Contacts of the helix formed by residues 260 - 271 (chain X) in PDB entry 2OI4
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 SER 260 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141X GLU* 2.5 36.2 + - - -
258X ARG* 4.2 17.2 - - - +
259X VAL* 1.3 75.1 - - - +
261X SER* 1.3 59.2 + - - +
262X GLU* 3.7 14.1 + - - -
263X CYS* 3.3 14.0 + - - +
264X GLN* 2.9 25.3 + - - +
289X TRP* 3.8 5.2 - - - -
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Residues in contact with SER 261 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258X ARG* 5.3 0.8 - - - +
259X VAL 3.7 1.0 + - - -
260X SER* 1.3 73.9 - - - +
262X GLU* 1.3 68.2 + - - +
264X GLN* 4.0 11.2 - - - +
265X HIS* 3.0 28.2 + - - +
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Residues in contact with GLU 262 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260X SER* 3.2 16.3 - - - -
261X SER* 1.3 86.2 + - - +
263X CYS* 1.3 62.9 + - - +
265X HIS* 3.4 5.1 + - - +
266X LEU* 3.1 9.9 + - - +
287X HIS* 3.1 26.9 - - + -
288X PRO* 4.7 15.0 - - + -
289X TRP* 3.9 23.3 - - + +
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Residues in contact with CYS 263 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141X GLU* 3.8 1.8 - - - +
232X LEU* 4.4 5.6 - - - -
236X VAL* 4.0 14.8 - - - -
259X VAL* 3.5 21.1 - - + -
260X SER* 3.2 21.1 + - - +
262X GLU* 1.3 73.5 - - - +
264X GLN* 1.4 65.4 + - - +
265X HIS 3.1 0.3 + - - -
266X LEU* 3.2 4.4 + - - +
267X ILE* 3.0 35.9 + - - +
289X TRP* 3.6 42.9 - - - +
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Residues in contact with GLN 264 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255X PHE* 3.6 42.0 - - + +
257X GLN 5.3 0.4 + - - -
259X VAL* 3.3 28.6 + - + +
260X SER 2.9 25.1 + - - +
261X SER* 4.0 9.0 - - - +
263X CYS* 1.4 71.3 - - - +
265X HIS* 1.3 57.0 + - - +
267X ILE* 3.6 1.7 + - - +
268X ARG* 2.9 62.9 + - - +
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Residues in contact with HIS 265 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261X SER 3.0 19.3 + - - +
262X GLU* 3.4 7.9 - - - +
263X CYS 3.1 0.4 - - - -
264X GLN* 1.3 75.8 - - - +
266X LEU* 1.3 53.8 + - - +
268X ARG* 3.2 6.1 + - - +
269X TRP* 2.8 57.4 + + + +
287X HIS* 3.0 26.3 + + - +
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Residues in contact with LEU 266 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148X PHE* 4.5 7.4 - - + -
232X LEU* 3.8 15.5 - - + -
262X GLU 3.1 10.8 + - - +
263X CYS* 3.2 8.3 + - - +
265X HIS* 1.3 76.7 + - - +
267X ILE* 1.3 64.0 + - - +
269X TRP* 3.3 14.7 + - + +
270X CYS* 3.0 36.0 + - - -
279X PRO* 4.7 0.2 - - + -
284X ILE* 4.1 18.6 - - + -
287X HIS* 3.9 35.0 - - + +
289X TRP* 3.8 27.4 - - + -
290X MET* 4.0 17.3 - - + -
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Residues in contact with ILE 267 (chain X).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229X GLY* 4.1 4.0 - - - +
232X LEU* 3.7 25.1 - - + -
233X TYR* 3.8 35.7 - - + +
236X VAL* 3.8 20.0 - - + -
253X VAL* 4.6 2.5 - - + -
255X PHE* 3.9 26.9 - - + -
263X CYS* 3.0 21.8 + - - +
264X GLN 3.7 7.4 - - - +
266X LEU* 1.3 72.5 - - - +
268X ARG* 1.3 58.0 + - - +
270X CYS* 3.3 5.9 + - - +
271X LEU* 3.0 47.4 + - + +
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Residues in contact with ARG 268 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253X VAL* 2.8 49.6 + - + +
255X PHE* 3.4 21.7 - - + +
264X GLN* 2.9 51.1 + - - +
265X HIS* 3.8 5.6 - - - +
267X ILE* 1.3 73.9 - - - +
269X TRP* 1.3 65.0 + - - +
271X LEU* 3.4 6.4 + - - +
272X ALA* 3.3 19.1 + - - +
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Residues in contact with TRP 269 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265X HIS* 2.8 33.2 + + + +
266X LEU* 3.4 8.1 - - + +
268X ARG* 1.3 73.0 - - - +
270X CYS* 1.3 65.3 + - - +
271X LEU 3.0 2.7 + - - -
272X ALA* 3.1 17.7 + - + +
277X ASP 3.3 27.3 + - - -
278X ARG* 3.8 2.2 + - - +
279X PRO* 3.4 38.7 - - + +
283X GLU* 3.8 45.8 - - + -
287X HIS* 3.9 30.5 - + - -
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Residues in contact with CYS 270 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148X PHE* 5.0 6.3 - - - -
225X VAL* 3.7 12.6 - - - +
226X TRP* 3.5 12.1 + - - -
228X LEU* 5.0 2.2 - - - -
229X GLY* 3.5 28.7 - - - -
232X LEU* 5.7 0.7 - - - -
266X LEU* 3.0 28.4 + - - +
267X ILE* 3.3 4.5 + - - +
269X TRP* 1.3 72.6 - - - +
271X LEU* 1.3 58.4 + - - +
278X ARG* 3.2 23.4 - - - -
279X PRO* 3.8 13.0 - - - -
284X ILE* 3.9 30.1 - - - -
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Residues in contact with LEU 271 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226X TRP* 3.1 63.9 - - + +
229X GLY* 4.0 9.2 - - - +
230X ILE* 3.9 9.6 - - + +
241X PRO* 4.4 11.4 - - + -
242X PHE* 4.2 14.4 - - + -
251X GLY 4.7 8.1 - - - +
253X VAL* 3.8 30.1 - - + -
267X ILE* 3.0 31.5 + - + +
268X ARG* 3.5 6.7 - - - +
269X TRP 3.0 0.6 - - - -
270X CYS* 1.3 79.6 - - - +
272X ALA* 1.3 63.6 + - - +
273X LEU* 3.4 3.3 + - - +
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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