Contacts of the helix formed by residues 216 - 226 (chain F) in PDB entry 5YUY
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 216 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212F LEU* 2.8 31.3 + - - +
213F LYS 4.5 1.6 + - - -
214F ARG 4.0 0.2 - - - -
215F PHE* 1.3 77.0 - - - +
217F LYS* 1.3 56.2 + - - -
219F GLY* 2.7 27.0 + - - -
220F ARG 3.5 3.6 + - - -
847G T 4.9 2.7 - - - -
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Residues in contact with LYS 217 (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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212F LEU* 4.8 2.7 - - - -
215F PHE 3.6 0.4 + - - -
216F GLY* 1.3 71.0 - - - -
218F PHE* 1.3 61.9 + - - +
220F ARG* 3.1 17.3 + - - +
221F ILE* 3.1 25.0 + - + +
846G C 4.7 6.5 - - - +
847G T 2.8 41.0 + - - +
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Residues in contact with PHE 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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183F GLY 3.7 20.6 - - - -
184F VAL* 4.0 20.6 - - + -
188F SER* 3.8 33.0 - - - -
192F LEU* 4.6 2.2 - - + -
215F PHE* 3.5 32.9 + + + +
216F GLY 3.1 0.2 - - - -
217F LYS* 1.3 76.9 - - - +
219F GLY* 1.3 57.1 + - - +
221F ILE* 3.2 16.8 + - + +
222F LEU* 2.9 53.2 + - + +
846G C 5.7 0.2 + - - -
847G T 4.8 1.6 + - - -
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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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208F LEU* 4.9 0.4 - - - -
211F LEU* 3.5 35.4 - - - +
212F LEU* 4.7 0.7 - - - -
215F PHE* 3.4 11.2 - - - +
216F GLY 2.7 17.8 + - - -
218F PHE* 1.3 74.9 - - - +
220F ARG* 1.3 54.9 + - - -
222F LEU* 3.5 6.8 + - - +
223F TRP* 3.0 27.9 + - - +
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Residues in contact with ARG 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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208F LEU* 3.9 34.0 - - + +
212F LEU* 3.8 36.2 - - + +
216F GLY 3.5 4.0 + - - -
217F LYS* 3.1 12.3 + - - +
219F GLY* 1.3 73.7 - - - +
221F ILE* 1.3 66.9 + - + +
223F TRP* 3.3 6.7 + - - +
224F GLU* 2.9 51.8 + - + +
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Residues in contact with ILE 221 (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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181F ILE* 5.8 2.7 - - + -
217F LYS* 3.1 22.7 + - + +
218F PHE* 3.6 20.2 - - + +
220F ARG* 1.3 87.7 - - + +
222F LEU* 1.3 58.1 + - + +
224F GLU* 3.2 10.6 + - - +
225F ARG* 2.8 68.2 + - + +
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Residues in contact with LEU 222 (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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178F LEU* 4.4 19.7 - - + -
181F ILE* 4.8 3.6 - - + -
184F VAL* 4.0 20.6 - - + -
192F LEU* 3.7 39.3 - - + -
203F VAL* 4.2 9.2 - - + -
211F LEU* 4.8 6.1 - - + -
215F PHE* 4.3 12.8 - - + -
218F PHE* 2.9 46.5 + - + +
219F GLY* 3.7 5.6 - - - +
221F ILE* 1.3 78.1 - - + +
223F TRP* 1.3 62.2 + - - +
225F ARG* 4.2 3.3 - - - +
226F SER* 2.8 32.1 + - - +
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Residues in contact with TRP 223 (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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203F VAL* 4.2 8.3 - - + -
204F GLN* 5.8 1.9 + - - +
206F CYS 4.1 12.2 + - - -
208F LEU* 3.7 60.4 - - + +
211F LEU* 3.8 16.3 - - + +
219F GLY 3.0 18.5 + - - +
220F ARG* 3.6 7.4 - - - +
222F LEU* 1.3 77.8 - - - +
224F GLU* 1.3 77.2 + - + +
226F SER* 3.5 6.4 + - - -
227F GLN* 2.9 54.8 + - - +
229F ILE* 4.3 16.6 - - + -
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Residues in contact with GLU 224 (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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220F ARG* 2.9 47.4 + - + +
221F ILE* 3.7 9.5 - - - +
223F TRP* 1.3 95.6 - - + +
225F ARG* 1.3 87.3 + - - +
227F GLN* 3.0 15.7 + - - +
229F ILE* 3.0 42.6 + - + +
230F ASP* 5.3 0.5 - - - -
231F GLU* 5.6 2.1 + - - +
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Residues in contact with ARG 225 (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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147F PHE* 3.2 50.2 - - + +
173F LEU* 3.5 4.9 - - - +
181F ILE* 4.1 27.9 - - + +
200F CYS* 4.4 1.7 - - - -
221F ILE* 2.8 54.6 + - + +
222F LEU* 4.2 2.0 - - - +
224F GLU* 1.3 96.1 + - - +
226F SER* 1.3 58.1 + - - +
228F GLY 3.0 15.6 + - - -
229F ILE 2.9 22.3 + - - -
230F ASP* 3.7 18.0 + - - +
231F GLU 5.1 0.2 - - - +
232F ARG* 3.5 34.4 - - - +
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Residues in contact with SER 226 (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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173F LEU* 3.7 3.1 - - - +
178F LEU* 3.8 16.5 - - - +
181F ILE* 4.8 1.4 - - - +
200F CYS* 3.6 28.2 - - - +
203F VAL* 3.2 28.2 - - - +
204F GLN* 2.6 37.5 + - - -
222F LEU 2.8 22.8 + - - -
223F TRP 4.0 3.4 - - - -
224F GLU 3.2 0.4 - - - -
225F ARG* 1.3 76.4 - - - +
227F GLN* 1.3 51.9 + - - +
228F GLY 3.5 0.2 - - - -
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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