Contacts of the helix formed by residues 269 - 288 (chain V) 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 V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1484O EDO 4.8 0.2 + - - -
267V HIS* 3.3 14.0 + - - -
268V ASP* 1.3 73.7 - - - +
270V LEU* 1.3 84.9 + - + +
273V GLY* 2.8 29.8 + - - -
274V PHE* 3.5 34.0 + + - -
277V ASN* 3.5 26.0 - - + +
293V ILE* 3.1 21.8 - - + -
294V HIS 3.3 9.5 + - - -
295V ARG* 3.8 11.7 - - + -
311V PHE* 4.1 8.7 - - - -
314V LEU* 2.9 36.1 + - - +
318V LEU* 3.6 26.2 - - + +
326V LEU* 3.7 19.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274O PHE* 5.7 0.2 - - - -
1484O EDO 3.0 44.3 + - - +
117V PHE* 5.9 0.2 - - + -
268V ASP 3.3 0.6 - - - -
269V TYR* 1.3 115.2 - - + +
271V THR* 1.3 65.8 + - - +
273V GLY* 3.7 4.2 + - - -
274V PHE* 4.0 18.4 - - + -
294V HIS 4.7 0.2 + - - -
295V ARG 3.9 6.3 - - - +
296V ALA 3.5 12.4 + - - +
297V MET* 4.0 10.5 - - + -
298V HIS* 3.7 39.5 - - + +
301V ILE* 4.9 4.9 - - + -
314V LEU* 4.4 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 271 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114O THR* 2.9 29.3 + - - +
117O PHE* 4.3 8.7 - - + -
118O THR* 2.9 41.6 + - - +
274O PHE* 3.9 16.4 + - - +
268V ASP* 3.1 20.6 - - - +
270V LEU* 1.3 75.0 - - - +
272V GLY* 1.3 61.9 + - - +
296V ALA* 3.6 19.6 + - + +
297V MET* 3.8 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 272 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114O THR* 3.7 6.8 - - - +
272O GLY 4.6 0.2 - - - +
273O GLY 3.7 1.6 - - - -
274O PHE 3.5 4.0 + - - -
275O THR* 3.1 46.4 + - - -
276O ALA 4.3 0.5 + - - -
267V HIS* 4.0 13.0 - - - -
268V ASP 2.9 15.6 + - - -
271V THR* 1.3 78.5 + - - +
273V GLY* 1.3 59.1 + - - +
276V ALA* 4.1 2.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 273 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272O GLY 3.9 0.4 - - - -
273O GLY* 3.8 17.0 - - - -
1484O EDO 4.5 3.4 - - - -
267V HIS* 4.0 0.5 + - - -
268V ASP 4.1 0.2 + - - -
269V TYR 2.8 19.6 + - - -
270V LEU 3.9 7.2 - - - -
271V THR 3.5 0.8 - - - -
272V GLY* 1.3 79.5 - - - +
274V PHE* 1.3 60.4 + - - -
275V THR 3.4 3.1 + - - -
276V ALA 3.5 2.4 + - - -
277V ASN* 2.8 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 274 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245O GLY 4.5 0.4 - - - -
271O THR* 3.9 13.5 + - - +
272O GLY 3.7 2.8 + - - -
297O MET* 6.1 1.1 - - - -
1484O EDO 4.7 9.2 + - - -
113V VAL* 3.6 26.5 - - + -
114V THR* 3.5 21.5 - - - +
117V PHE* 3.9 30.3 - + + -
269V TYR* 3.5 36.0 + + - -
270V LEU* 4.0 16.2 - - + -
273V GLY* 1.3 70.2 - - - -
275V THR* 1.3 59.4 + - - +
277V ASN* 4.1 3.1 - - + -
278V THR* 2.7 38.0 + - - +
314V LEU* 5.0 1.3 - - + -
317V ALA* 3.7 28.3 - - + -
321V SER* 3.7 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 275 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244O ALA 2.8 24.0 + - - +
