Contacts of the helix formed by residues 240 - 252 (chain S) in PDB entry 2QKK
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 ASN 240 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179S ARG* 5.1 2.0 - - - +
183S GLN 4.2 7.3 + - - -
184S ARG* 4.0 15.4 - - - +
187S ILE* 5.0 2.2 - - + -
213S PHE* 3.8 13.3 - - - -
238S VAL* 3.3 6.8 - - + +
239S ILE* 1.3 79.5 - - - +
241S LYS* 1.3 67.8 + - - +
242S GLU* 3.4 1.8 - - - -
243S ASP* 3.0 27.4 + - + +
244S PHE* 3.1 25.8 + - + -
19U T 2.7 56.4 + - - +
20U C 4.1 0.9 + - - -
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Residues in contact with LYS 241 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229S GLY 4.9 3.0 + - - -
230S TRP* 3.1 70.5 - - + +
238S VAL* 3.3 17.9 + - + +
239S ILE 3.4 2.2 + - - -
240S ASN* 1.3 76.9 - - - +
242S GLU* 1.3 58.0 + - - +
243S ASP 2.6 13.5 + - - -
244S PHE 3.1 0.3 + - - -
245S VAL* 3.0 32.9 + - + +
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Residues in contact with GLU 242 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184S ARG* 5.7 3.1 + - - -
239S ILE 5.2 1.0 + - - +
240S ASN 3.4 0.6 - - - -
241S LYS* 1.3 81.9 - - - +
243S ASP* 1.3 64.5 + - - +
245S VAL* 3.8 5.6 - - - +
246S ALA* 3.3 24.3 + - - +
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Residues in contact with ASP 243 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179S ARG* 5.4 2.4 + - - -
184S ARG* 2.5 45.7 + - - +
187S ILE* 4.0 15.3 - - + -
188S HIS* 2.9 27.5 + - + +
191S CYS* 5.1 0.6 - - - -
240S ASN* 3.2 31.4 + - - +
241S LYS 2.6 5.3 + - - -
242S GLU* 1.3 77.2 - - - +
244S PHE* 1.3 55.5 + - - +
245S VAL 2.7 15.6 + - - -
246S ALA* 2.8 14.4 + - - +
247S LEU* 3.0 11.7 + - - +
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Residues in contact with PHE 244 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187S ILE* 3.7 24.5 - - + -
213S PHE* 3.5 39.3 - + - -
214S THR* 3.5 17.3 - - + -
217S GLY* 3.7 13.9 - - - -
218S ILE* 3.3 36.9 - - + +
222S VAL* 4.2 13.5 - - + +
225S TRP* 3.9 19.5 - + - -
230S TRP* 4.1 18.0 - - + -
238S VAL* 5.3 0.9 - - + -
240S ASN* 3.1 20.9 + - + +
241S LYS 4.1 1.6 - - - +
243S ASP* 1.3 78.0 - - - +
245S VAL* 1.3 59.9 + - - +
247S LEU* 3.7 10.1 - - + +
248S GLU* 3.2 23.0 + - - +
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Residues in contact with VAL 245 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230S TRP* 3.2 30.7 - - + -
241S LYS* 3.1 33.4 - - + +
242S GLU* 3.8 6.5 - - - +
243S ASP 2.7 4.4 + - - -
244S PHE* 1.3 70.4 - - - +
246S ALA* 1.3 65.6 + - - +
247S LEU 2.9 5.2 + - - -
248S GLU* 3.1 5.5 + - - +
249S ARG* 2.9 24.7 + - + +
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Residues in contact with ALA 246 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188S HIS* 4.9 13.0 - - + +
191S CYS* 4.6 4.4 - - - -
242S GLU 3.3 11.7 + - - +
243S ASP* 2.8 14.0 + - - +
245S VAL* 1.3 77.4 - - - +
247S LEU* 1.3 55.7 + - - +
249S ARG* 3.1 10.4 - - - +
250S LEU* 2.9 29.6 - - - +
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Residues in contact with LEU 247 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187S ILE* 4.4 13.7 - - + +
190S ALA* 4.5 0.2 - - + -
191S CYS* 3.4 40.8 - - - +
194S ILE* 4.3 12.6 - - + -
214S THR* 4.9 3.8 - - + -
218S ILE* 3.5 37.2 - - + -
243S ASP 3.0 8.7 + - - +
244S PHE* 3.7 17.5 - - + +
245S VAL 2.9 2.6 + - - -
246S ALA* 1.3 74.4 - - - +
248S GLU* 1.3 53.7 + - - +
249S ARG 2.8 4.3 - - - -
250S LEU* 2.6 29.2 + - - +
251S THR* 2.9 15.4 + - - +
258S TRP* 4.2 18.8 - - + -
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Residues in contact with GLU 248 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218S ILE* 4.3 9.6 - - + +
222S VAL* 3.5 29.9 - - + +
226S LYS* 3.8 28.0 + - - +
230S TRP* 5.9 1.6 - - - -
244S PHE 3.2 13.2 + - - +
245S VAL* 3.1 5.9 + - - +
247S LEU* 1.3 79.7 - - - +
249S ARG* 1.3 61.8 + - - +
250S LEU 3.0 1.0 + - - -
251S THR* 3.1 26.8 + - + -
252S GLN* 3.2 33.7 + - + +
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Residues in contact with ARG 249 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245S VAL* 2.9 14.9 + - + +
246S ALA* 3.1 22.0 - - - +
248S GLU* 1.3 79.8 - - - +
250S LEU* 1.3 67.9 + - - +
252S GLN* 3.9 15.0 - - - +
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Residues in contact with LEU 250 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191S CYS* 3.6 37.5 - - + +
194S ILE* 3.9 23.3 - - + +
195S GLU* 4.1 26.0 - - + +
246S ALA 2.9 21.3 - - - +
247S LEU 2.6 14.1 + - - +
249S ARG* 1.3 91.8 - - + +
251S THR* 1.3 54.1 + - - +
252S GLN 2.7 25.7 + - - +
254S MET* 3.7 14.2 - - - +
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Residues in contact with THR 251 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194S ILE* 4.0 13.7 - - - +
218S ILE* 3.8 21.1 - - + +
247S LEU* 2.9 17.3 + - - +
248S GLU* 3.1 23.9 + - + -
250S LEU* 1.3 74.9 - - - +
252S GLN* 1.3 58.8 + - - +
253S GLY 3.3 0.9 + - - -
254S MET* 3.2 26.4 - - - +
256S ILE* 5.0 9.9 - - + +
258S TRP* 4.8 6.4 - - - +
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Residues in contact with GLN 252 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248S GLU* 3.2 36.6 - - + +
249S ARG* 3.9 13.8 - - - +
250S LEU 2.7 9.4 + - - +
251S THR* 1.3 78.5 + - - +
253S GLY* 1.3 60.3 + - - +
254S MET* 3.3 2.5 + - - +
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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