Contacts of the helix formed by residues 212 - 223 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145C PHE* 3.8 21.5 - - + -
148C TYR* 3.7 30.1 - - + -
156C PHE* 4.4 6.3 - - + -
166C LEU* 3.7 31.9 - - + +
210C ASN* 2.9 17.6 + - - +
211C PHE* 1.3 87.2 - - + +
213C ARG* 1.3 61.2 + - - +
215C PHE* 3.7 23.1 - - - +
216C ASN* 2.8 33.8 + - - +
1003C GOL 3.4 24.2 - - - +
298D TYR* 3.8 12.3 - - + -
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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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210C ASN* 4.3 1.1 + - - +
211C PHE 3.3 0.8 - - - -
212C MET* 1.3 78.1 - - - +
214C ASP* 1.3 63.5 + - - +
216C ASN* 3.4 1.9 + - - +
217C LYS* 3.1 50.3 + - - +
295D ASP* 3.7 23.6 + - - +
298D TYR* 3.5 48.5 - - + +
299D LEU 2.8 41.7 + - - +
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Residues in contact with ASP 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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194C PHE* 4.3 2.1 - - - -
198C GLN* 2.9 37.8 + - - +
201C LYS* 6.1 0.2 - - - +
211C PHE 3.2 9.4 + - - +
213C ARG* 1.3 79.4 - - - +
215C PHE* 1.3 61.0 + - - +
217C LYS* 3.4 16.9 + - - +
218C TYR* 2.9 29.7 + - - +
2001C ACT 3.5 16.6 - - - +
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Residues in contact with PHE 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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165C LEU* 3.9 16.2 - - + -
166C LEU 4.7 7.6 - - - -
167C PHE* 4.3 13.9 - + - -
171C HIS* 3.5 42.4 - + + -
191C LEU* 3.7 31.4 - - + -
194C PHE* 3.7 41.2 - + + -
211C PHE 2.8 19.3 + - - +
212C MET* 3.7 25.4 - - - +
213C ARG 3.3 0.2 - - - -
214C ASP* 1.3 72.1 - - - +
216C ASN* 1.3 58.8 + - - +
218C TYR* 3.2 4.6 + + - +
219C PHE* 2.9 38.9 + + + +
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Residues in contact with ASN 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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145C PHE* 4.3 7.0 - - - -
171C HIS* 2.8 32.3 + - - -
212C MET 2.8 17.2 + - - +
213C ARG 3.8 0.9 - - - +
214C ASP 3.3 0.4 - - - -
215C PHE* 1.3 73.2 - - - +
217C LYS* 1.3 58.4 + - - +
219C PHE* 3.4 4.1 + - - +
220C MET* 2.9 37.5 + - + +
230C LEU* 4.0 18.0 - - + +
234C LEU* 4.2 5.9 - - - +
297D LEU 2.9 28.1 + - - -
298D TYR* 3.0 24.1 + - - +
299D LEU* 4.1 8.1 - - + +
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Residues in contact with LYS 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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213C ARG* 3.1 42.3 + - - +
214C ASP* 3.7 15.3 + - - +
216C ASN* 1.3 75.9 - - + +
218C TYR* 1.3 57.9 + - - +
220C MET* 3.5 21.0 + - + +
221C ASP* 3.0 29.6 + - - +
299D LEU* 5.3 8.3 - - - -
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Residues in contact with TYR 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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102B ASN* 5.9 9.6 - - + -
190C GLN* 2.6 42.6 + - + +
191C LEU* 4.5 5.6 - - + -
194C PHE* 3.4 40.5 - + + -
197C LYS* 3.6 34.5 + - + +
198C GLN* 5.4 3.1 - - - -
214C ASP 2.9 17.4 + - - +
215C PHE* 3.2 9.8 + + - +
217C LYS* 1.3 76.4 - - - +
219C PHE* 1.3 61.0 + - - +
221C ASP* 3.5 6.0 + - - +
222C LEU* 2.9 39.6 + - + +
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Residues in contact with PHE 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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167C PHE* 4.7 4.3 - + - -
171C HIS* 3.8 47.8 - + + -
174C ILE* 4.0 13.5 - - + -
175C LEU* 3.7 29.2 - - + -
191C LEU* 4.2 3.4 - - + -
215C PHE* 2.9 34.9 + + + +
216C ASN* 3.6 6.1 - - - +
218C TYR* 1.3 77.4 - - - +
220C MET* 1.3 66.5 + - - +
222C LEU* 4.6 1.1 - - - -
223C PHE* 3.0 55.8 + + - +
225C ILE* 3.7 23.3 - - + -
230C LEU* 4.3 16.6 - - + -
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Residues in contact with MET 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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216C ASN* 2.9 25.2 + - + +
217C LYS* 3.6 25.6 - - + +
219C PHE* 1.3 75.4 - - - +
221C ASP* 1.3 56.1 + - - +
224C LYS* 2.9 25.8 + - - +
225C ILE* 2.9 36.0 + - + +
226C ASP* 4.0 0.9 - - - -
227C LYS* 3.6 39.0 - - + -
230C LEU* 3.6 22.7 - - + -
299D LEU* 4.1 18.4 - - + +
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Residues in contact with ASP 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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102B ASN* 2.9 33.6 + - - +
217C LYS 3.0 16.8 + - - +
218C TYR* 3.9 5.8 - - - +
219C PHE 3.3 0.2 - - - -
220C MET* 1.3 74.6 - - - +
222C LEU* 1.3 70.2 + - - +
224C LYS* 3.0 45.7 + - - +
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Residues in contact with LEU 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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101B PHE* 6.3 3.4 - - + -
102B ASN* 6.2 1.3 - - - +
186C PHE* 3.4 35.7 - - + -
187C SER 4.4 8.5 - - - +
188C PHE* 4.7 3.8 - - - +
190C GLN* 4.0 17.0 - - + +
191C LEU* 3.5 33.2 - - + +
218C TYR* 2.9 27.2 + - + +
219C PHE 3.4 2.9 + - - +
221C ASP* 1.3 84.2 + - - +
223C PHE* 1.3 89.0 + - + +
224C LYS* 3.5 1.4 + - - -
2003C ACT 3.7 4.7 - - - +
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Residues in contact with PHE 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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175C LEU* 3.8 17.9 - - + -
180C LEU* 3.8 18.5 - - + +
186C PHE* 3.7 30.5 - + - -
188C PHE* 3.7 27.1 - + - -
191C LEU* 3.8 25.1 - - + -
219C PHE* 3.0 55.4 + + - +
222C LEU* 1.3 97.7 - - + +
224C LYS* 1.3 71.5 + - - +
225C ILE* 3.4 21.5 - - + +
2003C ACT 3.4 14.4 - - - +
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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