Contacts of the helix formed by residues 8 - 34 (chain B) in PDB entry 4HYJ
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 VAL 8 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 1.3 78.5 - - - +
9B LEU* 1.3 58.1 + - - +
11B THR* 3.3 11.3 - - + +
12B GLN* 2.9 30.0 + - - +
211B LEU* 3.9 12.9 - - + +
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Residues in contact with LEU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.3 0.8 - - - +
8B VAL* 1.3 74.4 - - - +
10B ALA* 1.3 57.3 + - - +
11B THR 3.0 5.1 + - - -
12B GLN* 3.1 5.7 + - - +
13B TYR* 3.0 32.3 + - - +
316B LFA 5.1 8.4 - - + +
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Residues in contact with ALA 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 3.4 13.9 + - + +
9B LEU* 1.3 78.0 - - - +
11B THR* 1.3 56.4 + - - +
13B TYR* 4.7 5.7 - - - +
14B MET* 3.5 21.3 + - - +
215B LEU* 3.6 13.3 - - + +
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Residues in contact with THR 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.1 20.2 + - - +
8B VAL* 3.3 14.4 - - - +
9B LEU 3.0 0.4 - - - -
10B ALA* 1.3 76.9 - - - +
12B GLN* 1.3 68.0 + - - +
13B TYR 3.3 1.1 - - - -
14B MET* 3.6 3.1 - - - +
15B PHE* 3.2 33.0 + - + -
211B LEU* 3.9 33.9 + - + -
214B GLU* 4.5 7.3 - - - +
215B LEU* 3.4 27.4 + - - +
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Residues in contact with GLN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B VAL 2.9 19.9 + - - +
9B LEU* 3.7 5.6 - - - +
11B THR* 1.3 78.9 - - - +
13B TYR* 1.3 60.3 + - - +
15B PHE* 3.4 18.7 + - - +
16B TRP* 3.1 22.1 + - + +
62B LYS* 5.2 8.3 - - - +
63B ASP 5.8 2.2 - - - +
316B LFA 5.3 11.0 - - + -
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Residues in contact with TYR 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B LEU 3.0 17.1 + - - +
10B ALA* 4.7 4.9 - - - +
12B GLN* 1.3 75.2 - - - +
14B MET* 1.3 58.4 + - - +
16B TRP* 3.0 8.2 + - - +
17B VAL* 3.0 32.3 + - + +
316B LFA 3.5 34.9 - - + +
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Residues in contact with MET 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ALA 3.5 18.5 + - - +
11B THR* 3.4 6.1 + - - +
12B GLN 3.3 0.6 - - - -
13B TYR* 1.3 77.8 - - - +
15B PHE* 1.3 58.3 + - - +
17B VAL* 3.6 29.4 - - + +
18B GLY 2.9 22.9 + - - -
215B LEU* 3.6 25.1 - - + -
218B ASN* 3.3 34.7 + - + +
219B PHE* 3.5 40.4 - - + -
222B LEU* 5.0 4.9 - - + -
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Residues in contact with PHE 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 3.2 24.0 + - + -
12B GLN* 3.6 14.1 - - - +
13B TYR 3.2 0.6 - - - -
14B MET* 1.3 74.6 - - + +
16B TRP* 1.3 56.1 + - - +
18B GLY* 3.3 0.9 + - - -
19B PHE* 2.7 35.2 + - - +
57B HIS* 5.3 1.3 - - - -
58B TYR* 3.3 41.9 - + - +
61B MET* 3.4 52.7 - - + -
62B LYS* 4.4 13.7 - - - -
214B GLU* 4.1 35.2 - - + -
218B ASN* 3.5 9.9 - - - -
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Residues in contact with TRP 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLN* 3.1 27.7 - - + +
13B TYR* 3.0 11.5 + - - +
15B PHE* 1.3 79.1 - - - +
17B VAL* 1.3 56.8 + - - +
19B PHE* 3.2 21.1 + + + +
20B VAL* 2.8 35.6 + - - +
59B TYR* 5.7 0.4 - + - -
62B LYS* 3.4 52.4 + - + +
304B LFA 3.7 48.7 - - + -
316B LFA 4.8 2.2 - - + -
318B LFA 3.4 83.6 - - + +
