Contacts of the helix formed by residues 5267 - 5288 (chain c) in PDB entry 3A0B
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 SER5267 (chain c).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5151c TRP* 4.3 0.7 - - - -
5265c ILE* 2.5 31.8 + - - +
5266c TRP* 1.3 80.2 - - - +
5268c GLY* 1.3 71.6 + - - +
5269c GLU* 3.3 13.7 + - - +
5270c ALA* 3.8 10.1 + - - -
5271c TYR* 2.9 21.9 + - - -
5448c ALA* 4.4 5.8 - - - +
5451c ALA* 4.5 13.4 - - - +
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Residues in contact with GLY5268 (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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5151c TRP* 3.2 46.3 - - - +
5267c SER* 1.3 79.2 + - - +
5269c GLU* 1.3 60.5 + - - -
5271c TYR* 3.1 16.6 + - - +
6033c CLA 3.0 20.1 - - - +
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Residues in contact with GLU5269 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5151c TRP* 5.3 0.4 - - - -
5267c SER* 3.3 7.9 + - - +
5268c GLY* 1.3 73.2 - - - +
5270c ALA* 1.3 57.9 + - - +
5272c LEU* 2.7 35.1 + - + +
5273c SER* 3.3 3.5 + - - -
5444c HIS* 2.4 46.6 + - + +
5447c ARG* 2.8 55.2 + - - +
5448c ALA* 3.7 9.6 - - + -
5451c ALA* 5.6 1.9 - - - +
6032c CLA 4.5 5.3 - - + +
6033c CLA 3.9 10.8 - - - +
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Residues in contact with ALA5270 (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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5265c ILE* 2.6 33.0 - - + +
5267c SER* 3.8 8.2 + - - +
5268c GLY 3.3 0.2 - - - -
5269c GLU* 1.3 78.2 - - - +
5271c TYR* 1.3 53.5 + - - +
5273c SER* 2.3 35.1 + - - -
5274c TYR* 2.6 28.5 - - + +
5448c ALA* 3.5 22.5 - - + +
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Residues in contact with TYR5271 (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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5151c TRP* 3.4 46.9 + + + +
5153c ASP 5.1 0.7 + - - -
5154c LYS* 5.5 0.9 - - - -
5157c MET* 4.0 15.2 - - + +
5265c ILE 4.4 1.8 - - - -
5266c TRP* 2.6 64.2 + - - +
5267c SER 2.9 10.3 - - - -
5268c GLY 3.1 6.0 + - - +
5269c GLU 3.1 0.6 - - - -
5270c ALA* 1.3 78.4 - - - +
5272c LEU* 1.3 62.8 + - - +
5274c TYR* 4.2 5.5 - + - +
5275c SER* 3.1 21.0 + - - +
6031c CLA 3.4 50.5 + + + +
6033c CLA 3.0 22.3 - - + +
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Residues in contact with LEU5272 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5268c GLY 3.6 1.0 + - - -
5269c GLU* 2.7 18.9 + - + +
5271c TYR* 1.3 74.2 - - - +
5273c SER* 1.3 50.2 + - - +
5275c SER* 3.8 1.0 - - - -
5276c LEU* 2.6 54.6 + - + +
5444c HIS* 3.5 32.1 - - + +
6032c CLA 3.4 54.5 - - + -
6033c CLA 3.3 50.0 - - + +
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Residues in contact with SER5273 (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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5269c GLU 3.3 1.2 + - - -
5270c ALA* 2.3 28.8 + - - -
5272c LEU* 1.3 76.5 - - - +
5274c TYR* 1.3 80.7 + - - +
5275c SER 3.2 1.3 - - - -
5276c LEU* 2.9 19.2 + - - -
5277c GLY* 3.0 15.3 + - - +
5441c HIS* 4.0 9.4 + - - +
5444c HIS* 3.8 9.6 - - - -
5445c ALA* 3.3 39.2 - - - +
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Residues in contact with TYR5274 (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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5264c PHE* 3.4 32.5 - + + -
5265c ILE* 2.3 53.4 + - - +
5270c ALA* 2.6 36.7 + - + +
5271c TYR* 4.2 6.7 - + - +
5273c SER* 1.3 83.1 - - - +
5275c SER* 1.3 60.6 - - - +
5277c GLY 5.1 0.3 - - - -
5278c ALA* 4.2 5.4 + - - +
