Contacts of the helix formed by residues 348 - 366 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B LEU* 4.3 6.2 - - - +
332B HIS* 5.3 11.9 + - - -
345B ASP* 2.9 24.9 + - + +
347B ASP* 1.3 77.8 - - - +
349B PRO* 1.3 75.8 - - - +
350B SER* 3.9 10.3 + - - -
351B ALA* 3.2 27.2 + - + +
352B MET* 2.9 24.8 + - - +
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Residues in contact with PRO 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B ASP 3.4 9.4 - - - +
348B ASP* 1.3 91.3 - - - +
350B SER* 1.3 51.1 + - - +
352B MET 3.1 1.6 + - - -
353B ASP* 2.7 46.3 + - - +
373B ARG* 3.3 17.3 + - - +
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Residues in contact with SER 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B SER* 3.7 8.2 - - - +
328B THR* 3.1 34.2 + - - +
329B LEU* 3.9 20.6 - - - -
332B HIS* 6.2 1.3 - - - -
348B ASP* 3.4 10.5 + - - -
349B PRO* 1.3 78.6 - - - +
351B ALA* 1.3 58.0 + - - +
353B ASP* 3.0 10.9 + - - +
354B PHE* 2.8 31.0 + - - +
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Residues in contact with ALA 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B PHE* 4.3 21.1 - - + -
329B LEU* 4.1 1.7 - - + +
343B ILE 5.8 0.2 - - - +
344B TRP* 3.1 36.8 + - + +
345B ASP 3.8 9.4 - - - +
348B ASP* 3.2 28.2 + - + +
350B SER* 1.3 78.5 - - - +
352B MET* 1.3 62.3 + - - +
354B PHE* 3.4 3.7 + - - +
355B VAL* 3.3 16.1 + - - +
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Residues in contact with MET 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344B TRP* 4.0 20.8 - - + +
345B ASP 4.8 0.4 + - - -
346B LYS* 4.0 15.7 - - - +
348B ASP 2.9 18.2 + - - +
351B ALA* 1.3 74.3 - - - +
353B ASP* 1.3 61.8 + - - +
355B VAL* 3.8 25.1 - - + -
356B THR* 2.8 46.4 + - - +
373B ARG* 3.5 28.3 - - + +
376B ILE* 4.0 11.9 - - + -
377B LYS* 3.7 37.2 - - + +
380B ALA* 4.1 3.8 - - + -
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Residues in contact with ASP 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321B LEU* 3.7 27.4 - - + +
324B LYS* 5.7 3.3 - - - +
325B SER* 3.9 14.7 - - - -
349B PRO* 2.7 29.5 + - - +
350B SER* 3.4 7.9 + - - +
352B MET* 1.3 71.4 - - - +
354B PHE* 1.3 58.8 + - - +
356B THR* 3.6 5.5 - - - -
357B SER* 2.9 33.5 + - - -
373B ARG* 2.6 38.2 + - - -
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Residues in contact with PHE 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B ALA 3.9 3.6 - - - -
192B LEU* 3.3 34.1 - - + -
193B PHE* 3.8 38.4 - + + -
196B LEU* 3.6 21.5 - - + -
197B PHE* 4.3 4.5 - + - -
322B PHE* 3.6 21.8 - + - -
325B SER* 3.4 19.9 - - - +
326B ILE* 3.9 20.0 - - + -
329B LEU* 3.9 18.6 - - + -
350B SER 2.8 14.8 + - - +
351B ALA 3.6 5.2 - - - +
352B MET 3.3 0.2 - - - -
353B ASP* 1.3 77.1 - - - +
355B VAL* 1.3 62.5 + - + +
357B SER* 3.0 3.2 + - - -
358B ALA* 2.8 35.1 + - + +
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186B ILE* 4.4 4.0 - - + -
189B ALA* 3.4 29.2 - - + +
190B LYS* 4.0 17.9 - - + -
193B PHE* 4.7 0.7 - - + -
344B TRP* 3.3 31.9 - - + +
351B ALA 3.3 6.7 + - - +
352B MET* 3.8 20.2 - - + -
354B PHE* 1.3 83.5 - - + +
356B THR* 1.3 58.6 + - - +
359B ALA* 2.8 34.5 + - + +
376B ILE* 4.2 6.3 - - + -
380B ALA* 4.0 17.0 - - + -
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Residues in contact with THR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B TYR* 3.9 22.7 - - + -
321B LEU* 4.1 7.0 - - + -
352B MET* 2.8 32.7 + - - +
353B ASP* 3.6 6.7 - - - -
355B VAL* 1.3 76.7 - - - +
357B SER* 1.3 58.3 + - - +
360B ASN* 3.0 30.8 + - - +
373B ARG* 3.5 33.6 - - + +
376B ILE* 3.5 27.3 - - + +
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Residues in contact with SER 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B TYR* 3.1 35.4 - - - +
321B LEU* 3.8 9.2 - - - -
322B PHE* 3.2 25.9 - - - +
353B ASP 2.9 14.7 + - - -
354B PHE* 3.0 11.1 + - - -
356B THR* 1.3 75.3 - - - +
358B ALA* 1.3 73.6 + - - +
360B ASN* 3.3 1.4 + - - +
361B LEU* 3.0 30.3 + - - +
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Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B TRP* 3.8 14.4 - - + -
189B ALA* 3.9 11.9 - - + -
