Contacts of the helix formed by residues 272 - 286 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A PHE* 3.5 4.0 - - - -
256A ASP* 5.7 0.7 - - - -
259A LEU* 3.7 6.5 - - - -
270A GLY 4.8 0.9 - - - +
271A LEU* 1.3 76.2 - - - +
273A TYR* 1.3 65.5 + - - +
274A ARG* 3.6 9.1 + - - +
275A GLU* 3.0 39.1 + - - +
276A GLY 3.1 17.8 + - - -
274C ARG* 4.0 10.5 - - - +
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Residues in contact with TYR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PHE* 4.1 5.2 - - - -
259A LEU* 3.3 27.2 - - + +
272A THR* 1.3 73.1 - - - +
274A ARG* 1.3 66.6 + - + +
276A GLY* 3.3 3.1 + - - -
277A MET* 3.0 51.4 + - + +
314A LEU* 3.6 26.7 - - + -
317A ASP* 2.6 34.4 + - - -
327A ARG* 5.4 7.0 - - - -
256B ASP* 6.0 0.4 - - - +
268B VAL* 3.4 31.5 - - + +
269B GLY* 3.6 27.6 - - - -
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Residues in contact with ARG 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A THR* 3.2 8.4 + - - +
273A TYR* 1.3 81.3 - - + +
275A GLU* 1.3 58.8 + - + +
277A MET* 3.4 2.5 + - - +
278A TYR* 2.9 29.8 + - - +
327A ARG* 3.8 16.6 + - - +
219B MET* 3.4 12.4 - - + +
222B ILE* 3.5 16.8 + - - +
223B ASP* 2.7 41.3 + - - +
269B GLY* 3.7 32.5 - - - +
270B GLY 3.2 18.1 + - - -
272B THR* 4.0 11.3 - - - +
275B GLU* 2.8 42.6 + - - -
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Residues in contact with GLU 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ILE* 3.4 15.3 - - - +
227A ILE* 4.0 23.9 + - + +
271A LEU* 3.5 16.0 - - + +
272A THR* 3.0 34.3 + - - +
274A ARG* 1.3 78.8 - - + +
276A GLY* 1.3 62.0 + - - +
278A TYR* 3.2 8.0 + - - +
279A ILE* 3.0 29.8 + - - +
223B ASP* 6.4 0.7 - - - -
274C ARG* 2.8 45.1 + - - -
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Residues in contact with GLY 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A PHE* 4.7 6.2 - - - -
255A PHE* 3.6 26.7 - - - -
271A LEU* 4.5 4.8 - - - +
272A THR 3.1 9.9 + - - -
275A GLU* 1.3 76.9 - - - +
277A MET* 1.3 67.6 + - - +
279A ILE* 3.3 15.0 + - - +
280A ALA* 3.1 22.0 + - - +
318A VAL* 5.3 0.4 - - - +
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Residues in contact with MET 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255A PHE* 4.1 7.0 - - + -
273A TYR* 3.0 52.8 + - + +
274A ARG 3.8 4.0 - - - +
276A GLY* 1.3 77.9 - - - +
278A TYR* 1.3 57.9 + - - +
280A ALA* 3.2 1.7 + - - -
281A GLU* 2.8 37.3 + - - +
314A LEU* 4.3 1.1 - - + -
317A ASP* 3.7 33.7 - - + +
318A VAL* 3.8 36.1 - - + +
321A SER* 3.3 11.4 + - - +
327A ARG* 4.1 23.1 - - + +
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Residues in contact with TYR 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ILE* 3.6 25.1 - - + -
228A GLN* 3.4 31.2 + - - +
231A MET* 3.9 9.6 - - + +
232A GLU* 5.9 0.3 - - - +
274A ARG 2.9 17.4 + - - +
275A GLU 3.2 4.9 + - - +
277A MET* 1.3 75.5 - - - +
279A ILE* 1.3 67.1 + - - +
281A GLU* 3.6 10.5 - - - +
282A GLU* 2.9 48.1 + - + +
327A ARG* 4.0 9.6 - - - +
220B ARG* 3.4 26.9 - - + -
223B ASP* 4.4 10.8 - - + +
224B ARG* 2.8 48.9 + - + -
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL* 5.3 0.2 - - + -
