Contacts of the helix formed by residues 269 - 288 (chain R) in PDB entry 1UW9
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 TYR 269 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477H EDO 4.6 0.2 + - - -
267R HIS* 3.3 14.0 + - - -
268R ASP* 1.3 73.1 - - - +
270R LEU* 1.3 80.1 + - + +
273R GLY* 2.8 30.5 + - - -
274R PHE* 3.5 34.0 + + - -
277R ASN* 3.3 26.0 - - + +
293R ILE* 3.1 22.4 - - + -
294R HIS 3.4 9.1 + - - -
295R ARG* 3.8 15.3 - - + -
311R PHE* 4.1 9.7 - - - -
314R LEU* 2.9 35.2 + - - +
318R LEU* 3.5 26.7 - - + +
326R LEU* 3.8 18.8 - - + +
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Residues in contact with LEU 270 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273H GLY* 5.6 0.2 - - - -
1477H EDO 2.8 45.4 + - - +
117R PHE* 5.9 0.2 - - + -
268R ASP 3.3 0.6 - - - -
269R TYR* 1.3 113.9 - - + +
271R THR* 1.3 65.4 + - - +
273R GLY* 3.6 4.5 + - - -
274R PHE* 4.1 16.6 - - + -
295R ARG 3.9 5.6 - - - +
296R ALA 3.4 11.8 + - - +
297R MET* 3.9 11.4 - - + -
298R HIS* 3.7 40.6 - - + +
301R ILE* 4.8 4.7 - - + -
314R LEU* 4.3 17.9 - - + -
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Residues in contact with THR 271 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H THR* 2.9 29.3 + - - +
117H PHE* 4.3 7.9 - - + -
118H THR* 2.8 41.6 + - - +
274H PHE* 3.9 17.1 + - - +
268R ASP* 3.2 20.5 + - - +
270R LEU* 1.3 73.9 - - - +
272R GLY* 1.3 63.5 + - - +
296R ALA* 3.7 20.3 + - + +
297R MET* 3.8 23.1 - - + -
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Residues in contact with GLY 272 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H THR* 3.7 7.7 - - - +
272H GLY 4.7 0.2 - - - +
273H GLY 3.9 1.2 - - - -
274H PHE 3.6 3.3 + - - -
275H THR* 3.1 46.1 + - - -
276H ALA 4.3 0.3 + - - -
267R HIS* 3.9 13.2 - - - -
268R ASP 2.8 16.9 + - - -
271R THR* 1.3 79.2 + - - +
273R GLY* 1.3 59.4 + - - +
276R ALA* 4.0 2.5 - - - +
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Residues in contact with GLY 273 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H GLY 3.8 1.1 - - - -
273H GLY* 3.8 16.8 - - - -
1477H EDO 4.4 3.8 - - - -
267R HIS* 4.0 0.7 + - - -
269R TYR 2.8 20.2 + - - -
270R LEU 3.9 7.2 - - - -
271R THR 3.4 1.4 - - - -
272R GLY* 1.3 77.8 - - - +
274R PHE* 1.3 60.2 + - - -
275R THR 3.4 2.7 - - - -
276R ALA 3.4 2.8 + - - -
277R ASN* 2.8 29.3 + - - +
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Residues in contact with PHE 274 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H GLY 4.5 0.2 - - - -
271H THR* 3.9 13.5 + - - +
272H GLY 3.6 3.0 + - - -
297H MET* 6.0 0.4 - - - -
1477H EDO 4.8 11.0 - - - -
113R VAL* 3.6 25.1 - - + -
114R THR* 3.5 22.2 - - - +
117R PHE* 3.8 30.7 - + + -
269R TYR* 3.5 38.8 + + - -
270R LEU* 4.1 14.4 - - + -
273R GLY* 1.3 68.5 - - - -
275R THR* 1.3 58.7 + - - +
277R ASN* 4.1 2.9 - - + -
278R THR* 2.7 39.6 + - - +
314R LEU* 5.0 1.6 - - + -
317R ALA* 3.7 29.4 - - + -
321R SER* 4.0 14.1 - - - -
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Residues in contact with THR 275 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244H ALA 2.8 24.2 + - - +
245H GLY 3.6 7.4 - - - -
