Contacts of the helix formed by residues 12 - 36 (chain A) in PDB entry 1SEK
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 GLU 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A GLY* 1.3 71.7 - - - -
13A THR* 1.3 57.4 + - - +
15A LEU* 3.6 5.1 - - - +
16A GLN* 2.9 52.2 + - + +
87A ASP* 2.7 41.8 - - - +
90A ARG* 4.7 4.2 - - - +
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Residues in contact with THR 13 (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 GLY* 3.2 1.7 - - - -
12A GLU* 1.3 78.8 - - - +
14A ASP* 1.3 69.3 + - - +
16A GLN* 3.5 5.9 + - - +
17A LYS* 3.1 21.5 + - + +
20A ARG* 5.2 1.6 + - - -
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Residues in contact with ASP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLY* 3.2 21.8 + - - +
13A THR* 1.3 81.0 - - - +
15A LEU* 1.3 67.0 + - + +
17A LYS* 3.2 13.9 + - - +
18A ILE* 3.0 29.8 + - + +
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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
----------------------------------------------------------
11A GLY 3.0 22.0 + - - +
12A GLU* 3.2 9.6 + - - +
14A ASP* 1.3 78.5 - - + +
16A GLN* 1.3 63.3 + - + +
18A ILE* 3.4 8.1 + - + +
19A LEU* 3.1 22.7 + - - +
80A VAL* 4.8 9.6 - - + +
83A ASP* 4.0 38.6 - - + +
84A VAL* 4.1 23.9 - - + +
87A ASP* 3.7 25.1 - - + +
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Residues in contact with GLN 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU* 2.9 41.8 + - + +
13A THR* 3.8 6.5 - - - +
15A LEU* 1.3 74.5 - - - +
17A LYS* 1.3 57.3 + - - +
19A LEU* 3.4 18.8 + - - +
20A ARG* 2.9 43.3 + - - +
87A ASP* 4.6 14.7 + - - +
88A LEU* 5.5 5.9 - - - +
374A ASN* 3.2 28.0 + - - +
376A ASN* 5.0 3.1 + - - -
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Residues in contact with LYS 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 THR* 3.1 15.3 + - + +
14A ASP* 3.4 17.5 + - - +
16A GLN* 1.3 74.7 - - - +
18A ILE* 1.3 70.2 + - + +
20A ARG* 3.1 29.1 + - - +
21A GLU* 2.9 63.2 + - - +
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Residues in contact with ILE 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 ASP* 3.0 20.1 + - + +
15A LEU* 3.7 9.4 - - + +
17A LYS* 1.3 79.0 - - + +
19A LEU* 1.3 59.4 + - - +
21A GLU* 3.4 14.6 + - + +
22A SER* 2.9 35.1 + - - +
74A ALA 4.7 4.7 - - - +
75A LEU* 3.4 32.5 - - + -
76A PRO* 5.2 6.5 - - + -
80A VAL* 4.9 9.4 - - + -
84A VAL* 4.3 10.3 - - + -
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Residues in contact with LEU 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 3.1 11.3 + - - +
16A GLN* 3.5 21.5 - - - +
18A ILE* 1.3 81.0 - - - +
20A ARG* 1.3 57.7 + - - +
22A SER* 3.2 6.8 + - - -
23A ASN* 2.8 32.3 + - - +
48A PHE* 4.6 11.2 - - + -
51A LEU* 4.5 19.7 - - + -
75A LEU* 6.1 0.4 - - - -
84A VAL* 4.0 26.9 - - + +
85A PHE* 4.7 10.5 - - + -
88A LEU* 3.6 34.5 - - + -
374A ASN* 6.2 0.2 - - - +
376A ASN* 4.6 15.9 - - - +
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Residues in contact with ARG 20 (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 THR 5.2 1.4 + - - -
16A GLN* 2.9 31.0 + - - +
17A LYS* 3.1 37.7 + - - +
19A LEU* 1.3 77.6 - - - +
21A GLU* 1.3 58.7 + - - +
23A ASN* 3.4 1.4 + - - +
24A ASP* 2.9 42.8 + - - +
374A ASN* 4.8 5.6 + - - +
375A ARG* 3.6 70.0 - - - +
376A ASN* 3.3 23.6 - - - +
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Residues in contact with GLU 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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17A LYS* 2.9 58.1 + - - +
18A ILE* 3.7 12.8 - - + +
