Contacts of the helix formed by residues 266 - 278 (chain B) in PDB entry 2R8P
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 GLY 266 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B GLN* 2.9 23.0 + - - -
264B PRO* 3.2 3.3 - - - -
265B LEU* 1.3 78.5 - - - +
267B ASP* 1.3 60.0 + - - -
268B ALA 3.4 2.9 - - - -
269B GLU 3.3 3.6 + - - -
270B ILE* 2.9 29.1 + - - +
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Residues in contact with ASP 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B GLN* 3.4 29.0 + - - +
266B GLY* 1.3 72.1 - - - -
268B ALA* 1.3 62.5 + - - +
270B ILE* 3.3 8.4 + - - +
271B ALA* 3.0 23.2 + - - +
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Residues in contact with ALA 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B GLY 3.4 0.4 - - - -
267B ASP* 1.3 77.0 - - - +
269B GLU* 1.3 63.9 + - - +
271B ALA* 3.3 9.1 + - - +
272B LEU* 3.2 29.1 + - + +
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Residues in contact with GLU 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251B SER* 2.6 29.7 + - - +
252B PRO* 3.2 12.8 - - - +
253B ASN* 2.9 48.1 + - - +
254B LYS* 4.3 10.1 - - + -
265B LEU* 3.4 33.2 - - + +
266B GLY 3.3 2.4 + - - -
268B ALA* 1.3 80.1 - - - +
270B ILE* 1.3 57.6 + - - +
272B LEU* 3.2 7.7 + - - +
273B THR* 2.8 33.4 + - - +
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Residues in contact with ILE 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 3.6 31.8 - - + +
17B ASP* 3.7 8.1 - - - +
20B GLN* 3.5 44.4 - - + +
265B LEU* 4.1 14.1 - - + -
266B GLY 2.9 15.2 + - - +
267B ASP* 3.3 7.8 + - - +
269B GLU* 1.3 75.0 - - - +
271B ALA* 1.3 58.4 + - - +
273B THR* 3.1 7.5 + - - -
274B ARG* 2.9 57.4 + - - +
283B PRO* 6.2 0.2 - - + -
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Residues in contact with ALA 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B ASP 3.0 12.4 + - - +
268B ALA* 3.5 11.2 - - - +
269B GLU 3.3 0.2 - - - -
270B ILE* 1.3 77.3 - - - +
272B LEU* 1.3 63.1 + - + +
274B ARG* 3.4 1.1 + - - +
275B GLU* 3.2 20.8 + - - +
674B EDO 3.3 44.7 - - - +
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Residues in contact with LEU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B PRO* 3.7 21.3 - - + +
253B ASN* 3.5 26.7 - - - +
268B ALA* 3.2 16.4 + - + +
269B GLU* 3.2 13.9 + - - +
271B ALA* 1.3 77.4 - - + +
273B THR* 1.3 57.2 + - - +
275B GLU* 3.3 20.9 + - - +
276B GLN* 3.0 28.1 + - - +
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Residues in contact with THR 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B MET* 3.6 26.5 - - - -
31B MET* 3.7 11.7 - - + -
250B GLY 3.5 25.8 - - - +
251B SER* 3.3 22.2 - - - -
252B PRO* 4.0 0.4 - - - +
265B LEU* 4.3 3.1 - - - +
269B GLU* 2.8 23.8 + - - +
270B ILE* 3.1 6.0 + - - -
272B LEU* 1.3 74.7 - - - +
274B ARG* 1.3 64.7 + - - +
276B GLN* 3.2 1.7 + - - +
277B LEU* 2.9 35.8 + - + +
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Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ALA* 4.6 0.8 - - - +
16B MET* 3.8 11.3 - - + +
17B ASP* 2.6 43.0 + - - -
270B ILE* 2.9 31.9 + - - +
271B ALA* 3.5 10.1 - - - +
273B THR* 1.3 75.2 - - - +
275B GLU* 1.3 58.2 + - - +
277B LEU* 4.8 0.2 - - - -
278B GLY* 2.9 25.3 + - - -
279B TRP* 3.0 45.5 + - + +
280B LYS 5.2 2.2 - - - -
281B TYR 2.9 31.2 + - - -
282B ALA* 3.4 3.4 + - - +
283B PRO* 3.3 22.3 - - - +
674B EDO 3.9 27.4 - - - -
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B ALA* 3.2 9.2 + - - +
272B LEU* 3.6 26.9 - - - +
273B THR 3.1 0.8 - - - -
274B ARG* 1.3 77.8 - - - +
276B GLN* 1.3 61.6 + - - +
278B GLY* 3.4 10.8 + - - -
674B EDO 2.7 30.1 + - - -
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Residues in contact with GLN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B PHE* 5.9 3.0 - - - -
250B GLY* 3.3 40.9 + - - +
251B SER 4.5 2.2 + - - -
252B PRO* 3.4 30.4 - - + +
272B LEU 3.0 13.6 + - - +
273B THR 3.8 0.2 - - - +
275B GLU* 1.3 77.5 - - - +
277B LEU* 1.3 62.8 + - + +
278B GLY 3.5 0.5 + - - -
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Residues in contact with LEU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B GLU* 6.0 0.7 - - - +
9B ASN* 3.3 42.5 + - + +
12B ARG* 3.9 31.2 - - + -
13B ALA* 5.5 0.7 - - + +
16B MET* 4.9 5.8 - - + -
249B PHE* 4.0 17.9 - - + -
250B GLY* 3.6 24.0 - - - -
273B THR* 2.9 36.9 + - + +
274B ARG 4.1 2.2 - - - +
276B GLN* 1.3 79.2 - - + +
278B GLY* 1.3 61.1 + - - +
279B TRP* 4.1 11.4 - - + +
677B EDO 5.3 1.0 + - - -
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Residues in contact with GLY 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274B ARG 2.9 7.5 + - - -
275B GLU* 3.4 7.4 + - - -
276B GLN 3.3 4.4 + - - -
277B LEU* 1.3 77.5 - - - +
279B TRP* 1.3 51.6 + - - +
280B LYS* 3.6 1.2 + - - +
677B EDO 2.7 31.6 + - - -
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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