Contacts of the helix formed by residues 259 - 269 (chain B) in PDB entry 1EJD
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 LEU 259 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232B ARG* 3.6 29.2 - - + +
233B ILE* 5.6 0.4 - - + -
235B THR* 3.5 38.6 - - + -
236B GLY* 4.2 5.4 - - - +
239B LEU* 4.5 7.9 - - + -
255B GLN 5.0 2.2 - - - +
256B PRO* 2.9 11.3 + - + +
258B THR* 1.3 88.2 - - - +
260B ASP* 1.3 66.3 + - - +
261B ALA 3.3 2.7 - - - -
262B VAL* 3.1 31.6 + - + -
263B LEU* 2.9 28.8 + - + +
280B ILE* 4.2 10.8 - - + -
303B PRO* 5.5 3.1 - - + -
306B MET* 5.4 2.9 - - + -
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Residues in contact with ASP 260 (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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256B PRO 3.7 11.3 - - - +
257B ASP* 3.8 20.0 + - - +
258B THR 3.8 1.4 - - - -
259B LEU* 1.3 75.6 - - - +
261B ALA* 1.3 62.0 + - - +
263B LEU* 3.4 7.8 + - - +
264B ALA* 3.0 24.7 + - - +
300B PRO* 5.5 4.3 - - + +
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Residues in contact with ALA 261 (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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259B LEU 3.3 0.8 - - - -
260B ASP* 1.3 78.1 - - - +
262B VAL* 1.3 63.1 + - + +
264B ALA* 3.3 7.6 + - - +
265B LYS* 3.1 24.8 + - - +
300B PRO 3.8 9.9 + - - +
301B ALA* 3.8 9.0 - - - +
302B PHE* 3.6 37.9 - - + +
303B PRO* 4.9 1.3 - - + -
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Residues in contact with VAL 262 (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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236B GLY* 4.6 14.1 - - - +
239B LEU* 5.1 0.9 - - + -
259B LEU* 3.1 33.9 + - + +
261B ALA* 1.3 75.4 - - - +
263B LEU* 1.3 67.9 + - + +
265B LYS* 3.1 4.0 + - - +
266B LEU* 2.9 39.4 + - + +
302B PHE* 4.2 12.6 - - + -
303B PRO* 3.7 31.4 - - + -
306B MET* 3.9 10.8 - - + -
310B PHE* 4.1 14.4 - - + -
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Residues in contact with LEU 263 (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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239B LEU* 3.7 31.0 - - + -
256B PRO* 4.2 16.8 - - + +
259B LEU* 2.9 25.4 + - + +
260B ASP* 3.9 6.7 - - - +
262B VAL* 1.3 75.4 - - + +
264B ALA* 1.3 63.1 + - - +
266B LEU* 3.3 3.7 + - + +
267B ARG* 3.0 44.6 + - - +
273B ILE* 3.8 15.2 - - + +
275B THR* 4.0 27.1 - - + -
280B ILE* 4.2 20.2 - - + -
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Residues in contact with ALA 264 (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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260B ASP 3.0 17.8 + - - +
261B ALA* 3.7 8.1 - - - +
263B LEU* 1.3 75.5 - - - +
265B LYS* 1.3 62.8 + - - +
267B ARG* 3.3 12.5 + - - +
268B GLU* 3.1 31.9 + - - +
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Residues in contact with LYS 265 (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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261B ALA 3.1 13.6 + - - +
262B VAL 3.1 6.9 + - - +
264B ALA* 1.3 75.9 - - - +
266B LEU* 1.3 65.0 + - - +
268B GLU* 3.2 33.2 + - - +
269B ALA* 3.1 21.0 + - - +
292B VAL* 3.8 14.5 - - + +
293B THR 2.8 28.4 + - - +
294B VAL* 3.8 20.1 - - + +
295B ARG 5.4 1.0 - - - +
302B PHE* 4.2 15.3 - - + -
310B PHE* 3.6 24.1 - - + -
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Residues in contact with LEU 266 (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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239B LEU* 3.8 33.7 - - + -
240B VAL* 4.3 7.9 - - + +
243B ALA* 4.1 25.6 - - + -
262B VAL* 2.9 32.5 + - + +
263B LEU* 3.3 2.2 + - + -
265B LYS* 1.3 76.3 - - - +
267B ARG* 1.3 62.9 + - - +
269B ALA* 3.1 14.9 + - + +
270B GLY 3.3 0.2 + - - -
271B ALA* 3.1 24.2 + - + +
273B ILE* 3.6 18.4 - - + -
282B LEU* 4.0 7.4 - - + -
310B PHE* 3.6 23.1 - - + -
313B LEU* 4.1 9.4 - - + -
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Residues in contact with ARG 267 (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 LEU* 3.0 42.6 + - - +
264B ALA* 3.6 12.0 - - - +
265B LYS 3.2 0.2 - - - -
266B LEU* 1.3 77.1 - - - +
268B GLU* 1.3 56.1 + - + +
270B GLY* 2.9 20.3 + - - -
271B ALA 3.8 16.6 + - - +
273B ILE* 3.0 51.2 + - + +
274B GLU* 4.6 2.4 - - - +
275B THR* 4.8 7.3 + - - +
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Residues in contact with GLU 268 (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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264B ALA* 3.1 23.2 + - - +
265B LYS* 3.2 42.1 + - - +
267B ARG* 1.3 76.9 - - + +
269B ALA* 1.3 57.1 + - - +
270B GLY* 3.1 3.6 + - - -
290B LYS* 4.2 9.7 - - - +
291B ALA 4.8 1.2 - - - +
292B VAL* 3.8 14.6 - - + +
293B THR 4.5 2.1 + - - +
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Residues in contact with ALA 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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243B ALA* 6.1 1.1 - - + -
265B LYS 3.1 12.1 + - - +
266B LEU* 3.1 14.3 + - + +
268B GLU* 1.3 76.3 - - - +
270B GLY* 1.3 58.9 + - - +
271B ALA* 3.6 1.1 + - + -
284B MET* 4.1 3.2 - - + +
288B ARG 4.7 0.2 - - - +
289B PRO* 3.5 12.6 - - + +
290B LYS* 2.9 47.2 + - - +
292B VAL* 3.6 6.5 - - + +
310B PHE* 5.7 0.4 - - + -
313B LEU* 4.3 21.5 - - + -
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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