Contacts of the helix formed by residues 274 - 284 (chain B) in PDB entry 5Y7G
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 ASP 274 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237B LEU* 6.3 1.1 - - + -
269B CYS* 2.9 22.2 + - + +
272B GLN* 3.4 7.9 - - + +
273B ARG* 1.3 73.3 - - - +
275B PHE* 1.3 60.5 + - - +
276B ASP* 3.7 5.4 + - - +
277B LEU* 3.3 36.5 + - - +
278B ALA* 3.1 24.9 + - - +
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Residues in contact with PHE 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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270B GLU* 3.5 27.1 - - + -
273B ARG* 3.0 54.5 + - - -
274B ASP* 1.3 73.2 - - - +
276B ASP* 1.3 64.3 + - - +
277B LEU 3.2 2.2 - - - -
278B ALA* 3.8 3.8 - - - -
279B GLN* 2.7 33.3 + - - +
297B SER* 3.7 19.4 + - - +
298B LEU* 5.7 0.4 - - - -
300B ARG* 3.0 55.0 - - + -
301B GLY* 3.4 28.0 - - - -
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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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274B ASP* 3.7 5.0 + - - +
275B PHE* 1.3 79.5 - - - +
277B LEU* 1.3 60.2 + - - +
279B GLN* 3.8 5.5 - - - +
280B ARG* 3.3 38.0 + - - +
301B GLY* 5.2 4.2 - - - +
303B ARG* 2.9 38.6 + - - +
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Residues in contact with LEU 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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237B LEU* 5.2 12.6 - - + +
238B GLU* 6.1 1.6 - - - -
241B LEU* 3.9 31.6 - - + -
269B CYS* 4.3 13.9 - - - -
274B ASP* 3.3 26.0 + - - +
275B PHE 3.2 0.4 - - - -
276B ASP* 1.3 77.4 - - - +
278B ALA* 1.3 64.9 + - - +
280B ARG* 3.1 33.9 + - - +
281B LEU* 2.9 33.7 + - + +
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Residues in contact with ALA 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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266B ALA* 3.7 26.8 - - - +
269B CYS* 3.8 8.6 - - + +
270B GLU* 4.5 5.6 - - + +
274B ASP 3.1 23.8 + - - +
275B PHE* 3.3 3.3 + - - +
277B LEU* 1.3 77.7 - - - +
279B GLN* 1.3 64.7 + - - +
281B LEU* 3.1 3.1 + - - +
282B TYR* 2.9 30.6 + - + -
297B SER* 3.5 15.5 - - - +
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Residues in contact with GLN 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 PHE 2.7 19.7 + - - +
276B ASP* 3.8 7.4 - - - +
278B ALA* 1.3 71.5 - - - +
280B ARG* 1.3 73.9 + - - +
282B TYR* 2.8 28.7 + - - +
283B ARG* 2.9 52.9 + - + +
294B ALA* 4.3 7.2 - - + +
297B SER* 3.6 12.6 + - - -
298B LEU* 3.7 36.4 - - + +
303B ARG* 4.2 13.4 + - - +
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Residues in contact with ARG 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 ASP* 3.3 31.8 + - - +
277B LEU* 3.1 32.3 + - + +
279B GLN* 1.3 89.4 + - - +
281B LEU* 1.3 60.5 + - + +
283B ARG* 4.0 8.1 + - - +
284B GLN* 3.4 24.1 + - - +
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Residues in contact with LEU 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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241B LEU* 3.4 48.7 - - + -
262B LEU* 4.2 23.2 - - + +
265B PHE 4.8 0.2 - - - -
266B ALA* 3.8 31.2 - - + +
269B CYS* 4.4 5.6 - - - -
277B LEU* 2.9 26.7 + - + +
278B ALA 3.5 5.6 - - - +
280B ARG* 1.3 76.2 - - + +
282B TYR* 1.3 65.7 + - - +
283B ARG 3.2 0.2 - - - -
284B GLN* 3.0 34.8 + - - +
285B SER* 3.1 13.5 + - - -
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Residues in contact with TYR 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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263B PHE* 4.0 28.3 - + - -
266B ALA* 3.5 26.9 + - + -
267B GLN* 3.6 10.7 - - - +
270B GLU* 2.4 29.3 + - - -
278B ALA* 2.9 29.2 + - + -
279B GLN* 2.8 16.4 + - - +
281B LEU* 1.3 71.8 - - - +
283B ARG* 1.3 61.1 + - - +
285B SER* 3.2 21.3 + - - +
290B ALA* 3.3 16.6 - - - +
291B ARG* 4.5 0.7 + - - -
293B ARG* 3.4 51.6 + - + -
294B ALA* 3.7 16.6 - - + +
297B SER* 3.9 9.9 - - - -
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Residues in contact with ARG 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 GLN* 2.9 52.9 + - + +
280B ARG* 4.3 6.7 - - - +
281B LEU 3.2 0.4 - - - -
282B TYR* 1.3 77.9 - - - +
284B GLN* 1.3 57.7 + - + +
285B SER 3.6 4.9 + - - +
291B ARG* 5.9 3.1 - - - +
294B ALA* 4.0 6.1 - - + -
298B LEU* 4.5 5.1 - - - +
306B GLU* 6.3 0.4 - - - +
310B LEU* 3.8 46.0 - - - +
313B GLU* 4.9 5.1 + - - -
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Residues in contact with GLN 284 (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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246B GLY 5.6 1.6 - - - +
258B ARG* 4.5 10.5 + - - +
259B VAL* 4.1 4.7 - - - +
262B LEU* 3.4 23.3 - - + +
280B ARG* 3.4 23.8 + - - +
281B LEU* 3.0 32.7 + - - +
283B ARG* 1.3 75.5 - - + +
285B SER* 1.3 60.1 + - - +
286B SER* 3.9 1.8 + - - -
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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