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B TYR* 3.0 18.9 + - + +
14B MET* 3.6 33.2 - - + +
15B PHE 3.2 0.2 - - - -
16B TRP* 1.3 75.7 - - - +
18B GLY* 1.3 58.8 + - - +
20B VAL* 3.3 2.0 + - - +
21B GLY* 2.8 27.5 + - - -
222B LEU* 5.0 7.1 - - + +
318B LFA 3.7 33.4 - - + -
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Residues in contact with GLY 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B MET 2.9 10.5 + - - -
15B PHE 3.6 2.9 - - - -
17B VAL* 1.3 74.7 - - - +
19B PHE* 1.3 65.3 + - - +
21B GLY* 3.3 0.7 + - - -
22B MET* 2.9 29.1 + - - +
58B TYR* 4.0 14.4 - - - -
218B ASN* 3.6 21.7 - - - +
222B LEU* 4.5 10.8 - - - -
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Residues in contact with PHE 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PHE 2.7 18.9 + - - +
16B TRP* 3.3 26.0 - + + +
18B GLY* 1.3 74.1 - - - +
20B VAL* 1.3 67.6 + - + +
22B MET* 3.9 2.0 - - - +
23B ALA* 2.9 40.5 + - + +
55B ALA* 3.2 29.8 - - + -
58B TYR* 3.7 14.6 - - + +
59B TYR* 3.8 27.6 - + + +
62B LYS* 6.4 0.4 - - + -
304B LFA 4.0 37.5 - - + -
314B LFA 3.9 26.0 - - + -
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Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TRP 2.8 23.7 + - - +
17B VAL 3.7 4.5 - - - +
19B PHE* 1.3 80.6 - - + +
21B GLY* 1.3 68.9 + - - +
23B ALA* 4.0 3.0 - - - +
24B ALA* 2.9 29.8 + - + +
318B LFA 3.7 46.4 - - + -
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Residues in contact with GLY 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL 2.8 20.3 + - - -
18B GLY 3.7 1.1 - - - -
20B VAL* 1.3 75.8 - - - +
22B MET* 1.3 56.3 + - - +
24B ALA* 3.6 4.9 - - - +
25B GLY* 2.9 24.4 + - - -
222B LEU* 4.0 16.4 - - - -
226B VAL* 4.3 7.8 - - - +
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Residues in contact with MET 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLY 2.9 19.5 + - - +
19B PHE 3.9 0.2 - - - +
21B GLY* 1.3 73.1 - - - +
23B ALA* 1.3 66.0 - - - +
25B GLY* 3.2 1.5 + - - +
26B THR* 3.0 24.4 + - - -
51B THR* 3.4 30.3 - - - +
54B ALA* 3.7 21.8 - - + -
55B ALA* 3.7 10.8 - - - +
58B TYR* 4.1 12.1 - - + -
221B ASP* 3.6 44.6 - - + +
222B LEU* 3.6 15.3 - - + +
225B LYS* 3.8 15.0 - - + -
226B VAL* 4.3 15.0 - - - -
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 2.9 33.3 + - + +
20B VAL* 4.0 4.0 - - - +
22B MET* 1.3 76.8 - - - +
24B ALA* 1.3 61.9 + - - +
26B THR* 3.2 8.9 + - - -
27B LEU* 3.2 28.3 + - + +
52B PHE* 6.5 0.7 - - - -
55B ALA* 4.0 14.1 - - + +
314B LFA 5.3 7.9 - - + -
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Residues in contact with ALA 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B VAL* 2.9 22.9 + - + +
21B GLY* 3.6 5.4 - - - +
23B ALA* 1.3 74.0 - - - +
25B GLY* 1.3 56.6 + - - +
27B LEU* 3.2 11.5 + - - +
28B TYR* 2.8 38.3 + - - +
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Residues in contact with GLY 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLY 2.9 15.5 + - - -
22B MET 3.2 5.3 + - - -
24B ALA* 1.3 74.9 - - - +
26B THR* 1.3 56.6 + - - +
28B TYR* 3.7 5.1 - - - +
29B PHE* 2.9 48.1 + - - -
51B THR* 3.5 11.9 - - - -
226B VAL* 4.8 9.0 - - - -
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Residues in contact with THR 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B MET 3.0 10.5 + - - -
