Contacts of the helix formed by residues 272 - 286 (chain C) in PDB entry 4IXU
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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ARG* 4.0 10.5 - - - +
255C PHE* 3.4 5.1 - - - -
256C ASP* 5.6 0.4 - - - -
259C LEU* 3.7 6.1 - - - -
270C GLY 4.8 1.1 - - - +
271C LEU* 1.3 76.1 - - - +
273C TYR* 1.3 65.2 + - - +
274C ARG* 3.5 9.8 + - - +
275C GLU* 2.9 41.0 + - - +
276C GLY 3.1 17.5 + - - -
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Residues in contact with TYR 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ASP* 6.0 0.2 - - - +
268A VAL* 3.5 30.7 - - + +
269A GLY* 3.6 27.1 - - - +
255C PHE* 4.1 4.9 - - - -
259C LEU* 3.3 27.9 - - + +
272C THR* 1.3 74.1 - - - +
274C ARG* 1.3 67.0 + - + +
276C GLY* 3.3 1.2 + - - -
277C MET* 3.0 50.1 + - + +
314C LEU* 3.5 27.4 - - + -
317C ASP* 2.6 35.0 + - - +
327C ARG* 5.4 7.2 - - - -
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Residues in contact with ARG 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A MET* 3.3 12.2 - - - +
222A ILE* 3.6 17.8 + - - +
223A ASP* 2.7 42.1 + - - +
269A GLY* 3.6 33.7 - - - +
270A GLY 3.2 18.6 + - - -
272A THR* 4.0 11.3 - - - +
275A GLU* 2.8 42.6 + - - -
272C THR* 3.2 8.8 + - - +
273C TYR* 1.3 81.7 - - + +
275C GLU* 1.3 58.0 + - + +
277C MET* 3.4 2.5 + - - +
278C TYR* 2.9 29.2 + - - +
327C ARG* 3.8 15.2 + - - +
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Residues in contact with GLU 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ASP* 6.4 0.7 - - - -
274B ARG* 2.8 45.3 + - - -
222C ILE* 3.4 14.4 - - - +
227C ILE* 4.0 23.3 + - + +
271C LEU* 3.4 16.0 - - + +
272C THR* 2.9 34.0 + - - +
274C ARG* 1.3 77.5 - - + +
276C GLY* 1.3 58.4 + - - +
278C TYR* 3.1 8.3 + - - +
279C ILE* 3.0 34.4 + - - +
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Residues in contact with GLY 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C PHE* 4.7 6.6 - - - -
255C PHE* 3.6 26.9 - - - -
271C LEU* 4.5 4.4 - - - +
272C THR 3.1 10.5 + - - -
275C GLU* 1.3 74.8 - - - +
277C MET* 1.3 68.7 + - - +
279C ILE* 3.4 14.1 + - - +
280C ALA* 3.1 22.2 + - - +
318C VAL* 5.2 0.7 - - - +
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Residues in contact with MET 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C PHE* 4.1 9.0 - - + -
273C TYR* 3.0 52.1 + - + +
274C ARG* 3.7 4.7 - - - +
276C GLY* 1.3 76.5 - - - +
278C TYR* 1.3 59.3 + - - +
280C ALA* 3.2 1.1 + - - -
281C GLU* 2.8 37.9 + - - +
314C LEU* 4.4 1.1 - - + -
317C ASP* 3.8 31.0 - - + +
318C VAL* 3.8 35.4 - - + +
321C SER* 3.3 11.4 + - - +
327C ARG* 4.1 23.1 - - + +
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Residues in contact with TYR 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 3.4 25.8 - - + -
223A ASP* 4.3 10.8 - - + +
224A ARG* 3.0 50.7 + - + +
227C ILE* 3.8 21.8 - - + -
228C GLN* 3.6 29.0 + - - +
231C MET* 3.9 11.0 - - + -
232C GLU* 6.0 0.2 - - - +
274C ARG 2.9 17.6 + - - +
275C GLU 3.1 5.1 + - - +
277C MET* 1.3 77.6 - - - +
279C ILE* 1.3 63.8 + - - +
281C GLU* 3.3 9.9 + - - +
282C GLU* 2.9 47.8 + - + +
327C ARG* 4.0 8.7 - - - +
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Residues in contact with ILE 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C VAL* 5.3 0.4 - - + -
142C VAL* 4.2 25.1 - - + -
196C ILE* 4.0 22.4 - - + -
227C ILE* 3.8 19.7 - - + -
