Contacts of the helix formed by residues 277 - 292 (chain A) in PDB entry 3I5Y
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 PHE 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A PRO* 3.4 32.1 - - + -
243A PRO* 3.7 25.6 - - + -
271A ARG* 3.5 39.9 - - - +
272A LEU* 3.1 30.7 - - + +
274A GLU 3.1 4.0 + - - -
275A ILE 3.4 1.2 + - - -
276A GLY* 1.3 80.0 - - - +
278A ARG* 1.3 60.6 + - - +
279A ASP 3.3 2.5 - - - -
280A ASP* 3.1 7.0 + - - +
281A LEU* 2.9 30.9 + - + +
5B U 3.4 25.1 - - - -
6B U 3.4 37.7 - - - -
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Residues in contact with ARG 278 (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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272A LEU 3.3 8.0 + - - -
273A LEU* 3.6 37.2 - - + +
274A GLU 3.1 10.0 + - - +
275A ILE* 4.8 16.8 - - + +
276A GLY 3.7 1.2 - - - +
277A PHE* 1.3 77.8 - - - +
279A ASP* 1.3 62.5 + - - +
281A LEU* 3.3 4.2 + - - +
282A GLU* 2.9 54.8 + - + +
314A LYS 5.0 2.6 + - - -
315A LEU* 3.6 44.7 + - - +
317A ASN* 6.0 0.6 - - - +
318A ASN* 3.6 15.4 - - - +
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Residues in contact with ASP 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A GLY* 5.1 6.5 - - - +
277A PHE 3.3 0.8 - - - +
278A ARG* 1.3 79.8 - - - +
280A ASP* 1.3 65.4 + - - +
282A GLU* 3.4 17.1 + - - +
283A THR* 3.0 32.3 + - - -
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Residues in contact with ASP 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PRO* 4.0 23.0 - - + +
244A GLY* 4.7 4.0 + - - -
247A ILE* 3.6 26.6 - - + +
276A GLY 3.9 16.0 + - - +
277A PHE* 3.1 12.8 + - - +
279A ASP* 1.3 77.0 - - - +
281A LEU* 1.3 60.4 + - - +
283A THR* 3.4 1.8 + - - -
284A ILE* 2.9 34.4 + - - +
6B U 4.3 12.5 + - - +
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Residues in contact with LEU 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 4.5 15.9 - - + -
243A PRO* 4.2 14.8 - - + -
264A LYS* 5.9 3.4 - - + -
266A LEU* 3.4 43.1 - - + -
272A LEU* 3.8 36.3 - - + +
273A LEU* 4.8 6.5 - - + -
277A PHE 2.9 21.5 + - - +
278A ARG* 3.6 5.4 - - - +
280A ASP* 1.3 75.3 - - - +
282A GLU* 1.3 61.5 + - - +
284A ILE* 3.2 13.0 + - + +
285A SER* 2.8 32.3 + - - -
319A ILE* 4.2 8.0 - - + +
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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
----------------------------------------------------------
273A LEU* 6.4 0.4 - - + -
278A ARG* 2.9 50.9 + - + +
279A ASP* 3.7 15.6 - - - +
281A LEU* 1.3 78.3 - - + +
283A THR* 1.3 55.9 + - - +
285A SER* 3.9 0.9 - - - -
286A GLY* 2.9 26.2 + - - -
315A LEU 4.7 1.7 - - - +
318A ASN* 3.3 33.2 + - + +
319A ILE* 3.8 22.8 - - + +
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Residues in contact with THR 283 (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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247A ILE* 4.2 22.8 - - + +
251A GLU* 5.3 4.0 - - - +
279A ASP 3.0 15.6 + - - -
280A ASP* 3.6 8.5 + - - -
281A LEU 3.3 0.2 - - - -
282A GLU* 1.3 74.9 - - - +
284A ILE* 1.3 66.6 + - - +
286A GLY* 3.2 1.9 + - - -
287A ILE* 3.0 42.4 + - + +
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Residues in contact with ILE 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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184A VAL* 5.5 0.2 - - + -
186A VAL* 4.8 10.8 - - + -
243A PRO* 3.8 31.6 - - + +
246A LEU* 4.0 30.1 - - + -
247A ILE* 3.6 19.7 - - + -
250A LEU* 4.2 12.5 - - + +
264A LYS* 5.6 4.5 - - + -
280A ASP 2.9 26.2 + - - +
281A LEU* 3.5 18.2 - - + +
283A THR* 1.3 77.2 - - - +
285A SER* 1.3 62.5 + - - +
287A ILE* 3.4 2.7 + - - +
288A LEU* 3.1 39.7 + - + +
