Contacts of the helix formed by residues 260 - 275 (chain D) in PDB entry 3KDO
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 260 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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256D VAL 3.1 10.5 + - - -
257D VAL 4.0 9.0 - - - -
258D ILE 3.3 1.8 - - - -
259D THR* 1.3 82.1 - - - +
261D TRP* 1.3 68.5 + - - -
262D GLY 3.2 3.0 + - - -
263D ALA 3.7 1.1 + - - -
264D LEU* 3.3 25.6 + - - +
258J ILE 4.6 0.4 - - - -
260J GLY* 3.7 17.7 - - - -
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Residues in contact with TRP 261 (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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101D LEU* 4.0 15.5 - - + -
102D PRO* 3.9 17.9 - - + +
105D LEU* 3.5 29.0 - - + +
260D GLY* 1.3 77.0 - - - -
262D GLY* 1.3 62.2 + - - +
263D ALA 3.3 0.5 + - - -
264D LEU* 3.7 11.0 + - + +
265D ARG 4.6 2.1 + - - -
288D PHE* 6.3 0.9 - + - -
296D ILE* 6.4 1.1 - - + -
301D LEU* 3.6 24.7 - - + -
304D LEU* 3.7 36.6 - - + -
305D TYR* 3.6 38.6 - + - -
308D ILE* 4.0 15.2 - - + +
233J ASP* 4.1 7.8 - - - +
257J VAL 5.3 1.1 - - - -
258J ILE* 3.4 37.8 + - + +
284J MET* 4.4 17.0 - - + +
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Residues in contact with GLY 262 (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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102D PRO* 4.5 2.7 - - - +
261D TRP* 1.3 80.1 - - - +
263D ALA* 1.3 58.1 + - - +
265D ARG 5.5 0.2 - - - -
232J ALA 4.1 13.9 - - - -
233J ASP* 3.6 1.0 - - - -
234J LEU* 2.9 32.9 + - - +
237J MET* 3.8 9.0 - - - +
258J ILE 3.8 0.6 + - - -
259J THR* 2.9 27.3 + - - -
263J ALA* 4.9 2.2 - - - -
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Residues in contact with ALA 263 (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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234D LEU* 4.5 15.0 - - + -
237D MET* 5.4 0.7 - - + -
259D THR* 4.6 13.7 - - + +
260D GLY 3.7 2.2 + - - -
261D TRP 3.3 0.2 - - - -
262D GLY* 1.3 75.7 - - - +
264D LEU* 1.3 60.3 + - - +
265D ARG 3.4 2.5 - - - -
266D TYR* 3.2 5.3 + - - +
267D ILE* 2.9 32.4 + - + +
234J LEU* 4.4 8.7 - - + -
259J THR 4.3 1.4 + - - -
262J GLY 4.6 1.1 - - - -
263J ALA* 3.4 34.3 - - + +
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Residues in contact with LEU 264 (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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254D VAL* 4.6 9.0 - - + -
256D VAL* 3.9 30.5 - - + +
259D THR* 4.4 15.3 - - + -
260D GLY 3.3 17.8 + - - +
261D TRP* 3.7 9.7 + - + +
263D ALA* 1.3 78.6 - - - +
265D ARG* 1.3 59.9 + - - +
267D ILE* 3.4 7.2 + - + +
268D ARG* 2.9 31.6 + - + +
305D TYR* 3.3 39.3 - - + -
308D ILE* 4.0 22.9 - - + -
310D ILE* 4.3 10.1 - - + -
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Residues in contact with ARG 265 (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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99D ALA* 5.1 11.5 + - - +
101D LEU* 5.9 1.8 - - - +
135D GLU 2.7 28.3 + - - -
136D PHE* 3.6 35.7 - - - +
137D ASP* 4.6 12.7 + - - +
261D TRP 4.6 2.6 + - - +
262D GLY 5.5 0.2 - - - -
263D ALA 3.4 0.2 - - - -
264D LEU* 1.3 78.4 - - - +
266D TYR* 1.3 57.9 + - - +
268D ARG* 3.3 3.6 + - + +
269D ASP* 2.9 45.8 + - - +
308D ILE* 4.1 23.9 + - + +
233J ASP* 3.8 40.2 + - + +
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Residues in contact with TYR 266 (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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234D LEU* 3.9 17.3 - - + -
238D GLU* 2.4 39.1 + - + -
263D ALA 3.2 9.1 + - - +
265D ARG* 1.3 78.9 - - - +
267D ILE* 1.3 65.9 + - + +
269D ASP* 3.2 7.3 + - + +
270D LEU* 2.9 45.2 + - + +
233J ASP* 6.1 0.4 - - - +
234J LEU* 3.3 44.3 - - + +
235J LEU* 4.4 30.3 - - + +
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Residues in contact with ILE 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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230D ILE* 4.2 22.0 - - + -
