Contacts of the helix formed by residues 275 - 283 (chain B) in PDB entry 3Q36
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 GLN 275 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271B ILE* 3.2 27.7 - - - +
272B SER* 3.4 20.1 - - - +
273B LEU 3.0 1.0 - - - -
274B ASP* 1.3 88.0 + - - +
276B ILE* 1.3 54.7 + - - +
277B ASP 2.7 3.1 + - - -
278B LEU* 2.6 38.3 + - + +
279B LEU* 3.3 20.9 + - + +
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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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271B ILE* 5.2 2.0 - - + -
272B SER 4.3 10.3 - - - +
273B LEU* 3.9 15.9 - - + +
274B ASP 3.7 0.2 - - - -
275B GLN* 1.3 76.4 - - - +
277B ASP* 1.3 54.5 + - - +
279B LEU* 3.7 16.4 - - + +
280B SER* 2.6 35.3 + - - +
284B PHE* 4.1 11.4 - - + -
292B HIS* 3.3 31.0 - - + +
296B ARG* 5.1 1.8 - - - +
309B TYR* 3.7 7.4 - - - +
313B LEU* 4.4 15.3 - - + -
316B ILE* 5.3 3.4 - - + -
318B LEU* 4.5 17.9 - - + -
326B PHE* 3.7 29.6 - - + -
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Residues in contact with ASP 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 LEU 5.3 0.2 + - - -
274B ASP 4.9 6.1 + - - +
275B GLN 2.7 7.1 + - - +
276B ILE* 1.3 75.7 - - - +
278B LEU* 1.3 61.2 + - - +
280B SER* 3.5 13.0 + - - -
281B THR* 4.0 7.1 + - - -
292B HIS* 2.8 24.7 + - - -
296B ARG* 3.4 30.4 + - - +
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Residues in contact with LEU 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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275B GLN* 2.6 17.0 + - + +
277B ASP* 1.3 71.1 - - - +
279B LEU* 1.3 57.6 + - + +
280B SER 3.1 4.9 - - - -
281B THR* 3.0 25.9 + - + -
282B LYS* 3.3 44.0 + - + +
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Residues in contact with LEU 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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271B ILE* 3.7 32.1 - - + -
275B GLN* 3.3 17.9 + - + +
276B ILE* 3.3 17.2 + - + +
278B LEU* 1.3 77.6 - - + +
280B SER* 1.3 57.9 + - - +
282B LYS* 3.9 2.7 - - + -
283B SER* 3.0 11.1 + - - +
284B PHE* 2.9 45.4 + - + -
316B ILE* 5.3 0.7 - - + -
448B PHE* 3.7 24.2 - - + -
452B GLN* 3.8 29.2 - - - +
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Residues in contact with SER 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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276B ILE 2.6 22.4 + - - -
277B ASP 3.5 7.8 + - - -
278B LEU 3.1 0.8 - - - -
279B LEU* 1.3 78.6 - - - +
281B THR* 1.3 62.4 + - - +
282B LYS 3.5 0.2 - - - -
284B PHE* 3.5 30.0 - - - +
289B ARG* 3.4 31.5 - - - +
292B HIS* 2.8 32.9 - - - -
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Residues in contact with THR 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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277B ASP 4.3 6.4 + - - -
278B LEU* 3.0 15.2 + - + -
280B SER* 1.3 81.0 - - - +
282B LYS* 1.3 76.3 + - + +
284B PHE 5.4 0.9 - - - -
289B ARG* 3.4 36.2 + - - +
427B TYR* 5.0 0.8 + - - -
431B ILE* 4.3 13.3 - - - +
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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 LEU* 3.3 46.6 + - + +
279B LEU* 5.3 1.8 - - + -
281B THR* 1.3 98.3 - - + +
283B SER* 1.3 64.7 + - - +
284B PHE 3.8 0.4 - - - -
431B ILE* 3.6 14.7 - - - +
432B HIS* 3.3 19.9 + - + +
451B SER* 3.3 8.7 + - - -
455B LEU 5.7 4.7 - - - +
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Residues in contact with SER 283 (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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279B LEU* 3.0 10.2 + - - +
282B LYS* 1.3 80.5 - - - +
284B PHE* 1.3 64.9 + - - +
447B PHE* 3.3 19.5 - - - -
448B PHE* 3.4 41.6 - - - -
451B SER* 2.6 25.2 + - - -
452B GLN* 2.7 25.2 + - - -
455B LEU 5.3 1.2 + - - -
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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