Contacts of the helix formed by residues 32 - 61 (chain B) 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 GLN 32 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 3.5 26.2 - - + +
32A GLN* 4.1 14.3 - - + +
30B GLY 3.1 1.0 + - - -
31B LEU* 1.3 101.9 + - + +
33B PHE* 1.3 66.8 + - - +
34B PHE 3.1 3.3 + - - -
35B SER* 3.2 13.4 + - - +
36B ILE* 3.0 25.6 + - + +
88B PRO* 3.5 31.2 - - + +
155B BU1 3.9 16.8 - - - +
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Residues in contact with PHE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B HIS 4.3 4.3 - - - -
26B TRP* 4.6 8.5 - - - -
28B VAL* 3.3 44.4 - - + +
29B LYS* 5.1 0.9 - - - -
30B GLY 2.9 23.6 + - - +
31B LEU 3.2 2.4 - - - +
32B GLN* 1.3 77.0 - - - +
34B PHE* 1.3 75.4 + + + +
36B ILE* 3.7 2.0 - - - +
37B HIS* 2.8 63.4 + + + +
88B PRO* 4.8 0.2 - - - +
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Residues in contact with PHE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU 4.9 1.4 + - - -
32B GLN 3.2 0.6 - - - -
33B PHE* 1.3 92.5 - + + +
35B SER* 1.3 65.5 + - - +
37B HIS* 3.5 13.5 - + - +
38B GLU* 2.9 63.9 + - + +
153B ACY 6.2 2.0 - - + -
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Residues in contact with SER 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B GLN* 3.2 15.1 + - - +
34B PHE* 1.3 81.1 - - - +
36B ILE* 1.3 59.2 + - - +
38B GLU* 3.3 5.9 + - - +
39B TYR* 2.9 29.9 + - - +
155B BU1 3.0 38.6 + - - +
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Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR 4.6 1.3 - - - +
28B VAL* 3.8 24.0 - - + -
32B GLN* 3.0 20.6 + - + +
33B PHE 3.7 2.7 - - - +
35B SER* 1.3 77.4 + - - +
37B HIS* 1.3 57.4 + - - +
39B TYR* 3.2 5.4 + - + +
40B THR* 2.9 36.2 + - + +
88B PRO* 3.9 24.0 - - + +
91B VAL* 3.8 26.5 - - + -
92B ILE* 4.0 22.7 - - + -
95B ILE* 6.4 0.2 - - + -
155B BU1 3.4 36.1 - - + +
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Residues in contact with HIS 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B HIS* 2.8 70.2 + + - +
26B TRP* 5.4 2.9 - + - -
28B VAL* 4.6 1.1 - - + +
33B PHE* 2.8 42.7 + + + +
34B PHE* 3.3 16.8 + + - +
36B ILE* 1.3 77.3 - - - +
38B GLU* 1.3 80.7 + - - +
40B THR* 3.1 5.7 + - - -
41B GLU* 3.1 8.0 + - - +
162B ZN 2.0 37.7 - - - -
163B ZN 3.8 1.8 - - - -
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Residues in contact with GLU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B PHE* 2.9 52.8 + - + +
35B SER* 3.7 6.1 - - - +
37B HIS* 1.3 82.1 - - - +
39B TYR* 1.3 65.9 + - - +
41B GLU* 3.1 4.1 + - - +
42B LYS* 3.2 18.5 + - - +
151B ACY 3.3 24.5 - - + +
153B ACY 2.6 23.5 - - - +
161B ZN 2.1 28.3 - - - -
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Residues in contact with TYR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GOL 4.1 19.2 + - - -
35B SER 2.9 17.8 + - - +
36B ILE* 3.2 8.5 + - + +
38B GLU* 1.3 77.3 - - - +