231C MET* 3.9 27.7 - - + +
248C LEU* 4.9 2.7 - - + -
250C PHE* 4.6 7.2 - - + -
271C LEU* 3.8 28.3 - - + -
275C GLU 3.0 19.8 + - - +
276C GLY* 3.5 8.5 - - - +
277C MET 3.3 0.2 - - - -
278C TYR* 1.3 76.7 - - - +
280C ALA* 1.3 59.6 + - - +
282C GLU* 3.1 3.8 + - - +
283C ILE* 2.9 35.9 + - + +
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Residues in contact with ALA 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C LEU* 5.2 1.3 - - + -
250C PHE* 5.7 0.7 - - + -
276C GLY 3.1 10.4 + - - +
277C MET* 3.7 4.7 - - - +
279C ILE* 1.3 82.4 - - + +
281C GLU* 1.3 58.3 + - - +
283C ILE* 3.3 7.6 + - - +
284C HIS 2.9 24.4 + - - -
318C VAL* 3.6 14.1 - - + +
321C SER* 3.3 31.3 - - - +
322C SER* 3.4 24.9 - - - +
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Residues in contact with GLU 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 3.1 35.4 + - - +
277C MET* 2.8 20.8 + - - +
278C TYR* 3.6 4.6 - - - +
280C ALA* 1.3 75.8 - - - +
282C GLU* 1.3 58.5 + - - +
284C HIS* 3.3 3.8 + - - +
285C ASN* 2.9 35.7 + - - +
321C SER* 3.2 17.4 + - - +
325C GLN 4.2 11.3 - - - +
326C THR* 5.2 2.9 - - + -
327C ARG* 2.8 60.6 + - - +
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Residues in contact with GLU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 2.6 38.6 + - - -
224A ARG* 5.2 1.9 + - - -
231C MET* 3.9 14.9 - - + +
235C PHE* 3.6 23.2 - - + -
278C TYR* 2.9 46.7 + - + +
279C ILE 3.7 3.4 - - - +
281C GLU* 1.3 73.4 - - - +
283C ILE* 1.3 67.3 + - - +
285C ASN* 3.2 26.2 + - - +
286C THR* 3.2 16.8 + - - +
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Residues in contact with ILE 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C VAL* 4.2 15.0 - - + -
231C MET* 4.6 1.3 - - + -
235C PHE* 3.9 25.4 - - + -
246C ILE* 4.1 20.0 - - + -
248C LEU* 4.2 29.2 - - + -
279C ILE* 2.9 23.8 + - + +
280C ALA* 3.4 10.1 - - - +
282C GLU* 1.3 76.7 - - - +
284C HIS* 1.3 60.5 + - - +
286C THR* 2.7 26.1 + - - +
287C GLY 4.0 0.5 + - - -
289C LEU* 3.8 42.7 - - + +
322C SER* 4.7 2.0 - - - +
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Residues in contact with HIS 284 (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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24C HIS* 6.5 0.9 - + - -
280C ALA 2.9 6.5 + - - -
281C GLU* 3.3 7.6 + - - +
283C ILE* 1.3 77.2 - - - +
285C ASN* 1.3 72.6 + - - +
287C GLY* 3.0 21.9 + - - -
289C LEU* 5.4 2.5 - - - -
321C SER 3.5 14.1 - - - +
322C SER 3.3 18.9 + - - +
323C PHE* 3.5 9.3 - - - -
324C GLY* 3.4 37.7 + - - -
326C THR* 6.0 2.2 - - + -
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Residues in contact with ASN 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A ARG* 3.6 16.6 - - - +
281C GLU* 2.9 18.8 + - - +
282C GLU* 3.2 33.3 + - - +
284C HIS* 1.3 89.9 - - - +
286C THR* 1.3 62.0 + - - +
287C GLY* 3.1 0.9 + - - -
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Residues in contact with THR 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235C PHE* 3.5 36.3 - - + -
239C ILE* 4.2 7.6 - - + -
243C GLN* 4.8 4.0 + - - +
246C ILE* 3.5 18.6 - - + +
282C GLU 3.2 16.6 + - - +
283C ILE 2.7 16.5 + - - +
285C ASN* 1.3 79.1 - - - +
287C GLY* 1.3 59.8 + - - +
288C LEU* 3.0 32.3 + - - +
289C LEU 4.0 0.3 + - - -
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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