Contacts of the helix formed by residues 214 - 222 (chain C) in PDB entry 5E5R
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 214 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204C PHE* 4.3 25.1 - - + -
211C ASN* 3.1 25.5 + - + +
212C SER 3.1 0.8 - - - -
213C ALA* 1.3 78.7 - - + +
215C ASP* 1.3 54.1 + - - +
216C PRO* 3.3 2.2 - - - -
217C ILE* 2.8 34.0 + - + +
218C ILE* 2.9 21.8 + - + -
240C ASP 5.1 0.2 - - - +
241C LEU* 3.6 27.1 - - + -
274C VAL* 4.6 5.4 - - + -
275C PRO 3.6 21.3 - - - +
276C ILE* 3.7 31.0 - - + -
280C GLN* 3.9 8.5 - - - +
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Residues in contact with ASP 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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210C ASP* 5.2 4.3 - - - +
211C ASN 3.9 1.6 - - - +
212C SER* 3.3 33.7 + - - +
214C LEU* 1.3 76.0 - - - +
216C PRO* 1.3 70.2 - - + +
218C ILE* 3.9 6.4 - - - +
219C HIS* 2.9 27.3 + - - +
280C GLN* 3.5 17.2 + - - -
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Residues in contact with PRO 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 SER 4.1 3.6 - - - +
213C ALA 3.6 11.9 - - - +
214C LEU 3.5 4.7 - - - -
215C ASP* 1.3 93.7 - - + +
217C ILE* 1.3 59.3 + - + +
219C HIS* 3.9 6.1 + - + +
220C GLY* 2.9 23.6 + - - -
233C LEU* 3.9 8.6 - - + +
234C ASP* 3.8 37.6 + - + +
235C PRO 3.5 20.6 - - - +
236C PHE* 3.9 16.8 - - + -
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Residues in contact with ILE 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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117C MET* 3.8 11.8 - - + +
126C ILE* 4.1 22.9 - - + -
150C PHE* 4.2 23.1 - - + -
204C PHE* 6.2 1.8 - - + -
214C LEU* 2.8 21.2 + - + +
216C PRO* 1.3 76.2 - - + +
218C ILE* 1.3 67.5 + - + +
220C GLY* 3.1 1.9 + - - -
221C LEU* 2.8 40.7 + - + +
233C LEU* 4.6 3.1 - - + -
236C PHE* 4.1 32.8 - - + -
241C LEU* 4.3 25.4 - - + -
284C PHE* 4.8 2.7 - - + -
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Residues in contact with ILE 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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204C PHE* 6.5 0.2 - - + -
214C LEU* 2.9 28.9 + - + +
215C ASP* 3.9 6.1 - - - +
217C ILE* 1.3 80.2 - - + +
219C HIS* 1.3 61.5 + - - +
221C LEU* 3.2 19.1 + - + +
222C LYS* 3.3 36.6 + - - +
276C ILE* 4.7 2.9 - - + -
279C HIS* 5.7 0.4 - - + +
280C GLN* 3.8 55.4 - - + +
283C ALA* 4.0 10.8 - - + -
284C PHE* 4.2 20.0 - - + -
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Residues in contact with HIS 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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215C ASP 2.9 22.6 + - - +
216C PRO* 3.9 5.2 + - + +
218C ILE* 1.3 70.2 - - - +
220C GLY* 1.3 67.1 + - - +
222C LYS* 3.3 28.8 + - + +
223C GLY* 3.5 7.1 + - - -
232C PHE 5.8 2.8 + - - -
233C LEU* 6.2 0.4 - - - -
234C ASP* 3.6 28.1 + - - +
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Residues in contact with GLY 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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117C MET* 3.4 8.0 - - - +
216C PRO 2.9 16.8 + - - -
217C ILE 3.1 4.0 + - - -
219C HIS* 1.3 79.6 + - - +
221C LEU* 1.3 56.8 + - - +
223C GLY* 3.0 16.8 + - - -
224C VAL* 3.4 13.3 + - - +
231C THR* 3.7 10.5 - - - +
232C PHE 5.5 0.7 - - - -
233C LEU* 3.7 20.4 - - - -
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Residues in contact with LEU 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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117C MET* 4.3 2.0 - - + -
124C VAL* 3.7 42.6 - - + -
150C PHE* 5.8 0.9 - - + -
217C ILE* 2.8 26.4 + - + +
218C ILE* 3.2 14.8 + - + +
220C GLY* 1.3 71.7 - - - +
222C LYS* 1.3 61.2 + - - +
223C GLY 3.3 0.9 + - - -
224C VAL* 3.3 11.7 + - - +
225C VAL* 3.9 4.3 + - - +
283C ALA* 3.9 23.1 - - + +
284C PHE* 3.5 50.9 - - + +
287C ILE* 3.5 27.2 - - + +
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Residues in contact with LYS 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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218C ILE* 3.4 34.8 + - - +
219C HIS* 3.3 21.5 + - + +
220C GLY 3.2 0.8 - - - -
221C LEU* 1.3 76.0 - - - +
223C GLY* 1.3 57.5 + - - +
224C VAL 3.5 0.4 - - - -
225C VAL* 4.1 16.4 - - - +
229C LYS* 5.1 2.9 + - - -
279C HIS* 5.1 14.5 - - - -
283C ALA* 4.4 13.7 - - + +
226D GLU* 4.8 4.2 - - - +
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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