Contacts of the helix formed by residues 267 - 278 (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 ASP 267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LEU* 5.2 3.3 - - - +
265A PRO 3.5 6.6 + - - +
266A LEU* 1.3 76.4 - - - +
268A GLY* 1.3 63.1 + - - +
269A ASN* 3.4 29.8 + - - +
270A LEU* 3.4 23.6 + - - +
271A MET* 3.3 19.5 + - - +
296A TRP* 4.2 8.5 + - - -
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Residues in contact with GLY 268 (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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266A LEU 4.0 0.2 + - - -
267A ASP* 1.3 74.4 - - - +
269A ASN* 1.3 52.3 + - - +
271A MET* 3.0 8.2 + - - +
272A ASP* 2.8 35.5 + - - +
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Residues in contact with ASN 269 (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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267A ASP* 3.4 13.3 + - - +
268A GLY* 1.3 71.3 - - - +
270A LEU* 1.3 67.4 + - - +
271A MET 3.1 0.3 + - - -
272A ASP* 3.2 4.0 + - - +
273A PHE* 2.9 21.1 + - - +
294A HIS* 3.4 11.6 - - - -
295A PRO* 3.2 35.3 + - - +
296A TRP* 4.0 19.2 + - + -
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Residues in contact with LEU 270 (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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107A LEU* 4.2 19.5 - - + -
110A VAL* 6.0 0.7 - - + -
199A LEU* 4.5 7.2 - - + -
203A ILE* 3.8 27.1 - - + -
266A LEU* 3.7 31.0 - - + -
267A ASP* 3.4 29.0 + - - +
268A GLY 3.4 0.4 - - - -
269A ASN* 1.3 78.1 - - - +
271A MET* 1.3 57.2 + - + +
273A PHE* 3.5 2.3 - - - +
274A LEU* 3.1 27.8 + - + +
296A TRP* 3.4 48.3 - - + +
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Residues in contact with MET 271 (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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254A LEU* 3.5 31.2 - - + -
255A ARG* 3.6 30.1 - - + +
258A LEU* 4.1 9.6 - - - -
266A LEU* 4.4 22.2 - - + +
267A ASP 3.3 13.4 + - - +
268A GLY* 3.0 11.9 + - - +
270A LEU* 1.3 78.2 - - - +
272A ASP* 1.3 65.3 + - - +
274A LEU* 3.3 21.5 + - + +
275A HIS* 3.0 50.2 + - + +
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Residues in contact with ASP 272 (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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268A GLY 2.8 18.4 + - - +
269A ASN* 3.8 5.8 - - - +
271A MET* 1.3 71.8 - - - +
273A PHE* 1.3 62.8 + - - +
275A HIS* 3.4 9.6 + - - +
276A GLY* 3.0 21.3 + - - -
294A HIS* 3.0 23.5 + - + +
295A PRO* 5.7 0.2 - - - +
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Residues in contact with PHE 273 (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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114A GLN* 4.1 4.7 - - - -
118A LEU* 3.7 15.5 - - + -
199A LEU* 3.7 26.7 - - + -
269A ASN 2.9 16.7 + - - +
270A LEU* 3.5 6.1 - - - +
272A ASP* 1.3 77.7 - - - +
274A LEU* 1.3 60.5 + - - +
276A GLY* 3.2 9.5 + - - -
277A LEU* 3.2 33.8 + - + +
286A LEU* 4.3 3.4 - - + +
291A ALA* 3.3 34.1 - - + -
294A HIS* 3.3 35.1 + + + +
296A TRP* 3.5 31.9 - + + -
297A PHE* 3.6 18.8 - + - -
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Residues in contact with LEU 274 (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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196A GLY* 3.5 26.5 - - - +
199A LEU* 3.9 24.9 - - + -
200A ALA* 4.5 5.8 - - + +
203A ILE* 4.3 16.2 - - + -
208A LEU* 5.7 0.2 - - + -
254A LEU* 4.1 13.9 - - + -
258A LEU* 3.5 34.1 - - + -
270A LEU* 3.1 17.0 + - + +
271A MET* 3.6 16.8 - - - +
272A ASP 3.3 0.2 - - - -
273A PHE* 1.3 74.5 - - - +
275A HIS* 1.3 63.0 + - - +
277A LEU* 3.2 6.9 + - - +
278A LEU* 3.1 33.6 + - + +
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Residues in contact with HIS 275 (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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225A MET* 5.6 4.9 - - - -
252A ARG 5.4 1.1 - - - -
253A ASP* 5.1 5.3 - - - +
254A LEU* 3.6 39.9 + - + +
271A MET* 3.0 44.7 + - + +
272A ASP* 3.8 8.7 - - - +
274A LEU* 1.3 75.6 - - - +
276A GLY* 1.3 62.7 + - - +
278A LEU* 3.3 13.4 + - - +
279A GLN* 3.4 26.8 + - - +
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Residues in contact with GLY 276 (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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272A ASP 3.0 15.4 + - - -
273A PHE 3.2 5.6 + - - -
274A LEU 3.2 0.2 - - - -
275A HIS* 1.3 77.8 - - - +
277A LEU* 1.3 57.8 + - - +
279A GLN* 4.1 5.1 - - - +
284A MET 3.9 4.2 - - - +
285A ARG* 3.6 6.2 - - - -
286A LEU* 2.9 43.1 + - - -
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Residues in contact with LEU 277 (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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114A GLN* 3.7 26.2 - - - +
118A LEU* 5.6 1.6 - - + -
192A ILE* 3.9 29.2 - - + +
193A TRP* 4.2 2.8 - - - -
195A CYS* 4.1 2.9 - - + -
196A GLY* 3.8 26.2 - - - +
199A LEU* 4.1 6.7 - - + -
273A PHE* 3.2 40.0 + - + +
274A LEU* 3.6 6.5 - - - +
275A HIS 3.2 0.2 - - - -
276A GLY* 1.3 78.6 - - - +
278A LEU* 1.3 58.6 + - - +
279A GLN 3.4 0.4 - - - -
285A ARG* 3.0 26.5 + - - +
286A LEU* 3.8 26.2 - - + -
291A ALA* 4.4 6.7 - - + -
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Residues in contact with LEU 278 (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* 3.7 55.8 - - + +
196A GLY* 3.8 22.2 - - - +
197A CYS* 4.0 10.8 - - - -
208A LEU* 3.8 21.8 - - + -
209A PHE* 4.4 1.8 - - + -
225A MET* 3.6 33.4 - - + +
254A LEU* 4.3 5.4 - - + -
274A LEU* 3.1 27.6 + - + +
275A HIS* 3.3 11.0 + - - +
277A LEU* 1.3 77.0 - - - +
279A GLN* 1.3 61.6 + - - +
280A LEU 4.0 0.2 + - - -
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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