Contacts of the helix formed by residues 206 - 218 (chain C) in PDB entry 5YL4
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 ASN 206 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171C ILE* 3.4 17.2 - - - +
172C TYR 3.1 10.9 + - - +
174C ALA* 3.6 18.0 - - + +
177C VAL* 3.6 15.8 - - + +
204C VAL* 3.4 2.3 + - - +
205C ASP* 1.3 73.8 + - - +
207C GLU* 1.3 57.3 + - - +
209C ILE* 3.4 5.9 + - - +
210C TYR* 2.8 29.7 + - - +
227C LEU* 3.9 9.6 - - - +
231C ILE* 4.6 5.0 - - - +
501C GTP 2.8 65.8 + - - -
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Residues in contact with GLU 207 (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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174C ALA* 3.3 11.7 - - + +
175C PRO* 3.7 15.2 - - - +
176C GLN* 3.4 36.4 + - - +
205C ASP* 3.1 14.9 + - - +
206C ASN* 1.3 75.5 - - - +
208C ALA* 1.3 56.3 + - - +
210C TYR* 3.4 5.6 - - + +
211C ASP* 2.8 48.4 + - - +
304C LYS* 3.4 27.1 + - + +
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Residues in contact with ALA 208 (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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205C ASP* 3.0 18.2 + - + +
207C GLU* 1.3 79.5 - - - +
209C ILE* 1.3 58.7 + - - +
211C ASP* 3.6 5.3 + - - +
212C ILE* 3.1 32.5 + - - +
301C GLN 3.3 23.3 - - - +
302C MET* 3.6 15.5 - - - +
303C VAL 4.0 1.6 - - - +
304C LYS* 4.2 17.4 - - + +
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Residues in contact with ILE 209 (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 VAL* 3.4 23.1 - - + -
205C ASP 3.1 13.9 + - - +
206C ASN* 3.9 8.1 - - - +
208C ALA* 1.3 75.7 - - - +
210C TYR* 1.3 61.0 + - - +
212C ILE* 3.4 7.4 + - + +
213C CYS* 3.0 29.5 + - - -
227C LEU* 3.5 43.5 - - + +
230C LEU* 3.9 17.9 - - + -
231C ILE* 4.1 8.5 - - + -
302C MET* 3.4 39.7 - - + -
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Residues in contact with TYR 210 (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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176C GLN* 4.1 29.1 - - + +
177C VAL* 3.9 26.7 - - + -
206C ASN 2.8 18.9 + - - +
207C GLU* 3.4 8.7 - - - +
209C ILE* 1.3 74.4 - - - +
211C ASP* 1.3 65.3 + - - +
213C CYS* 3.4 2.9 + - - +
214C ARG* 3.1 59.9 + - - +
220C GLU 4.9 1.0 + - - -
221C ARG* 3.3 33.8 + - - +
222C PRO* 3.5 38.1 - - + +
227C LEU* 3.6 11.6 - - + +
327D ASP* 3.9 5.2 + - - -
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Residues in contact with ASP 211 (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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176C GLN* 5.0 0.5 + - - -
207C GLU* 2.8 29.0 + - - +
208C ALA* 4.0 4.7 - - - +
210C TYR* 1.3 74.2 - - - +
212C ILE* 1.3 53.3 + - - +
214C ARG* 2.8 37.1 + - - +
215C ARG* 2.8 57.6 + - - +
304C LYS* 2.6 38.9 + - - -
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Residues in contact with ILE 212 (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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208C ALA 3.1 25.3 + - - +
209C ILE* 3.8 9.2 - - + +
210C TYR 3.2 0.2 - - - -
211C ASP* 1.3 74.9 - - - +
213C CYS* 1.3 59.2 + - - +
215C ARG* 4.0 8.5 - - - +
216C ASN* 2.9 35.5 + - - +
217C LEU* 3.6 1.0 + - - +
230C LEU* 3.5 20.4 - - + -
275C VAL* 3.7 27.4 - - + -
299C ALA 3.4 24.2 - - - +
300C ASN* 4.0 15.9 - - - +
301C GLN 3.7 19.7 - - - +
302C MET* 4.3 11.9 - - + -
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Residues in contact with CYS 213 (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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209C ILE 3.0 20.3 + - - +
210C TYR 3.8 0.2 - - - +
211C ASP 3.4 0.2 - - - -
212C ILE* 1.3 77.2 - - - +
214C ARG* 1.3 59.3 + - - +
217C LEU* 3.4 31.1 + - - +
219C ILE* 3.2 26.8 + - + +
222C PRO* 3.5 23.1 - - + -
226C ASN* 3.9 27.8 - - - -
227C LEU* 4.1 10.8 - - - -
230C LEU* 4.0 16.2 - - - -
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Residues in contact with ARG 214 (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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176C GLN* 4.8 10.5 - - - +
210C TYR* 3.1 40.1 + - + +
211C ASP* 2.8 32.6 + - - +
213C CYS* 1.3 79.6 - - - +
215C ARG* 1.3 63.3 + - - +
218C ASP* 3.5 18.5 - - - +
219C ILE 3.4 20.5 - - - +
220C GLU* 4.0 13.7 - - - +
222C PRO* 3.8 10.1 - - + -
324D LYS* 6.6 0.2 - - - +
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Residues in contact with ARG 215 (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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211C ASP* 2.8 48.1 + - - +
212C ILE* 4.0 7.1 - - - +
214C ARG* 1.3 77.0 - - - +
216C ASN* 1.3 75.8 + - - +
218C ASP* 3.7 12.1 - - - +
280C LYS* 4.2 7.8 + - - -
299C ALA* 3.4 46.0 + - - +
300C ASN* 5.2 0.6 + - - -
304C LYS* 5.8 2.6 - - - +
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Residues in contact with ASN 216 (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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212C ILE* 2.9 22.2 + - - +
215C ARG* 1.3 99.2 + - - +
217C LEU* 1.3 61.6 + - - +
218C ASP* 3.5 0.6 - - - +
275C VAL* 3.1 41.4 + - + +
276C ILE* 4.2 1.9 - - - -
277C SER* 3.8 19.2 + - - -
280C LYS* 4.4 13.7 + - - +
300C ASN* 3.8 21.0 + - - -
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Residues in contact with LEU 217 (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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212C ILE 3.6 0.2 + - - -
213C CYS* 3.4 32.6 + - - +
216C ASN* 1.3 76.3 - - - +
218C ASP* 1.3 70.2 + - - +
219C ILE* 3.3 28.1 + - + +
226C ASN 5.6 1.3 - - - +
230C LEU* 5.0 5.2 - - + -
275C VAL* 3.8 27.8 - - + -
276C ILE 3.9 19.7 - - - +
277C SER* 4.2 12.7 - - - +
367C ASP* 3.8 36.5 - - + +
368C LEU* 4.1 13.7 - - + -
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Residues in contact with ASP 218 (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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213C CYS 3.4 2.0 + - - -
214C ARG 3.5 12.1 + - - +
215C ARG 3.7 11.5 - - - +
216C ASN 4.8 0.3 - - - +
217C LEU* 1.3 79.1 - - - +
219C ILE* 1.3 60.3 + - - +
220C GLU* 3.8 6.6 + - - +
277C SER* 5.0 3.7 + - - -
280C LYS* 3.2 32.4 + - - +
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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