20A ARG* 1.3 77.6 + - - +
22A SER* 1.3 63.2 + - - +
24A ASP* 3.3 9.0 + - - +
25A GLN* 3.2 25.8 + - - +
74A ALA* 5.7 1.1 - - + -
263A LYS* 4.9 13.5 + - - +
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Residues in contact with SER 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 ILE* 2.9 27.1 + - - +
19A LEU* 3.5 7.9 - - - -
21A GLU* 1.3 77.3 - - - +
23A ASN* 1.3 63.3 + - - +
25A GLN* 3.1 16.2 + - - +
26A PHE* 3.0 23.2 + - - +
51A LEU* 4.8 9.2 - - - -
73A LEU 3.1 24.1 + - - -
74A ALA* 3.5 15.0 + - - +
75A LEU* 4.1 4.8 - - - +
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Residues in contact with ASN 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 LEU* 2.8 19.9 + - + +
20A ARG 3.9 3.1 - - - +
22A SER* 1.3 72.7 - - - +
24A ASP* 1.3 60.6 + - - +
26A PHE* 4.4 1.8 - - - -
27A THR* 2.5 50.2 + - - -
47A ALA* 3.9 1.0 - - - +
48A PHE* 3.3 43.9 + - + +
51A LEU* 3.8 16.6 - - + +
376A ASN* 4.0 10.7 + - - +
377A SER* 3.3 36.6 + - - +
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Residues in contact with ASP 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 ARG* 2.9 32.4 + - - +
21A GLU* 3.4 9.1 - - - +
22A SER 3.2 0.2 - - - -
23A ASN* 1.3 84.8 + - - +
25A GLN* 1.3 61.0 + - - +
27A THR* 3.8 3.4 - - - -
28A ALA* 3.2 22.9 + - - +
262A PRO* 3.7 21.6 - - + +
263A LYS* 4.2 16.3 + - - +
266A SER* 4.6 7.6 + - - -
372A LYS* 5.7 2.4 - - - -
375A ARG 5.1 3.8 - - - +
376A ASN* 4.9 1.0 - - - +
377A SER* 5.0 7.8 + - - -
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Residues in contact with GLN 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 GLU 3.2 10.5 + - - +
22A SER* 3.1 21.2 + - - +
24A ASP* 1.3 76.3 - - - +
26A PHE* 1.3 76.6 + - - +
28A ALA* 3.5 1.9 + - - +
29A GLN* 2.7 58.0 + - - +
71A ARG 5.9 0.2 - - - -
72A ALA 3.2 25.0 + - - +
73A LEU 4.0 2.0 - - - -
74A ALA* 3.5 24.6 - - + +
262A PRO* 3.7 23.3 - - + +
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Residues in contact with PHE 26 (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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22A SER 3.0 18.7 + - - +
23A ASN* 4.1 2.2 - - - +
25A GLN* 1.3 78.8 - - - +
27A THR* 1.3 61.7 + - - +
29A GLN* 3.2 5.1 + - - +
30A MET* 2.8 50.2 + - - +
47A ALA* 3.5 17.5 - - + -
50A VAL* 4.4 8.5 - - + -
51A LEU* 3.8 25.6 - - + -
54A LEU* 3.7 27.1 - - + -
72A ALA* 3.4 28.0 - - + -
73A LEU* 4.2 5.4 - - + -
296A LEU* 3.9 13.0 - - + -
299A MET* 3.4 28.3 - - + -
301A ILE* 4.5 6.5 - - + -
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Residues in contact with THR 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 ASN* 2.5 44.7 + - - -
24A ASP* 3.8 4.7 - - - -
26A PHE* 1.3 77.8 - - - +
28A ALA* 1.3 58.7 + - - +
30A MET* 3.8 0.9 - - - +
31A PHE* 2.8 33.6 + - + +
45A LEU* 4.8 2.5 - - + +
47A ALA* 3.5 19.5 + - + +
48A PHE 4.7 0.2 + - - -
377A SER* 4.5 18.8 + - - +
379A PHE* 6.0 0.9 - - - -
380A SER* 4.0 22.4 - - - +
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Residues in contact with ALA 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 ASP 3.2 15.3 + - - +
25A GLN 3.8 4.7 - - - +
27A THR* 1.3 79.2 - - - +
29A GLN* 1.3 55.7 + - + +
31A PHE* 3.5 7.0 - - - +
32A SER* 2.7 33.7 + - - -
259A LEU 3.8 14.5 - - - +
260A LYS* 3.2 26.5 - - - +
262A PRO* 3.9 14.1 - - + -
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Residues in contact with GLN 29 (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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25A GLN* 2.7 42.4 + - - +
26A PHE* 3.2 5.6 + - - +
28A ALA* 1.3 78.2 - - + +
30A MET* 1.3 62.3 + - - +
