Contacts of the helix formed by residues 225 - 234 (chain C) in PDB entry 5EWL
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 225 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C PHE* 3.6 37.2 - - + -
222C THR* 3.7 31.2 - - + +
223C LYS 3.7 0.2 + - - -
224C ASN* 1.3 70.5 - - - +
226C THR* 1.3 63.2 + - - +
227C ALA* 3.3 3.4 - - - +
228C LEU* 3.4 13.5 + - + +
229C LEU* 3.2 31.9 + - + +
248C ASP 4.5 0.7 - - - +
251C ALA* 3.6 17.7 - - + -
252C VAL* 3.6 43.1 - - + +
255C SER* 3.4 15.6 + - - +
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Residues in contact with THR 226 (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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224C ASN* 3.2 25.1 + - - -
225C LEU* 1.3 75.1 - - - +
227C ALA* 1.4 60.0 + - - +
230C LEU* 2.8 36.5 + - + +
255C SER* 4.1 10.3 + - - -
258C MET* 5.8 2.1 - - - +
259C LEU* 3.8 34.0 - - + +
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Residues in contact with ALA 227 (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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224C ASN 5.1 1.9 + - - +
225C LEU* 3.3 1.0 - - - -
226C THR* 1.4 76.8 - - - +
228C LEU* 1.4 62.6 + - - +
230C LEU* 4.0 4.9 - - - +
231C GLU* 3.3 26.3 + - - +
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Residues in contact with LEU 228 (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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166C ILE* 3.8 26.7 - - + -
216C LEU* 3.6 31.7 - - + +
217C GLN 3.5 26.9 - - - +
218C PHE* 3.8 23.3 - - + -
225C LEU* 3.6 27.5 - - + +
227C ALA* 1.4 79.2 - - - +
229C LEU* 1.3 66.9 + - + +
231C GLU* 3.2 12.6 - - - +
232C ALA 3.2 19.1 + - - -
252C VAL* 5.2 1.1 - - + -
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Residues in contact with LEU 229 (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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166C ILE* 4.5 10.8 - - + -
225C LEU* 3.2 29.2 + - + +
228C LEU* 1.3 84.9 - - + +
230C LEU* 1.4 60.7 + - - +
231C GLU 3.2 0.2 - - - -
232C ALA* 3.3 3.5 + - + -
233C LYS* 2.8 30.1 + - - +
240C ILE* 5.7 0.2 - - + -
252C VAL* 3.8 20.4 - - + +
255C SER* 3.6 23.6 - - - -
256C ALA* 3.8 19.5 - - + +
259C LEU* 3.5 20.6 - - + -
261C MET* 3.4 24.5 - - + +
268C TRP* 4.1 14.1 - - + -
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Residues in contact with LEU 230 (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 THR* 2.8 21.9 + - + +
227C ALA* 4.0 5.8 - - - +
229C LEU* 1.4 75.2 - - - +
231C GLU* 1.4 61.0 + - - +
233C LYS* 3.3 9.2 + - - +
234C GLU* 3.2 27.8 + - - +
259C LEU* 3.9 15.0 - - + +
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Residues in contact with GLU 231 (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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214C LYS* 2.9 30.3 + - - +
216C LEU* 3.4 16.4 - - + +
227C ALA 3.3 15.7 + - - +
228C LEU* 3.2 14.7 - - - +
230C LEU* 1.4 75.7 - - - +
232C ALA* 1.4 59.1 + - - +
234C GLU* 3.6 16.6 + - - +
235C LEU* 3.7 14.7 - - + +
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Residues in contact with ALA 232 (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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164C ILE* 3.4 31.9 - - + +
166C ILE* 4.7 10.1 - - + -
216C LEU* 3.7 20.8 - - + +
228C LEU 3.2 4.9 + - - +
229C LEU* 3.3 11.9 + - - +
231C GLU* 1.4 76.4 - - - +
233C LYS* 1.3 63.8 + - - +
235C LEU* 3.4 20.9 + - - +
237C ALA 4.6 0.9 - - - +
240C ILE* 5.6 2.2 - - + +
261C MET* 4.2 10.5 - - + +
266C TYR* 5.5 1.7 - - - -
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Residues in contact with LYS 233 (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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229C LEU 2.8 20.3 + - - +
230C LEU* 3.3 8.9 + - - +
232C ALA* 1.3 73.1 - - - +
234C GLU* 1.3 61.8 + - + +
235C LEU 3.4 8.3 + - - +
259C LEU* 2.8 39.8 + - + +
260C ASP* 4.7 8.8 - - - +
261C MET* 3.7 21.0 - - + +
266C TYR* 3.3 27.6 + - - +
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Residues in contact with GLU 234 (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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230C LEU 3.2 11.4 + - - +
231C GLU* 3.7 13.5 - - - +
232C ALA 3.3 0.6 - - - -
233C LYS* 1.3 78.7 - - + +
235C LEU* 1.4 59.8 + - + +
236C GLU 4.0 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