Contacts of the helix formed by residues 273 - 288 (chain D) in PDB entry 1IR1
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 GLY 273 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267D HIS* 4.2 0.7 - - - -
269D TYR* 2.9 18.9 + - - +
270D LEU 3.6 7.2 + - - -
271D THR 3.5 1.4 - - - -
272D GLY* 1.3 80.0 - - - +
274D PHE* 1.3 60.7 + - - -
275D THR 3.3 3.1 - - - -
276D ALA 3.4 2.9 + - - -
277D ASN* 2.9 28.8 + - - +
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Residues in contact with PHE 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D VAL* 3.6 29.8 - - + -
114D THR* 3.6 18.6 - - - +
117D PHE* 3.6 33.4 - + - -
269D TYR* 3.6 39.3 - + - -
270D LEU* 4.1 18.2 - - + -
273D GLY* 1.3 70.5 - - - -
275D THR* 1.3 60.6 + - - +
277D ASN* 3.7 4.3 - - + +
278D THR* 2.8 37.4 + - - +
314D LEU* 4.8 4.9 - - + -
317D ALA* 3.9 14.6 - - + -
321D SER* 4.4 12.3 - - - -
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Residues in contact with THR 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114D THR* 3.2 24.2 + - - +
247D CYS* 5.6 7.9 - - - -
273D GLY* 3.3 0.8 - - - -
274D PHE* 1.3 80.4 - - - +
276D ALA* 1.3 63.0 + - - +
278D THR* 3.5 4.8 + - - -
279D THR* 3.3 23.0 + - - +
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Residues in contact with ALA 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D THR 6.3 0.7 - - - -
247D CYS* 4.7 16.4 - - - +
250D MET* 3.4 32.7 - - + +
267D HIS* 4.2 6.3 - - + +
272D GLY* 4.1 14.8 - - - +
273D GLY 3.4 7.0 + - - +
274D PHE 3.3 0.4 - - - -
275D THR* 1.3 77.7 - - - +
277D ASN* 1.3 65.6 + - - +
279D THR* 3.3 4.8 + - - -
280D LEU* 3.1 17.3 + - - +
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Residues in contact with ASN 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267D HIS* 3.0 31.2 + - + +
269D TYR* 3.5 16.0 - - + +
273D GLY 2.9 18.7 + - - +
274D PHE* 3.3 7.2 + - - +
276D ALA* 1.3 78.3 - - - +
278D THR* 1.3 56.3 + - - +
280D LEU* 3.2 3.8 + - - +
281D SER* 2.8 27.5 + - - -
291D LEU* 4.6 2.3 - - - +
293D ILE* 3.4 19.6 - - - +
318D LEU* 3.9 8.1 - - - +
321D SER* 2.9 25.8 + - - +
322D GLY 3.3 21.6 + - - +
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Residues in contact with THR 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D GLY 4.6 14.8 + - - +
113D VAL* 5.5 4.7 + - - +
148D PHE* 6.3 0.9 - - + -
274D PHE* 2.8 22.7 + - - +
275D THR* 3.9 6.0 - - - -
277D ASN* 1.3 77.0 - - - +
279D THR* 1.3 63.1 + - - +
281D SER* 3.3 4.3 + - - -
282D HIS* 3.1 50.6 + - + +
321D SER* 2.9 28.9 + - - +
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Residues in contact with THR 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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247D CYS* 5.4 8.7 - - + -
250D MET* 4.0 15.5 - - + -
251D MET* 4.1 19.3 - - + -
275D THR* 3.3 14.5 + - - +
276D ALA* 3.3 11.2 + - - -
277D ASN 3.2 0.6 - - - -
278D THR* 1.3 78.6 - - - +
280D LEU* 1.3 62.4 + - - +
282D HIS* 3.4 8.4 + - - +
283D TYR* 3.1 20.3 + - - +
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Residues in contact with LEU 280 (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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242D ALA* 4.4 13.0 - - + -
250D MET* 4.1 19.1 - - + -
251D MET* 5.0 2.9 - - - -
254D ALA* 4.0 27.1 - - + -
265D VAL* 5.1 2.9 - - + -
266D MET 4.7 0.7 - - - +
267D HIS* 3.5 39.7 - - + -
276D ALA 3.1 10.3 + - - +
277D ASN* 3.6 7.6 - - - +
279D THR* 1.3 78.9 - - - +
281D SER* 1.3 61.5 + - - +
283D TYR* 3.1 8.6 + - + +
284D CYS* 2.8 50.4 + - - -
291D LEU* 4.0 13.5 - - + -
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Residues in contact with SER 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149D GLN* 3.2 23.2 + - - -
