Contacts of the helix formed by residues 274 - 295 (chain B) in PDB entry 1USK
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 274 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B MET* 3.4 25.1 - - - -
271B ASP* 4.6 5.4 + - - -
272B PRO 3.5 1.2 - - - -
273B SER* 1.3 80.8 + - - +
275B PRO* 1.3 75.5 - - - +
277B VAL* 3.3 20.9 + - - +
278B TRP* 3.4 7.4 + - - -
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Residues in contact with PRO 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TRP* 4.6 10.1 - - + -
21B MET* 3.7 6.1 - - + -
226B GLU* 5.6 1.3 - - + -
229B GLY 5.2 4.9 - - - +
248B MET* 5.1 13.7 - - + -
249B PRO* 3.9 38.6 - - + +
250B LYS 5.0 2.7 - - - +
251B ARG* 6.2 1.8 - - - -
252B TYR* 4.2 7.1 - - + -
273B SER 3.6 5.8 - - - +
274B GLY* 1.3 83.9 - - - +
276B TYR* 1.3 72.2 - - + +
277B VAL 3.2 0.4 - - - -
278B TRP* 3.2 14.1 + - + +
279B ILE* 3.1 30.0 + - + +
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Residues in contact with TYR 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TRP* 3.8 30.7 - + - +
21B MET* 3.1 22.0 - - + +
22B GLU* 3.9 2.3 - - - +
77B LEU* 5.3 4.3 - - + -
99B PRO 3.1 28.5 - - - -
100B GLY* 3.8 13.4 + - - -
102B THR* 4.0 7.1 - - - +
118B ALA* 4.4 4.2 - - + +
119B GLY 5.8 0.2 + - - -
226B GLU* 2.4 41.6 + - + +
249B PRO* 5.3 2.5 - - + +
275B PRO* 1.3 78.4 - - + +
277B VAL* 1.3 62.9 + - - +
278B TRP 3.3 0.4 - - - -
279B ILE* 3.6 26.0 - - + +
280B THR* 2.8 30.5 + - - +
331B PHE* 5.5 1.2 - - - -
1347B LEU* 3.6 31.1 + - + -
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B MET* 3.5 37.5 - - + +
24B ASN* 5.0 5.2 - - + +
25B GLY* 3.4 23.8 - - - +
261B ILE* 5.7 1.3 - - + -
265B LEU* 3.8 30.1 - - + -
271B ASP 4.1 17.0 - - - +
272B PRO 4.9 0.9 - - - +
274B GLY 3.3 16.4 + - - +
275B PRO 3.2 0.2 - - - -
276B TYR* 1.3 77.7 - - - +
278B TRP* 1.3 72.4 + - + +
281B TYR* 3.2 23.9 + - + +
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Residues in contact with TRP 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B TYR* 3.7 32.5 - + + -
253B ASP* 3.7 25.7 - - + +
258B ASN* 3.7 22.9 - - + -
261B ILE* 3.5 40.8 - - + -
262B VAL* 3.6 22.4 - - + -
265B LEU* 4.5 3.6 - - + -
272B PRO* 2.9 32.1 + - + -
273B SER 4.7 0.6 - - - -
274B GLY 3.4 16.5 + - - -
275B PRO* 3.2 9.8 + - + +
277B VAL* 1.3 83.0 - - + +
279B ILE* 1.3 59.6 + - - +
281B TYR* 3.4 3.3 + + + -
282B ALA* 2.9 26.3 + - - +
314B VAL* 3.3 28.3 - - + +
315B ILE* 3.6 8.0 - - + +
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B PRO 3.1 25.1 - - - +
117B THR* 2.9 52.7 + - - +
118B ALA* 3.6 2.5 - - - +
119B GLY 5.5 0.2 - - - +
249B PRO* 4.3 11.7 - - + -
252B TYR* 4.0 13.2 - - + -
275B PRO 3.1 18.4 + - - +
276B TYR* 3.6 28.7 - - + -
278B TRP* 1.3 75.7 - - - +
280B THR* 1.3 56.7 - - - +
282B ALA* 3.6 2.4 + - - +
283B ALA 3.2 12.6 + - - -
315B ILE* 4.2 13.2 - - + -
329B PHE* 3.9 24.0 - - + -
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Residues in contact with THR 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 5.1 0.2 - - + -
22B GLU* 3.3 45.4 - - + +
25B GLY 4.7 0.2 - - - -
26B ALA* 3.8 17.0 - - + +
74B ILE* 4.1 8.5 - - + -
77B LEU* 5.8 0.3 - - - +
99B PRO* 3.3 26.0 + - + +
