Contacts of the helix formed by residues 274 - 295 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C MET* 3.7 22.9 - - - +
271C ASP* 4.6 3.6 + - - -
272C PRO 3.4 1.8 - - - -
273C SER* 1.3 80.4 + - - +
275C PRO* 1.3 73.8 - - - +
276C TYR 3.3 3.8 + - - -
277C VAL* 3.4 13.2 + - - +
278C TRP* 3.2 17.9 - - - -
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Residues in contact with PRO 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C TRP* 4.3 9.9 - - + -
21C MET* 4.3 4.9 - - + -
226C GLU* 5.4 0.9 - - + -
229C GLY 5.2 0.9 - - - +
248C MET* 4.2 27.8 - - + -
249C PRO* 3.9 31.6 - - + +
250C LYS 5.3 2.0 - - - +
252C TYR* 4.3 7.5 - - + +
273C SER 3.7 4.2 - - - +
274C GLY* 1.3 83.9 - - - +
276C TYR* 1.3 74.8 + - + +
278C TRP* 3.3 12.4 + - + +
279C ILE* 3.2 31.1 + - + +
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Residues in contact with TYR 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C TRP* 3.8 28.7 - + - +
21C MET* 3.6 23.0 - - + +
22C GLU* 3.8 2.3 - - - +
77C LEU* 5.2 4.7 - - + -
99C PRO 3.1 28.7 - - - -
100C GLY* 3.7 13.2 + - - -
102C THR* 3.8 7.6 - - - +
118C ALA* 4.4 4.1 - - + +
226C GLU* 2.4 46.5 + - + +
249C PRO* 5.3 3.2 - - + +
274C GLY 3.3 1.0 - - - -
275C PRO* 1.3 80.3 - - + +
277C VAL* 1.3 62.8 + - - +
278C TRP 3.3 0.4 - - - -
279C ILE* 3.6 24.3 - - + +
280C THR* 2.9 31.1 + - - +
331C PHE* 5.6 0.7 - - - -
1347C LEU* 3.7 25.9 + - + -
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Residues in contact with VAL 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C MET* 3.2 34.1 + - + +
24C ASN* 5.2 3.6 - - + -
25C GLY* 3.4 24.1 - - - +
28C GLN* 6.4 0.2 - - + -
261C ILE* 5.7 1.1 - - + -
265C LEU* 3.8 29.4 - - + -
271C ASP 3.9 20.4 - - - +
272C PRO 4.6 2.2 - - - +
274C GLY 3.6 17.9 - - - +
275C PRO 3.3 0.2 - - - -
276C TYR* 1.3 77.5 - - - +
278C TRP* 1.3 73.2 + - + +
281C TYR* 3.1 25.0 + - + +
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Residues in contact with TRP 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252C TYR* 3.7 23.8 - + + -
253C ASP* 3.6 25.1 - - - +
258C ASN* 3.6 37.7 - - + -
261C ILE* 3.5 38.1 - - + -
262C VAL* 3.8 13.5 - - + -
265C LEU* 4.7 3.4 - - + -
272C PRO* 2.9 32.8 + - + -
273C SER 5.2 0.7 - - - -
274C GLY 3.2 24.4 + - - -
275C PRO* 3.3 6.2 + - + +
277C VAL* 1.3 82.6 - - + +
279C ILE* 1.3 60.4 + - - +
280C THR 3.3 0.2 - - - -
281C TYR* 4.1 4.3 - - + -
282C ALA 3.0 22.3 + - - -
314C VAL* 3.3 28.4 - - + +
315C ILE* 3.4 18.6 - - + +
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Residues in contact with ILE 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C PRO* 3.0 26.0 - - - +
117C THR* 3.0 51.4 + - - +
118C ALA* 3.7 1.6 - - - +
249C PRO* 4.3 10.5 - - + -
252C TYR* 4.1 13.9 - - + -
275C PRO* 3.2 20.7 + - + +
276C TYR* 3.6 27.8 - - + +
278C TRP* 1.3 75.3 - - - +
280C THR* 1.3 61.2 + - - +
282C ALA* 3.5 4.1 + - - +
283C ALA 3.2 8.8 + - - -
315C ILE* 4.0 12.6 - - + -
329C PHE* 4.1 21.3 - - + -
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Residues in contact with THR 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLU* 3.2 48.1 - - + +
26C ALA* 3.7 19.5 - - + +
74C ILE* 4.2 8.7 - - + -
99C PRO* 3.2 22.2 - - + +
276C TYR* 2.9 24.1 + - - +
277C VAL 3.9 1.8 - - - -
278C TRP 3.3 0.4 - - - -