142A VAL* 4.2 25.6 - - + -
196A ILE* 4.0 16.4 - - + -
227A ILE* 3.8 25.1 - - + -
231A MET* 3.9 27.6 - - + +
248A LEU* 4.9 2.7 - - + -
250A PHE* 4.6 8.3 - - + -
271A LEU* 3.7 30.3 - - + -
275A GLU 3.0 18.9 + - - +
276A GLY* 3.3 8.0 + - - +
278A TYR* 1.3 76.8 - - - +
280A ALA* 1.3 59.9 + - - +
282A GLU* 3.2 2.1 + - - +
283A ILE* 2.9 39.7 + - + +
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Residues in contact with ALA 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A LEU* 5.3 1.6 - - + -
250A PHE* 5.7 0.9 - - + -
276A GLY 3.1 9.8 + - - +
277A MET* 3.6 3.8 - - - +
279A ILE* 1.3 80.9 - - - +
281A GLU* 1.3 58.2 + - - +
283A ILE* 3.2 8.0 + - - +
284A HIS 2.8 24.9 + - - -
318A VAL* 3.6 13.7 - - + +
321A SER* 3.5 31.5 - - - +
322A SER* 3.3 25.5 - - - +
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A MET* 2.8 20.1 + - - +
278A TYR* 3.6 5.3 - - - +
280A ALA* 1.3 74.0 - - - +
282A GLU* 1.3 56.6 + - - +
284A HIS* 3.2 4.7 + - - +
285A ASN* 2.8 36.7 + - - +
321A SER* 3.2 22.4 + - - +
325A GLN 4.1 10.0 - - - +
326A THR* 5.1 3.4 - - + -
327A ARG* 2.7 59.2 + - - +
220B ARG* 3.1 34.2 + - - +
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A MET* 3.9 14.1 - - + +
232A GLU* 6.1 1.2 - - - +
235A PHE* 3.5 24.3 - - + -
278A TYR* 2.9 47.2 + - + +
279A ILE 3.7 3.4 - - - +
281A GLU* 1.3 73.7 - - - +
283A ILE* 1.3 65.6 - - - +
285A ASN* 3.1 24.7 + - - +
286A THR* 3.2 18.4 + - - +
220B ARG* 2.6 39.9 + - - -
224B ARG* 5.1 1.5 + - - -
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A VAL* 4.2 13.9 - - + -
231A MET* 4.7 1.3 - - + -
235A PHE* 3.8 25.5 - - + -
246A ILE* 4.2 19.1 - - + -
248A LEU* 4.2 28.7 - - + -
279A ILE* 2.9 24.5 + - + +
280A ALA* 3.3 9.6 - - - +
282A GLU* 1.3 76.5 - - - +
284A HIS* 1.3 60.6 + - - +
286A THR* 2.8 26.7 + - - +
287A GLY 4.1 0.3 + - - -
289A LEU* 3.8 43.0 - - + +
322A SER* 4.6 2.0 - - - +
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Residues in contact with HIS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A ALA 2.8 9.9 + - - -
281A GLU* 3.2 7.8 + - - +
283A ILE* 1.3 73.8 - - - +
285A ASN* 1.3 71.3 + - - +
287A GLY* 2.9 23.2 + - - -
289A LEU* 5.5 2.2 - - - -
321A SER 3.5 13.7 - - - +
322A SER 3.3 18.4 + - - +
323A PHE* 3.4 10.7 - - - -
324A GLY* 3.3 34.2 + - - -
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Residues in contact with ASN 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A GLU* 2.8 22.8 + - - +
282A GLU* 3.1 35.4 + - - +
284A HIS* 1.3 87.2 - - - +
286A THR* 1.3 60.8 + - - +
287A GLY 3.2 0.6 + - - -
220B ARG* 3.5 15.8 - - - +
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Residues in contact with THR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A PHE* 3.6 34.3 - - + -
239A ILE* 4.1 13.9 - - + -
243A GLN* 4.7 5.5 + - - +
246A ILE* 3.5 19.0 - - + +
282A GLU 3.2 15.4 + - - +
283A ILE 2.8 15.8 + - - +
284A HIS 3.1 0.2 - - - -
285A ASN* 1.3 76.4 - - - +
287A GLY* 1.3 60.2 + - - +
288A LEU* 2.9 28.0 + - - +
289A 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
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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