Contacts of the helix formed by residues 265 - 280 (chain C) in PDB entry 7CE1
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 265 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89C GLU* 3.4 25.7 - - - +
237C ILE* 3.6 31.2 + - - +
263C SER* 3.0 6.7 + - - -
264C ILE* 1.3 80.7 - - - +
266C GLY* 1.3 59.6 + - - +
267C SER* 3.0 2.8 + - - -
268C SER* 2.8 31.2 + - - -
269C THR* 3.0 13.6 + - - -
292C LYS* 4.2 1.3 - - - +
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Residues in contact with GLY 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C GLU* 2.9 8.5 + - - -
91C MET* 4.6 0.7 - - - -
265C SER* 1.3 72.2 - - - +
267C SER* 1.3 60.7 + - - +
269C THR* 3.5 9.8 - - - -
270C ILE* 3.5 25.6 + - - +
291C SER* 3.7 2.7 - - - -
292C LYS 3.3 24.0 + - - -
293C GLN* 5.1 1.1 - - - +
294C SER 6.0 0.2 - - - -
297C PHE* 3.9 19.8 - - - -
298C LEU* 4.3 1.9 - - - +
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Residues in contact with SER 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C GLU* 3.0 21.5 + - - +
90C LEU* 3.8 17.3 - - - -
91C MET* 2.5 42.9 + - - +
241C LEU* 3.1 21.1 - - - +
265C SER* 3.0 2.5 - - - -
266C GLY* 1.3 75.7 - - - +
268C SER* 1.3 65.0 + - - +
269C THR 3.2 0.2 - - - -
270C ILE* 3.3 20.1 - - - +
271C ALA 3.6 0.7 + - - -
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Residues in contact with SER 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C ILE* 3.9 21.3 - - - +
237C ILE* 4.2 7.6 - - - +
241C LEU* 3.8 9.8 - - - +
244C ILE* 3.7 27.2 - - - +
263C SER* 3.5 8.3 + - - -
265C SER* 2.8 29.0 + - - -
267C SER* 1.3 75.6 - - - +
269C THR* 1.3 55.1 + - - +
271C ALA* 3.4 1.3 + - - +
272C LEU* 2.8 37.1 + - - +
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Residues in contact with THR 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C SER* 2.7 22.9 + - - -
265C SER 3.0 4.3 + - - -
266C GLY* 3.5 9.0 - - - -
268C SER* 1.3 79.6 + - - +
270C ILE* 1.3 57.6 + - - +
272C LEU* 3.2 7.2 + - - +
273C VAL* 2.8 35.1 + - + +
289C ILE* 3.9 19.3 - - + -
291C SER* 2.5 39.6 + - - +
298C LEU* 4.6 5.2 - - + -
305C ILE* 4.3 16.2 - - + -
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Residues in contact with ILE 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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90C LEU* 4.5 15.3 - - + -
91C MET* 4.5 20.6 - - + -
241C LEU* 5.5 1.3 - - + -
266C GLY 3.5 6.3 + - - +
267C SER 3.3 14.1 - - - +
269C THR* 1.3 76.1 - - - +
271C ALA* 1.3 64.2 + - + +
273C VAL* 3.3 7.8 + - - +
274C ALA* 2.8 28.4 + - - +
297C PHE* 3.8 10.1 - - + -
298C LEU* 3.5 29.2 - - + -
301C ILE* 6.4 2.5 - - + -
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Residues in contact with ALA 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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241C LEU* 3.7 51.4 - - + +
244C ILE* 4.2 6.7 - - + -
245C ARG* 3.4 13.5 - - + -
267C SER 3.9 0.2 - - - +
268C SER 3.4 4.0 + - - +
269C THR 3.3 0.6 - - - -
270C ILE* 1.3 80.6 - - + +
272C LEU* 1.3 65.5 + - - +
274C ALA* 3.3 8.7 + - - +
275C GLY 3.2 16.5 + - - -
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Residues in contact with LEU 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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202C ILE* 3.7 33.0 - - + -
235C ILE* 5.8 0.7 - - + -
244C ILE* 3.8 29.3 - - + +
247C PHE* 4.4 13.9 - - + -
248C GLY* 4.0 5.6 - - - -
251C LEU* 5.9 0.7 - - + -
261C ILE* 3.7 28.9 - - + -
