Contacts of the helix formed by residues 225 - 234 (chain B) in PDB entry 3QEK
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 LEU 225 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B PHE* 3.8 28.5 - - + -
222B THR* 3.5 30.3 - - + +
223B LYS 3.1 9.9 + - - +
224B ASN* 1.3 73.6 - - - +
226B THR* 1.3 59.9 + - - +
227B ALA 3.5 2.0 - - - -
228B LEU* 3.1 15.7 + - + +
229B LEU* 2.9 35.8 + - + +
251B ALA* 3.5 46.2 - - + +
252B VAL* 3.6 16.2 - - + +
255B SER* 3.8 15.3 + - - +
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Residues in contact with THR 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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224B ASN* 3.5 4.2 - - - -
225B LEU* 1.3 78.4 + - - +
227B ALA* 1.3 59.4 + - - +
229B LEU* 3.2 1.6 + - - +
230B LEU* 2.8 52.8 + - + +
255B SER* 4.9 7.6 + - - -
259B LEU* 4.3 25.7 - - + +
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Residues in contact with ALA 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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224B ASN 5.3 1.7 + - - +
225B LEU 3.5 0.2 - - - -
226B THR* 1.3 78.6 - - - +
228B LEU* 1.3 62.1 + - - +
230B LEU* 3.6 9.4 + - - +
231B GLU* 3.3 27.6 + - - +
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Residues in contact with LEU 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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166B ILE* 4.4 17.7 - - + -
216B LEU* 3.5 36.8 - - + +
217B GLN 3.7 17.9 - - - +
218B PHE* 3.4 36.8 - - + +
225B LEU* 3.1 16.5 + - + +
226B THR 3.1 0.8 - - - -
227B ALA* 1.3 79.6 - - - +
229B LEU* 1.3 71.9 + - + +
231B GLU* 3.2 26.4 - - - +
232B ALA 3.3 4.2 + - - -
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Residues in contact with LEU 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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166B ILE* 3.9 27.6 - - + -
225B LEU* 2.9 26.6 + - + +
228B LEU* 1.3 79.6 - - + +
230B LEU* 1.3 57.2 + - - +
232B ALA* 3.0 7.1 + - + +
233B LYS 2.8 23.7 + - - -
252B VAL* 4.0 15.0 - - + +
255B SER* 3.4 35.0 - - - -
256B ALA* 3.5 22.0 - - + +
259B LEU* 3.7 16.2 - - + -
261B MSE 3.4 27.1 - - + +
268B TRP* 4.8 2.0 - - + -
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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 THR* 2.8 39.9 + - + +
227B ALA* 3.8 8.7 - - - +
229B LEU* 1.3 73.8 - - - +
231B GLU* 1.3 64.5 + - - +
233B LYS* 3.1 25.0 + - + +
234B GLU* 2.9 24.8 + - - +
259B LEU* 4.3 20.0 - - + -
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Residues in contact with GLU 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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214B LYS* 4.0 13.5 + - + -
216B LEU* 3.8 24.5 - - + +
227B ALA* 3.3 16.3 + - - +
228B LEU* 3.2 12.7 + - - +
230B LEU* 1.3 77.8 - - - +
232B ALA* 1.3 62.9 + - - +
234B GLU* 3.5 10.8 + - - +
235B LEU* 3.4 21.7 - - - +
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Residues in contact with ALA 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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164B ILE* 4.2 17.2 - - + +
166B ILE* 4.9 1.6 - - + -
216B LEU* 3.6 23.7 - - + +
228B LEU 3.3 1.6 + - - -
229B LEU* 3.0 16.7 + - + +
231B GLU* 1.3 81.2 - - - +
233B LYS* 1.3 61.3 + - - +
235B LEU* 3.1 28.5 + - - +
237B ALA 4.7 3.8 - - - +
238B ARG* 5.2 0.3 + - - -
240B ILE* 4.9 6.4 - - + +
261B MSE 3.8 14.6 - - + -
266B TYR* 6.1 0.6 - - - -
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Residues in contact with LYS 233 (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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229B LEU 2.8 13.4 + - - +
230B LEU* 3.1 27.1 + - + +
232B ALA* 1.3 76.0 - - - +
234B GLU* 1.3 62.1 + - - +
235B LEU 3.2 8.8 + - - +
238B ARG* 4.0 10.7 + - - +
259B LEU* 2.9 32.9 + - - +
260B ASP* 4.7 6.1 + - - +
261B MSE 3.7 24.2 - - - +
266B TYR* 4.0 17.5 - - - +
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Residues in contact with GLU 234 (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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230B LEU 2.9 15.1 + - - +
231B GLU* 3.7 9.9 - - - +
232B ALA 3.2 0.6 - - - -
233B LYS* 1.3 77.8 - - - +
235B LEU* 1.3 65.7 + - + +
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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