Contacts of the helix formed by residues 266 - 283 (chain A) in PDB entry 1QZE
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 ASN 266 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A PHE* 4.2 7.1 - - + -
235A LEU* 3.7 29.8 - - + +
238A GLN* 3.3 20.2 + - - +
240A GLN* 3.2 27.1 + - - +
262A LEU 3.9 3.7 + - - +
263A GLY 4.2 3.1 + - - +
265A GLU* 1.3 85.9 - - - +
267A PRO* 1.3 69.2 - - - +
268A GLN* 3.3 11.4 + - - +
269A LEU* 3.5 2.0 + - - +
270A LEU* 3.2 25.0 + - - +
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Residues in contact with PRO 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A GLU 3.3 11.2 - - - +
266A ASN* 1.3 83.1 - - - +
268A GLN* 1.3 76.4 + - + +
269A LEU 3.2 0.7 + - - -
270A LEU* 3.7 11.2 - - + -
271A GLN* 3.3 25.5 + - - +
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Residues in contact with GLN 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LEU 5.6 0.5 + - - -
234A PHE* 3.1 50.0 - - + +
238A GLN* 5.3 1.2 - - - +
266A ASN* 3.1 8.1 + - - +
267A PRO* 1.3 90.8 - - + +
269A LEU* 1.3 56.0 + - - +
271A GLN* 3.0 30.4 + - - +
272A GLN* 4.5 2.6 + - - +
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LEU* 3.5 49.4 - - + +
234A PHE* 3.7 2.6 - - + -
235A LEU* 3.2 37.9 - - + -
241A PHE* 6.1 0.2 - - + -
263A GLY* 5.3 7.2 - - - +
266A ASN 3.5 3.6 + - - +
268A GLN* 1.3 77.0 - - - +
270A LEU* 1.3 61.3 + - - +
271A GLN 3.1 2.5 - - - -
272A GLN* 2.8 4.8 + - - +
273A ILE* 2.6 58.0 + - + +
280A PHE* 3.2 35.2 - - + -
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Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LEU* 5.1 2.9 - - + +
263A GLY 2.8 31.4 - - - +
264A GLN* 3.7 23.8 - - + -
266A ASN 3.2 15.8 + - - +
267A PRO* 3.4 11.0 + - + -
269A LEU* 1.3 78.2 - - - +
271A GLN* 1.3 62.5 + - - +
272A GLN 3.2 0.7 + - - -
273A ILE* 3.3 23.9 - - + +
274A SER* 3.4 15.9 + - - -
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Residues in contact with GLN 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A PRO 3.3 10.9 + - - +
268A GLN* 3.0 30.5 + - - +
270A LEU* 1.3 79.5 - - - +
272A GLN* 1.3 80.2 + - - +
274A SER* 3.3 12.0 + - - -
275A ARG* 5.3 2.8 - - - +
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Residues in contact with GLN 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LEU* 4.3 17.0 - - + +
268A GLN 4.6 2.7 - - - +
269A LEU* 2.8 8.8 + - - +
271A GLN* 1.3 107.5 - - + +
273A ILE* 1.3 52.1 + - - +
274A SER 2.9 2.2 - - - -
275A ARG* 2.6 13.7 + - - +
276A HIS* 2.6 69.6 + - + +
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LEU* 5.2 1.1 - - - +
259A LEU* 3.5 31.4 - - + -
263A GLY* 5.1 6.5 - - - +
269A LEU* 2.6 50.0 + - + +
270A LEU* 3.3 27.4 - - + +
272A GLN* 1.3 73.3 - - - +
274A SER* 1.3 63.1 + - - +
276A HIS* 3.9 9.8 - - - +
277A GLN* 2.7 40.4 + - + +
280A PHE* 3.7 32.5 - - + -
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Residues in contact with SER 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU* 3.4 15.9 - - - -
271A GLN* 3.3 17.7 + - - -
272A GLN 2.7 4.4 + - - -
273A ILE* 1.3 83.8 - - - +
275A ARG* 1.3 76.2 + - - +
277A GLN* 4.4 15.5 + - - +