263C SER* 6.4 0.2 - - - -
268C SER 2.8 19.2 + - - +
269C THR* 3.6 6.5 - - - +
271C ALA* 1.3 79.4 - - - +
273C VAL* 1.3 62.3 + - + +
275C GLY* 3.3 2.1 + - - -
276C PHE* 3.1 43.3 + - + -
289C ILE* 5.3 3.8 - - + -
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Residues in contact with VAL 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C THR* 2.8 28.3 + - + +
270C ILE* 3.6 7.2 - - - +
272C LEU* 1.3 76.2 - - + +
274C ALA* 1.3 54.8 + - - +
276C PHE* 3.2 9.1 + - + +
277C GLU* 2.7 51.5 + - - +
283C ILE* 3.9 16.4 - - + -
289C ILE* 4.6 16.8 - - + -
302C GLN* 3.9 21.8 - - + +
305C ILE* 4.3 21.3 - - + -
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Residues in contact with ALA 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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245C ARG* 5.0 6.1 - - + -
270C ILE 2.8 13.7 + - - +
271C ALA* 3.4 13.5 - - - +
272C LEU 3.2 0.2 - - - -
273C VAL* 1.3 78.6 - - - +
275C GLY* 1.3 56.1 + - - +
277C GLU* 3.2 11.0 - - - +
278C ALA* 3.1 28.6 + - - +
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Residues in contact with GLY 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245C ARG* 3.0 28.9 - - - +
248C GLY* 4.4 0.4 - - - -
249C LYS* 3.6 14.2 - - - +
271C ALA 3.2 8.3 + - - -
272C LEU 3.3 3.3 + - - -
273C VAL 3.2 0.2 - - - -
274C ALA* 1.3 77.6 - - - +
276C PHE* 1.3 64.0 + - - +
278C ALA* 3.5 4.6 + - - +
279C ALA* 3.0 25.6 + - - +
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Residues in contact with PHE 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C GLY* 3.4 33.4 - - - -
251C LEU* 4.5 12.8 - - + -
252C MET* 3.6 17.3 - - + -
261C ILE* 3.4 35.2 - - + -
272C LEU* 3.1 32.2 + - + +
273C VAL* 3.5 13.0 - - + +
275C GLY* 1.3 75.7 - - - +
277C GLU* 1.3 63.7 + - - +
279C ALA* 3.4 2.2 + - - +
280C GLY 3.1 17.7 + - - -
281C VAL* 3.1 27.1 + - + +
283C ILE* 5.0 6.1 - - + -
287C ILE* 3.6 31.4 - - + -
289C ILE* 4.2 11.4 - - + -
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Residues in contact with GLU 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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273C VAL* 2.7 29.4 + - - +
274C ALA* 3.2 15.3 - - - +
276C PHE* 1.3 75.3 - - - +
278C ALA* 1.3 57.8 + - - +
280C GLY* 3.0 21.0 + - - -
281C VAL* 4.0 8.5 + - - +
283C ILE* 3.1 24.4 - - - +
302C GLN* 3.4 13.3 + - - -
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Residues in contact with ALA 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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249C LYS* 5.2 4.3 - - + -
274C ALA 3.1 12.8 + - - +
275C GLY* 3.9 6.5 - - - +
277C GLU* 1.3 74.1 - - - +
279C ALA* 1.3 62.2 + - - +
280C GLY* 3.0 5.8 + - - -
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Residues in contact with ALA 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C LYS* 3.6 33.1 - - + +
252C MET* 4.2 15.3 - - + -
253C GLN* 4.6 8.7 - - + +
275C GLY 3.0 18.3 + - - +
276C PHE 3.9 3.8 - - - +
278C ALA* 1.3 75.8 - - - +
280C GLY* 1.3 61.3 + - - +
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Residues in contact with GLY 280 (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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276C PHE 3.1 1.2 + - - -
277C GLU 3.0 15.5 + - - -
278C ALA 3.0 1.5 - - - -
279C ALA* 1.3 82.3 - - - +
281C VAL* 1.3 60.6 + - - +
286C ASP* 4.9 0.9 - - - +
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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