Contacts of the helix formed by residues 272 - 287 (chain D) in PDB entry 1PQ3
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 THR 272 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255D PHE* 3.6 4.4 - - - -
259D LEU* 4.2 5.7 - - - +
270D GLY 3.7 0.6 + - - -
271D LEU* 1.3 76.5 - - - +
273D TYR* 1.3 65.0 + - - +
274D ARG* 3.1 20.4 - - + +
275D GLU* 2.9 48.5 + - + +
276D GLY 2.9 18.9 + - - -
274F ARG* 4.1 5.7 + - - -
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Residues in contact with TYR 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D PHE* 4.1 10.9 - - - -
259D LEU* 3.8 25.4 - - + +
272D THR* 1.3 73.7 + - - +
274D ARG* 1.3 67.4 + - + +
276D GLY* 3.2 1.4 + - - -
277D MET* 3.0 46.2 + - + +
314D LEU* 3.5 31.6 - - + -
317D ASP* 2.5 29.7 + - - -
327D ARG* 5.6 5.8 - - - -
256E ASP* 5.6 1.8 - - - +
268E VAL* 3.1 29.2 - - + +
269E GLY* 3.3 34.1 - - - +
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Residues in contact with ARG 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D THR* 3.1 12.4 - - + +
273D TYR* 1.3 80.1 - - + +
275D GLU* 1.3 51.4 + - - +
277D MET* 3.1 4.6 + - - +
278D TYR* 2.7 33.8 + - - +
327D ARG* 3.8 15.3 + - - +
219E MET* 3.2 28.1 - - - +
222E ILE* 3.7 17.0 + - - +
223E ASP* 2.6 49.4 + - - +
269E GLY* 3.7 19.5 - - - +
270E GLY 3.5 10.3 + - - -
272E THR* 4.2 4.8 - - - +
275E GLU* 2.5 46.9 + - - -
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Residues in contact with GLU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D ILE* 3.7 15.7 - - - +
227D ILE* 4.0 25.5 + - + +
271D LEU* 3.7 12.4 - - + +
272D THR* 2.9 30.7 + - + +
274D ARG* 1.3 73.4 - - + +
276D GLY* 1.3 66.7 + - - +
278D TYR* 3.2 9.2 + - - +
279D ILE* 2.9 31.8 + - - +
223E ASP* 5.7 2.2 - - - +
274F ARG* 2.5 43.5 + - - -
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Residues in contact with GLY 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D PHE* 4.6 6.9 - - - -
255D PHE* 3.4 29.6 - - - -
271D LEU* 4.5 11.8 - - - +
272D THR 2.9 10.9 + - - -
275D GLU* 1.3 77.6 - - - +
277D MET* 1.3 68.0 + - - +
279D ILE* 3.3 6.6 + - - +
280D ALA* 3.2 20.4 + - - +
318D VAL* 5.1 0.3 - - - +
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Residues in contact with MET 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255D PHE* 5.1 0.7 - - + -
273D TYR* 3.0 49.4 + - + +
274D ARG* 3.5 9.0 - - - +
276D GLY* 1.3 76.6 - - - +
278D TYR* 1.3 59.2 + - - +
280D ALA* 3.3 3.0 + - + +
281D GLU* 2.8 37.2 + - - +
314D LEU* 5.1 0.9 - - - +
317D ASP* 3.3 32.1 - - - +
318D VAL* 3.4 29.2 - - + +
321D SER* 3.8 15.5 - - - +
327D ARG* 4.2 26.9 - - + +
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Residues in contact with TYR 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ILE* 3.7 24.5 - - + -
228D GLN* 3.1 31.2 + - + +
231D MET* 4.1 12.3 - - + -
274D ARG 2.7 15.7 + - - +
275D GLU* 3.4 13.5 - - - +
277D MET* 1.3 77.4 - - - +
279D ILE* 1.3 63.2 + - - +
281D GLU* 3.7 8.2 - - - +
282D GLU* 2.9 36.2 + - - +
327D ARG* 3.9 12.5 - - - +
220E ARG* 3.3 41.1 + - + -
223E ASP* 4.5 10.8 - - + +
224E ARG* 3.1 34.3 - - + -
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Residues in contact with ILE 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 5.3 0.4 - - + -
142D VAL* 4.2 22.2 - - + -
196D ILE* 3.8 29.6 - - + -
227D ILE* 3.9 14.6 - - + -
231D MET* 3.9 33.4 - - + +
248D LEU* 5.1 1.3 - - + -
250D PHE* 4.8 6.5 - - + -
271D LEU* 3.8 23.8 - - + -
275D GLU 2.9 19.5 + - - +
276D GLY* 3.6 6.5 - - - +
277D MET 3.3 0.2 - - - -