40B THR* 1.3 61.6 + - + +
42B LYS* 3.4 7.0 + - + +
43B ALA* 3.0 24.5 + - + +
92B ILE* 6.4 1.1 - - + -
95B ILE* 3.7 35.2 - - + -
99B TYR* 3.8 27.0 + - - -
135B SER* 3.9 8.8 + - - -
139B ILE* 3.9 10.6 - - + +
155B BU1 3.6 28.9 - - - -
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Residues in contact with THR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 3.8 17.4 - - + +
24B TYR* 3.9 22.9 - - + -
25B HIS* 3.1 22.1 - - - +
36B ILE* 2.9 24.5 + - + +
37B HIS 3.1 6.1 + - - -
39B TYR* 1.3 75.3 - - + +
41B GLU* 1.3 60.9 + - - +
43B ALA* 3.6 8.0 - - - +
44B TYR* 2.8 34.6 + - - +
91B VAL* 4.0 16.4 - - + -
95B ILE* 4.0 14.1 - - + -
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Residues in contact with GLU 41 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B HIS* 3.6 15.3 - - + -
37B HIS 3.1 9.4 + - - +
38B GLU* 3.1 13.4 - - - +
40B THR* 1.3 75.3 + - - +
42B LYS* 1.3 65.7 + - - +
44B TYR* 3.3 31.0 + - + +
45B GLU* 3.0 37.7 + - - +
151B ACY 3.3 18.2 - - + +
153B ACY 3.3 10.6 - - - +
161B ZN 2.1 35.9 - - - -
162B ZN 4.6 0.9 - - - -
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Residues in contact with LYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLU 3.2 9.1 + - - +
39B TYR* 3.7 9.4 - - + +
41B GLU* 1.3 79.9 - - - +
43B ALA* 1.3 61.5 + - - +
45B GLU* 3.2 15.9 + - - +
46B GLU* 3.0 60.6 + - - +
49B GLU* 5.4 6.1 + - - -
151B ACY 4.0 21.2 - - + +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B PHE* 3.6 18.6 - - + -
39B TYR* 3.0 23.6 + - + +
40B THR* 3.6 9.6 - - + +
41B GLU 3.2 0.4 - - - -
42B LYS* 1.3 76.8 - - - +
44B TYR* 1.3 62.3 + - - +
46B GLU* 3.3 15.1 + - - +
47B MSE 3.0 25.1 + - - +
95B ILE* 5.6 2.7 - - + -
99B TYR* 3.6 22.4 - - - +
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Residues in contact with TYR 44 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TRP* 3.2 21.7 - - + +
21B PHE* 3.8 27.3 - - + -
22B HIS* 3.4 53.3 + + + -
25B HIS* 3.6 25.2 + + - -
40B THR 2.8 27.2 + - - +
41B GLU* 3.6 34.7 + - + +
43B ALA* 1.3 74.9 - - - +
45B GLU* 1.3 73.7 + - + +
47B MSE 3.1 3.5 + - - +
48B ALA 2.9 24.8 + - - -
163B ZN 3.6 6.8 - - - -
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Residues in contact with GLU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B GLU* 3.0 28.9 + - - +
42B LYS* 3.2 19.9 + - + +
44B TYR* 1.3 91.9 - - + +
46B GLU* 1.3 61.5 - - + +
48B ALA* 3.4 7.7 + - - +
49B GLU* 3.1 30.4 + - - +
151B ACY 3.1 10.5 - - - +
164B ZN 2.3 35.8 - - - -
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Residues in contact with GLU 46 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS* 3.0 44.8 + - - +
43B ALA* 3.6 15.1 - - - +
44B TYR 3.2 0.2 - - - -
45B GLU* 1.3 76.4 - - - +
47B MSE 1.3 67.1 + - + +
49B GLU* 3.3 17.1 + - - +
50B LEU* 2.9 27.7 + - - +
99B TYR* 4.3 9.2 + - - -
131B LYS* 3.0 38.2 + - - -
132B TYR* 4.6 1.8 + - - +
