Contacts of the helix formed by residues 263 - 276 (chain D) in PDB entry 7CR3
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 THR 263 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251D TYR* 3.4 21.7 - - - -
261D PHE 4.5 0.7 - - - -
262D ASP* 1.3 89.3 + - + +
264D TYR* 1.3 62.8 + - - +
265D ALA* 3.3 17.1 + - - +
266D ASP* 3.4 18.1 + - - +
267D ALA* 3.5 13.5 + - - +
114G THR* 4.2 27.6 - - - +
115G ILE* 4.2 15.2 - - + +
116G LYS* 5.2 2.7 - - + +
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Residues in contact with TYR 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244D ILE* 3.5 33.2 + - + +
247D SER* 4.5 2.2 - - - -
248D PHE* 3.5 40.9 - + + +
251D TYR* 3.7 24.2 + + + -
263D THR* 1.3 73.2 - - - +
265D ALA* 1.3 59.6 + - - +
267D ALA* 3.5 3.0 + - + +
268D LEU* 3.0 57.5 + - + +
107G LEU* 6.4 0.4 - - + -
111G VAL* 4.2 17.3 - - + -
114G THR* 4.1 18.1 + - + +
201G ARG* 4.2 27.8 - - - +
205G ILE* 5.0 4.6 - - + +
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Residues in contact with ALA 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D THR* 3.2 10.1 + - - +
264D TYR* 1.3 76.6 - - - +
266D ASP* 1.3 60.9 + - - +
268D LEU* 3.1 6.7 + - - +
269D TRP* 2.9 26.9 + - - +
111G VAL* 4.2 23.5 - - + +
114G THR* 4.5 2.6 - - - +
115G ILE* 4.0 27.1 - - + -
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Residues in contact with ASP 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG* 3.3 24.0 + - - +
260D HIS 4.0 11.4 - - - +
261D PHE* 4.7 2.0 - - - -
262D ASP* 4.5 8.0 - - - +
263D THR* 3.4 27.1 + - - +
264D TYR 3.5 0.2 - - - -
265D ALA* 1.3 76.5 - - - +
267D ALA* 1.3 56.8 + - - +
269D TRP* 3.2 7.8 + - - +
270D TRP* 2.9 27.0 + - - +
283D LYS* 3.6 29.3 - - - +
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Residues in contact with ALA 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D SER* 2.5 26.0 + - - +
251D TYR* 3.8 24.7 - - + -
261D PHE* 3.5 28.6 - - + -
263D THR 3.5 9.8 + - - +
264D TYR* 3.6 11.9 - - + +
265D ALA 3.2 0.6 - - - -
266D ASP* 1.3 78.8 - - - +
268D LEU* 1.3 54.1 + - - +
270D TRP* 3.2 4.3 + - - +
271D GLY 3.0 19.9 + - - -
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Residues in contact with LEU 268 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243D LEU* 4.2 20.3 - - + +
244D ILE* 4.8 9.4 - - + -
247D SER* 3.5 21.5 - - - +
264D TYR* 3.0 49.3 + - + +
265D ALA* 3.1 8.7 + - - +
267D ALA* 1.3 73.0 - - - +
269D TRP* 1.3 64.7 + - - +
271D GLY* 3.3 1.0 + - - -
272D LEU* 3.0 25.1 + - - +
107G LEU* 5.7 3.6 - - + -
111G VAL* 4.0 23.6 - - + -
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Residues in contact with TRP 269 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B TRP* 6.3 0.2 - + - -
284B TYR* 5.2 0.8 - - + +
285B PRO* 4.0 27.8 + - + -
291B ARG* 3.8 60.1 - - + +
294B ALA* 4.6 7.9 - - + -
295B ALA* 4.8 4.5 - - + -
265D ALA 2.9 12.5 + - - +
266D ASP* 3.2 11.0 + - - +
268D LEU* 1.3 77.2 - - - +
270D TRP* 1.3 63.2 + - - +
272D LEU* 3.4 26.4 + - + +
273D ILE* 3.0 59.1 + - + +
280D TYR* 3.8 16.1 - + - -
282D ASP* 3.7 23.5 + - - -
283D LYS* 4.3 12.3 - - + -
