Contacts of the helix formed by residues 267 - 279 (chain A) in PDB entry 1EBF
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 TYR 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A PRO* 4.0 33.0 - - + -
249A LYS* 5.9 5.8 - - + -
251A LEU* 3.0 46.8 - - + +
263A LYS* 3.9 7.3 + - - -
264A LEU* 2.9 16.0 + - + +
266A ASP* 1.3 99.6 - - + +
268A ASP* 1.3 54.9 + - - +
269A LYS* 2.7 20.7 + - - +
270A ASP* 3.5 16.2 + - + +
271A LEU* 4.4 5.5 + - - +
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Residues in contact with ASP 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A PHE* 5.9 0.2 - - - -
193A LYS* 3.2 37.9 - - + +
194A PHE* 3.9 12.4 - - - +
195A SER* 2.5 50.8 + - - -
264A LEU* 4.1 4.2 - - - +
265A SER* 3.5 16.5 + - - +
266A ASP 3.9 0.4 - - - -
267A TYR* 1.3 76.2 - - - +
269A LYS* 1.3 58.5 + - - +
271A LEU* 4.2 4.1 - - - +
272A THR* 2.4 40.9 + - - +
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Residues in contact with LYS 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193A LYS* 5.6 0.2 - - - +
266A ASP* 3.8 20.1 + - - +
267A TYR* 2.7 11.4 + - - +
268A ASP* 1.3 77.8 - - - +
270A ASP* 1.3 66.6 + - - +
272A THR* 3.3 5.3 - - - -
273A GLN* 3.0 35.9 + - - +
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Residues in contact with ASP 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A TYR* 3.5 8.3 + - + +
269A LYS* 1.3 80.3 - - - +
271A LEU* 1.3 58.0 + - + +
273A GLN* 3.2 9.7 + - - +
274A LEU* 2.7 36.5 + - - +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PHE* 5.9 0.2 - - + -
184A PHE* 3.6 20.4 - - + -
194A PHE* 3.2 52.0 - - + -
244A GLN* 6.1 0.7 - - - +
246A LEU* 5.6 5.6 - - + +
267A TYR 4.4 5.4 + - - +
268A ASP* 3.6 7.0 + - - +
269A LYS 3.4 0.6 - - - -
270A ASP* 1.3 81.6 - - + +
272A THR* 1.3 57.4 + - - +
274A LEU* 3.8 14.2 - - + +
275A LYS* 2.8 33.1 + - - +
285A LEU* 4.4 1.0 - - + +
302A ILE* 4.0 26.0 - - + -
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Residues in contact with THR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A PHE* 4.3 7.6 - - - -
191A ASP* 6.2 5.8 - - + -
192A VAL 5.1 6.6 + - - +
193A LYS* 4.9 10.7 + - - +
268A ASP* 2.4 36.6 + - - +
269A LYS* 3.3 5.8 - - - -
271A LEU* 1.3 77.8 - - - +
273A GLN* 1.3 62.1 + - + +
275A LYS* 3.6 9.6 + - + +
276A LYS* 3.1 25.9 + - + +
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Residues in contact with GLN 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A LYS* 3.0 34.7 + - - +
270A ASP* 3.7 6.1 + - - +
272A THR* 1.3 79.6 - - + +
274A LEU* 1.3 63.9 + - - +
276A LYS* 3.4 17.4 + - + +
277A GLU* 3.1 22.2 + - - +
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Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A GLN* 5.9 2.9 - - - +
270A ASP 2.7 20.9 + - - +
271A LEU* 3.8 14.1 - - + +
273A GLN* 1.3 72.5 - - - +
275A LYS* 1.3 63.6 + - - +
277A GLU* 3.3 18.5 + - + +
278A ALA* 3.2 19.6 + - - +
285A LEU* 3.7 23.8 - - + -
302A ILE* 4.4 24.9 - - + -
304A LYS* 5.4 8.7 - - + +
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Residues in contact with LYS 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A PHE* 2.9 36.4 + - + +
185A SER* 4.0 17.9 - - - +
186A THR 5.0 2.5 - - - +
188A GLN 5.7 0.7 - - - -
189A ALA* 6.0 0.9 - - - +
190A ASN* 2.7 57.3 + - - +
191A ASP* 4.5 0.2 - - - +
192A VAL 3.7 11.1 + - - +
271A LEU 2.8 16.7 + - - +
272A THR* 3.7 8.5 - - + +
274A LEU* 1.3 76.4 - - - +
276A LYS* 1.3 58.0 - - - +
278A ALA* 3.2 4.3 + - - +
279A ALA* 2.9 28.3 + - + +
285A LEU* 3.5 21.4 - - + +
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Residues in contact with LYS 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A THR* 3.1 18.9 + - + +
273A GLN* 3.5 18.2 - - + +
274A LEU 3.2 0.2 - - - -
275A LYS* 1.3 74.9 - - - +
277A GLU* 1.3 64.7 + - - +
279A ALA* 3.0 18.7 + - + +
280A THR* 3.0 18.2 + - - +
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Residues in contact with GLU 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273A GLN 3.1 10.8 + - - +
274A LEU* 3.3 21.9 + - + +
276A LYS* 1.3 80.1 - - - +
278A ALA* 1.3 57.7 + - - +
280A THR* 3.1 27.1 - - + -
281A GLU* 3.1 32.2 + - + +
304A LYS* 4.6 6.2 + - - -
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A LEU 3.2 6.6 + - - +
275A LYS 3.4 9.9 - - - +
276A LYS 3.1 0.6 - - - -
277A GLU* 1.3 71.6 - - - +
279A ALA* 1.3 56.2 + - - +
280A THR 2.9 5.4 - - - -
281A GLU* 3.2 3.9 + - - +
282A ASN 3.1 7.3 + - - -
283A LYS* 2.7 48.4 + - + +
284A VAL* 4.7 0.9 - - - -
285A LEU* 3.7 31.2 - - + -
304A LYS* 4.2 18.6 - - + +
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A SER 6.0 1.1 - - - +
189A ALA* 5.5 12.6 - - + -
275A LYS* 2.9 16.7 + - + +
276A LYS* 3.0 14.1 + - + +
278A ALA* 1.3 76.4 - - - +
280A THR* 1.3 59.4 + - - +
282A ASN* 3.8 7.2 + - - +
283A LYS 3.7 3.1 + - - +
307A TYR* 3.8 17.3 + - - +
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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