Contacts of the helix formed by residues 213 - 226 (chain A) in PDB entry 2PK9
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 213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172A LEU* 3.7 8.9 - - - +
211A GLY 3.7 0.6 - - - -
212A THR* 1.3 94.0 - - + +
214A ASP* 1.3 77.8 + - - +
215A GLU* 3.1 14.1 + - - +
216A GLU* 3.0 36.0 + - - +
217A GLN* 2.9 23.2 + - - +
151D ARG* 3.6 12.1 - - - +
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Residues in contact with ASP 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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172A LEU* 3.5 16.7 - - + +
180A LEU* 5.0 13.6 - - + +
213A ASN* 1.3 76.6 - - - +
215A GLU* 1.3 74.5 + - - +
217A GLN* 4.1 2.5 - - - +
218A LEU* 3.6 26.3 + - + +
241A LYS* 5.8 10.2 - - + -
151D ARG* 3.3 24.6 + - - -
154D GLU* 4.6 9.9 - - - +
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Residues in contact with GLU 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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213A ASN* 3.1 10.3 + - - +
214A ASP* 1.3 91.4 - - - +
216A GLU* 1.3 67.4 + - - +
218A LEU* 3.4 11.8 + - - +
219A LYS* 3.2 20.1 + - - +
241A LYS* 6.0 1.7 - - - +
70D LYS* 3.6 47.2 - - - +
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Residues in contact with GLU 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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210A PRO 4.3 4.0 - - - +
211A GLY* 4.1 4.6 - - - -
212A THR* 3.4 39.8 + - - +
213A ASN* 3.0 21.7 + - - +
215A GLU* 1.3 75.0 - - - +
217A GLN* 1.3 60.0 + - - +
219A LYS* 3.3 15.2 + - - +
220A LEU* 2.8 52.1 + - + +
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Residues in contact with GLN 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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172A LEU* 3.4 31.0 + - + +
173A TRP* 3.5 19.1 + - - +
175A ARG 5.2 1.0 + - - -
180A LEU* 3.8 20.6 - - + -
209A PHE* 2.8 51.5 + - - +
211A GLY* 3.1 20.6 + - - -
213A ASN 2.9 19.0 + - - +
214A ASP 4.1 4.3 - - - +
216A GLU* 1.3 75.8 - - - +
218A LEU* 1.3 62.8 + - - +
220A LEU* 3.2 5.0 + - - +
221A ILE* 3.0 31.9 + - + +
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Residues in contact with LEU 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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177A PRO* 3.7 29.8 - - + +
180A LEU* 4.0 21.8 - - + +
181A MET* 3.8 21.1 - - + -
214A ASP* 3.6 16.0 + - + +
215A GLU* 3.4 15.1 + - - +
216A GLU 3.3 0.6 - - - -
217A GLN* 1.3 78.5 - - - +
219A LYS* 1.3 63.4 + - - +
221A ILE* 2.9 8.8 + - - +
222A PHE* 2.9 61.7 + - + -
241A LYS* 5.5 4.5 - - + +
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Residues in contact with LYS 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 GLU 3.2 10.8 + - - +
216A GLU* 3.5 16.2 - - - +
218A LEU* 1.3 77.7 - - - +
220A LEU* 1.3 70.5 + - - +
222A PHE* 3.3 5.0 + - - -
223A ASP* 2.9 62.1 + - - +
249A ARG* 3.3 23.2 + - - +
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Residues in contact with LEU 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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208A LEU 5.7 0.4 - - - +
209A PHE* 3.4 20.6 - - + -
210A PRO* 3.7 23.3 - - + +
211A GLY* 3.5 35.0 - - - +
216A GLU* 2.8 36.7 + - + +
217A GLN* 3.5 5.6 - - - +
218A LEU 3.2 0.2 - - - -
219A LYS* 1.3 80.1 - - - +
221A ILE* 1.3 66.3 + - - +
223A ASP* 3.8 21.2 + - + +
224A ILE* 3.9 10.9 + - - +
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Residues in contact with ILE 221 (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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175A ARG 4.1 6.5 - - - +
177A PRO* 4.3 13.0 - - + -
180A LEU* 3.9 25.8 - - + -
193A TRP* 3.7 37.7 - - + -
209A PHE* 3.6 22.0 - - + -
217A GLN* 3.0 27.9 + - + +
218A LEU* 2.9 8.8 + - - +
220A LEU* 1.3 76.3 - - - +
222A PHE* 1.3 54.1 + - + +
224A ILE* 3.0 6.1 + - - +
225A MET* 2.7 37.8 + - + +
280A LEU* 3.7 22.7 - - + -
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Residues in contact with PHE 222 (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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177A PRO* 4.6 5.8 - - + -
181A MET* 4.3 8.7 - - + -
218A LEU* 2.9 55.6 + - + +
219A LYS* 4.5 3.6 - - - -
221A ILE* 1.3 75.3 - - + +
223A ASP* 1.3 63.6 + - - +
226A GLY* 3.1 41.3 + - - +
227A THR* 3.8 17.7 - - + -
228A PRO* 3.6 31.6 - - + -
233A TRP* 5.8 0.4 - + - -
246A ILE* 5.0 11.9 - - + -
249A ARG* 3.5 32.6 - - - +
250A PRO 5.0 0.2 - - - +
280A LEU* 4.0 18.4 - - + -
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Residues in contact with ASP 223 (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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219A LYS* 2.9 50.2 + - - +
220A LEU* 4.0 13.6 - - + +
221A ILE 3.2 0.8 - - - -
222A PHE* 1.3 75.7 - - - +
224A ILE* 1.3 59.7 + - + +
226A GLY 4.8 0.2 - - - -
249A ARG* 2.5 41.4 + - - +
250A PRO 5.0 3.2 - - - +
252A ARG* 3.3 40.9 + - - +
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Residues in contact with ILE 224 (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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208A LEU* 4.3 24.9 - - + +
209A PHE* 4.5 7.0 - - + -
220A LEU 4.1 7.2 - - - +
221A ILE 3.0 5.8 + - - +
223A ASP* 1.3 84.1 - - + +
225A MET* 1.3 79.6 + - + +
226A GLY 3.2 4.0 - - - -
251A PRO* 3.6 0.3 - - - +
252A ARG* 2.8 62.3 + - - +
254A LEU* 4.0 13.7 - - + -
257A VAL* 3.8 31.2 - - + -
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Residues in contact with MET 225 (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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193A TRP* 4.1 10.8 - - + -
209A PHE* 4.1 16.6 - - + -
221A ILE* 2.7 30.9 + - + +
224A ILE* 1.3 87.2 - - + +
226A GLY* 1.3 58.8 + - - +
227A THR 4.8 0.3 - - - +
251A PRO* 3.4 17.9 - - - +
252A ARG 5.8 0.4 - - - +
254A LEU* 3.6 42.4 - - + -
275A HIS* 5.6 3.8 - - - -
278A LEU* 3.6 32.5 - - + +
280A LEU* 3.9 28.2 - - + +
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Residues in contact with GLY 226 (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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222A PHE* 3.1 34.1 + - - -
224A ILE 3.2 4.0 + - - -
225A MET* 1.3 84.2 - - - +
227A THR* 1.3 67.3 + - - +
249A ARG 3.5 14.1 - - - -
250A PRO 4.0 1.6 - - - -
251A PRO* 3.6 15.3 - - - +
280A LEU* 3.4 4.7 - - - +
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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