278D TYR* 1.3 75.3 - - - +
280D ALA* 1.3 65.8 + - - +
282D GLU* 3.2 4.5 + - - +
283D ILE* 3.0 33.0 + - + +
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Residues in contact with ALA 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D LEU* 5.3 2.9 - - + -
250D PHE* 5.6 1.3 - - + -
276D GLY 3.2 10.2 + - - +
277D MET* 3.6 7.4 - - + +
279D ILE* 1.3 81.5 - - - +
281D GLU* 1.3 62.9 + - - +
283D ILE* 3.2 7.3 + - - +
284D HIS* 3.0 22.5 + - - +
318D VAL* 3.7 9.9 - - + +
321D SER* 3.6 25.1 - - - +
322D SER* 3.5 27.1 - - - +
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Residues in contact with GLU 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277D MET* 2.8 27.1 + - - +
278D TYR* 3.7 6.7 - - - +
280D ALA* 1.3 71.1 - - - +
282D GLU* 1.3 65.6 + - - +
284D HIS* 3.2 7.6 + - - +
285D ASN* 2.9 34.7 + - - +
321D SER* 3.4 19.5 + - - +
325D GLN 4.5 6.5 - - - +
326D THR* 4.5 4.3 - - - +
327D ARG* 2.9 63.4 + - - +
220E ARG* 3.8 24.6 + - - +
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Residues in contact with GLU 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D MET* 3.6 32.1 - - + -
232D GLU* 5.5 2.8 - - - +
235D PHE* 3.9 13.6 - - + -
278D TYR* 2.9 28.7 + - + +
279D ILE 3.2 4.9 + - - +
281D GLU* 1.3 75.0 - - - +
283D ILE* 1.3 65.3 + - - +
285D ASN* 3.1 24.2 + - - +
286D THR* 3.3 11.3 + - - +
220E ARG* 2.5 33.3 + - - -
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Residues in contact with ILE 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D VAL* 4.3 19.1 - - + -
231D MET* 4.5 3.6 - - + -
235D PHE* 3.7 22.7 - - + -
246D ILE* 4.7 8.1 - - + -
248D LEU* 3.3 44.9 - - + -
279D ILE* 3.0 18.6 + - + +
280D ALA* 3.2 9.8 + - - +
282D GLU* 1.3 74.7 - - - +
284D HIS* 1.3 62.8 + - - +
286D THR* 2.5 30.6 + - - +
287D GLY 3.7 0.3 + - - -
288D LEU 4.7 0.5 + - - -
289D LEU* 4.1 35.6 + - + -
322D SER* 4.9 1.6 - - - +
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Residues in contact with HIS 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280D ALA 3.0 10.7 + - - +
281D GLU* 3.4 10.8 - - - +
283D ILE* 1.3 76.4 - - - +
285D ASN* 1.3 66.5 + - - +
287D GLY* 2.9 23.1 + - - -
289D LEU* 5.7 2.5 - - - -
321D SER 3.8 6.7 - - - +
322D SER 3.3 19.5 + - - +
323D PHE* 3.4 9.3 - - - -
324D GLY* 3.2 40.1 + - - -
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Residues in contact with ASN 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281D GLU* 2.9 29.5 + - - +
282D GLU* 3.1 25.5 + - - +
284D HIS* 1.3 84.4 - - - +
286D THR* 1.3 60.1 + - + +
287D GLY* 4.5 0.2 - - - -
220E ARG* 3.9 17.4 - - - +
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Residues in contact with THR 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D PHE* 3.7 36.6 - - + -
239D ILE* 4.1 9.2 - - + -
243D GLN* 4.5 3.8 - - - +
246D ILE* 3.7 10.3 - - + +
282D GLU 3.5 11.0 - - - +
283D ILE* 2.5 24.1 + - - +
285D ASN* 1.3 77.9 - - - +
287D GLY* 1.3 62.6 + - - +
288D LEU* 3.0 35.1 + - - +
289D LEU 4.2 1.4 + - - -
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Residues in contact with GLY 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283D ILE 3.7 0.2 + - - -
284D HIS* 2.9 15.6 + - - -
285D ASN 3.3 0.6 - - - -
286D THR* 1.3 79.9 + - - +
288D LEU* 1.3 63.2 + - - +
289D LEU 3.6 3.2 + - - +
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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
------------------------------------------------------------
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