Contacts of the helix formed by residues 272 - 278 (chain B) in PDB entry 5DQE
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 ARG 272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270B ASP* 2.9 21.8 + - - +
271B VAL* 1.3 81.6 - - - +
273B GLN* 1.3 62.1 + - + +
274B ILE 3.3 0.7 + - - -
275B TYR* 3.5 40.3 + - + +
276B ASP 5.2 0.2 + - - -
446B ARG* 3.1 30.1 - - + +
447B ASP* 3.2 40.4 + - - +
448B VAL* 4.8 6.3 - - - +
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Residues in contact with GLN 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 VAL* 5.3 4.5 - - + -
270B ASP* 3.3 25.8 - - + +
271B VAL 3.0 1.2 - - - -
272B ARG* 1.3 79.6 - - + +
274B ILE* 1.3 63.7 + - + +
275B TYR 3.6 0.2 - - - -
276B ASP* 3.9 9.2 - - - +
277B LYS* 5.6 0.3 - - - +
502B 5E4 5.8 0.5 - - - +
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Residues in contact with ILE 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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269B VAL* 4.9 10.1 - - + -
270B ASP 4.8 3.1 - - - +
271B VAL* 3.1 15.4 + - - +
273B GLN* 1.3 86.0 - - + +
275B TYR* 1.3 66.1 + - - +
276B ASP* 3.0 7.3 + - - -
277B LYS* 3.0 14.1 + - - +
278B PHE* 3.1 30.9 - - + -
285B LEU* 3.6 22.9 - - + -
299B LEU* 4.3 14.6 - - + -
425B ALA* 4.2 10.5 - - + -
444B LEU* 3.8 22.2 - - + -
502B 5E4 4.3 18.8 - - + -
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Residues in contact with TYR 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 VAL* 3.3 38.7 + - + +
272B ARG* 3.5 31.9 + - + +
273B GLN 3.6 0.2 - - - -
274B ILE* 1.3 77.5 - - - +
276B ASP* 1.3 59.4 + - + +
278B PHE* 3.3 20.4 + - - +
279B PRO 4.8 2.3 - - - +
280B GLU* 4.9 11.4 - - - +
285B LEU* 3.9 18.3 + - + +
286B ARG* 3.6 60.5 - - + +
289B TYR* 5.3 0.2 - - + -
446B ARG* 2.9 39.8 + - - -
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Residues in contact with ASP 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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273B GLN 3.9 15.1 - - - +
274B ILE 3.9 0.2 - - - -
275B TYR* 1.3 78.0 - - + +
277B LYS* 1.3 86.3 + - - +
278B PHE 3.2 4.1 + - - +
350B PHE 5.0 0.9 - - - -
351B GLY* 3.6 15.1 + - - -
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Residues in contact with LYS 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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273B GLN 5.6 0.2 - - - +
274B ILE* 3.0 11.5 + - - +
276B ASP* 1.3 96.4 - - - +
278B PHE* 1.3 71.1 + - + +
348B CYS* 3.8 6.8 - - - +
351B GLY* 4.0 10.4 + - - +
404B GLU* 3.5 35.2 + - - +
405B ASN* 5.0 8.1 - - - +
407B THR* 2.8 32.6 + - + +
502B 5E4 3.5 33.6 - - + +
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Residues in contact with PHE 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 ILE* 3.1 44.0 - - + -
275B TYR 3.3 13.7 + - - +
276B ASP 3.2 2.5 - - - +
277B LYS* 1.3 88.6 - - + +
279B PRO* 1.3 78.3 - - + +
280B GLU* 4.6 3.5 - - - +
285B LEU* 3.5 24.2 - - + +
348B CYS* 4.1 3.4 - - - -
351B GLY* 3.0 14.4 - - - +
407B THR* 3.3 33.9 - - + -
408B ILE 3.8 18.6 - - - -
409B LEU* 4.1 20.2 - - + -
425B ALA* 3.5 22.0 - - + -
426B TYR 4.4 0.7 - - - -
427B VAL* 4.3 11.7 - - + -
502B 5E4 5.1 0.2 - - + -
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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