Contacts of the helix formed by residues 240 - 252 (chain W) 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 W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179W ARG* 5.2 3.2 - - - +
184W ARG* 4.2 10.9 - - - +
187W ILE* 4.5 4.9 - - + -
213W PHE* 3.9 16.6 - - - -
238W VAL* 3.6 4.1 - - - +
239W ILE* 1.3 82.8 - - - +
241W LYS* 1.3 68.6 + - - +
242W GLU* 3.5 1.6 - - - -
243W ASP* 3.1 27.2 + - + +
244W PHE* 3.0 32.1 + - + -
19Z T 2.4 49.4 + - - +
20Z C 5.5 0.3 - - - +
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Residues in contact with LYS 241 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E GLY* 5.7 0.7 - - - -
138E ASP* 3.6 44.7 + - + +
229W GLY 5.1 1.8 + - - -
230W TRP* 3.2 70.3 - - + +
238W VAL* 3.5 12.8 + - + +
239W ILE 3.1 6.7 + - - +
240W ASN* 1.3 72.0 - - - +
242W GLU* 1.3 71.0 + - - +
244W PHE* 2.7 5.9 + - - +
245W VAL* 2.7 32.4 + - + +
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Residues in contact with GLU 242 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E HIS* 3.5 27.6 - - - +
137E GLY 6.3 0.9 - - - +
138E ASP 5.9 3.0 - - - +
184W ARG* 4.2 13.3 + - - -
188W HIS* 4.7 4.7 - - + -
239W ILE 5.1 0.4 + - - -
240W ASN* 5.8 0.2 - - - -
241W LYS* 1.3 83.3 - - - +
243W ASP* 1.3 66.6 + - - +
245W VAL* 2.8 10.5 + - - +
246W ALA* 2.7 38.0 + - + +
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Residues in contact with ASP 243 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179W ARG* 5.7 0.3 + - - -
184W ARG* 3.2 24.5 + - - -
187W ILE* 3.2 28.7 - - + -
188W HIS* 2.7 39.0 + - - +
240W ASN* 3.1 33.6 + - - +
241W LYS 2.9 2.4 + - - -
242W GLU* 1.3 86.2 - - - +
244W PHE* 1.3 51.7 + - - +
246W ALA* 3.1 5.0 + - - +
247W LEU* 2.8 36.5 + - - +
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Residues in contact with PHE 244 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187W ILE* 4.7 10.5 - - + +
213W PHE* 3.9 40.2 - + - -
214W THR* 4.5 9.2 - - - -
217W GLY* 3.4 37.0 - - - -
218W ILE* 3.7 7.6 - - + +
222W VAL* 3.6 19.5 - - + +
225W TRP* 4.1 18.8 - + - -
230W TRP* 3.8 17.0 - + + -
238W VAL* 5.2 3.4 - - + -
240W ASN* 3.0 27.7 + - + +
241W LYS* 2.7 11.2 + - - +
243W ASP* 1.3 72.6 - - - +
245W VAL* 1.3 68.4 + - - +
247W LEU* 3.3 15.5 + - + +
248W GLU* 2.9 22.2 + - - +
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Residues in contact with VAL 245 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230W TRP* 3.7 17.7 - - + -
241W LYS* 2.7 53.2 + - + +
242W GLU* 2.8 10.5 + - - +
244W PHE* 1.3 69.7 - - - +
246W ALA* 1.3 55.6 + - - +
248W GLU* 2.7 30.7 + - + +
249W ARG* 3.1 10.6 + - + +
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Residues in contact with ALA 246 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188W HIS* 5.1 8.3 - - + +
191W CYS* 4.8 4.5 - - - -
242W GLU* 2.7 18.5 + - + +
243W ASP* 3.3 11.2 - - - +
245W VAL* 1.3 73.5 - - - +
247W LEU* 1.3 62.5 + - - +
249W ARG* 3.1 18.0 + - - +
250W LEU* 3.1 21.9 - - + +
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Residues in contact with LEU 247 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187W ILE* 4.5 10.5 - - + +
188W HIS* 6.1 0.2 - - + -
190W ALA 4.1 7.9 - - - +
191W CYS* 3.3 30.4 - - - -
194W ILE* 3.5 20.4 - - + +
214W THR* 4.0 26.9 - - + +
218W ILE* 4.2 28.3 - - + -
243W ASP 2.8 19.8 + - - +
244W PHE* 3.7 13.7 - - + +
245W VAL 3.1 0.2 + - - -
246W ALA* 1.3 73.7 - - - +
248W GLU* 1.3 53.6 + - - +
250W LEU* 3.7 3.4 + - - +
251W THR* 2.6 29.7 + - - +
258W TRP* 4.2 12.1 - - + -
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Residues in contact with GLU 248 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218W ILE* 3.8 21.6 - - + +
222W VAL* 4.8 13.6 - - + +
226W LYS* 3.2 35.2 + - + +
230W TRP* 6.3 1.3 - - + -
244W PHE 2.9 10.6 + - - +
245W VAL* 2.7 21.2 + - + +
247W LEU* 1.3 70.3 - - - +
249W ARG* 1.3 65.7 + - - +
251W THR* 3.0 26.1 - - - +
252W GLN* 3.4 28.1 + - - +
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Residues in contact with ARG 249 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198W LYS* 4.7 5.2 + - - +
245W VAL* 3.1 6.6 + - + +
246W ALA* 3.1 16.7 + - - +
248W GLU* 1.3 75.2 - - - +
250W LEU* 1.3 72.5 + - - +
252W GLN* 2.7 45.3 + - + +
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Residues in contact with LEU 250 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191W CYS* 3.5 39.9 - - + +
194W ILE* 3.5 31.4 - - + +
195W GLU* 4.2 23.6 - - + +
198W LYS* 3.4 18.2 - - + +
246W ALA* 3.1 21.8 - - + +
247W LEU 4.0 2.0 - - - +
248W GLU 3.5 0.2 - - - -
249W ARG* 1.3 94.1 - - + +
251W THR* 1.3 62.5 + - - +
252W GLN 3.2 0.9 + - - -
254W MET* 3.4 17.2 - - - +
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Residues in contact with THR 251 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194W ILE* 4.7 3.7 - - - +
218W ILE* 4.3 15.5 - - + +
247W LEU* 2.6 25.1 + - - +
248W GLU* 3.0 24.3 + - - +
249W ARG 2.8 0.6 + - - -
250W LEU* 1.3 77.6 - - - +
252W GLN* 1.3 60.6 + - - +
253W GLY 3.3 0.3 + - - -
254W MET* 2.9 33.4 + - - +
256W ILE* 4.4 18.8 - - + -
258W TRP* 5.5 5.6 - - + +
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Residues in contact with GLN 252 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198W LYS* 2.5 34.9 + - - +
248W GLU* 3.4 36.5 + - - +
249W ARG* 2.7 24.4 + - + +
251W THR* 1.3 73.9 - - - +
253W GLY* 1.3 59.2 + - - +
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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