279C ILE* 1.3 75.5 - - - +
281C TYR* 1.3 66.5 + - - +
282C ALA 3.1 1.3 - - - -
283C ALA* 3.0 12.5 + - - +
284C VAL* 3.2 12.5 + - - +
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Residues in contact with TYR 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C GLY* 3.4 25.9 + - - +
28C GLN* 3.8 4.7 - - + -
29C ALA* 3.4 27.7 - - + +
32C ASP* 2.5 35.4 + - - +
33C ILE* 6.5 0.4 - - + -
261C ILE* 3.4 32.6 - - + +
277C VAL* 3.1 19.4 + - + +
278C TRP* 3.5 10.1 - + + +
280C THR* 1.3 74.6 - - - +
282C ALA* 1.3 57.7 + - - +
284C VAL* 3.2 6.4 + - - +
285C GLN* 3.0 51.4 + - + +
314C VAL* 3.4 29.6 - - + -
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Residues in contact with ALA 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C THR* 4.3 1.8 - - + -
278C TRP 3.0 18.6 + - - +
279C ILE 3.6 6.7 - - - +
280C THR 3.1 0.2 - - - -
281C TYR* 1.3 72.9 - - - +
283C ALA* 1.3 56.8 + - - +
285C GLN* 3.4 4.5 + - - +
286C SER* 2.7 38.7 + - - -
313C THR* 3.6 32.2 - - + +
314C VAL* 4.2 1.3 - - + +
315C ILE* 3.7 19.5 - - + -
318C LEU* 4.4 2.7 - - + -
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Residues in contact with ALA 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ILE* 3.5 34.7 - - + +
97C ILE* 3.9 15.3 - - + +
99C PRO* 4.4 3.6 - - + -
117C THR* 3.7 25.5 - - - +
279C ILE 3.2 6.1 + - - +
280C THR* 3.0 12.6 + - - +
282C ALA* 1.3 74.7 - - - +
284C VAL* 1.3 63.9 + - - +
286C SER* 3.3 4.0 + - - -
287C LEU* 3.1 17.8 + - - +
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Residues in contact with VAL 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 6.1 1.3 - - + -
7C VAL* 5.6 0.7 - - + -
26C ALA* 4.1 29.8 - - + +
29C ALA* 3.7 11.4 - - + -
30C ILE* 4.0 20.2 - - + -
33C ILE* 3.8 20.6 - - + -
44C LEU* 4.5 6.9 - - + +
74C ILE* 4.0 22.4 - - + -
280C THR 3.2 12.0 + - - +
281C TYR 3.6 6.5 - - - +
283C ALA* 1.3 73.0 - - - +
285C GLN* 1.3 59.0 + - - +
287C LEU* 3.4 7.8 + - + +
288C ALA* 3.0 27.0 + - - +
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Residues in contact with GLN 285 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ALA* 5.2 0.4 - - + -
33C ILE* 4.5 12.3 - - + -
281C TYR* 3.0 43.3 + - + +
282C ALA* 3.6 7.6 - - - +
283C ALA 3.3 0.2 - - - -
284C VAL* 1.3 76.3 - - - +
286C SER* 1.3 58.2 + - - +
288C ALA* 3.4 6.7 + - - +
289C THR* 3.0 33.0 + - - +
312C ASN 4.4 6.9 + - - +
313C THR* 3.1 21.0 - - + +
314C VAL* 2.9 36.4 + - - +
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Residues in contact with SER 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C ILE* 4.9 4.5 - - - -
117C THR* 4.3 1.2 - - - +
282C ALA 2.7 22.2 + - - -
283C ALA* 3.6 7.2 - - - -
284C VAL 3.2 0.2 - - - -
285C GLN* 1.3 74.8 - - - +
287C LEU* 1.3 64.3 + - - +
289C THR* 3.4 1.6 + - - -
290C ALA 3.3 16.5 + - - -
306C LEU* 3.4 20.5 - - - +
311C ALA* 3.9 9.8 - - - +
313C THR* 3.6 4.2 - - - +
318C LEU* 3.6 12.0 - - - +
320C TRP* 3.4 34.3 - - - -
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Residues in contact with LEU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 3.7 42.2 - - + -
44C LEU* 5.3 3.4 - - + -
72C TYR* 4.0 17.9 - - + -
74C ILE* 4.5 8.7 - - + -
95C LEU* 3.9 33.4 - - + -
97C ILE* 4.5 10.0 - - + +
283C ALA 3.1 13.2 + - - +
284C VAL* 3.7 11.4 - - + +
