Contacts of the helix formed by residues 314 - 337 (chain D) in PDB entry 1Y8Q
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 314 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290D GLN 6.4 0.7 - - - -
313D LEU* 1.3 76.5 - - - +
315D VAL* 1.3 66.6 + - - +
316D LYS* 3.0 25.7 + - - +
317D SER* 2.8 48.4 + - - -
318D TYR* 3.3 11.8 + - - -
370D MET* 3.9 5.4 - - - -
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Residues in contact with VAL 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D LEU* 4.6 9.2 - - + -
287D VAL* 3.7 20.4 - - + -
314D ASP* 1.3 72.8 - - - +
316D LYS* 1.3 61.3 - - - +
318D TYR* 3.5 2.2 + - - +
319D ALA* 3.2 19.9 + - - +
361D LEU* 3.9 19.0 - - + +
364D HIS* 3.3 53.6 - - + +
370D MET* 3.7 18.2 - - + +
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Residues in contact with LYS 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287D VAL* 3.7 25.2 - - - +
288D GLN* 3.6 22.9 - - - +
290D GLN* 5.1 19.3 - - - +
314D ASP* 3.0 23.3 + - - +
315D VAL* 1.3 79.6 - - - +
317D SER* 1.3 76.9 + - - +
319D ALA* 3.0 6.3 + - - +
320D ARG* 3.0 55.0 + - - +
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Residues in contact with SER 317 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313D LEU* 3.7 30.6 - - - +
314D ASP* 2.8 31.8 + - - -
316D LYS* 1.3 94.9 + - - +
318D TYR* 1.3 58.2 + - - +
320D ARG* 3.2 8.1 + - - +
321D LEU* 2.9 28.2 + - - +
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Residues in contact with TYR 318 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311D GLN 3.9 3.8 + - - -
312D VAL* 3.8 5.8 - - + -
313D LEU* 3.0 59.1 + - + +
314D ASP 3.3 15.6 + - - -
315D VAL 4.0 5.4 - - - +
317D SER* 1.3 73.8 - - - +
319D ALA* 1.3 60.7 + - - +
321D LEU* 3.7 19.3 - - + -
322D PHE* 2.9 23.0 + - - +
356D THR* 4.0 13.0 - - + -
357D SER* 3.0 30.0 - - - +
360D ASN* 3.2 36.5 + - + -
361D LEU* 4.3 9.6 - - + +
370D MET* 3.7 20.4 - - + -
371D LYS 3.7 8.1 + - - -
372D SER* 4.2 3.1 - - - -
373D ARG* 4.5 4.2 + - + +
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Residues in contact with ALA 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D PHE* 4.2 13.5 - - + -
284D TRP* 3.5 27.6 - - + -
287D VAL* 4.5 10.3 - - + -
288D GLN* 5.2 3.1 - - - +
315D VAL 3.2 13.2 + - - +
316D LYS* 3.0 14.6 + - - +
318D TYR* 1.3 77.2 - - - +
320D ARG* 1.3 64.4 + - + +
322D PHE* 3.2 9.2 - - - +
323D SER 3.1 16.6 + - - -
361D LEU* 4.3 8.7 - - + -
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Residues in contact with ARG 320 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D TRP* 4.4 2.0 - - + -
288D GLN* 3.7 27.6 - - - +
316D LYS* 3.0 52.4 + - - +
317D SER* 3.2 8.4 + - - +
319D ALA* 1.3 74.6 - - - +
321D LEU* 1.3 59.6 + - - +
323D SER* 2.8 24.4 + - - +
324D LYS* 2.8 16.5 + - - +
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Residues in contact with LEU 321 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D LEU* 5.3 6.5 - - + -
317D SER 2.9 16.8 + - - +
318D TYR* 3.7 24.0 - - + +
320D ARG* 1.3 73.1 - - - +
322D PHE* 1.3 66.0 + - - +
324D LYS* 3.1 33.2 + - + +
325D SER* 2.9 25.5 + - - -
353D ASP* 3.7 41.5 - - + +
356D THR* 4.6 7.9 - - + -