245O GLY 3.6 7.4 - - - -
246O THR* 3.3 33.4 - - - +
247O CYS* 3.4 6.4 + - - +
250O MET* 4.7 7.9 - - + -
267O HIS* 5.0 0.9 - - + -
272O GLY* 3.1 24.7 + - - -
276O ALA* 3.8 19.1 - - + -
114V THR* 3.1 9.2 + - - -
274V PHE* 1.3 78.2 - - - +
276V ALA* 1.3 63.1 + - - +
279V SER* 3.3 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 276 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247O CYS* 3.7 11.3 - - - -
272O GLY 4.3 1.0 + - - -
275O THR* 3.7 36.8 - - + -
276O ALA* 4.4 2.1 - - - +
247V CYS* 4.1 6.1 - - - -
250V MET* 3.5 19.4 - - - +
267V HIS* 4.3 4.0 - - - +
272V GLY 4.1 3.8 - - - +
273V GLY 3.5 7.7 + - - +
274V PHE 3.4 0.4 - - - -
275V THR* 1.3 78.0 - - - +
277V ASN* 1.3 63.6 + - - +
279V SER* 3.3 3.8 + - - -
280V LEU* 2.9 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 277 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267V HIS* 2.8 35.1 + - + +
269V TYR* 3.5 16.5 - - + +
273V GLY 2.8 21.9 + - - +
274V PHE* 3.8 6.7 - - + +
275V THR 3.3 0.2 - - - -
276V ALA* 1.3 75.5 - - - +
278V THR* 1.3 55.1 + - - +
280V LEU* 3.2 3.1 + - - +
281V ALA* 2.9 26.9 + - - +
291V LEU* 4.4 2.2 - - - +
293V ILE* 3.1 24.2 - - - +
318V LEU* 3.6 6.2 - - - +
321V SER* 3.0 20.2 + - - +
322V GLY 3.0 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 278 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245O GLY 3.2 24.6 + - - +
246O THR* 3.7 13.2 - - + -
111V GLY 4.4 14.7 + - - +
113V VAL* 5.3 4.3 + - - +
148V PHE* 6.0 1.6 - - + -
149V VAL* 6.3 1.6 - - + -
274V PHE* 2.7 19.8 + - - +
277V ASN* 1.3 71.2 - - - +
279V SER* 1.3 66.8 + - - +
281V ALA* 3.3 2.4 + - - +
282V ILE* 3.0 36.3 + - + +
320V MET 5.6 0.7 - - - +
321V SER* 2.8 34.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 279 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246O THR* 3.4 4.1 - - - +
247O CYS* 2.8 30.1 + - - +
248O GLU* 2.6 30.5 + - - +
250V MET* 4.5 1.1 - - - -
251V MET* 3.8 19.9 - - - +
275V THR 3.3 4.7 + - - -
276V ALA 3.4 9.2 - - - -
278V THR* 1.3 78.6 - - - +
280V LEU* 1.3 56.9 + - - +
282V ILE* 3.3 8.4 + - - +
283V TYR* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242V ALA* 4.2 7.9 - - + -
250V MET* 3.9 23.6 - - + -
251V MET* 4.1 12.3 - - - +
254V ALA* 3.8 29.6 - - + -
265V ILE* 3.9 15.7 - - + -
267V HIS* 3.6 36.1 - - + +
276V ALA 2.9 17.8 + - - +
277V ASN* 3.2 5.8 + - - +
279V SER* 1.3 76.0 - - - +
281V ALA* 1.3 57.7 + - - +
283V TYR* 3.2 4.8 + - + +
284V CYS* 2.9 29.8 + - - -
291V LEU* 3.7 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 281 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149V VAL* 5.8 0.2 - - - -
150V GLY 4.5 4.9 - - - +
152V PRO* 3.5 16.0 - - + +
277V ASN 2.9 16.3 + - - +
278V THR 3.6 1.8 - - - +
280V LEU* 1.3 77.8 - - - +
282V ILE* 1.3 58.0 + - + +
284V CYS 3.3 0.7 + - - -
