Contacts of the helix formed by residues 211 - 220 (chain A) 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 SER 211 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A GLN* 4.5 2.9 + - - -
186A GLU* 3.1 35.8 - - - +
209A THR* 2.9 10.5 + - - -
210A ASN* 1.3 78.6 + - - +
212A MET* 1.3 63.7 + - - +
213A PHE* 3.5 9.4 + - - +
214A THR* 2.6 30.7 + - - -
215A ILE* 3.1 23.8 + - - +
260A HIS* 4.7 0.4 - - - -
4C C 3.8 1.6 - - - -
5C A 5.2 3.8 - - - -
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Residues in contact with MET 212 (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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211A SER* 1.3 70.3 - - - +
213A PHE* 1.3 60.6 + - - +
214A THR 2.9 0.3 + - - -
215A ILE* 3.6 19.7 - - + -
216A ASN* 2.6 78.0 + - - +
260A HIS* 3.3 34.5 - - + +
3C A 5.0 4.3 - - - +
4C C 3.0 48.1 + - - +
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Residues in contact with PHE 213 (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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183A GLN* 3.4 41.7 - - + +
187A ILE* 4.5 10.8 - - + -
211A SER* 3.7 6.5 - - - +
212A MET* 1.3 81.0 - - - +
214A THR* 1.3 58.4 + - - +
217A GLY* 3.3 12.9 + - - -
221A TRP* 3.5 24.8 - + - -
240A ASN* 4.1 18.8 - - + -
244A PHE* 3.6 38.2 - + - -
4C C 4.7 11.3 + - - +
26D T 3.8 26.9 - - - +
27D C 3.4 35.7 - - - -
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Residues in contact with THR 214 (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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186A GLU* 3.9 1.8 - - - +
187A ILE* 3.5 40.4 + - + +
190A ALA* 4.6 4.0 - - + -
209A THR* 5.2 4.0 - - + +
211A SER* 2.6 31.5 + - - -
212A MET 2.9 0.2 - - - -
213A PHE* 1.3 76.5 - - - +
215A ILE* 1.3 68.1 + - - +
217A GLY* 3.0 1.6 + - - -
218A ILE* 2.8 24.3 + - - +
244A PHE* 4.2 6.5 - - + -
247A LEU* 4.0 19.1 - - + -
258A TRP* 4.1 17.3 - - + -
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Residues in contact with ILE 215 (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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209A THR* 3.8 17.3 - - + +
211A SER 3.1 12.9 + - - +
212A MET* 3.1 22.4 + - + +
214A THR* 1.3 80.0 - - - +
216A ASN* 1.3 60.7 + - - +
218A ILE* 3.5 7.8 - - - +
219A THR* 2.9 42.3 + - + +
258A TRP* 3.9 26.7 - - + +
259A MET 3.5 36.1 - - - +
260A HIS* 3.8 16.4 - - + +
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Residues in contact with ASN 216 (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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212A MET* 2.6 57.0 + - - +
215A ILE* 1.3 77.0 - - - +
217A GLY* 1.3 63.7 + - - +
220A ASN* 3.1 21.9 + - - +
221A TRP* 3.0 56.5 + - + +
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Residues in contact with GLY 217 (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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213A PHE 3.3 7.4 + - - -
214A THR 3.0 6.4 + - - -
216A ASN* 1.3 81.4 - - - +
218A ILE* 1.3 67.4 + - - +
219A THR 2.8 2.6 + - - -
220A ASN 3.0 2.6 + - - -
221A TRP* 3.8 19.0 - - - -
222A VAL* 3.0 23.4 + - - +
225A TRP* 5.1 0.2 - - - -
244A PHE* 3.8 19.5 - - - -
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Residues in contact with ILE 218 (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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214A THR 2.8 15.8 + - - +
215A ILE* 3.5 7.4 - - - +
217A GLY* 1.3 69.8 - - - -
219A THR* 1.3 78.4 + - + +
222A VAL* 3.3 18.8 - - + +
223A GLN* 4.5 3.1 + - - -
244A PHE* 3.9 10.2 - - + +
247A LEU* 3.6 32.3 - - + -
248A GLU* 4.0 28.2 - - + +
251A THR* 4.0 11.9 - - + -
258A TRP* 3.4 43.1 - - + +
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Residues in contact with THR 219 (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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215A ILE* 2.9 26.1 + - + +
217A GLY 2.8 4.0 + - - -
218A ILE* 1.3 93.3 - - + +
220A ASN* 1.3 80.4 + - - +
223A GLN* 3.5 18.6 + - - +
258A TRP* 3.7 12.3 - - + +
2002A MES 3.5 26.5 - - - +
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Residues in contact with ASN 220 (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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216A ASN* 3.1 20.7 + - + +
217A GLY 3.0 4.6 + - - -
218A ILE 3.6 0.2 - - - -
219A THR* 1.3 106.1 + - - +
221A TRP* 1.3 77.8 + - + +
222A VAL* 3.1 1.9 - - - +
223A GLN* 2.9 27.9 + - - +
224A GLY* 3.7 3.1 + - - -
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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