Contacts of the helix formed by residues 8 - 34 (chain A) in PDB entry 4KXW
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 8 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LYS 3.6 2.0 + - - +
7A PRO* 1.3 75.8 - - - +
9A GLN* 1.3 58.2 + - - +
10A GLN* 3.4 18.2 + - - +
11A LYS* 2.8 36.2 + - - +
12A LEU* 2.9 28.4 + - - +
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Residues in contact with GLN 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASP* 1.3 73.2 - - - +
10A GLN* 1.3 58.0 + - + +
12A LEU* 3.4 27.2 + - - +
13A GLN* 2.8 30.2 + - - +
16A LYS* 4.9 11.5 - - - +
222A GLU* 4.4 9.0 - - - +
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Residues in contact with GLN 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ASP* 3.2 16.8 + - - +
9A GLN* 1.3 75.9 - - + +
11A LYS* 1.3 59.4 + - - +
13A GLN* 3.4 6.9 + - + +
14A ALA* 2.9 27.5 + - - +
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Residues in contact with LYS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 3.8 22.2 - - + -
8A ASP* 2.8 26.2 + - - +
10A GLN* 1.3 72.3 - - - +
12A LEU* 1.3 57.3 + - - +
14A ALA* 3.2 5.5 + - + +
15A LEU* 2.9 35.0 + - + +
53A PHE 3.4 23.4 + - - -
54A HIS* 3.1 26.6 + - + +
284A ILE* 3.8 30.0 - - + +
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A PRO* 3.6 28.9 - - + +
8A ASP 2.9 21.5 + - - +
9A GLN* 3.4 36.1 - - - +
11A LYS* 1.3 75.8 - - - +
13A GLN* 1.3 61.8 + - - +
15A LEU* 3.1 7.0 + - + +
16A LYS* 3.0 32.1 + - - +
221A VAL* 3.7 26.5 - - + +
222A GLU* 3.6 40.6 - - + +
225A CYS* 4.4 4.5 - - - -
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Residues in contact with GLN 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLN* 2.8 21.4 + - - +
10A GLN* 3.8 7.6 - - + +
12A LEU* 1.3 72.9 - - - +
14A ALA* 1.3 58.0 + - - +
16A LYS* 3.2 30.5 + - - +
17A ASP* 2.8 56.4 + - - +
277A GLN 4.1 5.9 + - - -
279A GLN* 3.5 49.6 + - + +
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN 2.9 17.4 + - - +
11A LYS* 3.2 8.7 + - + +
13A GLN* 1.3 75.4 - - - +
15A LEU* 1.3 53.6 + - - +
17A ASP* 3.4 11.8 + - - +
18A THR* 2.7 37.1 + - - -
21A ARG* 4.3 2.4 + - - +
280A SER* 6.5 0.2 - - - -
282A LYS 5.2 8.1 - - - +
284A ILE* 3.8 22.4 - - + -
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LYS* 2.9 32.2 + - + +
12A LEU* 3.1 13.4 + - + +
14A ALA* 1.3 72.9 - - - +
16A LYS* 1.3 59.6 + - - +
18A THR* 3.3 5.1 + - - +
19A ALA* 2.9 25.3 + - - +
49A ALA* 3.5 37.7 - - + +
50A VAL* 4.2 7.2 - - + -
53A PHE* 3.9 13.7 - - + +
54A HIS* 4.3 5.6 - - + -
221A VAL* 4.0 13.9 - - + +
225A CYS* 3.6 31.2 - - - -
284A ILE* 3.6 20.0 - - + -
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Residues in contact with LYS 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A GLN* 4.9 11.3 - - - +
12A LEU* 3.0 26.1 + - - +
13A GLN* 3.2 31.2 + - - +
15A LEU* 1.3 72.3 - - - +
17A ASP* 1.3 66.1 + - - +
19A ALA* 3.2 7.5 + - - +
20A ASN* 2.9 34.7 + - - +
46A GLU* 5.6 3.6 - - + +
221A VAL* 3.9 32.5 - - + -
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Residues in contact with ASP 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLN* 2.8 39.8 + - - +
14A ALA* 3.5 8.6 - - - +
16A LYS* 1.3 74.9 - - - +
18A THR* 1.3 57.2 + - - +
20A ASN* 3.3 2.9 + - - +
21A ARG* 2.9 44.4 + - - +
277A GLN 3.9 0.9 - - - +
278A ILE* 3.5 22.1 - - + +
279A GLN* 2.9 27.2 + - - +
