Contacts of the helix formed by residues 275 - 289 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273W GLY 4.3 0.6 + - - -
274W MET* 1.3 74.3 - - - +
276W GLU* 1.3 68.7 + - - +
277W GLU* 2.7 9.1 + - - +
278W ASP* 2.4 49.7 + - - -
279W ALA* 3.1 5.2 + - - +
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Residues in contact with GLU 276 (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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274W MET 3.2 2.4 + - - -
275W SER* 1.3 70.9 - - - +
277W GLU* 1.3 59.0 + - - +
279W ALA* 3.2 14.0 - - - +
280W THR 3.2 1.9 + - - -
303W ARG 3.7 0.2 - - - +
304W ALA* 2.9 49.6 - - - +
305W LEU 3.5 1.7 + - - -
307W ALA* 2.9 37.9 + - + +
308W SER* 2.7 28.4 + - - -
330W ARG* 2.8 40.0 + - - +
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Residues in contact with GLU 277 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275W SER* 2.7 11.8 + - - +
276W GLU* 1.3 71.7 - - - +
278W ASP* 1.3 64.3 + - - +
279W ALA 3.1 1.8 - - - -
280W THR* 3.1 6.2 + - - -
281W LEU* 3.1 49.3 + - + +
330W ARG* 4.3 6.3 + - - +
342W TYR* 3.1 33.7 + - - -
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Residues in contact with ASP 278 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274W MET* 4.2 13.4 - - + -
275W SER* 2.4 36.0 + - - +
277W GLU* 1.3 77.1 - - - +
279W ALA* 1.3 56.9 + - - +
281W LEU* 4.1 13.5 - - - +
282W ASN* 2.8 43.9 + - - +
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Residues in contact with ALA 279 (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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271W SER* 4.3 2.5 - - - -
274W MET* 3.9 21.2 - - + -
275W SER 3.1 8.9 + - - +
276W GLU 3.2 12.6 - - - +
278W ASP* 1.3 78.8 - - - +
280W THR* 1.3 61.3 + - - +
282W ASN* 4.0 1.4 - - - +
283W LEU* 3.1 12.0 + - - +
301W TYR* 2.9 44.1 + - + -
304W ALA* 3.9 15.0 - - + -
334W ASN* 4.8 0.2 - - - +
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Residues in contact with THR 280 (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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276W GLU 3.2 0.4 + - - -
277W GLU* 3.1 13.0 + - - -
279W ALA* 1.3 75.7 - - - +
281W LEU* 1.3 54.5 + - - +
283W LEU* 2.7 7.6 + - - +
284W ASN* 2.6 33.8 + - - +
330W ARG* 2.4 35.5 + - - -
333W ALA* 4.2 3.7 - - - +
334W ASN* 3.6 13.4 + - - -
337W ALA* 3.5 14.6 - - + -
342W TYR* 3.2 45.5 - - + -
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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
----------------------------------------------------------
245W PRO* 4.6 14.5 - - + +
277W GLU* 3.1 43.9 + - + +
278W ASP* 4.0 13.2 - - - +
280W THR* 1.3 73.9 - - - +
282W ASN* 1.3 56.8 + - - +
284W ASN* 3.6 6.8 - - - +
285W ALA* 2.7 37.7 + - - +
342W TYR* 3.7 28.7 - - + -
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Residues in contact with ASN 282 (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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232W MET* 3.5 22.9 - - - -
234W THR* 4.8 4.8 - - - +
245W PRO* 4.0 24.7 - - - +
248W VAL* 4.1 22.4 - - + +
249W ALA* 4.6 0.2 - - - +
274W MET* 3.4 24.2 - - - -
278W ASP* 2.8 28.3 + - - +
279W ALA 4.0 2.0 - - - +
281W LEU* 1.3 73.4 - - - +
283W LEU* 1.3 60.1 + - - +
285W ALA* 3.6 5.4 - - - +
286W ILE* 2.9 33.4 + - - +
