Contacts of the helix formed by residues 348 - 366 (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 348 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329D LEU* 4.8 1.5 - - - +
332D HIS* 4.9 9.9 + - - -
345D ASP* 3.1 23.9 + - + +
347D ASP* 1.3 77.6 - - - +
349D PRO* 1.3 74.2 - - - +
350D SER* 2.7 28.8 + - - -
351D ALA* 2.7 24.3 + - + +
352D MET* 2.9 25.4 + - - +
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Residues in contact with PRO 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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347D ASP 3.4 8.7 - - - +
348D ASP* 1.3 91.8 - - - +
350D SER* 1.3 51.9 + - - +
353D ASP* 2.7 46.4 + - - +
373D ARG* 3.2 15.8 + - - +
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Residues in contact with SER 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324D LYS* 4.9 3.3 - - - +
325D SER* 3.6 9.2 - - - -
328D THR* 3.9 27.4 - - - -
329D LEU* 3.4 21.2 - - - +
332D HIS* 3.9 11.1 + - - -
348D ASP* 2.7 20.6 + - - -
349D PRO* 1.3 76.6 - - - +
351D ALA* 1.3 61.5 + - - +
353D ASP* 3.5 10.3 - - - +
354D PHE* 2.8 31.2 + - - +
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Residues in contact with ALA 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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193D PHE* 4.0 22.2 - - + -
329D LEU* 4.4 2.7 - - + -
343D ILE 5.7 0.4 - - - +
344D TRP* 2.9 36.5 + - + -
345D ASP 3.7 16.6 - - - +
348D ASP* 2.7 28.7 + - + +
350D SER* 1.3 73.2 + - - +
352D MET* 1.3 60.9 + - - +
354D PHE* 3.6 3.5 - - - +
355D VAL 3.4 12.8 + - - -
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Residues in contact with MET 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344D TRP* 4.0 17.3 - - + +
345D ASP 4.7 0.2 + - - -
346D LYS 4.1 15.5 - - - +
348D ASP 2.9 14.6 + - - +
351D ALA* 1.3 77.2 - - - +
353D ASP* 1.3 56.1 + - - +
354D PHE 3.2 0.2 - - - -
355D VAL* 4.1 15.5 - - + -
356D THR* 2.7 50.0 + - - +
373D ARG* 3.3 30.5 - - + +
376D ILE* 3.7 22.7 - - + -
377D LYS* 3.6 41.1 - - + +
380D ALA* 4.1 5.4 - - + -
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Residues in contact with ASP 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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321D LEU* 3.7 29.8 - - + +
324D LYS* 3.2 21.4 + - - +
325D SER* 3.8 13.7 - - - -
349D PRO* 2.7 35.6 + - - +
350D SER* 3.0 4.9 + - - +
352D MET* 1.3 72.9 - - - +
354D PHE* 1.3 60.6 + - - +
356D THR* 3.7 4.1 - - - -
357D SER* 2.8 31.1 + - - -
373D ARG* 3.0 24.7 + - - -
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Residues in contact with PHE 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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189D ALA 3.8 7.4 - - - -
192D LEU* 3.4 31.0 - - + -
193D PHE* 3.6 44.2 - + + -
196D LEU* 3.8 12.3 - - + -
197D PHE* 4.0 13.5 - + - -
322D PHE* 3.8 20.6 - + - -
325D SER* 3.4 18.6 + - - +
326D ILE* 4.0 12.1 - - + -
329D LEU* 3.9 17.5 - - + -
350D SER 2.8 15.9 + - - +
351D ALA 3.6 5.6 - - - +
353D ASP* 1.3 76.6 - - - +
355D VAL* 1.3 65.6 + - + +
357D SER* 3.0 3.3 + - - -
358D ALA* 2.8 35.0 + - + +
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Residues in contact with VAL 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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186D ILE* 4.2 9.0 - - + -
189D ALA* 3.8 37.2 - - + +
190D LYS* 4.0 13.5 - - + +
193D PHE* 4.7 0.7 - - + -
344D TRP* 3.3 31.9 - - + +
351D ALA 3.4 6.4 + - - +
352D MET* 3.5 9.8 + - + -
354D PHE* 1.3 83.8 - - + +
356D THR* 1.3 63.2 + - - +
359D ALA* 2.9 30.5 + - - +
376D ILE* 4.3 2.9 - - + -
380D ALA* 4.1 25.1 - - + -
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Residues in contact with THR 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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318D TYR* 4.0 21.5 - - + -
321D LEU* 4.6 3.4 - - + -
352D MET* 2.7 38.6 + - - +
353D ASP* 3.7 5.6 - - - -
355D VAL* 1.3 78.0 - - - +
357D SER* 1.3 63.4 + - - +
360D ASN* 3.1 25.5 + - - +
373D ARG* 3.5 37.9 - - + +
376D ILE* 3.7 26.1 - - + +
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Residues in contact with SER 357 (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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318D TYR* 3.0 36.6 - - - +
321D LEU* 3.9 9.6 - - - -
322D PHE* 3.2 25.5 - - - +
353D ASP 2.8 18.6 + - - -
354D PHE* 3.0 5.9 + - - -
356D THR* 1.3 77.9 - - - +
358D ALA* 1.3 72.3 + - - -
360D ASN* 3.3 2.6 + - - +
361D LEU* 3.1 29.8 + - - +
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Residues in contact with ALA 358 (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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188D TRP* 3.7 10.6 - - + -
