Contacts of the helix formed by residues 273 - 283 (chain Y) in PDB entry 1O1F
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 GLY 273 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178Y LEU* 4.6 1.1 - - - -
261Y LEU 3.8 11.0 - - - -
262Y PHE 4.0 12.2 + - - -
264Y PRO* 4.0 11.3 - - - +
272Y ALA* 1.3 75.8 - - - +
274Y ILE* 1.3 66.4 + - - -
275Y HIS* 3.3 6.6 - - - -
276Y GLU* 2.9 23.7 + - - +
277Y THR* 3.0 12.2 + - - -
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Residues in contact with ILE 274 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153Y LEU* 3.6 27.4 - - + +
155Y SER* 5.7 1.1 - - - +
160Y THR* 3.6 21.3 - - + -
178Y LEU* 3.4 25.5 - - + +
261Y LEU* 3.2 40.3 + - + +
262Y PHE* 3.6 25.8 - - + -
273Y GLY* 1.3 68.2 - - - -
275Y HIS* 1.3 58.0 + - - +
277Y THR* 3.3 7.3 + - + -
278Y THR* 2.9 31.6 + - - -
309Y ILE* 6.2 2.9 - - + -
313Y MET* 3.9 18.6 - - + -
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Residues in contact with HIS 275 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262Y PHE* 3.4 35.5 - + + -
273Y GLY* 2.9 7.8 + - - -
274Y ILE* 1.3 73.0 - - - +
276Y GLU* 1.3 98.3 + - + +
278Y THR* 3.5 3.5 - - - -
279Y TYR* 3.3 20.4 + - - +
313Y MET* 3.4 28.5 - - - -
316Y GLU* 3.2 53.6 + - + -
317Y ILE* 3.8 9.9 - - + +
320Y LEU* 4.9 6.9 - - + +
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Residues in contact with GLU 276 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272Y ALA* 4.1 20.5 - - + +
273Y GLY 2.9 11.7 + - - +
275Y HIS* 1.3 100.6 + - + +
277Y THR* 1.3 53.4 + - - +
279Y TYR* 3.2 8.0 + - - +
280Y ASN* 2.8 52.4 + - - +
320Y LEU* 4.5 13.5 - - + -
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Residues in contact with THR 277 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160Y THR* 6.1 0.4 - - + -
162Y ASN* 2.9 31.6 - - - +
176Y MET* 3.8 20.2 - - + +
178Y LEU* 5.2 16.5 - - + +
272Y ALA* 4.0 18.4 + - - +
273Y GLY 3.0 13.4 + - - -
274Y ILE* 3.5 12.6 - - + +
276Y GLU* 1.3 76.1 - - - +
278Y THR* 1.3 62.8 + - - +
280Y ASN* 3.1 8.7 + - - +
281Y SER* 3.1 23.7 + - - -
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Residues in contact with THR 278 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151Y ILE* 3.6 6.3 - - + +
153Y LEU* 3.9 2.6 - - - +
162Y ASN* 3.4 20.0 + - - +
274Y ILE 2.9 15.6 + - - -
275Y HIS 3.5 10.1 - - - -
277Y THR* 1.3 72.9 - - - +
279Y TYR* 1.3 63.1 - - - +
281Y SER* 3.4 4.3 - - - -
282Y ILE* 3.0 35.6 + - + +
297Y ASN* 3.2 34.8 + - - +
313Y MET* 3.0 17.7 - - + +
317Y ILE* 4.1 15.0 - - + -
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Residues in contact with TYR 279 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275Y HIS 3.3 10.5 + - - +
276Y GLU* 3.2 8.5 + - - +
278Y THR* 1.3 79.5 - - - +
280Y ASN* 1.3 80.1 + - - +
282Y ILE* 2.9 25.3 + - - +
283Y MET* 2.9 56.3 + - + +
294Y TYR* 3.4 22.0 - + - -
317Y ILE* 5.1 4.9 - - + -
320Y LEU* 3.3 63.0 + - + +
321Y ALA 4.3 0.9 - - - -
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Residues in contact with ASN 280 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176Y MET* 4.8 13.9 - - + -
272Y ALA* 4.9 5.2 - - - +
276Y GLU* 2.8 41.1 + - - +
277Y THR* 3.1 8.9 + - - +
279Y TYR* 1.3 91.3 - - - +
281Y SER* 1.3 62.1 + - - +
283Y MET* 3.2 6.3 + - - +
284Y LYS* 3.1 25.6 + - - +
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Residues in contact with SER 281 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151Y ILE* 3.6 13.2 - - - -
162Y ASN* 3.6 15.7 - - - +
164Y PRO* 3.4 12.5 - - - +
174Y ALA* 2.4 31.7 + - - +
176Y MET* 3.8 7.6 - - - +
277Y THR 3.1 11.5 + - - -
278Y THR 3.4 11.4 - - - -
280Y ASN* 1.3 74.0 - - - +
282Y ILE* 1.3 60.3 - - - +
284Y LYS* 3.1 24.0 + - - +
285Y CYS* 3.4 15.2 + - - -
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Residues in contact with ILE 282 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151Y ILE* 3.7 22.7 - - + -
278Y THR* 3.0 32.8 - - + +
279Y TYR* 2.9 11.3 + - - +
281Y SER* 1.3 80.2 - - - +
283Y MET* 1.3 56.8 + - - +
284Y LYS 3.0 5.1 + - - -
285Y CYS* 3.2 18.8 + - - +
290Y ARG* 3.4 27.9 + - + +
293Y LEU* 4.5 13.0 - - + -
294Y TYR* 3.6 59.2 - - + +
297Y ASN* 4.6 1.8 - - - +
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Residues in contact with MET 283 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279Y TYR* 2.9 58.6 + - + +
280Y ASN* 3.2 7.0 + - - +
282Y ILE* 1.3 70.5 - - - +
284Y LYS* 1.4 56.8 + - - +
285Y CYS 3.5 0.4 - - - -
290Y ARG* 3.9 43.7 + - - +
294Y TYR* 3.4 23.8 - - + +
322Y PRO* 4.0 24.5 - - + -
325Y MET* 6.0 0.9 - - + -
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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