Contacts of the helix formed by residues 335 - 358 (chain D) in PDB entry 5Y1Z
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 335 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.8 27.4 - - + -
14B LEU* 4.1 25.1 - - + -
15B ALA 4.5 0.2 - - - +
18B GLU* 3.3 11.4 - - - -
288D PHE* 4.9 5.2 - - + -
289D PRO* 4.7 5.6 - - + +
291D TRP* 3.6 20.6 - - - -
332D VAL* 3.2 10.5 + - - +
333D LYS 3.2 0.4 - - - -
334D LYS* 1.3 82.1 - - + +
336D LYS* 1.3 55.6 + - - +
337D SER 3.3 2.0 - - - -
338D ILE* 3.0 13.6 + - - -
339D PHE* 2.7 35.0 + - - +
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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
----------------------------------------------------------
18B GLU* 3.3 8.0 + - - +
332D VAL* 3.1 26.8 + - + +
333D LYS* 3.6 12.9 + - - +
335D THR* 1.3 75.6 - - - +
337D SER* 1.3 58.7 + - - +
339D PHE* 3.5 2.6 + - - +
340D ASN* 2.9 31.2 + - + +
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Residues in contact with SER 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU* 2.8 26.1 + - - -
21B ILE* 4.0 23.4 - - - +
22B ARG* 6.1 2.2 - - - -
336D LYS* 1.3 71.0 - - - +
338D ILE* 1.3 69.4 + - - +
340D ASN* 3.0 7.4 + - - +
341D SER* 2.8 27.9 + - - -
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Residues in contact with ILE 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B LEU* 4.2 17.5 - - + +
17B TYR* 4.4 10.1 - - + -
18B GLU* 3.0 29.5 + - + +
21B ILE* 3.4 32.8 - - + -
291D TRP* 3.9 16.2 - - + -
309D GLY* 5.8 0.8 - - - -
310D GLN* 3.5 29.4 - - - +
335D THR* 3.5 9.2 - - - +
337D SER* 1.3 72.4 - - - +
339D PHE* 1.3 58.0 + - - +
341D SER* 3.0 10.5 + - - -
342D ALA* 2.8 27.2 + - - +
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Residues in contact with PHE 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D TRP* 4.0 3.1 - + - -
290D PHE 3.7 20.2 - - - -
291D TRP* 3.7 34.4 - + + -
292D PRO* 4.0 15.5 - - + -
328D ILE* 3.8 33.2 - - + -
330D PHE* 3.9 8.5 - + - -
332D VAL* 3.7 28.9 - - + -
335D THR* 2.7 21.1 + - - +
336D LYS 3.7 3.4 - - - +
338D ILE* 1.3 72.3 - - - +
340D ASN* 1.3 62.3 + - + +
342D ALA* 3.0 3.6 + - - +
343D MET* 2.8 55.3 + - + +
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Residues in contact with ASN 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336D LYS* 2.9 20.2 + - + +
337D SER* 3.0 7.4 + - - +
339D PHE* 1.3 79.8 - - + +
341D SER* 1.3 57.5 + - - +
343D MET* 3.1 9.4 + - - +
344D GLN* 2.8 51.8 + - - +
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Residues in contact with SER 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLN* 6.5 1.6 - - - -
309D GLY* 5.5 1.8 - - - -
337D SER* 2.8 19.0 + - - -
338D ILE* 3.3 10.9 - - - -
340D ASN* 1.3 75.5 + - - +
342D ALA* 1.3 62.7 + - - +
344D GLN* 3.0 14.7 + - - +
345D GLU* 2.9 23.6 + - - +
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Residues in contact with ALA 342 (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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291D TRP* 3.8 20.6 - - + +
292D PRO* 4.1 9.0 - - + -
308D PHE* 3.8 29.5 - - - +
309D GLY* 4.0 14.1 - - - +
338D ILE 2.8 15.9 + - - +
339D PHE* 3.0 7.6 + - - +
341D SER* 1.3 71.4 - - - +
343D MET* 1.3 64.4 + - - +
345D GLU* 3.0 5.8 + - - +
346D MET* 2.9 22.5 + - - +
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Residues in contact with MET 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282D TRP* 3.8 29.8 - - + -
