Contacts of the helix formed by residues 272 - 287 (chain A) in PDB entry 5ULM
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 272 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273A ARG* 1.3 67.4 + - - +
274A GLU* 3.4 8.6 - - - +
275A SER* 3.5 16.3 + - - +
276A ILE* 3.2 29.3 + - + +
302A ARG* 6.5 0.4 - - + -
306A ILE* 4.6 23.6 - - + -
307A GLU* 4.6 19.5 - - - +
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Residues in contact with ARG 273 (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 PHE* 1.3 78.5 - - - +
274A GLU* 1.3 73.5 + - + +
276A ILE* 3.1 5.1 + - - +
277A LEU* 3.0 39.7 + - + +
306A ILE* 5.8 5.6 - - + +
310A THR* 3.4 33.0 - - - +
312A ASP* 2.7 31.9 + - - +
313A ILE* 4.0 18.1 - - + +
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Residues in contact with GLU 274 (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 PHE 3.4 5.0 - - - +
273A ARG* 1.3 99.6 + - + +
275A SER* 1.3 57.3 + - - +
277A LEU* 3.4 10.7 + - + +
278A ASN* 2.9 44.1 + - - +
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Residues in contact with SER 275 (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 PHE* 3.5 20.0 + - - +
274A GLU* 1.3 76.0 - - - +
276A ILE* 1.3 65.0 + - - +
278A ASN* 3.5 5.6 + - - +
279A ASP* 3.1 34.3 + - - +
302A ARG* 2.8 24.5 + - - -
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Residues in contact with ILE 276 (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 PHE* 3.2 15.7 + - + +
273A ARG 3.1 8.1 + - - +
275A SER* 1.3 76.0 - - - +
277A LEU* 1.3 63.9 + - - +
279A ASP* 3.3 3.7 + - - +
280A ILE* 3.0 37.7 + - + +
299A ILE* 4.1 7.3 - - + +
302A ARG* 3.4 48.9 - - + +
303A VAL* 3.7 30.1 - - + +
306A ILE* 4.1 11.9 - - + -
313A ILE* 3.6 23.8 - - + -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ARG* 3.0 32.0 + - + +
274A GLU* 3.7 10.8 - - + +
275A SER 3.3 0.4 - - - -
276A ILE* 1.3 77.2 - - - +
278A ASN* 1.3 62.1 + - - +
280A ILE* 3.3 7.2 + - + +
281A ARG* 3.1 24.7 + - - +
312A ASP* 3.6 54.3 - - + +
313A ILE* 3.9 12.6 - - + -
316A ASN* 3.8 19.7 - - + +
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Residues in contact with ASN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A GLU* 2.9 30.3 + - - +
275A SER* 4.0 5.9 - - - +
276A ILE 3.3 0.2 - - - -
277A LEU* 1.3 76.9 - - - +
279A ASP* 1.3 61.6 + - - +
281A ARG* 2.8 38.1 + - - +
282A LYS* 3.0 28.8 + - - +
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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
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275A SER* 3.1 17.0 + - - +
276A ILE* 3.8 2.7 - - - +
278A ASN* 1.3 79.1 - - - +
280A ILE* 1.3 59.8 + - - +
282A LYS* 2.8 40.2 + - - +
283A ALA* 2.9 29.6 + - - +
295A GLU* 5.5 0.4 - - - +
299A ILE* 3.5 16.9 - - + +
302A ARG* 2.8 37.4 + - - +
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Residues in contact with ILE 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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276A ILE* 3.0 40.0 + - + +
277A LEU* 3.3 7.2 + - - +
279A ASP* 1.3 74.6 - - - +
281A ARG* 1.3 59.8 + - - +
283A ALA* 3.3 4.4 + - - +
284A ARG* 2.9 33.3 + - - +
296A LEU* 4.9 2.2 - - + -
299A ILE* 3.9 21.3 - - + -
313A ILE* 4.3 12.6 - - + +
316A ASN* 3.5 35.9 - - + +
317A LEU* 4.1 29.8 - - + +
320A SER* 4.2 12.8 - - - +
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Residues in contact with ARG 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 LEU 3.1 13.4 + - - +
278A ASN* 2.8 33.8 + - - +
280A ILE* 1.3 74.9 - - - +
282A LYS* 1.3 65.7 + - - +
284A ARG* 3.4 9.7 + - - +
285A ASN* 3.1 22.1 + - + +
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Residues in contact with LYS 282 (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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278A ASN 3.0 13.2 + - - +
279A ASP* 2.8 49.6 + - - +
281A ARG* 1.3 76.7 - - - +
283A ALA* 1.3 60.2 + - - +
285A ASN* 3.1 8.3 + - - +
286A LEU* 2.9 47.9 + - + +
287A TYR* 6.0 1.3 - - + -
295A GLU* 4.8 12.3 - - - -
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Residues in contact with ALA 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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279A ASP 2.9 21.4 + - - +
280A ILE* 3.4 9.2 - - - +
282A LYS* 1.3 77.4 - - - +
284A ARG* 1.3 57.7 + - - +
287A TYR* 2.9 45.0 + - - +
292A LEU* 3.6 13.5 - - + +
295A GLU* 3.5 25.6 - - + -
296A LEU* 4.6 4.0 - - + -
299A ILE* 4.2 3.8 - - + -
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Residues in contact with ARG 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 2.9 25.6 + - - +
281A ARG* 3.4 8.0 + - + +
283A ALA* 1.3 74.8 - - - +
285A ASN* 1.3 60.5 + - - +
287A TYR 3.6 10.3 - - - +
288A THR* 5.4 2.3 - - - +
292A LEU* 4.4 8.6 - - + +
316A ASN* 4.6 8.2 + - - -
319A LEU* 3.7 37.0 + - - +
320A SER* 3.7 27.6 - - - +
322A ARG* 6.0 0.6 - - - +
323A ASP* 2.6 43.7 + - - +
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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 ARG* 3.1 13.3 + - + +
282A LYS* 3.5 10.1 - - - +
284A ARG* 1.3 78.7 - - - +
286A LEU* 1.3 69.2 + - + +
287A TYR 5.0 0.3 - - - +
288A THR* 6.1 0.2 - - - +
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Residues in contact with LEU 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 LYS* 2.9 36.2 + - + +
285A ASN* 1.3 80.8 - - - +
287A TYR* 1.3 99.0 + - + +
288A THR* 5.7 0.3 - - - +
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Residues in contact with TYR 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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282A LYS* 6.0 1.6 - - + -
283A ALA* 2.9 24.3 + - - +
284A ARG 3.6 9.7 - - - +
285A ASN 4.8 0.2 - - - -
286A LEU* 1.3 114.5 - - + +
288A THR* 1.3 71.3 + - - +
291A GLU* 3.9 19.5 - - + -
292A LEU* 3.5 31.7 - - - +
295A GLU* 3.9 41.3 + - + -
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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