246H THR* 3.3 34.5 - - - +
247H CYS* 3.4 5.6 - - - +
250H MET* 4.7 7.0 - - + -
267H HIS* 5.0 1.1 - - + -
272H GLY* 3.2 23.6 + - - -
276H ALA* 3.8 18.2 - - + -
114R THR* 3.1 9.1 + - - +
274R PHE* 1.3 77.7 - - - +
276R ALA* 1.3 62.4 + - - +
278R THR 3.5 0.2 + - - -
279R SER* 3.3 23.9 + - - -
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Residues in contact with ALA 276 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247H CYS* 3.7 11.5 - - - -
272H GLY 4.3 1.0 + - - -
275H THR* 3.8 37.2 - - + -
276H ALA* 4.4 1.9 - - - +
247R CYS* 4.1 5.4 - - - -
250R MET* 3.5 19.5 - - - +
267R HIS* 4.3 4.0 - - - +
272R GLY 4.0 2.9 - - - +
273R GLY 3.4 7.9 + - - +
275R THR* 1.3 78.4 - - - +
277R ASN* 1.3 57.8 + - - +
279R SER* 3.3 3.6 + - - -
280R LEU* 2.9 24.9 + - - +
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Residues in contact with ASN 277 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267R HIS* 2.7 34.9 + - + +
269R TYR* 3.3 17.2 - - + +
273R GLY 2.8 22.0 + - - +
274R PHE* 3.2 7.4 + - + +
276R ALA* 1.3 74.3 - - - +
278R THR* 1.3 58.0 + - - +
280R LEU* 3.2 3.3 + - - +
281R ALA* 2.9 26.3 + - - +
291R LEU* 4.5 2.0 - - - +
293R ILE* 3.2 24.0 - - - +
318R LEU* 3.6 6.8 - - - +
321R SER* 3.0 18.6 + - - +
322R GLY 3.1 19.4 - - - +
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Residues in contact with THR 278 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245H GLY 3.1 25.7 + - - +
246H THR* 3.7 12.8 - - + -
111R GLY 4.4 14.9 + - - +
113R VAL* 5.4 4.7 + - - +
148R PHE* 6.0 0.9 - - + -
149R VAL* 6.4 1.3 - - + -
274R PHE* 2.7 23.2 + - - +
277R ASN* 1.3 69.5 - - - +
279R SER* 1.3 65.3 + - - +
281R ALA* 3.3 2.4 + - - +
282R ILE* 3.0 37.3 + - + +
320R MET 5.7 0.7 - - - +
321R SER* 2.8 34.4 + - - +
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Residues in contact with SER 279 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H THR* 3.4 4.4 - - - +
247H CYS* 2.7 30.3 + - - +
248H GLU* 2.6 30.8 + - - +
250R MET* 4.5 0.7 - - - -
251R MET* 3.8 18.7 - - - +
275R THR 3.3 5.5 + - - -
276R ALA* 3.5 9.2 - - - -
278R THR* 1.3 78.2 - - - +
280R LEU* 1.3 62.8 + - - +
282R ILE* 3.3 9.0 + - - +
283R TYR* 3.0 21.3 + - - +
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Residues in contact with LEU 280 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242R ALA* 4.2 8.3 - - + -
250R MET* 3.9 25.1 - - + -
251R MET* 4.1 10.7 - - - +
254R ALA* 3.7 30.3 - - + -
265R ILE* 3.9 15.5 - - + -
267R HIS* 3.6 34.8 - - + +
276R ALA 2.9 14.4 + - - +
277R ASN* 3.6 8.1 - - - +
279R SER* 1.3 74.8 - - - +
281R ALA* 1.3 57.8 + - - +
283R TYR* 3.1 4.9 + - + +
284R CYS* 2.9 33.9 + - - -
291R LEU* 3.7 17.0 - - + -
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Residues in contact with ALA 281 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149R VAL* 5.6 0.8 - - - +
150R GLY 4.5 4.7 - - - +
152R PRO* 3.5 15.6 - - + +
277R ASN 2.9 16.1 + - - +
278R THR 3.3 2.2 + - - +
280R LEU* 1.3 75.7 - - - +
282R ILE* 1.3 58.6 + - + +
284R CYS 3.3 0.9 + - - -
285R ARG* 2.9 26.9 + - - +
291R LEU* 3.7 13.3 - - + +
321R SER 3.6 20.9 - - - +
322R GLY* 3.8 22.7 - - - +
