Contacts of the helix formed by residues 267 - 281 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B PRO* 3.6 35.4 - - + -
249B LYS* 4.4 13.5 - - + -
251B LEU* 2.6 52.5 - - + +
263B LYS* 2.7 52.3 + - + +
264B LEU* 2.9 10.3 + - + +
266B ASP* 1.3 89.0 - - + +
268B ASP* 1.3 57.9 + - - +
269B LYS* 2.8 15.1 + - - +
270B ASP* 3.7 18.0 + - - +
271B LEU* 4.6 5.9 + - - +
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Residues in contact with ASP 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B LYS* 3.5 20.2 - - + +
194B PHE* 3.5 20.2 - - - +
195B SER* 2.8 51.0 + - - -
264B LEU* 4.0 4.9 - - - +
265B SER* 3.5 17.8 + - - +
266B ASP 3.7 1.4 - - - -
267B TYR* 1.3 76.0 - - - +
269B LYS* 1.3 55.4 + - + +
270B ASP 3.6 0.4 - - - -
271B LEU* 3.8 3.7 + - - +
272B THR* 2.6 45.4 + - - +
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Residues in contact with LYS 269 (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 ASP 4.6 16.2 - - - +
267B TYR* 2.8 5.0 + - - +
268B ASP* 1.3 77.2 - - + +
270B ASP* 1.3 69.3 + - - +
272B THR* 3.1 6.4 + - - -
273B GLN* 2.9 34.7 + - + +
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Residues in contact with ASP 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LYS* 2.9 37.5 - - - +
267B TYR* 3.7 12.8 + - - +
268B ASP 3.6 0.2 - - - -
269B LYS* 1.3 77.0 - - - +
271B LEU* 1.3 62.1 + - + +
273B GLN* 3.2 18.0 + - - +
274B LEU* 2.9 27.8 + - - +
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Residues in contact with LEU 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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181B PHE* 5.1 2.2 - - + -
184B PHE* 3.5 22.9 - - + -
194B PHE* 3.6 48.2 - - + -
246B LEU* 4.8 14.4 - - + +
267B TYR 4.6 4.4 + - - +
268B ASP* 3.8 7.2 + - - +
270B ASP* 1.3 78.8 - - + +
272B THR* 1.3 55.7 + - - +
274B LEU* 3.8 13.8 - - + +
275B LYS* 2.7 36.9 + - - +
285B LEU* 4.6 0.8 - - + +
302B ILE* 3.8 28.9 - - + -
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Residues in contact with THR 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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184B PHE* 4.2 9.0 - - - -
192B VAL 5.3 0.9 + - - -
193B LYS* 4.2 25.4 + - - +
268B ASP* 2.6 33.3 + - - +
269B LYS* 3.1 6.7 + - - -
271B LEU* 1.3 76.2 - - - +
273B GLN* 1.3 59.8 + - + +
275B LYS* 3.4 13.0 - - + +
276B LYS* 2.9 39.8 + - - +
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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 LYS* 2.9 21.4 + - + +
270B ASP* 3.3 20.0 - - - +
272B THR* 1.3 75.4 - - + +
274B LEU* 1.3 67.5 + - - +
276B LYS* 3.0 8.0 + - - +
277B GLU* 2.9 24.1 + - - +
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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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244B GLN* 6.1 1.6 - - - +
270B ASP 2.9 16.4 + - - +
271B LEU* 3.8 12.8 - - + +
273B GLN* 1.3 74.0 - - - +
275B LYS* 1.3 63.8 + - - +
277B GLU* 3.1 22.0 + - - +
278B ALA* 3.0 22.0 + - - +
285B LEU* 3.7 27.8 - - + -
302B ILE* 4.2 24.9 - - + -
304B LYS* 3.8 25.6 - - + +
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Residues in contact with LYS 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B PHE* 3.2 42.2 + - + +
185B SER* 4.8 9.4 + - - +
190B ASN* 2.8 32.0 - - - +
191B ASP* 3.5 8.4 - - - +
192B VAL 2.7 34.4 + - - +
271B LEU 2.7 22.3 + - - +
272B THR* 3.4 12.3 - - + +
274B LEU* 1.3 74.4 - - - +
276B LYS* 1.3 65.3 + - - +
278B ALA* 3.3 3.3 + - - +
279B ALA* 3.1 23.2 + - + +
285B LEU* 3.5 13.1 - - - +
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Residues in contact with LYS 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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272B THR* 2.9 24.2 + - - +
273B GLN* 3.4 9.2 - - - +
275B LYS* 1.3 77.9 - - - +
277B GLU* 1.3 65.6 + - - +
279B ALA* 3.0 10.2 + - + +
280B THR* 2.8 26.4 + - - +
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Residues in contact with GLU 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 2.9 11.7 + - - +
274B LEU* 3.4 26.8 - - - +
276B LYS* 1.3 76.5 - - - +
278B ALA* 1.3 63.4 + - - +
280B THR* 2.9 28.9 + - + +
281B GLU* 3.0 36.2 + - + +
304B LYS* 4.1 15.5 + - - -
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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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185B SER* 5.4 0.7 - - - +
274B LEU 3.0 9.1 + - - +
275B LYS 3.6 8.3 - - - +
277B GLU* 1.3 78.7 - - - +
279B ALA* 1.3 58.4 + - - +
281B GLU* 2.9 12.5 + - - +
283B LYS* 2.8 46.7 + - + +
284B VAL 4.5 1.1 - - - +
285B LEU* 3.9 26.5 - - + -
304B LYS* 4.1 17.5 - - + +
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Residues in contact with ALA 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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186B THR 5.5 4.9 - - - +
189B ALA* 6.5 0.9 - - - -
275B LYS* 3.1 14.2 + - + +
276B LYS* 3.0 13.6 + - + +
278B ALA* 1.3 75.4 - - - +
280B THR* 1.3 58.7 + - - +
282B ASN* 2.9 21.5 + - - +
283B LYS 3.5 8.7 + - - -
307B TYR* 3.7 13.4 + - - +
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Residues in contact with THR 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 LYS* 2.8 16.8 + - - +
277B GLU* 2.9 19.3 + - + +
279B ALA* 1.3 77.0 - - - +
281B GLU* 1.3 71.4 + - + +
282B ASN* 3.3 5.2 + - - +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B GLU* 3.0 45.7 - - - +
278B ALA* 2.9 10.7 + - - +
280B THR* 1.3 86.6 - - + +
282B ASN* 1.3 69.1 + - - +
283B LYS* 3.1 29.1 + - + +
304B LYS* 4.3 8.7 - - - +
306B ASP* 5.3 0.7 - - - +
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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