Contacts of the helix formed by residues 25 - 55 (chain W) in PDB entry 2DYS
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 GLY 25 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W LEU* 5.7 2.0 - - - +
22W LEU 3.2 7.1 + - - +
23W LYS 3.3 2.2 + - - -
24W GLY* 1.3 80.1 - - - +
26W ALA* 1.3 58.5 + - - -
27W THR* 3.2 4.0 - - - -
28W ASP* 3.0 22.4 + - - +
29W ASN* 3.2 14.7 + - - -
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Residues in contact with ALA 26 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25W GLY* 1.3 67.3 - - - -
27W THR* 1.3 65.1 + - - +
28W ASP 3.3 0.2 - - - -
29W ASN* 3.3 16.2 - - + +
30W ILE* 3.2 29.4 + - + +
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Residues in contact with THR 27 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309P CDL 3.8 31.1 + - + +
24W GLY 5.8 1.3 - - - -
25W GLY 3.1 1.7 + - - -
26W ALA* 1.3 74.5 - - - +
28W ASP* 1.3 74.1 + - - +
30W ILE* 2.9 14.7 + - + +
31W LEU* 2.9 32.6 + - + +
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Residues in contact with ASP 28 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56P GLN* 4.5 1.4 - - - +
59P ARG* 3.8 13.6 + - - +
63P ARG* 2.9 30.3 + - - -
309P CDL 4.1 6.6 + - - -
21W HIS 3.2 19.3 - - - +
22W LEU* 3.1 12.8 - - - +
24W GLY* 2.6 35.4 + - - -
25W GLY 3.3 11.4 - - - +
27W THR* 1.3 79.4 - - - +
29W ASN* 1.3 62.9 + - - +
31W LEU* 3.9 2.6 - - - +
32W TYR* 2.9 27.2 + - - +
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Residues in contact with ASN 29 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18W LEU* 6.2 1.0 - - - +
22W LEU* 4.0 34.2 + - - +
25W GLY 3.2 18.4 + - - -
26W ALA* 3.3 17.1 - - + +
28W ASP* 1.3 81.6 - - - +
30W ILE* 1.3 63.5 + - + +
32W TYR* 3.4 3.8 + - - +
33W ARG* 3.0 41.3 + - - +
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Residues in contact with ILE 30 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26W ALA* 3.2 19.3 - - + +
27W THR* 2.9 16.3 + - + +
29W ASN* 1.3 73.4 - - + +
31W LEU* 1.3 67.7 + - - +
33W ARG* 2.9 22.4 + - - +
34W VAL* 2.9 36.5 + - + +
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Residues in contact with LEU 31 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P LEU* 3.7 27.1 - - + -
55P TYR* 4.0 27.4 - - + -
56P GLN* 3.3 27.6 - - + +
59P ARG* 4.2 7.6 - - - +
309P CDL 4.1 31.6 - - + -
27W THR* 2.9 25.2 + - + +
28W ASP* 3.9 3.8 - - - +
30W ILE* 1.3 73.5 - - - +
32W TYR* 1.3 53.8 + - - +
34W VAL* 3.3 12.0 + - + +
35W THR* 2.8 37.1 + - - -
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Residues in contact with TYR 32 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N PHE* 3.7 16.1 - + - -
15P PRO* 3.7 17.7 - - + -
16P TRP* 3.7 26.9 - + + -
56P GLN* 3.6 7.5 + - - -
21W HIS* 4.4 6.7 - + - -
22W LEU* 4.3 17.3 - - + -
28W ASP 2.9 19.3 + - - +
29W ASN* 3.5 5.4 - - - +
31W LEU* 1.3 76.9 - - - +
33W ARG* 1.3 61.6 + - + +
35W THR* 3.3 2.0 + - - -
36W MET* 2.8 61.7 + - + +
101W CHD 3.4 51.2 - + + +
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Residues in contact with ARG 33 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29W ASN* 3.0 29.9 + - - +
30W ILE* 2.9 20.2 + - - +
32W TYR* 1.3 85.0 - - + +
34W VAL* 1.3 55.0 + - + +
36W MET* 4.1 1.2 - - - +
37W THR* 2.5 38.7 + - - -
101W CHD 3.2 57.5 + - + -
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Residues in contact with VAL 34 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P LEU* 4.5 10.5 - - + -
309P CDL 5.4 7.9 - - + -
30W ILE* 2.9 33.5 + - + +
31W LEU* 3.4 13.7 - - + +
33W ARG* 1.3 74.3 - - + +
35W THR* 1.3 65.4 + - - +
37W THR* 3.3 5.5 + - - -
38W LEU* 3.0 48.6 + - + +
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Residues in contact with THR 35 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P TRP* 4.1 5.6 - - + -
19P THR* 3.9 28.7 - - + +
49P THR* 4.5 1.6 - - - +
52P LEU* 3.7 30.8 - - + +
53P THR* 4.4 4.9 - - - +
56P GLN* 2.7 32.5 + - - +
31W LEU 2.8 16.7 + - - -
32W TYR 3.5 4.0 - - - -
34W VAL* 1.3 75.7 - - - +
36W MET* 1.3 58.4 + - - +
38W LEU* 3.2 5.4 + - - +
39W CYS* 2.9 36.4 + - - -
