Contacts of the helix formed by residues 210 - 221 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A TYR* 2.9 32.3 + - + -
208A ASN 4.0 0.8 + - - -
209A LEU* 1.3 69.6 - - - +
211A TYR* 1.3 63.2 + - - +
212A ALA* 3.4 11.8 - - - +
213A ARG* 3.0 38.7 + - - +
214A LEU* 2.9 23.9 + - - +
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Residues in contact with TYR 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A ALA* 3.9 27.8 + - + -
208A ASN* 6.3 0.4 - - + -
209A LEU* 2.9 53.4 + - + +
210A ASP* 1.3 70.6 - - - +
212A ALA* 1.3 57.1 + - - +
214A LEU* 3.6 5.5 - - + +
215A ARG* 2.8 33.4 + - - +
225A LEU* 4.0 1.5 - - + +
227A ALA* 4.4 1.1 - - + +
229A MSE 5.5 1.7 - - - +
232A ILE* 4.1 18.7 - - - +
242A PRO* 4.3 17.5 - - + -
243A SER 4.2 4.5 - - - -
244A PRO* 3.4 43.5 - - + +
247A HIS* 3.7 25.3 - - + +
248A CYS* 3.9 16.4 - - - -
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Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A ASP* 3.4 10.5 - - - +
211A TYR* 1.3 81.0 - - - +
213A ARG* 1.3 61.9 + - - +
215A ARG* 3.4 4.2 + - - +
216A LYS* 3.2 17.2 + - - +
247A HIS* 3.3 30.3 + - + +
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Residues in contact with ARG 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TYR* 3.6 38.9 + - + +
184A ASP* 2.9 31.7 + - - +
187A GLU* 2.8 33.5 + - - -
210A ASP* 3.0 29.9 + - + +
212A ALA* 1.3 77.2 - - - +
214A LEU* 1.3 66.2 + - - +
216A LYS* 3.0 21.3 + - + +
217A ILE* 3.0 29.6 + - + +
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Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A TYR* 4.5 11.2 - - + +
181A ILE* 6.0 0.9 - - + -
183A TYR* 3.8 20.4 - - + +
186A LEU* 3.5 31.9 - - + -
198A ILE* 4.5 13.3 - - + +
200A ALA* 3.5 29.6 - - + -
209A LEU* 4.5 10.3 - - + -
210A ASP 2.9 25.0 + - - +
211A TYR* 3.6 9.2 - - + +
213A ARG* 1.3 77.0 - - - +
215A ARG* 1.3 57.8 + - - +
217A ILE* 3.2 8.3 + - + +
218A ALA* 2.8 29.5 + - - +
225A LEU* 4.0 15.1 - - + +
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Residues in contact with ARG 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A TYR 2.8 16.3 + - - +
212A ALA 3.4 6.3 - - - +
214A LEU* 1.3 74.6 - - - +
216A LYS* 1.3 65.8 + - - +
218A ALA* 3.2 2.2 + - - +
219A ASP* 2.7 81.0 + - - +
225A LEU* 3.6 9.8 - - + +
247A HIS* 2.8 47.3 + - + +
248A CYS 5.6 0.6 + - - -
249A HIS* 3.2 34.9 + - - -
270A ARG* 5.3 7.1 - - - +
274A ARG 5.9 0.2 + - - -
286A TYR* 4.0 8.9 + - - -
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Residues in contact with LYS 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU* 2.9 31.5 + - - +
212A ALA 3.2 9.1 + - - +
213A ARG* 3.0 23.9 + - + +
215A ARG* 1.3 78.9 - - - +
217A ILE* 1.3 64.9 + - - +
219A ASP* 3.2 5.8 + - - +
220A ASP* 2.9 51.2 + - - +
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Residues in contact with ILE 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A TYR* 3.8 12.6 - - + +
186A LEU* 4.0 17.3 - - + -
187A GLU* 3.5 58.1 - - + +
190A ALA* 4.0 9.6 - - + -
198A ILE* 4.4 9.4 - - + -
213A ARG* 3.0 27.0 + - + +
214A LEU* 3.5 9.2 - - + +
216A LYS* 1.3 78.3 - - + +
218A ALA* 1.3 64.4 + - - +
220A ASP* 3.2 11.8 + - - +
221A ASN* 3.0 36.3 + - - +
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Residues in contact with ALA 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A ILE* 4.0 18.8 - - + +
214A LEU 2.8 14.2 + - - +
215A ARG* 3.5 9.4 - - - +
216A LYS 3.2 0.2 - - - -
217A ILE* 1.3 78.1 - - - +
219A ASP* 1.3 56.9 + - - +
221A ASN* 3.2 1.6 + - - -
222A GLY 2.9 8.0 + - - -
223A ALA* 2.7 48.2 + - - +
224A TYR 4.5 0.7 - - - -
225A LEU* 4.1 23.1 - - + +
249A HIS* 5.2 0.7 - - + -
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Residues in contact with ASP 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215A ARG* 2.7 60.3 + - - +
216A LYS* 3.9 4.7 - - - +
218A ALA* 1.3 73.6 - - - +
220A ASP* 1.3 67.1 + - - +
222A GLY* 3.0 15.5 + - - +
223A ALA 4.5 2.0 - - - +
249A HIS* 4.0 10.4 + - - -
274A ARG* 5.3 3.3 + - - -
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Residues in contact with ASP 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU* 3.7 10.5 - - + +
216A LYS* 2.9 55.4 + - - +
217A ILE* 3.3 13.2 - - - +
219A ASP* 1.3 79.3 - - - +
221A ASN* 1.3 67.8 + - - +
222A GLY 3.3 0.4 + - - -
156C ASP* 5.2 2.4 - - - +
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Residues in contact with ASN 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A GLU* 4.9 2.4 + - - +
190A ALA* 3.3 43.8 - - - +
191A SER* 3.4 15.0 - - - +
194A HIS* 5.1 7.0 - - - -
195A PRO* 4.2 22.3 - - + +
198A ILE* 5.4 0.2 - - - +
217A ILE* 3.0 26.4 + - - +
218A ALA* 3.2 3.2 + - - +
219A ASP 3.1 0.4 - - - -
220A ASP* 1.3 82.6 - - - +
222A GLY* 1.3 65.6 + - - +
223A ALA* 3.3 2.8 + - + +
156C ASP* 4.2 27.3 - - + +
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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