Contacts of the helix formed by residues 272 - 288 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267P TYR* 3.0 35.0 + - + +
270P GLN* 3.5 4.4 + - + +
271P GLY* 1.3 73.8 - - - +
273P LYS* 1.3 62.8 + - - +
274P TRP* 3.2 4.4 + - - +
275P ARG* 2.9 52.9 + - - +
276P ALA* 3.1 18.2 + - - +
1S G 5.4 0.7 - - - -
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Residues in contact with LYS 273 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267P TYR 5.0 0.7 - - - -
268P SER* 5.0 6.3 - - - +
271P GLY 2.8 13.8 + - - +
272P ASP* 1.3 71.6 - - - +
274P TRP* 1.3 66.1 + - + +
276P ALA* 3.4 7.2 + - - +
277P ALA* 2.9 28.2 + - - +
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Residues in contact with TRP 274 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272P ASP* 3.2 3.7 - - - +
273P LYS* 1.3 80.8 - - + +
275P ARG* 1.3 64.7 + - - +
277P ALA* 3.5 20.0 + - + +
278P GLY 3.2 14.7 + - - -
4Q C 3.2 81.8 - + + +
5Q A 4.0 9.2 - - - -
1S G 3.2 23.0 - - + -
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Residues in contact with ARG 275 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267P TYR* 3.4 30.9 + - + -
272P ASP* 2.9 42.3 + - + +
274P TRP* 1.3 75.9 - - - +
276P ALA* 1.3 59.5 + - - +
278P GLY* 3.0 3.5 + - - -
279P TYR* 3.0 38.6 + - + -
1S G 2.9 90.1 + - + +
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Residues in contact with ALA 276 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264P ALA* 3.9 25.5 - - + +
267P TYR* 4.3 3.7 - - + +
268P SER* 3.9 20.2 - - - +
272P ASP 3.1 12.4 + - - +
273P LYS* 3.6 9.4 - - - +
275P ARG* 1.3 73.9 - - - +
277P ALA* 1.3 59.7 + - - +
278P GLY 3.0 1.3 - - - -
279P TYR* 3.1 8.7 + - - +
280P ALA* 2.8 30.6 + - - +
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Residues in contact with ALA 277 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273P LYS 2.9 17.8 + - - +
274P TRP* 3.6 26.9 - - + +
276P ALA* 1.3 75.4 - - - +
278P GLY* 1.3 56.7 - - - +
280P ALA* 3.5 6.9 + - - +
281P LYS* 2.8 30.2 + - - +
1S G 4.8 4.5 - - - +
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Residues in contact with GLY 278 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274P TRP 3.2 6.5 + - - -
275P ARG 3.0 5.6 + - - -
276P ALA 3.0 0.8 - - - -
277P ALA* 1.3 75.5 - - - +
279P TYR* 1.3 64.5 + - - +
281P LYS* 3.1 9.4 + - - +
282P ALA* 3.1 21.1 + - - +
304P GLY 4.8 1.7 - - - +
309P MET* 4.4 1.1 - - - +
1S G 3.3 39.6 - - - +
2S C 4.8 2.7 - - - +
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Residues in contact with TYR 279 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260P LEU* 4.2 24.2 - - + -
263P LEU* 3.4 37.4 - - + +
264P ALA* 3.7 19.7 - - + -
267P TYR* 3.7 8.9 - + - -
275P ARG* 3.0 39.3 + - + -
276P ALA* 3.1 6.5 + - - +
278P GLY* 1.3 74.4 - - - +
280P ALA* 1.3 53.7 + - - +
282P ALA* 3.1 2.4 + - - +
283P ILE* 2.6 41.8 + - + +
309P MET* 3.7 27.1 - - + -
312P LYS* 3.6 8.6 - - + -
1S G 2.7 54.7 + - - -
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Residues in contact with ALA 280 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264P ALA* 5.0 2.8 - - + +
276P ALA 2.8 16.1 + - - +
277P ALA* 3.6 9.0 - - - +
279P TYR* 1.3 74.0 - - - +
281P LYS* 1.3 63.7 - - - +
283P ILE* 4.3 8.3 - - - +
284P ASN* 2.7 45.8 + - - +
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Residues in contact with LYS 281 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277P ALA 2.8 15.6 + - - +
