Contacts of the helix formed by residues 272 - 290 (chain B) in PDB entry 1QK0
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 TRP 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B GLY* 2.8 30.9 + - - -
269B TRP 3.7 12.8 - - - -
270B LEU 3.4 0.2 - - - -
271B GLY* 1.3 79.2 - - - +
273B PRO* 1.3 78.8 - - + +
274B ALA* 4.6 4.3 - - + +
275B ASN* 2.9 27.9 + - - +
276B GLN* 3.2 6.9 + - - +
319B GLN 3.8 16.4 - - - -
320B GLY* 3.3 28.0 - - - -
321B ASN* 3.6 26.9 - - + +
364B TRP* 3.9 21.8 - + + -
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Residues in contact with PRO 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B GLY 3.3 2.2 - - - +
272B TRP* 1.3 91.6 - - + +
274B ALA* 1.3 62.5 + - - +
275B ASN 3.1 1.9 + - - -
276B GLN* 3.2 31.7 + - - +
277B ASP* 4.4 2.3 + - - +
320B GLY 5.5 3.1 - - - +
321B ASN* 4.3 9.4 - - - +
322B ALA* 6.0 3.8 - - + +
323B VAL* 6.1 0.7 - - + -
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Residues in contact with ALA 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B TRP* 3.3 4.4 - - + +
273B PRO* 1.3 79.3 - - - +
275B ASN* 1.3 64.6 + - - +
276B GLN 3.6 0.2 - - - -
278B PRO* 3.3 22.2 - - - +
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Residues in contact with ASN 275 (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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227B VAL* 4.2 10.3 - - + +
228B THR* 3.6 23.5 - - - +
269B TRP 2.8 24.0 + - - -
270B LEU* 3.7 17.5 - - - +
272B TRP* 2.9 26.2 + - - +
274B ALA* 1.3 83.5 - - - +
276B GLN* 1.3 65.5 + - - +
277B ASP 3.5 1.3 - - - -
278B PRO* 3.4 5.2 - - - +
279B ALA* 3.1 26.0 + - - +
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Residues in contact with GLN 276 (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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270B LEU 3.7 10.5 - - - +
271B GLY* 2.8 24.7 + - - +
272B TRP 3.2 8.4 + - - +
273B PRO* 3.2 22.1 + - - +
275B ASN* 1.3 76.8 - - - +
277B ASP* 1.3 63.1 + - - +
279B ALA* 3.7 3.0 - - - +
280B ALA* 3.0 24.3 + - - +
323B VAL* 3.7 17.2 - - - +
329B TYR* 5.5 3.8 - - + -
332B ALA* 3.7 28.8 - - + +
333B ILE* 4.3 7.0 - - + +
336B LEU* 3.6 17.5 - - + +
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Residues in contact with ASP 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B PRO 4.4 3.0 + - - +
276B GLN* 1.3 74.9 - - - +
278B PRO* 1.3 77.5 - - + +
280B ALA* 3.1 2.2 + - - +
281B GLN* 2.8 41.1 + - - +
336B LEU* 3.8 17.8 - - + +
340B HIS* 2.8 27.0 + - - -
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Residues in contact with PRO 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B VAL* 4.2 18.6 - - + +
274B ALA 3.3 25.4 - - - +
275B ASN* 3.4 7.4 - - - +
277B ASP* 1.3 96.5 - - + +
279B ALA* 1.3 55.6 + - - +
281B GLN* 3.3 9.3 + - + +
282B LEU* 2.9 29.8 + - - +
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B VAL* 3.8 15.8 - - + +
270B LEU* 3.7 32.3 - - + -
275B ASN 3.1 19.8 + - - +
276B GLN* 3.7 3.4 - - - +
278B PRO* 1.3 77.0 - - - +
280B ALA* 1.3 64.8 + - - +
282B LEU* 3.0 4.2 + - - +
283B PHE* 2.9 35.2 + - + -
333B ILE* 4.1 6.7 - - + -
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Residues in contact with ALA 280 (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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276B GLN 3.0 14.5 + - - +
277B ASP 3.6 3.1 - - - +
279B ALA* 1.3 76.1 - - - +
281B GLN* 1.3 58.4 + - - +
283B PHE 3.4 0.2 + - - -
284B ALA* 2.9 32.7 + - - +
333B ILE* 3.8 12.9 - - + +
336B LEU* 3.4 41.5 - - + -
337B LEU* 3.7 13.9 - - + +
340B HIS* 4.0 5.3 - - + +
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Residues in contact with GLN 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ASP* 2.8 34.8 + - - +
278B PRO* 3.5 9.1 - - + +
280B ALA* 1.3 72.9 - - - +
282B LEU* 1.3 58.4 + - - +
284B ALA* 3.9 1.2 - - - +
285B ASN* 2.9 49.9 + - - +
340B HIS* 3.7 31.3 - - + +
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Residues in contact with LEU 282 (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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223B LEU* 3.5 39.7 - - + +
