Contacts of the helix formed by residues 272 - 278 (chain B) in PDB entry 4EOZ
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 HIS 272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B GLN* 2.9 23.3 + - - -
221B SER* 2.8 31.2 + - - -
222B GLN* 3.6 14.4 - - - -
225B LEU* 4.4 15.9 - - + +
233B TYR* 3.6 18.4 - - + +
267B GLU 3.5 20.6 - - - -
268B LEU 4.2 4.5 - - - +
269B ILE 3.1 3.3 + - - -
271B LYS* 1.3 87.2 + - + +
273B MSE 1.3 61.2 + - - +
274B LYS 3.5 2.2 - - - -
275B THR* 3.2 15.8 + - - -
276B ILE* 3.0 34.9 + - + +
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Residues in contact with MSE 273 (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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269B ILE* 2.8 18.3 + - + +
270B SER* 3.2 36.6 - - - +
271B LYS 3.8 0.4 - - - -
272B HIS* 1.3 74.9 - - - +
274B LYS* 1.3 69.2 + - + +
276B ILE* 3.3 3.3 + - - +
277B VAL* 3.0 28.6 + - - +
303B PHE* 3.5 24.0 - - + -
306B VAL* 2.9 37.2 - - + -
307B PRO 4.2 5.2 - - - +
308B ASN* 4.0 5.4 - - - +
309B GLY* 3.8 21.5 - - - +
312B THR* 3.9 21.1 - - + +
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Residues in contact with LYS 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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272B HIS 3.5 0.4 - - - -
273B MSE 1.3 83.2 - - + +
275B THR* 1.3 58.6 + - - +
277B VAL* 3.9 2.4 - - + +
278B GLU* 2.9 61.0 + - + +
312B THR* 4.4 15.7 - - + +
315B GLU* 5.2 9.6 + - - -
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Residues in contact with THR 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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225B LEU* 4.4 25.6 - - + -
271B LYS 5.6 0.2 + - - -
272B HIS* 3.2 19.7 + - - -
273B MSE 3.2 0.6 - - - -
274B LYS* 1.3 80.5 - - - +
276B ILE* 1.3 60.4 + - - +
278B GLU* 4.3 8.2 + - - +
279B MSE 3.6 25.9 + - + +
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Residues in contact with ILE 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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225B LEU* 3.6 30.5 - - + -
230B ALA* 3.9 19.6 - - + +
233B TYR* 3.8 33.4 - - + -
234B ILE* 4.1 30.5 - - + -
268B LEU 5.5 0.2 - - - +
269B ILE* 6.5 0.2 - - - -
272B HIS* 3.0 21.2 + - + +
273B MSE 3.7 6.5 - - - +
275B THR* 1.3 76.6 - - - +
277B VAL* 1.3 64.5 + - - +
278B GLU 3.7 0.2 + - - -
279B MSE 3.8 19.3 + - - +
283B GLY* 4.1 2.4 - - - -
299B MSE 4.3 3.2 - - + +
303B PHE* 4.1 15.9 - - + -
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B MSE 3.0 11.8 + - - +
274B LYS* 3.9 4.5 - - + +
276B ILE* 1.3 78.9 - - - +
278B GLU* 1.3 58.9 + - + +
279B MSE 3.3 0.4 - - - -
283B GLY* 3.4 1.9 - - - -
284B LEU* 3.0 34.1 + - + +
285B VAL* 4.5 0.5 + - - +
299B MSE 4.1 10.8 - - - -
303B PHE* 3.3 35.2 - - + -
312B THR* 4.3 14.6 - - + +
313B MSE 3.9 18.6 - - + -
316B CYS* 3.5 34.3 - - + -
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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 LYS* 2.9 54.7 + - + +
275B THR* 4.3 7.1 + - - +
277B VAL* 1.3 79.5 - - + +
279B MSE 1.3 65.4 - - - +
280B GLU* 3.4 3.3 + - - -
316B CYS* 4.7 10.3 - - + -
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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