Contacts of the helix formed by residues 251 - 275 (chain C) in PDB entry 2D2C
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 ASP 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144C PHE* 3.0 33.4 - - + -
250C GLN* 1.3 72.0 + - - +
252C PRO* 1.3 62.1 - - - +
253C ASN* 3.2 21.3 + - - +
254C ARG* 2.6 65.9 + - + +
255C VAL* 3.1 5.7 + - - +
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Residues in contact with PRO 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C LEU* 5.1 8.1 - - + -
42C PRO* 5.1 10.5 - - + -
144C PHE* 5.8 0.4 - - + -
250C GLN 2.9 16.6 - - - +
251C ASP* 1.3 76.8 - - - +
253C ASN* 1.3 53.1 + - + +
254C ARG 2.6 6.3 + - - -
255C VAL* 2.5 32.2 + - + +
256C LYS* 2.7 17.6 + - - +
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Residues in contact with ASN 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251C ASP* 3.2 15.9 + - - +
252C PRO* 1.3 77.9 - - - +
254C ARG* 1.3 55.1 + - - +
256C LYS* 3.9 36.1 + - - +
257C TRP* 3.1 42.1 - - - +
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Residues in contact with ARG 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80A TRP* 3.0 77.5 - - + +
56B VAL* 4.5 8.3 - - - +
144C PHE* 4.2 29.0 - - - +
250C GLN* 3.6 27.6 - - - +
251C ASP* 2.6 47.4 + - + +
253C ASN* 1.3 79.2 - - - +
255C VAL* 1.3 59.7 + - - -
256C LYS 3.5 0.2 - - - -
257C TRP* 4.4 6.4 - - - +
258C MET* 3.8 17.0 + - - +
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Residues in contact with VAL 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 4.6 6.3 - - + -
57B LEU* 6.1 2.9 - - + -
250C GLN* 3.1 38.4 - - + +
251C ASP 3.7 6.7 - - - +
252C PRO* 2.5 17.7 + - + +
254C ARG* 1.3 72.8 - - - +
256C LYS* 1.3 69.2 + - - +
258C MET* 3.0 16.1 - - + +
259C ILE* 2.9 35.5 + - + +
5G VAL* 4.7 16.8 - - + -
9G VAL* 5.0 11.9 - - + +
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Residues in contact with LYS 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C PRO 2.7 14.8 + - - +
253C ASN* 3.9 33.9 + - - +
255C VAL* 1.3 75.3 - - - +
257C TRP* 1.3 91.1 + - + +
259C ILE* 2.5 35.9 + - - +
260C ALA* 2.5 19.2 + - + -
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Residues in contact with TRP 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253C ASN* 3.1 31.4 + - - +
254C ARG* 4.6 5.6 - - - +
256C LYS* 1.3 114.4 - - - +
258C MET* 1.3 58.6 + - - +
260C ALA* 3.6 20.0 - - + +
261C PHE* 2.8 29.5 + - - +
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Residues in contact with MET 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 5.5 9.6 - - + +
53B ALA* 3.6 41.1 - - + +
56B VAL* 3.9 27.4 - - + -
57B LEU* 4.5 7.0 - - + -
254C ARG 3.8 11.7 + - - +
255C VAL* 3.0 22.8 + - + +
256C LYS 3.2 1.0 - - - -
257C TRP* 1.3 78.6 - - - +
259C ILE* 1.3 72.0 + - + +
261C PHE* 3.3 9.7 - - - +
262C ILE* 3.2 27.3 + - + +
9G VAL 4.9 0.7 - - - +
12G THR* 3.9 25.6 - - + +
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Residues in contact with ILE 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C VAL* 2.9 27.1 + - + +
256C LYS* 2.5 20.1 + - - +
258C MET* 1.3 78.2 - - + +
260C ALA* 1.3 56.7 + - - +
261C PHE 2.8 5.4 - - - -
262C ILE* 2.8 34.0 + - + +
263C CYS* 3.3 15.7 + - - -
5G VAL* 5.2 3.8 - - + -
8G LEU* 3.5 16.4 - - + -
12G THR* 3.2 35.4 - - + -
10H LEU* 6.3 2.5 - - + -
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C LYS* 2.5 19.2 + - + +
257C TRP* 3.6 33.7 - - + +
