Contacts of the helix formed by residues 240 - 252 (chain A) in PDB entry 2QK9
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179A ARG* 3.4 9.9 - - - +
183A GLN* 4.3 3.2 - - - +
184A ARG* 3.7 6.5 - - - +
187A ILE* 4.3 1.8 - - + +
213A PHE* 3.5 19.1 - - - -
238A VAL* 3.4 4.5 - - + +
239A ILE* 1.3 75.2 - - - +
241A LYS* 1.3 59.1 + - - +
242A GLU 3.4 2.5 - - - -
243A ASP* 3.1 29.1 + - + +
244A PHE* 2.8 50.1 + - + -
1002A GOL 4.1 0.4 - - - -
30C T 3.0 50.0 + - - +
31C C 4.5 0.2 + - - -
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Residues in contact with LYS 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A TRP* 3.2 68.6 - - + +
238A VAL* 3.6 15.5 + - - +
239A ILE 3.3 4.6 + - - +
240A ASN* 1.3 76.3 - - - +
242A GLU* 1.3 62.7 + - + +
243A ASP 3.1 0.2 + - - -
244A PHE* 3.2 1.7 + - - +
245A VAL* 2.8 45.4 + - + +
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Residues in contact with GLU 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ILE 5.1 1.0 + - - -
240A ASN 3.4 0.4 - - - -
241A LYS* 1.3 82.3 - - + +
243A ASP* 1.3 63.1 + - - +
245A VAL* 3.4 6.8 + - - +
246A ALA* 3.0 25.5 + - - +
1002A GOL 2.9 41.4 + - - -
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Residues in contact with ASP 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A ARG* 2.9 31.3 + - - +
187A ILE* 3.8 28.4 - - + +
188A HIS* 2.9 24.2 + - + +
191A CYS* 4.7 1.0 - - - -
240A ASN* 3.1 24.8 + - - +
241A LYS 3.1 0.8 - - - -
242A GLU* 1.3 75.3 - - - +
244A PHE* 1.3 65.5 + - - +
245A VAL 3.2 0.2 + - - -
246A ALA* 3.3 4.7 + - - +
247A LEU* 3.0 22.7 + - - +
1002A GOL 3.0 28.2 + - - -
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Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ILE* 3.5 29.8 - - + -
213A PHE* 3.7 36.8 - + - -
214A THR* 4.0 9.2 - - - -
217A GLY* 3.4 23.6 - - - -
218A ILE* 3.7 18.7 - - + +
222A VAL* 4.1 17.4 - - + +
225A TRP* 3.7 23.6 - + - -
230A TRP* 4.1 10.5 - - + -
238A VAL* 5.1 1.8 - - + -
240A ASN* 2.8 36.2 + - + +
241A LYS 4.0 2.2 - - - +
243A ASP* 1.3 74.0 - - - +
245A VAL* 1.3 56.9 + - - +
247A LEU* 3.7 13.1 - - + +
248A GLU* 2.9 29.6 + - - +
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Residues in contact with VAL 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A TRP* 4.0 17.0 - - + -
241A LYS* 2.8 46.5 + - + +
242A GLU* 3.6 7.6 - - - +
243A ASP 3.1 0.2 - - - -
244A PHE* 1.3 73.2 - - - +
246A ALA* 1.3 64.9 + - - +
248A GLU* 3.2 6.1 + - - +
249A ARG* 3.0 28.0 + - + +
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Residues in contact with ALA 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A HIS* 4.8 9.4 - - + -
191A CYS* 4.4 10.1 - - - -
242A GLU 3.0 17.1 + - - +
243A ASP* 3.6 5.6 - - - +
245A VAL* 1.3 79.4 - - - +
247A LEU* 1.3 62.1 + - - +
249A ARG* 3.5 8.0 + - - +
250A LEU* 3.2 27.3 + - + +
1003A GOL 4.9 4.7 - - - +
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Residues in contact with LEU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187A ILE* 4.3 12.6 - - + +
190A ALA* 4.6 0.2 - - + -
191A CYS* 3.7 28.8 - - - +
194A ILE* 3.7 26.2 - - + -
214A THR* 4.1 16.2 - - + -
218A ILE* 3.6 33.2 - - + -
243A ASP 3.0 16.9 + - - +
244A PHE* 3.7 11.0 - - + +
245A VAL 3.2 0.2 - - - -
246A ALA* 1.3 77.0 - - - +
248A GLU* 1.3 62.5 + - - +
250A LEU* 3.1 4.0 + - + +
251A THR* 3.0 18.7 + - + +
258A TRP* 3.9 20.2 - - + -
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Residues in contact with GLU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ILE* 3.7 16.1 - - + +
222A VAL* 3.4 26.4 - - + +
226A LYS* 3.3 30.9 + - - +
230A TRP* 5.6 0.5 - - - -
244A PHE 2.9 17.1 + - - +
245A VAL* 3.2 5.2 + - - +
247A LEU* 1.3 73.1 - - - +
249A ARG* 1.3 67.6 + - - +
251A THR* 2.6 30.4 + - - +
252A GLN* 3.4 21.2 + - - +
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Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LYS* 4.3 3.5 + - - -
245A VAL* 3.0 20.2 + - + +
246A ALA* 3.8 8.3 - - - +
248A GLU* 1.3 75.9 - - - +
250A LEU* 1.3 65.0 + - + +
252A GLN* 3.2 27.2 + - + +
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Residues in contact with LEU 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A CYS* 3.4 43.1 - - + +
194A ILE* 3.5 18.9 - - + +
195A GLU* 4.2 36.3 - - + +
198A LYS* 3.0 36.8 + - + +
246A ALA* 3.2 16.1 + - + +
247A LEU 3.1 8.8 + - - +
249A ARG* 1.3 83.1 - - + +
251A THR* 1.3 58.1 + - - +
254A MET* 3.8 0.3 - - - +
1003A GOL 4.6 3.6 - - - -
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Residues in contact with THR 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194A ILE* 4.1 7.2 - - + -
218A ILE* 4.3 17.3 - - + +
247A LEU* 3.0 19.9 + - + +
248A GLU* 2.6 30.5 + - - +
250A LEU* 1.3 75.3 - - - +
252A GLN* 1.3 67.5 + - - +
253A GLY 3.3 0.3 + - - -
254A MET* 3.1 21.9 + - - +
256A ILE* 3.7 28.9 - - + -
258A TRP* 4.3 4.3 - - + +
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Residues in contact with GLN 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A LYS* 3.0 25.3 + - - +
248A GLU* 3.6 33.2 + - - +
249A ARG* 3.4 20.6 - - + +
250A LEU 3.1 2.4 - - - -
251A THR* 1.3 80.1 + - - +
253A GLY* 1.3 62.1 + - - +
254A MET 3.4 0.5 + - - -
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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