5441c HIS* 5.6 2.2 - - - -
5445c ALA* 5.1 1.1 - - + -
6029c CLA 3.4 36.8 + + + +
6031c CLA 3.0 75.6 - + + +
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Residues in contact with SER5275 (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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5271c TYR* 3.1 16.9 + - - +
5272c LEU 3.8 0.7 - - - -
5274c TYR* 1.3 76.7 - - - +
5276c LEU* 1.3 58.8 + - - +
5278c ALA* 3.9 10.9 - - - +
5279c LEU* 4.5 4.0 + - - +
6031c CLA 2.9 48.9 + - - +
6033c CLA 3.0 52.6 + - - +
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Residues in contact with LEU5276 (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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5272c LEU* 2.6 44.2 + - + +
5273c SER* 2.9 8.0 + - - +
5275c SER* 1.3 74.5 - - - +
5277c GLY* 1.3 57.1 + - - +
5278c ALA 2.5 18.4 + - - -
5279c LEU* 2.7 26.0 + - - +
5280c SER 3.7 1.2 + - - -
5437c PHE* 3.2 40.8 - - + +
5440c GLY* 3.8 18.6 - - - +
5441c HIS* 3.6 6.7 - - - +
5444c HIS* 4.2 4.9 - - + -
6032c CLA 4.1 26.7 - - + -
6033c CLA 4.6 3.8 - - - +
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Residues in contact with GLY5277 (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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5273c SER 3.0 11.3 + - - -
5274c TYR 5.1 0.2 - - - -
5276c LEU* 1.3 84.2 - - - +
5278c ALA* 1.3 59.4 + - - +
5279c LEU 3.5 0.2 - - - -
5280c SER* 3.9 12.4 - - - -
5281c MET* 3.9 10.9 + - - +
5438c LEU* 4.8 1.5 - - - +
5441c HIS* 3.6 26.2 - - - +
6029c CLA 3.7 25.2 - - - +
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Residues in contact with ALA5278 (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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5274c TYR 4.2 2.4 + - - +
5275c SER 3.9 13.9 - - - +
5276c LEU 2.5 5.9 + - - +
5277c GLY* 1.3 73.8 - - - +
5279c LEU* 1.3 59.7 + - - +
5281c MET* 2.8 27.8 + - - +
5282c MET* 3.1 21.7 + - + +
6025c CLA 3.5 31.2 - - + -
6029c CLA 4.4 3.8 - - - -
6031c CLA 4.1 18.4 - - + +
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Residues in contact with LEU5279 (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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5275c SER 4.6 8.5 - - - +
5276c LEU* 2.7 7.9 + - - +
5278c ALA* 1.3 77.0 - - - +
5280c SER* 1.3 55.1 + - - +
5282c MET* 2.9 13.5 + - + +
5283c GLY 2.5 34.1 + - - -
5437c PHE* 3.1 37.5 - - + -
6026c CLA 3.3 48.6 - - + +
6031c CLA 4.8 7.2 - - - +
6033c CLA 4.4 26.7 - - + +
6034c CLA 4.2 19.3 - - + -
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Residues in contact with SER5280 (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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5276c LEU 3.7 3.0 + - - -
5277c GLY 3.9 12.1 - - - -
5278c ALA 3.2 0.6 - - - -
5279c LEU* 1.3 77.0 - - - +
5281c MET* 1.3 62.4 + - - +
5283c GLY 3.4 0.2 + - - -
5284c PHE* 2.8 37.9 + - - -
5434c ALA* 2.3 34.0 + - - +
5437c PHE* 3.6 9.4 - - - -
5438c LEU* 2.9 42.9 - - - +
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Residues in contact with MET5281 (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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5223c TRP* 5.8 5.4 - - + -
5277c GLY 3.9 6.1 + - - +
5278c ALA* 2.8 16.4 + - - +
5280c SER* 1.3 80.8 - - - +
5282c MET* 1.3 52.0 + - + +
5284c PHE* 3.5 8.9 + - - +
5285c ILE* 2.7 41.5 + - + +
5438c LEU* 5.9 0.4 - - - +
6025c CLA 3.9 30.1 - - + -
6029c CLA 4.7 15.2 - - + +
6030c CLA 3.6 46.9 - - + -
6054c BCR 4.7 8.7 - - - -
6055c DGD 5.4 0.5 - - - +
