Contacts of the helix formed by residues 314 - 336 (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 314 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 1.3 77.7 - - - +
315B VAL* 1.3 66.3 + - - +
316B LYS* 3.8 12.6 - - - +
317B SER* 2.7 40.5 + - - -
318B TYR* 3.2 11.8 + - - -
320B ARG* 5.2 1.9 + - - -
370B MET* 3.9 5.8 - - - -
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Residues in contact with VAL 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B LEU* 4.3 17.0 - - + -
287B VAL* 4.0 19.3 - - + -
314B ASP* 1.3 73.4 - - - +
316B LYS* 1.3 65.1 + - - +
318B TYR* 3.0 7.3 + - - +
319B ALA* 3.0 19.6 + - - +
361B LEU* 4.1 18.1 - - + +
364B HIS* 3.7 41.3 - - + +
370B MET* 3.8 17.3 - - + +
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Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B VAL* 3.6 28.9 - - - +
288B GLN* 3.1 41.8 + - - +
289B SER 4.9 0.2 + - - -
290B GLN* 3.4 27.0 + - + +
314B ASP* 3.3 12.2 + - - +
315B VAL* 1.3 78.2 - - - +
317B SER* 1.3 63.0 - - - +
319B ALA* 3.1 4.2 + - - +
320B ARG* 3.0 50.6 + - - +
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Residues in contact with SER 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 3.6 31.0 - - - +
314B ASP* 2.7 32.7 + - - -
316B LYS* 1.3 75.3 - - - +
318B TYR* 1.3 57.9 + - - +
320B ARG* 3.0 29.7 + - - +
321B LEU* 2.9 26.0 + - - +
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Residues in contact with TYR 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B GLN 3.9 4.3 + - - -
312B VAL* 3.8 8.7 - - + -
313B LEU* 3.1 59.0 + - + +
314B ASP 3.2 16.5 + - - -
315B VAL* 3.0 7.6 + - - +
317B SER* 1.3 74.6 - - - +
319B ALA* 1.3 59.2 + - - +
321B LEU* 3.6 18.4 - - + -
322B PHE* 3.0 22.9 + - - +
356B THR* 3.9 13.0 - - + -
357B SER* 3.1 26.0 - - - +
360B ASN* 3.3 32.2 + - + -
361B LEU* 4.1 14.5 - - + +
370B MET* 3.9 20.2 - - + -
371B LYS 3.7 8.1 + - - -
372B SER* 4.3 2.3 - - - -
373B ARG* 4.6 3.3 + - + +
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B PHE* 4.0 20.9 - - + -
284B TRP* 3.6 14.5 - - + -
287B VAL* 4.0 11.0 - - + -
288B GLN* 3.6 17.7 - - - +
315B VAL 3.0 11.5 + - - +
316B LYS 3.1 8.0 + - - +
318B TYR* 1.3 76.3 - - - +
320B ARG* 1.3 64.0 + - - +
322B PHE* 3.3 7.7 + - - +
323B SER 3.1 18.5 + - - -
361B LEU* 4.1 9.1 - - + +
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Residues in contact with ARG 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B TRP* 4.9 3.1 - - + -
288B GLN* 3.8 22.4 - - - +
314B ASP* 4.5 2.8 + - - -
316B LYS* 3.0 42.0 + - - +
317B SER* 3.0 36.2 + - - +
319B ALA* 1.3 77.5 - - - +
321B LEU* 1.3 62.0 + - - +
323B SER* 3.5 6.1 + - - -
324B LYS* 3.0 25.1 + - - +
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Residues in contact with LEU 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B LEU* 5.6 5.4 - - + -
317B SER 2.9 15.5 + - - +
318B TYR* 3.6 17.7 - - + +
319B ALA 3.2 0.2 - - - -
320B ARG* 1.3 74.7 - - - +
322B PHE* 1.3 59.5 + - - +
324B LYS* 3.6 10.1 - - + +
325B SER* 2.9 34.2 + - - -