357D SER* 3.9 7.0 - - - -
373D ARG* 5.2 4.3 - - - -
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Residues in contact with PHE 322 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192D LEU* 4.4 2.2 - - + -
196D LEU* 5.7 0.7 - - + -
251D PRO 4.0 4.5 - - - -
254D LEU* 4.5 5.2 - - + -
255D PHE* 3.9 44.2 - + + -
258D LEU* 4.6 7.9 - - + -
259D PHE* 3.8 18.6 - + - -
284D TRP* 5.1 0.7 - + - -
318D TYR 2.9 14.8 + - - +
319D ALA* 3.2 12.8 - - - +
321D LEU* 1.3 77.5 - - - +
323D SER* 1.3 62.8 + - - +
325D SER* 3.0 16.1 + - - -
326D ILE* 3.2 40.8 - - + +
354D PHE* 3.8 25.6 - + - -
357D SER* 3.2 21.7 + - - +
358D ALA* 4.1 21.1 - - + -
361D LEU* 4.1 5.6 - - + -
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Residues in contact with SER 323 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D PRO* 3.5 31.0 - - - +
284D TRP* 3.8 22.2 - - - -
319D ALA 3.1 2.6 + - - -
320D ARG* 2.8 24.1 + - - +
322D PHE* 1.3 78.5 - - - +
324D LYS* 1.3 63.7 + - - +
326D ILE* 3.3 3.1 + - - +
327D GLU* 3.1 33.4 + - - +
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Residues in contact with LYS 324 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320D ARG 2.8 18.2 + - - +
321D LEU* 3.1 31.8 + - + +
323D SER* 1.3 77.7 + - - +
325D SER* 1.3 65.9 + - - +
327D GLU* 3.4 14.9 + - - +
328D THR* 3.3 30.3 + - - +
350D SER* 4.9 5.5 - - - +
353D ASP* 3.2 21.0 + - - -
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Residues in contact with SER 325 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321D LEU 2.9 13.8 + - - -
322D PHE* 3.0 15.4 + - - -
324D LYS* 1.3 81.0 - - - +
326D ILE* 1.3 59.8 + - - +
328D THR* 3.4 1.3 + - - +
329D LEU* 2.8 36.6 + - - +
350D SER* 3.6 27.1 - - - -
353D ASP* 3.8 8.3 - - - -
354D PHE* 3.4 30.0 - - - -
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Residues in contact with ILE 326 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D PHE* 4.5 8.2 - - + -
249D TYR* 3.5 31.0 - - + +
251D PRO* 4.1 16.2 - - + -
254D LEU* 3.5 29.8 - - + -
322D PHE* 3.2 44.6 + - + +
323D SER 3.3 7.1 + - - +
324D LYS 3.3 1.0 - - - -
325D SER* 1.3 73.8 + - - +
327D GLU* 1.3 67.5 + - - +
329D LEU* 3.8 5.1 - - - +
330D ARG* 2.9 25.6 + - - +
354D PHE* 4.0 18.8 - - + -
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Residues in contact with GLU 327 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D PRO* 4.3 13.4 - - + +
323D SER* 3.1 20.7 + - - +
324D LYS* 3.6 15.4 - - - +
326D ILE* 1.3 78.3 - - - +
328D THR* 1.3 60.9 + - - +
330D ARG* 3.2 38.9 + - - +
331D VAL* 3.1 21.7 - - - +
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Residues in contact with THR 328 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324D LYS* 3.3 20.8 + - - +
325D SER 3.9 5.6 - - - -
326D ILE 3.2 0.2 - - - -
327D GLU* 1.3 77.5 - - - +
329D LEU* 1.3 65.4 + - - +
331D VAL* 3.0 17.8 + - + +
332D HIS* 3.0 43.7 + - + +
350D SER* 3.9 16.8 - - - -
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Residues in contact with LEU 329 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D PHE* 3.7 34.3 - - + -
197D PHE* 3.8 27.6 - - + -
325D SER 2.8 31.0 + - - +
326D ILE 3.8 2.7 - - - +
328D THR* 1.3 72.3 - - - +
