Contacts of the helix formed by residues 209 - 219 (chain C) in PDB entry 3P9K
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 GLY 209 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206C GLY 3.2 5.6 + - - -
207C GLY 3.0 4.9 - - - -
208C VAL* 1.3 79.3 - - - +
210C ALA* 1.3 65.9 + - - +
211C THR 3.2 3.3 + - - -
212C VAL* 3.3 7.9 - - - +
213C ALA* 3.1 23.7 + - - +
226C ASN* 3.5 27.8 - - - -
239C PHE* 3.7 8.2 - - - -
244C HIS* 4.4 1.1 - - - -
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Residues in contact with ALA 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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178C LYS* 3.7 34.1 - - + +
181C SER* 5.3 2.2 - - - -
182C ILE* 4.1 21.7 - - + +
206C GLY 4.7 0.8 + - - -
208C VAL* 3.5 8.2 + - + +
209C GLY* 1.3 77.4 - - - +
211C THR* 1.3 57.3 + - - +
213C ALA* 3.6 6.4 - - - +
214C ALA* 3.1 29.3 + - - +
239C PHE* 4.1 10.0 - - + -
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Residues in contact with THR 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C SER* 3.3 28.9 + - - -
182C ILE* 6.5 0.2 - - - +
185C THR* 3.6 20.3 + - - +
188C LEU* 5.8 1.6 - - + -
203C ASP* 3.4 20.6 - - - +
206C GLY 5.3 5.4 + - - -
209C GLY* 3.2 1.4 - - - -
210C ALA* 1.3 74.8 - - - +
212C VAL* 1.3 66.6 + - - +
214C ALA* 3.2 5.4 + - - +
215C ILE* 3.1 27.3 + - + +
260C LEU* 3.6 18.8 - - + -
262C LYS* 4.6 11.6 - - + +
403C SAH 4.4 6.4 + - - -
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Residues in contact with VAL 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C LEU* 4.0 16.8 - - + +
203C ASP* 3.7 18.5 + - + -
209C GLY* 3.3 14.3 - - - +
211C THR* 1.3 79.4 - - - +
213C ALA* 1.3 60.8 + - - +
215C ILE* 3.3 8.5 + - - +
216C ALA* 2.8 28.9 + - - +
224C GLY* 3.7 28.3 - - - -
225C VAL 3.8 13.0 - - - +
226C ASN* 3.9 17.0 - - + +
242C VAL* 3.7 23.3 - - + -
260C LEU* 5.5 0.4 - - - -
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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 GLY 3.1 15.4 + - - +
210C ALA* 3.6 6.1 - - - +
211C THR 3.1 0.2 - - - -
212C VAL* 1.3 79.2 - - - +
214C ALA* 1.3 59.6 + - - +
216C ALA* 3.2 2.6 + - - +
217C ALA* 2.9 29.1 + - - +
239C PHE* 3.5 38.4 - - + -
240C PRO* 4.8 3.0 - - + +
242C VAL* 3.5 12.1 - - + -
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Residues in contact with ALA 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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182C ILE* 6.2 4.0 - - + -
185C THR* 4.0 19.5 - - + -
189C LEU* 3.8 7.4 - - + +
210C ALA 3.1 17.9 + - - +
211C THR 3.2 4.5 + - - +
213C ALA* 1.3 75.5 - - - +
215C ILE* 1.3 62.9 + - - +
217C ALA* 3.3 8.6 + - - +
218C HIS* 3.1 22.5 + - - +
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Residues in contact with ILE 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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185C THR* 4.0 13.0 - - + -
188C LEU* 4.6 4.0 - - + -
189C LEU* 4.2 13.2 - - + -
195C PHE* 3.5 35.9 - - + -
201C LEU* 3.5 26.2 - - + -
211C THR* 3.1 18.4 + - + +
212C VAL* 3.6 6.7 - - - +
214C ALA* 1.3 78.3 - - - +
216C ALA* 1.3 62.6 + - - +
218C HIS* 3.1 1.7 + - - +
219C TYR* 3.1 28.3 + - + +
222C ILE* 4.0 14.5 - - + +
260C LEU* 3.8 24.9 - - + -
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Residues in contact with ALA 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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212C VAL 2.8 17.9 + - - +
213C ALA 3.6 5.4 - - - +
215C ILE* 1.3 73.8 - - - +
217C ALA* 1.3 66.5 + - - +
219C TYR 3.2 24.4 - - - +
220C PRO* 3.7 5.2 - - - +
222C ILE* 4.7 14.9 - - + +
224C GLY* 4.9 5.4 - - - +
240C PRO 4.1 17.3 - - - +
241C GLY* 4.1 16.6 - - - +
242C VAL* 4.3 3.1 - - + -
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Residues in contact with ALA 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 ALA 2.9 17.0 + - - +
214C ALA* 3.5 9.9 - - - +
215C ILE 3.2 0.2 - - - -
216C ALA* 1.3 76.9 - - - +
218C HIS* 1.3 60.5 + - - +
219C TYR 3.6 0.3 + - - -
220C PRO* 4.4 6.4 - - - +
240C PRO 5.3 1.5 + - - +
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Residues in contact with HIS 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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189C LEU* 3.7 39.6 + - + +
214C ALA 3.1 13.7 + - - +
215C ILE 3.1 8.3 + - - +
217C ALA* 1.3 79.5 - - - +
219C TYR* 1.3 95.2 + + + +
220C PRO* 3.6 6.9 - - - +
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Residues in contact with TYR 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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189C LEU* 3.8 19.1 + - + +
192C TYR 4.3 11.8 + - - -
193C HIS* 4.8 1.9 + - - -
195C PHE* 3.8 21.7 - - + +
196C GLU* 3.7 35.7 + - + +
197C GLY 5.5 1.3 - - - -
215C ILE* 3.1 17.6 + - + -
216C ALA 3.2 10.6 - - - +
217C ALA 3.4 0.2 - - - -
218C HIS* 1.3 107.2 + + + +
220C PRO* 1.3 60.7 - - - +
221C THR* 3.0 9.9 - - - +
222C ILE* 2.9 50.2 + - + +
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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