Contacts of the helix formed by residues 208 - 215 (chain C) in PDB entry 3JXI
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 ASN 208 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165C ARG* 3.5 26.9 + - - +
166C LEU* 4.1 2.6 - - - +
167C THR* 3.1 41.7 + - - +
203C ALA* 2.9 14.8 + - - +
204C GLU 4.2 0.8 + - - -
206C THR* 3.4 15.5 - - + +
207C GLY* 1.3 76.7 - - - +
209C MET* 1.3 67.9 + - - +
210C ARG 3.4 1.7 + - - -
211C GLU* 3.2 25.0 + - - +
212C PHE* 3.0 23.7 + - - +
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Residues in contact with MET 209 (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 LEU* 2.8 43.1 - - + +
203C ALA* 3.3 12.3 + - + -
204C GLU* 3.5 39.2 - - + +
208C ASN* 1.3 76.7 - - - +
210C ARG* 1.3 54.8 + - + +
212C PHE* 3.3 2.8 + - - +
213C ILE* 2.8 50.6 + - + +
246C LYS* 3.0 65.3 - - + +
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Residues in contact with ARG 210 (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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208C ASN 3.5 0.2 - - - -
209C MET* 1.3 74.5 - - + +
211C GLU* 1.3 65.9 + - - +
213C ILE* 3.4 6.0 + - - +
214C ASN* 3.0 34.1 + - - +
246C LYS 3.6 18.4 - - - +
247C GLY* 4.0 23.3 - - - +
296C LYS* 5.5 3.6 - - - +
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Residues in contact with GLU 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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165C ARG* 5.1 4.0 + - - -
167C THR* 4.0 15.3 + - + -
208C ASN* 3.2 27.1 + - - +
209C MET 3.4 0.2 - - - -
210C ARG* 1.3 77.1 - - - +
212C PHE* 1.3 57.4 + - - +
214C ASN* 3.5 2.9 - - - +
215C SER* 2.8 33.3 + - - -
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Residues in contact with PHE 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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166C LEU* 3.6 26.9 - - + -
167C THR* 3.3 23.2 - - + +
179C THR* 3.4 28.0 + - - -
180C CYS* 3.8 18.6 - - - -
181C LEU* 3.5 30.5 - - + +
182C PRO* 5.8 0.7 - - - +
199C LEU* 4.1 22.2 - - + -
200C LEU* 4.1 20.2 - - + -
203C ALA* 3.6 18.6 - - + -
208C ASN* 3.0 22.1 + - - +
209C MET 3.4 3.4 - - - +
211C GLU* 1.3 74.4 - - - +
213C ILE* 1.3 67.1 + - - +
214C ASN 3.3 0.3 + - - -
215C SER* 3.4 12.4 + - - +
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Residues in contact with ILE 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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181C LEU* 3.9 7.2 - - - -
200C LEU* 3.8 27.6 - - + -
209C MET* 2.8 27.9 + - + +
210C ARG* 3.9 5.8 - - - +
212C PHE* 1.3 74.3 - - + +
214C ASN* 1.3 60.1 + - - +
215C SER 3.7 1.6 + - - +
226C THR* 4.5 1.7 - - - -
227C ALA* 3.7 25.2 + - + +
228C LEU* 5.1 0.8 + - + +
243C LEU* 3.9 21.5 - - + +
246C LYS* 3.7 44.6 - - + +
248C ALA* 3.5 35.0 - - + +
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Residues in contact with ASN 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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210C ARG* 3.0 25.0 + - - +
211C GLU* 3.5 3.4 - - - +
213C ILE* 1.3 80.3 - - - +
215C SER* 1.3 65.1 + - - +
216C PRO* 3.2 7.4 - - - +
226C THR* 3.7 20.8 + - + +
228C LEU* 6.0 0.5 - - - +
247C GLY 3.1 23.2 + - - -
248C ALA* 3.4 6.9 - - - +
249C ASP* 2.8 40.1 + - + +
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Residues in contact with SER 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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167C THR* 4.6 6.5 - - - -
172C ARG* 4.7 5.4 - - - -
177C GLY 4.3 5.0 + - - -
178C LYS* 6.2 0.2 - - - -
179C THR* 3.5 26.6 + - - +
182C PRO* 5.3 4.2 - - - +
211C GLU* 2.8 17.1 + - - -
212C PHE* 3.4 12.8 + - - +
213C ILE 3.4 1.8 - - - +
214C ASN* 1.3 76.3 - - - +
216C PRO* 1.4 74.5 + - - +
217C PHE* 3.9 4.9 + - - -
225C GLN 3.9 4.7 - - - +
226C THR* 4.4 6.1 - - - -
227C ALA 5.0 1.0 + - - -
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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