280A SER* 3.0 29.8 + - - +
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Residues in contact with THR 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ALA 2.7 24.6 + - - -
15A LEU* 3.5 7.4 - - - -
17A ASP* 1.3 76.3 - - - +
19A ALA* 1.3 63.6 + - - +
21A ARG* 3.1 20.7 + - - +
22A LEU* 2.9 32.7 + - + +
49A ALA* 3.9 11.9 - - + -
53A PHE* 3.8 31.4 - - + -
88A GLU* 3.9 16.9 + - + +
284A ILE* 3.8 16.8 + - - +
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Residues in contact with ALA 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU 2.9 13.5 + - - +
16A LYS 3.2 9.2 + - - +
18A THR* 1.3 74.9 - - - +
20A ASN* 1.3 57.4 + - - +
22A LEU* 3.2 6.3 + - - +
23A ARG* 3.0 33.4 + - - +
45A ALA* 3.5 34.5 - - - +
46A GLU* 3.8 27.6 - - + +
49A ALA* 3.8 2.2 - - + +
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Residues in contact with ASN 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LYS* 2.9 26.8 + - - +
17A ASP* 3.8 0.8 + - - +
19A ALA* 1.3 73.9 - - - +
21A ARG* 1.3 64.5 + - - +
23A ARG* 3.0 33.4 + - - +
24A ILE* 3.0 27.2 + - - +
46A GLU* 5.6 0.4 + - - -
247A GLY* 6.0 0.3 - - - -
274A ILE* 3.6 20.1 - - + +
277A GLN* 4.2 29.7 + - - +
278A ILE* 3.7 19.7 - - + +
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Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ALA* 4.3 1.8 + - - +
17A ASP* 2.9 20.8 + - - +
18A THR* 3.5 25.4 + - - +
20A ASN* 1.3 75.1 - - - +
22A LEU* 1.3 58.0 + - - +
24A ILE* 3.3 7.7 + - + +
25A SER* 2.9 30.1 + - - -
88A GLU* 2.8 28.7 + - - +
278A ILE* 3.8 25.3 - - + +
280A SER 2.9 25.1 + - - -
281A LYS* 3.8 15.7 - - - +
282A LYS 3.5 18.6 + - - -
283A LYS* 3.8 15.9 - - - +
284A ILE* 5.1 0.4 - - - +
1010A EDO 3.4 26.9 + - - +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A THR* 2.9 22.8 + - + +
19A ALA* 3.2 6.0 + - - +
21A ARG* 1.3 76.4 - - - +
23A ARG* 1.3 62.1 + - - +
25A SER* 3.4 1.7 + - - -
26A SER* 2.9 30.3 + - - -
45A ALA* 3.9 20.9 - - + +
48A MET* 4.0 5.6 - - + -
49A ALA* 3.9 14.8 - - + +
81A ILE* 3.7 17.8 - - + +
84A ALA* 3.7 31.7 - - + +
85A VAL* 3.6 37.0 - - + +
88A GLU* 4.6 7.4 - - + -
1010A EDO 4.4 7.0 - - - -
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Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ALA* 3.0 18.7 + - - +
20A ASN* 3.0 35.9 + - - +
22A LEU* 1.3 74.9 - - - +
24A ILE* 1.4 62.3 + - - +
26A SER* 3.2 4.7 + - - -
27A ILE* 3.0 29.0 + - - +
42A CYS* 3.0 40.8 + - - +
45A ALA* 3.7 15.7 - - + +
46A GLU* 2.8 44.0 + - - -
81A ILE* 5.5 1.1 - - - -
246A ARG* 2.8 42.3 + - - +
247A GLY* 4.2 5.6 - - - -
274A ILE* 4.2 19.7 - - + -
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Residues in contact with ILE 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ASN 3.0 15.8 + - - +
21A ARG* 3.7 9.6 - - + +
23A ARG* 1.4 75.6 - - - +
25A SER* 1.3 60.0 + - - +
27A ILE* 3.3 3.5 + - - +
28A GLN* 2.8 54.0 + - + +
271A ILE* 3.9 27.8 - - + +
274A ILE* 3.7 29.8 - - + -
275A TYR* 3.8 29.4 - - + +
278A ILE* 3.9 15.3 - - + -
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Residues in contact with SER 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG 2.9 16.5 + - - -
22A LEU 3.8 0.4 - - - -
24A ILE* 1.3 77.8 - - - +
26A SER* 1.4 56.8 + - - +
28A GLN* 3.2 13.6 + - - +
29A ALA* 2.8 32.2 + - - +
80A PRO 4.9 1.8 + - - -
84A ALA* 3.6 22.3 - - - +
97A LEU* 3.3 30.2 - - - +