150D GLY 3.7 0.2 + - - -
152D PRO* 3.5 10.3 - - - +
277D ASN 2.8 16.1 + - - -
278D THR 3.5 4.5 - - - -
279D THR 3.3 0.2 - - - -
280D LEU* 1.3 76.3 - - - +
282D HIS* 1.3 62.6 + - - +
284D CYS 3.4 0.2 + - - -
285D ARG 3.2 17.0 + - - -
291D LEU* 3.9 12.1 - - - +
321D SER 3.1 26.3 + - - -
322D GLY* 3.3 20.4 - - - -
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Residues in contact with HIS 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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111D GLY 6.0 0.2 - - - -
149D GLN* 3.2 42.7 + - + +
278D THR* 3.1 39.5 + - + +
279D THR* 3.7 7.2 - - - +
281D SER* 1.3 77.1 - - - +
283D TYR* 1.3 65.0 + - - +
285D ARG* 3.3 3.1 + - - +
286D ASP* 3.1 31.4 + - - +
321D SER 5.1 1.6 + - - -
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Residues in contact with TYR 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D MET* 3.3 32.8 - - + -
254D ALA* 3.8 26.9 - - + -
255D VAL* 3.6 31.3 - - + +
258D ARG* 3.6 15.9 - - - +
279D THR 3.1 14.0 + - - +
280D LEU* 3.1 14.3 + - + +
282D HIS* 1.3 76.1 - - - +
284D CYS* 1.3 68.1 + - - +
286D ASP* 3.2 3.7 + - - -
287D ASN* 3.0 54.7 + - - +
289D LEU* 3.9 20.0 - - + -
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Residues in contact with CYS 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D PRO* 4.0 11.9 - - + -
153D HIS* 3.6 1.2 - - - -
265D VAL* 3.9 26.5 - - - -
280D LEU* 2.8 32.7 + - - +
281D SER 3.7 5.2 - - - +
282D HIS 3.3 0.2 - - - -
283D TYR* 1.3 78.9 - - - +
285D ARG* 1.3 55.8 + - - +
287D ASN 4.5 0.2 - - - +
288D GLY* 3.0 26.5 + - - -
289D LEU* 3.0 43.6 + - - +
291D LEU* 4.1 11.9 - - + -
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Residues in contact with ARG 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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213A ARG* 3.8 47.1 - - - +
215A ARG* 3.7 19.1 - - - +
216A ASP* 6.0 1.3 + - - -
149D GLN* 3.3 58.9 + - - +
151D PRO 3.0 23.2 + - - -
152D PRO* 2.7 28.5 + - + +
153D HIS* 4.6 5.3 + - - -
281D SER 3.2 4.8 + - - -
282D HIS 3.6 5.2 - - - +
283D TYR 3.3 0.2 - - - -
284D CYS* 1.3 78.6 - - - +
286D ASP* 1.3 69.2 + - - +
287D ASN 3.4 0.7 + - - -
288D GLY* 3.8 3.1 + - - -
372D PRO* 5.1 6.7 - - - +
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Residues in contact with ASP 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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214A TRP* 5.0 13.2 + - - -
215A ARG* 3.1 19.5 + - - +
252A LYS* 3.6 30.7 + - - +
258D ARG* 5.4 0.5 + - - -
282D HIS* 3.1 22.6 + - - +
283D TYR* 3.8 5.3 - - - +
285D ARG* 1.3 82.5 - - - +
287D ASN* 1.3 71.3 + - - +
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Residues in contact with ASN 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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215A ARG* 3.6 17.2 + - - +
258D ARG* 3.2 36.1 + - + +
283D TYR* 3.0 63.2 + - + +
284D CYS 4.6 0.2 - - - +
286D ASP* 1.3 89.8 + - - +
288D GLY* 1.3 64.1 + - - +
289D LEU* 3.4 5.7 + - + +
59V PRO* 3.8 18.9 - - - +
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Residues in contact with GLY 288 (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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215A ARG* 3.6 19.8 - - - +
153D HIS* 3.7 18.3 + - - -
161D LYS* 4.8 7.3 + - - -
263D PRO 4.5 2.3 - - - +
284D CYS 3.0 6.5 + - - -
285D ARG 3.8 2.5 + - - -
286D ASP 3.7 0.8 - - - -
287D ASN* 1.3 78.3 - - - +
289D LEU* 1.3 59.7 + - - +
290D LEU* 4.0 2.4 + - - +
59V PRO* 3.5 22.7 - - - +
60V GLY* 4.3 4.0 + - - -
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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