Contacts of the strand formed by residues 296 - 301 (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 ILE 296 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219D LEU* 5.3 7.0 - - + -
220D GLU 3.6 8.5 - - - +
221D ILE* 4.7 16.8 - - + -
247D LEU* 5.1 10.5 - - + -
257D VAL* 4.7 5.2 - - + -
261D VAL* 4.6 7.9 - - + -
294D PRO 4.4 0.2 - - - +
295D LYS* 1.3 80.5 - - - +
297D SER* 1.3 69.7 + - - +
298D ILE* 5.2 6.5 - - + +
311D ILE 4.1 0.2 - - - +
312D THR* 3.3 2.4 - - - +
313D ILE* 3.1 48.8 + - + +
318D TYR* 3.4 36.6 - - + +
336D ILE* 3.6 29.6 - - + -
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Residues in contact with SER 297 (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* 3.3 7.1 - - - +
220D GLU* 2.8 55.7 + - - +
295D LYS* 4.2 2.1 - - - +
296D ILE* 1.3 71.1 - - - +
298D ILE* 1.3 67.2 + - - +
299D TYR* 4.7 1.8 - - - -
310D ARG* 4.2 19.4 + - - -
311D ILE 3.4 4.5 - - - -
312D THR* 2.6 32.7 + - - +
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Residues in contact with ILE 298 (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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216D ILE* 3.7 31.2 - - + -
218D LYS 3.8 2.9 - - - -
219D LEU* 3.4 19.7 - - + -
247D LEU* 4.7 14.8 - - + -
249D LEU* 6.0 0.7 - - + -
296D ILE* 5.2 6.5 - - + +
297D SER* 1.3 75.9 - - - +
299D TYR* 1.3 65.8 + - - +
300D LEU* 3.7 19.3 + - + +
310D ARG* 3.4 2.1 - - - -
311D ILE* 3.0 52.4 + - + +
343D LEU* 6.3 0.7 - - + -
345D ILE* 4.6 16.2 - - + -
349D VAL* 4.6 19.3 - - + -
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Residues in contact with TYR 299 (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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216D ILE* 3.5 6.1 - - - +
217D LEU* 2.7 37.4 + - + -
218D LYS* 3.0 52.1 + - + +
219D LEU 4.7 0.7 - - - -
220D GLU* 2.6 44.6 + - + -
297D SER* 4.7 1.1 - - - -
298D ILE* 1.3 75.7 - - - +
300D LEU* 1.3 57.8 + - - +
308D SER* 3.9 19.3 - - - +
309D PHE 3.6 4.5 - - - +
310D ARG* 2.9 41.0 + - + -
386D PHE* 3.7 35.2 - + + -
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Residues in contact with LEU 300 (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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204D THR* 4.1 9.2 - - + +
214D ILE* 3.7 28.7 - - + -
215D GLU 3.8 7.9 - - - +
216D ILE* 3.7 26.5 - - + -
217D LEU* 4.3 0.7 - - - -
298D ILE* 3.7 16.8 - - + +
299D TYR* 1.3 82.7 - - - +
301D ARG* 1.3 65.0 + - - +
308D SER* 3.3 4.7 - - - -
309D PHE* 3.0 54.6 + - + -
311D ILE* 4.4 9.4 - - + -
345D ILE* 5.0 1.8 - - + -
366D PHE* 3.7 26.0 - - + -
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Residues in contact with ARG 301 (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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204D THR* 2.9 26.3 + - - +
205D PRO* 3.6 8.8 - - + +
207D LYS* 5.9 0.7 - - - +
215D GLU* 2.7 52.5 + - + -
217D LEU* 3.8 20.2 - - + +
300D LEU* 1.3 72.8 - - - +
302D ASP* 1.3 74.1 + - - +
305D SER* 3.0 40.7 + - - +
307D ARG 4.0 7.4 - - - +
309D PHE* 4.2 0.6 - - - -
388D THR* 3.4 16.0 + - - -
389D GLU* 5.6 0.4 + - - -
392D ALA* 3.5 30.3 - - - +
393D SER* 3.5 26.0 + - - +
394D ASN 4.1 0.2 - - - +
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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