Contacts of the helix formed by residues 277 - 287 (chain Z) in PDB entry 1XDM
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 GLU 277 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275Z SER* 2.8 9.0 + - - +
276Z GLU* 1.3 80.5 - - - +
278Z ASP* 1.3 53.4 + - - +
279Z ALA 3.5 0.2 - - - -
280Z THR* 4.0 1.7 - - - -
281Z LEU* 2.7 54.1 + - + +
330Z ARG* 3.6 16.8 + - - +
342Z TYR* 3.1 26.3 + - - -
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Residues in contact with ASP 278 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245Z PRO* 4.9 5.9 - - - +
274Z MET* 4.6 7.4 - - + -
275Z SER* 2.8 28.5 + - - +
277Z GLU* 1.3 77.5 - - - +
279Z ALA* 1.3 61.0 + - - +
280Z THR 3.0 6.1 + - - -
281Z LEU* 3.3 22.5 - - - +
282Z ASN* 3.3 34.9 + - - +
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Residues in contact with ALA 279 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232Z MET* 4.9 0.7 - - - -
271Z SER* 4.0 4.0 - - - -
274Z MET* 3.9 22.6 - - + +
275Z SER 2.8 14.1 + - - +
276Z GLU 4.5 0.9 - - - +
278Z ASP* 1.3 78.4 - - - +
280Z THR* 1.3 57.6 + - - +
283Z LEU* 3.4 9.6 + - - +
301Z TYR* 2.4 53.4 + - + -
304Z ALA* 3.6 17.7 - - + -
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Residues in contact with THR 280 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276Z GLU 2.5 9.0 + - - -
277Z GLU 4.1 5.2 - - - -
278Z ASP 3.0 0.6 - - - -
279Z ALA* 1.3 78.6 - - - +
281Z LEU* 1.3 67.1 + - - +
282Z ASN 3.3 1.1 - - - -
283Z LEU 3.4 1.0 + - - -
284Z ASN* 2.9 25.3 + - - +
330Z ARG* 2.5 29.9 + - - +
333Z ALA 4.0 8.3 - - - +
334Z ASN* 2.8 18.1 + - - +
337Z ALA* 3.8 6.2 - - + +
342Z TYR* 3.3 46.2 - - + -
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Residues in contact with LEU 281 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245Z PRO* 3.7 22.7 - - + +
246Z GLU* 5.3 0.3 - - - +
277Z GLU* 2.7 41.7 + - + +
278Z ASP* 3.3 26.7 - - - +
280Z THR* 1.3 79.4 - - - +
282Z ASN* 1.3 63.0 + - - +
284Z ASN* 3.0 13.3 + - - +
285Z ALA* 3.0 14.0 + - - +
342Z TYR* 4.3 13.5 - - + -
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Residues in contact with ASN 282 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232Z MET* 3.4 24.0 - - + -
234Z THR* 4.6 4.4 - - - +
245Z PRO* 2.7 50.7 - - - +
248Z VAL* 3.9 24.5 - - + +
249Z ALA* 4.3 0.5 - - - +
274Z MET* 4.1 11.3 - - - -
278Z ASP* 3.3 21.6 + - - +
280Z THR 3.3 0.4 - - - -
281Z LEU* 1.3 70.5 - - - +
283Z LEU* 1.3 58.4 + - - +
284Z ASN 2.8 6.2 + - - -
285Z ALA* 3.0 3.1 + - - +
286Z ILE* 2.8 34.1 + - + +
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Residues in contact with LEU 283 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232Z MET* 4.3 2.6 - - + +
269Z PHE* 4.2 14.1 - - + -
279Z ALA 3.4 7.4 + - - +
280Z THR 3.4 1.6 + - - -
282Z ASN* 1.3 77.6 - - - +
284Z ASN* 1.3 56.1 + - - +
286Z ILE* 3.9 12.6 - - + -
287Z ASN 3.5 7.4 + - - -
297Z LEU 3.1 27.6 - - - +
298Z SER 3.5 9.6 - - - +
299Z PHE* 3.4 41.5 - - + -
301Z TYR* 3.3 23.1 - - + +
334Z ASN 4.0 1.6 - - - +
337Z ALA* 2.7 45.1 - - + +
338Z ALA 4.3 1.3 - - - +
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Residues in contact with ASN 284 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280Z THR 2.9 13.1 + - - +
281Z LEU* 3.2 11.9 - - - +
282Z ASN 2.9 0.8 - - - -
283Z LEU* 1.3 77.3 - - - +
285Z ALA* 1.3 66.9 + - - +
287Z ASN* 2.9 15.1 + - - +
288Z LEU* 3.2 31.0 + - - +
336Z GLN 3.3 2.8 - - - +
337Z ALA* 3.6 4.0 - - - +
340Z GLY* 2.8 38.6 + - - -
342Z TYR* 2.9 42.1 + - + +
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Residues in contact with ALA 285 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245Z PRO 3.3 34.1 - - - +
246Z GLU* 3.8 18.4 - - + +
249Z ALA* 3.4 5.7 - - + +
281Z LEU 3.0 6.7 + - - +
282Z ASN 3.0 5.3 + - - +
284Z ASN* 1.3 79.6 - - - +
286Z ILE* 1.3 51.1 + - - +
288Z LEU* 2.6 16.7 + - - +
289Z CYS* 2.6 35.5 + - - -
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Residues in contact with ILE 286 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232Z MET* 3.9 22.7 - - + -
248Z VAL* 5.4 0.7 - - + -
249Z ALA* 3.2 24.9 - - + +
252Z THR* 3.8 12.3 - - + +
253Z VAL* 3.6 21.8 - - + +
269Z PHE* 3.4 46.9 - - + -
282Z ASN* 2.8 17.6 + - + +
283Z LEU* 3.9 9.6 - - + +
285Z ALA* 1.3 76.3 - - - +
287Z ASN* 1.3 59.5 + - - +
288Z LEU 3.1 3.3 + - - -
289Z CYS* 3.6 3.8 + - - +
293Z LYS* 3.9 3.5 - - - +
297Z LEU* 3.5 30.1 - - + +
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Residues in contact with ASN 287 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283Z LEU 3.5 0.6 + - - +
284Z ASN 2.9 8.2 + - - +
286Z ILE* 1.3 77.4 - - - +
288Z LEU* 1.3 62.7 + - - +
293Z LYS* 3.6 14.0 + - - +
295Z TRP 5.6 0.4 + - - -
297Z LEU* 3.3 36.7 + - - +
337Z ALA 3.4 16.4 - - - +
338Z ALA* 2.7 39.4 + - - +
339Z LYS* 4.3 3.8 - - - +
340Z GLY* 4.0 10.2 - - - +
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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
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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