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Residues in contact with SER 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LYS* 3.5 30.5 + - - +
281A LEU* 2.8 21.7 + - - -
282A GLU 3.9 2.0 - - - -
284A ILE* 1.3 76.1 - - - +
286A GLY* 1.3 58.2 + - - +
288A LEU* 3.9 4.6 - - - +
289A ASN* 3.0 38.9 + - - +
318A ASN 4.4 2.2 + - - -
319A ILE* 3.5 31.9 + - - +
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Residues in contact with GLY 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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282A GLU 2.9 17.7 + - - -
283A THR* 3.2 2.0 + - - -
285A SER* 1.3 75.0 - - - +
287A ILE* 1.3 58.7 + - - +
289A ASN* 3.4 6.4 + - - +
290A GLU* 2.9 30.2 + - - +
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Residues in contact with ILE 287 (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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247A ILE* 5.3 2.2 - - + +
250A LEU* 4.1 30.1 - - + +
251A GLU* 4.3 21.8 - - + +
254A SER* 3.9 30.5 - - - +
283A THR* 3.0 36.3 + - + +
284A ILE* 3.8 4.3 - - - +
286A GLY* 1.3 74.5 - - - +
288A LEU* 1.3 66.7 + - + +
290A GLU* 3.2 4.9 + - - -
291A LYS* 3.0 36.3 + - + +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A VAL* 4.5 21.8 - - + -
250A LEU* 4.1 20.2 - - + -
254A SER* 6.0 0.2 - - - -
258A PHE* 4.0 37.4 - - + +
261A VAL* 4.3 12.6 - - + -
264A LYS* 4.6 15.9 - - + -
284A ILE* 3.1 31.5 + - + +
285A SER* 4.0 4.0 - - - +
287A ILE* 1.3 79.5 - - + +
289A ASN* 1.3 61.0 + - - +
291A LYS* 4.2 2.4 - - - -
292A ASN* 3.4 24.8 + - - +
299A ILE* 3.6 25.1 - - + +
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Residues in contact with ASN 289 (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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264A LYS* 4.9 1.2 + - - -
285A SER* 3.0 31.8 + - - +
286A GLY* 3.7 7.0 - - - +
287A ILE 3.1 0.2 - - - -
288A LEU* 1.3 77.7 - - - +
290A GLU* 1.3 64.6 + - - +
291A LYS 3.4 0.3 + - - -
292A ASN* 3.7 9.9 + - - +
295A SER 4.1 0.3 - - - +
296A ALA* 3.1 43.4 + - + +
299A ILE* 3.7 15.1 + - - +
318A ASN 5.7 2.0 + - - -
321A ASN* 2.9 38.8 + - - +
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Residues in contact with GLU 290 (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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286A GLY 2.9 18.2 + - - +
287A ILE* 3.2 5.6 + - - +
289A ASN* 1.3 77.1 - - - +
291A LYS* 1.3 90.1 + - + +
292A ASN 3.5 4.9 + - - +
296A ALA* 5.7 1.6 - - - -
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Residues in contact with LYS 291 (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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254A SER* 3.2 30.7 - - - +
255A ASN* 3.2 28.0 - - - +
258A PHE* 4.8 5.6 - - + +
259A ARG* 3.2 32.8 + - + +
287A ILE* 3.0 26.9 + - + +
288A LEU* 4.2 2.9 - - - +
290A GLU* 1.3 107.7 + - + +
292A ASN* 1.3 64.0 + - - +
293A SER* 3.5 0.5 + - - -
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Residues in contact with ASN 292 (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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258A PHE 5.1 0.4 + - - -
259A ARG* 3.4 13.4 + - - +
260A PHE* 4.2 1.6 - - - +
261A VAL* 3.0 32.5 + - - +
288A LEU 3.4 14.8 + - - +
289A ASN* 3.8 5.0 - - - +
290A GLU 3.3 6.2 - - - +
291A LYS* 1.3 79.1 - - - +
293A SER* 1.3 62.8 + - - +
294A LYS* 3.2 21.2 + - - +
295A SER* 3.2 30.5 + - - +
298A ASN* 3.2 23.8 + - - +
299A ILE* 4.2 10.2 - - + +
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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
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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