98A LEU* 5.6 0.2 - - - +
1010A EDO 4.0 10.5 - - - -
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Residues in contact with SER 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU 2.9 21.7 + - - -
23A ARG* 3.2 5.8 + - - -
25A SER* 1.4 75.4 - - - +
27A ILE* 1.3 60.5 + - - +
29A ALA* 4.1 0.3 - - - +
30A THR* 2.8 33.7 + - - +
38A PRO* 4.2 6.0 - - - +
41A CYS* 3.3 37.9 - - - +
42A CYS* 5.4 0.7 - - - -
80A PRO* 4.0 10.7 + - - -
81A ILE* 3.5 19.4 - - - +
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Residues in contact with ILE 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ARG 3.0 19.0 + - - +
24A ILE* 3.7 4.5 - - - +
26A SER* 1.3 74.3 - - - +
28A GLN* 1.3 65.1 + - - +
30A THR* 3.4 5.2 + - - -
31A THR* 2.9 32.8 + - - +
38A PRO* 4.3 15.9 - - + -
42A CYS* 4.5 4.9 - - - -
248A ILE* 4.1 17.5 - - + -
262A LEU* 4.2 13.7 - - + -
267A ALA* 3.8 26.9 - - + -
270A ILE* 3.9 14.8 - - + -
271A ILE* 3.9 12.8 - - + -
274A ILE* 3.9 26.7 - - + -
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Residues in contact with GLN 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 2.8 36.7 + - - +
25A SER* 3.7 17.5 + - - +
27A ILE* 1.3 73.9 - - - +
29A ALA* 1.3 58.6 + - - +
31A THR* 3.9 3.9 - - - -
32A ALA* 2.9 30.8 + - - +
98A LEU* 3.9 21.2 - - + +
271A ILE* 3.6 23.3 - - + +
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A SER* 2.8 18.4 + - - +
26A SER* 4.1 3.8 - - - +
28A GLN* 1.3 78.7 - - - +
30A THR* 1.4 58.2 + - - +
32A ALA* 3.4 6.0 + - - +
33A ALA* 2.9 28.6 + - - +
80A PRO* 4.8 6.3 - - + +
97A LEU* 3.3 32.1 - - + +
98A LEU* 4.5 4.8 - - + +
100A LEU* 3.7 18.9 - - + +
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Residues in contact with THR 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 2.8 22.6 + - - +
27A ILE* 3.4 4.2 + - - -
29A ALA* 1.4 72.6 - - - +
31A THR* 1.3 63.2 + - - +
34A GLY* 2.8 24.8 + - - -
35A SER 3.4 24.3 + - - +
36A GLY* 3.9 0.7 - - - -
37A HIS 3.8 16.4 - - - +
38A PRO* 3.5 28.0 - - + +
80A PRO* 3.8 15.7 - - + -
100A LEU* 3.7 19.3 - - + -
261A PRO* 3.7 7.4 - - - +
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ILE* 2.9 20.2 + - - +
28A GLN* 4.0 3.6 - - - -
30A THR* 1.3 77.0 + - - +
32A ALA* 1.3 62.4 + - - +
34A GLY* 3.3 10.7 + - - -
261A PRO* 4.5 3.3 - - - +
262A LEU* 2.9 35.4 + - - +
264A LYS* 3.3 45.2 + - + +
267A ALA* 3.5 19.0 - - + +
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Residues in contact with ALA 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A GLN 2.9 19.8 + - - +
29A ALA* 3.6 5.4 - - - +
31A THR* 1.3 78.2 - - - +
33A ALA* 1.3 62.5 + - - +
98A LEU* 3.7 28.0 - - + +
102A LYS* 5.9 3.8 - - - -
264A LYS* 4.3 9.7 + - - +
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA 2.9 16.6 + - - +
30A THR 3.8 0.2 - - - +
32A ALA* 1.3 77.5 - - - +
34A GLY* 1.3 61.6 + - - +
35A SER* 3.6 20.9 + - - +
98A LEU 5.1 0.6 + - - -
100A LEU* 3.5 26.2 + - + +
101A ARG* 4.1 15.5 - - + -
102A LYS* 6.3 2.0 - - - +
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Residues in contact with GLY 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A THR 2.8 8.3 + - - -
31A THR 3.3 7.5 + - - -
32A ALA 3.3 3.4 - - - -
33A ALA* 1.3 76.9 - - - +
35A SER* 1.3 61.1 + - - +
261A PRO* 3.7 19.2 - - - +
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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