259C ILE* 1.3 76.4 - - - +
261C PHE* 1.3 59.2 + - - +
263C CYS* 4.1 7.6 + - - +
264C LEU* 3.4 25.7 + - - +
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Residues in contact with PHE 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B PHE* 5.5 5.4 - + - -
49B ALA* 5.7 7.9 - - + -
52B VAL* 5.6 14.1 - - + -
257C TRP 2.8 17.1 + - - +
258C MET* 3.3 10.5 - - - +
259C ILE 2.8 0.6 - - - -
260C ALA* 1.3 78.3 - - - +
262C ILE* 1.3 69.5 + - + +
264C LEU* 3.0 25.8 + - + +
265C VAL* 3.2 25.6 + - + -
30D VAL* 3.5 28.9 - - + -
33D GLY* 3.6 12.6 - - - -
34D ALA* 3.4 38.6 - - + -
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Residues in contact with ILE 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B ALA* 6.2 4.0 - - + -
53B ALA* 5.6 4.7 - - + -
258C MET* 3.5 25.6 - - + +
259C ILE* 2.8 23.6 + - + +
261C PHE* 1.3 74.7 - - + +
263C CYS* 1.3 56.2 + - - +
264C LEU 2.5 4.6 + - - -
265C VAL* 2.4 36.2 + - - +
266C MET* 2.5 48.7 + - + +
12G THR* 4.1 30.5 - - + +
16G LEU* 4.1 17.9 - - + -
10H LEU* 5.7 4.3 - - + -
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Residues in contact with CYS 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C ILE* 3.3 20.3 + - - -
260C ALA* 4.1 11.2 - - - +
262C ILE* 1.3 82.5 - - - +
264C LEU* 1.3 62.5 + - + +
266C MET* 3.3 13.2 - - - -
267C LEU* 2.9 40.0 + - + +
10H LEU* 5.0 16.6 - - - -
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Residues in contact with LEU 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260C ALA 3.4 21.8 - - - +
261C PHE* 3.0 23.3 + - + +
262C ILE 2.5 6.3 + - - -
263C CYS* 1.3 76.8 - - + +
265C VAL* 1.3 54.1 + - + +
267C LEU* 3.1 11.8 + - + +
268C ALA* 2.5 38.2 + - - +
29D GLY 5.4 8.7 - - - +
30D VAL* 4.6 15.4 - - + +
33D GLY* 5.9 3.4 - - - -
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Residues in contact with VAL 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B MET* 4.9 7.9 - - + +
46B GLY* 4.6 13.2 - - - +
49B ALA* 4.4 25.1 - - + -
261C PHE* 3.7 33.4 - - + +
262C ILE* 2.4 18.7 + - + +
264C LEU* 1.3 70.8 - - - +
266C MET* 1.3 58.8 + - - +
268C ALA* 2.6 31.1 + - + -
269C GLN* 2.9 37.8 + - + +
30D VAL* 4.2 11.4 - - + -
16G LEU* 5.3 5.4 - - + -
19G ALA* 5.6 0.7 - - + -
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Residues in contact with MET 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C ILE* 2.5 32.5 + - + +
263C CYS* 3.3 25.8 - - - +
265C VAL* 1.3 72.1 - - - +
267C LEU* 1.3 62.0 + - + +
269C GLN* 2.8 27.3 + - - +
270C LEU* 3.5 7.6 - - - +
15G GLY 3.0 29.2 - - - +
16G LEU* 4.0 14.6 - - + -
18G TYR* 3.5 29.0 - - + -
10H LEU* 4.3 24.2 - - + -
11H VAL* 5.7 1.8 - - - -
14H THR* 3.8 28.2 - - + +
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Residues in contact with LEU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C CYS* 2.9 34.5 + - + +
264C LEU* 3.1 11.1 + - + +
265C VAL 2.6 4.2 + - - -
266C MET* 1.3 80.6 - - + +
268C ALA* 1.3 64.1 + - - +
270C LEU* 2.8 31.3 - - + +
271C MET* 2.9 31.1 + - + +
14H THR* 4.4 13.9 - - + -
17H ILE* 5.4 9.9 - - + -
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Residues in contact with ALA 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45B MET* 4.6 10.1 - - - -
264C LEU 2.5 20.7 + - - +
265C VAL* 2.6 7.8 + - - +
267C LEU* 1.3 68.5 - - - +
269C GLN* 1.3 55.4 + - - +
270C LEU 2.4 17.4 + - - -
271C MET* 2.9 4.7 + - - +
272C LEU* 2.8 24.2 + - - +
26D THR* 4.8 16.6 - - - +