292D PRO* 3.6 25.4 - - - -
324D MET* 4.6 0.4 - - - -
325D SER 5.5 1.3 - - - +
328D ILE* 4.4 15.0 - - + -
339D PHE* 2.8 42.9 + - + +
340D ASN* 3.5 15.0 - - - +
342D ALA* 1.3 71.4 - - - +
344D GLN* 1.3 64.9 + - - +
346D MET* 3.0 36.6 + - + +
347D GLU* 2.9 41.1 + - - +
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Residues in contact with GLN 344 (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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340D ASN* 2.8 38.4 + - - +
341D SER* 3.0 15.1 + - - +
343D MET* 1.3 75.2 - - - +
345D GLU* 1.3 62.9 + - - +
347D GLU* 3.0 24.9 + - - +
348D VAL* 3.1 17.2 + - - +
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Residues in contact with GLU 345 (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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110B GLN* 6.2 1.1 - - - -
268D ASN* 5.7 2.6 - - - +
270D PHE* 3.5 15.6 - - - +
271D CYS* 3.6 20.0 - - - -
308D PHE* 3.5 9.0 - - + -
309D GLY* 2.4 38.8 + - - -
311D HIS* 2.6 29.9 + - - -
341D SER 2.9 12.4 + - - +
342D ALA* 3.5 5.6 - - - +
344D GLN* 1.3 74.9 - - - +
346D MET* 1.3 63.2 + - - +
348D VAL* 3.0 19.2 + - - +
349D TYR* 3.1 10.4 + - - +
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Residues in contact with MET 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280D LEU* 3.7 17.7 - - + -
292D PRO* 3.9 7.9 - - + -
308D PHE* 3.3 29.3 - - + -
324D MET* 3.5 47.8 - - + +
325D SER 5.4 0.4 - - - +
342D ALA 2.9 12.6 + - - +
343D MET* 3.0 34.5 + - + +
345D GLU* 1.3 75.5 - - - +
347D GLU* 1.3 66.4 + - + +
349D TYR* 3.0 6.2 + - - +
350D VAL* 2.8 35.1 + - + +
362D TYR* 4.1 20.0 - - + +
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Residues in contact with GLU 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343D MET* 2.9 35.0 + - - +
344D GLN* 3.0 15.6 + - - +
346D MET* 1.3 85.3 - - + +
348D VAL* 1.3 57.7 + - + +
350D VAL* 3.1 7.6 + - + +
351D GLU* 2.7 30.3 + - - +
362D TYR* 4.6 9.0 - - - +
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Residues in contact with VAL 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268D ASN* 4.2 19.1 - - - +
271D CYS* 3.6 24.2 - - + -
344D GLN* 3.1 13.7 + - + +
345D GLU* 3.0 10.2 + - - +
347D GLU* 1.3 75.4 - - + +
349D TYR* 1.3 63.7 + - - +
351D GLU* 3.0 9.6 + - - +
352D ASN* 2.8 33.6 + - - +
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Residues in contact with TYR 349 (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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270D PHE 4.0 4.5 - - - -
271D CYS* 3.5 35.6 - - - +
272D GLU 4.2 1.3 - - - -
273D PRO* 3.8 27.1 - - + +
274D CYS 4.9 0.5 + - - -
277D PRO* 4.0 16.5 - - - +
278D HIS* 3.4 24.8 + + - +
280D LEU* 3.4 39.3 - - + -
294D LYS* 3.9 20.9 - - + +
308D PHE* 3.8 16.8 - + + -
345D GLU 3.1 5.0 + - - +
346D MET 3.0 7.6 + - - +
348D VAL* 1.3 77.9 - - - +
350D VAL* 1.3 67.8 + - - +
352D ASN* 3.0 3.8 + - - +
353D ILE* 2.8 39.4 + - + +
360D PHE* 5.3 0.7 - + - -
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Residues in contact with VAL 350 (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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280D LEU* 3.7 26.5 - - + -
346D MET* 2.8 26.0 + - + +
347D GLU* 3.1 8.7 + - + +
349D TYR* 1.3 70.5 - - - +
351D GLU* 1.3 66.1 + - - +
353D ILE* 3.0 10.7 - - - +
354D ARG* 2.9 46.5 + - - +
360D PHE* 3.9 31.6 - - + -
362D TYR* 3.8 21.1 - - - +
