Contacts of the helix formed by residues 261 - 280 (chain D) in PDB entry 1Y8R
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 261 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255D ARG* 3.5 17.5 + - - +
258D SER* 3.4 11.2 + - - -
259D SER 2.7 1.2 + - - -
260D ASP* 1.3 87.5 - - + +
262D TYR* 1.3 68.1 + - - +
263D GLU 3.5 1.6 - - - -
264D GLU* 3.1 30.1 + - - +
265D ASP* 2.9 37.4 + - - -
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Residues in contact with TYR 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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258D SER 3.3 7.1 + - - -
259D SER* 2.9 17.9 + - - +
261D THR* 1.3 77.1 - - - +
263D GLU* 1.3 80.6 + - + +
266D SER* 2.6 58.8 + - - -
292D VAL* 3.4 32.1 + - - +
293D ARG* 3.8 30.3 - - - +
296D PHE* 3.5 22.4 - + - -
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Residues in contact with GLU 263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261D THR 3.5 0.4 - - - -
262D TYR* 1.3 94.8 - - + +
264D GLU* 1.3 65.0 + - - +
266D SER* 3.9 4.8 - - - -
267D GLU* 3.3 45.6 + - - +
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Residues in contact with GLU 264 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D LYS* 3.7 23.2 + - - +
255D ARG* 4.6 4.9 + - - -
261D THR* 3.1 33.1 + - + +
262D TYR 2.9 4.4 + - - -
263D GLU* 1.3 76.8 - - - +
265D ASP* 1.3 68.9 + - - +
267D GLU* 3.1 20.7 + - - +
268D LEU* 3.2 7.4 + - + +
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Residues in contact with ASP 265 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D PHE* 3.8 18.7 - - + -
253D LYS* 5.1 3.3 - - - +
255D ARG* 2.8 42.7 + - - -
257D PRO* 4.2 2.5 - - + -
258D SER 2.8 26.0 + - - +
261D THR* 2.9 16.5 + - - +
262D TYR 3.7 1.3 - - - +
264D GLU* 1.3 70.3 - - - +
266D SER* 1.3 70.2 + - - +
267D GLU 2.9 1.3 - - - -
268D LEU* 2.7 10.3 + - - -
269D LEU* 2.7 26.5 + - - +
296D PHE* 4.0 12.6 - - + -
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Residues in contact with SER 266 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D TYR* 2.6 68.3 + - - -
263D GLU* 3.8 7.6 - - - -
265D ASP* 1.3 73.4 - - - +
267D GLU* 1.3 65.9 + - - +
269D LEU* 4.5 0.4 - - - -
270D LEU* 3.1 30.0 + - - +
292D VAL* 3.7 20.3 - - - +
296D PHE* 3.8 5.2 - - - -
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Residues in contact with GLU 267 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D GLU* 3.3 32.1 + - - +
264D GLU* 3.1 12.6 + - - +
265D ASP 2.7 4.0 + - - -
266D SER* 1.3 77.6 - - - +
268D LEU* 1.3 65.1 + - - +
270D LEU* 3.3 11.3 + - - +
271D GLN* 3.0 21.2 + - - +
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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
----------------------------------------------------------
249D PHE* 3.2 30.7 - - + -
252D ASP* 5.6 2.7 - - + -
253D LYS* 3.5 35.4 - - + -
264D GLU* 3.2 7.7 + - + +
265D ASP* 2.7 12.5 + - - +
267D GLU* 1.3 76.4 - - - +
269D LEU* 1.3 52.2 + - - +
271D GLN* 2.9 15.8 + - + +
272D ILE* 2.7 47.9 + - + +
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Residues in contact with LEU 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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245D VAL* 3.9 13.9 - - + +
246D LEU* 4.0 17.9 - - + -
249D PHE* 3.4 34.8 - - + -
257D PRO* 3.8 24.5 - - + -
265D ASP 2.7 18.6 + - - +
268D LEU* 1.3 73.5 - - - +
270D LEU* 1.3 57.8 + - - +
272D ILE* 3.3 4.3 + - + +
273D ARG* 2.7 31.2 + - - +
291D PHE* 3.8 7.9 - - + -
292D VAL* 3.5 22.4 - - + -
295D CYS* 4.3 9.9 - - - -
296D PHE* 3.9 22.7 - - + -
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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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266D SER* 3.1 19.9 + - - +
267D GLU* 3.3 8.7 + - - +
269D LEU* 1.3 78.2 - - - +
271D GLN* 1.3 56.7 + - - +
273D ARG* 3.4 19.3 + - - +
274D ASN* 2.7 28.2 - - - +
289D GLU* 3.3 40.8 - - + +
291D PHE* 3.8 17.3 - - + -
292D VAL* 3.9 11.9 - - + -
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Residues in contact with GLN 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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267D GLU 3.0 12.3 + - - +
