Contacts of the strand formed by residues 296 - 301 (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 ILE 296 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219C LEU* 5.3 7.2 - - + -
220C GLU 3.6 8.3 - - - +
221C ILE* 4.7 17.5 - - + -
247C LEU* 5.1 10.1 - - + -
257C VAL* 4.7 4.3 - - + -
261C VAL* 4.6 7.6 - - + -
295C LYS* 1.3 80.4 - - - +
297C SER* 1.3 69.1 + - - +
298C ILE* 5.2 6.4 - - + +
312C THR* 3.3 2.3 - - - +
313C ILE* 3.1 48.4 + - + +
318C TYR* 3.4 35.9 - - + +
336C ILE* 3.6 30.1 - - + -
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Residues in contact with SER 297 (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* 3.3 7.6 - - - +
220C GLU* 2.8 56.3 + - - +
295C LYS* 4.2 1.9 - - - +
296C ILE* 1.3 72.7 + - - +
298C ILE* 1.3 66.7 + - - +
299C TYR* 4.7 2.2 - - - -
310C ARG* 4.2 19.9 + - - -
311C ILE 3.4 4.0 - - - -
312C THR* 2.6 33.3 + - - +
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Residues in contact with ILE 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216C ILE* 3.7 31.2 - - + -
218C LYS 3.8 2.9 - - - -
219C LEU* 3.4 18.8 - - + -
247C LEU* 4.7 14.6 - - + -
249C LEU* 6.0 0.7 - - + -
296C ILE* 5.2 7.2 - - + +
297C SER* 1.3 74.7 - - - +
299C TYR* 1.3 64.5 + - - +
300C LEU* 3.7 20.5 + - + +
310C ARG* 3.4 1.4 - - - -
311C ILE* 3.0 52.8 + - + +
343C LEU* 6.3 0.9 - - + -
345C ILE* 4.6 16.4 - - + -
349C VAL* 4.6 18.6 - - + -
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Residues in contact with TYR 299 (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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84A THR* 4.0 9.5 - - - +
216C ILE* 3.5 5.7 - - - +
217C LEU* 2.7 37.5 + - + -
218C LYS* 3.0 50.8 + - + +
219C LEU 4.7 0.4 - - - -
220C GLU* 2.6 44.1 + - + -
297C SER* 4.7 1.1 - - - -
298C ILE* 1.3 76.5 - - - +
300C LEU* 1.3 57.4 + - - +
308C SER* 3.9 20.0 - - - +
309C PHE 3.6 3.8 - - - -
310C ARG* 2.9 41.8 + - + -
386C PHE* 3.7 30.7 - + + -
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Residues in contact with LEU 300 (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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204C THR* 4.1 10.1 - - + +
214C ILE* 3.7 28.7 - - + -
215C GLU 3.8 7.9 - - - +
216C ILE* 3.7 26.9 - - + -
217C LEU* 4.3 0.7 - - - -
298C ILE* 3.7 16.6 - - + +
299C TYR* 1.3 81.4 - - - +
301C ARG* 1.3 65.0 + - - +
302C ASP 3.4 0.2 + - - -
308C SER* 3.3 4.2 - - - -
309C PHE* 3.0 54.2 + - + -
311C ILE* 4.4 9.2 - - + -
345C ILE* 5.0 1.6 - - + -
366C PHE* 3.7 25.8 - - + -
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Residues in contact with ARG 301 (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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204C THR* 2.9 24.7 + - - +
205C PRO* 3.6 8.8 - - + +
207C LYS* 5.9 0.2 - - - +
215C GLU* 2.7 52.7 + - + -
217C LEU* 3.8 21.2 - - + +
300C LEU* 1.3 72.6 - - - +
302C ASP* 1.3 74.8 + - - +
305C SER* 3.0 39.5 + - - +
307C ARG 4.0 6.5 - - - +
308C SER* 4.2 0.2 - - - -
309C PHE* 4.2 0.6 - - - -
388C THR* 3.4 16.6 + - - +
389C GLU* 5.6 0.4 + - - -
392C ALA* 3.4 30.3 - - - +
393C SER* 3.5 24.7 + - - +
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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