353B ASP* 3.7 51.1 - - + +
356B THR* 4.1 18.2 - - + -
357B SER* 3.8 7.4 - - - -
373B ARG* 5.3 4.9 - - + -
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Residues in contact with PHE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU* 4.5 1.8 - - + -
196B LEU* 5.8 0.2 - - + -
251B PRO 3.9 17.3 - - - -
254B LEU* 4.4 4.3 - - + -
255B PHE* 3.9 27.8 - + - -
258B LEU* 4.3 14.8 - - + -
259B PHE* 3.8 17.7 - + - -
284B TRP* 5.1 1.3 - + - -
318B TYR 3.0 14.1 + - - +
319B ALA 3.4 9.9 - - - +
320B ARG 3.3 0.2 - - - -
321B LEU* 1.3 76.0 - - - +
323B SER* 1.3 63.3 + - - +
325B SER* 2.8 16.5 + - - -
326B ILE* 3.2 35.8 + - + +
354B PHE* 3.6 30.3 - + - -
357B SER* 3.2 22.2 + - - +
358B ALA* 4.2 15.7 - - + -
361B LEU* 4.1 9.4 - - + -
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Residues in contact with SER 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PRO* 3.3 29.5 - - - +
252B VAL* 5.9 0.2 - - - +
284B TRP* 3.7 29.9 - - - -
319B ALA 3.1 3.9 + - - -
320B ARG* 3.8 5.4 - - - -
322B PHE* 1.3 82.1 - - - +
324B LYS* 1.3 61.8 + - - +
326B ILE* 3.4 2.8 + - - +
327B GLU* 3.2 36.7 + - - +
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Residues in contact with LYS 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ARG 3.0 19.5 + - - +
321B LEU* 3.3 12.8 + - + +
323B SER* 1.3 73.2 - - - +
325B SER* 1.3 66.7 + - - +
327B GLU* 3.2 32.9 + - - +
328B THR* 3.2 27.5 + - - +
353B ASP* 5.7 3.1 - - - +
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Residues in contact with SER 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B LEU 2.9 16.2 + - - -
322B PHE* 2.8 21.3 + - - -
324B LYS* 1.3 73.7 - - - +
326B ILE* 1.3 56.2 + - - +
328B THR* 3.2 7.6 + - - -
329B LEU* 2.8 35.2 + - - +
350B SER* 3.7 14.1 - - - -
353B ASP* 3.9 9.9 - - - -
354B PHE* 3.4 40.5 - - - +
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Residues in contact with ILE 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PHE* 4.4 8.5 - - + -
249B TYR* 3.5 36.8 - - + +
251B PRO* 4.1 13.9 - - + -
254B LEU* 3.9 19.3 - - + -
322B PHE* 3.2 55.3 + - + +
323B SER 3.6 4.5 - - - +
325B SER* 1.3 74.5 + - - +
327B GLU* 1.3 66.4 + - - +
329B LEU* 4.3 5.8 - - - -
330B ARG* 2.8 24.8 + - - +
354B PHE* 3.9 18.6 - - + -
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Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B PRO* 4.4 8.0 - - + +
323B SER* 3.2 28.0 + - - +
324B LYS* 3.2 27.1 + - + +
326B ILE* 1.3 77.0 - - - +
328B THR* 1.3 62.5 + - - +
330B ARG* 3.2 43.0 + - - +
331B VAL* 3.3 15.1 - - - +
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Residues in contact with THR 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LYS* 3.2 22.8 + - - -
325B SER* 3.2 6.2 + - - -
326B ILE 3.2 0.6 - - - -
327B GLU* 1.3 77.1 - - - +
329B LEU* 1.3 65.9 + - - +
331B VAL* 3.2 8.3 + - - +
332B HIS* 3.2 42.0 + - + +
350B SER* 3.1 28.6 + - - +
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Residues in contact with LEU 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B PHE* 3.5 36.1 - - + -
