Contacts of the helix formed by residues 251 - 275 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144P PHE* 2.9 32.5 - - + -
250P GLN* 1.3 71.7 + - - +
252P PRO* 1.3 63.3 - - - +
253P ASN* 3.1 21.5 + - - +
254P ARG* 2.6 66.8 + - + +
255P VAL* 3.1 5.1 + - - +
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Residues in contact with PRO 252 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P LEU* 5.1 9.4 - - + -
42P PRO* 5.1 10.5 - - + -
144P PHE* 5.4 0.4 - - + -
250P GLN 2.8 17.0 - - - +
251P ASP* 1.3 76.1 - - - +
253P ASN* 1.3 52.9 + - - +
254P ARG 2.6 7.3 + - - -
255P VAL* 2.5 33.4 + - + +
256P LYS* 2.7 17.0 + - - +
4T LEU* 6.0 5.6 - - + -
5T VAL* 6.4 2.7 - - + -
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Residues in contact with ASN 253 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251P ASP* 3.1 15.7 + - - +
252P PRO* 1.3 78.7 - - + +
254P ARG* 1.3 56.1 + - - +
256P LYS* 4.0 34.9 + - - +
257P TRP* 3.1 43.0 - - - +
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Residues in contact with ARG 254 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N PHE* 6.2 0.2 - - + -
80N TRP* 2.9 86.2 - - + +
56O VAL* 4.6 7.5 - - - +
144P PHE* 4.2 27.8 - - - +
250P GLN* 3.7 26.3 - - - +
251P ASP* 2.6 48.2 + - + +
252P PRO 2.6 4.9 + - - -
253P ASN* 1.3 75.5 - - - +
255P VAL* 1.3 59.6 + - - -
257P TRP* 4.3 6.0 - - - +
258P MET* 3.8 17.2 + - - +
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Residues in contact with VAL 255 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56O VAL* 5.4 2.5 - - + +
57O LEU* 5.3 5.2 - - + -
250P GLN* 3.0 38.8 - - + +
251P ASP 3.7 6.5 - - - +
252P PRO* 2.5 17.9 + - + +
254P ARG* 1.3 72.5 - - - +
256P LYS* 1.3 69.0 + - - +
258P MET* 3.0 16.7 - - + +
259P ILE* 2.9 34.5 + - + +
5T VAL* 4.3 23.1 - - + +
9T VAL* 4.8 14.8 - - + +
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Residues in contact with LYS 256 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252P PRO 2.7 14.1 + - - +
253P ASN* 4.0 30.0 + - - +
255P VAL* 1.3 74.9 - - - +
257P TRP* 1.3 95.7 + - + +
259P ILE* 2.5 34.8 + - - +
260P ALA* 2.5 19.4 + - + -
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Residues in contact with TRP 257 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78N PHE* 6.0 7.9 - + - -
253P ASN* 3.1 31.7 + - - +
254P ARG* 4.5 5.2 - - - +
256P LYS* 1.3 114.5 - - - +
258P MET* 1.3 57.9 + - - +
260P ALA* 3.6 20.8 - - + +
261P PHE* 2.8 29.5 + - - +
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Residues in contact with MET 258 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52O VAL* 3.9 15.3 - - + +
53O ALA* 3.3 36.3 - - + -
56O VAL* 3.6 30.1 - - + -
57O LEU* 3.9 8.7 - - + -
254P ARG 3.8 9.1 + - - +
255P VAL* 3.0 21.0 + - + +
256P LYS 3.1 0.6 - - - -
257P TRP* 1.3 78.2 - - - +
259P ILE* 1.3 67.2 + - + +
261P PHE* 3.2 9.9 - - - +
262P ILE* 3.2 31.0 + - - +
9T VAL 4.4 0.7 - - - +
12T THR* 3.5 29.6 - - + +
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Residues in contact with ILE 259 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255P VAL* 2.9 26.0 + - + +
256P LYS* 2.5 23.3 + - - +
258P MET* 1.3 77.1 - - + +
260P ALA* 1.3 56.7 + - - +
261P PHE 2.8 4.7 - - - -
262P ILE* 2.8 34.0 + - + +
263P CYS* 3.3 17.0 + - - -
5T VAL* 4.9 4.7 - - + -
8T LEU* 3.1 37.9 - - + +
12T THR* 3.1 21.5 - - + -
10U LEU* 6.1 5.6 - - + -
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Residues in contact with ALA 260 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256P LYS* 2.5 19.0 + - + +
