP* 3.0 38.6 + - - +
399A THR* 3.4 41.0 + - + +
400A GLU* 4.5 8.7 + - - +
403A LYS* 4.7 2.8 - - - +
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Residues in contact with GLN 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A LYS 4.7 3.3 - - - +
27A PHE* 3.1 36.5 - - + -
31A ARG* 5.5 12.1 - - + +
272A GLU* 3.2 35.4 + - + +
273A LYS* 3.8 9.2 - - - +
274A LYS 3.3 0.2 - - - -
275A ARG* 1.3 95.1 - - - +
277A PHE* 1.3 65.4 + - + +
279A LYS* 3.3 25.4 + - - +
280A GLN* 3.4 21.4 + - - +
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Residues in contact with PHE 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLY 4.7 3.6 - - - -
31A ARG* 4.0 33.7 - - + -
32A LYS 4.4 3.6 - - - -
33A ILE* 3.1 37.5 - - + +
248A ILE* 5.0 2.9 - - + -
256A ARG* 3.9 19.1 - - + -
257A HIS* 3.9 40.8 - + + -
260A MET* 3.8 24.7 - - + -
261A VAL* 5.3 2.5 - - + -
273A LYS* 3.2 35.9 + - + +
274A LYS* 3.5 9.9 - - - +
275A ARG 3.2 0.4 - - - -
276A GLN* 1.3 78.2 - - + +
278A LEU* 1.3 62.5 + - + +
280A GLN* 3.1 21.0 + - - +
281A ARG* 3.2 8.3 + - - +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A HIS* 3.7 26.9 - - + +
261A VAL* 4.3 11.7 - - + -
274A LYS 3.1 16.3 + - - +
277A PHE* 1.3 72.5 - - - +
279A LYS* 1.3 60.3 + - - +
280A GLN 3.0 2.2 - - - -
281A ARG* 3.6 16.3 - - - +
282A ILE* 3.0 32.6 + - - +
315A PHE* 4.3 13.2 - - + -
316A TYR* 4.5 18.2 - - + -
319A VAL* 4.4 14.4 - - + -
320A PHE* 3.9 26.5 - - + -
395A LEU* 3.7 20.6 - - + -
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Residues in contact with LYS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 3.2 30.8 + - - +
27A PHE* 4.7 5.6 - - + -
275A ARG* 2.9 38.9 + - + +
276A GLN* 3.7 36.4 + - - +
277A PHE 3.2 0.2 - - - -
278A LEU* 1.3 76.5 - - - +
280A GLN* 1.3 60.2 + - - +
282A ILE 4.1 0.7 - - - -
283A TRP 3.7 3.3 + - - -
392A TYR* 3.3 34.0 + - + -
395A LEU* 3.6 15.7 - - + -
396A ASP* 4.8 9.5 + - - +
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Residues in contact with GLN 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A TYR* 4.5 5.8 - - + -
24A PHE* 3.3 28.8 - - + -
27A PHE* 3.4 45.6 - - + -
31A ARG 2.7 27.7 + - - -
32A LYS* 3.5 4.8 - - - +
33A ILE* 3.3 35.0 + - + +
276A GLN 3.5 12.4 + - - +
277A PHE 3.1 8.2 + - - +
278A LEU 3.0 0.4 - - - -
279A LYS* 1.3 78.6 - - - +
281A ARG* 1.3 62.8 + - - +
283A TRP* 3.6 3.0 + - - +
284A LEU* 3.2 27.0 + - - +
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Residues in contact with ARG 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ILE* 4.0 12.5 - - + +
62A LEU* 4.3 27.3 - - + +
65A ILE* 5.0 2.6 - - - +
66A ASP* 2.6 42.2 + - - -
257A HIS* 3.7 27.5 + - - +
277A PHE 3.2 10.5 + - - +
278A LEU* 3.2 20.7 + - + +
280A GLN* 1.3 76.7 - - - +
282A ILE* 1.3 61.1 + - + +
284A LEU* 3.2 6.4 + - - +
285A GLU* 2.7 70.4 + - + +
315A PHE* 5.6 6.3 - - - -
316A TYR* 6.4 1.1 - - - -
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Residues in contact with ILE 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A LEU 3.0 16.7 + - - +
280A GLN 3.4 0.2 - - - -