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Residues in contact with LEU 283 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232W MET* 4.6 1.1 - - + +
269W PHE* 4.8 5.8 - - + -
279W ALA 3.1 14.6 + - - +
280W THR* 2.7 14.5 + - - +
282W ASN* 1.3 69.4 - - - +
284W ASN* 1.3 68.1 + - - +
286W ILE* 3.0 22.6 + - + +
287W ASN* 3.2 14.2 + - - +
297W LEU 3.0 26.7 - - - +
298W SER 3.8 9.6 - - - +
299W PHE* 3.6 35.9 - - + -
301W TYR* 3.5 17.2 + - + +
334W ASN* 4.2 4.0 - - - +
337W ALA* 3.6 15.6 - - + +
338W ALA* 4.1 7.9 - - - +
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Residues in contact with ASN 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 THR 2.6 18.6 + - - +
281W LEU* 3.6 7.8 - - - +
283W LEU* 1.3 70.2 - - - +
285W ALA* 1.3 69.1 + - - +
287W ASN* 3.1 11.6 + - - +
288W LEU* 3.4 22.4 + - - +
337W ALA* 3.2 13.8 + - - +
340W GLY* 2.8 36.6 + - - -
341W GLN 2.9 0.3 + - - -
342W TYR* 2.8 46.8 + - + +
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Residues in contact with ALA 285 (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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245W PRO* 3.9 24.7 - - + +
246W GLU* 4.4 7.0 - - + +
249W ALA* 3.7 15.7 - - + -
281W LEU 2.7 21.6 + - - +
282W ASN 3.6 5.2 - - - +
284W ASN* 1.3 72.5 - - - +
286W ILE* 1.3 53.8 - - - +
287W ASN 2.7 0.5 + - - -
288W LEU* 2.4 39.6 + - - +
289W CYS* 3.0 7.7 + - - -
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Residues in contact with ILE 286 (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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232W MET* 3.9 26.5 - - + -
248W VAL* 5.8 0.9 - - + -
249W ALA* 3.4 26.6 - - + +
252W THR* 4.0 4.5 - - + -
253W VAL* 3.4 19.9 - - + +
269W PHE* 3.6 31.0 - - + -
282W ASN 2.9 22.4 - - - +
283W LEU* 3.0 11.1 + - + +
285W ALA* 1.3 77.5 - - - +
287W ASN* 1.3 59.2 + - - +
288W LEU 3.2 0.9 + - - -
289W CYS* 3.6 8.2 - - - +
293W LYS* 3.6 16.8 - - - +
297W LEU* 3.8 27.4 - - + -
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Residues in contact with ASN 287 (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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283W LEU* 3.2 5.5 + - - +
284W ASN 3.1 9.9 + - - +
285W ALA 2.7 6.3 + - - -
286W ILE* 1.3 70.4 - - - +
288W LEU* 1.3 55.9 + - - +
293W LYS* 2.6 26.1 + - - +
297W LEU* 3.2 45.2 + - - +
337W ALA 3.1 5.9 - - - +
338W ALA 2.3 35.6 + - - +
339W LYS 3.7 17.8 + - - +
340W GLY* 3.9 4.7 - - - -
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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
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284W ASN* 3.4 26.4 + - - +
285W ALA* 2.4 25.4 + - - +
287W ASN* 1.3 78.7 - - - +
289W CYS* 1.3 64.3 + - - +
290W PRO* 2.9 10.2 - - - +
293W LYS* 3.7 3.0 + - - +
340W GLY* 3.9 18.8 - - - +
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Residues in contact with CYS 289 (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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246W GLU* 4.8 2.0 - - - +
249W ALA* 3.6 17.7 - - + -
250W MET* 3.5 47.3 - - - -
253W VAL* 4.0 17.0 - - + -
285W ALA 3.0 5.0 + - - -
286W ILE 3.6 15.4 + - - +
288W LEU* 1.3 73.1 - - - +
290W PRO* 1.3 63.4 - - - +
291W LEU* 2.6 24.4 + - - +
293W LYS* 3.4 17.7 + - - +
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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