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Residues in contact with MET 36 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N PHE* 4.1 11.9 - - + -
15P PRO* 3.8 11.9 - - + +
18P LEU* 5.0 9.2 - - + -
19P THR* 3.6 26.9 - - + -
22P LEU* 5.6 0.7 - - - -
32W TYR* 2.8 49.5 + - + +
33W ARG* 4.1 1.8 - - - +
35W THR* 1.3 74.7 - - - +
37W THR* 1.3 58.3 + - - +
39W CYS* 3.5 4.4 + - - +
40W LEU* 2.9 49.8 + - + +
101W CHD 3.6 50.3 - - + +
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Residues in contact with THR 37 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33W ARG 2.5 25.5 + - - -
34W VAL* 3.6 5.2 - - - -
36W MET* 1.3 72.5 - - - +
38W LEU* 1.3 61.9 + - + +
40W LEU* 4.9 1.3 - - - -
41W GLY* 2.7 34.3 + - - -
101W CHD 3.9 46.5 - - + +
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Residues in contact with LEU 38 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P LEU* 4.1 0.3 - - - +
45P ILE* 3.9 18.0 - - + +
48P THR* 4.2 13.7 - - + -
49P THR* 3.3 20.0 - - + -
52P LEU* 3.5 31.0 - - + -
309P CDL 6.1 0.9 - - + -
34W VAL* 3.0 30.0 + - + +
35W THR 3.6 1.1 - - - +
37W THR* 1.3 81.2 - - + +
39W CYS* 1.3 54.2 + - - +
41W GLY* 5.1 0.4 - - - -
42W GLY* 2.7 33.1 + - - -
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Residues in contact with CYS 39 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P THR* 3.7 38.6 - - + -
22P LEU* 4.0 20.4 - - + -
23P SER 4.8 0.2 - - - -
26P LEU* 4.2 7.1 - - - +
49P THR* 3.5 27.4 - - - -
35W THR* 2.9 22.1 + - - +
36W MET* 3.8 7.0 - - - +
38W LEU* 1.3 76.6 - - - +
40W LEU* 1.3 55.4 + - + +
42W GLY 3.9 0.2 - - - -
43W THR* 2.6 38.4 + - - -
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Residues in contact with LEU 40 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P LEU* 5.9 2.5 - - + -
22P LEU* 4.1 19.5 - - + -
36W MET* 2.9 36.5 + - + +
37W THR* 4.2 2.0 - - - +
39W CYS* 1.3 72.8 - - - +
41W GLY* 1.3 65.8 + - - +
43W THR* 3.4 6.2 + - + +
44W LEU* 3.0 31.5 + - + +
101W CHD 3.5 52.5 - - + +
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Residues in contact with GLY 41 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37W THR* 2.7 22.8 + - - -
38W LEU* 5.1 0.2 - - - -
40W LEU* 1.3 71.3 - - - +
42W GLY* 1.3 53.0 + - - +
44W LEU* 3.0 15.0 + - - +
45W TYR* 2.8 34.6 + - - +
----------------------------------------------------------
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Residues in contact with GLY 42 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26P LEU* 3.2 22.4 - - - +
42P LEU* 3.6 2.1 - - - +
45P ILE* 4.5 15.9 - - - +
38W LEU 2.7 21.9 + - - -
41W GLY* 1.3 71.7 - - - -
43W THR* 1.3 51.6 + - - +
45W TYR* 3.4 9.1 - - - +
46W SER* 2.7 31.5 + - - -
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Residues in contact with THR 43 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110N LEU* 5.9 0.9 - - + -
22P LEU* 3.5 28.9 - - + +
25P LEU* 4.2 14.3 - - + +
26P LEU* 3.6 7.2 - - - +
39W CYS 2.6 22.9 + - - -
40W LEU* 3.6 8.7 - - + -
42W GLY* 1.3 73.3 - - - +
44W LEU* 1.3 67.2 + - + +
46W SER* 2.4 23.4 + - - +
47W LEU* 3.0 25.6 + - + +
----------------------------------------------------------
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Residues in contact with LEU 44 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40W LEU* 3.0 21.6 + - + +
41W GLY* 3.0 13.1 + - - +
43W THR* 1.3 74.8 - - + +
45W TYR* 1.3 67.5 + - - +
47W LEU* 3.1 20.7 + - + +
48W TYR* 3.1 21.3 + - - +
----------------------------------------------------------
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Residues in contact with TYR 45 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P MET* 5.7 2.0 - - + +
39P SER* 4.6 6.6 + - - -
41P THR* 4.0 34.8 + - + +
42P LEU* 3.9 29.6 - - + -
45P ILE* 4.2 12.8 - - + -
41W GLY 2.8 13.2 + - - +
42W GLY* 3.4 9.4 - - - +
44W LEU* 1.3 77.5 - - - +
46W SER* 1.3 62.0 + - - +
48W TYR* 3.1 27.6 + + - +
49W CYS* 3.0 39.9 + - - -
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Residues in contact with SER 46 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110N LEU* 5.5 2.9 - - - +
