Contacts of the helix formed by residues 275 - 288 (chain X) 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 SER 275 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273X GLY 4.0 1.0 + - - -
274X MET* 1.3 77.5 - - - +
276X GLU* 1.3 64.6 + - - +
277X GLU* 2.9 20.6 + - - +
278X ASP* 2.6 30.6 + - - -
279X ALA* 2.9 21.3 + - - +
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Residues in contact with GLU 276 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274X MET 3.8 0.6 + - - -
275X SER* 1.3 73.4 - - - +
277X GLU* 1.3 52.3 + - - +
279X ALA* 3.9 2.9 + - - +
280X THR* 2.5 32.7 + - - -
303X ARG 4.4 3.8 - - - +
304X ALA* 3.6 32.5 - - - +
306X GLN 4.4 1.9 - - - -
307X ALA* 4.1 9.9 + - + +
308X SER* 2.7 50.3 + - - -
330X ARG* 2.9 34.1 + - - +
334X ASN* 3.9 2.3 + - - +
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Residues in contact with GLU 277 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275X SER* 2.9 9.9 + - - +
276X GLU* 1.3 76.8 - - - +
278X ASP* 1.3 54.3 + - - +
279X ALA 3.0 1.3 - - - -
280X THR* 2.6 6.6 + - - -
281X LEU* 2.6 53.7 + - + +
330X ARG* 3.8 12.7 + - - +
342X TYR* 2.4 36.9 + - - -
344X HIS* 2.8 35.7 + - + +
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Residues in contact with ASP 278 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245X PRO* 5.9 1.9 - - - +
274X MET* 3.8 14.5 - - + +
275X SER* 2.6 48.6 + - - +
277X GLU* 1.3 73.4 - - - +
279X ALA* 1.3 57.7 + - - +
281X LEU* 4.2 15.9 - - - +
282X ASN* 3.0 42.5 + - - +
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Residues in contact with ALA 279 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232X MET* 4.3 0.5 - - - +
271X SER* 3.9 1.8 - - - -
274X MET* 3.7 22.8 - - + +
275X SER 2.9 16.9 + - - +
276X GLU 3.9 3.1 - - - +
278X ASP* 1.3 78.6 - - - +
280X THR* 1.3 59.7 + - - +
283X LEU* 3.3 11.1 + - - +
301X TYR* 2.6 37.1 + - + -
304X ALA* 3.5 26.5 - - + -
334X ASN* 3.8 1.6 - - - -
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Residues in contact with THR 280 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276X GLU 2.5 19.8 + - - -
277X GLU* 2.6 18.6 + - - -
279X ALA* 1.3 72.0 - - - +
281X LEU* 1.3 65.7 + - - +
284X ASN* 2.9 25.3 + - - +
330X ARG* 2.5 12.9 + - - +
333X ALA 3.6 11.7 - - - +
334X ASN* 2.4 27.9 + - - +
337X ALA* 3.2 22.7 - - + +
342X TYR* 3.6 30.5 - - + -
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Residues in contact with LEU 281 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245X PRO* 4.3 20.0 - - + -
277X GLU* 2.6 38.6 + - + +
278X ASP* 4.0 14.6 - - - +
280X THR* 1.3 71.5 - - - +
282X ASN* 1.3 59.1 + - - +
284X ASN* 3.0 9.4 + - - +
285X ALA* 2.6 38.2 + - - +
342X TYR* 3.8 23.8 - - + -
344X HIS* 3.9 24.2 - - + +
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Residues in contact with ASN 282 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232X MET* 3.2 17.9 - - - -
234X THR* 5.6 1.4 - - - +
245X PRO* 3.3 26.2 - - - +
248X VAL* 3.6 33.5 - - + +
249X ALA* 5.9 0.2 - - - -
274X MET* 3.7 18.2 - - - -
278X ASP* 3.0 23.9 + - - +
281X LEU* 1.3 73.2 - - - +
283X LEU* 1.3 66.9 + - - +
285X ALA* 3.8 7.0 - - - +
286X ILE* 2.8 32.0 + - + +
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Residues in contact with LEU 283 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232X MET* 4.4 3.5 - - + -
269X PHE* 4.7 2.9 - - + -
279X ALA 3.3 9.9 + - - +
281X LEU 3.3 0.8 - - - -
282X ASN* 1.3 76.3 - - - +
284X ASN* 1.3 61.6 + - - +
286X ILE* 3.1 10.6 + - + +
287X ASN* 2.8 35.3 + - - +
297X LEU* 3.2 17.7 - - + +
298X SER 3.6 29.2 - - - +
299X PHE* 3.8 7.6 - - + -
301X TYR* 3.3 22.4 - - + +
334X ASN 3.6 23.8 - - - +
337X ALA* 3.4 16.4 - - + +
338X ALA* 3.7 6.1 - - - +
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Residues in contact with ASN 284 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280X THR 2.9 14.4 + - - +
281X LEU* 3.1 11.3 + - - +
283X LEU* 1.3 75.2 - - - +
285X ALA* 1.3 56.7 + - - +
287X ASN* 2.6 28.8 + - - +
288X LEU* 3.0 31.8 + - - +
336X GLN 3.9 0.2 - - - +
337X ALA* 2.9 17.6 + - - +
340X GLY* 3.1 31.4 + - - -
341X GLN 3.2 0.2 + - - -
342X TYR* 3.1 35.1 + - + +
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Residues in contact with ALA 285 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245X PRO* 2.8 39.9 - - + +
246X GLU* 4.4 10.3 - - - +
249X ALA* 3.4 10.2 - - + +
281X LEU 2.6 20.0 + - - +
282X ASN* 3.8 3.6 - - - +
284X ASN* 1.3 76.0 - - - +
286X ILE* 1.3 56.7 + - - +
288X LEU* 3.0 10.5 + - - +
289X CYS* 3.0 24.8 + - - -
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Residues in contact with ILE 286 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232X MET* 3.6 33.2 - - + -
248X VAL* 5.7 0.7 - - + -
249X ALA* 3.8 27.1 - - - +
252X THR* 4.1 7.6 - - + +
253X VAL* 3.9 8.2 - - + +
269X PHE* 3.6 31.0 - - + -
282X ASN* 2.8 26.0 + - + +
283X LEU* 3.3 6.3 - - - +
284X ASN 2.8 0.2 + - - -
285X ALA* 1.3 72.2 - - - +
287X ASN* 1.3 60.4 + - - +
288X LEU 3.0 5.9 + - - -
289X CYS* 3.5 15.6 + - - +
293X LYS* 3.6 11.6 - - - +
297X LEU* 3.3 29.4 - - + -
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Residues in contact with ASN 287 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283X LEU* 2.8 35.2 - - - +
284X ASN 2.6 11.5 + - - +
286X ILE* 1.3 72.7 - - - +
288X LEU* 1.3 63.9 + - - +
289X CYS 3.5 0.7 - - - -
293X LYS* 3.3 16.7 + - - +
296X LYS* 5.8 0.2 - - - +
297X LEU* 3.3 32.6 + - - +
337X ALA 3.8 7.4 - - - +
338X ALA 2.6 29.8 + - - +
339X LYS 4.7 1.1 - - - -
340X GLY* 4.2 9.6 - - - +
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Residues in contact with LEU 288 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284X ASN* 3.0 34.2 + - - +
285X ALA* 3.0 13.2 + - - +
287X ASN* 1.3 85.9 - - - +
289X CYS* 1.3 63.6 + - - +
290X PRO* 3.5 6.1 - - - +
293X LYS* 4.4 0.2 - - - -
340X GLY* 3.7 27.8 - - - +
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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
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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