286C SER* 1.3 75.4 - - - +
288C ALA* 1.3 62.8 + - - +
290C ALA* 3.3 7.9 + - + +
291C LEU* 3.1 43.9 + - + +
302C LEU* 4.7 5.4 - - + -
306C LEU* 4.8 0.7 - - - -
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Residues in contact with ALA 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ILE* 3.7 23.6 - - + -
39C ILE* 3.7 22.5 - - + +
44C LEU* 4.6 4.5 - - + -
284C VAL 3.0 17.6 + - - +
285C GLN* 3.7 4.7 - - - +
287C LEU* 1.3 74.4 - - - +
289C THR* 1.3 64.9 + - - +
291C LEU* 3.6 6.9 + - - +
292C GLU* 3.1 34.0 + - - +
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Residues in contact with THR 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C GLN* 3.0 19.9 + - - +
286C SER 3.6 6.3 - - - -
288C ALA* 1.3 75.5 - - - +
290C ALA* 1.3 64.5 + - - +
292C GLU* 3.4 9.1 + - - +
293C ARG* 3.0 57.4 + - + +
306C LEU* 4.7 0.2 - - + -
310C GLY 4.0 8.1 - - - +
311C ALA* 4.2 13.9 - - + +
312C ASN 5.0 6.1 + - - +
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Residues in contact with ALA 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C SER 3.3 10.1 + - - +
287C LEU* 3.3 9.8 + - + +
289C THR* 1.3 79.5 - - - +
291C LEU* 1.3 57.0 + - - +
294C THR* 2.7 35.9 + - - +
302C LEU* 3.5 39.9 - - + +
305C ASP* 3.5 14.1 - - - +
306C LEU* 3.9 11.4 - - + -
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Residues in contact with LEU 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C ILE* 4.7 19.1 - - + -
39C ILE* 3.6 31.9 - - + +
40C LYS* 5.6 0.9 - - - +
44C LEU* 4.8 4.3 - - + -
72C TYR* 3.8 23.8 - - + +
287C LEU* 3.1 40.9 + - + +
288C ALA* 3.9 7.2 - - - +
289C THR 3.3 0.2 - - - -
290C ALA* 1.3 77.5 - - - +
292C GLU* 1.3 56.5 + - - +
294C THR* 4.3 0.2 - - - -
295C GLY* 3.1 28.8 + - - -
296C SER 3.6 20.4 + - - +
297C ASP* 4.8 1.6 - - + -
302C LEU* 3.9 15.3 - - + -
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Residues in contact with GLU 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ILE* 6.0 1.4 - - - +
38C GLY 4.2 13.0 - - - +
39C ILE* 4.3 24.6 - - + +
40C LYS* 3.5 36.3 + - + +
288C ALA* 3.1 26.4 + - - +
289C THR* 3.8 7.5 + - - +
291C LEU* 1.3 79.3 - - - +
293C ARG* 1.3 63.0 + - - +
295C GLY 3.7 2.8 + - - -
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Residues in contact with ARG 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C THR* 3.0 36.8 + - + +
292C GLU* 1.3 79.5 - - - +
294C THR* 1.3 58.8 + - - +
305C ASP* 2.9 47.6 + - - +
306C LEU* 4.1 4.4 - - - +
309C ASN* 3.6 26.3 + - - +
310C GLY 3.0 28.9 + - - -
311C ALA* 5.2 0.4 - - - +
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Residues in contact with THR 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290C ALA 2.7 18.8 + - - +
293C ARG* 1.3 77.8 - - + +
295C GLY* 1.3 65.8 + - - +
296C SER* 3.1 25.6 + - - -
301C ALA* 4.6 5.6 - - + +
302C LEU* 3.6 7.5 - - + +
305C ASP* 3.2 43.5 - - + +
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Residues in contact with GLY 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C LYS* 5.3 10.3 - - - -
291C LEU 3.1 16.2 + - - -
292C GLU 3.7 5.1 + - - -
293C ARG 3.5 2.2 - - - -
294C THR* 1.3 77.1 - - - +
296C SER* 1.3 57.5 + - - +
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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