226B LEU* 4.2 14.8 - - + -
227B VAL* 3.7 15.9 - - + -
243B LEU* 4.1 26.9 - - + -
278B PRO 2.9 13.6 + - - +
279B ALA 3.4 8.5 - - - +
281B GLN* 1.3 74.5 - - - +
283B PHE* 1.3 70.1 + - + +
285B ASN* 3.2 10.2 + - + +
286B VAL* 3.0 31.0 + - + +
501B NAG 5.5 3.8 - - + -
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Residues in contact with PHE 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 3.8 32.3 - - + -
224B ALA 5.3 2.2 - - - -
227B VAL* 5.4 1.8 - - + -
262B LEU* 4.3 2.9 - - + -
263B ASP 3.6 17.7 - - - -
264B ALA* 3.5 30.1 - - + -
270B LEU* 3.8 14.6 - - + -
279B ALA* 2.9 44.0 + - + +
280B ALA* 4.1 0.9 - - - -
282B LEU* 1.3 78.6 - - + +
284B ALA* 1.3 63.2 - - - +
286B VAL* 3.2 8.5 + - - +
287B TYR 3.0 18.0 + - - -
299B LEU* 3.8 22.2 - - + -
333B ILE* 3.9 11.4 - - + -
337B LEU* 4.0 12.1 - - + -
342B TRP* 3.5 21.3 - - + -
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Residues in contact with ALA 284 (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 ALA 2.9 19.2 + - - +
281B GLN 3.9 1.8 - - - +
283B PHE* 1.3 76.0 - - - +
285B ASN* 1.3 57.5 + - - +
287B TYR* 3.2 3.1 + - - +
288B LYS* 2.8 34.3 + - - +
337B LEU* 4.3 2.9 - - - +
340B HIS* 3.3 39.5 - - + +
342B TRP* 4.0 22.8 - - + -
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Residues in contact with ASN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLN* 2.9 47.0 + - - +
282B LEU* 3.2 8.7 + - + +
284B ALA* 1.3 72.3 - - - +
286B VAL* 1.3 58.0 + - - +
288B LYS* 3.4 25.7 + - - +
289B ASN* 2.7 37.9 + - - +
340B HIS* 6.1 0.2 - - - +
501B NAG 4.5 17.3 - - + +
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Residues in contact with VAL 286 (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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223B LEU* 4.1 24.5 - - + -
243B LEU* 4.7 4.0 - - + -
246B ILE* 4.1 21.8 - - + +
247B ASN* 5.1 4.6 + - + +
250B VAL* 4.8 10.1 - - + -
262B LEU* 3.7 22.0 - - + -
282B LEU* 3.0 30.4 + - + +
283B PHE 3.2 7.8 + - - +
285B ASN* 1.3 76.6 - - - +
287B TYR* 1.3 65.8 + - - +
289B ASN* 3.8 1.4 - - - +
290B ALA* 3.2 21.5 + - - +
296B LEU* 5.0 1.5 - - + +
501B NAG 4.2 17.0 - - - +
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Residues in contact with TYR 287 (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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283B PHE 3.0 4.9 + - - -
284B ALA 3.2 7.6 - - - +
286B VAL* 1.3 77.0 - - - +
288B LYS* 1.3 67.3 + - + +
290B ALA 3.1 8.3 + - - -
292B SER* 3.0 52.9 + - - -
293B PRO* 3.5 27.5 + - + +
296B LEU* 3.8 27.3 - - + +
341B GLY 4.1 13.2 - - - -
342B TRP* 3.5 69.0 + + + -
343B SER 4.7 5.2 + - - -
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Residues in contact with LYS 288 (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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284B ALA 2.8 22.1 + - - +
285B ASN* 3.4 27.9 + - - +
287B TYR* 1.3 77.2 - - + +
289B ASN* 1.3 62.3 + - - +
291B SER* 3.0 15.2 + - - -
292B SER* 4.2 11.2 + - - +
340B HIS* 2.7 34.7 + - - +
341B GLY* 4.1 21.1 - - - +
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Residues in contact with ASN 289 (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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247B ASN* 3.3 14.9 + - - +
285B ASN 2.7 24.4 + - - +
286B VAL 3.8 3.6 - - - +
288B LYS* 1.3 73.6 - - - +
290B ALA* 1.3 56.7 + - - +
291B SER* 3.2 3.9 + - - -
501B NAG 1.4 69.8 + - + +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B ASN* 3.7 12.6 - - - +
250B VAL* 4.2 10.8 - - + -
251B THR* 3.5 30.2 - - + +
254B ASN* 5.6 1.0 + - - -
286B VAL 3.2 14.8 + - - +
287B TYR 3.1 3.6 + - - +
289B ASN* 1.3 76.0 - - - +
291B SER* 1.3 71.2 + - - +
292B SER 3.3 1.6 - - - -
293B PRO* 3.3 27.2 - - + +
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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
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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