Contacts of the helix formed by residues 0 - 28 (chain D) in PDB entry 3KWO
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 ALA 0 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MSE 1.3 72.4 + - - +
2D SER* 3.1 4.6 + - - +
3D VAL* 3.3 6.2 + - - +
4D THR* 3.7 12.5 + - - +
116D GLU* 3.0 40.7 + - + +
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Residues in contact with MSE 1 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D ALA* 1.3 83.4 - - - +
2D SER* 1.3 56.5 + - - +
4D THR* 3.2 13.1 + - - +
5D LYS* 2.8 34.1 + - + +
63D GLU* 3.6 35.9 - - - +
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Residues in contact with SER 2 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D ALA* 3.1 3.1 + - - +
1D MSE 1.3 79.6 - - - +
3D VAL* 1.3 62.1 + - - +
5D LYS* 3.8 7.8 - - - +
6D GLN* 3.0 23.9 + - - +
112D ALA* 4.1 18.6 + - - +
115D LYS* 5.7 4.0 - - - +
116D GLU* 3.3 12.5 + - - +
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Residues in contact with VAL 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D ALA 4.0 1.6 - - - +
1D MSE 3.3 0.4 - - - -
2D SER* 1.3 77.3 - - - +
4D THR* 1.3 58.2 + - - +
6D GLN* 3.3 4.3 + - - +
7D LEU* 3.0 34.6 + - + +
61D LEU* 3.8 25.1 - - + -
109D LEU* 4.0 2.8 - - + +
112D ALA* 3.4 31.0 - - + +
113D ALA* 3.7 9.2 - - - +
116D GLU* 3.1 36.2 + - + +
118D ASP* 3.9 11.7 - - - +
121D THR* 4.0 13.0 - - + -
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Residues in contact with THR 4 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0D ALA 3.7 6.6 + - - +
1D MSE 3.2 26.6 + - - +
3D VAL* 1.3 74.3 - - - +
5D LYS* 1.3 65.0 + - - +
7D LEU* 3.8 7.0 - - - +
8D LEU* 3.0 35.5 + - - +
58D VAL* 4.7 9.4 - - - +
61D LEU* 3.8 37.2 - - + +
63D GLU* 3.8 32.3 - - + +
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Residues in contact with LYS 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D MSE 2.8 21.6 + - + +
2D SER* 3.8 8.3 - - - +
4D THR* 1.3 78.4 + - - +
6D GLN* 1.3 58.3 + - - +
8D LEU* 3.7 9.7 - - + +
9D GLN* 2.9 27.9 + - + +
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Residues in contact with GLN 6 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D SER 3.0 18.3 + - - +
3D VAL* 3.3 3.3 + - - +
5D LYS* 1.3 77.0 - - - +
7D LEU* 1.3 56.4 + - - +
9D GLN* 3.3 10.7 + - - +
10D MSE 2.9 41.9 + - + +
105D GLU* 2.8 52.9 + - - +
108D LYS* 3.6 31.6 + - + +
109D LEU* 3.8 33.0 - - + +
112D ALA* 5.1 3.8 - - + -
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Residues in contact with LEU 7 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D VAL* 3.0 23.9 + - + +
4D THR* 3.8 3.1 - - - +
5D LYS 3.4 0.2 - - - -
6D GLN* 1.3 75.7 - - - +
8D LEU* 1.3 58.8 + - - +
10D MSE 3.2 3.9 + - - +
11D GLN* 2.8 24.3 + - - +
54D CYS* 3.5 20.5 - - - +
57D ARG* 3.5 37.2 - - + -
58D VAL* 3.4 23.8 - - + +
61D LEU* 3.7 20.6 - - + -
109D LEU* 3.9 28.5 - - + -
121D THR* 4.5 2.0 - - + +
124D PHE* 4.0 18.4 - - + -
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Residues in contact with LEU 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D THR* 3.0 31.0 + - - +
5D LYS* 3.7 7.6 - - + +
7D LEU* 1.3 74.9 - - - +
9D GLN* 1.3 65.5 + - - +
11D GLN* 3.3 23.7 + - - +
12D ALA* 3.1 19.1 + - - +
58D VAL* 4.0 15.9 - - + -
63D GLU* 5.5 3.1 - - + -
64D LYS 3.5 26.2 - - - +
65D ALA* 3.9 5.8 - - - -
66D ILE* 3.8 25.9 - - + +
75D ASN* 5.6 2.2 + - - +
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Residues in contact with GLN 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D LYS* 2.9 15.0 + - + +
6D GLN* 3.5 16.8 - - - +
8D LEU* 1.3 75.7 - - - +
10D MSE 1.3 62.4 + - - +
12D ALA* 3.2 4.9 + - - +
13D ASP* 3.0 52.6 + - - +
75D ASN* 3.0 25.9 + - - +
77D LYS* 3.0 37.6 + - + +
101D TYR* 4.7 1.1 - - - +
105D GLU* 4.0 16.6 - - - +
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Residues in contact with MSE 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLN* 2.9 35.7 + - + +
