Contacts of the helix formed by residues 270 - 298 (chain A) in PDB entry 1YG1
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 ARG 270 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A LEU* 3.7 26.3 + - - +
267A LYS 4.0 5.6 - - - +
268A LEU 3.3 6.7 + - - +
269A PHE* 1.3 76.1 + - - +
271A MET* 1.3 67.3 + - - +
272A ARG* 4.0 32.4 - - + +
273A SER* 3.2 39.4 + - - +
274A LEU* 3.4 11.8 + - - +
276A TRP* 6.0 6.5 - - - -
400A THR* 3.5 21.8 + - - +
401A GLU* 3.3 32.2 + - - -
404A LEU* 5.0 3.6 - - - -
466A LYS* 4.5 16.9 - - - +
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Residues in contact with MET 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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270A ARG* 1.3 74.4 - - - +
272A ARG* 1.3 65.2 + - + +
274A LEU* 3.2 21.7 + - - +
275A ARG* 3.4 16.7 + - + +
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Residues in contact with ARG 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ARG* 3.2 29.8 - - + +
271A MET* 1.3 77.7 - - + +
273A SER* 1.3 66.9 + - - +
275A ARG* 3.3 40.6 + - - +
276A TRP* 3.5 23.7 - - + +
462A GLU* 3.0 42.8 + - + +
466A LYS* 4.0 23.4 - - - +
470A GLU* 5.7 3.4 + - - -
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Residues in contact with SER 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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267A LYS* 4.1 20.9 + - - +
270A ARG* 3.2 36.8 + - - +
271A MET 3.2 0.6 - - - -
272A ARG* 1.3 81.9 - - - +
274A LEU* 1.3 56.8 + - - +
276A TRP* 3.2 22.4 + - - +
277A GLN* 2.6 39.6 + - - +
404A LEU* 6.1 0.5 - - - +
407A SER* 5.3 7.1 - - - -
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A LYS* 5.3 8.1 - - - +
270A ARG 3.4 6.8 + - - +
271A MET* 3.2 18.0 + - - +
273A SER* 1.3 78.1 - - - +
275A ARG* 1.3 65.5 + - - +
276A TRP 3.2 0.2 + - - -
277A GLN* 3.2 18.1 + - + +
278A LEU* 3.1 46.2 + - + +
414A VAL* 5.5 6.5 - - + -
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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
----------------------------------------------------------
271A MET* 3.6 15.1 - - - +
272A ARG* 3.5 33.8 - - - +
273A SER 3.2 1.0 - - - -
274A LEU* 1.3 77.4 - - - +
276A TRP* 1.3 66.2 + - + +
278A LEU* 3.1 17.2 + - + +
279A LEU* 2.9 25.7 + - - +
455A TYR* 4.7 22.9 + - + +
458A LEU* 3.6 19.7 + - - +
459A ILE* 3.7 17.6 - - + +
462A GLU* 3.3 39.4 + - - +
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Residues in contact with TRP 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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270A ARG* 6.0 6.3 - - - -
272A ARG* 3.5 21.0 + - + +
273A SER* 3.7 16.8 - - - -
274A LEU 3.2 0.2 - - - -
275A ARG* 1.3 82.4 - - + +
277A GLN* 1.3 79.7 + - - +
279A LEU* 2.7 29.9 - - + +
280A SER* 2.9 14.6 + - - +
392A SER 5.6 2.2 - - - +
395A PRO* 5.3 1.8 - - + -
396A ALA* 3.1 50.5 - - + -
399A ILE* 4.3 17.5 - - + -
400A THR* 5.7 3.1 - - - -
407A SER* 5.6 3.8 - - - -
459A ILE* 2.8 58.0 - - + +
462A GLU* 5.5 1.5 + - - -
463A THR* 4.7 11.7 - - + -
466A LYS* 4.8 6.7 - - - -
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Residues in contact with GLN 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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267A LYS* 4.3 16.3 - - - +
273A SER* 2.6 41.7 + - - +
274A LEU* 3.2 15.9 + - + +
276A TRP* 1.3 88.6 - - - +
