Contacts of the helix formed by residues 222 - 232 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B MET* 4.0 8.1 - - - -
220B ASP* 2.8 19.0 + - - -
221B ILE* 1.3 76.3 - - - +
223B SER* 1.3 65.0 + - - +
224B THR* 3.6 9.4 + - - -
225B LYS* 3.1 32.3 + - - +
226B ILE* 3.1 20.4 + - - +
778B NAD 5.5 2.7 - - - -
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Residues in contact with SER 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASN* 3.3 29.5 + - - -
19B PRO* 3.0 22.9 + - - -
21B THR* 4.5 1.3 - - - +
23B MET* 4.8 2.0 - - - +
24B HIS* 3.6 14.9 + - - -
221B ILE 3.9 1.4 + - - -
222B SER* 1.3 70.3 - - - +
224B THR* 1.3 68.4 + - - +
226B ILE* 3.0 9.7 + - - +
227B ARG* 2.9 33.2 + - - +
778B NAD 4.6 8.7 + - - -
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Residues in contact with THR 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B SER* 3.2 8.4 - - - -
223B SER* 1.3 80.2 - - - +
225B LYS* 1.3 58.6 + - + +
227B ARG* 3.3 29.3 + - - +
228B ARG* 2.9 51.4 + - - +
231B ARG* 5.1 1.5 + - - +
259B GLU* 5.7 0.7 - - - +
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Residues in contact with LYS 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A TRP* 3.2 18.8 + - - +
217A ILE* 3.6 36.7 - - + +
220B ASP* 2.9 29.8 + - - +
222B SER* 3.1 25.4 + - - +
224B THR* 1.3 74.8 - - + +
226B ILE* 1.3 61.5 + - - +
228B ARG* 3.6 18.2 - - - +
229B ALA* 2.9 28.1 + - - +
198C TYR* 3.1 28.4 + - - +
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Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ILE* 5.0 2.9 - - + -
19B PRO* 4.0 18.2 - - + -
21B THR* 3.8 17.9 - - + -
221B ILE* 3.7 21.5 - - + -
222B SER 3.1 16.5 + - - +
223B SER* 3.0 10.4 + - - +
225B LYS* 1.3 76.0 - - + +
227B ARG* 1.3 66.2 + - - +
229B ALA* 3.1 5.9 + - - +
230B LEU* 2.9 40.1 + - + +
236B ILE* 4.0 22.8 - - + +
239B LEU* 3.8 27.1 - - + -
240B VAL* 4.3 6.1 - - + -
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Residues in contact with ARG 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B ASN* 3.0 41.0 + - - +
19B PRO* 4.2 3.4 - - + -
57B LYS* 6.2 2.2 - - - +
58B LYS 5.0 6.4 + - - -
59B GLY 4.6 1.7 + - - -
223B SER* 2.9 29.5 + - - +
224B THR* 3.3 31.1 + - - +
226B ILE* 1.3 75.4 - - - +
228B ARG* 1.3 65.2 + - - +
230B LEU* 3.1 10.9 + - - +
231B ARG* 2.9 38.9 + - - +
254B TYR* 3.4 42.6 - - + +
259B GLU* 3.0 35.6 + - - +
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Residues in contact with ARG 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B THR* 2.9 39.6 + - - +
225B LYS* 3.6 21.2 - - - +
227B ARG* 1.3 78.3 - - - +
229B ALA* 1.3 63.7 + - - +
231B ARG* 3.3 29.9 + - - +
232B ARG* 3.2 66.4 + - - +
234B GLN* 5.9 0.4 - - - +
198C TYR* 3.2 43.4 + - + +
199C GLU* 4.4 24.7 + - - +
201C ASP* 4.2 0.2 - - - -
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A ILE* 5.2 9.4 - - + -
225B LYS 2.9 21.6 + - - +
226B ILE* 3.1 4.7 + - - +
228B ARG* 1.3 73.7 - - - +
230B LEU* 1.3 59.2 + - - +
232B ARG* 3.1 3.1 + - - -
233B GLY 3.1 3.3 + - - -
234B GLN* 2.7 59.8 + - + +
235B SER 5.0 2.0 - - - +
236B ILE* 4.0 18.2 - - + -
239B LEU* 6.2 0.2 - - + -
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ILE* 2.9 35.4 + - + +
227B ARG* 3.6 5.2 - - - +
229B ALA* 1.3 71.4 - - - +
231B ARG* 1.3 67.5 + - - +
233B GLY* 2.9 14.9 + - - +
234B GLN 4.7 5.6 - - - +
236B ILE* 3.9 29.2 - - + -
248B ILE* 3.9 24.2 - - + -
249B GLU* 5.9 4.5 - - + -
254B TYR* 3.7 43.3 - - + +
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Residues in contact with ARG 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B THR* 5.1 1.0 + - - +
227B ARG* 2.9 14.3 + - - +
228B ARG* 3.5 50.1 - - - +
230B LEU* 1.3 76.9 - - - +
232B ARG* 1.3 62.2 + - + +
233B GLY 3.5 0.5 + - - -
254B TYR* 4.4 5.8 + - + -
255B SER* 3.6 37.9 - - - +
256B SER* 3.6 13.0 - - - +
259B GLU* 3.4 36.3 + - - +
201C ASP* 2.9 41.9 + - - +
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Residues in contact with ARG 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B ARG* 3.2 29.9 + - - +
229B ALA 3.1 7.9 + - - +
230B LEU 3.0 1.0 - - - -
231B ARG* 1.3 81.4 - - + +
233B GLY* 1.3 64.2 + - - +
234B GLN* 3.3 21.8 + - + +
198C TYR* 2.6 51.3 + - - -
199C GLU 4.2 0.4 - - - -
200C SER 3.6 3.0 - - - +
201C ASP* 2.8 46.2 + - - +
204C TRP* 3.3 49.1 + - + +
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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