Contacts of the helix formed by residues 251 - 264 (chain D) in PDB entry 2EWY
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 GLN 251 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249D LEU 3.3 1.4 + - - -
250D PRO* 1.3 68.2 - - - +
252D LYS* 1.3 67.6 + - - +
254D PHE* 2.8 33.0 + - - +
255D ASP* 2.9 43.7 + - - +
338D PRO* 3.9 15.4 - - - +
339D SER 2.9 17.0 + - - +
340D THR* 5.2 2.2 + - - +
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Residues in contact with LYS 252 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D LEU* 4.7 22.0 - - + +
232D GLU* 2.9 35.9 + - - +
250D PRO* 3.1 2.9 + - + +
251D GLN* 1.3 78.7 - - - +
253D VAL* 1.3 62.8 + - + +
255D ASP* 3.6 10.0 + - - +
256D ALA* 3.2 20.8 + - - +
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Residues in contact with VAL 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D LEU* 3.8 28.9 - - + -
226D LEU* 4.0 9.4 - - + -
228D LEU* 4.4 9.9 - - + -
232D GLU* 4.4 12.3 - - + +
233D TYR* 3.8 25.6 - - + -
249D LEU* 3.9 16.2 - - + -
250D PRO* 2.7 33.2 + - + +
252D LYS* 1.3 72.2 - - + +
254D PHE* 1.3 67.9 + - - +
256D ALA* 3.0 6.4 + - - +
257D VAL* 2.8 21.7 + - - +
343D LEU* 5.8 1.6 - - + -
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Residues in contact with PHE 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249D LEU* 3.9 24.7 - - + +
250D PRO 3.1 2.2 + - - -
251D GLN* 2.8 22.2 + - - +
253D VAL* 1.3 75.3 - - - +
255D ASP* 1.3 63.5 + - - +
257D VAL* 3.1 1.8 + - + +
258D VAL* 2.8 52.3 + - + +
275D TRP* 3.5 28.9 - - + -
276D THR* 5.5 1.8 - - - -
334D PHE* 3.8 10.3 - + - -
336D ILE* 3.4 32.8 - - + -
337D SER 3.7 11.2 - - - -
338D PRO* 3.5 37.9 - - + -
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Residues in contact with ASP 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D GLN* 2.9 43.9 + - - +
252D LYS* 3.7 10.0 - - - +
254D PHE* 1.3 84.0 - - - +
256D ALA* 1.3 65.9 + - - +
258D VAL* 3.1 5.0 + - - +
259D GLU* 2.8 26.5 + - - +
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Residues in contact with ALA 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D LEU* 3.9 27.2 - - + +
228D LEU* 4.2 14.4 - - + -
252D LYS 3.2 11.3 + - - +
253D VAL 3.0 9.5 + - - +
255D ASP* 1.3 77.9 - - - +
257D VAL* 1.3 64.3 + - - +
259D GLU* 3.5 14.2 + - - +
260D ALA* 3.0 22.5 + - - +
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Residues in contact with VAL 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D LEU* 3.9 6.7 - - + -
221D ILE* 3.5 30.7 - - + -
226D LEU* 3.8 13.2 - - + -
249D LEU* 3.5 24.2 - - + -
253D VAL 2.8 20.3 + - - +
254D PHE* 3.4 6.5 - - + +
256D ALA* 1.3 68.6 - - - +
258D VAL* 1.3 58.1 + - + +
260D ALA* 2.9 4.9 + - - +
261D VAL* 2.7 48.4 + - + +
296D ILE* 4.7 4.5 - - + -
334D PHE* 5.3 1.8 - - + -
336D ILE* 4.3 21.8 - - + -
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Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254D PHE* 2.8 59.3 + - + +
255D ASP* 3.6 5.6 - - - +
257D VAL* 1.3 75.1 - - + +
259D GLU* 1.3 67.0 + - - +
261D VAL* 3.7 6.2 - - - +
262D ALA* 2.8 24.2 + - + +
275D TRP* 3.8 37.4 - - + +
334D PHE* 4.2 14.6 - - + -
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Residues in contact with GLU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255D ASP 2.8 21.0 + - - +
256D ALA* 3.5 10.9 - - - +
258D VAL* 1.3 73.5 - - - +
260D ALA* 1.3 59.4 + - - +
262D ALA* 3.2 6.3 + - - +
263D ARG* 2.8 68.1 + - + +
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Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ILE* 3.8 28.7 - - + -
226D LEU* 4.7 6.7 - - + -
256D ALA 3.0 13.7 + - - +
257D VAL 2.9 10.4 + - - +
259D GLU* 1.3 80.4 + - - +
261D VAL* 1.3 65.1 + - - +
262D ALA 3.0 1.0 + - - -
263D ARG* 3.1 8.3 + - - +
264D ALA* 3.1 21.8 + - - +
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Residues in contact with VAL 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ILE* 4.5 9.9 - - + -
257D VAL* 2.7 41.2 + - + +
258D VAL* 3.7 6.3 - - - +
260D ALA* 1.3 72.7 - - - +
262D ALA* 1.3 63.3 + - - +
264D ALA* 3.7 7.1 + - - +
265D SER* 3.4 13.2 + - - -
275D TRP* 4.3 16.8 - - + -
293D PHE* 3.8 26.8 - - + -
294D PRO* 4.1 11.7 - - + +
296D ILE* 4.6 7.4 - - + -
318D TYR* 3.8 25.1 - - + +
334D PHE* 5.0 4.9 - - + -
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Residues in contact with ALA 262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258D VAL* 2.8 16.0 + - + +
259D GLU* 3.3 11.7 - - - +
261D VAL* 1.3 75.9 - - - +
263D ARG* 1.3 68.3 + - + +
265D SER* 2.8 18.1 + - - -
266D LEU* 3.1 25.4 + - + +
275D TRP* 4.5 19.0 - - + +
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Residues in contact with ARG 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D GLU* 2.8 55.3 + - + +
260D ALA* 3.1 8.0 + - - +
262D ALA* 1.3 72.8 - - + +
264D ALA* 1.3 56.0 + - - +
265D SER 2.9 6.9 + - - -
266D LEU* 3.7 18.4 + - + +
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Residues in contact with ALA 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D ILE* 6.0 0.9 - - + -
222D GLY* 6.1 0.9 - - - -
260D ALA 3.1 13.5 + - - +
261D VAL 4.0 4.7 - - - +
262D ALA 2.9 2.2 + - - -
263D ARG* 1.3 73.6 - - - +
265D SER* 1.3 64.8 + - - +
267D ILE* 5.0 0.2 - - - +
292D TYR 3.2 9.0 - - - +
293D PHE 5.2 0.2 - - - -
294D PRO* 4.1 25.9 - - + +
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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