25P LEU* 4.1 10.2 - - - +
26P LEU* 4.0 5.7 - - - +
29P SER* 3.8 22.9 + - - -
42P LEU* 3.9 20.4 - - - +
42W GLY 2.7 11.5 + - - -
43W THR* 2.4 34.7 + - - +
45W TYR* 1.3 77.0 - - - +
47W LEU* 1.3 59.9 + - - +
49W CYS* 3.2 3.9 + - - +
50W LEU* 3.0 22.7 + - - +
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Residues in contact with LEU 47 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110N LEU* 3.9 36.1 - - + -
43W THR* 3.0 26.0 + - + +
44W LEU* 3.1 24.4 + - + +
46W SER* 1.3 77.0 - - - +
48W TYR* 1.3 62.8 + - - +
50W LEU* 3.4 14.5 + - + +
51W GLY* 3.0 19.4 + - - -
----------------------------------------------------------
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Residues in contact with TYR 48 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44W LEU 3.1 11.1 + - - +
45W TYR* 3.1 35.6 + + - +
47W LEU* 1.3 78.7 - - - +
49W CYS* 1.3 61.0 + - - +
51W GLY* 3.1 3.5 + - - -
52W TRP* 2.9 48.8 + + + +
----------------------------------------------------------
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Residues in contact with CYS 49 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29P SER* 6.0 0.2 - - - +
33P MET* 3.7 37.1 - - + +
42P LEU* 4.0 16.8 - - + -
45W TYR* 3.0 48.7 + - - -
46W SER* 3.5 9.0 - - - +
48W TYR* 1.3 79.8 - - - +
50W LEU* 1.3 56.0 + - - +
52W TRP* 3.4 7.8 + - - +
53W ALA* 3.0 29.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 50 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110N LEU* 5.4 12.8 - - + -
114N ALA* 3.7 39.5 - - + -
117N MET* 4.1 14.8 - - + -
118N VAL* 4.1 8.3 - - + -
46W SER 3.0 12.6 + - - +
47W LEU* 3.5 17.7 - - + +
48W TYR 3.2 0.2 - - - -
49W CYS* 1.3 72.1 - - - +
51W GLY* 1.3 71.0 + - - +
53W ALA* 3.3 4.3 + - - -
54W SER* 2.9 44.1 + - - +
----------------------------------------------------------
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Residues in contact with GLY 51 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47W LEU 3.0 14.9 + - - -
48W TYR* 3.1 4.0 + - - -
50W LEU* 1.3 85.0 - - - +
52W TRP* 1.3 63.7 + - - +
54W SER* 3.4 15.2 + - - -
55W PHE* 3.6 15.5 - - - -
----------------------------------------------------------
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Residues in contact with TRP 52 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33P MET* 4.8 8.7 - - + -
37P PHE* 3.7 35.2 - + + -
48W TYR* 2.9 37.0 + + + +
49W CYS* 3.5 12.8 - - - +
51W GLY* 1.3 79.3 - - - +
53W ALA* 1.3 78.7 + - + +
54W SER 3.2 1.4 + - - -
55W PHE* 3.3 6.1 + - - +
57W HIS* 3.1 66.4 + + + -
----------------------------------------------------------
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Residues in contact with ALA 53 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118N VAL* 3.7 30.0 - - + +
119N GLU* 4.3 6.1 + - - +
33P MET* 5.3 0.4 - - + -
37P PHE* 3.8 33.4 - - + -
49W CYS 3.0 16.8 + - - +
50W LEU* 4.0 2.7 - - - +
52W TRP* 1.3 86.7 - - + +
54W SER* 1.3 61.0 + - - +
55W PHE 3.2 6.5 + - - +
46Y LYS* 4.9 0.3 + - - -
----------------------------------------------------------
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Residues in contact with SER 54 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N MET* 3.1 47.3 - - - +
118N VAL* 4.2 1.5 - - - +
50W LEU* 2.9 28.1 + - - +
51W GLY* 3.5 10.5 - - - -
52W TRP 3.1 0.6 - - - -
53W ALA* 1.3 78.8 - - - +
55W PHE* 1.3 66.9 + - - +
42Y HIS* 3.1 14.5 + - - -
46Y LYS* 2.9 25.3 + - - -
----------------------------------------------------------
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Residues in contact with PHE 55 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117N MET* 5.7 2.0 - - + -
51W GLY* 3.6 16.6 - - - -
52W TRP 3.3 7.0 + - - +
53W ALA* 4.0 5.5 - - - +
54W SER* 1.3 84.1 - - - +
56W PRO* 1.3 74.8 - - + +
57W HIS* 3.1 28.8 + - + +
42Y HIS* 3.6 31.0 - + - -
45Y LEU* 6.0 2.7 - - + -
46Y LYS* 4.8 5.8 - - + -
----------------------------------------------------------
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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