32A SER* 3.3 7.6 + - - -
33A GLU* 3.3 25.5 + - - +
72A ALA* 5.2 5.5 + - - +
262A PRO* 6.4 0.2 - - + -
299A MET* 3.4 44.6 + - + +
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Residues in contact with MET 30 (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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26A PHE* 2.8 34.0 + - + +
27A THR 3.9 2.5 - - - +
29A GLN* 1.3 73.9 - - - +
31A PHE* 1.3 64.0 + - - +
33A GLU* 3.3 3.8 + - - +
34A VAL* 3.0 29.7 + - + +
45A LEU* 3.8 16.4 - - + -
46A SER 3.9 14.1 - - - +
47A ALA* 3.8 28.0 - - + -
50A VAL* 4.2 4.9 - - + -
290A THR* 4.9 8.3 - - + -
292A LEU* 3.6 31.2 - - + -
295A VAL* 4.0 16.4 - - + -
296A LEU* 5.3 2.9 - - + -
299A MET* 3.8 12.3 - - - +
329A GLN* 4.0 12.3 - - - +
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Residues in contact with PHE 31 (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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27A THR* 2.8 20.4 + - + +
28A ALA* 3.5 7.4 - - - +
29A GLN 3.3 0.2 - - - -
30A MET* 1.3 77.7 - - - +
32A SER* 1.3 66.7 + - - +
34A VAL* 3.4 1.4 + - - +
35A VAL* 3.0 38.7 + - + +
45A LEU* 3.7 20.6 - - + +
256A GLU* 3.9 32.5 - - + -
259A LEU* 4.3 20.9 - - + -
368A PHE* 3.7 32.8 - + - -
380A SER* 3.7 18.8 - - - +
381A GLY* 4.1 10.3 - - - -
382A VAL* 3.8 23.3 - - + -
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Residues in contact with SER 32 (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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28A ALA 2.7 17.8 + - - -
29A GLN* 3.3 8.0 + - - -
30A MET 3.4 0.2 - - - -
31A PHE* 1.3 83.6 - - - +
33A GLU* 1.3 63.4 + - - +
35A VAL* 3.8 5.1 - - - +
36A LYS* 2.9 42.7 + - - +
256A GLU 5.7 1.1 - - - -
260A LYS* 4.0 30.8 - - - +
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Residues in contact with GLU 33 (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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29A GLN 3.3 14.2 + - - +
30A MET 3.3 8.4 + - - +
31A PHE 3.3 0.6 - - - -
32A SER* 1.3 82.2 - - - +
34A VAL* 1.3 60.8 + - - +
36A LYS* 3.3 29.0 + - - +
37A ALA* 3.2 22.3 + - - +
295A VAL* 3.8 24.0 - - + +
298A ASN* 3.3 37.2 + - - +
299A MET* 3.9 20.5 - - + +
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Residues in contact with VAL 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 MET* 3.0 21.0 + - + +
31A PHE 4.0 0.2 - - - +
33A GLU* 1.3 72.3 - - - +
35A VAL* 1.3 66.3 + - - +
37A ALA* 3.2 3.4 + - - -
38A ASN* 2.6 46.1 + - - +
43A VAL* 3.5 19.3 - - + -
45A LEU* 3.9 31.6 - - + -
288A THR* 5.2 1.1 - - + -
290A THR* 4.2 35.2 - - + +
295A VAL* 4.2 10.5 - - + -
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Residues in contact with VAL 35 (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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31A PHE* 3.0 44.2 + - + +
32A SER* 4.2 6.3 - - - +
34A VAL* 1.3 77.4 - - + +
36A LYS* 1.3 69.6 + - + +
38A ASN* 3.3 22.1 + - - +
39A PRO* 3.7 4.9 - - - +
43A VAL* 4.6 7.6 - - + -
45A LEU* 5.7 1.1 - - + -
256A GLU* 3.3 44.6 - - + +
382A VAL* 4.3 15.0 - - + -
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Residues in contact with LYS 36 (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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32A SER* 2.9 29.0 + - - +
33A GLU* 3.3 36.0 + - - +
34A VAL 3.2 0.2 - - - -
35A VAL* 1.3 83.8 - - + +
37A ALA* 1.3 58.2 + - - +
38A ASN 3.3 1.1 + - - -
39A PRO* 3.6 12.6 - - - +
257A GLN* 6.2 2.0 - - - +
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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