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Residues in contact with MET5282 (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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5278c ALA* 3.4 35.0 - - + +
5279c LEU* 2.9 14.9 + - + +
5281c MET* 1.3 75.6 - - + +
5283c GLY* 1.3 49.8 + - - +
5284c PHE 2.9 5.2 - - - -
5285c ILE* 3.0 8.5 - - - +
5286c ALA* 2.7 38.3 + - - +
6025c CLA 3.1 56.1 - - + -
6026c CLA 3.1 33.4 - - + +
6031c CLA 3.9 33.0 - - + +
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Residues in contact with GLY5283 (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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5279c LEU 2.5 15.2 + - - -
5282c MET* 1.3 73.2 - - - +
5284c PHE* 1.3 57.5 + - - +
5286c ALA* 3.8 5.4 - - - -
5287c THR* 2.9 28.9 + - - -
5430c HIS* 3.5 6.5 - - - +
5434c ALA* 3.2 14.3 - - - +
6026c CLA 3.2 32.3 - - - +
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Residues in contact with PHE5284 (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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5280c SER* 2.8 37.3 + - - -
5281c MET* 3.5 9.6 - - - +
5283c GLY* 1.3 76.6 - - - +
5285c ILE* 1.3 55.7 + - - +
5286c ALA 2.7 14.4 + - - -
5287c THR* 3.0 15.2 + - + +
5288c CYS* 3.1 14.6 + - - +
5431c PHE* 3.3 50.3 - + - -
5434c ALA* 3.6 8.1 - - + -
5435c PHE* 3.9 19.5 - + + -
5438c LEU* 4.8 9.4 - - + -
6055c DGD 3.5 56.3 - - + +
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Residues in contact with ILE5285 (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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5223c TRP* 4.8 7.9 - - + -
5224c ILE* 3.2 37.0 - - + -
5225c VAL* 4.3 2.3 - - + +
5281c MET* 2.7 31.7 + - + +
5282c MET* 3.0 20.2 - - - -
5284c PHE* 1.3 72.0 - - - +
5286c ALA* 1.3 57.7 + - - +
5288c CYS* 4.2 1.6 - - - -
5289c PHE* 2.8 42.0 + - + +
6025c CLA 3.3 35.7 - - + -
6055c DGD 3.9 25.5 - - + +
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Residues in contact with ALA5286 (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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5282c MET 2.7 19.5 + - - +
5283c GLY 3.7 5.2 - - - +
5284c PHE 2.7 0.8 + - - -
5285c ILE* 1.3 77.5 - - - +
5287c THR* 1.3 54.1 + - - +
5288c CYS 2.6 4.1 + - - -
5289c PHE* 2.4 34.2 + - - +
5290c VAL* 3.2 6.9 + - - +
5430c HIS* 4.0 11.2 - - + -
6025c CLA 4.2 10.8 - - - +
6026c CLA 3.3 33.3 - - + +
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Residues in contact with THR5287 (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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5295a PHE* 3.4 28.4 - - + -
5283c GLY 2.9 10.6 + - - -
5284c PHE* 3.0 9.1 + - + +
5286c ALA* 1.3 77.0 - - - +
5288c CYS* 1.3 59.7 + - - +
5290c VAL* 3.6 14.3 - - - +
5291c TRP* 3.5 17.3 - - - +
5427c ALA* 3.2 19.5 + - - +
5430c HIS* 2.9 30.6 - - - +
5431c PHE* 3.0 17.7 + - + -
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Residues in contact with CYS5288 (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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5163a ILE* 3.8 21.5 - - - -
5295a PHE* 5.7 4.9 - - - -
5225c VAL* 3.5 10.9 - - + +
5284c PHE 3.1 8.4 + - - +
5285c ILE 4.7 0.7 - - - +
5286c ALA 2.6 5.5 + - - -
5287c THR* 1.3 80.0 - - - +
5289c PHE* 1.3 57.6 + - - +
5291c TRP* 3.8 4.7 - - - -
5292c PHE* 3.0 39.1 + - + -
6055c DGD 2.8 59.2 - - + -
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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
------------------------------------------------------------
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