197B PHE* 3.6 31.4 - - + -
325B SER 2.8 23.9 + - - +
326B ILE 3.8 0.2 - - - +
328B THR* 1.3 74.4 - - + +
330B ARG* 1.3 63.5 + - - +
332B HIS* 3.1 12.7 + - + +
333B LEU* 3.0 23.0 + - - +
342B LEU* 3.8 12.6 - - + +
348B ASP* 4.3 7.0 - - - +
350B SER* 3.9 23.3 - - - +
351B ALA* 4.1 5.6 - - - +
354B PHE* 3.9 23.3 - - + -
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Residues in contact with ARG 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B PHE* 3.8 8.2 - - + -
248B GLY 2.9 21.5 + - - -
249B TYR* 2.8 58.9 + - + -
250B ASP* 4.2 2.0 + - - +
251B PRO* 4.0 9.6 - - - +
326B ILE 2.8 17.2 + - - +
327B GLU* 3.2 41.6 + - - +
329B LEU* 1.3 74.3 - - - +
331B VAL* 1.3 65.2 + - + +
333B LEU* 3.6 5.6 + - - +
334B ALA* 3.1 23.7 + - - +
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Residues in contact with VAL 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLU 3.3 15.9 - - - +
328B THR* 3.2 9.1 + - + +
329B LEU 3.1 0.6 - - - -
330B ARG* 1.3 81.6 - - + +
332B HIS* 1.3 70.4 + - + +
334B ALA* 3.1 6.5 + - + +
335B GLU* 2.9 51.1 + - + +
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Residues in contact with HIS 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B THR* 3.2 33.9 + - + +
329B LEU* 3.1 15.1 + - + +
331B VAL* 1.3 81.7 - - + +
333B LEU* 1.3 63.0 + - - +
335B GLU* 3.2 26.1 + - - +
336B LYS* 3.4 26.9 + - - +
342B LEU* 4.4 15.9 - - + -
348B ASP* 5.3 12.4 + - - -
350B SER* 6.2 1.5 - - - -
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Residues in contact with LEU 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B LEU 4.6 0.2 - - - +
197B PHE* 3.7 32.8 - - + +
241B LYS* 4.8 4.7 - - - +
245B LYS* 6.0 2.7 - - + -
249B TYR* 3.6 36.1 - - + +
329B LEU 3.0 15.7 + - - +
330B ARG 3.8 5.2 - - - +
332B HIS* 1.3 77.4 - - - +
334B ALA* 1.3 61.2 + - - +
336B LYS* 3.4 11.8 + - + +
337B GLY 3.7 13.0 - - - +
340B ALA* 3.2 32.8 - - + +
341B GLU 4.2 0.4 - - - +
342B LEU* 3.8 21.5 - - + +
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Residues in contact with ALA 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ARG 3.1 17.8 + - - +
331B VAL* 3.1 7.1 + - - +
333B LEU* 1.3 72.9 - - - +
335B GLU* 1.3 63.6 + - + +
336B LYS 3.1 5.9 + - - -
337B GLY* 3.3 14.1 + - - -
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Residues in contact with GLU 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B VAL* 2.9 39.5 + - + +
332B HIS* 3.2 19.4 + - - +
334B ALA* 1.3 77.1 - - + +
336B LYS* 1.3 59.1 + - - +
337B GLY 3.3 0.7 - - - -
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Residues in contact with LYS 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332B HIS* 3.4 19.0 + - - +
333B LEU* 3.7 6.7 - - - +
334B ALA 3.1 1.4 - - - -
335B GLU* 1.3 78.4 - - - +
337B GLY* 1.3 61.3 + - - +
340B ALA* 3.6 21.1 - - + +
341B GLU 4.3 13.7 - - - +
342B LEU* 3.8 30.0 - - + +
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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