Contacts of the helix formed by residues 208 - 220 (chain F) in PDB entry 6ACQ
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 SER 208 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A GLU 4.8 0.8 + - - -
202F LEU* 4.1 6.1 - - - -
207F ALA* 1.3 74.8 - - - +
209F VAL* 1.3 59.6 + - - +
210F GLU* 3.7 19.8 + - - -
211F ASP* 3.3 27.3 + - - +
212F ILE* 2.8 30.6 + - - +
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Residues in contact with VAL 209 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202F LEU* 3.8 26.3 - - + +
208F SER* 1.3 75.1 - - - +
210F GLU* 1.3 77.7 + - + +
212F ILE* 3.2 2.9 + - - +
213F ASP* 3.0 26.5 + - - +
227F LEU* 3.7 21.1 - - + -
263F TYR* 5.8 1.1 - - - +
277F PHE* 4.2 22.7 - - + +
278F TYR* 3.5 36.8 - - + -
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Residues in contact with GLU 210 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F SER* 3.8 15.6 + - - +
209F VAL* 1.3 100.8 + - + +
211F ASP* 1.3 63.5 + - - +
213F ASP* 3.6 1.4 + - - +
214F LYS* 2.9 28.8 + - - +
278F TYR* 4.2 15.0 - - + -
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Residues in contact with ASP 211 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A PRO 4.6 2.8 - - - +
177A VAL* 3.3 27.3 - - + +
178A GLU* 2.9 30.4 + - - +
186A VAL* 5.5 0.7 - - - -
207F ALA* 4.5 7.9 - - + -
208F SER* 3.2 24.8 + - - +
209F VAL 3.2 0.6 - - - -
210F GLU* 1.3 84.0 - - - +
212F ILE* 1.3 65.0 + - - +
214F LYS* 3.8 9.8 + - - +
215F ALA* 2.9 27.0 + - - +
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Residues in contact with ILE 212 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 4.0 17.2 - - + +
190A ILE* 4.4 2.9 - - + -
198F ALA* 3.7 33.4 - - + +
201F ILE* 3.8 13.0 - - + -
202F LEU* 3.7 35.0 - - + +
207F ALA* 3.6 19.3 - - + +
208F SER 2.8 22.5 + - - +
209F VAL 3.6 4.0 - - - +
211F ASP* 1.3 79.5 - - - +
213F ASP* 1.3 70.6 + - - +
215F ALA* 3.4 2.4 + - - +
216F MET* 3.2 22.9 + - - +
226F PRO* 4.2 4.9 - - + -
227F LEU* 4.0 9.6 - - + -
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Residues in contact with ASP 213 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209F VAL 3.0 11.2 + - - +
210F GLU 4.1 1.8 - - - +
212F ILE* 1.3 75.9 - - - +
214F LYS* 1.3 65.2 + - - +
216F MET* 3.3 1.0 + - - -
217F LYS* 3.1 32.2 + - - +
225F GLY* 3.5 20.4 - - - -
226F PRO* 3.0 10.8 - - - +
227F LEU* 3.0 26.6 + - - +
228F GLU* 3.0 27.9 + - - +
278F TYR* 2.6 32.1 + - - +
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Residues in contact with LYS 214 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 4.9 0.2 - - + -
175A ASP* 2.9 40.9 + - - +
176A PRO 4.4 12.5 + - - -
177A VAL* 4.1 11.9 - - + -
210F GLU 2.9 20.4 + - - +
211F ASP* 3.8 13.3 + - - +
212F ILE 3.4 0.2 - - - -
213F ASP* 1.3 77.3 - - - +
215F ALA* 1.3 57.5 + - - +
217F LYS* 3.3 9.4 + - - +
218F LEU* 2.9 45.0 + - + +
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Residues in contact with ALA 215 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 3.7 20.6 - - + +
150A GLU* 4.6 0.7 - - - +
177A VAL* 4.4 9.0 - - + -
186A VAL* 4.0 15.9 - - + -
187A VAL* 3.6 21.5 - - + +
211F ASP 2.9 18.3 + - - +
212F ILE 3.8 3.6 - - - +
214F LYS* 1.3 78.5 - - - +
216F MET* 1.3 54.4 + - - +
219F GLY* 2.6 34.5 + - - -
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Residues in contact with MET 216 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A VAL* 4.4 2.2 - - - -
187A VAL* 3.9 28.9 - - - +
190A ILE* 3.7 39.5 - - + -
191A LEU* 4.4 7.6 - - + -
194F MET* 5.8 0.7 - - + -
212F ILE 3.2 11.4 + - - +
213F ASP 3.3 1.7 + - - +
215F ALA* 1.3 75.3 - - - +
217F LYS* 1.3 61.2 + - - +
220F ALA* 3.0 49.9 + - + +
222F HIS* 3.4 27.7 + - + +
225F GLY* 4.5 2.0 - - - -
226F PRO* 3.5 38.1 - - + -
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Residues in contact with LYS 217 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213F ASP* 3.1 26.2 + - - +
214F LYS* 3.7 8.3 - - - +
216F MET* 1.3 77.1 - - - +
218F LEU* 1.3 64.1 + - + +
221F ASN* 3.0 28.4 - - - +
222F HIS 3.2 19.7 + - - +
223F PRO 4.0 15.9 + - - +
224F MET* 3.9 0.9 - - - -
225F GLY 3.7 15.9 - - - +
228F GLU* 3.8 25.3 + - - -
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Residues in contact with LEU 218 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A MET* 3.5 19.2 - - - +
147A LYS* 4.9 12.9 + - + -
148A LEU* 3.7 27.6 + - + +
175A ASP* 3.9 28.9 - - + +
214F LYS* 2.9 38.4 + - + +
217F LYS* 1.3 80.6 - - + +
219F GLY* 1.3 63.3 + - - +
220F ALA 3.5 0.2 - - - -
221F ASN* 4.1 3.5 + - - +
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Residues in contact with GLY 219 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PHE* 4.5 13.7 - - - -
146A MET* 4.3 12.3 - - - +
148A LEU* 3.7 16.3 - - - +
187A VAL* 4.3 13.2 - - - +
191A LEU* 5.4 1.6 - - - +
215F ALA 2.6 24.0 + - - -
218F LEU* 1.3 77.1 - - - +
220F ALA* 1.3 56.9 + - - +
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Residues in contact with ALA 220 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A VAL* 5.0 0.4 - - + -
191A LEU* 3.9 20.9 - - + -
223A PRO* 4.3 5.2 - - - +
229A LEU* 6.1 1.1 - - + +
215F ALA 3.9 0.2 + - - -
216F MET* 3.0 32.3 + - + +
219F GLY* 1.3 76.4 - - - +
221F ASN* 1.3 73.4 + - - +
222F HIS* 3.3 25.7 + - - +
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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