Contacts of the helix formed by residues 274 - 295 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D MET* 3.6 26.2 - - - -
271D ASP* 4.5 5.7 + - - -
272D PRO 3.5 1.6 - - - -
273D SER* 1.3 81.3 + - - +
275D PRO* 1.3 74.5 - - - +
276D TYR 3.3 3.2 + - - -
277D VAL* 3.4 9.3 + - - +
278D TRP* 3.2 18.8 + - - -
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Residues in contact with PRO 275 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D TRP* 4.4 7.2 - - + -
21D MET* 4.1 9.4 - - + -
226D GLU* 5.6 1.1 - - + -
229D GLY 5.3 0.7 - - - +
248D MET* 4.3 26.7 - - + -
249D PRO* 3.9 35.2 - - + +
250D LYS 5.2 2.0 - - - +
252D TYR* 4.3 6.6 - - + -
273D SER 3.6 4.6 - - - +
274D GLY* 1.3 85.1 - - - +
276D TYR* 1.3 71.2 + - + +
277D VAL 3.3 0.4 - - - -
278D TRP* 3.3 12.4 + - + +
279D ILE* 3.1 29.8 + - + +
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Residues in contact with TYR 276 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D TRP* 3.8 29.2 - + - +
21D MET* 3.8 20.2 - - + +
22D GLU* 3.9 2.5 - - - +
77D LEU* 5.3 4.5 - - + -
99D PRO 3.2 28.0 - - - -
100D GLY* 3.7 16.0 + - - -
102D THR* 3.9 6.6 - - - +
118D ALA* 4.5 4.2 - - + +
119D GLY 5.6 0.2 + - - -
226D GLU* 2.5 40.2 + - + +
249D PRO* 5.3 2.9 - - + +
274D GLY 3.3 1.0 - - - -
275D PRO* 1.3 80.1 - - + +
277D VAL* 1.3 60.9 + - - +
278D TRP 3.3 0.7 - - - -
279D ILE* 3.6 27.5 - - + +
280D THR* 2.8 32.9 + - - +
331D PHE* 5.5 1.6 - - - -
1347D LEU* 3.6 27.5 + - + -
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Residues in contact with VAL 277 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D MET* 3.5 39.6 - - + +
24D ASN* 4.8 5.6 - - + +
25D GLY* 3.3 22.3 - - - +
261D ILE* 5.9 0.7 - - + -
265D LEU* 3.6 31.6 - - + -
271D ASP 4.1 16.6 - - - +
272D PRO* 5.0 0.9 - - + +
274D GLY* 3.6 12.8 - - - +
275D PRO 3.3 0.4 - - - -
276D TYR* 1.3 77.9 - - - +
278D TRP* 1.3 72.7 + - + +
281D TYR* 3.2 23.6 + - + +
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Residues in contact with TRP 278 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252D TYR* 3.7 32.5 - + + -
253D ASP* 3.7 23.4 - - + +
258D ASN* 3.7 25.6 - - + -
261D ILE* 3.5 36.3 - - + -
262D VAL* 3.6 25.4 - - + -
265D LEU* 4.7 4.0 - - + -
272D PRO* 2.9 34.3 + - + -
273D SER 4.7 1.3 - - - -
274D GLY 3.2 19.6 + - - -
275D PRO* 3.3 7.3 + - + +
277D VAL* 1.3 83.3 - - + +
279D ILE* 1.3 58.9 + - - +
280D THR 3.3 1.6 - - - -
281D TYR* 3.3 4.1 + - + -
282D ALA* 3.0 24.8 + - - +
314D VAL* 3.4 28.7 - - + +
315D ILE* 3.6 6.2 - - + +
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Residues in contact with ILE 279 (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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99D PRO 3.1 22.0 - - - +
117D THR* 3.1 50.7 + - - +
118D ALA* 3.8 1.8 - - - +
249D PRO* 4.2 13.0 - - + -
252D TYR* 4.0 17.3 - - + +
275D PRO 3.1 20.6 + - - +
276D TYR* 3.6 26.9 - - + -
278D TRP* 1.3 75.2 - - - +
280D THR* 1.3 60.3 + - - +
282D ALA* 3.5 4.3 + - - +
283D ALA 3.3 9.2 + - - -
315D ILE* 4.2 12.1 - - + -
329D PHE* 4.0 22.0 - - + -
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Residues in contact with THR 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 5.2 0.2 - - + -
22D GLU* 3.1 46.9 - - + +
26D ALA* 3.8 16.4 - - + -
74D ILE* 4.2 7.6 - - + -
77D LEU* 5.8 0.2 - - - +
99D PRO* 3.3 25.4 - - + +
276D TYR* 2.8 28.0 + - - +
277D VAL 4.2 2.5 - - - -
278D TRP 3.3 0.4 - - - -