276B TYR* 2.8 25.7 + - - +
277B VAL 4.1 1.3 - - - -
279B ILE* 1.3 75.8 - - - +
281B TYR* 1.3 64.1 + - - +
282B ALA 3.2 0.2 - - - -
283B ALA* 3.1 10.9 + - - +
284B VAL* 3.1 14.7 + - - +
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Residues in contact with TYR 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLY* 3.4 25.7 + - - +
28B GLN* 3.7 11.0 - - + -
29B ALA* 3.4 29.2 + - + +
32B ASP* 2.5 36.4 + - - +
33B ILE* 6.4 0.2 - - + -
261B ILE* 3.8 26.0 - - + +
277B VAL* 3.2 20.3 + - + +
278B TRP* 3.4 9.4 + + + +
280B THR* 1.3 75.4 - - - +
282B ALA* 1.3 57.7 + - - +
284B VAL* 3.3 4.5 + - - +
285B GLN* 3.0 54.6 + - + +
314B VAL* 3.6 20.4 - - + -
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Residues in contact with ALA 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B THR* 4.3 2.0 - - + -
278B TRP 2.9 16.8 + - - +
279B ILE 3.7 6.1 - - - +
280B THR 3.2 0.2 - - - -
281B TYR* 1.3 77.1 - - - +
283B ALA* 1.3 52.4 + - - +
285B GLN* 3.4 12.2 + - - +
286B SER* 2.7 36.9 + - - -
313B THR* 3.4 26.7 - - + +
314B VAL* 4.3 2.7 - - + -
315B ILE* 3.7 19.3 - - + -
318B LEU* 4.5 3.1 - - + -
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Residues in contact with ALA 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 3.7 29.8 - - + +
97B ILE* 4.0 14.2 - - + +
99B PRO* 4.3 3.4 - - + -
117B THR* 3.5 28.9 - - + +
279B ILE 3.2 6.4 + - - +
280B THR* 3.1 12.0 + - - +
282B ALA* 1.3 75.1 - - - +
284B VAL* 1.3 64.5 + - - +
286B SER* 3.3 4.8 + - - -
287B LEU* 3.2 17.7 + - - +
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 6.1 1.8 - - + -
7B VAL* 5.8 1.1 - - + -
26B ALA* 4.1 27.8 - - + +
29B ALA* 3.6 24.5 - - + -
30B ILE* 4.0 21.1 - - + -
33B ILE* 4.0 14.6 - - + -
44B LEU* 4.4 7.7 - - + +
74B ILE* 4.3 20.9 - - + -
280B THR 3.1 13.1 + - - +
281B TYR 3.3 1.1 + - - +
283B ALA* 1.3 72.7 - - - +
285B GLN* 1.3 64.5 + - - +
287B LEU* 3.4 8.1 + - + +
288B ALA* 3.0 21.8 + - - +
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Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ALA* 5.3 0.4 - - + -
33B ILE* 4.6 10.5 - - + -
281B TYR* 3.0 43.8 + - + +
282B ALA* 3.5 11.2 - - - +
284B VAL* 1.3 78.4 - - - +
286B SER* 1.3 51.8 + - - +
288B ALA* 3.5 6.4 + - - +
289B THR* 2.7 37.5 + - - +
312B ASN 4.1 7.1 + - - +
313B THR* 3.4 24.7 - - + +
314B VAL* 3.1 27.4 + - - +
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Residues in contact with SER 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 4.7 4.5 - - - -
117B THR* 4.2 0.6 - - - +
282B ALA 2.7 22.5 + - - -
283B ALA* 3.5 9.1 - - - -
284B VAL 3.2 0.2 - - - -
285B GLN* 1.3 74.3 - - - +
287B LEU* 1.3 64.7 + - - +
289B THR* 3.2 1.6 + - - -
290B ALA 3.2 17.7 + - - -
306B LEU* 3.4 22.4 - - - +
311B ALA* 4.3 9.4 - - - -
313B THR* 4.0 2.8 - - - +
318B LEU* 3.8 5.9 - - - +
320B TRP* 3.4 35.7 - - - -
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Residues in contact with LEU 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B VAL* 3.7 41.7 - - + -
44B LEU* 5.4 3.8 - - + -
72B TYR* 3.9 28.9 - - + -
74B ILE* 4.5 9.9 - - + -
95B LEU* 4.1 19.5 - - + -
97B ILE* 4.4 11.8 - - + +
283B ALA 3.2 10.9 + - - +
284B VAL* 3.4 9.8 + - + +
286B SER* 1.3 78.8 - - - +
