Contacts of the helix formed by residues 277 - 296 (chain W) in PDB entry 5IY6
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 277 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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268W LYS* 5.7 4.8 - - + +
269W THR 4.4 11.4 - - - +
271W LEU 5.8 0.2 + - - -
272W ARG* 3.7 25.3 + - - +
276W THR* 1.3 77.2 + - - +
278W GLU* 1.4 65.0 + - - +
279W GLN* 4.2 6.1 - - + +
280W ARG* 2.9 44.2 + - + +
281W LEU* 2.9 34.8 + - - +
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Residues in contact with GLU 278 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263W LEU* 4.8 10.2 - - + +
268W LYS* 4.6 5.0 - - + +
269W THR* 2.9 33.7 + - - +
272W ARG* 2.8 40.1 + - + +
277W ASP* 1.4 73.8 - - - +
279W GLN* 1.4 62.6 + - - +
281W LEU* 3.2 11.0 + - + +
282W ARG* 3.0 26.0 + - - +
329W PHE* 3.8 27.3 - - + +
330W LEU* 6.0 2.5 - - + -
332W PHE* 5.6 1.2 - - - +
333W LEU* 3.8 27.3 - - + +
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Residues in contact with GLN 279 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260W GLN* 3.6 24.6 + - - +
263W LEU* 3.4 27.4 - - + +
264W GLU* 2.8 32.5 + - - +
268W LYS* 4.0 20.4 - - + +
277W ASP* 3.3 5.6 - - + +
278W GLU* 1.4 76.9 + - - +
280W ARG* 1.4 63.1 + - + +
282W ARG* 2.7 62.5 + - - +
283W ASP 3.1 5.7 + - - -
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Residues in contact with ARG 280 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273W ILE 4.1 0.8 + - - -
274W LYS* 2.7 32.7 + - - +
275W GLU* 3.2 16.2 + - - +
276W THR* 3.3 23.2 + - - +
277W ASP* 2.9 42.2 + - + +
279W GLN* 1.4 75.4 - - + +
281W LEU* 1.3 57.4 - - - +
283W ASP* 3.0 13.1 - - - +
284W GLU* 3.0 32.2 + - + +
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Residues in contact with LEU 281 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276W THR* 3.3 22.9 - - + +
277W ASP 2.9 17.3 + - - +
278W GLU* 3.5 12.3 - - + +
280W ARG* 1.3 70.7 - - - +
282W ARG* 1.3 60.8 + - - +
284W GLU* 3.0 15.5 + - + +
285W TYR* 2.9 51.8 + - + +
316W GLN* 5.9 2.5 - - - +
326W ALA* 3.5 45.1 - - + +
329W PHE* 4.3 20.4 - - + -
330W LEU* 5.4 1.1 - - + +
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Residues in contact with ARG 282 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256W LEU* 4.3 22.2 - - + +
259W CYS 5.9 0.2 - - - -
260W GLN* 3.0 46.4 + - + +
263W LEU* 4.3 15.0 - - + -
278W GLU 3.0 16.6 + - - +
279W GLN* 2.7 53.4 + - - +
281W LEU* 1.3 74.1 - - - +
283W ASP* 1.4 95.5 + - - +
285W TYR* 3.3 17.4 + - + +
286W ARG* 3.0 47.3 + - - +
330W LEU* 5.8 3.1 - - + -
399W LEU* 4.9 8.7 - - + -
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Residues in contact with ASP 283 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279W GLN 3.1 6.3 + - - +
280W ARG* 3.0 17.5 + - - +
282W ARG* 1.4 104.4 + - - +
284W GLU* 1.3 60.5 + - - +
286W ARG* 3.7 4.3 - - - +
287W ARG* 2.8 35.3 + - - +
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Residues in contact with GLU 284 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280W ARG* 3.0 21.4 + - + +
281W LEU* 3.0 21.0 + - + +
283W ASP* 1.3 78.5 - - - +
285W TYR* 1.3 64.2 + - + +
287W ARG* 3.3 13.3 + - - +
288W LEU* 3.3 24.0 + - - +
315W LEU* 4.0 20.2 - - + +
316W GLN* 4.2 31.2 - - + +
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Residues in contact with TYR 285 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256W LEU* 5.6 3.4 - - + -
281W LEU* 2.9 34.8 + - + +
282W ARG* 3.6 15.9 - - + +
284W GLU* 1.3 78.1 - - + +
286W ARG* 1.3 65.0 + - - +
288W LEU* 3.3 17.6 + - + +
289W VAL* 3.2 23.2 + - - +
316W GLN* 5.2 7.6 - - - -
323W ILE* 6.0 0.7 - - + -
326W ALA* 3.4 35.4 + - + +
330W LEU* 3.8 27.3 - - + +
399W LEU* 5.2 15.0 - - + -
403W PHE* 3.0 52.3 - + + -
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Residues in contact with ARG 286 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253W ARG* 4.4 11.9 - - - +
256W LEU* 3.9 24.0 - - + +
257W ASP* 2.7 40.5 + - - +
260W GLN* 2.8 29.2 + - - +
282W ARG* 3.0 35.3 + - - +
283W ASP* 3.7 7.9 - - - +
