Contacts of the helix formed by residues 269 - 280 (chain B) in PDB entry 5KYT
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 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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265B MET* 4.1 3.5 - - - +
267B ARG 3.3 7.1 + - - +
268B PHE* 1.3 82.3 - - - +
270B GLU* 1.3 70.3 + - - +
271B GLU* 2.8 33.1 + - - +
272B LEU* 3.0 34.3 + - + +
273B PHE* 3.1 21.8 + - - +
275B ARG* 5.4 1.0 + - - -
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Residues in contact with GLU 270 (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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268B PHE* 3.8 20.8 - - + -
269B GLU* 1.3 78.0 + - - +
271B GLU* 1.3 68.7 + - + +
273B PHE* 3.4 4.0 + - - +
274B LEU* 3.2 35.2 + - + +
294B PHE* 3.2 36.5 - - + +
295B PHE* 4.6 4.0 - - + -
298B SER* 3.6 14.7 + - - -
300B LEU* 3.9 17.2 - - + +
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Residues in contact with GLU 271 (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 GLU* 2.8 20.8 + - - +
270B GLU* 1.3 78.2 - - + +
272B LEU* 1.3 67.2 + - - +
274B LEU* 3.5 3.3 + - - +
275B ARG* 2.9 40.8 + - - +
300B LEU* 5.9 5.6 - - + -
304B TYR* 4.0 19.1 + - - +
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Residues in contact with LEU 272 (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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45B ALA* 3.6 18.8 - - + +
46B HIS* 4.0 33.0 - - + +
265B MET* 3.9 31.9 - - + -
267B ARG 5.3 2.9 - - - +
269B GLU* 3.0 26.8 + - + +
271B GLU* 1.3 75.2 - - - +
273B PHE* 1.3 54.2 + - - +
275B ARG* 3.4 29.0 + - - +
276B SER* 2.7 46.9 + - - +
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Residues in contact with PHE 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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238B LEU* 3.6 20.5 - - + +
240B VAL* 3.4 30.5 - - + -
265B MET* 3.9 11.1 - - + +
268B PHE* 3.3 26.7 - + + -
269B GLU 3.1 13.2 + - - +
270B GLU 3.4 10.3 - - - +
272B LEU* 1.3 76.9 - - - +
274B LEU* 1.3 59.8 + - - +
276B SER 3.2 1.6 + - - -
277B LEU* 2.9 61.7 + - + +
285B ALA* 4.1 10.3 - - + -
287B LEU* 3.2 32.8 - - + -
295B PHE* 3.9 19.5 - + + -
331B PHE* 5.7 1.3 - + - -
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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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270B GLU* 3.2 26.0 + - + +
271B GLU* 4.2 1.6 - - - +
273B PHE* 1.3 76.3 - - - +
275B ARG* 1.3 64.3 + - - +
277B LEU* 3.4 12.9 + - + +
278B GLN* 3.1 23.0 + - - +
295B PHE* 4.1 13.7 - - + -
300B LEU* 3.8 21.8 - - + -
301B ILE* 4.2 14.8 - - + +
304B TYR* 3.5 38.6 - - + +
306B LEU* 4.0 9.9 - - + +
331B PHE* 4.0 32.8 - - + -
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Residues in contact with ARG 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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269B GLU* 5.4 0.8 + - - -
271B GLU* 2.9 43.9 + - - +
272B LEU* 3.5 33.1 - - - +
274B LEU* 1.3 76.8 - - - +
276B SER* 1.3 58.1 + - - +
278B GLN* 3.3 5.6 + - - +
279B ASP* 2.8 53.0 + - - +
304B TYR* 3.9 22.3 + - + -
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Residues in contact with SER 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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45B ALA* 3.3 25.5 - - - +
238B LEU* 4.1 15.0 - - - -
265B MET* 4.8 0.2 - - - -
272B LEU* 2.7 31.3 + - - +
273B PHE* 3.6 3.4 - - - -
275B ARG* 1.3 74.6 - - - +
277B LEU* 1.3 66.8 + - - +
278B GLN 3.1 1.6 - - - -
279B ASP* 4.4 1.6 - - - +
280B TYR* 2.8 50.8 + - - +
282B ILE* 3.8 2.4 - - - +
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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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238B LEU* 3.6 17.6 - - + +
273B PHE* 2.9 38.9 + - + +
274B LEU* 3.4 15.5 + - + +
276B SER* 1.3 73.3 - - - +
278B GLN* 1.3 62.0 + - - +
281B LYS* 3.2 3.1 + - - -
282B ILE* 3.0 53.4 + - + +
285B ALA* 4.0 16.8 - - + -
306B LEU* 3.8 15.4 - - + -
308B ASN* 5.5 1.0 - - - +
309B LEU* 4.4 16.6 - - + -
312B ILE* 6.2 0.2 - - + -
331B PHE* 4.1 24.7 - - + -
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Residues in contact with GLN 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 LEU 3.1 10.4 + - - +
275B ARG* 3.4 9.7 + - - +
277B LEU* 1.3 79.4 - - - +
279B ASP* 1.3 81.1 + - - +
281B LYS* 3.0 25.3 + - - +
303B LYS 4.4 1.6 - - - +
304B TYR* 3.1 28.0 - - + +
305B ASP* 2.9 52.3 + - + +
306B LEU* 4.1 0.6 - - + +
308B ASN* 5.4 0.3 + - - -
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Residues in contact with ASP 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 ARG* 2.8 40.1 + - - +
276B SER* 4.5 2.7 - - - +
278B GLN* 1.3 100.9 + - - +
280B TYR* 1.3 72.7 + - + +
281B LYS* 3.7 5.0 + - - +
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Residues in contact with TYR 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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43B THR* 3.5 19.8 - - + +
45B ALA* 3.9 21.4 + - + -
48B GLU* 4.1 20.3 - - - +
50B ASN* 4.9 0.4 - - - -
236B ALA* 4.0 11.5 - - + +
261B ARG* 3.6 41.8 + - - +
263B VAL* 3.9 16.8 - - + -
276B SER* 2.8 48.5 + - - +
279B ASP* 1.3 85.5 - - + +
281B LYS* 1.3 72.2 + - - +
282B ILE* 3.4 14.0 + - + -
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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