Contacts of the helix formed by residues 216 - 226 (chain C) in PDB entry 4OE5
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 GLY 216 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208C SER* 5.8 2.0 - - - -
212C PHE* 5.9 2.5 - - - -
214C ALA* 3.3 9.6 - - - +
215C ILE* 1.3 78.7 - - - +
217C GLY* 1.3 56.8 + - - +
218C ASN* 3.0 4.7 - - - -
219C LEU* 2.8 48.5 + - - +
220C ALA 4.0 1.2 + - - -
232C TRP* 4.6 4.8 + - - -
285C THR* 6.5 0.2 - - - -
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Residues in contact with GLY 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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166C LEU* 4.6 16.0 - - - +
170C PHE* 4.5 9.7 - - - -
215C ILE* 3.2 18.5 - - - +
216C GLY* 1.3 75.6 - - - +
218C ASN* 1.3 57.2 + - - +
219C LEU 3.3 0.3 + - - -
220C ALA* 3.4 4.4 + - - +
221C GLY* 2.8 25.1 + - - -
232C TRP* 4.6 10.5 - - - -
245C VAL* 5.2 4.5 - - - -
249C LEU* 6.0 1.2 - - - +
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Residues in contact with ASN 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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165C GLU 6.5 0.2 - - - -
166C LEU* 5.6 0.8 - - - +
169C PHE* 3.5 40.6 - - + +
170C PHE* 5.4 5.0 - - - -
173C ASN* 2.7 28.7 + - - +
216C GLY* 3.0 2.1 + - - -
217C GLY* 1.3 74.6 - - - +
219C LEU* 1.3 67.1 + - + +
220C ALA 3.2 0.2 - - - -
221C GLY* 3.7 3.0 - - - +
222C ALA* 3.1 35.6 + - - +
223C PRO* 3.8 0.3 - - - +
283C ASN* 4.0 3.2 + - - +
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Residues in contact with LEU 219 (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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206C ALA* 3.7 19.2 - - + +
207C ILE 3.5 31.6 - - - +
208C SER* 4.2 12.3 - - - -
212C PHE* 6.5 0.2 - - + -
215C ILE 5.6 0.2 - - - +
216C GLY* 2.8 25.5 + - - +
218C ASN* 1.3 79.3 - - + +
220C ALA* 1.3 55.5 + - - +
223C PRO* 3.2 12.0 - - - +
232C TRP* 5.3 4.0 - - - +
283C ASN* 2.9 50.6 + - - +
284C PHE 4.3 1.6 - - - +
285C THR* 3.6 28.9 - - - +
314C GLU* 5.4 1.1 - - - +
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Residues in contact with ALA 220 (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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206C ALA* 4.0 4.9 - - + -
216C GLY 4.0 0.6 + - - -
217C GLY 3.4 4.9 + - - +
218C ASN 3.2 0.2 - - - -
219C LEU* 1.3 78.0 - - - +
221C GLY* 1.3 64.2 + - - +
222C ALA 3.5 0.7 - - - -
223C PRO* 3.4 1.4 - - - +
224C ALA* 3.3 25.7 + - - +
230C VAL* 3.9 20.1 - - + +
232C TRP* 3.9 37.2 - - + -
249C LEU* 6.3 0.7 - - + -
259C ILE* 4.1 14.1 - - + +
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Residues in contact with GLY 221 (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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128C PHE* 3.6 22.9 - - - -
170C PHE* 4.4 10.8 - - - -
173C ASN* 5.1 1.8 - - - -
217C GLY 2.8 18.3 + - - -
218C ASN* 4.1 2.0 - - - -
220C ALA* 1.3 77.4 - - - +
222C ALA* 1.3 56.4 + - - +
224C ALA* 3.5 1.3 + - - -
225C LEU* 2.9 30.7 + - - +
249C LEU* 5.7 1.5 - - - +
259C ILE* 4.9 3.1 - - - +
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Residues in contact with ALA 222 (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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173C ASN* 3.8 15.3 - - - +
218C ASN* 3.1 33.7 + - - +
221C GLY* 1.3 74.6 - - - +
223C PRO* 1.4 70.4 - - + +
225C LEU* 3.3 7.2 + - - +
226C MET* 3.2 28.6 + - + +
283C ASN* 5.2 2.7 - - - +
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Residues in contact with PRO 223 (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* 4.2 21.3 - - + -
218C ASN 3.8 0.4 - - - +
219C LEU 3.2 26.7 - - - +
220C ALA* 3.4 6.3 - - - +
222C ALA* 1.4 92.3 - - + +
224C ALA* 1.3 64.5 + - - +
226C MET* 3.1 7.6 + - + -
228C ASN* 2.9 43.2 + - + +
230C VAL* 4.1 13.5 - - + -
283C ASN* 3.8 11.7 - - - +
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Residues in contact with ALA 224 (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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116C TRP* 2.8 30.0 + - + -
128C PHE* 4.0 9.9 - - + -
220C ALA 3.3 18.9 + - - +
221C GLY 3.8 3.1 - - - +
223C PRO* 1.3 77.9 - - - +
225C LEU* 1.3 63.5 + - - +
227C GLY 3.0 2.6 + - - -
228C ASN 3.5 15.5 - - - +
230C VAL* 4.1 2.6 - - + +
254C LEU* 5.2 0.2 - - + -
258C ILE* 4.3 8.7 - - + -
259C ILE* 4.0 25.6 - - + -
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Residues in contact with LEU 225 (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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116C TRP* 4.9 0.7 - - - -
121C ILE* 3.6 13.6 - - + +
124C ARG* 2.8 25.1 + - - +
125C ALA* 3.8 34.1 - - + +
128C PHE* 3.8 26.0 - - + -
170C PHE 5.3 0.9 - - - +
173C ASN* 3.4 49.6 - - + +
174C ALA* 3.8 3.4 - - + +
177C ALA* 4.0 10.8 - - + -
221C GLY 2.9 18.5 + - - +
222C ALA* 3.5 5.4 - - - +
223C PRO 3.2 0.2 - - - -
224C ALA* 1.3 76.7 - - - +
226C MET* 1.3 62.1 + - - +
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Residues in contact with MET 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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121C ILE* 5.1 1.8 - - + -
124C ARG* 3.7 10.9 + - - +
177C ALA* 3.8 28.7 - - + -
180C LEU* 4.1 25.1 - - + -
197C TYR* 5.2 8.9 - - + +
198C ARG 4.5 1.2 - - - +
199C GLY* 3.3 23.7 + - - -
222C ALA* 3.3 15.7 - - + +
223C PRO* 3.1 9.3 + - + +
225C LEU* 1.3 80.7 - - + +
227C GLY* 1.3 56.4 + - - +
228C ASN* 3.4 9.8 + - - +
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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