285W TYR* 1.3 74.8 - - - +
287W ARG* 1.3 60.6 + - - +
289W VAL* 3.3 9.5 + - - -
290W GLU* 2.8 69.8 + - + +
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Residues in contact with ARG 287 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283W ASP* 2.8 22.3 + - - +
284W GLU* 3.5 7.9 - - - +
285W TYR 3.2 0.6 - - - -
286W ARG* 1.3 75.9 - - - +
288W LEU* 1.4 67.1 + - - +
290W GLU* 4.1 5.7 - - - +
291W GLY* 3.1 27.0 + - - +
311W PRO* 6.3 0.8 - - - +
315W LEU* 3.8 41.0 - - + +
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Residues in contact with LEU 288 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284W GLU 3.3 18.6 + - - +
285W TYR* 3.3 18.3 + - + +
286W ARG 3.2 0.2 - - - -
287W ARG* 1.4 80.3 - - - +
289W VAL* 1.4 66.4 + - + +
291W GLY* 3.2 6.6 + - - -
292W LEU* 3.4 20.0 + - + +
308W PRO 5.8 0.9 - - - +
311W PRO* 3.6 25.4 - - + +
312W ASP* 3.7 42.2 - - + +
315W LEU* 3.6 25.8 - - + -
316W GLN* 4.1 11.2 - - + +
403W PHE* 5.8 2.7 - - + -
406W LEU* 6.1 4.5 - - + -
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Residues in contact with VAL 289 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251W LEU* 4.5 24.2 - - + -
253W ARG* 5.5 7.4 - - + -
256W LEU* 4.2 15.9 - - + -
285W TYR 3.2 6.1 + - - +
286W ARG* 3.6 20.9 - - - +
288W LEU* 1.4 76.2 - - + +
290W GLU* 1.3 70.8 + - + +
292W LEU* 3.1 22.8 + - + +
293W ARG* 3.1 11.4 + - - +
418W ILE* 5.2 2.4 - - - +
433W LEU* 4.0 26.5 - - + -
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Residues in contact with GLU 290 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253W ARG* 2.8 44.1 + - + +
286W ARG* 2.8 68.8 + - + +
287W ARG* 4.1 5.4 - - - +
289W VAL* 1.3 74.5 - - + +
291W GLY* 1.3 64.2 + - - +
293W ARG* 3.0 25.3 + - - +
294W GLU* 3.4 11.4 + - - +
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Residues in contact with GLY 291 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287W ARG* 3.1 28.4 + - - +
288W LEU 3.2 3.6 + - - -
290W GLU* 1.3 76.9 - - - +
292W LEU* 1.4 55.3 + - - +
294W GLU* 3.2 9.9 + - - +
295W ALA* 3.1 30.5 + - - +
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Residues in contact with LEU 292 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288W LEU* 3.4 22.0 + - + +
289W VAL* 3.1 13.9 + - + +
291W GLY* 1.4 70.1 - - - +
293W ARG* 1.3 59.7 + - - +
295W ALA* 4.4 4.7 - - + -
296W SER* 2.7 50.6 + - - +
307W ASN* 3.3 36.3 - - - +
308W PRO* 4.8 20.6 - - + +
311W PRO* 4.5 18.6 - - + -
418W ILE* 4.4 12.6 - - + -
433W LEU* 5.0 10.3 - - + -
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Residues in contact with ARG 293 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253W ARG* 3.6 28.1 - - - +
289W VAL 3.1 9.3 + - - +
290W GLU* 3.0 16.4 + - - +
292W LEU* 1.3 76.9 - - - +
294W GLU* 1.3 93.6 + - - +
296W SER* 4.6 0.4 + - - -
297W ALA 4.1 3.3 - - - +
418W ILE* 4.4 9.3 - - + +
421W PHE* 2.3 82.1 + - + -
423W ASP* 4.2 13.1 + - - -
430W ASN* 3.4 26.2 + - - -
431W PRO* 3.6 10.5 - - + +
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Residues in contact with GLU 294 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253W ARG* 5.3 3.1 + - - -
290W GLU 3.4 8.6 + - - +
291W GLY* 3.2 9.4 + - - +
292W LEU 3.2 0.4 - - - -
293W ARG* 1.3 118.8 + - - +
295W ALA* 1.4 61.3 + - - +
297W ALA 5.1 3.3 + - - +
421W PHE* 4.7 4.1 - - - -
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Residues in contact with ALA 295 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291W GLY 3.1 18.2 + - - +
292W LEU* 4.2 6.1 - - + +
294W GLU* 1.4 76.8 - - - +
296W SER* 1.3 65.7 + - - +
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Residues in contact with SER 296 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292W LEU* 2.7 54.5 + - - +
293W ARG* 5.3 0.2 - - - -
294W GLU 3.7 0.6 - - - -
295W ALA* 1.3 76.3 - - - +
297W ALA* 1.4 59.4 + - - +
300W GLU 4.9 0.9 - - - +
301W THR* 5.5 1.7 + - - -
303W ALA* 5.5 2.9 - - - -
307W ASN* 4.6 1.9 + - - -
418W ILE* 3.6 28.8 - - - +
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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