288B ALA* 1.3 56.4 + - - +
290B ALA* 3.5 4.6 + - + +
291B LEU* 3.1 47.8 + - + +
302B LEU* 4.5 4.9 - - + -
306B LEU* 4.9 1.6 - - - -
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Residues in contact with ALA 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ILE* 3.7 24.9 - - + -
39B ILE* 3.7 23.7 - - + +
44B LEU* 4.6 4.7 - - + -
284B VAL 3.0 17.5 + - - +
285B GLN* 3.8 4.9 - - - +
286B SER 3.2 0.2 - - - -
287B LEU* 1.3 76.0 - - - +
289B THR* 1.3 63.6 + - - +
291B LEU* 3.7 6.1 + - - +
292B GLU* 3.2 27.8 + - - +
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Residues in contact with THR 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B GLN* 2.7 22.8 + - - +
286B SER 3.2 6.3 + - - -
288B ALA* 1.3 78.5 - - - +
290B ALA* 1.3 56.8 + - - +
292B GLU* 3.6 5.4 + - - +
293B ARG* 3.2 59.5 + - + +
306B LEU* 4.7 0.4 - - + -
310B GLY 4.1 0.2 - - - +
311B ALA* 4.0 24.5 - - + +
312B ASN 4.8 6.5 + - - +
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Residues in contact with ALA 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B SER 3.2 14.7 + - - +
287B LEU* 3.9 5.2 - - - +
288B ALA 3.3 0.2 - - - -
289B THR* 1.3 75.8 - - - +
291B LEU* 1.3 58.8 + - - +
294B THR* 2.6 36.6 + - - +
302B LEU* 3.4 35.7 - - + +
305B ASP* 3.5 19.7 - - - +
306B LEU* 3.9 10.3 - - + +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 4.3 28.0 - - + -
39B ILE* 3.8 21.3 - - + +
40B LYS* 5.7 0.5 - - - +
44B LEU* 4.4 12.6 - - + -
72B TYR* 4.1 15.7 - - + +
287B LEU* 3.1 42.1 + - + +
288B ALA* 4.0 4.5 - - - +
289B THR 3.4 0.2 - - - -
290B ALA* 1.3 76.0 - - - +
292B GLU* 1.3 58.3 + - - +
294B THR* 4.3 0.4 - - - -
295B GLY* 3.1 27.2 + - - -
296B SER 3.5 20.8 - - - +
297B ASP* 4.8 0.9 - - + -
302B LEU* 3.8 20.0 - - + -
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Residues in contact with GLU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLY 5.2 3.7 - - - +
39B ILE* 3.7 23.0 - - + +
40B LYS* 3.9 36.8 - - + +
288B ALA* 3.2 17.7 + - - +
289B THR* 4.0 5.5 - - - +
290B ALA 3.2 0.4 - - - -
291B LEU* 1.3 80.8 - - - +
293B ARG* 1.3 61.4 + - - +
295B GLY* 4.2 3.3 + - - -
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Residues in contact with ARG 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B THR* 3.2 37.7 + - - +
291B LEU 3.5 0.2 - - - -
292B GLU* 1.3 79.0 - - - +
294B THR* 1.3 64.2 + - + +
305B ASP* 3.1 36.3 + - - +
306B LEU* 4.3 3.8 - - - +
309B ASN* 3.7 30.8 + - - +
310B GLY 2.8 28.9 + - - -
311B ALA* 5.3 0.8 - - - +
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Residues in contact with THR 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ALA 2.6 18.2 + - - +
293B ARG* 1.3 78.0 - - - +
295B GLY* 1.3 62.9 + - - +
296B SER* 3.2 21.1 + - - -
301B ALA* 4.4 8.1 - - + +
302B LEU* 3.5 10.4 - - + +
305B ASP* 3.3 43.1 - - + +
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Residues in contact with GLY 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 6.1 4.3 - - - -
291B LEU 3.1 17.9 + - - -
292B GLU 4.2 3.5 + - - -
293B ARG 3.5 1.6 - - - -
294B THR* 1.3 79.9 + - - +
296B SER* 1.3 59.7 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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