Contacts of the helix formed by residues 273 - 282 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B ARG* 3.9 21.8 + - - +
271B ASP 3.4 3.7 + - - +
272B LEU* 1.3 75.5 - - - +
274B GLU* 1.3 66.7 + - - +
275B GLU* 3.2 7.6 - - + +
276B GLU* 2.8 35.2 + - + +
277B ILE* 2.9 20.7 + - - +
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Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 4.1 10.4 + - - +
267B ARG* 4.1 27.2 + - - +
272B LEU 3.8 0.6 + - - -
273B GLU* 1.3 73.7 + - - +
275B GLU* 1.3 54.9 + - + +
277B ILE* 3.2 16.7 + - - +
278B GLU* 2.7 75.7 + - - +
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273B GLU* 3.2 4.6 - - + +
274B GLU* 1.3 79.9 - - + +
276B GLU* 1.3 59.9 + - + +
278B GLU* 3.4 11.5 + - - +
279B ALA* 2.8 33.2 + - - +
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Residues in contact with GLU 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272B LEU* 3.4 21.9 - - + +
273B GLU* 2.8 46.7 + - + +
275B GLU* 1.3 77.0 - - + +
277B ILE* 1.3 58.0 + - - +
279B ALA* 3.4 4.1 + - - +
280B LEU* 2.9 28.6 + - - +
310B ASP* 5.5 0.9 - - - +
311B ARG* 3.8 32.4 + - - +
321B TRP* 3.4 35.2 - - + +
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Residues in contact with ILE 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 5.5 1.1 - - - +
263B PRO* 4.9 6.7 - - + -
266B PHE* 3.4 49.4 - - + +
267B ARG* 4.0 22.0 - - + -
272B LEU* 3.8 28.3 - - + +
273B GLU 2.9 15.4 + - - +
274B GLU* 3.4 20.0 - - - +
276B GLU* 1.3 73.7 - - - +
278B GLU* 1.3 61.4 + - + +
280B LEU* 2.8 26.2 + - - +
281B LEU* 2.9 28.9 + - + +
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Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B GLU* 2.7 62.6 + - - +
275B GLU* 3.8 11.1 + - - +
277B ILE* 1.3 74.2 - - + +
279B ALA* 1.3 55.8 + - - +
281B LEU* 3.7 10.5 + - + +
282B LYS* 3.2 27.1 + - - +
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Residues in contact with ALA 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B GLU 2.8 18.9 + - - +
276B GLU* 3.6 7.9 - - - +
278B GLU* 1.3 75.6 - - - +
280B LEU* 1.3 64.4 + - - +
282B LYS* 3.5 11.7 + - + +
283B ALA* 3.4 18.7 + - - +
321B TRP* 5.3 1.8 - - + +
324B PHE* 3.9 22.9 - - + -
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B PHE* 3.9 25.1 - - + -
272B LEU* 4.0 6.5 - - + -
276B GLU 2.9 7.8 + - - +
277B ILE* 2.8 11.8 + - - +
279B ALA* 1.3 76.7 - - - +
281B LEU* 1.3 63.0 + - - +
283B ALA* 3.2 17.8 + - + +
284B GLY 3.7 9.0 + - - +
287B PRO 4.2 1.8 - - - +
288B ALA* 3.6 27.5 - - + +
291B VAL* 3.5 41.7 - - + -
321B TRP* 3.6 30.7 - - + -
324B PHE* 4.4 17.7 - - + -
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Residues in contact with LEU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262B LEU* 4.0 37.0 - - + -
263B PRO* 3.8 25.1 - - + -
266B PHE* 4.4 6.5 - - + -
277B ILE* 2.9 32.3 + - + +
278B GLU* 4.0 9.0 - - + +
280B LEU* 1.3 70.8 - - - +
282B LYS* 1.3 63.0 + - - +
283B ALA 2.9 5.2 - - - -
284B GLY* 3.0 17.1 + - - +
285B PRO* 5.3 0.7 - - + +
288B ALA* 4.4 9.4 - - + -
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Residues in contact with LYS 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278B GLU 3.2 15.9 + - - +
279B ALA* 3.7 11.7 - - - +
280B LEU 3.3 0.2 - - - -
281B LEU* 1.3 78.1 - - - +
283B ALA* 1.3 59.1 + - - +
284B GLY 3.3 0.4 + - - -
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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