Contacts of the helix formed by residues 272 - 279 (chain B) in PDB entry 6FEQ
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 272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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266B PHE* 4.6 1.8 - - + -
269B PRO* 3.2 20.1 + - + +
271B GLN* 1.3 92.5 + - + +
273B ALA* 1.3 58.5 + - - +
274B LEU 3.3 1.6 - - - -
275B GLY* 3.6 11.8 - - - +
276B TYR* 2.8 30.8 + - - +
341B PHE* 4.1 28.4 - - + -
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Residues in contact with ALA 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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256B LEU* 3.7 24.5 - - + -
266B PHE* 3.8 26.1 - - + -
269B PRO 3.6 3.0 + - - +
270B ALA 3.8 10.8 - - - +
271B GLN 3.3 2.2 - - - -
272B GLU* 1.3 79.0 - - - +
274B LEU* 1.3 61.6 + - - +
276B TYR* 3.8 5.6 + - - +
277B PHE* 3.7 14.9 + - + -
294B PHE* 3.4 29.4 - - + -
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Residues in contact with LEU 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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287A TYR* 3.8 39.3 - - + +
250B PHE* 5.7 3.3 - - + -
270B ALA 4.8 1.2 + - - -
271B GLN 4.2 7.0 + - - +
272B GLU 3.3 0.2 - - - -
273B ALA* 1.3 79.4 - - - +
275B GLY* 1.3 63.2 + - - +
277B PHE* 3.3 13.3 + - - +
278B GLU* 3.5 16.8 + - + +
284B CYS* 3.9 30.5 - - + -
290B PRO* 4.4 22.4 - - + -
293B PHE* 4.4 13.7 - - + -
294B PHE* 3.6 11.3 - - + -
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Residues in contact with GLY 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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271B GLN 4.6 1.2 + - - -
272B GLU* 3.3 19.5 + - - +
274B LEU* 1.3 77.0 - - - +
276B TYR* 1.3 63.6 + - - +
278B GLU* 3.8 14.3 + - - +
279B SER* 3.8 10.6 + - - -
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Residues in contact with TYR 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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265B MET 5.1 0.4 - - - -
266B PHE* 3.8 27.8 - + + -
272B GLU 2.8 16.1 + - - +
273B ALA 4.0 4.9 - - - +
274B LEU 3.2 0.6 - - - -
275B GLY* 1.3 79.2 - - - +
277B PHE* 1.3 85.6 + + - +
279B SER* 3.3 11.2 + - - -
280B ALA* 3.2 21.4 + - + +
335B ILE* 3.2 37.7 + - + +
336B TYR* 3.5 19.1 - + + -
339B SER* 3.5 27.4 - - - -
340B SER 5.2 1.3 - - - -
341B PHE* 4.1 19.5 - + + -
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Residues in contact with PHE 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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258B LEU* 4.3 20.9 - - + -
265B MET* 4.5 12.8 - - + -
266B PHE* 4.6 8.5 - + + -
273B ALA* 3.7 7.3 + - + -
274B LEU 3.3 7.6 + - - +
276B TYR* 1.3 102.2 - + - +
278B GLU* 1.3 65.3 + - - +
279B SER 3.2 0.7 - - - -
280B ALA* 3.1 26.5 + - + +
282B TYR* 3.2 19.3 + + + +
293B PHE* 4.7 9.2 - - + -
294B PHE* 3.5 43.3 - + + -
297B ILE* 3.5 31.4 - - + -
332B LEU* 6.2 3.6 - - + -
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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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287A TYR* 5.6 0.9 + - - -
274B LEU* 3.5 18.0 + - + +
275B GLY* 4.2 9.0 - - - +
276B TYR 3.4 0.8 - - - -
277B PHE* 1.3 77.4 - - - +
279B SER* 1.3 60.3 + - - +
280B ALA 3.5 0.3 + - - -
281B GLY* 3.7 9.0 + - - -
282B TYR 3.2 18.8 - - - +
283B HIS* 3.3 20.4 - - - +
284B CYS* 2.5 41.1 + - - +
293B PHE* 4.9 2.0 - - + -
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Residues in contact with SER 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 GLY 3.8 8.3 + - - -
276B TYR* 3.3 14.5 + - - -
277B PHE 3.2 0.2 - - - -
278B GLU* 1.3 76.3 - - - +
280B ALA* 1.3 61.4 + - - +
281B GLY* 3.4 0.6 + - - -
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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