7D LEU* 3.2 6.3 + - - +
9D GLN* 1.3 76.4 - - - +
11D GLN* 1.3 58.5 + - - +
13D ASP* 3.8 7.0 - - + +
14D ALA* 2.8 32.4 + - - +
50D LEU* 4.7 3.5 - - + +
54D CYS* 3.7 16.3 - - - -
102D LEU* 3.9 22.2 - - + -
105D GLU* 3.8 35.0 - - + +
106D PHE* 3.7 48.5 - - + -
109D LEU* 4.1 13.0 - - + -
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Residues in contact with GLN 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D LEU 2.8 14.6 + - - +
8D LEU* 3.5 18.5 - - - +
10D MSE 1.3 76.0 - - - +
12D ALA* 1.3 62.6 + - - +
14D ALA* 3.4 4.1 + - - +
15D HIS* 3.1 18.4 + - - +
51D PHE* 3.3 48.3 - - + +
54D CYS* 4.0 12.5 - - + +
55D ALA* 3.9 20.3 - - - +
65D ALA* 3.9 3.7 - - - +
66D ILE* 2.9 54.1 + - + +
72D LEU* 4.4 0.8 - - + +
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Residues in contact with ALA 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU 3.1 10.1 + - - +
9D GLN 3.6 7.4 - - - +
11D GLN* 1.3 80.5 - - - +
13D ASP* 1.3 56.9 + - - +
15D HIS* 3.4 4.3 + - - +
16D HIS* 3.0 26.0 + - - +
66D ILE* 4.4 2.2 - - + -
72D LEU* 3.8 37.5 - - + +
75D ASN* 3.9 23.3 - - + -
76D ALA* 4.0 8.8 - - - +
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Residues in contact with ASP 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLN* 3.0 34.3 + - - +
10D MSE 3.9 8.2 - - + +
12D ALA* 1.3 73.0 - - - +
14D ALA* 1.3 62.6 + - - +
16D HIS* 3.2 5.4 + - - +
17D LEU* 2.8 38.5 + - + +
76D ALA* 3.5 2.1 - - - +
77D LYS 2.7 28.9 + - - -
78D SER* 3.4 6.7 + - - -
101D TYR* 2.5 43.6 + - + -
102D LEU* 5.2 4.9 - - + -
105D GLU* 4.5 3.1 - - - +
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Residues in contact with ALA 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D MSE 2.8 17.5 + - - +
11D GLN 3.7 5.4 - - - +
13D ASP* 1.3 77.7 - - - +
15D HIS* 1.3 61.8 + - - +
17D LEU* 3.4 0.8 + - - +
18D TRP* 2.9 24.4 + - - +
47D MSE 3.7 22.8 - - - +
50D LEU* 3.9 18.6 - - + +
51D PHE* 3.6 30.1 - - - +
102D LEU* 5.6 0.8 - - - +
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Residues in contact with HIS 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D GLN 3.1 14.5 + - - +
12D ALA 3.6 8.6 + - - +
14D ALA* 1.3 76.8 - - - +
16D HIS* 1.3 65.7 + - - +
18D TRP* 3.2 19.0 + + - +
19D VAL* 3.0 45.1 + - + +
51D PHE* 3.8 23.6 - + + -
69D GLN* 5.4 10.7 - - + +
72D LEU* 3.7 40.7 - - + +
73D MSE 5.6 3.7 - - + -
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Residues in contact with HIS 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ALA 3.0 14.8 + - - +
13D ASP 3.2 8.3 + - - +
15D HIS* 1.3 81.6 + - - +
17D LEU* 1.3 56.9 + - - +
19D VAL* 3.3 9.1 + - + +
20D LYS* 2.9 38.9 + - + +
76D ALA* 3.8 19.3 - - + +
78D SER* 2.4 47.8 + - - +
79D PRO 3.5 14.1 - - - -
80D LYS* 3.7 27.3 - - + +
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Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D ASP* 2.8 24.2 + - + +
16D HIS* 1.3 70.5 - - - +
18D TRP* 1.3 57.9 + - - +
20D LYS* 3.6 31.4 - - - +
21D PHE* 2.7 48.7 + - + -
47D MSE 3.7 20.4 - - + -
78D SER* 3.8 17.9 - - - +
98D ASP* 3.7 26.0 - - + +
101D TYR* 5.0 0.7 - - + -
102D LEU* 3.7 42.8 - - + -
----------------------------------------------------------
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Residues in contact with TRP 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ALA 2.9 14.1 + - - +
15D HIS* 3.4 23.3 - + - +
17D LEU* 1.3 78.9 - - - +
19D VAL* 1.3 91.8 + - + +
22D HIS* 2.7 56.8 + + - -
44D TYR* 3.2 37.0 + - - +
47D MSE 3.9 11.1 - - + +
48D ALA* 3.7 23.5 - - + +
51D PHE* 6.3 0.4 - - + -
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Residues in contact with VAL 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D HIS* 3.0 33.9 + - + +
16D HIS* 3.6 10.3 - - + +
18D TRP* 1.3 96.8 - - + +
20D LYS* 1.3 63.8 + - - +
22D HIS* 3.1 17.4 + - + +
23D ASN* 3.3 10.7 + - + +
26D TRP* 5.4 3.3 - - + -
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Residues in contact with LYS 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D HIS* 2.9 32.5 + - + +