279D ILE* 1.3 75.7 - - - +
281D TYR* 1.3 63.4 + - - +
283D ALA* 3.2 10.6 + - - +
284D VAL* 3.3 13.3 + - - +
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Residues in contact with TYR 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25D GLY* 3.4 24.4 - - - +
28D GLN* 3.6 14.4 - - + -
29D ALA* 3.4 29.2 - - + +
32D ASP* 2.7 34.1 + - - +
33D ILE* 6.5 0.4 - - + -
261D ILE* 3.6 25.4 - - + +
277D VAL* 3.2 19.8 + - + +
278D TRP* 3.5 9.9 - + + +
280D THR* 1.3 76.2 - - - +
282D ALA* 1.3 57.0 + - - +
284D VAL* 3.4 5.4 + - - +
285D GLN* 3.1 54.8 + - + +
314D VAL* 3.5 22.9 - - + -
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Residues in contact with ALA 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117D THR* 4.2 2.9 - - + -
278D TRP 3.0 16.6 + - - +
279D ILE 3.7 6.3 - - - +
280D THR 3.2 0.2 - - - -
281D TYR* 1.3 76.0 - - - +
283D ALA* 1.3 54.8 + - - +
285D GLN* 3.7 13.0 - - - +
286D SER* 2.7 36.9 + - - -
313D THR* 3.5 26.6 - - + +
314D VAL* 4.5 1.1 - - + -
315D ILE* 3.8 20.2 - - + -
318D LEU* 4.4 2.9 - - + -
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Residues in contact with ALA 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D ILE* 3.2 37.0 - - + +
97D ILE* 4.2 15.0 - - + +
99D PRO* 4.2 5.8 - - + -
117D THR* 3.5 27.1 - - + +
279D ILE 3.3 7.0 + - - +
280D THR 3.2 11.3 + - - +
282D ALA* 1.3 75.4 - - - +
284D VAL* 1.3 63.5 + - - +
286D SER* 3.7 3.3 + - - -
287D LEU* 3.5 13.5 + - - +
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Residues in contact with VAL 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 5.8 2.9 - - + -
7D VAL* 5.6 0.4 - - + -
26D ALA* 4.0 28.9 - - + +
29D ALA* 3.7 22.0 - - + -
30D ILE* 4.0 20.0 - - + -
33D ILE* 4.0 15.3 - - + -
44D LEU* 4.5 7.6 - - + -
74D ILE* 4.1 20.9 - - + -
280D THR 3.3 13.3 + - - +
281D TYR 3.8 0.7 - - - +
282D ALA 3.4 0.2 - - - -
283D ALA* 1.3 73.7 - - - +
285D GLN* 1.3 64.9 + - - +
286D SER 3.2 0.2 - - - -
287D LEU* 3.2 8.2 + - + +
288D ALA* 3.1 21.3 + - - +
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Residues in contact with GLN 285 (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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29D ALA* 5.4 0.4 - - + -
33D ILE* 4.6 13.0 - - + -
281D TYR* 3.1 46.9 + - + +
282D ALA* 3.7 8.6 - - - +
283D ALA 3.4 0.2 - - - -
284D VAL* 1.3 77.6 - - - +
286D SER* 1.3 52.8 + - - +
288D ALA* 3.7 6.0 + - - +
289D THR* 2.8 36.3 + - - -
312D ASN 4.2 7.2 + - - +
313D THR* 3.3 24.0 - - + +
314D VAL* 3.1 29.5 + - - +
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Residues in contact with SER 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97D ILE* 4.9 4.3 - - - -
117D THR* 4.4 1.3 - - - +
282D ALA 2.7 23.0 + - - -
283D ALA* 4.1 6.3 - - - -
284D VAL 3.2 0.2 - - - -
285D GLN* 1.3 74.7 - - - +
287D LEU* 1.3 66.0 + - - +
289D THR* 3.4 0.7 + - - -
290D ALA* 3.2 11.4 + - - +
306D LEU* 3.2 29.2 - - - +
311D ALA* 4.2 8.7 - - - -
313D THR* 3.8 9.7 - - - +
318D LEU* 3.9 1.4 - - - +
320D TRP* 3.4 36.7 - - - -
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Residues in contact with LEU 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D VAL* 3.7 38.4 - - + -
44D LEU* 5.4 2.7 - - + -
72D TYR* 3.9 32.1 - - + -
74D ILE* 4.2 11.9 - - + -
95D LEU* 4.4 19.7 - - + -
97D ILE* 4.6 7.5 - - + +
283D ALA 3.5 10.5 + - - +
284D VAL* 3.2 11.1 + - + +
286D SER* 1.3 79.9 - - - +
288D ALA* 1.3 59.6 + - - +