192B LEU* 3.9 28.0 - - + -
259B PHE* 4.3 6.5 - - + -
322B PHE* 4.2 14.8 - - + -
354B PHE* 2.8 24.0 + - + +
357B SER* 1.3 74.2 + - - +
359B ALA* 1.3 65.3 + - - +
361B LEU* 3.2 2.9 + - - +
362B ARG 3.1 17.3 + - - -
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Residues in contact with ALA 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B CYS* 3.6 10.1 - - - +
186B ILE* 4.0 22.9 - - + -
189B ALA* 3.7 13.8 - - + +
355B VAL* 2.8 21.7 + - + +
356B THR 3.7 3.4 - - - +
358B ALA* 1.3 77.5 - - - +
360B ASN* 1.3 58.2 + - - +
362B ARG* 3.1 3.0 + - - +
363B MET* 2.9 43.4 + - + +
376B ILE* 4.3 5.4 - - + -
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Residues in contact with ASN 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B TYR* 3.3 31.4 - - + -
356B THR* 3.0 16.0 + - - +
357B SER 4.0 2.0 - - - +
359B ALA* 1.3 76.2 - - - +
361B LEU* 1.3 62.4 + - - +
363B MET* 3.5 12.1 - - - +
364B HIS* 3.1 17.8 + - - +
370B MET* 3.1 34.8 - - - +
371B LYS 2.7 46.0 + - - +
376B ILE* 3.3 13.5 - - - +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255B PHE* 3.6 30.1 - - + -
259B PHE* 3.4 31.9 - - + -
282B LEU* 4.2 8.5 - - + +
315B VAL* 4.1 36.1 - - + +
318B TYR* 4.1 9.4 - - + +
319B ALA* 4.1 8.5 - - + +
322B PHE* 4.1 20.0 - - + -
357B SER 3.0 23.7 + - - +
358B ALA 3.6 0.4 - - - +
359B ALA 3.2 0.2 - - - -
360B ASN* 1.3 74.6 - - - +
362B ARG* 1.3 64.1 + - - +
364B HIS* 3.6 4.4 + - - +
365B ILE* 3.1 28.1 + - - +
370B MET* 5.3 1.1 - - - -
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Residues in contact with ARG 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B ILE 4.0 7.0 + - - -
176B ARG 4.4 14.3 + - - -
179B PRO* 3.3 31.8 - - - +
185B CYS* 3.6 21.3 - - + +
188B TRP* 3.0 73.6 - - + +
206B VAL 4.7 2.0 + - - -
259B PHE* 4.2 1.7 - - + -
262B ASP* 6.2 1.2 - - - +
263B ILE* 4.9 12.6 - - - +
266B LEU* 5.7 3.0 - - - +
358B ALA 3.1 11.6 + - - +
359B ALA 3.6 7.0 - - - +
361B LEU* 1.3 76.9 - - - +
363B MET* 1.3 64.7 + - - +
365B ILE* 3.0 22.3 + - - +
366B PHE* 3.1 35.8 + - + -
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Residues in contact with MET 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B PRO* 3.9 36.1 - - + +
185B CYS* 3.3 23.3 - - + -
186B ILE* 4.1 9.4 - - + -
359B ALA* 2.9 33.8 + - + +
360B ASN* 3.5 28.7 - - - +
362B ARG* 1.3 77.4 - - - +
364B HIS* 1.3 62.7 + - - +
366B PHE* 3.1 7.4 + - - -
368B MET* 2.9 38.6 + - + +
369B ASN 3.7 19.1 - - - +
370B MET* 4.0 3.1 - - - -
371B LYS* 4.3 6.7 - - + -
376B ILE* 4.4 7.2 - - + -
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Residues in contact with HIS 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280B VAL* 6.0 0.2 - - - +
282B LEU* 4.3 25.4 - - + +
315B VAL* 3.7 30.4 - - + +
360B ASN 3.1 14.9 + - - +
361B LEU* 3.8 5.6 - - - +
363B MET* 1.3 76.2 - - - +
365B ILE* 1.3 71.3 + - - +
367B SER* 2.9 16.8 + - - -
368B MET 3.9 11.6 + - - -
370B MET* 4.2 14.9 - - - +
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Residues in contact with ILE 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B PHE* 3.6 42.2 - - + +
263B ILE* 3.8 23.8 - - + -
278B PRO 4.5 1.0 - - - +
279B PRO* 3.4 26.0 - - + +
280B VAL* 3.1 44.7 + - - +
282B LEU* 3.9 12.6 - - + -
361B LEU 3.1 16.6 + - - +
362B ARG* 3.0 12.0 + - - +
364B HIS* 1.3 80.3 - - - +
366B PHE* 1.3 65.2 + - + +
367B SER* 3.4 2.9 + - - -
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Residues in contact with PHE 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B ASN 4.4 0.4 - - - -
179B PRO* 3.4 43.3 - - + +
263B ILE* 4.9 4.5 - - + -
266B LEU* 4.1 14.1 - - + -
273B TRP* 3.7 29.6 - + - -
277B LYS 5.3 6.9 - - - +
278B PRO 5.7 0.4 - - - -
279B PRO* 3.7 20.0 - - + -
362B ARG* 3.1 44.0 + - + -
363B MET 3.1 0.4 + - - +
364B HIS 3.0 1.2 - - - -
365B ILE* 1.3 92.1 - - + +
367B SER* 1.3 60.9 + - - +
368B MET* 2.9 39.2 + - + +
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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) + - + + + + + -
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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