234D LEU* 3.9 25.8 - - + +
237D MET* 4.1 32.5 - - + -
238D GLU* 5.3 1.6 - - + +
241D LEU* 4.2 14.2 - - + +
254D VAL* 4.2 17.9 - - + -
259D THR* 4.8 4.5 - - + -
263D ALA* 2.9 23.6 + - + +
264D LEU* 3.8 10.1 - - + +
266D TYR* 1.3 81.1 - - + +
268D ARG* 1.3 58.9 + - - +
270D LEU* 3.3 4.1 + - - +
271D ALA* 2.9 30.8 + - + +
278D ILE* 5.9 1.3 - - + -
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Residues in contact with ARG 268 (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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137D ASP* 3.4 25.0 + - - +
138D GLY 2.9 24.4 + - - -
140D ALA* 4.3 15.6 - - - +
264D LEU* 2.9 19.0 + - + +
265D ARG* 3.5 5.8 - - - +
267D ILE* 1.3 77.3 - - - +
269D ASP* 1.3 85.9 + - - +
271D ALA* 3.5 2.1 + - - +
272D ALA* 3.0 49.3 + - - +
278D ILE* 3.7 27.0 - - + +
308D ILE* 3.1 39.1 + - + +
309D GLY* 4.1 6.7 + - - -
310D ILE* 5.0 4.0 - - + +
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Residues in contact with ASP 269 (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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137D ASP* 4.5 7.9 - - - +
265D ARG* 2.9 36.5 + - - +
266D TYR* 3.2 8.4 + - + +
268D ARG* 1.3 104.7 + - - +
270D LEU* 1.3 59.9 + - - +
272D ALA* 3.4 1.6 + - - +
273D ASP* 2.9 36.1 + - - +
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Residues in contact with LEU 270 (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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238D GLU* 4.0 21.8 - - + +
241D LEU* 3.8 19.5 - - + -
266D TYR* 2.9 46.6 + - + +
267D ILE* 3.6 5.4 - - + +
269D ASP* 1.3 75.3 - - - +
271D ALA* 1.3 65.4 + - - +
273D ASP* 3.2 14.8 + - + +
274D TYR* 3.0 55.8 + - + +
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Residues in contact with ALA 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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241D LEU* 4.3 19.2 - - + +
252D ALA* 4.9 2.0 - - + -
267D ILE* 2.9 18.1 + - + +
268D ARG 3.8 1.6 - - - +
270D LEU* 1.3 75.9 - - - +
272D ALA* 1.3 62.3 + - - +
274D TYR* 3.0 8.1 + - - +
275D GLY 3.0 5.0 + - - -
276D LEU* 2.8 39.3 + - + +
278D ILE* 3.7 28.9 - - + -
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Residues in contact with ALA 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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140D ALA* 4.4 19.3 - - + -
141D PHE* 5.7 1.5 - - - -
268D ARG* 3.0 43.0 + - - +
269D ASP 3.6 2.9 - - - +
271D ALA* 1.3 77.3 - - - +
273D ASP* 1.3 57.9 + - - +
275D GLY* 2.7 24.5 + - - -
276D LEU 4.2 7.1 + - - +
278D ILE* 5.1 0.9 - - + +
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Residues in contact with ASP 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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269D ASP* 2.9 19.1 + - - +
270D LEU* 3.5 18.2 - - + +
272D ALA* 1.3 78.6 - - - +
274D TYR* 1.3 63.8 + - + +
275D GLY* 3.3 0.7 + - - -
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Residues in contact with TYR 274 (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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238D GLU 4.9 1.5 + - - -
241D LEU* 3.9 34.1 - - + -
242D GLU* 3.9 27.2 + - + +
245D ALA* 3.4 26.8 - - + +
246D ASP* 6.1 0.4 - - - -
270D LEU* 3.0 47.9 + - + +
271D ALA 3.0 7.6 + - - +
273D ASP* 1.3 78.9 - - + +
275D GLY* 1.3 61.5 + - - +
276D LEU* 3.9 19.5 - - + +
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Residues in contact with GLY 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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141D PHE* 3.5 23.6 - - - -
249D LEU 5.0 0.7 - - - +
250D LYS* 4.3 5.2 - - - +
272D ALA 2.7 17.7 + - - -
273D ASP 3.1 1.6 + - - -
274D TYR* 1.3 80.4 - - - +
276D LEU* 1.3 62.8 + - - +
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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