290D ALA* 3.4 5.0 + - - +
291D LEU* 3.2 46.3 + - + +
302D LEU* 4.7 6.1 - - + -
306D LEU* 5.0 1.1 - - - -
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Residues in contact with ALA 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE* 3.8 24.0 - - + -
39D ILE* 3.7 25.9 - - + +
44D LEU* 4.4 6.5 - - + -
284D VAL 3.1 15.8 + - - +
285D GLN* 4.0 3.6 - - - +
287D LEU* 1.3 74.2 - - - +
289D THR* 1.3 62.4 + - - +
290D ALA 3.4 0.2 - - - -
291D LEU* 3.6 4.2 + - - -
292D GLU* 3.2 32.0 + - - +
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Residues in contact with THR 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D GLN 2.8 21.8 + - - -
286D SER 3.6 6.1 - - - +
288D ALA* 1.3 76.7 - - - +
290D ALA* 1.3 62.6 + - - +
292D GLU* 3.4 20.1 + - - +
293D ARG* 3.4 31.2 + - - +
310D GLY 4.0 9.4 - - - +
311D ALA* 3.9 27.2 - - + +
312D ASN 4.9 6.9 + - - +
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Residues in contact with ALA 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D SER 3.2 14.2 + - - +
287D LEU* 3.8 4.3 - - + +
288D ALA 3.4 0.2 - - - -
289D THR* 1.3 81.9 - - - +
291D LEU* 1.3 55.0 + - - +
293D ARG* 4.5 0.4 - - - +
294D THR* 2.5 37.8 + - - +
302D LEU* 3.4 33.9 - - + +
305D ASP* 3.4 21.8 - - - +
306D LEU* 3.9 9.6 - - + +
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Residues in contact with LEU 291 (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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3D ILE* 4.6 20.6 - - + -
39D ILE* 3.6 35.1 - - + +
40D LYS* 5.1 1.6 - - - +
44D LEU* 5.0 4.0 - - + -
72D TYR* 4.3 14.8 - - + +
287D LEU* 3.2 37.5 + - + +
288D ALA* 4.0 7.9 - - - +
289D THR 3.3 0.4 - - - -
290D ALA* 1.3 75.0 - - - +
292D GLU* 1.3 65.5 + - - +
294D THR* 4.3 0.9 - - - -
295D GLY* 3.2 21.0 + - - -
296D SER 3.5 21.3 - - - +
297D ASP* 4.9 1.1 - - + -
302D LEU* 3.8 20.6 - - + -
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Residues in contact with GLU 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE* 5.9 1.2 - - - +
38D GLY 3.7 22.3 - - - +
39D ILE* 4.5 12.7 - - + +
40D LYS* 3.6 32.9 + - + -
288D ALA* 3.2 21.6 + - - +
289D THR* 3.7 12.3 + - - +
290D ALA 3.3 0.2 - - - -
291D LEU* 1.3 79.4 - - - +
293D ARG* 1.3 62.8 + - + +
294D THR 3.7 0.2 + - - -
295D GLY 3.9 2.9 + - - -
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Residues in contact with ARG 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289D THR* 3.4 24.1 + - - +
292D GLU* 1.3 78.3 - - + +
294D THR* 1.3 70.7 + - + +
305D ASP* 2.9 47.7 + - - +
306D LEU* 3.9 7.9 - - - +
309D ASN* 3.3 29.9 + - - +
310D GLY 2.9 30.1 + - - +
311D ALA* 5.3 0.2 - - - +
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Residues in contact with THR 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D ALA 2.5 21.2 + - - +
291D LEU* 4.3 0.2 - - - -
293D ARG* 1.3 80.0 - - + +
295D GLY* 1.3 62.9 + - - +
296D SER* 3.1 23.1 + - - -
301D ALA* 5.1 3.4 - - - +
302D LEU* 3.9 6.0 - - + +
305D ASP* 3.2 44.9 - - + +
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Residues in contact with GLY 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D LYS* 5.4 9.9 - - - -
291D LEU 3.2 19.1 + - - -
292D GLU 3.9 4.6 + - - -
293D ARG 3.6 1.2 - - - -
294D THR* 1.3 79.4 + - - +
296D SER* 1.3 61.4 + - - +
297D ASP* 4.0 1.0 + - - +
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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