278A LEU* 1.3 64.3 + - - +
280A SER* 3.0 20.4 + - - -
281A ILE* 3.0 19.3 + - - +
407A SER 5.9 0.7 - - - -
410A SER* 4.4 1.3 - - - +
411A ALA* 3.8 33.5 - - + +
414A VAL* 3.6 30.3 - - + -
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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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274A LEU* 3.1 45.7 + - + +
275A ARG* 3.1 16.8 + - + +
277A GLN* 1.3 78.3 - - + +
279A LEU* 1.3 62.0 + - - +
281A ILE* 3.2 24.7 + - + +
282A ILE* 3.6 10.3 + - - +
414A VAL* 5.5 4.3 - - + -
418A VAL* 6.0 3.6 - - + -
455A TYR* 5.6 15.7 - - + +
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Residues in contact with LEU 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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275A ARG 2.9 24.6 + - - +
276A TRP* 2.7 37.0 + - + +
278A LEU* 1.3 72.9 - - - +
280A SER* 1.3 90.1 + - - +
282A ILE* 2.7 26.9 - - - +
283A VAL* 3.1 8.0 + - + -
392A SER* 5.5 0.9 - - - +
452A THR* 3.7 29.9 - - + +
455A TYR* 3.4 30.9 - - + -
456A ILE* 4.1 13.2 - - + -
459A ILE* 3.3 17.7 - - + -
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Residues in contact with SER 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A TRP* 2.9 18.3 + - - +
277A GLN* 3.0 14.7 + - - -
279A LEU* 1.3 84.4 - - - +
281A ILE* 1.3 61.0 + - - +
283A VAL* 2.7 31.8 - - - +
284A LEU* 2.9 9.2 + - - +
389A LEU* 6.6 0.2 - - - -
392A SER* 2.9 28.3 + - - -
411A ALA* 5.2 6.5 - - - +
415A GLY* 4.9 10.1 - - - -
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Residues in contact with ILE 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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277A GLN 3.0 14.7 + - - +
278A LEU* 3.4 16.2 - - + +
279A LEU 3.1 0.2 - - - -
280A SER* 1.3 76.1 - - - +
282A ILE* 1.3 58.5 + - + +
284A LEU* 3.1 9.5 + - - +
285A MET* 3.0 36.2 + - + +
414A VAL* 2.9 34.3 - - + +
415A GLY* 2.9 23.1 - - - +
418A VAL* 2.9 49.6 - - + +
419A HIS* 3.3 17.7 + - - +
422A SER* 4.7 1.6 - - - +
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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 4.0 7.0 - - - +
279A LEU* 2.7 32.5 - - + +
281A ILE* 1.3 81.2 - - + +
283A VAL* 1.3 61.9 + - - +
285A MET* 2.9 34.6 + - + +
286A GLY 3.5 3.1 + - - -
448A ILE* 2.8 39.3 - - + +
449A CYS* 5.0 2.1 + - - -
451A LEU* 3.3 17.5 - - + -
452A THR* 2.8 46.8 + - - +
455A TYR* 4.3 4.3 - - + -
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 3.1 6.1 + - + -
280A SER* 2.7 36.8 - - - +
282A ILE* 1.3 76.1 - - - +
284A LEU* 1.3 64.0 + - + +
286A GLY 3.1 11.1 + - - -
287A GLY 3.6 1.7 + - - -
352A CYS* 5.0 1.3 - - - -
384A VAL* 3.2 48.6 - - + +
388A ALA* 3.5 31.6 - - + +
389A LEU* 5.5 5.2 - - + +
392A SER* 6.1 2.0 - - - -
449A CYS* 5.9 2.2 - - - +
452A THR* 3.8 22.9 - - + -
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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
----------------------------------------------------------
280A SER 2.9 8.9 + - - +
281A ILE* 3.3 10.3 - - - +
283A VAL* 1.3 81.8 - - + +
285A MET* 1.3 65.2 + - - +
287A GLY* 3.0 11.7 + - - +
288A GLN* 3.3 7.2 + - + +
384A VAL 5.2 2.7 - - - +
385A ILE 5.0 11.0 - - - +
389A LEU* 4.6 22.2 - - + -
415A GLY* 3.5 18.6 - - - +
416A GLY* 4.0 7.6 - - - +
419A HIS* 2.9 48.8 - - + +
420A TRP* 5.4 1.8 - - + +