330D ARG* 1.3 63.2 + - - +
331D VAL 3.0 0.2 + - - -
332D HIS* 3.1 10.0 + - + +
333D LEU* 2.9 24.1 + - - +
342D LEU* 3.9 16.1 - - + +
348D ASP* 4.8 0.9 - - - +
350D SER* 3.4 26.5 - - - +
351D ALA* 4.2 5.6 - - + +
354D PHE* 3.9 23.3 - - + -
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Residues in contact with ARG 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D PHE* 4.0 6.4 - - + -
248D GLY 3.3 18.4 + - - -
249D TYR* 2.9 50.5 + - + -
250D ASP* 4.4 1.6 + - - +
251D PRO* 3.9 11.9 - - - +
326D ILE 2.9 18.9 + - - +
327D GLU* 3.2 43.9 + - - +
329D LEU* 1.3 73.3 - - - +
331D VAL* 1.3 61.0 + - + +
333D LEU* 3.7 7.9 + - - +
334D ALA* 3.1 24.9 + - - +
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Residues in contact with VAL 331 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327D GLU 3.1 20.2 - - - +
328D THR* 3.0 10.2 + - - +
330D ARG* 1.3 79.6 - - + +
332D HIS* 1.3 64.3 + - + +
333D LEU 3.0 1.3 - - - -
334D ALA* 3.0 7.1 + - + +
335D GLU* 2.9 52.0 + - + +
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Residues in contact with HIS 332 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328D THR* 3.0 40.2 + - + +
329D LEU* 3.1 11.0 + - + +
331D VAL* 1.3 82.4 - - + +
333D LEU* 1.3 60.5 + - - +
335D GLU* 3.6 22.1 + - - +
336D LYS* 3.3 26.0 + - - +
342D LEU* 3.9 13.4 - - + +
348D ASP* 4.9 9.7 + - - -
350D SER* 3.9 14.5 + - - -
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Residues in contact with LEU 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197D PHE* 4.0 22.7 - - + +
241D LYS* 4.6 4.0 - - - +
249D TYR* 3.3 39.0 - - + +
329D LEU 2.9 15.6 + - - +
330D ARG 3.7 5.8 - - - +
332D HIS* 1.3 76.0 - - - +
334D ALA* 1.3 65.5 + - - +
336D LYS* 3.0 18.9 + - - +
337D GLY 3.8 7.8 + - - +
340D ALA* 3.0 35.7 - - + +
342D LEU* 3.8 24.6 - - + +
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Residues in contact with ALA 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D ARG 3.1 14.3 + - - +
331D VAL* 3.0 7.9 + - + +
333D LEU* 1.3 80.7 - - - +
335D GLU* 1.3 62.6 + - + +
336D LYS 3.4 0.3 + - - -
337D GLY* 3.5 14.7 + - - +
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Residues in contact with GLU 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331D VAL* 2.9 36.2 + - + +
332D HIS* 3.6 27.9 + - - +
333D LEU 3.1 0.2 - - - -
334D ALA* 1.3 78.8 - - + +
336D LYS* 1.3 60.2 + - + +
337D GLY 3.4 0.4 + - - -
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Residues in contact with LYS 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D HIS 3.3 14.1 - - - +
333D LEU 3.0 6.2 + - - +
335D GLU* 1.3 79.6 - - + +
337D GLY* 1.3 57.1 + - - +
340D ALA* 3.4 24.4 - - + +
341D GLU 2.9 25.4 + - - +
342D LEU* 3.5 26.6 - - + +
343D ILE* 5.1 8.7 - - - +
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Residues in contact with GLY 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D LEU* 3.8 6.1 + - - +
334D ALA* 3.5 11.6 + - - +
335D GLU 3.4 4.0 + - - -
336D LYS* 1.3 80.6 - - - +
338D ASP* 1.3 65.1 + - - -
339D GLY 3.7 1.2 + - - -
340D ALA* 3.7 11.4 + - - +
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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