Contacts of the helix formed by residues 212 - 223 (chain A) in PDB entry 2E52
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 MET 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145A PHE* 3.8 18.8 - - + -
148A TYR* 3.7 31.4 - - + -
156A PHE* 4.2 9.9 - - + -
166A LEU* 3.8 27.8 - - + +
210A ASN* 2.8 18.2 + - - +
211A PHE* 1.3 88.0 - - + +
213A ARG* 1.3 61.4 + - - +
215A PHE* 3.7 23.4 - - - +
216A ASN* 2.8 32.7 + - - +
1004A GOL 3.3 24.2 - - - +
298B TYR* 3.8 12.6 - - + -
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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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210A ASN* 4.3 1.0 + - - +
211A PHE 3.4 0.6 - - - -
212A MET* 1.3 77.0 - - - +
214A ASP* 1.3 64.9 + - - +
216A ASN* 3.5 1.9 + - - +
217A LYS* 3.1 52.1 + - - +
295B ASP* 4.0 17.8 + - - +
298B TYR* 3.6 48.6 - - + +
299B LEU* 2.7 42.2 + - - +
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Residues in contact with ASP 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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194A PHE* 4.3 2.4 - - - -
198A GLN* 2.9 37.5 + - - +
201A LYS* 4.2 15.9 + - - +
211A PHE* 3.3 12.9 + - - +
213A ARG* 1.3 81.7 - - - +
215A PHE* 1.3 61.3 + - - +
217A LYS* 3.3 18.9 + - - +
218A TYR* 2.9 24.1 + - - +
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Residues in contact with PHE 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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165A LEU* 3.8 19.7 - - + -
166A LEU 4.6 7.9 - - - -
167A PHE* 4.1 16.6 - + - -
171A HIS* 3.7 42.4 - + - -
191A LEU* 3.8 26.0 - - + -
194A PHE* 3.7 41.2 - + + -
211A PHE* 2.8 16.4 + + - +
212A MET* 3.7 25.1 - - - +
213A ARG 3.3 0.2 - - - -
214A ASP* 1.3 77.4 - - - +
216A ASN* 1.3 59.8 + - - +
218A TYR* 3.2 5.6 + + + +
219A PHE* 2.8 38.2 + + + +
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Residues in contact with ASN 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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145A PHE* 4.3 7.4 - - - -
171A HIS* 2.8 31.2 + - - -
212A MET 2.8 17.1 + - - +
213A ARG 3.8 1.1 - - - +
215A PHE* 1.3 71.9 - - - +
217A LYS* 1.3 57.0 + - + +
219A PHE* 3.5 4.4 + - - +
220A MET* 2.9 38.0 + - + +
230A LEU* 4.0 8.7 - - + +
234A LEU* 4.3 6.1 - - - +
297B LEU 2.9 28.1 + - - -
298B TYR* 3.1 24.9 + - - +
299B LEU* 3.7 16.8 - - + +
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Residues in contact with LYS 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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213A ARG* 3.1 42.9 + - + +
214A ASP* 3.6 20.0 + - - +
215A PHE 3.2 0.2 - - - -
216A ASN* 1.3 75.4 - - + +
218A TYR* 1.3 58.5 + - - +
220A MET* 3.4 19.1 + - + +
221A ASP* 2.9 40.0 + - - +
299B LEU 5.4 5.6 - - - -
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Residues in contact with TYR 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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190A GLN* 2.5 46.5 + - + +
191A LEU* 4.4 6.5 - - + -
194A PHE* 3.4 43.5 - + + -
197A LYS* 3.8 25.2 + - + +
198A GLN* 5.6 1.1 - - - -
214A ASP 2.9 13.9 + - - +
215A PHE* 3.4 13.0 - + - +
217A LYS* 1.3 74.6 - - - +
219A PHE* 1.3 58.2 + - - +
221A ASP* 3.4 7.2 + - - +
222A LEU* 2.8 44.5 + - + +
102D ASN* 3.8 22.5 + - + -
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Residues in contact with PHE 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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167A PHE* 4.4 3.4 - + - -
171A HIS* 3.7 48.7 - + + -
174A ILE* 4.0 13.7 - - + -
175A LEU* 3.6 36.3 - - + -
191A LEU* 4.4 3.6 - - + -
215A PHE* 2.8 38.0 + + + +
216A ASN* 3.6 7.0 - - - +
218A TYR* 1.3 77.4 - - - +
220A MET* 1.3 63.5 + - - +
222A LEU* 4.8 0.4 - - - -
223A PHE* 3.0 49.6 + + - +
225A ILE* 3.6 22.2 - - + -
230A LEU* 4.2 16.2 - - + -
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Residues in contact with MET 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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216A ASN* 2.9 33.1 + - + +
217A LYS* 3.6 19.3 - - + +
219A PHE* 1.3 76.4 - - - +
221A ASP* 1.3 61.2 + - - +
224A LYS* 2.8 27.2 + - - -
225A ILE* 3.0 30.6 + - + +
226A ASP 4.0 0.7 - - - -
227A LYS* 3.5 42.8 - - + -
230A LEU* 3.5 24.0 - - + -
299B LEU* 4.1 18.8 - - + +
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Residues in contact with ASP 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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217A LYS* 2.9 26.3 + - - +
218A TYR* 3.8 5.9 - - - +
220A MET* 1.3 80.1 - - - +
222A LEU* 1.3 65.1 + - - +
224A LYS* 3.7 14.1 + - - +
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Residues in contact with LEU 222 (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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186A PHE* 3.2 45.0 - - + -
187A SER 4.4 10.3 - - - +
188A PHE* 4.9 2.0 - - - +
190A GLN* 4.2 13.5 - - + -
191A LEU* 3.6 31.6 - - + +
218A TYR* 2.8 31.3 + - + +
219A PHE* 4.0 2.7 - - - +
221A ASP* 1.3 75.4 - - - +
223A PHE* 1.3 84.9 + - + +
224A LYS* 3.7 4.5 + - - +
101D PHE* 6.4 2.5 - - + -
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Residues in contact with PHE 223 (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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175A LEU* 3.9 14.8 - - + -
180A LEU* 3.9 24.6 - - + +
186A PHE* 3.7 25.8 - + - -
188A PHE* 3.6 33.7 - + - -
191A LEU* 3.7 26.9 - - + -
219A PHE* 3.0 57.4 + + - +
222A LEU* 1.3 98.3 - - + +
224A LYS* 1.3 70.7 + - - +
225A ILE* 3.7 20.9 - - + +
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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