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Residues in contact with MET 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ILE* 3.0 13.1 + - + +
282A ILE* 2.9 57.7 - - + +
283A VAL 3.1 0.4 - - - -
284A LEU* 1.3 74.9 - - - +
286A GLY* 1.3 59.3 + - - +
289A GLN* 2.7 63.7 + - + +
419A HIS* 2.9 29.0 + - + +
422A SER* 3.9 25.8 - - - +
423A ASN 4.6 0.7 - - - -
426A VAL* 5.4 1.3 - - - -
448A ILE* 3.3 29.4 - - + -
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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 3.5 4.2 + - - -
283A VAL 3.1 9.8 + - - -
285A MET* 1.3 78.2 - - - +
287A GLY* 1.3 57.8 + - - +
289A GLN* 4.1 3.3 - - - +
290A LEU* 2.9 31.4 - - - +
359A LEU* 6.1 3.6 - - - -
380A VAL* 3.8 3.4 - - - +
384A VAL* 3.7 16.6 - - - -
385A ILE* 3.4 3.6 - - - +
445A PHE* 5.6 3.6 - - - -
448A ILE* 5.3 0.4 - - - +
449A CYS* 5.0 12.3 - - - -
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Residues in contact with GLY 287 (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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283A VAL 3.6 5.5 + - - -
284A LEU* 3.0 9.0 + - - -
286A GLY* 1.3 81.4 - - - +
288A GLN* 1.3 56.4 + - - +
291A SER* 3.2 19.4 + - - -
385A ILE* 2.9 53.0 - - - +
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Residues in contact with GLN 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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40A ASN* 4.4 10.7 + - - -
284A LEU* 3.3 8.2 + - + +
287A GLY* 1.3 69.4 - - - +
289A GLN* 1.3 57.4 + - - +
290A LEU 3.0 1.8 - - - -
291A SER* 2.7 22.2 + - - -
292A GLY* 2.7 45.7 + - - +
419A HIS* 2.8 31.6 - - + +
420A TRP* 4.4 30.7 - - + -
423A ASN* 4.8 8.5 + - - +
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Residues in contact with GLN 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 MET* 2.7 58.4 + - + +
286A GLY* 4.1 0.6 - - - +
288A GLN* 1.3 73.7 - - - +
290A LEU* 1.3 61.3 + - - +
292A GLY* 3.6 0.8 + - - -
293A VAL* 3.0 31.1 + - - +
419A HIS* 4.2 0.2 - - + -
423A ASN* 2.8 51.1 - - + +
426A VAL* 4.3 6.8 - - - +
427A GLY* 5.3 1.4 + - - -
441A SER* 5.3 0.7 + - - -
444A VAL* 5.2 1.0 - - - +
445A PHE* 2.9 47.2 + - + +
448A ILE* 3.7 13.2 - - - +
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Residues in contact with LEU 290 (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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286A GLY* 2.9 24.8 + - - +
287A GLY 3.8 0.7 - - - +
288A GLN 3.0 0.4 - - - -
289A GLN* 1.3 80.6 - - - +
291A SER* 1.3 61.0 + - - +
293A VAL* 2.7 29.7 - - + +
294A ASN* 3.0 23.9 + - + +
359A LEU* 4.0 24.2 - - + -
363A LEU* 5.6 2.2 - - + -
376A SER* 5.5 3.6 - - - +
377A ILE* 5.1 6.7 - - + -
380A VAL* 3.6 36.8 - - + -
385A ILE* 4.1 4.9 - - + -
442A PHE* 5.8 4.5 - - + -
445A PHE* 4.5 4.6 - - + -
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Residues in contact with SER 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 5.5 0.3 - - - +
287A GLY 3.2 10.0 + - - -
288A GLN* 2.7 41.8 + - - -
290A LEU* 1.3 82.1 - - - +
292A GLY* 1.3 66.2 + - - +
294A ASN* 3.1 18.3 + - - +
295A ALA* 4.1 3.3 + - - +
381A ILE* 6.6 0.2 - - - -
385A ILE* 5.6 4.3 - - - -
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Residues in contact with GLY 292 (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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40A ASN* 4.5 11.2 - - - -