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Residues in contact with TRP 270 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246D ALA* 4.5 7.2 - - + -
247D SER* 4.2 11.9 - - - -
250D VAL* 3.7 32.3 - - + -
261D PHE* 3.5 34.5 - + + -
266D ASP 2.9 9.7 + - - +
267D ALA 3.4 11.2 - - - +
269D TRP* 1.3 80.1 - - - +
271D GLY* 1.3 85.9 + - - +
273D ILE* 3.1 5.5 + - + -
274D THR* 3.0 49.1 + - + +
275D LEU* 6.2 2.0 - - + -
283D LYS* 2.9 34.8 + - + -
285D PRO* 3.7 14.1 - - + +
294D ALA* 4.0 24.7 - - + -
269G TRP* 6.3 0.2 - + - -
280G TYR* 3.0 23.0 + + - -
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Residues in contact with GLY 271 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243D LEU* 3.5 19.7 - - - -
247D SER* 4.4 2.5 - - - -
267D ALA 3.0 13.3 + - - -
268D LEU 3.3 0.6 + - - -
270D TRP* 1.3 94.2 - - - +
272D LEU* 1.3 61.6 + - - +
274D THR* 3.4 2.0 + - - -
275D LEU* 3.0 33.4 + - - +
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Residues in contact with LEU 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ALA* 3.6 40.2 - - + +
298B THR* 3.8 22.7 - - + -
299B LEU* 4.5 11.4 - - + -
243D LEU* 3.6 16.4 - - + +
268D LEU 3.0 16.8 + - - +
269D TRP* 3.9 22.0 - - + +
271D GLY* 1.3 75.7 - - - +
273D ILE* 1.3 56.3 + - + +
275D LEU* 4.8 2.0 - - - +
276D THR* 2.5 43.6 + - + +
278D ILE* 6.5 0.2 - - + -
305D PHE* 5.0 6.5 - - + -
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Residues in contact with ILE 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B THR* 6.5 0.4 - - + -
269D TRP* 3.0 65.5 + - + +
270D TRP* 3.8 5.8 - - - +
272D LEU* 1.3 81.5 - - + +
274D THR* 1.3 63.2 + - + +
276D THR* 3.3 4.0 + - - -
278D ILE* 3.1 42.7 + - + +
279D GLY* 3.3 6.3 + - - +
280D TYR* 3.6 47.3 - - + +
282D ASP* 5.3 3.4 - - - +
280G TYR* 5.9 1.1 - - + -
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Residues in contact with THR 274 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270D TRP* 3.0 39.1 + - + +
271D GLY* 3.4 9.4 + - - -
273D ILE* 1.3 79.1 - - + +
275D LEU* 1.3 71.0 + - - +
276D THR 3.1 2.0 - - - -
277D THR* 2.7 26.5 + - - -
279D GLY 4.9 2.7 - - - +
302D VAL* 3.9 9.6 - - - +
278G ILE* 4.2 18.6 - - - +
280G TYR* 3.1 35.4 - - + +
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Residues in contact with LEU 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D GLY 4.6 0.7 - - - +
242D CYS* 4.5 4.3 - - - +
243D LEU* 3.7 30.3 - - + +
246D ALA* 5.5 7.6 - - + -
270D TRP* 6.2 2.0 - - + -
271D GLY* 3.0 17.9 + - - +
272D LEU* 4.8 1.6 - - - +
274D THR* 1.3 90.9 + - - +
276D THR* 1.3 59.7 + - - +
277D THR* 3.2 1.1 - - - +
297D PHE 4.4 9.2 - - - +
298D THR* 4.9 6.3 - - - -
301D GLY* 3.6 25.8 - - - -
302D VAL* 3.5 21.9 - - + +
305D PHE* 3.3 51.5 - - + +
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Residues in contact with THR 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B THR* 3.9 13.2 - - - +
298B THR* 4.5 8.7 + - - +
299B LEU* 4.3 8.7 - - + -
302B VAL* 4.7 14.7 - - + +
272D LEU* 2.5 37.8 + - + +
273D ILE 3.3 8.7 + - - -
275D LEU* 1.3 75.9 - - + +
277D THR* 1.3 74.6 + - - +
278D ILE* 3.2 19.0 + - - +
305D PHE* 4.1 26.5 - - + +
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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