Contacts of the helix formed by residues 259 - 269 (chain A) in PDB entry 2P8Q
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 ALA 259 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A CYS* 4.3 15.0 - - + -
255A TYR* 3.0 17.2 + - + +
257A GLY 3.4 2.0 + - - -
258A PRO* 1.3 83.3 - - + +
260A LEU* 1.3 76.4 + - + +
261A PHE 3.4 1.6 - - - -
262A ALA* 3.4 10.4 + - - +
263A ILE* 3.1 27.6 + - + +
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Residues in contact with LEU 260 (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 MET* 4.1 6.7 - - + -
223A CYS* 3.9 19.5 - - - -
241A LEU* 3.8 32.8 - - + -
245A MET* 4.2 15.5 - - + -
252A MET* 3.9 28.0 - - - +
255A TYR* 2.9 29.5 + - + +
256A MET* 3.9 20.6 - - + +
259A ALA* 1.3 71.7 - - + +
261A PHE* 1.3 69.1 + - - +
263A ILE* 3.2 4.0 + - + -
264A THR* 2.9 31.4 + - + +
282A PHE* 4.5 11.9 - - + -
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Residues in contact with PHE 261 (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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256A MET* 3.1 30.3 + - + +
257A GLY* 4.6 7.4 - - - +
260A LEU* 1.3 76.3 - - - +
262A ALA* 1.3 70.0 + - + +
264A THR* 4.0 4.0 - - - -
265A ILE* 2.8 64.2 + - + +
283A TRP* 4.0 11.2 - + - -
318A ALA* 3.9 23.1 - - + -
321A TYR* 3.5 39.5 - + + -
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Residues in contact with ALA 262 (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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257A GLY 5.4 1.7 + - - +
258A PRO 6.0 0.4 - - - +
259A ALA* 3.4 11.2 + - - +
260A LEU 3.3 0.2 - - - -
261A PHE* 1.3 87.7 - - + +
263A ILE* 1.3 63.8 + - + +
265A ILE* 4.1 4.3 - - - +
266A GLU* 3.1 26.7 + - - +
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Residues in contact with ILE 263 (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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223A CYS* 4.7 14.6 - - + +
226A THR* 3.5 22.0 - - + +
227A GLN* 2.8 39.0 - - + +
234A ARG* 5.8 0.2 + - - -
238A LEU* 3.8 22.9 - - + -
241A LEU* 4.1 9.2 - - + -
259A ALA* 3.1 20.4 + - + +
260A LEU* 3.2 9.4 + - - +
262A ALA* 1.3 79.5 - - + +
264A THR* 1.3 58.4 + - - +
266A GLU* 3.6 6.0 - - + +
267A ALA* 3.1 24.8 + - - +
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Residues in contact with THR 264 (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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238A LEU* 4.8 6.1 - - + -
241A LEU* 4.7 7.2 - - + -
260A LEU* 2.9 23.5 + - - +
261A PHE 3.3 3.5 + - - -
263A ILE* 1.3 79.7 - - + +
265A ILE* 1.3 65.3 + - - +
267A ALA* 3.5 8.6 + - - +
268A MET* 3.2 27.6 + - - +
279A GLY* 3.8 4.4 - - - -
282A PHE* 3.7 42.9 - - + -
283A TRP* 3.2 27.7 + - - -
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Residues in contact with ILE 265 (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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261A PHE* 2.8 71.5 + - + +
262A ALA* 4.1 5.6 - - - +
264A THR* 1.3 75.4 - - - +
266A GLU* 1.3 65.8 + - - +
268A MET* 3.2 17.6 + - - +
269A LYS* 3.2 40.7 + - - +
283A TRP* 3.4 26.0 - - + +
321A TYR* 5.0 3.6 - - + -
322A LEU* 4.6 7.0 - - + -
325A ILE* 4.1 14.7 - - + +
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Residues in contact with GLU 266 (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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227A GLN* 6.1 3.4 - - - +
234A ARG* 4.8 10.7 + - - +
262A ALA 3.1 19.0 + - - +
263A ILE* 3.6 7.0 - - + +
265A ILE* 1.3 78.1 - - - +
267A ALA* 1.3 63.9 + - - +
269A LYS* 3.3 18.3 + - - +
270A SER* 3.3 17.8 + - - -
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Residues in contact with ALA 267 (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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234A ARG* 4.4 6.0 - - - +
238A LEU* 4.0 16.4 - - + -
263A ILE 3.1 16.6 + - - +
264A THR* 3.7 9.0 - - - +
265A ILE 3.3 0.4 - - - -
266A GLU* 1.3 76.7 - - - +
268A MET* 1.3 63.4 + - - +
270A SER* 3.1 18.9 - - - -
275A VAL* 3.7 29.2 - - + +
276A ALA* 3.2 13.5 + - - -
279A GLY* 4.0 8.1 - - - -
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Residues in contact with MET 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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264A THR 3.2 12.4 + - - +
265A ILE* 3.2 13.2 + - - +
267A ALA* 1.3 80.0 - - - +
269A LYS* 1.3 59.0 + - - +
270A SER 3.4 1.6 + - - +
276A ALA* 3.8 19.8 - - - +
279A GLY 3.5 19.5 - - - +
280A ILE* 3.8 15.9 - - + +
283A TRP* 3.6 31.0 - - + -
322A LEU* 3.8 16.6 - - + -
325A ILE* 3.8 32.3 - - + +
326A LEU* 3.5 36.1 - - + -
329A THR* 5.0 5.4 + - - -
351A CYS* 5.5 0.4 - - - -
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Residues in contact with LYS 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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265A ILE* 3.2 26.5 + - + +
266A GLU* 3.3 19.2 + - - +
267A ALA 3.2 0.6 - - - -
268A MET* 1.3 76.0 - - - +
270A SER* 1.3 64.4 + - - +
271A ASP* 3.6 1.6 + - - +
325A ILE* 3.9 37.5 - - + -
332A LYS* 5.7 3.0 + - - -
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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