257P TRP* 3.6 34.3 - - + +
259P ILE* 1.3 75.9 - - - +
261P PHE* 1.3 58.9 + - - +
263P CYS* 4.1 7.6 + - - +
264P LEU* 3.4 25.5 + - - +
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Residues in contact with PHE 261 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O PHE* 4.9 12.1 - + - -
49O ALA* 5.8 7.4 - - - -
52O VAL* 5.9 9.9 - - + -
257P TRP 2.8 13.0 + - - +
258P MET* 3.2 14.6 - - - +
259P ILE 2.8 1.0 - - - -
260P ALA* 1.3 77.3 - - - +
262P ILE* 1.3 69.7 + - + +
264P LEU* 3.1 18.5 + - + +
265P VAL* 3.3 16.7 + - + -
30Q VAL* 3.0 44.6 - - + -
33Q GLY* 3.4 12.6 - - - -
34Q ALA* 3.0 44.2 - - + -
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Residues in contact with ILE 262 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49O ALA* 5.5 5.8 - - + -
53O ALA* 5.8 2.0 - - + -
258P MET* 3.2 22.4 + - + +
259P ILE* 2.8 28.7 + - + +
261P PHE* 1.3 70.7 - - - +
263P CYS* 1.3 55.3 + - - +
264P LEU 2.5 1.4 + - - -
265P VAL* 2.4 35.8 + - - +
266P MET* 2.6 49.4 + - + -
12T THR* 3.8 38.1 - - - +
13T LEU* 5.6 0.4 - - - -
16T LEU* 4.0 18.4 - - + -
10U LEU* 5.5 3.8 - - + -
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Residues in contact with CYS 263 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259P ILE* 3.3 21.0 + - - -
260P ALA* 4.1 11.2 - - - +
262P ILE* 1.3 81.3 - - - +
264P LEU* 1.3 61.4 + - + +
266P MET* 3.3 13.2 - - - -
267P LEU* 2.9 40.8 + - + +
10U LEU* 4.6 20.6 - - - -
14U THR* 6.1 0.2 - - - -
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Residues in contact with LEU 264 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260P ALA 3.4 21.8 - - - +
261P PHE* 3.3 18.6 - - + +
262P ILE 2.5 5.9 + - - -
263P CYS* 1.3 77.5 - - + +
265P VAL* 1.3 53.7 + - - +
267P LEU* 3.1 10.8 + - + +
268P ALA* 2.5 36.9 + - - +
26Q THR* 5.0 3.7 - - - +
29Q GLY* 4.4 21.3 - - - +
30Q VAL* 3.7 16.3 - - + +
33Q GLY* 5.4 3.6 - - - -
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Residues in contact with VAL 265 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O MET* 4.0 20.9 - - + +
46O GLY* 4.1 11.4 - - - +
48O PHE* 6.5 0.2 - - + -
49O ALA* 4.8 11.9 - - + +
261P PHE* 3.6 21.8 - - + +
262P ILE* 2.4 18.5 + - + +
264P LEU* 1.3 70.3 - - - +
266P MET* 1.3 55.0 + - - +
267P LEU 2.6 3.6 + - - -
268P ALA* 2.6 30.3 + - - -
269P GLN* 2.9 37.2 + - + +
30Q VAL* 3.5 25.4 - - + -
16T LEU* 4.9 7.4 - - + -
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Residues in contact with MET 266 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262P ILE* 2.6 34.4 + - + -
263P CYS* 3.3 25.6 - - - +
265P VAL* 1.3 72.4 - - - +
267P LEU* 1.3 62.2 + - + +
269P GLN* 2.9 24.4 - - - +
270P LEU* 3.6 3.5 - - - +
15T GLY 2.7 32.8 - - - +
16T LEU* 3.9 14.4 - - - -
18T TYR* 3.3 32.3 - - + -
10U LEU* 4.0 24.0 - - + -
11U VAL* 5.4 1.6 - - - -
14U THR* 3.8 28.1 - - + +
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Residues in contact with LEU 267 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263P CYS* 2.9 34.2 + - + +
264P LEU* 3.5 9.4 - - + +
265P VAL 2.6 4.6 + - - -
266P MET* 1.3 77.7 - - + +
268P ALA* 1.3 62.8 + - - +
270P LEU* 2.8 31.8 + - + +
271P MET* 3.0 30.2 + - + +
26Q THR* 4.5 7.4 - - + -
14U THR* 4.0 19.1 - - + -
17U ILE* 5.1 12.3 - - + -
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Residues in contact with ALA 268 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O MET* 3.8 14.1 - - - -
264P LEU 2.5 21.0 + - - +
265P VAL 2.6 3.6 + - - +
267P LEU* 1.3 66.3 - - - +
