Contacts of the helix formed by residues 272 - 288 (chain F) in PDB entry 3HX0
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 ASP 272 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267F TYR* 3.4 25.3 + - + +
268F SER* 5.2 0.4 - - - -
270F GLN* 3.6 4.5 - - + +
271F GLY* 1.3 70.9 - - - +
273F LYS* 1.3 65.4 + - - +
274F TRP* 3.1 3.1 + - - +
275F ARG* 2.9 56.2 + - - +
276F ALA* 3.2 18.9 + - - +
1I G 5.3 0.2 - - - -
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Residues in contact with LYS 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F SER* 5.7 2.5 - - - +
271F GLY 2.5 17.6 + - - +
272F ASP* 1.3 69.6 - - - +
274F TRP* 1.3 70.1 + - + +
276F ALA* 3.6 5.9 + - - +
277F ALA* 3.1 26.6 + - - +
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Residues in contact with TRP 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272F ASP* 3.3 3.0 + - - +
273F LYS* 1.3 85.0 - - + +
275F ARG* 1.3 66.7 + - - +
276F ALA 3.2 1.6 - - - -
277F ALA* 3.2 13.6 + - + +
278F GLY 3.0 17.5 + - - -
4G C 3.2 76.2 - + + +
5G A 3.9 29.8 - + + -
6G A 5.3 5.4 - - - -
1I G 3.4 30.9 + + + -
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Residues in contact with ARG 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267F TYR* 3.2 57.7 + - + -
272F ASP* 2.9 38.8 + - + +
274F TRP* 1.3 75.8 - - - +
276F ALA* 1.3 61.9 + - - +
278F GLY* 3.0 10.6 + - - -
279F TYR* 3.3 19.7 + - + -
1I G 3.4 58.3 + - + +
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Residues in contact with ALA 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F ALA* 3.7 28.2 - - + +
267F TYR* 4.3 5.1 - - + +
268F SER* 3.7 21.1 - - - +
272F ASP 3.2 10.0 + - - +
273F LYS* 3.6 9.4 - - - +
275F ARG* 1.3 80.2 - - - +
277F ALA* 1.3 62.7 + - - +
278F GLY 3.0 1.0 + - - -
279F TYR* 3.0 18.1 + - - +
280F ALA* 3.1 11.7 + - - +
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Residues in contact with ALA 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273F LYS 3.1 17.7 + - - +
274F TRP* 3.2 20.4 + - + +
276F ALA* 1.3 75.3 - - - +
278F GLY* 1.3 60.7 + - - +
280F ALA* 3.2 18.6 - - - +
5G A 2.6 50.9 + - + +
1I G 4.7 0.7 - - - +
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Residues in contact with GLY 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F TRP 3.0 9.3 + - - -
275F ARG 3.0 2.9 + - - -
276F ALA 3.0 1.0 - - - -
277F ALA* 1.3 76.1 - - - +
279F TYR* 1.3 65.0 + - - +
281F LYS* 3.2 7.0 + - - +
282F ALA* 3.1 19.3 + - - +
304F GLY 5.0 1.9 - - - +
309F MET* 4.8 0.2 - - - -
5G A 4.6 0.9 - - - -
1I G 3.2 39.6 - - - +
2I C 5.1 5.2 - - - +
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Residues in contact with TYR 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F LEU* 3.7 27.1 - - + -
263F LEU* 3.5 33.3 - - + +
264F ALA* 3.9 17.3 - - + -
267F TYR* 3.4 24.0 - + - -
275F ARG* 3.3 14.4 - - + -
276F ALA* 3.0 8.1 + - - +
278F GLY* 1.3 74.3 - - - +
280F ALA* 1.3 53.9 + - - +
282F ALA* 2.9 2.8 + - - +
283F ILE* 2.7 41.8 + - + +
309F MET* 3.6 30.5 - - + -
312F LYS* 3.3 14.0 + - - -
1I G 2.5 48.0 + - - -
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Residues in contact with ALA 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F ALA* 5.1 2.2 - - + +
276F ALA 3.1 8.8 + - - +
277F ALA* 3.2 20.4 - - - +
279F TYR* 1.3 77.5 - - - +
281F LYS* 1.3 62.4 + - - +
283F ILE* 3.3 10.4 + - - +
284F ASN* 2.8 33.7 + - - +
5G A 4.7 8.3 - - - +
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Residues in contact with LYS 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277F ALA 3.4 1.2 + - - -