189D ALA* 4.1 13.5 - - + -
192D LEU* 4.1 17.0 - - + -
259D PHE* 3.8 13.0 - - + -
322D PHE* 4.1 21.5 - - + -
354D PHE* 2.8 26.4 + - + +
357D SER* 1.3 73.3 + - - +
359D ALA* 1.3 62.5 + - - +
361D LEU 3.7 0.2 + - - -
362D ARG* 3.3 21.0 + - - +
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Residues in contact with ALA 359 (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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185D CYS* 3.5 6.0 - - - +
186D ILE* 3.8 24.5 - - + +
188D TRP* 5.1 0.2 - - - -
189D ALA* 3.6 15.9 - - + +
355D VAL* 2.9 23.1 + - + +
356D THR 4.0 2.0 - - - +
358D ALA* 1.3 75.4 - - - +
360D ASN* 1.3 64.7 + - - +
362D ARG* 3.3 5.1 - - - +
363D MET* 3.0 37.3 + - + +
376D ILE* 4.8 2.9 - - + -
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Residues in contact with ASN 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318D TYR* 3.2 41.6 - - + -
356D THR* 3.1 21.9 + - - +
357D SER 3.3 2.4 + - - +
359D ALA* 1.3 73.0 - - - +
361D LEU* 1.3 68.2 + - - +
363D MET* 3.0 16.6 + - - +
364D HIS* 2.8 24.1 + - - +
370D MET* 3.2 17.7 - - + +
371D LYS 2.8 44.5 + - - +
376D ILE* 3.6 5.4 - - - +
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Residues in contact with LEU 361 (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* 3.6 21.5 - - + -
259D PHE* 3.5 41.5 - - + -
282D LEU* 4.3 7.7 - - + +
315D VAL* 3.9 35.4 - - + +
318D TYR* 4.3 7.6 - - + +
319D ALA* 4.2 9.0 - - + +
322D PHE* 4.1 18.6 - - + -
357D SER 3.1 21.1 + - - +
358D ALA 3.9 0.2 - - - +
360D ASN* 1.3 75.3 - - - +
362D ARG* 1.3 64.9 + - - +
364D HIS* 3.2 6.4 + - - +
365D ILE* 3.0 28.5 + - - +
370D MET* 5.5 1.3 - - - -
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Residues in contact with ARG 362 (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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175D ILE 3.4 9.6 + - - -
176D ARG 3.1 21.6 + - - -
179D PRO* 3.1 32.9 - - - +
185D CYS* 3.8 17.9 - - + +
188D TRP* 3.0 69.6 - - + +
206D VAL 4.4 3.4 + - - -
208D PRO* 6.2 1.0 - - - +
259D PHE* 4.0 4.0 - - + -
263D ILE* 5.4 7.5 - - - +
266D LEU* 5.3 2.2 - - - +
358D ALA 3.3 6.6 + - - +
359D ALA 3.3 10.5 - - - +
360D ASN 3.1 0.2 - - - -
361D LEU* 1.3 78.2 - - - +
363D MET* 1.3 65.0 + - - +
365D ILE* 3.0 25.5 + - + +
366D PHE* 3.2 34.7 + - - -
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Residues in contact with MET 363 (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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182D PRO* 3.7 36.1 - - + +
185D CYS* 3.3 26.6 - - + -
186D ILE* 4.5 5.2 - - + -
359D ALA* 3.0 29.2 + - + +
360D ASN* 3.0 33.2 - - - +
362D ARG* 1.3 78.0 - - - +
364D HIS* 1.3 64.0 + - - +
366D PHE* 3.1 10.0 + - - -
367D SER 3.2 0.3 + - - -
368D MET* 2.9 39.9 + - + +
369D ASN 3.8 15.9 - - - +
370D MET* 4.8 1.6 - - - -
371D LYS* 4.2 7.4 - - + +
376D ILE* 4.2 10.3 - - + -
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Residues in contact with HIS 364 (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 VAL* 5.8 0.5 - - - +
282D LEU* 4.3 19.2 - - + +
315D VAL* 3.3 40.8 - - + +
360D ASN 2.8 15.0 + - - +
361D LEU* 3.5 11.7 - - - +
363D MET* 1.3 74.0 - - - +
365D ILE* 1.3 59.9 + - - +
367D SER* 2.8 21.7 + - - -
368D MET 3.9 12.9 + - - -
370D MET* 4.3 15.8 - - + +
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Residues in contact with ILE 365 (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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259D PHE* 3.7 37.0 - - + +
263D ILE* 3.6 43.5 - - + -
278D PRO 4.7 0.3 - - - +
279D PRO* 3.6 17.9 - - + +
280D VAL* 3.1 51.8 + - - +
282D LEU* 3.7 14.1 - - + -
361D LEU 3.0 14.4 + - - +
362D ARG* 3.0 13.1 + - + +
364D HIS* 1.3 78.7 - - - +
366D PHE* 1.3 61.6 + - + +
367D SER* 3.2 4.2 + - - -
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Residues in contact with PHE 366 (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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177D ASN 3.7 7.2 - - - -
178D THR* 4.9 0.4 - - - -
179D PRO* 3.2 39.0 - - + +
263D ILE* 4.2 4.7 - - + -
266D LEU* 3.7 21.3 - - + -
273D TRP* 4.2 11.7 - + - -
277D LYS* 5.4 11.2 - - - +
278D PRO 6.0 0.2 - - - -
279D PRO* 3.8 18.6 - - + -
362D ARG* 3.2 48.2 - - - -
363D MET 3.1 9.1 + - - +
365D ILE* 1.3 90.7 - - + +
367D SER* 1.3 69.5 + - - +
368D MET* 3.5 21.4 + - + +
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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
------------------------------------------------------------
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