Contacts of the helix formed by residues 205 - 215 (chain C) in PDB entry 4KEU
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 205 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203C THR* 3.0 19.1 + - + +
204C ASP* 1.4 78.1 + - - +
206C ILE* 1.3 63.6 + - - +
207C ASP* 3.1 22.6 + - - +
208C TYR* 3.3 29.1 + - + +
209C ILE* 3.5 16.3 + - - +
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Residues in contact with ILE 206 (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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204C ASP 2.7 11.4 + - - +
205C ASN* 1.3 72.1 + - - +
207C ASP* 1.3 73.1 + - - +
209C ILE* 3.5 4.9 + - + +
210C LYS* 3.0 52.6 + - - +
238C THR* 3.3 27.4 - - + +
241C ARG* 4.2 32.5 - - + +
242C LEU* 3.0 42.0 - - + -
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Residues in contact with ASP 207 (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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205C ASN* 3.1 11.0 + - - +
206C ILE* 1.3 87.9 - - - +
208C TYR* 1.3 66.2 + - - +
210C LYS* 3.3 11.1 + - - +
211C LYS* 3.0 23.7 + - - +
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Residues in contact with TYR 208 (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 ASN 4.8 0.9 + - - -
173C ALA* 3.8 26.2 - - - -
176C ASN* 3.3 39.6 + - - -
178C GLY* 3.4 8.0 + - - -
179C LEU* 3.0 44.2 + - + -
200C LEU* 3.6 26.7 - - + -
203C THR* 4.9 7.2 - - + -
205C ASN* 3.3 28.4 + - + +
207C ASP* 1.3 79.7 - - - +
209C ILE* 1.3 65.0 + - - +
211C LYS* 3.1 23.9 + - + +
212C ILE* 3.3 20.1 + - + +
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Residues in contact with ILE 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* 3.4 41.7 - - + +
203C THR* 3.8 21.3 - - + +
205C ASN 3.5 15.7 + - - +
206C ILE* 3.8 6.3 - - - +
207C ASP 3.3 0.4 - - - -
208C TYR* 1.3 78.2 - - + +
210C LYS* 1.3 64.5 + - - +
212C ILE* 3.2 14.0 + - - +
213C ALA* 3.2 10.0 + - - +
219C ILE* 3.5 37.5 - - + +
221C LEU* 4.6 3.6 - - + -
238C THR* 3.8 22.2 - - + -
242C LEU* 3.9 15.0 - - + -
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Residues in contact with LYS 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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206C ILE* 3.0 41.7 + - + +
207C ASP* 3.7 9.6 + - - +
208C TYR 3.3 0.2 - - - -
209C ILE* 1.3 73.8 - - - +
211C LYS* 1.3 61.3 + - - +
213C ALA* 3.3 3.5 + - - +
214C ASP* 2.8 39.0 + - - +
241C ARG* 3.9 12.5 - - - +
242C LEU* 3.9 12.1 - - + -
245C ASP* 2.6 33.6 + - - +
247C TYR* 3.7 43.0 - - + +
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Residues in contact with LYS 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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176C ASN* 6.1 0.2 - - - +
179C LEU* 3.9 38.0 - - + +
207C ASP 3.0 13.1 + - - +
208C TYR* 3.1 19.2 + - + +
210C LYS* 1.3 76.9 - - - +
212C ILE* 1.3 62.5 + - - +
214C ASP* 3.3 10.2 + - + +
215C LYS* 3.0 40.6 + - - +
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Residues in contact with ILE 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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179C LEU* 4.1 28.3 - - + +
182C GLN* 2.9 41.5 + - - +
197C ILE* 3.7 28.9 - - + -
200C LEU* 3.6 32.8 - - + -
208C TYR* 3.3 32.3 + - + +
209C ILE 3.2 7.5 + - - +
211C LYS* 1.3 77.6 - - - +
213C ALA* 1.3 61.8 + - - +
215C LYS 3.2 5.7 + - - -
216C GLY 3.5 1.9 + - - -
217C SER* 3.6 5.2 + - - -
219C ILE* 4.1 10.8 - - + -
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Residues in contact with ALA 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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209C ILE 3.2 7.4 + - - +
210C LYS 3.8 3.4 - - - +
212C ILE* 1.3 76.0 - - - +
214C ASP* 1.3 57.8 + - - +
216C GLY* 2.8 19.8 + - - -
217C SER 3.5 11.7 - - - -
219C ILE* 4.0 15.0 - - + +
247C TYR* 3.6 29.8 - - + -
250C LYS* 3.1 38.2 + - + -
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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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210C LYS* 2.8 32.0 + - - +
211C LYS* 3.5 9.2 - - + +
213C ALA* 1.3 73.2 - - - +
215C LYS* 1.4 59.1 + - + +
216C GLY* 3.2 5.0 + - - -
247C TYR* 2.9 30.6 + - - -
250C LYS* 5.3 0.7 + - - +
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Residues in contact with LYS 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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179C LEU* 4.8 8.1 - - + -
182C GLN* 3.2 34.0 - - + +
186C THR* 5.5 0.9 - - + +
192C PRO* 3.4 21.3 - - - +
211C LYS* 3.0 33.2 + - + +
212C ILE 3.2 1.1 + - - +
214C ASP* 1.4 75.1 - - + +
216C GLY* 1.3 57.0 + - - +
217C SER 3.7 1.1 - - - -
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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