Contacts of the helix formed by residues 273 - 288 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267C HIS* 4.2 0.5 - - - -
269C TYR 3.0 17.6 + - - +
270C LEU 3.6 7.2 + - - -
271C THR 3.5 1.2 - - - -
272C GLY* 1.3 80.1 - - - +
274C PHE* 1.3 61.5 + - - -
275C THR* 3.3 3.6 - - - -
276C ALA 3.4 2.7 + - - -
277C ASN* 2.9 28.4 + - - +
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Residues in contact with PHE 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C VAL* 3.6 26.0 - - + -
114C THR* 3.5 23.6 - - - +
117C PHE* 3.5 35.4 - + - -
269C TYR* 3.6 38.6 - + - -
270C LEU* 4.1 18.2 - - + -
273C GLY* 1.3 69.5 - - - -
275C THR* 1.3 58.4 + - - +
277C ASN* 3.7 3.8 - - + +
278C THR* 2.7 39.9 + - - +
314C LEU* 4.9 4.5 - - + -
317C ALA* 3.9 14.6 - - + -
321C SER* 4.0 11.6 + - - -
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Residues in contact with THR 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C THR* 3.2 23.6 + - - +
247C CYS* 5.7 7.0 - - - -
273C GLY 3.3 0.6 - - - -
274C PHE* 1.3 78.3 - - - +
276C ALA* 1.3 64.0 + - - +
278C THR* 3.4 4.3 + - - -
279C THR* 3.3 24.5 + - - +
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Residues in contact with ALA 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246C THR 6.4 0.2 - - - -
247C CYS* 5.0 16.8 - - - -
250C MET* 3.4 28.8 - - + +
267C HIS* 4.2 7.4 - - + +
272C GLY* 4.1 15.3 - - - +
273C GLY* 3.4 7.4 + - - +
274C PHE 3.4 0.2 - - - -
275C THR* 1.3 80.3 - - - +
277C ASN* 1.3 63.6 + - - +
279C THR* 3.3 6.6 + - - -
280C LEU 3.1 17.5 + - - -
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Residues in contact with ASN 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267C HIS* 2.9 30.3 + - + +
269C TYR* 3.5 14.9 - - + +
273C GLY 2.9 19.1 + - - +
274C PHE* 3.7 7.6 - - + +
275C THR 3.2 0.2 - - - -
276C ALA* 1.3 78.3 - - - +
278C THR* 1.3 56.5 + - - +
280C LEU* 3.3 3.7 + - - +
281C SER* 2.8 27.5 + - - -
291C LEU* 4.7 2.3 - - - +
293C ILE* 3.4 17.3 - - - +
318C LEU* 3.8 11.7 - - - +
321C SER* 3.1 21.1 + - - +
322C GLY 3.3 22.4 + - - -
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Residues in contact with THR 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLY 4.5 16.3 + - - +
113C VAL* 5.6 4.7 + - - +
148C PHE* 6.2 1.3 - - + -
274C PHE* 2.7 23.2 + - - +
275C THR* 3.9 5.7 - - - -
276C ALA 3.3 0.2 - - - -
277C ASN* 1.3 74.7 - - - +
279C THR* 1.3 65.8 + - - +
281C SER* 3.4 3.1 + - - -
282C HIS* 3.1 50.9 + - + +
321C SER* 2.9 27.9 + - - +
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Residues in contact with THR 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247C CYS* 5.8 8.1 - - + -
250C MET* 3.9 15.3 - - + -
251C MET* 4.0 17.9 - - + -
275C THR* 3.3 13.7 + - - +
276C ALA* 3.3 11.1 + - - -
277C ASN 3.2 0.2 - - - -
278C THR* 1.3 79.2 - - - +
280C LEU* 1.3 62.8 + - - +
282C HIS* 3.3 7.5 + - - +
283C TYR* 3.1 20.3 + - + +
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Residues in contact with LEU 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C ALA* 4.3 13.5 - - + -
250C MET* 3.9 21.5 - - + -
251C MET* 4.9 2.2 - - - -
254C ALA* 3.8 29.2 - - + -
265C VAL* 5.0 3.1 - - + -
266C MET 4.6 0.7 - - - +
267C HIS* 3.6 38.6 - - + -
276C ALA 3.1 11.2 + - - +
277C ASN* 3.3 8.5 + - - +
279C THR* 1.3 76.7 - - - +
281C SER* 1.3 60.0 + - - +
283C TYR* 3.2 9.5 + - + +
284C CYS* 2.8 44.5 + - - -
291C LEU* 3.8 13.9 - - + -
