Contacts of the helix formed by residues 267 - 278 (chain C) 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 ASP 267 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C LEU* 5.5 2.4 - - - +
255C ARG* 4.7 2.7 - - - +
265C PRO* 3.7 7.3 + - + +
266C LEU* 1.3 75.4 - - - +
268C GLY* 1.3 54.0 + - - +
269C ASN* 2.8 35.6 + - - +
270C LEU* 2.9 29.8 + - - +
271C MET 3.3 7.0 + - - -
296C TRP* 5.0 3.5 + - - -
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Residues in contact with GLY 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C ARG* 3.7 23.7 - - - +
266C LEU 3.8 1.2 + - - -
267C ASP* 1.3 71.1 - - - +
269C ASN* 1.3 56.4 + - - +
270C LEU 3.3 0.4 - - - -
271C MET* 3.7 9.6 - - - -
272C ASP* 3.1 27.2 + - - +
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Residues in contact with ASN 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C ASP* 2.8 20.8 + - - +
268C GLY* 1.3 78.5 - - - +
270C LEU* 1.3 60.3 + - - +
272C ASP* 4.0 2.4 - - - +
273C PHE 3.7 1.7 + - - -
294C HIS* 3.3 24.8 - - - -
295C PRO* 3.4 43.9 + - - +
296C TRP* 3.8 13.6 - - + +
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Residues in contact with LEU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C LEU* 4.2 16.4 - - + -
199C LEU* 3.9 29.6 - - + -
203C ILE* 4.5 5.6 - - + -
266C LEU* 4.0 29.8 - - + -
267C ASP* 2.9 12.9 + - - +
269C ASN* 1.3 76.6 - - - +
271C MET* 1.3 65.2 + - + +
272C ASP 3.2 2.2 - - - -
273C PHE* 3.2 5.0 + - + +
274C LEU* 2.6 47.5 + - + +
296C TRP* 3.5 42.6 - - + +
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Residues in contact with MET 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C ILE* 5.1 0.9 - - + -
254C LEU* 5.2 4.7 - - - -
255C ARG* 3.9 45.8 - - + +
258C LEU* 4.5 6.3 - - + -
266C LEU* 3.7 51.8 - - + +
267C ASP 3.3 3.8 + - - +
268C GLY* 3.8 12.3 - - - -
270C LEU* 1.3 92.4 - - + +
272C ASP* 1.3 62.2 + - - +
274C LEU* 3.7 32.8 - - + +
275C HIS* 3.1 38.3 + - + -
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Residues in contact with ASP 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268C GLY 3.1 19.4 + - - +
269C ASN* 4.0 6.7 - - - +
270C LEU 3.2 0.2 - - - -
271C MET* 1.3 74.7 - - - +
273C PHE* 1.3 65.5 + - - +
275C HIS* 3.0 16.0 + - - +
276C GLY* 3.1 10.2 + - - -
294C HIS* 3.2 21.7 + - + +
295C PRO* 5.7 0.3 - - - +
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Residues in contact with PHE 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLN* 4.2 3.6 - - + -
118C LEU* 3.7 14.6 - - + -
199C LEU* 3.5 30.3 - - + -
269C ASN 3.9 3.6 - - - +
270C LEU* 3.2 11.8 + - + +
272C ASP* 1.3 78.3 - - - +
274C LEU* 1.3 63.0 + - - +
275C HIS 3.0 1.2 + - - -
276C GLY* 3.1 12.7 + - - -
277C LEU* 3.2 30.7 - - + +
286C LEU* 4.2 3.7 - - + +
291C ALA* 3.6 33.0 - - + -
294C HIS* 3.4 42.1 + + + +
296C TRP* 3.5 28.7 - + + -
297C PHE* 3.5 20.2 - + - -
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Residues in contact with LEU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C GLY* 3.9 13.9 - - - +
199C LEU* 3.6 38.6 - - + -
200C ALA* 4.2 5.8 - - + +
203C ILE* 4.2 10.1 - - + -
254C LEU* 4.4 9.2 - - + +
258C LEU* 3.5 32.5 - - + -
270C LEU* 2.6 25.7 + - + +
271C MET* 3.7 23.6 - - + +
273C PHE* 1.3 75.9 - - - +
275C HIS* 1.3 61.5 + - - +
277C LEU* 4.0 3.0 + - - +
278C LEU* 3.5 30.2 + - + +
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Residues in contact with HIS 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C MET* 5.6 1.9 - - - -
254C LEU* 3.5 40.6 - - + +
255C ARG* 6.1 2.3 - - + +
271C MET* 3.1 26.8 + - + +
272C ASP* 3.0 13.9 + - - +
274C LEU* 1.3 76.5 - - + +
276C GLY* 1.3 57.6 + - - +
278C LEU* 2.8 26.4 + - - +
279C GLN* 3.3 25.4 + - - +
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Residues in contact with GLY 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272C ASP 3.1 6.1 + - - -
273C PHE 3.1 7.9 + - - -
275C HIS* 1.3 76.1 - - - +
277C LEU* 1.3 60.0 + - - +
279C GLN* 3.3 21.1 + - - +
284C MET 5.0 1.6 - - - -
285C ARG* 3.3 2.6 - - - -
286C LEU* 3.3 41.9 + - - -
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Residues in contact with LEU 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C GLN* 3.6 22.9 - - - +
118C LEU* 5.1 5.2 - - + -
192C ILE* 3.8 20.4 - - + +
193C TRP* 3.6 17.9 + - - -
195C CYS* 3.7 8.5 - - + -
196C GLY* 3.5 33.2 - - - +
199C LEU* 4.2 7.6 - - + -
273C PHE* 3.2 45.8 - - + +
274C LEU 4.3 5.2 - - - +
275C HIS 3.2 0.8 - - - -
276C GLY* 1.3 74.9 - - - +
278C LEU* 1.3 59.2 + - - +
279C GLN 3.3 3.9 + - - -
285C ARG* 3.4 15.4 + - - +
286C LEU* 4.1 11.7 - - + +
291C ALA* 4.9 3.1 - - + -
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Residues in contact with LEU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C TRP* 3.2 50.5 - - + +
196C GLY* 4.1 20.6 - - - +
197C CYS* 4.1 11.0 - - - -
200C ALA* 4.9 0.7 - - + -
208C LEU* 3.9 16.8 - - + -
209C PHE* 4.1 8.3 - - + -
225C MET* 3.7 40.9 - - + +
254C LEU* 5.1 7.0 - - + -
274C LEU* 3.5 29.3 + - + +
275C HIS* 2.8 15.8 + - - +
277C LEU* 1.3 72.6 - - - +
279C GLN* 1.3 63.1 + - - +
280C LEU 3.7 1.0 + - - -
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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