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Residues in contact with GLU 351 (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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347D GLU 2.7 16.4 + - - +
348D VAL* 3.4 11.0 - - + +
350D VAL* 1.3 73.6 - - - +
352D ASN* 1.3 67.6 + - - +
354D ARG* 3.1 10.3 + - - +
355D ARG* 2.8 23.9 + - - +
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Residues in contact with ASN 352 (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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268D ASN* 5.4 1.8 + - - +
271D CYS* 3.1 38.5 + - - +
272D GLU* 4.9 3.0 - - - +
273D PRO* 4.2 10.3 - - + +
348D VAL* 2.8 24.0 + - - +
349D TYR 3.4 7.4 - - - +
351D GLU* 1.3 74.8 - - - +
353D ILE* 1.3 58.5 + - - +
355D ARG* 2.9 37.9 + - - +
356D LYS* 2.8 28.6 + - - +
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Residues in contact with ILE 353 (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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273D PRO* 4.0 16.4 - - + +
277D PRO* 3.7 26.2 - - + -
278D HIS 5.9 0.4 - - - +
349D TYR* 2.8 31.5 + - + +
350D VAL* 3.0 25.4 - - - +
352D ASN* 1.3 77.2 - - - +
354D ARG* 1.3 58.2 + - - +
356D LYS* 3.0 2.0 + - - +
357D PHE* 2.8 46.0 + - + +
359D VAL 4.3 2.2 - - - +
360D PHE* 4.3 18.2 - - + -
377D MET* 3.4 31.2 - - + -
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Residues in contact with ARG 354 (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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326D LYS* 5.9 0.2 - - - +
350D VAL* 2.9 29.0 + - - +
351D GLU* 3.4 11.9 - - - +
353D ILE* 1.3 79.4 - - - +
355D ARG* 1.3 59.2 + - - +
358D GLY* 2.8 34.4 + - - +
359D VAL* 3.9 7.6 - - - +
360D PHE* 3.5 42.5 + - + +
362D TYR* 3.5 29.3 + - - -
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Residues in contact with ARG 355 (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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273D PRO* 5.8 1.4 - - - +
351D GLU 2.8 12.2 + - - +
352D ASN* 2.9 47.8 + - - +
354D ARG* 1.3 79.0 - - - +
356D LYS* 1.3 65.7 + - - +
358D GLY* 4.7 0.9 + - - -
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Residues in contact with LYS 356 (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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273D PRO* 3.2 36.3 + - + -
274D CYS 3.6 18.0 + - - -
275D SER* 4.0 8.6 + - - +
352D ASN 2.8 15.6 + - - +
353D ILE* 3.8 3.4 - - - +
355D ARG* 1.3 86.2 - - - +
357D PHE* 1.3 83.1 + - + +
391D ILE* 3.6 28.4 - - + +
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Residues in contact with PHE 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273D PRO* 4.6 2.5 - - + -
274D CYS 3.8 8.3 - - - -
275D SER* 3.3 26.7 - - - -
277D PRO* 3.7 20.9 - - + -
353D ILE* 2.8 37.4 + - + +
356D LYS* 1.3 102.2 - - + +
358D GLY* 1.3 57.1 + - - +
359D VAL 3.5 4.0 - - - +
377D MET* 4.4 11.4 - - - -
389D ALA* 3.5 36.4 - - + +
390D LYS* 4.4 6.7 - - - -
391D ILE* 3.7 50.3 - - - +
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Residues in contact with GLY 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354D ARG* 2.8 24.7 + - - +
355D ARG 4.6 0.6 + - - -
356D LYS 3.8 0.4 - - - -
357D PHE* 1.3 77.7 - - - +
359D VAL* 1.3 61.4 + - - +
391D ILE* 5.9 0.7 - - - -
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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