44A LEU* 3.7 18.4 - - - +
71A TRP* 5.8 1.5 - - - -
288A GLN* 2.7 30.1 + - - -
289A GLN* 4.1 0.9 - - - -
291A SER* 1.3 75.8 + - - +
293A VAL* 1.3 59.6 + - - +
296A ILE* 3.2 16.0 - - - +
423A ASN* 6.3 1.1 - - - -
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Residues in contact with VAL 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A GLN* 3.0 17.0 - - - +
290A LEU* 2.7 39.5 - - + +
292A GLY* 1.3 77.8 - - - +
294A ASN* 1.3 59.0 + - - +
295A ALA 3.4 0.2 - - - -
296A ILE* 3.3 8.7 - - + -
297A TYR* 2.6 47.8 + - + +
423A ASN* 5.9 1.1 - - - +
432A PHE* 6.1 6.3 - - + -
441A SER* 5.2 2.0 - - - +
442A PHE* 5.0 9.6 - - + -
445A PHE* 4.0 21.8 - - + -
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Residues in contact with ASN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A LEU* 3.0 21.2 + - + +
291A SER* 3.1 15.3 + - - +
293A VAL* 1.3 77.8 - - - +
295A ALA* 1.3 59.6 + - - +
297A TYR* 5.1 0.9 - - - -
298A TYR* 3.0 24.6 + - - +
311A GLU* 3.9 5.7 - - - +
312A GLU* 2.6 34.1 + - - +
317A VAL* 2.9 24.7 - - - +
321A THR* 5.3 0.2 - - - +
373A PRO* 5.5 2.6 - - - +
377A ILE* 3.1 21.4 - - - +
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 2.9 22.6 - - + +
178A GLN* 3.3 31.2 - - - +
291A SER 4.1 4.7 + - - +
293A VAL 3.4 0.2 - - - -
294A ASN* 1.3 80.0 - - - +
296A ILE* 1.4 51.3 + - - +
298A TYR* 2.7 27.5 - - - +
299A TYR* 5.0 0.5 - - - +
309A VAL* 5.1 1.0 - - - +
312A GLU* 3.3 12.7 + - + +
313A HIS* 3.4 23.0 - - + +
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Residues in contact with ILE 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ALA 5.2 0.2 - - - +
44A LEU* 2.9 49.1 - - + +
47A GLN 5.9 0.7 - - - +
62A MET* 3.4 34.8 - - + +
68A THR* 5.5 1.6 - - + -
71A TRP* 3.7 21.3 - - + +
292A GLY 3.2 16.2 - - - +
293A VAL* 3.1 20.0 - - + +
295A ALA* 1.4 72.0 - - - +
297A TYR* 1.3 71.5 + - - +
298A TYR 2.7 14.8 - - - +
299A TYR 4.4 0.2 - - - -
300A ALA* 3.0 14.7 + - - +
428A LEU* 6.5 0.4 - - + -
432A PHE* 5.0 11.2 - - + -
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Residues in contact with TYR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A MET* 5.0 0.7 - - - -
293A VAL* 2.6 35.4 + - + +
294A ASN* 4.8 0.9 - - - +
296A ILE* 1.3 70.1 - - + +
298A TYR* 1.3 57.4 + - - +
299A TYR 3.2 0.3 + - - -
300A ALA* 2.7 34.7 + - + +
301A ASP* 2.6 55.5 + - + +
303A ILE* 5.8 0.7 - - + -
363A LEU 5.6 2.2 + - - -
432A PHE* 5.5 10.1 - + + -
437A LEU 5.6 0.2 - - - -
438A GLY* 3.8 24.9 - - - -
439A PRO* 5.7 0.2 - - - +
442A PHE* 3.3 42.1 - + - -
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Residues in contact with TYR 298 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASN* 3.0 22.2 + - - +
295A ALA 2.7 14.7 - - - +
296A ILE 2.7 15.4 - - - +
297A TYR* 1.3 80.7 - - - +
299A TYR* 1.3 67.6 + - - +
300A ALA 3.0 0.2 - - - -
303A ILE* 5.9 3.6 - - + -
305A LEU 5.7 1.0 + - - -
306A SER* 6.6 0.2 - - - -
308A GLY 3.4 27.1 + - - -
309A VAL* 3.5 32.1 - - + -
310A PRO* 4.5 3.3 - - - +
311A GLU* 3.3 54.7 + - + +
312A GLU* 3.9 6.7 - - + -
316A TYR* 5.0 0.7 + - - -
369A VAL* 4.0 19.9 - - + +
370A SER* 5.8 1.9 - - - -
373A PRO* 6.0 0.2 - - + -
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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
------------------------------------------------------------
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