269P GLN* 1.3 53.1 + - - +
270P LEU 2.5 17.3 + - - -
271P MET* 2.9 4.0 + - - +
272P LEU* 2.8 22.7 + - - +
26Q THR* 3.5 13.9 + - - +
27Q VAL* 3.8 17.4 - - - +
30Q VAL* 3.2 25.8 - - + -
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Residues in contact with GLN 269 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O VAL* 3.1 34.4 - - + +
45O MET* 3.1 21.6 - - + +
265P VAL* 2.9 35.2 - - + +
266P MET* 2.9 35.4 - - - +
268P ALA* 1.3 71.8 - - - +
270P LEU* 1.3 60.2 + - - +
273P ILE* 3.0 25.5 - - - +
16T LEU* 5.1 1.2 - - - +
18T TYR* 2.9 32.3 - - - +
19T ALA* 4.0 11.4 - - - +
22T GLN* 3.2 7.0 - - - +
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Residues in contact with LEU 270 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266P MET 3.6 14.4 - - - +
267P LEU* 2.8 21.3 - - + +
268P ALA 2.5 5.9 + - - -
269P GLN* 1.3 76.5 + - - +
271P MET* 1.3 55.2 + - - +
272P LEU 2.8 3.1 - - - -
273P ILE* 2.5 33.1 + - + +
274P LEU* 2.6 43.1 + - + +
18T TYR* 3.5 17.9 - - + +
22T GLN* 3.4 19.1 - - - +
25T LYS* 6.2 0.2 - - - -
14U THR* 5.2 6.5 - - + +
17U ILE* 5.5 6.1 - - + -
18U ALA* 4.5 23.3 - - + +
21U VAL* 5.5 2.9 - - + -
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Residues in contact with MET 271 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267P LEU* 3.0 25.2 + - + +
268P ALA 2.9 3.4 + - - +
270P LEU* 1.3 87.3 - - - +
272P LEU* 1.3 56.8 + - - +
274P LEU* 3.2 29.7 - - + +
275P LYS* 3.0 26.0 + - - +
22Q LEU* 3.3 33.7 - - + -
23Q ALA* 2.9 45.2 - - + +
26Q THR* 3.2 35.9 - - + +
21U VAL* 6.3 1.8 - - - -
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Residues in contact with LEU 272 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O TYR* 2.4 45.5 - - + +
41O PRO* 3.1 37.9 - - + -
42O VAL* 3.0 24.2 - - + +
45O MET* 4.0 4.9 - - + -
268P ALA 2.8 9.4 + - - +
270P LEU 2.8 1.0 - - - -
271P MET* 1.3 79.0 - - - +
273P ILE* 1.3 56.2 + - - +
275P LYS* 5.2 1.6 - - + -
276P LYS* 2.8 14.8 - - + +
23Q ALA* 4.6 1.3 - - + +
24Q PHE* 3.0 36.6 - - + -
27Q VAL* 3.6 28.5 - - + -
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Residues in contact with ILE 273 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39O VAL* 4.9 7.9 - - + -
42O VAL* 3.7 11.9 - - + -
269P GLN 3.0 18.2 - - - +
270P LEU* 2.5 32.7 + - + +
272P LEU* 1.3 74.3 - - - +
274P LEU* 1.3 60.6 + - + +
275P LYS 2.9 6.7 - - - +
276P LYS* 4.1 5.4 - - - +
278P GLN* 2.6 33.2 + - + +
22T GLN* 2.8 52.7 - - + +
23T GLN* 5.7 0.2 - - - -
25T LYS* 3.4 39.9 - - + +
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Residues in contact with LEU 274 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270P LEU* 2.6 49.4 + - + +
271P MET* 3.2 44.2 - - + +
273P ILE* 1.3 70.6 - - + +
275P LYS* 1.3 71.6 + - - +
278P GLN* 2.7 25.9 - - + +
279P VAL* 3.6 3.3 - - - +
19Q MET* 4.9 12.3 - - + -
22Q LEU* 5.3 3.4 - - + -
25T LYS* 6.3 1.3 - - - -
18U ALA* 5.8 0.7 - - + -
21U VAL* 4.3 28.7 - - + -
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Residues in contact with LYS 275 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1306O OPC 3.6 40.0 + - - +
271P MET 3.0 12.3 + - - +
272P LEU* 5.0 1.1 - - + +
273P ILE 2.9 0.9 - - - +
274P LEU* 1.3 94.1 - - - +
276P LYS* 1.3 98.6 + - + +
278P GLN 2.8 8.3 + - - -
279P VAL* 3.1 25.0 + - + -
17Q GLN* 6.5 1.3 - - - -
19Q MET* 5.0 6.0 - - + +
20Q ASN* 4.4 37.1 - - + +
23Q ALA* 4.7 2.5 - - + -
24Q PHE* 4.8 13.9 - - + -
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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