278F GLY* 3.2 8.4 + - - +
280F ALA* 1.3 76.4 - - - +
282F ALA* 1.3 66.7 + - - +
284F ASN* 3.3 8.9 + - + +
285F ALA* 2.9 23.6 + - + +
303F PRO 5.3 2.5 - - - +
304F GLY* 4.7 19.5 - - - +
5G A 3.6 38.0 + - - +
2I C 6.0 3.4 - - - +
3I C 6.4 2.7 - - - -
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Residues in contact with ALA 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F LEU* 5.3 2.9 - - + -
278F GLY 3.1 8.6 + - - +
279F TYR 2.9 8.6 + - - +
281F LYS* 1.3 77.7 - - - +
283F ILE* 1.3 63.6 + - + +
285F ALA* 3.1 16.9 + - - +
286F LEU* 3.2 19.7 + - + +
304F GLY 3.8 21.0 + - - +
305F ILE* 4.6 4.9 - - + +
309F MET* 3.6 37.0 - - + -
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Residues in contact with ILE 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257F THR* 3.6 21.5 - - - +
260F LEU* 4.1 21.1 - - + +
261F GLU* 3.6 51.8 - - + +
264F ALA* 4.4 6.7 - - + -
279F TYR* 2.7 29.1 + - + +
280F ALA* 3.6 7.9 - - - +
282F ALA* 1.3 73.8 - - - +
284F ASN* 1.3 58.4 + - - +
286F LEU* 3.1 7.8 + - - +
287F LYS* 2.9 51.5 + - + +
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Residues in contact with ASN 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280F ALA* 2.8 28.5 + - - +
281F LYS* 3.7 8.9 - - + +
282F ALA 3.3 0.2 - - - -
283F ILE* 1.3 76.1 - - - +
285F ALA* 1.3 67.3 + - - +
287F LYS* 3.7 17.0 + - - +
288F SER* 2.9 28.2 + - - -
575F TRP* 3.2 56.1 - - + +
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Residues in contact with ALA 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281F LYS* 2.9 14.3 + - + +
282F ALA* 3.1 14.3 + - - +
284F ASN* 1.3 76.0 - - - +
286F LEU* 1.3 60.4 + - - +
288F SER* 3.7 4.6 + - - -
289F PHE* 3.3 20.1 + - - +
302F ILE* 3.8 31.4 - - + +
303F PRO 4.2 11.4 - - - +
304F GLY* 5.0 1.3 - - - -
305F ILE* 4.6 6.5 - - + -
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Residues in contact with LEU 286 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F ASN* 4.2 1.1 - - - +
252F HIS 5.1 0.9 + - - -
253F ASN* 3.3 30.2 + - + +
256F ILE* 3.9 24.5 - - + -
257F THR* 3.7 24.0 - - + -
260F LEU* 4.0 14.8 - - + -
282F ALA* 3.5 14.1 - - + +
283F ILE* 3.1 5.1 + - - +
284F ASN 3.0 0.4 - - - -
285F ALA* 1.3 74.0 - - - +
287F LYS* 1.3 56.1 + - - +
288F SER 2.9 4.9 - - - -
289F PHE* 2.7 31.0 + - - +
293F VAL* 4.9 7.9 - - + -
302F ILE* 4.4 10.8 - - + -
305F ILE* 3.6 24.7 - - + -
309F MET* 6.4 0.2 - - + -
313F ILE* 4.4 12.6 - - + -
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Residues in contact with LYS 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247F GLN 4.9 2.4 - - - +
249F ALA* 4.6 7.1 - - - +
250F THR 4.2 6.9 - - - +
251F ASN* 3.0 44.9 + - + +
257F THR* 3.9 10.8 - - + +
261F GLU* 4.6 10.4 + - - +
283F ILE* 2.9 39.7 + - + +
284F ASN* 3.2 20.1 + - - +
286F LEU* 1.3 73.3 - - - +
288F SER* 1.3 56.4 + - - +
289F PHE 5.1 1.2 - - - +
575F TRP* 4.5 19.1 - - + -
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Residues in contact with SER 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247F GLN* 5.0 9.9 - - - +
249F ALA* 5.8 6.3 - - - +
284F ASN 2.9 15.2 + - - -
285F ALA* 3.9 5.2 - - - -
286F LEU 2.9 0.8 - - - -
287F LYS* 1.3 77.2 - - - +
289F PHE* 1.3 62.4 + - - +
290F HIS* 3.4 3.1 + - - -
575F TRP* 3.6 24.5 - - - -
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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
------------------------------------------------------------
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