Contacts of the helix formed by residues 210 - 221 (chain C) in PDB entry 1EJI
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 ASP 210 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C TYR* 2.9 32.1 + - + +
208C ASN 4.0 0.6 + - - -
209C LEU* 1.3 69.1 - - - +
211C TYR* 1.3 64.5 + - - +
212C ALA* 3.5 12.0 - - - +
213C ARG* 2.9 38.5 + - - +
214C LEU* 2.9 24.5 + - - +
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Residues in contact with TYR 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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200C ALA* 3.8 29.4 + - + -
208C ASN* 6.3 0.7 - - + -
209C LEU* 2.9 53.4 + - + +
210C ASP* 1.3 71.1 - - - +
212C ALA* 1.3 57.5 + - - +
214C LEU* 3.7 5.5 - - + +
215C ARG* 2.8 33.3 + - - +
225C LEU* 4.0 1.7 - - + +
227C ALA* 4.4 2.0 - - + +
229C MSE 5.5 1.6 - - - +
232C ILE* 4.1 19.2 - - - +
242C PRO* 4.3 14.8 - - + -
243C SER 4.3 4.9 - - - -
244C PRO* 3.5 44.1 - - + +
247C HIS* 3.7 25.3 - - + +
248C CYS* 4.0 16.6 - - - -
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Residues in contact with ALA 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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210C ASP* 3.5 10.3 - - - +
211C TYR* 1.3 82.0 - - - +
213C ARG* 1.3 60.3 + - - +
215C ARG* 3.4 4.5 + - - +
216C LYS* 3.2 17.3 + - - +
247C HIS* 3.3 31.6 + - + +
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Residues in contact with ARG 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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183C TYR* 3.7 36.8 + - + +
184C ASP* 2.7 34.1 + - - +
187C GLU* 2.8 33.3 + - - -
210C ASP* 2.9 30.6 + - + +
212C ALA* 1.3 75.8 - - - +
214C LEU* 1.3 67.5 + - - +
216C LYS* 3.0 19.2 + - + +
217C ILE* 3.0 27.6 + - + +
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Residues in contact with LEU 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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172C TYR* 4.5 9.6 - - + +
181C ILE* 6.0 0.9 - - + -
183C TYR* 3.8 20.9 - - + +
186C LEU* 3.5 32.3 - - + -
198C ILE* 4.5 15.4 - - + +
200C ALA* 3.5 30.1 - - + -
209C LEU* 4.5 9.9 - - + -
210C ASP 2.9 24.1 + - - +
211C TYR* 3.7 9.4 - - + +
213C ARG* 1.3 76.7 - - - +
215C ARG* 1.3 58.0 + - - +
217C ILE* 3.2 8.1 + - + +
218C ALA* 2.8 28.9 + - - +
225C LEU* 4.0 15.1 - - + +
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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
----------------------------------------------------------
211C TYR 2.8 16.0 + - - +
212C ALA 3.4 5.4 - - - +
214C LEU* 1.3 78.3 - - - +
216C LYS* 1.3 63.1 + - - +
218C ALA* 3.2 2.9 + - - +
219C ASP* 2.5 81.7 + - - +
225C LEU* 3.6 10.2 - - + +
247C HIS* 2.7 47.8 + - + +
248C CYS 5.6 0.6 - - - -
249C HIS* 3.3 31.8 + - - -
270C ARG* 5.7 1.0 - - - +
274C ARG* 3.2 34.8 - - - +
286C TYR* 4.3 0.2 + - - -
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Residues in contact with LYS 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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187C GLU* 2.8 31.0 + - - +
212C ALA 3.2 8.7 + - - +
213C ARG* 3.0 21.0 + - + +
215C ARG* 1.3 80.0 - - - +
217C ILE* 1.3 68.3 + - + +
219C ASP* 3.2 5.8 + - - +
220C ASP* 2.9 52.7 + - - +
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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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183C TYR* 3.8 11.2 - - + +
186C LEU* 4.0 18.4 - - + -
187C GLU* 3.5 56.8 - - + +
190C ALA* 4.0 9.6 - - + -
198C ILE* 4.3 9.0 - - + -
213C ARG* 3.0 25.2 + - + +
214C LEU* 3.5 10.8 - - + +
216C LYS* 1.3 81.9 - - + +
218C ALA* 1.3 64.5 + - - +
220C ASP* 3.2 10.2 + - - +
221C ASN* 3.0 37.1 + - - +
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Residues in contact with ALA 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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198C ILE* 4.1 18.3 - - + +
214C LEU 2.8 14.2 + - - +
215C ARG* 3.4 10.1 - - - +
217C ILE* 1.3 77.2 - - - +
219C ASP* 1.3 57.1 + - - +
221C ASN* 3.2 1.7 + - - -
222C GLY 2.9 8.5 + - - -
223C ALA* 2.7 47.1 + - - +
224C TYR 4.5 0.7 - - - -
225C LEU* 4.1 22.2 - - + +
249C HIS* 5.2 0.4 - - + -
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Residues in contact with ASP 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 ARG* 2.5 60.5 + - - +
216C LYS* 3.8 4.5 - - - +
218C ALA* 1.3 73.0 - - - +
220C ASP* 1.3 68.1 + - - +
222C GLY* 3.0 15.5 + - - +
223C ALA 4.4 1.7 - - - +
249C HIS* 4.0 11.5 + - - -
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Residues in contact with ASP 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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156A ASP* 4.7 4.5 - - - +
187C GLU* 3.7 10.2 - - + +
216C LYS* 2.9 55.5 + - - +
217C ILE* 3.3 13.5 - - - +
218C ALA 3.2 0.2 - - - -
219C ASP* 1.3 78.4 - - - +
221C ASN* 1.3 66.3 + - - +
222C GLY 3.7 0.2 + - - -
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Residues in contact with ASN 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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156A ASP* 3.3 26.8 - - - +
187C GLU* 4.9 2.6 + - - +
190C ALA* 3.1 45.4 - - - +
191C SER* 3.4 14.7 - - - +
194C HIS* 5.0 5.7 - - - -
195C PRO* 4.3 22.5 - - + +
217C ILE* 3.0 26.4 + - - +
218C ALA* 3.2 4.0 + - - +
219C ASP 3.2 0.2 - - - -
220C ASP* 1.3 82.0 - - - +
222C GLY* 1.3 66.6 + - - +
223C ALA* 3.3 3.1 + - + +
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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