Contacts of the helix formed by residues 245 - 259 (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 SER 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B SER* 5.0 1.8 + - - -
244B ALA* 1.3 76.1 - - - +
246B GLU* 1.3 65.7 + - - +
247B ASP* 3.4 6.9 + - - +
248B ASP* 3.1 31.9 + - - +
249B ALA* 2.8 21.1 + - - +
273B ARG* 3.6 31.9 - - - +
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Residues in contact with GLU 246 (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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244B ALA 4.0 0.2 + - - -
245B SER* 1.3 72.2 - - - +
247B ASP* 1.3 67.2 + - - +
249B ALA 3.4 0.2 + - - -
250B THR* 2.9 28.8 + - - -
273B ARG* 3.4 34.6 + - + +
276B SER* 3.5 29.9 - - - +
277B GLY* 3.5 16.6 + - - -
278B SER* 4.1 3.4 + - - +
279B ALA* 3.6 10.1 - - + +
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Residues in contact with ASP 247 (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 LYS* 5.0 9.3 + - - +
245B SER* 3.2 6.7 + - - +
246B GLU* 1.3 82.8 - - - +
248B ASP* 1.3 67.9 + - - +
250B THR* 3.4 7.7 - - - -
251B ALA* 3.3 19.2 + - - +
278B SER* 3.7 14.4 + - - -
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Residues in contact with ASP 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER* 4.5 5.0 - - - -
170B ASP* 5.4 0.9 - - - +
218B PHE* 3.6 25.9 - - + -
220B PRO* 3.5 14.0 - - - +
221B GLY* 3.0 37.8 + - - -
222B THR 4.6 2.4 + - - +
223B LYS* 4.9 3.3 + - - -
244B ALA* 4.0 6.7 - - + -
245B SER* 3.1 21.5 + - - +
247B ASP* 1.3 79.0 - - - +
249B ALA* 1.3 65.2 + - - +
251B ALA* 3.3 6.6 + - - +
252B VAL* 3.0 26.5 + - - +
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Residues in contact with ALA 249 (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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242B LEU* 4.0 22.2 - - + -
244B ALA* 3.7 7.5 - - + +
245B SER 2.8 20.7 + - - +
246B GLU 3.7 4.5 - - - +
248B ASP* 1.3 72.1 - - - +
250B THR* 1.3 57.6 + - - +
252B VAL* 3.2 2.8 + - - +
253B TYR* 2.8 42.2 + - + -
274B GLU* 4.0 13.9 - - + -
279B ALA* 3.9 15.9 - - + -
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Residues in contact with THR 250 (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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246B GLU 2.9 13.2 + - - -
247B ASP* 3.4 11.2 - - - -
249B ALA* 1.3 78.9 - - - +
251B ALA* 1.3 63.0 + - - +
253B TYR* 3.3 9.7 + - - +
254B LYS* 3.0 43.2 + - + +
278B SER* 2.5 28.9 + - - +
279B ALA* 3.3 10.4 + - - +
282B TYR* 3.7 28.9 - - + -
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Residues in contact with ALA 251 (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 THR 4.1 5.4 - - - +
223B LYS* 3.6 33.7 - - + +
225B LEU* 3.5 15.3 - - + -
247B ASP 3.3 9.5 + - - +
248B ASP* 3.3 10.3 + - - +
250B THR* 1.3 78.7 - - - +
252B VAL* 1.3 63.2 + - - +
254B LYS* 3.8 9.0 - - - +
255B SER* 3.0 28.2 + - - -
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Residues in contact with VAL 252 (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* 5.0 5.2 - - + -
218B PHE* 4.1 19.5 - - + -
225B LEU* 3.7 18.2 - - + -
229B LEU* 4.0 13.1 - - + +
242B LEU* 4.1 26.5 - - + -
248B ASP 3.0 16.5 + - - +
249B ALA* 3.5 8.5 - - - +
251B ALA* 1.3 76.9 - - - +
253B TYR* 1.3 57.9 + - - +
255B SER* 3.3 2.4 + - - -
256B ALA* 2.8 28.9 + - - +
268B TRP* 3.9 28.9 - - + -
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Residues in contact with TYR 253 (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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242B LEU* 3.8 21.1 - - + -
249B ALA* 2.8 30.4 + - + +
250B THR* 3.6 6.7 - - - +
252B VAL* 1.3 73.7 - - - +
254B LYS* 1.3 56.1 + - - +
256B ALA* 3.9 4.1 - - - +
257B ALA* 3.0 31.1 + - - +
262B THR* 4.4 3.4 - - - +
268B TRP* 4.1 17.7 - + - -
270B VAL* 3.6 2.6 - - + +
274B GLU* 2.6 37.9 + - - +
279B ALA 3.4 26.7 - - - -
282B TYR* 3.5 19.5 - - + +
283B ALA* 3.6 12.8 - - - -
284B PRO* 3.8 13.5 - - + -
287B ILE* 3.3 29.4 - - + +
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Residues in contact with LYS 254 (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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250B THR* 3.0 33.2 + - + +
251B ALA* 3.8 7.4 - - - +
253B TYR* 1.3 74.3 - - - +
255B SER* 1.3 62.9 + - - +
257B ALA* 3.3 7.0 + - - +
258B MSE 3.1 27.6 + - + +
282B TYR* 3.3 56.9 + - + -
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Residues in contact with SER 255 (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 LYS 3.9 11.4 + - - -
225B LEU* 3.8 19.4 + - - +
226B THR* 4.9 7.1 + - - -
229B LEU* 3.4 21.3 - - - -
251B ALA 3.0 19.3 + - - -
252B VAL 3.7 0.2 - - - -
254B LYS* 1.3 74.1 - - - +
256B ALA* 1.3 65.3 + - - +
258B MSE 3.2 19.2 + - - +
259B LEU* 3.3 17.3 + - - +
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Residues in contact with ALA 256 (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* 3.5 14.5 - - + +
252B VAL 2.8 21.0 + - - +
253B TYR 3.9 1.6 - - - +
255B SER* 1.3 73.5 - - - +
257B ALA* 1.3 62.1 + - - +
259B LEU 3.0 7.8 + - - -
261B MSE 2.9 35.9 + - + +
262B THR* 3.7 10.1 - - + -
268B TRP* 3.7 32.3 - - + -
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Residues in contact with ALA 257 (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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253B TYR 3.0 19.3 + - - +
254B LYS* 3.5 7.2 - - - +
255B SER 3.2 0.2 - - - -
256B ALA* 1.3 77.9 - - - +
258B MSE 1.3 63.0 + - - +
260B ASP* 3.0 19.4 + - - +
262B THR* 3.8 21.5 - - + +
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Residues in contact with MSE 258 (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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254B LYS* 3.1 18.9 + - + +
255B SER* 3.3 13.2 - - - +
257B ALA* 1.3 78.6 - - - +
259B LEU* 1.3 65.7 + - + +
260B ASP* 3.4 3.8 + - - +
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Residues in contact with LEU 259 (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* 4.3 30.3 - - + +
229B LEU* 3.7 31.2 - - + -
230B LEU* 4.3 20.2 - - + -
233B LYS* 2.9 33.3 + - - +
255B SER 3.4 13.5 - - - +
256B ALA 3.0 5.9 + - - +
257B ALA 3.0 0.8 - - - -
258B MSE 1.3 84.5 - - + +
260B ASP* 1.3 66.3 + - - +
261B MSE 3.3 15.0 - - - -
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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