278P GLY* 3.1 14.4 - - - +
280P ALA* 1.3 76.2 - - - +
282P ALA* 1.3 59.4 + - - +
284P ASN* 4.1 5.2 - - - +
285P ALA* 3.3 21.1 + - + +
303P PRO* 5.1 4.8 + - - +
304P GLY* 4.4 24.7 - - - +
515P SER* 6.0 2.2 - - - -
1S G 6.0 2.0 - - - +
2S C 5.4 4.7 - - - +
3S C 6.0 3.9 - - - -
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Residues in contact with ALA 282 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260P LEU* 6.0 0.4 - - + -
278P GLY 3.1 10.4 + - - +
279P TYR 3.5 5.8 - - - +
280P ALA 3.1 0.4 - - - -
281P LYS* 1.3 73.2 - - - +
283P ILE* 1.3 60.6 + - + +
284P ASN 3.0 1.8 - - - -
285P ALA* 2.7 28.8 + - - +
286P LEU* 2.8 17.9 + - + +
304P GLY 3.6 21.1 + - - +
305P ILE* 4.0 7.8 - - + +
309P MET* 3.9 29.8 - - + -
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Residues in contact with ILE 283 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257P THR* 3.9 11.3 - - - +
260P LEU* 3.5 24.9 - - + +
261P GLU* 3.4 55.0 - - + +
264P ALA* 4.1 8.3 - - + -
279P TYR* 2.6 37.1 + - + +
280P ALA* 4.0 6.5 - - - +
282P ALA* 1.3 72.9 - - + +
284P ASN* 1.3 64.7 + - - +
286P LEU* 3.3 14.7 - - - +
287P LYS* 3.3 37.3 + - - +
309P MET* 6.0 0.2 - - - -
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Residues in contact with ASN 284 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280P ALA* 2.7 40.9 + - - +
281P LYS* 4.1 4.9 - - - +
283P ILE* 1.3 77.8 - - - +
285P ALA* 1.3 66.1 + - - +
286P LEU 3.1 0.6 + - - -
287P LYS* 3.3 21.8 + - - +
288P SER* 3.5 9.0 + - - -
511P ALA* 5.4 5.9 - - - +
575P TRP* 2.8 56.5 + - + +
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Residues in contact with ALA 285 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281P LYS* 3.3 14.6 + - + +
282P ALA* 2.7 16.7 + - - +
284P ASN* 1.3 76.9 - - - +
286P LEU* 1.3 63.0 + - - +
288P SER* 3.5 17.7 + - - +
289P PHE* 4.4 2.6 - - - +
302P ILE* 4.2 16.0 - - + +
303P PRO* 3.9 22.0 - - + +
305P ILE* 5.0 1.3 - - + -
575P TRP* 6.0 2.0 - - - -
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Residues in contact with LEU 286 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253P ASN* 3.6 26.6 + - + +
256P ILE* 4.4 11.2 - - + -
257P THR* 3.9 16.4 - - + -
260P LEU* 3.8 28.7 - - + -
282P ALA* 2.8 13.4 + - + +
283P ILE* 3.3 12.6 - - - +
285P ALA* 1.3 74.8 - - - +
287P LYS* 1.3 69.0 + - - +
289P PHE* 2.8 27.2 + - + +
293P VAL* 5.0 8.5 - - + -
299P ALA* 6.3 0.4 - - + -
302P ILE* 4.2 13.7 - - + -
305P ILE* 3.8 23.6 - - + -
309P MET* 6.3 0.2 - - + -
313P ILE* 4.5 13.2 - - + -
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Residues in contact with LYS 287 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249P ALA* 5.5 3.8 - - - +
250P THR 4.1 17.5 + - - +
251P ASN* 3.1 36.6 + - + +
252P HIS 5.1 0.7 + - - -
257P THR* 4.1 7.5 + - + -
261P GLU* 2.9 29.5 + - - -
283P ILE* 3.3 25.0 + - - +
284P ASN* 3.5 13.3 + - - +
286P LEU* 1.3 78.3 - - - +
288P SER* 1.3 57.4 + - - +
289P PHE 3.0 8.3 + - - +
575P TRP* 4.0 29.8 - - + -
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Residues in contact with SER 288 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284P ASN 3.5 3.8 + - - -
285P ALA* 3.7 11.5 - - - +
286P LEU 2.9 5.1 + - - -
287P LYS* 1.3 74.9 - - - +
289P PHE* 1.3 55.5 + - - +
575P TRP* 4.3 25.1 - - - -
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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