268D LEU* 2.9 24.3 + - + +
270D LEU* 1.3 73.5 - - - +
272D ILE* 1.3 57.1 + - + +
273D ARG 3.0 1.3 - - - -
274D ASN* 2.8 30.3 + - - +
275D ASP* 2.8 23.5 + - - +
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Residues in contact with ILE 272 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D VAL* 4.0 13.9 - - + +
248D LYS* 3.5 27.6 - - + +
249D PHE* 3.9 37.5 - - + +
252D ASP* 3.8 23.6 - - + +
268D LEU* 2.7 35.2 + - + +
269D LEU* 3.8 4.0 - - - +
271D GLN* 1.3 74.8 - - + +
273D ARG* 1.3 63.1 + - - +
275D ASP* 3.0 12.8 - - - +
276D VAL* 3.0 32.2 + - + +
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Residues in contact with ARG 273 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D VAL* 3.9 11.4 - - + +
269D LEU 2.7 17.8 + - - +
270D LEU* 3.4 15.8 + - - +
271D GLN 3.0 0.2 - - - -
272D ILE* 1.3 77.2 - - - +
274D ASN* 1.3 89.8 + - - +
277D LEU* 3.1 37.8 + - + +
284D PRO* 3.4 28.8 + - - +
285D ASP* 4.9 1.8 - - - +
287D LEU* 3.5 31.2 + - + -
289D GLU* 3.1 42.5 + - - +
291D PHE* 3.8 22.9 - - + -
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Residues in contact with ASN 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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270D LEU 2.7 23.3 - - - +
271D GLN* 2.8 16.6 + - - +
273D ARG* 1.3 97.4 + - - +
275D ASP* 1.3 67.3 + - - +
277D LEU* 3.1 4.3 + - - +
278D ASP* 2.9 34.5 + - - +
284D PRO* 4.6 12.4 - - + +
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Residues in contact with ASP 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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248D LYS* 3.8 20.4 + - - -
271D GLN* 2.8 35.5 + - - +
272D ILE* 3.0 16.6 - - - +
274D ASN* 1.3 75.1 - - - +
276D VAL* 1.3 64.7 + - - +
278D ASP* 3.8 7.2 + - - +
279D SER* 2.6 41.0 + - - +
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Residues in contact with VAL 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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244D GLN* 3.9 27.1 - - + +
245D VAL* 4.3 12.3 - - + -
248D LYS* 4.0 20.9 - - + -
272D ILE* 3.0 41.3 + - + +
273D ARG 4.0 1.6 - - - +
275D ASP* 1.3 84.1 - - - +
277D LEU* 1.3 69.6 + - + +
279D SER* 3.4 9.3 + - - -
280D LEU* 3.2 26.2 + - + +
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Residues in contact with LEU 277 (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 PHE* 3.6 42.4 - - + +
245D VAL* 5.2 0.9 - - + -
273D ARG* 3.1 37.2 + - + +
274D ASN 3.9 1.6 - - - +
276D VAL* 1.3 82.6 - - + +
278D ASP* 1.3 62.1 + - - +
280D LEU* 3.4 12.3 + - + +
282D ILE* 3.0 42.5 + - + +
283D SER 4.6 1.6 - - - +
284D PRO* 3.4 40.6 - - + +
286D LEU* 5.7 1.8 - - + -
287D LEU* 3.9 14.1 - - + +
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Residues in contact with ASP 278 (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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274D ASN* 2.9 32.5 + - - +
275D ASP* 3.8 6.4 + - - +
277D LEU* 1.3 71.8 - - - +
279D SER* 1.3 56.0 + - - +
280D LEU 2.9 5.2 - - - -
281D GLY* 2.6 26.0 + - - +
282D ILE 4.0 3.2 - - - +
284D PRO* 3.2 26.3 - - - +
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Residues in contact with SER 279 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D ASP* 2.6 27.9 + - - +
276D VAL* 3.5 8.8 - - - -
277D LEU 3.4 0.2 - - - -
278D ASP* 1.3 77.0 - - - +
280D LEU* 1.3 64.3 + - - +
281D GLY 3.2 1.1 + - - -
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Residues in contact with LEU 280 (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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220D LEU 5.5 6.3 - - - +
221D GLU* 6.0 2.9 - - - -
222D VAL 4.8 7.0 - - - +
224D TRP* 3.9 28.7 + - + +
225D SER* 5.1 0.3 + - - -
240D TYR* 5.7 1.1 - - + -
241D PHE* 4.4 15.3 - - + -
244D GLN* 4.9 11.9 - - + +
276D VAL* 3.2 26.9 - - + +
277D LEU* 3.4 8.7 + - - +
278D ASP 2.9 1.4 - - - -
279D SER* 1.3 81.3 - - - +
281D GLY* 1.3 65.9 + - - +
282D ILE* 3.0 34.4 - - + +
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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
------------------------------------------------------------
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