Contacts of the helix formed by residues 206 - 219 (chain S) in PDB entry 5JPQ
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 206 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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204S GLY 3.3 6.0 + - - +
205S PHE* 1.3 74.4 - - - +
207S GLU* 1.3 68.4 + - + +
208S GLN* 2.8 8.0 + - + +
209S ARG* 2.8 20.4 + - + +
210S ILE* 3.4 6.6 + - - +
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Residues in contact with GLU 207 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205S PHE 3.7 2.2 + - - -
206S ASN* 1.3 72.7 - - + +
208S GLN* 1.3 62.2 + - - +
209S ARG 3.5 0.2 + - - -
210S ILE* 3.6 13.2 + - - +
211S ASN* 3.6 11.1 + - - +
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Residues in contact with GLN 208 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206S ASN* 2.8 9.9 + - + +
207S GLU* 1.3 77.7 - - + +
209S ARG* 1.3 60.0 + - - +
211S ASN* 3.4 10.1 + - - +
212S ARG* 3.3 17.5 + - - +
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Residues in contact with ARG 209 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205S PHE* 4.8 7.6 - - + -
206S ASN* 2.8 17.6 + - + +
208S GLN* 1.3 73.7 - - - +
210S ILE* 1.3 68.7 + - - +
211S ASN 3.1 1.8 - - - -
212S ARG* 2.9 18.8 + - - +
213S ILE* 2.9 14.7 + - - +
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Residues in contact with ILE 210 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197S ILE* 5.0 13.9 - - + +
200S LEU* 4.7 20.0 - - + -
201S LYS* 5.7 1.3 - - - +
205S PHE* 4.8 11.2 - - + +
206S ASN 3.4 7.0 + - - +
207S GLU* 3.8 12.3 - - - +
209S ARG* 1.3 77.6 - - - +
211S ASN* 1.3 57.0 + - - +
213S ILE* 3.4 6.8 + - - +
214S LEU* 3.0 30.1 + - - +
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Residues in contact with ASN 211 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207S GLU 3.6 7.4 + - - +
208S GLN* 3.4 12.7 + - - +
209S ARG 3.1 0.8 - - - -
210S ILE* 1.3 77.3 - - - +
212S ARG* 1.3 64.0 + - - +
214S LEU* 4.0 5.1 - - - +
215S ASP* 3.0 26.3 + - - +
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Residues in contact with ARG 212 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175S LEU* 6.5 0.9 - - + -
208S GLN 3.3 8.9 + - - +
209S ARG* 2.9 12.1 + - - +
211S ASN* 1.3 78.4 - - - +
213S ILE* 1.3 58.0 + - - +
215S ASP* 3.9 3.9 - - - +
216S ALA* 3.0 29.7 + - - +
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Residues in contact with ILE 213 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175S LEU* 5.9 7.6 - - + -
209S ARG 2.9 10.2 + - - +
210S ILE* 3.6 10.5 - - - +
212S ARG* 1.3 76.7 - - - +
214S LEU* 1.3 56.2 + - - +
216S ALA* 3.1 9.1 + - - +
217S ALA* 2.9 28.2 + - - +
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Residues in contact with LEU 214 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195S LEU* 5.8 8.7 - - + -
210S ILE 3.0 18.0 + - - +
211S ASN* 4.0 5.6 - - - +
213S ILE* 1.3 75.6 - - - +
215S ASP* 1.3 57.9 + - - +
217S ALA* 3.3 7.8 + - - +
218S LYS* 3.0 27.0 + - - +
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Residues in contact with ASP 215 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211S ASN 3.0 19.4 + - - +
212S ARG* 3.9 5.2 - - - +
214S LEU* 1.3 72.6 - - - +
216S ALA* 1.3 59.6 + - - +
218S LYS* 3.7 6.4 - - - +
219S LYS* 3.1 31.5 + - - +
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Residues in contact with ALA 216 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171S GLU* 4.3 28.5 - - + +
172S LEU* 5.6 1.6 - - - +
175S LEU* 6.1 3.1 - - + -
212S ARG 3.0 15.2 + - - +
213S ILE* 3.2 13.2 - - - +
215S ASP* 1.3 76.4 - - - +
217S ALA* 1.3 58.6 + - - +
219S LYS* 3.7 2.4 - - - +
220S SER* 3.1 28.9 + - - -
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Residues in contact with ALA 217 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169S PHE* 6.2 1.6 - - - -
192S ARG* 3.9 37.3 - - + +
193S GLY* 5.7 0.4 - - - -
195S LEU* 5.6 3.6 - - + -
213S ILE 2.9 13.6 + - - +
214S LEU* 3.6 11.0 - - - +
215S ASP 3.2 0.2 - - - -
216S ALA* 1.3 75.1 - - - +
218S LYS* 1.3 64.1 + - - +
220S SER* 3.3 17.9 - - - -
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Residues in contact with LYS 218 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214S LEU 3.0 16.5 + - - +
215S ASP* 3.7 9.0 - - - +
216S ALA 3.4 0.2 - - - -
217S ALA* 1.3 79.1 - - - +
219S LYS* 1.3 58.2 + - + +
220S SER 3.1 5.2 + - - +
30T ARG 5.4 1.3 - - - +
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Residues in contact with LYS 219 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215S ASP 3.1 16.6 + - - +
216S ALA* 3.7 2.9 - - - +
218S LYS* 1.3 75.6 - - + +
220S SER* 1.3 64.8 + - - +
221S ILE* 3.5 3.5 + - - +
30T ARG* 4.6 23.6 - - + +
116T PHE* 5.6 9.7 - - + +
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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