Contacts of the helix formed by residues 273 - 284 (chain A) in PDB entry 1H3F
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 GLU 273 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ARG* 3.9 25.9 + - - +
271A ASP 4.0 4.9 - - - +
272A LEU* 1.3 74.7 - - - +
274A GLU* 1.3 67.1 + - - +
275A GLU* 4.3 12.1 - - + +
276A GLU* 2.7 43.0 + - + +
277A ILE* 3.0 12.6 + - - +
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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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17A ARG* 4.8 8.5 + - - +
267A ARG* 3.0 48.7 + - - +
272A LEU 3.9 0.6 + - - +
273A GLU* 1.3 72.5 + - - +
275A GLU* 1.3 57.7 + - - +
277A ILE* 3.2 14.7 + - - +
278A GLU* 3.0 39.5 + - + +
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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
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273A GLU* 4.3 8.9 - - + +
274A GLU* 1.3 75.8 - - - +
276A GLU* 1.3 76.9 + - + +
278A GLU* 3.5 8.2 + - - +
279A ALA* 3.1 22.7 + - - +
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Residues in contact with GLU 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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271A ASP 4.9 0.2 - - - +
272A LEU* 3.4 21.5 - - + +
273A GLU* 2.7 50.2 + - + +
275A GLU* 1.3 82.5 - - + +
277A ILE* 1.3 66.1 + - - +
279A ALA* 3.3 5.0 + - - +
280A LEU* 3.1 26.1 + - - +
310A ASP* 5.6 0.9 - - - +
311A ARG* 3.7 32.4 + - - +
321A TRP* 3.6 25.6 - - + -
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Residues in contact with ILE 277 (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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263A PRO* 4.8 7.9 - - + -
266A PHE* 3.6 46.2 - - + -
267A ARG* 4.1 24.7 - - + +
272A LEU* 3.9 28.0 - - + +
273A GLU 3.0 13.5 + - - +
274A GLU* 3.2 19.9 + - - +
276A GLU* 1.3 76.1 - - - +
278A GLU* 1.3 66.5 + - - +
280A LEU* 3.2 10.0 + - - +
281A LEU* 3.0 37.9 + - + +
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Residues in contact with GLU 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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267A ARG* 4.7 8.0 + - - -
274A GLU* 3.0 30.4 + - + +
275A GLU* 3.8 8.3 - - - +
277A ILE* 1.3 77.3 - - - +
279A ALA* 1.3 53.6 + - - +
281A LEU* 3.1 24.7 + - - +
282A LYS* 2.7 37.8 + - - +
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Residues in contact with ALA 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 GLU 3.1 18.7 + - - +
276A GLU* 3.5 8.5 - - - +
278A GLU* 1.3 76.5 - - - +
280A LEU* 1.3 63.1 + - - +
282A LYS* 3.4 21.0 + - - +
283A ALA* 3.0 21.5 + - - +
321A TRP* 4.7 4.9 - - + +
324A PHE* 4.3 21.2 - - + -
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Residues in contact with LEU 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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266A PHE* 3.7 35.4 - - + -
272A LEU* 3.9 14.4 - - + -
276A GLU 3.1 14.7 + - - +
277A ILE* 3.2 9.6 + - - +
279A ALA* 1.3 74.1 - - - +
281A LEU* 1.3 67.4 + - - +
283A ALA* 3.0 19.4 + - + +
284A GLY 3.4 9.9 + - - +
287A PRO 4.8 5.4 - - - +
288A ALA* 4.1 13.0 + - + +
291A VAL* 3.7 38.8 - - + -
321A TRP* 3.8 13.5 - - + -
324A PHE* 3.8 23.3 - - + -
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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
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259A ASP 5.8 0.4 - - - +
262A LEU* 4.1 35.0 - - + -
263A PRO* 4.1 21.3 - - + -
266A PHE* 5.0 3.6 - - + -
267A ARG* 6.3 0.2 - - - +
277A ILE* 3.0 31.4 + - + +
278A GLU* 3.5 29.8 - - - +
280A LEU* 1.3 74.5 - - - +
282A LYS* 1.3 55.4 + - - +
284A GLY* 2.6 30.7 + - - -
285A PRO* 5.0 0.5 - - - +
288A ALA* 4.4 7.9 - - + -
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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 GLU 2.7 20.1 + - - +
279A ALA* 3.6 18.8 - - - +
281A LEU* 1.3 72.5 - - - +
283A ALA* 1.3 60.9 + - - +
284A GLY* 3.4 0.7 + - - -
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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 ALA 3.0 12.9 + - - +
280A LEU 3.0 13.8 + - - +
281A LEU 2.9 0.8 + - - -
282A LYS* 1.3 77.3 - - - +
284A GLY* 1.3 56.7 + - - +
287A PRO* 3.7 26.6 - - + +
324A PHE* 4.3 24.0 - - + -
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Residues in contact with GLY 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 LEU 3.4 1.4 + - - +
281A LEU* 2.6 22.2 + - - -
282A LYS 3.2 1.5 - - - -
283A ALA* 1.3 74.5 - - - +
285A PRO* 1.3 76.0 - - - +
286A VAL* 5.5 0.7 - - - -
287A PRO* 3.1 14.6 - - - +
288A ALA* 3.1 18.2 + - - +
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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