281A ARG* 1.3 78.9 - - + +
283A TRP* 1.3 50.7 + - - +
285A GLU* 3.2 12.6 + - - +
286A GLY* 2.6 33.8 + - - -
316A TYR* 3.5 25.8 - - - +
384A LEU* 5.5 0.6 - - + +
388A PHE* 3.7 32.6 - - + +
391A LYS* 3.8 7.9 - - + -
392A TYR* 3.6 54.7 - - + +
395A LEU* 3.7 15.3 - - + -
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Residues in contact with TRP 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A SER* 3.6 15.3 - - - -
20A PHE* 3.0 32.4 + + - -
23A TYR* 3.2 54.0 - + + +
24A PHE* 3.6 19.1 - + - -
279A LYS 3.7 1.0 + - - +
280A GLN 3.6 6.9 + - - +
281A ARG 3.3 0.2 - - - -
282A ILE* 1.3 78.5 - - - +
284A LEU* 1.3 63.3 + - - +
286A GLY* 3.2 2.8 + - - -
287A PHE* 3.0 51.6 + + - -
377A LEU* 3.7 35.7 - - + -
378A LEU* 3.6 24.0 - - + -
384A LEU* 4.4 14.1 - - + -
392A TYR* 3.5 25.6 + - - +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 4.1 20.0 - - + -
24A PHE* 3.8 24.0 - - + -
33A ILE* 3.8 23.8 - - + -
34A ILE* 4.3 20.2 - - + -
42A ILE* 4.5 3.4 - - + -
58A ILE* 3.5 29.0 - - + +
61A ALA* 5.9 3.4 - - + -
62A LEU* 3.7 25.6 - - + -
65A ILE* 4.9 2.9 - - + -
280A GLN 3.2 15.9 + - - +
281A ARG* 3.2 7.1 + - - +
283A TRP* 1.3 80.9 - - - +
285A GLU* 1.3 61.8 + - - +
287A PHE* 3.3 1.6 + - - +
288A ALA 3.0 19.2 + - - -
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 4.0 13.5 - - + -
281A ARG* 2.7 55.1 + - - +
282A ILE* 3.6 19.6 + - - +
284A LEU* 1.3 73.6 - - - +
286A GLY* 1.3 62.5 + - - +
288A ALA* 3.5 6.5 + - - +
289A ALA* 3.1 25.3 + - - +
316A TYR* 4.9 1.6 + - - -
388A PHE* 3.5 15.1 - - + -
391A LYS* 3.3 27.1 + - - +
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A ILE 2.6 20.3 + - - -
283A TRP 3.2 2.7 + - - -
285A GLU* 1.3 75.1 - - - +
287A PHE* 1.3 59.1 + - - +
289A ALA* 3.5 4.9 + - - +
290A ASP 3.5 15.1 + - - +
291A LEU* 4.1 8.0 - - - +
384A LEU* 4.1 16.9 - - - +
385A LYS 5.3 0.3 + - - -
388A PHE* 3.6 26.6 - - - -
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Residues in contact with PHE 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 3.5 29.2 - - + -
20A PHE* 3.4 43.1 - + + -
46A MET* 3.9 13.2 - - + -
54A THR* 5.4 1.0 + - - -
55A ASN* 3.6 5.9 - - - +
58A ILE* 3.9 16.6 - - + +
283A TRP* 3.0 58.1 + + - +
284A LEU 4.0 0.2 - - - +
286A GLY* 1.3 71.9 - - - +
288A ALA* 1.3 59.5 + - - +
289A ALA 2.8 4.9 - - - -
290A ASP* 2.8 23.0 + - - +
291A LEU* 4.0 13.7 - - + -
378A LEU* 3.6 25.6 - - + -
384A LEU* 4.2 9.2 - - + -
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ASN* 3.0 35.7 - - + +
58A ILE* 3.4 29.3 - - + +
59A SER* 4.9 4.0 - - - +
62A LEU* 5.6 2.2 - - + -
284A LEU 3.0 17.0 + - - +
285A GLU* 4.0 7.0 - - - +
287A PHE* 1.3 76.6 - - - +
289A ALA* 1.3 57.3 + - - +
290A ASP* 4.1 1.2 - - - +
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A GLU 3.1 17.6 + - - +
286A GLY 3.5 2.2 - - - +
287A PHE 2.8 0.8 - - - -
288A ALA* 1.3 79.4 - - - +
290A ASP* 1.3 66.9 + - - +
385A LYS* 2.7 35.8 + - + +
388A PHE* 3.3 30.1 - - + -
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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