Contacts of the helix formed by residues 251 - 264 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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249C LEU 3.3 1.0 + - - -
250C PRO* 1.3 68.6 - - - +
252C LYS* 1.3 66.8 + - - +
254C PHE* 2.8 32.5 + - - +
255C ASP* 2.9 42.7 + - - +
338C PRO* 3.9 16.6 - - - +
339C SER 2.9 17.4 + - - +
340C THR* 5.2 1.8 + - - +
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Residues in contact with LYS 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228C LEU* 4.7 20.9 - - + +
232C GLU* 2.9 34.7 + - - +
250C PRO* 3.1 3.0 + - + -
251C GLN* 1.3 77.0 - - - +
253C VAL* 1.3 64.0 + - + +
255C ASP* 3.6 10.4 + - - +
256C ALA* 3.2 20.1 + - - +
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Residues in contact with VAL 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C LEU* 3.8 28.7 - - + -
226C LEU* 4.0 9.6 - - + -
228C LEU* 4.4 8.5 - - + -
232C GLU* 4.4 12.6 - - + +
233C TYR* 3.8 24.9 - - + -
249C LEU* 3.9 16.8 - - + -
250C PRO* 2.7 33.0 + - + +
252C LYS* 1.3 71.5 - - + +
254C PHE* 1.3 65.9 + - - +
256C ALA* 3.0 7.4 + - - +
257C VAL* 2.8 21.1 + - - +
343C LEU* 5.8 1.6 - - + -
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Residues in contact with PHE 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C LEU* 3.9 25.0 - - + +
250C PRO 3.1 2.4 + - - -
251C GLN* 2.8 22.2 + - - +
253C VAL* 1.3 76.6 - - - +
255C ASP* 1.3 62.9 + - - +
257C VAL* 3.0 2.9 + - + +
258C VAL* 2.8 50.8 + - + +
275C TRP* 3.5 28.9 - - + -
276C THR* 5.5 1.8 - - - -
334C PHE* 3.8 10.5 - + - -
336C ILE* 3.4 33.2 - - + -
337C SER 3.7 10.8 - - - -
338C PRO* 3.5 39.0 - - + -
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Residues in contact with ASP 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251C GLN* 2.9 42.8 + - - +
252C LYS* 3.7 9.4 - - - +
254C PHE* 1.3 84.3 - - - +
256C ALA* 1.3 64.7 + - - +
258C VAL* 3.1 4.6 + - - +
259C GLU* 2.8 26.5 + - - +
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Residues in contact with ALA 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C LEU* 3.9 27.6 - - + +
228C LEU* 4.2 14.8 - - + -
252C LYS 3.2 11.5 + - - +
253C VAL 3.0 8.2 + - - +
255C ASP* 1.3 77.6 - - - +
257C VAL* 1.3 63.5 + - - +
259C GLU* 3.5 13.9 + - - +
260C ALA* 3.0 22.9 + - - +
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Residues in contact with VAL 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219C LEU* 3.9 6.7 - - + -
221C ILE* 3.5 30.1 - - + -
226C LEU* 3.8 13.2 - - + -
249C LEU* 3.5 24.9 - - + -
253C VAL 2.8 20.1 + - - +
254C PHE* 3.4 6.3 - - + +
256C ALA* 1.3 69.8 - - - +
258C VAL* 1.3 58.1 + - + +
260C ALA* 2.9 4.0 + - - +
261C VAL* 2.7 49.2 + - + +
296C ILE* 4.7 4.7 - - + -
334C PHE* 5.3 1.6 - - + -
336C ILE* 4.3 21.5 - - + -
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Residues in contact with VAL 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254C PHE* 2.8 58.0 + - + +
255C ASP* 3.6 5.4 - - - +
257C VAL* 1.3 73.4 - - + +
259C GLU* 1.3 67.1 + - - +
261C VAL* 3.1 6.3 + - - +
262C ALA* 2.8 24.2 + - + +
275C TRP* 3.8 38.0 - - + +
334C PHE* 4.2 13.9 - - + -
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Residues in contact with GLU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ASP 2.8 20.2 + - - +
256C ALA* 3.5 11.3 - - - +
258C VAL* 1.3 75.1 - - - +
260C ALA* 1.3 58.0 + - - +
262C ALA* 3.2 6.0 + - - +
263C ARG* 2.8 67.6 + - + +
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ILE* 3.8 29.8 - - + -
226C LEU* 4.7 6.3 - - + -
256C ALA 3.0 13.7 + - - +
257C VAL 2.9 10.6 + - - +
259C GLU* 1.3 81.0 - - - +
261C VAL* 1.3 65.0 + - - +
262C ALA 3.0 1.0 + - - -
263C ARG* 3.1 8.4 + - - +
264C ALA* 3.1 21.8 + - - +
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Residues in contact with VAL 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ILE* 4.4 10.5 - - + +
257C VAL* 2.7 41.1 + - + +
258C VAL* 3.7 6.7 - - - +
260C ALA* 1.3 73.0 - - - +
262C ALA* 1.3 63.9 + - - +
264C ALA* 3.7 6.8 + - - +
265C SER* 3.4 13.7 + - - -
275C TRP* 4.3 17.7 - - + -
293C PHE* 3.8 26.0 - - + -
294C PRO* 4.1 11.9 - - + +
296C ILE* 4.6 7.6 - - + -
318C TYR* 3.8 24.5 - - + +
334C PHE* 5.0 4.7 - - + -
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Residues in contact with ALA 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C VAL* 2.8 16.3 + - + +
259C GLU* 3.3 11.0 - - - +
261C VAL* 1.3 75.9 - - - +
263C ARG* 1.3 67.8 + - + +
265C SER* 2.8 18.9 + - - -
266C LEU* 3.1 24.3 + - + +
275C TRP* 4.5 20.6 - - + +
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Residues in contact with ARG 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C GLU* 2.8 56.5 + - + +
260C ALA* 3.7 6.7 - - - +
262C ALA* 1.3 71.4 - - - +
264C ALA* 1.3 56.9 + - - +
265C SER 2.9 6.6 + - - -
266C LEU* 3.7 19.5 + - + +
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Residues in contact with ALA 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ILE* 6.0 0.7 - - + -
222C GLY* 6.1 0.9 - - - -
260C ALA 3.1 13.5 + - - +
261C VAL 4.0 5.4 - - - +
262C ALA 2.9 1.6 + - - -
263C ARG* 1.3 74.4 - - - +
265C SER* 1.3 65.6 + - - +
267C ILE* 5.0 0.2 - - - +
292C TYR 3.2 8.3 - - - +
293C PHE 5.2 0.2 - - - -
294C PRO* 4.1 25.7 - - + +
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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