Contacts of the helix formed by residues 222 - 237 (chain q) in PDB entry 5K0Y
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 GLU 222 (chain q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217q MET 3.5 2.3 + - - +
218q LYS* 3.4 26.0 - - - +
219q GLU* 4.7 3.8 - - - +
220q ALA 3.3 0.2 - - - -
221q LYS* 1.4 75.4 - - - +
223q LYS* 1.4 60.9 + - - +
224q ARG 3.2 1.1 + - - -
225q GLN* 3.2 33.3 + - + +
226q GLU* 4.1 10.1 + - + +
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Residues in contact with LYS 223 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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755A C 5.3 6.5 + - - -
219q GLU 4.7 3.9 + - - +
220q ALA 3.2 18.7 + - - +
221q LYS 3.1 0.4 - - - +
222q GLU* 1.4 77.0 - - - +
224q ARG* 1.4 59.3 + - - +
226q GLU* 3.2 40.8 + - - +
227q GLN* 3.2 43.0 + - + +
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Residues in contact with ARG 224 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A A 5.8 1.1 - - - +
276A U 3.7 20.8 + - - -
277A U 3.6 54.7 + - - -
221q LYS* 3.3 43.3 + - + +
223q LYS* 1.4 75.1 - - - +
225q GLN* 1.4 92.0 + - - +
227q GLN* 3.3 9.3 + - + +
228q ILE* 3.0 33.3 + - + +
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Residues in contact with GLN 225 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A C 4.6 9.3 + - - +
276A U 3.3 29.8 + - - +
221q LYS 4.2 2.1 - - - +
222q GLU* 3.2 39.8 + - + +
224q ARG* 1.4 105.0 + - - +
226q GLU* 1.4 63.1 + - + +
228q ILE* 3.4 1.7 + - - +
229q ALA* 3.0 27.2 + - - +
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Residues in contact with GLU 226 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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774A U 3.3 38.7 - - + +
222q GLU* 4.2 9.4 - - + +
223q LYS* 3.2 46.8 + - - +
225q GLN* 1.4 77.0 - - + +
227q GLN* 1.4 63.0 + - - +
229q ALA* 3.8 3.4 - - - +
230q LYS* 3.1 31.2 + - + +
233q ARG* 4.7 2.9 + - - -
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Residues in contact with GLN 227 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223q LYS* 3.2 45.3 + - + +
224q ARG* 3.7 10.5 - - + +
225q GLN 3.3 0.4 - - - -
226q GLU* 1.4 78.5 + - - +
228q ILE* 1.4 63.5 + - + +
230q LYS* 3.3 43.1 + - - +
231q ARG* 3.4 11.4 + - - +
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Residues in contact with ILE 228 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A U 3.4 49.4 - - + +
277A U 3.8 19.3 - - - +
224q ARG* 3.0 34.5 + - + +
225q GLN 3.9 3.6 - - - +
227q GLN* 1.4 74.1 - - + +
229q ALA* 1.4 61.8 + - - +
231q ARG* 3.4 49.2 + - - +
232q ARG* 3.8 4.0 - - - +
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Residues in contact with ALA 229 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
774A U 3.2 27.6 - - - +
225q GLN 3.0 18.4 + - - +
226q GLU* 3.8 3.4 - - - +
228q ILE* 1.4 77.0 - - - +
230q LYS* 1.4 61.2 + - - +
232q ARG* 3.4 24.6 + - - +
233q ARG* 3.3 23.8 + - - +
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Residues in contact with LYS 230 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753A C 4.4 4.3 + - - +
754A C 3.7 40.3 + - - +
782A G 5.4 0.8 - - - +
783A G 3.3 29.2 + - - +
226q GLU* 3.1 19.4 + - + +
227q GLN* 3.3 44.2 + - - +
229q ALA* 1.4 71.6 - - - +
231q ARG* 1.4 60.6 + - - +
232q ARG 3.1 5.4 - - - -
233q ARG* 3.1 28.3 + - - +
234q LEU* 3.1 24.0 + - - +
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Residues in contact with ARG 231 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A A 3.2 56.9 + - - +
227A A 3.1 20.1 + - - -
276A U 4.4 7.9 + - - -
884A U 3.2 12.3 + - - -
885A U 3.8 12.3 + - - -
227q GLN 3.4 12.1 + - - +
228q ILE* 3.4 40.1 + - - +
229q ALA 3.4 0.2 - - - -
230q LYS* 1.4 75.6 - - - +
232q ARG* 1.4 82.4 + - - +
234q LEU* 3.9 13.9 - - + +
235q SER* 3.4 22.0 + - - -
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Residues in contact with ARG 232 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A A 3.5 15.7 + - - +
228A A 3.2 28.5 + - - -
274A G 4.9 9.1 + - - -
276A U 4.4 3.2 + - - -
885A U 3.3 34.4 + - - -
886A U 4.8 3.4 + - - -
228q ILE* 3.8 8.7 - - - +
229q ALA* 3.6 12.1 - - - +
230q LYS 3.1 0.8 - - - -
231q ARG* 1.4 109.2 - - - +
233q ARG* 1.4 62.5 + - + +
234q LEU 3.3 0.2 - - - -
235q SER* 3.0 18.7 + - - -
236q SER* 3.0 17.2 + - - -
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Residues in contact with ARG 233 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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753A C 4.5 10.8 - - - +
754A C 3.3 46.5 + - - +
774A U 3.1 51.7 + - - -
775A G 3.2 36.2 + - - +
226q GLU 4.7 1.0 + - - -
229q ALA* 3.3 31.5 + - - +
230q LYS* 3.4 23.7 - - - +
232q ARG* 1.4 76.0 - - + +
234q LEU* 1.4 59.5 + - - +
236q SER* 3.4 22.0 - - - -
237q LEU* 4.3 5.4 + - - +
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Residues in contact with LEU 234 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752A C 5.2 1.6 - - - +
753A C 3.8 26.7 + - - +
784A G 3.5 30.1 - - - +
785A G 6.4 1.1 - - - -
230q LYS 3.1 15.5 + - - +
231q ARG* 3.9 12.3 - - + +
233q ARG* 1.4 77.2 - - - +
235q SER* 1.4 57.9 + - - +
236q SER 3.4 0.2 + - - -
237q LEU* 3.0 24.1 + - - +
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Residues in contact with SER 235 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A A 3.4 26.7 - - - -
227A A 3.0 23.8 + - - -
231q ARG 3.4 11.2 + - - -
232q ARG 3.0 17.5 + - - -
234q LEU* 1.4 77.6 - - - +
236q SER* 1.4 64.6 + - - +
237q LEU* 3.4 7.3 + - - +
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Residues in contact with SER 236 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232q ARG 3.0 14.9 + - - -
233q ARG* 3.4 13.5 + - - -
234q LEU 3.3 0.2 - - - -
235q SER* 1.4 80.0 + - - +
237q LEU* 1.4 71.9 + - - +
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Residues in contact with LEU 237 (chain q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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752A C 3.4 48.0 + - - +
753A C 3.8 14.8 - - - +
233q ARG 4.3 4.4 + - - +
234q LEU* 3.0 20.3 + - - +
235q SER 3.8 5.9 - - - +
236q SER* 1.4 92.3 - - - +
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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