Contacts of the helix formed by residues 245 - 259 (chain C) in PDB entry 3QEL
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168C SER* 5.1 1.4 + - - -
244C ALA* 1.3 76.7 - - - +
246C GLU* 1.3 67.2 + - - +
247C ASP* 3.1 5.9 + - - +
248C ASP* 3.2 23.6 + - - +
249C ALA* 2.8 21.6 + - - +
273C ARG* 3.5 30.1 - - - +
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Residues in contact with GLU 246 (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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245C SER* 1.3 73.9 - - - +
247C ASP* 1.3 57.7 + - - +
249C ALA* 3.5 4.0 + - - +
250C THR* 2.7 38.2 + - - -
273C ARG* 3.9 18.9 + - + +
276C SER* 3.7 26.2 - - - +
277C GLY* 5.4 0.9 - - - -
278C SER* 4.6 8.1 - - - +
279C ALA* 4.1 3.4 - - + +
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Residues in contact with ASP 247 (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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245C SER* 3.2 6.3 + - - +
246C GLU* 1.3 80.9 - - - +
248C ASP* 1.3 63.8 + - - +
250C THR* 3.4 8.5 - - - +
251C ALA* 3.4 18.7 + - - +
278C SER* 4.2 10.7 + - - -
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Residues in contact with ASP 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168C SER* 5.2 3.5 - - - -
170C ASP* 5.4 0.7 - - - +
218C PHE* 3.7 26.2 - - + -
220C PRO* 3.6 12.8 - - - +
221C GLY* 2.9 35.2 + - - -
222C THR 3.8 10.2 + - - +
225C LEU* 4.2 0.9 - - - +
244C ALA* 3.9 13.2 - - + -
245C SER* 3.2 16.0 + - - +
247C ASP* 1.3 76.5 - - - +
249C ALA* 1.3 66.8 + - - +
250C THR 3.2 1.1 - - - -
251C ALA* 3.2 5.4 + - - +
252C VAL* 3.0 26.9 + - - +
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Residues in contact with ALA 249 (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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242C LEU* 4.2 9.0 - - + -
244C ALA* 3.7 7.0 - - + +
245C SER 2.8 19.3 + - - +
246C GLU* 3.6 4.7 - - - +
248C ASP* 1.3 75.5 - - - +
250C THR* 1.3 57.2 + - - +
252C VAL* 3.3 2.1 + - - +
253C TYR* 2.9 44.8 + - + -
274C GLU* 3.8 38.4 - - + +
279C ALA* 4.4 1.3 - - + -
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Residues in contact with THR 250 (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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246C GLU 2.7 19.5 + - - -
247C ASP* 3.4 11.9 - - - -
249C ALA* 1.3 78.4 - - - +
251C ALA* 1.3 57.8 + - - +
253C TYR* 3.1 11.3 + - - +
254C LYS* 2.8 44.3 + - + +
278C SER* 2.9 20.6 + - - +
279C ALA* 3.6 9.3 - - - +
282C TYR* 3.5 31.2 - - + -
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Residues in contact with ALA 251 (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 THR 3.6 24.9 - - - +
223C LYS* 4.3 13.0 - - + +
225C LEU* 3.6 10.8 - - + -
247C ASP 3.4 8.5 + - - +
248C ASP* 3.2 7.5 + - - +
250C THR* 1.3 80.3 - - - +
252C VAL* 1.3 57.4 + - - +
254C LYS* 4.0 7.4 - - - +
255C SER* 2.9 35.9 + - - -
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Residues in contact with VAL 252 (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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166C ILE* 5.1 6.7 - - + -
218C PHE* 4.0 22.2 - - + -
225C LEU* 3.6 18.2 - - + -
228C LEU* 5.3 2.5 - - + -
229C LEU* 3.6 16.8 - - + +
242C LEU* 4.2 19.5 - - + -
248C ASP 3.0 16.5 + - - +
249C ALA 3.5 7.2 - - - +
251C ALA* 1.3 77.0 - - - +
253C TYR* 1.3 52.2 + - + +
256C ALA* 2.6 39.2 + - - +
268C TRP* 4.0 28.9 - - + -
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Residues in contact with TYR 253 (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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242C LEU* 3.8 21.3 - - + -
249C ALA* 2.9 25.9 + - + -
250C THR* 3.4 9.0 - - - +
252C VAL* 1.3 76.5 - - - +
254C LYS* 1.3 57.5 + - - +
256C ALA* 3.6 4.7 - - + +
257C ALA* 2.8 32.0 + - - +
268C TRP* 4.3 15.5 - + - -
270C VAL* 3.5 2.6 - - - +
274C GLU* 2.7 42.5 + - - +
279C ALA* 3.4 25.4 - - + -
282C TYR* 3.5 20.6 - - + +
283C ALA* 3.6 13.5 - - + -
284C PRO* 3.8 19.2 - - + +
287C ILE* 3.3 24.8 - - + +
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Residues in contact with LYS 254 (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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250C THR* 2.8 41.3 + - + +
251C ALA* 4.0 6.7 - - - +
253C TYR* 1.3 71.3 - - - +
255C SER* 1.3 64.3 + - - +
257C ALA* 3.0 19.6 + - - +
258C MET* 3.3 8.3 + - - +
282C TYR* 3.7 44.6 + - + -
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Residues in contact with SER 255 (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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223C LYS 3.6 18.7 + - - -
224C ASN* 5.0 0.2 - - - -
225C LEU* 3.6 19.3 + - - -
226C THR* 4.2 6.1 + - - -
229C LEU* 3.6 18.8 - - - -
251C ALA 2.9 19.7 + - - -
254C LYS* 1.3 74.9 - - - +
256C ALA* 1.3 63.7 + - - +
257C ALA 3.1 1.2 + - - -
258C MET* 3.2 16.8 + - - +
259C LEU* 3.4 17.5 + - - +
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Residues in contact with ALA 256 (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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229C LEU* 3.5 16.3 - - + +
252C VAL 2.6 23.7 + - - +
253C TYR* 3.6 6.1 - - - +
255C SER* 1.3 73.4 - - - +
257C ALA* 1.3 60.5 + - - +
259C LEU* 3.6 6.7 + - - +
261C MET* 3.2 29.4 + - + +
262C THR* 4.8 3.4 - - - +
268C TRP* 3.6 36.1 - - + -
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Residues in contact with ALA 257 (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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253C TYR 2.8 13.8 + - - +
254C LYS* 3.3 13.5 - - - +
255C SER 3.0 0.6 - - - -
256C ALA* 1.3 76.0 - - - +
258C MET* 1.3 66.8 + - - +
260C ASP* 3.1 16.8 + - - +
262C THR* 4.3 18.4 - - - -
282C TYR 5.7 2.5 - - - +
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Residues in contact with MET 258 (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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254C LYS 3.3 6.5 + - - +
255C SER* 3.2 11.2 + - - +
257C ALA* 1.3 78.2 - - - +
259C LEU* 1.3 61.9 + - + +
260C ASP* 2.9 16.5 - - - +
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Residues in contact with LEU 259 (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 THR* 3.9 28.9 - - - +
229C LEU* 3.6 32.5 - - + -
230C LEU* 4.1 13.2 - - + +
233C LYS* 5.6 3.0 - - + +
255C SER 3.4 14.7 + - - +
256C ALA 4.1 4.3 - - - +
257C ALA 3.1 1.0 - - - -
258C MET* 1.3 78.6 - - + +
260C ASP* 1.3 68.9 + - - +
261C MET* 3.2 19.4 + - - +
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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