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Residues in contact with SER 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149C GLN* 3.2 22.1 + - - -
150C GLY 3.7 0.2 + - - -
152C PRO* 3.6 7.7 - - - +
277C ASN 2.8 17.9 + - - -
278C THR 3.6 4.7 - - - -
279C THR 3.3 0.2 - - - -
280C LEU* 1.3 76.9 - - - +
282C HIS* 1.3 62.5 + - - +
284C CYS 3.4 0.5 + - - -
285C ARG 3.2 16.8 + - - -
291C LEU* 3.9 12.9 - - - +
321C SER 3.1 25.7 + - - -
322C GLY* 3.3 21.1 - - - -
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Residues in contact with HIS 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C GLY 5.9 0.7 - - - -
149C GLN* 3.3 43.9 + - + +
278C THR* 3.1 39.9 + - + +
279C THR* 3.8 5.6 - - - +
281C SER* 1.3 77.4 - - - +
283C TYR* 1.3 67.2 + - - +
285C ARG* 3.3 3.3 + - - +
286C ASP* 3.1 33.5 + - - +
321C SER 4.8 1.6 + - - -
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Residues in contact with TYR 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C MET* 3.4 28.7 - - + -
254C ALA* 3.8 29.4 - - + -
255C VAL* 3.6 31.9 - - + +
258C ARG* 3.6 16.6 - - - +
279C THR* 3.1 13.2 + - + +
280C LEU* 3.5 13.2 - - + +
282C HIS* 1.3 77.2 - - - +
284C CYS* 1.3 65.3 + - - +
286C ASP* 3.2 5.1 + - + +
287C ASN* 3.0 56.0 + - - +
289C LEU* 3.9 18.4 - - + -
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Residues in contact with CYS 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152C PRO* 4.0 12.6 - - + -
153C HIS* 3.7 1.0 - - - -
265C VAL* 3.9 26.9 - - - -
280C LEU* 2.8 36.2 + - - +
281C SER 3.7 5.6 - - - +
282C HIS 3.2 0.2 - - - -
283C TYR* 1.3 80.3 - - - +
285C ARG* 1.3 57.0 + - - +
288C GLY* 3.0 24.6 + - - -
289C LEU* 3.1 42.2 + - - +
291C LEU* 4.1 11.9 - - + -
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Residues in contact with ARG 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C GLN* 3.5 53.4 + - - +
151C PRO 2.9 26.1 + - - -
152C PRO* 3.2 25.7 + - + +
153C HIS* 4.6 6.1 + - - +
281C SER 3.2 7.1 + - - -
282C HIS 3.3 2.7 + - - +
284C CYS* 1.3 78.2 - - - +
286C ASP* 1.3 67.8 + - - +
287C ASN 3.3 0.7 + - - -
288C GLY* 3.7 2.3 + - - -
372C PRO* 5.0 8.5 - - - +
213D ARG* 3.5 48.3 - - + +
214D TRP* 6.2 2.5 - - - +
215D ARG* 3.5 19.4 - - + +
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Residues in contact with ASP 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C ARG* 5.4 0.2 + - - -
282C HIS* 3.1 24.5 + - - +
283C TYR* 3.2 6.6 + - + +
285C ARG* 1.3 81.3 - - - +
287C ASN* 1.3 71.4 + - - +
214D TRP* 5.0 13.0 + - - -
215D ARG* 3.0 19.5 + - - +
252D LYS* 2.9 31.4 + - - +
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Residues in contact with ASN 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C ARG* 3.2 35.5 + - + +
283C TYR* 3.0 63.8 + - + +
284C CYS 4.6 0.2 - - - +
285C ARG 3.1 0.2 - - - -
286C ASP* 1.3 90.4 + - - +
288C GLY* 1.3 61.7 + - - +
289C LEU* 3.4 6.3 + - + +
215D ARG* 3.5 17.8 + - - +
59U PRO* 3.7 19.1 - - - +
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Residues in contact with GLY 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C HIS* 3.8 16.4 + - - -
161C LYS* 4.8 7.6 + - - -
263C PRO 4.5 2.3 - - - +
284C CYS 3.0 6.7 + - - -
285C ARG 3.7 3.9 + - - -
287C ASN* 1.3 77.2 - - - +
289C LEU* 1.3 61.1 + - - +
290C LEU* 4.0 2.8 + - - +
215D ARG* 3.6 20.0 - - - +
59U PRO* 3.6 22.0 - - - +
60U GLY* 4.2 4.5 + - - -
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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