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Residues in contact with ARG 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLN 5.3 2.5 - - - +
272A GLN* 2.6 13.3 + - - +
274A SER* 1.3 86.6 + - - +
276A HIS* 1.3 70.7 + - + +
277A GLN* 3.4 4.2 + - - -
278A GLU* 4.5 10.7 - - - +
279A GLN* 4.2 3.3 - - - +
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Residues in contact with HIS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A LEU* 4.2 19.2 - - + +
272A GLN* 2.6 58.6 + - + +
273A ILE* 3.5 5.6 - - - -
275A ARG* 1.3 88.9 + - + +
277A GLN* 1.3 61.3 - - - +
278A GLU 2.8 7.4 + - - -
279A GLN* 2.9 28.3 + - + +
280A PHE* 2.8 22.1 + - + +
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Residues in contact with GLN 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A LEU* 4.4 20.7 - - + +
273A ILE* 2.7 22.3 + - + +
274A SER* 4.4 13.8 + - - +
275A ARG 3.4 2.0 - - - -
276A HIS* 1.3 77.7 - - - +
278A GLU* 1.3 62.3 + - + +
280A PHE* 3.9 7.9 - - + -
281A ILE* 2.9 49.4 + - + +
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ARG 4.5 10.2 - - - +
276A HIS* 2.8 1.4 + - - -
277A GLN* 1.3 83.5 + - + +
279A GLN* 1.3 73.4 + - - +
281A ILE* 4.9 1.6 - - - -
282A GLN* 2.5 48.1 + - - +
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Residues in contact with GLN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LEU* 5.1 11.0 - - + -
275A ARG 4.2 2.6 - - - +
276A HIS* 2.9 43.0 + - + +
278A GLU* 1.3 89.6 + - - +
280A PHE* 1.3 66.6 + - - +
282A GLN* 3.6 8.2 - - + +
283A MET* 3.1 25.3 + - - +
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Residues in contact with PHE 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LEU* 5.4 10.7 - - + +
235A LEU* 5.9 0.2 - - + -
241A PHE* 3.3 42.5 - + - -
244A MET* 3.8 35.2 - - + -
255A LEU* 5.0 4.3 - - + -
259A LEU* 5.3 4.0 - - + -
263A GLY* 6.2 1.1 - - - -
269A LEU* 3.2 40.6 - - + -
273A ILE* 3.7 21.3 - - + -
276A HIS* 2.8 17.3 + - + +
277A GLN* 4.0 8.7 - - + +
279A GLN* 1.3 77.5 - - - +
281A ILE* 1.3 74.7 + - + +
283A MET* 3.2 24.0 + - + +
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A LEU* 5.1 22.2 - - + -
277A GLN* 2.9 39.4 + - + +
278A GLU* 5.0 1.8 - - - -
280A PHE* 1.3 83.6 - - + +
282A GLN* 1.3 78.3 + - - +
283A MET 3.0 8.6 + - - -
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Residues in contact with GLN 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A GLU* 2.5 42.1 + - - +
279A GLN* 3.6 10.1 - - + +
280A PHE 3.3 0.2 - - - -
281A ILE* 1.3 89.9 - - - +
283A MET* 1.3 59.5 + - - +
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Residues in contact with MET 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A LEU* 4.0 29.2 - - + +
233A GLU* 5.5 4.0 - - - +
236A ARG* 3.7 57.0 + - + -
241A PHE* 4.8 15.9 - - + -
245A ARG* 4.5 17.1 + - - +
279A GLN 3.1 13.8 + - - +
280A PHE* 3.7 14.6 - - + +
281A ILE 3.0 6.3 - - - -
282A GLN* 1.3 82.5 - - - +
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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
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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