Contacts of the helix formed by residues 222 - 229 (chain B) in PDB entry 1QK0
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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171B LEU* 3.3 29.8 - - - -
219B GLU* 2.7 28.9 + - - +
220B PRO 4.3 1.3 - - - -
221B ASP* 1.3 78.7 - - - +
223B LEU* 1.3 76.1 + - - +
224B ALA 3.2 2.6 - - - +
225B ASN* 3.1 21.1 + - - +
226B LEU 3.7 2.4 + - - -
242B TYR* 3.7 24.5 - - - -
246B ILE* 3.7 9.1 - - - +
262B LEU* 5.8 0.3 - - - +
263B ASP* 5.0 1.0 + - - -
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Residues in contact with LEU 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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219B GLU 4.7 0.2 + - - -
222B SER* 1.3 80.0 + - - +
224B ALA* 1.3 65.5 + - - +
226B LEU* 3.1 33.9 + - + +
227B VAL* 3.5 3.6 + - - +
242B TYR* 5.2 0.4 - - + -
243B LEU* 4.0 15.5 - - + -
246B ILE* 3.2 29.4 - - + -
262B LEU* 3.6 40.8 - - + -
263B ASP 4.5 5.8 + - - +
282B LEU* 3.5 23.4 - - + +
283B PHE* 3.8 27.1 - - + -
286B VAL* 4.1 13.0 - - + -
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Residues in contact with ALA 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 3.6 - - - +
223B LEU* 1.3 78.7 - - - +
225B ASN* 1.3 61.3 + - - +
227B VAL* 3.2 13.7 + - - +
228B THR 3.5 8.5 + - - -
263B ASP* 5.0 6.0 + - - +
264B ALA* 5.5 0.4 - - - -
265B GLY 4.3 11.7 - - - +
269B TRP* 3.4 49.3 + - + +
270B LEU* 4.1 23.1 - - + +
283B PHE* 5.2 1.4 - - - -
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Residues in contact with ASN 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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176B CYS* 3.6 33.1 - - - +
177B ALA* 3.4 10.5 - - - +
221B ASP* 2.9 46.5 + - - +
222B SER* 3.1 9.9 + - - +
224B ALA* 1.3 78.6 - - - +
226B LEU* 1.3 57.5 + - - +
229B ASN* 2.6 63.6 + - + +
235B CYS* 3.9 2.4 - - - +
242B TYR* 5.1 0.2 - - + -
269B TRP* 3.4 12.4 - - - -
901B IOB 5.4 1.2 - - - -
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Residues in contact with LEU 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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222B SER 4.0 7.2 - - - +
223B LEU* 3.1 25.9 + - + +
225B ASN* 1.3 77.9 - - + +
227B VAL* 1.3 60.4 + - - +
230B LEU* 3.3 38.1 - - + +
235B CYS* 4.1 9.9 - - + +
239B GLN* 3.9 41.0 - - + +
242B TYR* 4.0 22.9 - - + -
243B LEU* 3.8 30.5 - - + -
282B LEU* 4.2 10.1 - - + -
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Residues in contact with VAL 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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223B LEU 3.8 5.6 - - - +
224B ALA* 3.5 9.0 - - - +
225B ASN 3.1 0.8 - - - -
226B LEU* 1.3 80.8 - - - +
228B THR* 1.3 63.9 + - + +
230B LEU* 5.4 0.7 - - - -
270B LEU* 3.6 24.5 - - + -
275B ASN* 4.2 22.2 - - + +
278B PRO* 4.2 14.2 - - + +
279B ALA* 3.8 26.0 - - + +
282B LEU* 3.7 26.0 - - + -
283B PHE* 5.4 0.9 - - + -
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Residues in contact with THR 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 ALA 3.5 2.4 + - - -
227B VAL* 1.3 90.0 - - + +
229B ASN* 1.3 72.7 + - - +
230B LEU 3.7 2.4 + - - -
231B GLY* 4.8 1.7 + - - -
269B TRP* 2.8 36.7 + - + +
270B LEU* 4.1 1.1 - - + -
275B ASN* 3.6 35.4 - - - +
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Residues in contact with ASN 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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177B ALA* 3.6 13.7 - - + +
225B ASN* 2.6 47.2 + - - +
228B THR* 1.3 89.5 + - - +
230B LEU* 1.3 55.7 + - - +
231B GLY* 2.8 6.5 - - - +
232B THR* 2.8 25.3 + - - +
235B CYS* 3.3 21.8 - - - +
269B TRP* 4.0 8.7 - - - +
901B IOB 6.3 1.0 - - - +
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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