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Residues in contact with MSE 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA* 3.6 21.5 - - - +
17B LEU* 3.7 26.0 - - + -
18B TRP* 3.7 11.4 - - - +
21B PHE* 3.4 26.5 - - + -
43B ALA 3.0 18.2 + - - +
44B TYR 3.1 7.2 + - - +
46B GLU* 1.3 86.4 - - + +
48B ALA* 1.3 64.7 + - - +
50B LEU* 3.2 20.8 + - + +
51B PHE* 2.9 24.1 + - - +
99B TYR* 5.3 1.8 - - + +
102B LEU* 3.9 19.7 - - + -
132B TYR* 3.2 27.4 - - + +
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Residues in contact with ALA 48 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TRP* 3.7 26.3 - - + +
44B TYR 2.9 8.3 + - - +
45B GLU* 3.6 10.8 - - - +
46B GLU 3.3 0.2 - - - -
47B MSE 1.3 75.7 - - - +
49B GLU* 1.3 63.4 + - + +
51B PHE* 3.3 11.5 - - - +
52B ASP* 3.2 22.2 + - - +
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LYS* 5.4 6.2 + - - -
45B GLU* 3.1 17.8 + - - +
46B GLU* 3.6 22.3 - - - +
48B ALA* 1.3 75.9 - - + +
50B LEU* 1.3 57.5 + - - +
52B ASP* 3.3 6.7 + - - +
53B SER* 2.9 35.1 + - - +
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Residues in contact with LEU 50 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B MSE 4.5 6.1 - - + +
14B ALA* 4.0 16.2 - - + -
46B GLU 2.9 18.0 + - - +
47B MSE 3.2 21.7 + - + +
49B GLU* 1.3 77.5 - - - +
51B PHE* 1.3 57.6 + - - +
53B SER* 4.3 2.7 - - - -
54B CYS* 2.9 39.4 + - - -
102B LEU* 4.1 20.2 - - + -
106B PHE* 3.6 28.7 - - + -
124B PHE* 3.6 29.6 - - + -
128B ASN* 4.8 4.5 - - - +
132B TYR* 5.3 0.7 - - - +
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Residues in contact with PHE 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 3.4 54.9 - - + +
14B ALA* 3.6 11.3 - - + +
15B HIS* 3.9 32.5 - + + +
18B TRP* 6.3 0.7 - - + -
47B MSE 2.9 12.6 + - - +
48B ALA* 3.3 15.3 - - - +
50B LEU* 1.3 75.4 - - - +
52B ASP* 1.3 68.4 + - + +
54B CYS 3.5 0.2 + - - -
55B ALA* 3.2 24.8 + - + +
66B ILE 5.0 2.2 - - - -
72B LEU* 4.0 17.9 - - + -
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Residues in contact with ASP 52 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA 3.2 9.7 + - - +
49B GLU* 3.7 9.4 - - - +
51B PHE* 1.3 85.4 - - + +
53B SER* 1.3 59.6 + - - +
55B ALA* 3.4 5.7 + - - +
56B GLU* 2.9 59.5 + - - +
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Residues in contact with SER 53 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLU* 2.9 23.6 + - - +
50B LEU* 3.8 5.3 - - - -
52B ASP* 1.3 76.5 + - - +
54B CYS* 1.3 63.1 + - - +
56B GLU* 3.9 6.3 - - - +
57B ARG* 3.0 24.8 + - - +
124B PHE* 4.0 26.9 - - - -
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Residues in contact with CYS 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.6 28.9 - - + +
10B MSE 3.8 28.7 - - - -
11B GLN* 4.0 10.8 - - + -
50B LEU* 2.9 42.8 + - - +
51B PHE 3.9 3.4 - - - +
52B ASP 3.2 0.2 - - - -
53B SER* 1.3 76.0 - - - +
55B ALA* 1.3 65.7 + - - +