23B ALA* 3.5 11.0 + - - -
24B ALA 3.2 0.6 - - - -
25B GLY* 1.3 74.3 - - - +
27B LEU* 1.3 59.3 + - - +
30B LEU* 2.8 56.0 + - + +
48B ALA* 3.8 18.0 - - + +
51B THR* 2.9 17.5 + - - -
52B PHE* 3.1 38.0 + - + -
303B LFA 4.6 4.9 - - + -
306B LFA 4.9 5.8 - - + -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA* 3.2 14.3 + - + +
24B ALA* 3.5 13.2 - - - +
26B THR* 1.3 80.8 - - - +
28B TYR* 1.3 58.5 + - - +
30B LEU* 3.1 3.6 + - - +
31B VAL* 2.8 40.4 + - + +
306B LFA 3.7 39.5 - - + -
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Residues in contact with TYR 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA 2.8 22.4 + - - +
25B GLY* 3.7 3.4 - - - +
27B LEU* 1.3 71.9 - - - +
29B PHE* 1.3 88.5 + + - +
31B VAL* 3.1 6.3 + - + +
32B GLU* 3.0 55.2 + - + +
226B VAL* 6.4 0.9 - - + -
230B LEU* 3.5 27.8 - - + +
233B PHE* 3.3 24.6 - + - -
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Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLY* 2.9 41.1 + - - +
28B TYR* 1.3 93.2 - + - +
30B LEU* 1.3 63.0 + - - +
32B GLU* 3.9 3.2 - - - +
33B ARG* 3.0 24.3 + - - +
44B ALA* 3.7 26.5 - - + +
47B ALA* 3.8 28.7 - - + -
48B ALA* 3.9 8.1 - - + -
51B THR* 4.4 11.4 - - + -
225B LYS 4.8 0.4 - - - -
226B VAL* 4.0 12.6 - - + -
229B GLY* 3.6 40.8 - - - -
230B LEU* 3.8 10.8 - - + -
233B PHE* 4.0 20.2 - + + -
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Residues in contact with LEU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A PHE* 5.9 2.7 - - + -
26B THR* 2.8 42.6 + - + +
27B LEU* 3.6 3.6 - - - +
29B PHE* 1.3 73.9 - - - +
31B VAL* 1.3 61.7 + - - +
33B ARG* 3.3 32.1 - - - +
34B ASN* 4.3 2.3 + - - +
45B THR* 5.5 0.7 - - - -
48B ALA* 3.7 16.8 - - + -
303B LFA 4.2 32.1 - - + -
306B LFA 4.0 45.6 - - + +
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Residues in contact with VAL 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B LEU* 2.8 28.5 + - + +
28B TYR* 3.7 6.1 - - + +
30B LEU* 1.3 73.3 - - - +
32B GLU* 1.3 73.7 + - + +
33B ARG 3.4 0.3 + - - -
34B ASN* 4.0 9.9 + - - +
35B SER* 4.6 3.6 + - - -
306B LFA 4.3 28.1 - - + +
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Residues in contact with GLU 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B TYR* 3.0 49.3 + - + +
29B PHE* 4.1 4.5 - - - +
31B VAL* 1.3 85.7 - - + +
33B ARG* 1.3 64.2 + - - +
34B ASN 3.3 0.4 - - - -
35B SER* 2.4 38.3 + - - -
36B LEU* 3.6 6.6 + - - +
233B PHE* 3.5 33.8 - - + -
237B LYS* 4.4 6.6 + - - -
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Residues in contact with ARG 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B PHE 3.0 13.5 + - - +
30B LEU* 3.3 27.6 - - - +
31B VAL 3.2 0.6 - - - -
32B GLU* 1.3 75.6 - - - +
34B ASN* 1.3 64.0 + - - +
36B LEU* 3.1 17.8 + - - +
41B ARG* 3.3 47.7 + - + +
44B ALA* 3.9 12.3 - - + -
45B THR* 2.7 33.2 + - - +
303B LFA 6.0 1.0 - - - +
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Residues in contact with ASN 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B LEU 4.3 1.6 + - - +
31B VAL 4.0 7.4 + - - +
32B GLU 3.3 0.6 - - - -
33B ARG* 1.3 78.2 - - - +
35B SER* 1.3 58.8 + - - +
36B LEU 3.1 0.2 - - - -
41B ARG* 3.0 32.3 + - - +
306B LFA 6.1 5.6 - - + -
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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