27D VAL* 5.2 4.4 - - + +
30D VAL* 3.5 27.4 - - + -
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Residues in contact with GLN 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 3.5 25.1 - - + +
45B MET* 3.9 18.2 - - + +
46B GLY* 5.1 0.4 - - - +
265C VAL* 2.9 35.3 + - + +
266C MET* 2.8 36.8 - - - +
268C ALA* 1.3 71.4 - - - +
270C LEU* 1.3 60.5 + - - +
272C LEU* 4.0 4.0 - - - -
273C ILE* 3.0 25.3 - - - +
16G LEU* 5.4 1.4 - - - +
18G TYR* 3.1 30.5 - - - -
19G ALA* 4.3 14.4 - - + +
22G GLN* 3.5 11.1 - - + +
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Residues in contact with LEU 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C MET 3.5 14.6 - - - +
267C LEU* 2.8 21.8 - - + +
268C ALA 2.4 6.5 + - - -
269C GLN* 1.3 77.2 + - - +
271C MET* 1.3 55.0 + - - +
272C LEU 2.8 4.0 - - - -
273C ILE* 2.5 35.4 + - + +
274C LEU* 2.5 44.6 + - + +
18G TYR* 3.8 15.7 - - + +
22G GLN* 3.7 16.8 - - - +
14H THR* 5.4 6.1 - - + +
17H ILE* 5.6 7.2 - - + -
18H ALA* 4.6 22.0 - - + +
21H VAL* 5.4 3.8 - - + -
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Residues in contact with MET 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267C LEU* 2.9 33.1 + - + +
268C ALA 2.9 8.9 + - - +
270C LEU* 1.3 84.3 - - - +
272C LEU* 1.3 57.3 + - - +
274C LEU* 3.1 29.9 - - + +
275C LYS* 3.0 30.3 + - - +
22D LEU* 4.8 25.4 - - + -
23D ALA* 4.9 17.8 - - - +
26D THR* 4.5 26.7 - - + +
21H VAL* 6.5 0.4 - - - -
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Residues in contact with LEU 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B TYR* 3.3 31.9 - - + +
39B VAL* 5.0 0.5 - - - +
41B PRO* 4.0 10.8 - - + -
42B VAL* 2.9 27.6 - - + +
45B MET* 3.2 31.9 - - + -
268C ALA 2.8 11.9 + - - +
269C GLN* 4.0 2.5 - - - -
270C LEU 2.8 0.6 - - - -
271C MET* 1.3 80.7 - - - +
273C ILE* 1.3 57.7 + - - +
275C LYS* 5.5 1.3 - - + -
276C LYS* 2.9 30.8 - - + +
23D ALA* 5.0 5.4 - - + +
24D PHE* 4.5 17.3 - - + -
27D VAL* 4.0 23.6 - - + -
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Residues in contact with ILE 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B VAL* 6.0 2.5 - - + -
42B VAL* 4.0 11.4 - - + -
269C GLN 3.0 19.1 - - - +
270C LEU* 2.5 36.0 + - + +
272C LEU* 1.3 76.0 - - - +
274C LEU* 1.3 60.1 + - + +
275C LYS 3.0 6.5 - - - +
276C LYS* 4.1 5.6 - - - +
278C GLN* 2.6 33.9 + - + +
22G GLN* 3.0 47.8 - - + +
25G LYS* 3.5 39.9 - - + +
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Residues in contact with LEU 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C LEU* 2.5 49.4 + - + +
271C MET* 3.1 44.2 - - + +
273C ILE* 1.3 71.4 - - + +
275C LYS* 1.3 72.0 + - - +
278C GLN* 2.7 26.2 - - + +
279C VAL* 3.6 3.4 - - - +
18H ALA* 6.2 0.2 - - + -
21H VAL* 4.2 29.8 - - + -
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Residues in contact with LYS 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271C MET 3.0 11.4 + - - +
272C LEU* 5.0 1.6 - - + +
273C ILE 3.0 1.6 - - - +
274C LEU* 1.3 93.8 - - - +
276C LYS* 1.3 101.6 + - + +
278C GLN 2.8 7.8 + - - -
279C VAL* 3.2 24.1 + - + -
306C OPC 2.9 55.0 - - - -
19D MET* 5.0 15.0 - - + -
20D ASN* 5.0 12.2 - - + +
23D ALA* 5.2 11.4 - - + -
24D PHE* 5.6 11.0 - - + -
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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
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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