57B ARG* 3.3 3.3 + - - +
58B VAL* 3.1 28.1 + - - +
124B PHE* 4.2 12.3 - - - -
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B GLN* 3.9 17.6 - - - +
51B PHE* 3.2 17.3 + - + +
52B ASP* 3.7 7.6 - - - +
54B CYS* 1.3 78.7 - - - +
56B GLU* 1.3 64.5 + - + +
58B VAL* 3.1 7.0 + - - +
59B LEU* 3.0 29.8 + - + +
65B ALA* 3.5 25.7 - - + +
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASP* 2.9 49.5 + - - +
53B SER* 4.2 4.8 - - - +
55B ALA* 1.3 77.9 - - + +
57B ARG* 1.3 57.9 + - - +
59B LEU* 3.3 11.3 + - + +
60B GLN* 2.9 46.0 + - - +
134D LYS* 5.3 7.8 + - - +
137D TRP* 3.6 31.2 - - + -
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Residues in contact with ARG 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 3.5 28.7 - - + -
53B SER 3.0 18.4 + - - +
54B CYS 3.7 4.3 - - - +
56B GLU* 1.3 73.6 - - - +
58B VAL* 1.3 66.3 + - - +
60B GLN* 3.0 40.5 + - - +
61B LEU* 2.9 47.8 + - + +
118B ASP* 2.8 31.3 + - - -
120B THR* 3.5 20.8 - - - +
121B THR* 2.9 19.1 + - + +
124B PHE* 5.6 6.5 - - + -
133D GLU* 3.3 32.3 + - - +
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Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B THR* 4.2 6.5 - - - +
7B LEU* 3.5 28.0 - - + -
8B LEU* 4.0 25.6 - - + +
11B GLN* 5.4 0.2 - - - +
54B CYS 3.1 16.3 + - - +
55B ALA* 3.1 9.8 + - - +
57B ARG* 1.3 76.0 - - - +
59B LEU* 1.3 63.8 + - - +
61B LEU* 3.2 14.1 + - - +
62B GLY 3.3 0.3 + - - -
63B GLU* 3.1 45.5 + - + +
64B LYS 3.6 21.3 - - - +
65B ALA* 4.7 0.9 - - - -
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Residues in contact with LEU 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA* 3.0 25.3 + - + +
56B GLU* 3.6 12.3 - - + +
58B VAL* 1.3 77.0 - - - +
60B GLN* 1.3 61.9 + - - +
62B GLY* 3.0 15.1 + - - -
63B GLU 3.4 16.8 - - - +
64B LYS* 4.2 5.8 - - + -
65B ALA* 3.8 23.1 - - + +
137D TRP* 3.7 40.6 - - + +
----------------------------------------------------------
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLU* 2.9 40.3 + - - +
57B ARG* 3.0 39.7 + - - +
59B LEU* 1.3 77.9 - - - +
61B LEU* 1.3 59.6 + - - +
62B GLY* 3.2 3.2 + - - -
120B THR* 5.2 2.4 - - - +
130D ALA 5.5 0.2 - - - +
133D GLU* 4.3 6.5 - - + +
134D LYS* 4.1 30.7 + - - +
137D TRP* 3.5 45.4 - - + +
----------------------------------------------------------
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Residues in contact with LEU 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B VAL* 3.6 31.6 - - + -
4B THR* 3.8 23.2 - - + +
7B LEU* 3.9 9.4 - - + -
57B ARG* 2.9 49.2 + - - +
58B VAL 3.6 4.9 - - - +
59B LEU 3.1 0.4 - - - -
60B GLN* 1.3 78.0 - - - +
62B GLY* 1.3 58.3 + - - +
63B GLU* 3.4 7.0 + - - +
116B GLU* 5.9 0.2 - - - +
118B ASP* 3.9 10.3 - - - +
133D GLU* 6.3 0.2 - - - -
----------------------------------------------------------
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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