17D LEU* 3.6 16.0 - - - +
19D VAL* 1.3 79.5 - - - +
21D PHE* 1.3 59.7 + - + +
23D ASN* 2.9 28.8 + - + +
24D TYR* 3.2 34.0 + - + +
78D SER* 4.0 0.4 + - - -
79D PRO* 2.3 42.8 + - - +
80D LYS* 5.0 0.7 - - - +
81D VAL* 3.9 27.0 - - + +
98D ASP* 2.7 27.0 + - - +
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Residues in contact with PHE 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 2.7 43.7 + - + +
20D LYS* 1.3 71.1 - - + +
22D HIS* 1.3 65.5 + - - +
24D TYR* 3.3 25.4 + + + +
25D HIS* 3.0 22.2 + - - +
40D THR* 3.9 9.6 - - - +
43D ALA* 3.6 29.6 - - + -
44D TYR* 3.8 17.3 - - + -
47D MSE 3.5 30.5 - - + -
95D ILE* 4.0 7.4 - - + -
98D ASP* 3.4 28.3 - - + -
99D TYR* 3.8 27.1 - + - -
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Residues in contact with HIS 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D TRP* 2.7 61.1 + + - -
19D VAL* 3.1 12.0 + - + +
21D PHE* 1.3 74.5 - - - +
23D ASN* 1.3 59.0 + - - +
25D HIS* 3.1 6.1 + + - +
26D TRP* 2.9 75.2 + + + -
44D TYR* 3.4 48.9 + + - -
----------------------------------------------------------
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Residues in contact with ASN 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D VAL* 3.3 6.8 + - + +
20D LYS* 2.9 19.1 + - + +
22D HIS* 1.3 78.6 - - - +
24D TYR* 1.3 60.6 + - + +
26D TRP* 4.1 11.7 - - + -
27D ASN* 2.9 42.6 + - - +
81D VAL* 4.0 12.9 + - - +
83D LYS 3.0 24.0 + - - -
84D ASP* 3.6 8.0 - - - +
86D PHE* 3.4 19.4 - - - -
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Residues in contact with TYR 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D LYS* 3.2 31.6 + - + +
21D PHE* 3.6 32.1 - + - +
22D HIS 3.3 0.2 - - - -
23D ASN* 1.3 75.3 - - + +
25D HIS* 1.3 61.7 + - - +
28D VAL* 3.2 30.5 + - - +
36D ILE* 4.7 1.0 - - - +
40D THR* 3.7 14.6 - - + -
81D VAL* 3.9 8.2 - - + +
86D PHE* 4.0 26.9 - + - -
91D VAL* 3.9 16.8 - - + +
94D LEU* 3.4 32.8 - - + +
95D ILE* 3.8 25.1 - - + -
98D ASP* 2.6 30.0 + - - -
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Residues in contact with HIS 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D PHE 3.0 11.9 + - - +
22D HIS* 3.3 10.3 - - - +
24D TYR* 1.3 77.9 - - - +
26D TRP* 1.3 80.0 + + - +
28D VAL* 4.3 0.9 - - - +
33D PHE* 4.3 5.7 - - - -
37D HIS* 2.7 82.2 + + - +
40D THR* 3.2 18.4 + - - +
41D GLU* 3.5 25.1 + - + -
44D TYR* 3.5 15.1 + + + -
162D ZN 2.0 36.1 - - - -
----------------------------------------------------------
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Residues in contact with TRP 26 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D VAL* 5.4 3.4 - - + -
22D HIS* 2.9 55.7 + + + +
23D ASN* 4.1 7.6 - - + -
25D HIS* 1.3 100.9 - + - +
27D ASN* 1.3 80.8 + - - +
28D VAL 3.5 4.9 + - - +
29D LYS* 5.3 1.4 + - - -
33D PHE* 4.5 6.6 - - - -
37D HIS* 5.0 4.0 - + - -
162D ZN 4.4 6.4 - - - -
----------------------------------------------------------
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Residues in contact with ASN 27 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ASN* 2.9 33.6 + - - +
24D TYR 4.1 0.7 - - - -
26D TRP* 1.3 98.4 + - - +
28D VAL* 1.3 66.4 + - - +
29D LYS* 3.3 21.0 + - - +
84D ASP* 3.1 33.1 + - - +
85D CYS* 3.5 0.3 - - - -
86D PHE* 3.1 21.9 + - + -
----------------------------------------------------------
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Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D TYR 3.2 18.7 + - - +
25D HIS 4.3 4.0 - - - +
26D TRP 4.4 1.0 - - - +
27D ASN* 1.3 81.6 - - - +
29D LYS* 1.3 72.3 + - - +
33D PHE* 3.3 50.3 - - + +
36D ILE* 4.0 26.0 - - + -
37D HIS 4.6 1.6 - - - +
86D PHE* 3.4 14.3 - - - +
88D PRO* 3.9 23.3 - - + -
91D VAL* 4.1 9.4 - - + -
----------------------------------------------------------
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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