285V ARG* 2.9 27.9 + - - +
291V LEU* 3.8 13.1 - - + +
321V SER 3.6 21.8 - - - +
322V GLY* 3.7 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 282 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246O THR* 3.8 25.6 - - + -
248O GLU* 5.7 3.6 - - - +
149V VAL* 4.2 32.5 - - + -
278V THR* 3.0 26.9 + - + +
279V SER* 3.6 8.7 - - - +
280V LEU 3.3 0.2 - - - -
281V ALA* 1.3 74.6 - - + +
283V TYR* 1.3 65.7 + - - +
285V ARG* 3.3 7.5 + - - +
286V ASP* 2.9 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 283 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251V MET* 4.3 23.1 - - + -
254V ALA* 3.8 31.9 - - + -
255V VAL* 3.5 33.6 - - + +
258V LYS* 3.3 25.5 - - - +
279V SER 3.0 13.7 + - - +
280V LEU* 3.2 9.6 + - + +
282V ILE* 1.3 75.8 - - - +
284V CYS* 1.3 62.8 + - - +
286V ASP* 3.2 4.0 + - + -
287V ASN* 2.9 63.3 + - + +
289V LEU* 4.1 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 284 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152V PRO* 3.8 12.8 - - + -
153V HIS* 3.7 1.0 + - - -
265V ILE* 3.7 30.5 - - - -
280V LEU* 2.9 21.5 + - - +
281V ALA 3.5 5.4 - - - +
282V ILE 3.2 0.2 - - - -
283V TYR* 1.3 75.9 - - - +
285V ARG* 1.3 61.1 + - - +
287V ASN* 5.2 0.2 - - - -
288V GLY* 2.8 27.5 + - - -
289V LEU* 3.1 43.2 + - - +
291V LEU* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 285 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H ARG* 3.7 48.2 - - - +
215H ARG* 3.7 16.4 - - - +
216H ASP* 5.9 1.8 - - - -
149V VAL* 3.3 41.2 + - + +
151V HYP 2.8 24.9 + - - -
152V PRO* 2.8 31.3 + - + +
153V HIS* 4.7 5.0 - - - -
281V ALA 2.9 13.7 + - - +
282V ILE* 3.3 11.9 + - + +
284V CYS* 1.3 78.3 - - - +
286V ASP* 1.3 71.4 + - - +
287V ASN 3.3 1.0 + - - -
288V GLY* 3.6 6.1 + - - -
372V PRO* 5.0 6.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 286 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H TRP* 5.3 10.7 + - - -
215H ARG* 3.0 19.4 + - - +
252H LYS* 3.4 35.2 + - - -
282V ILE* 2.9 34.4 + - - +
283V TYR* 3.2 5.9 + - - +
285V ARG* 1.3 85.3 - - - +
287V ASN* 1.3 69.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 287 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H ARG* 3.5 20.7 + - - +
258V LYS* 2.9 37.2 + - + +
283V TYR* 2.9 67.5 + - + +
284V CYS* 4.7 0.7 - - - +
286V ASP* 1.3 87.7 - - - +
288V GLY* 1.3 65.2 + - - +
289V LEU* 3.4 5.5 + - + +
63W VAL* 6.0 0.2 - - - -
65W CYS* 4.0 14.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 288 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H ARG* 3.6 16.6 - - - +
153V HIS* 3.7 19.1 - - - -
161V LYS* 4.0 5.3 + - - -
284V CYS 2.8 11.2 + - - -
285V ARG 3.6 5.1 + - - -
287V ASN* 1.3 78.3 - - - +
289V LEU* 1.3 57.7 + - - -
65W CYS* 3.6 14.2 - - - +
66W LEU* 3.4 20.3 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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