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Residues in contact with ILE 282 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246H THR* 3.8 24.7 - - + -
248H GLU* 5.7 4.0 - - - +
149R VAL* 4.2 32.1 - - + -
278R THR* 3.0 25.6 + - + +
279R SER* 3.6 9.0 - - - +
280R LEU 3.3 0.2 - - - -
281R ALA* 1.3 74.5 - - + +
283R TYR* 1.3 66.2 + - - +
285R ARG* 3.3 7.6 + - + +
286R ASP* 2.9 38.5 + - - +
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Residues in contact with TYR 283 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251R MET* 4.3 23.6 - - + -
254R ALA* 3.8 31.4 - - + -
255R VAL* 3.4 32.9 - - + +
258R LYS* 3.3 25.2 - - + +
279R SER 3.0 13.5 + - - +
280R LEU* 3.1 9.8 + - + +
282R ILE* 1.3 77.5 - - - +
284R CYS* 1.3 62.6 + - - +
286R ASP* 3.1 3.5 + - - +
287R ASN* 2.9 64.6 + - + +
289R LEU* 4.1 11.7 - - + -
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Residues in contact with CYS 284 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152R PRO* 3.8 12.3 - - + -
153R HIS* 3.7 1.0 + - - -
265R ILE* 3.7 30.3 - - - -
280R LEU* 2.9 21.0 + - - +
281R ALA 3.5 7.9 - - - +
283R TYR* 1.3 75.6 - - - +
285R ARG* 1.3 59.4 + - - +
287R ASN 4.6 0.2 - - - +
288R GLY* 2.8 27.0 + - - -
289R LEU* 3.1 41.7 + - - +
290R PHE 4.4 0.2 - - - -
291R LEU* 4.0 18.2 - - + -
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Residues in contact with ARG 285 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213O ARG* 3.7 49.5 - - - +
215O ARG* 3.8 15.6 - - - +
216O ASP* 6.0 1.3 - - - -
149R VAL* 3.4 39.6 + - + +
151R HYP 2.8 24.4 + - - -
152R PRO* 2.8 31.3 + - + +
153R HIS* 4.7 4.9 - - - +
281R ALA 2.9 13.8 + - - +
282R ILE* 3.5 11.4 - - - +
284R CYS* 1.3 77.4 - - - +
286R ASP* 1.3 73.1 + - - +
287R ASN 3.4 0.5 + - - -
288R GLY* 3.6 6.1 + - - -
372R PRO* 5.0 6.9 - - - +
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Residues in contact with ASP 286 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214O TRP* 5.3 9.9 + - - -
215O ARG* 3.1 18.2 + - - +
252O LYS* 3.4 35.3 + - - -
282R ILE* 2.9 33.5 + - - +
283R TYR* 3.1 5.5 + - - +
285R ARG* 1.3 86.1 - - - +
287R ASN* 1.3 70.1 + - - +
288R GLY 3.7 0.2 - - - -
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Residues in contact with ASN 287 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M CYS* 3.9 14.7 - - - +
215O ARG* 3.5 21.0 + - - +
258R LYS* 2.8 39.1 + - + +
283R TYR* 2.9 67.3 + - + +
284R CYS* 4.7 0.4 - - - +
286R ASP* 1.3 87.2 - - - +
288R GLY* 1.3 65.0 + - - +
289R LEU* 3.4 4.8 + - + +
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Residues in contact with GLY 288 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M CYS* 3.6 14.8 - - - +
66M LEU* 3.4 21.0 - - - +
215O ARG* 3.6 16.6 - - - +
153R HIS* 3.7 19.1 - - - -
161R LYS* 4.0 4.8 + - - -
284R CYS 2.8 10.6 + - - -
285R ARG 3.6 4.9 + - - -
287R ASN* 1.3 79.0 - - - +
289R LEU* 1.3 57.4 + - - -
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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
------------------------------------------------------------
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