Contacts of the helix formed by residues 222 - 232 (chain C) in PDB entry 1KQN
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 222 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C MET* 4.0 10.5 - - - +
220C ASP* 2.9 21.5 + - - -
221C ILE* 1.3 75.2 - - - +
223C SER* 1.3 64.2 + - - +
224C THR* 3.5 8.7 + - - -
225C LYS* 3.0 33.5 + - - +
226C ILE* 2.9 22.2 + - - +
779C NAD 5.6 2.9 - - - -
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Residues in contact with SER 223 (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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18C ASN* 3.4 28.4 + - - -
19C PRO* 3.0 19.4 + - - -
21C THR* 4.2 2.4 - - - +
23C MET* 5.0 1.6 - - - +
24C HIS* 3.6 15.8 + - - -
221C ILE 3.8 1.4 + - - -
222C SER* 1.3 72.2 - - - +
224C THR* 1.3 58.5 + - - +
226C ILE* 3.0 10.4 + - - +
227C ARG* 2.8 40.2 + - - +
779C NAD 4.6 9.1 + - - -
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Residues in contact with THR 224 (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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222C SER* 3.2 9.3 + - - +
223C SER* 1.3 78.9 - - - +
225C LYS* 1.3 56.8 + - + +
227C ARG* 3.4 28.7 + - - +
228C ARG* 3.0 50.2 + - - +
231C ARG* 5.1 1.6 + - - -
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Residues in contact with LYS 225 (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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220C ASP* 2.5 34.6 + - - +
222C SER* 3.0 25.3 + - - +
224C THR* 1.3 73.5 - - + +
226C ILE* 1.3 66.8 + - - +
228C ARG* 3.3 20.1 + - - +
229C ALA* 3.0 23.4 + - - +
216D TRP* 3.2 26.0 + - - +
217D ILE* 3.7 25.9 - - + +
198F TYR* 3.3 24.9 + - - +
199F GLU* 5.9 1.3 - - - -
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Residues in contact with ILE 226 (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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19C PRO* 3.9 20.9 - - + -
21C THR* 3.7 21.1 - - + -
221C ILE* 3.5 22.7 - - + -
222C SER 2.9 19.0 + - - +
223C SER* 3.0 8.7 + - - +
225C LYS* 1.3 76.0 - - - +
227C ARG* 1.3 64.1 + - - +
229C ALA* 3.2 6.7 + - - +
230C LEU* 3.0 25.8 + - + +
236C ILE* 3.8 28.9 - - + -
239C LEU* 3.9 26.9 - - + -
240C VAL* 4.3 6.3 - - + -
217D ILE* 4.5 4.9 - - + -
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Residues in contact with ARG 227 (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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18C ASN* 2.9 45.7 + - - +
19C PRO* 4.0 4.3 - - + -
57C LYS* 6.1 5.3 - - - +
58C LYS 4.9 6.9 + - - -
59C GLY 4.6 2.4 + - - -
223C SER* 2.8 34.9 + - - +
224C THR* 3.4 31.6 + - - +
226C ILE* 1.3 72.9 - - - +
228C ARG* 1.3 63.5 + - - +
230C LEU* 3.2 9.5 + - - +
231C ARG* 2.9 37.9 + - - +
254C TYR* 3.3 35.1 - - + +
259C GLU* 2.8 38.6 + - - +
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Residues in contact with ARG 228 (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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224C THR* 3.0 38.3 + - - +
225C LYS* 3.5 23.9 - - - +
226C ILE 3.2 0.2 - - - -
227C ARG* 1.3 76.2 - - - +
229C ALA* 1.3 65.2 + - - +
231C ARG* 3.4 26.2 + - - +
232C ARG* 3.2 65.2 + - - +
234C GLN* 5.8 0.2 - - - +
198F TYR* 3.1 46.6 + - + +
199F GLU* 4.2 27.5 + - - +
201F ASP* 4.3 0.7 - - - -
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Residues in contact with ALA 229 (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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225C LYS 3.0 13.1 + - - +
226C ILE* 3.4 10.3 - - - +
228C ARG* 1.3 77.9 - - - +
230C LEU* 1.3 56.7 + - - +
232C ARG 3.2 5.5 + - - -
234C GLN* 2.8 58.5 + - + +
235C SER 4.8 2.2 - - - +
236C ILE* 3.7 18.4 - - + -
239C LEU* 6.0 0.4 - - + -
26D ARG* 6.0 0.9 - - - +
217D ILE* 4.9 10.5 - - + -
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Residues in contact with LEU 230 (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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226C ILE* 3.0 33.3 + - + +
227C ARG* 3.6 6.3 - - - +
229C ALA* 1.3 70.9 - - - +
231C ARG* 1.3 66.3 + - - +
232C ARG 3.0 2.0 - - - -
233C GLY* 2.9 14.4 + - - +
234C GLN 4.5 6.7 - - - +
236C ILE* 3.8 29.2 - - + -
245C GLN* 6.2 0.2 - - + -
248C ILE* 3.7 24.2 - - + -
249C GLU* 6.1 1.8 - - - +
254C TYR* 3.4 47.3 - - + +
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Residues in contact with ARG 231 (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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224C THR* 5.1 1.6 + - - +
227C ARG* 2.9 27.7 + - - +
228C ARG* 3.5 34.2 - - - +
230C LEU* 1.3 77.2 - - - +
232C ARG* 1.3 61.4 + - + +
233C GLY 3.4 1.9 + - - -
254C TYR* 4.4 4.7 - - + +
255C SER* 3.5 41.0 + - - +
256C SER* 3.5 15.5 - - - +
259C GLU* 3.4 37.4 + - - +
201F ASP* 2.8 37.9 + - - +
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Residues in contact with ARG 232 (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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228C ARG* 3.2 33.0 + - - +
229C ALA 3.2 4.5 + - - +
230C LEU 3.0 1.0 - - - -
231C ARG* 1.3 80.3 - - + +
233C GLY* 1.3 62.0 + - - +
234C GLN* 3.2 23.6 + - + +
198F TYR* 2.8 48.1 + - - -
199F GLU 4.2 0.2 - - - -
200F SER 3.5 4.2 + - - +
201F ASP* 2.7 49.9 + - - +
204F TRP* 3.5 45.4 + - + +
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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