Contacts of the helix formed by residues 2 - 28 (chain C) 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 SER 2 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 1.3 79.6 - - - +
3C VAL* 1.3 66.0 + - - +
4C THR* 3.6 9.5 + - - -
5C LYS* 3.2 30.0 + - - +
6C GLN* 2.9 18.0 + - - +
112C ALA* 4.4 2.2 - - - -
116C GLU* 3.6 13.2 - - - -
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Residues in contact with VAL 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER* 1.3 71.6 - - - +
4C THR* 1.3 60.7 + - + +
6C GLN* 3.3 4.0 + - - +
7C LEU* 2.8 46.8 + - + +
61C LEU* 3.8 8.1 - - + -
109C LEU* 4.1 3.0 - - + +
112C ALA* 3.6 7.1 - - + +
113C ALA* 3.6 35.9 - - + +
116C GLU* 2.9 39.3 + - + +
118C ASP* 3.7 21.5 - - - +
121C THR* 3.9 10.3 - - + -
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Residues in contact with THR 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER* 3.6 8.5 + - - -
3C VAL* 1.3 73.7 - - + +
5C LYS* 1.3 64.9 + - - +
7C LEU* 3.2 7.2 + - + +
8C LEU* 2.8 38.2 + - - +
58C VAL* 4.8 7.4 - - + -
61C LEU* 3.6 39.9 - - + +
63C GLU* 4.7 27.7 + - + +
116C GLU* 6.0 0.2 - - - +
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Residues in contact with LYS 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 3.4 46.3 - - + +
2C SER* 3.2 18.3 + - - +
4C THR* 1.3 83.5 + - - +
6C GLN* 1.3 57.1 + - - +
8C LEU* 3.4 12.2 + - + +
9C GLN* 3.0 22.5 + - - +
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Residues in contact with GLN 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 3.6 29.9 - - + +
2C SER 2.9 17.7 + - - +
3C VAL* 3.7 4.5 - - - +
5C LYS* 1.3 75.7 - - - +
7C LEU* 1.3 63.9 + - - +
9C GLN* 3.2 4.5 + - - +
10C MSE 3.0 40.4 + - + +
105C GLU* 2.8 49.8 + - - +
108C LYS* 4.1 14.4 + - + +
109C LEU* 3.8 32.3 - - + +
112C ALA* 5.1 1.3 - - + -
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Residues in contact with LEU 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C VAL* 2.8 42.7 + - + +
4C THR* 3.7 1.3 - - - +
6C GLN* 1.3 71.0 - - - +
8C LEU* 1.3 52.6 + - - +
10C MSE 3.2 4.4 + - + +
11C GLN* 2.8 30.1 + - - +
54C CYS* 3.6 24.4 - - - +
57C ARG* 3.6 31.4 - - + -
58C VAL* 3.4 23.1 - - + -
61C LEU* 3.8 9.2 - - + -
109C LEU* 3.7 31.2 - - + -
121C THR* 4.4 4.0 - - + -
124C PHE* 4.2 14.8 - - + -
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Residues in contact with LEU 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C THR* 2.8 30.2 + - - +
5C LYS* 3.7 11.9 - - + +
7C LEU* 1.3 69.1 - - - +
9C GLN* 1.3 67.2 + - - +
11C GLN* 3.2 23.1 + - - +
12C ALA* 3.1 19.1 + - - +
58C VAL* 3.9 19.1 - - + -
63C GLU* 5.4 6.7 - - + -
64C LYS 3.6 25.4 - - - +
65C ALA* 4.1 0.7 - - - -
66C ILE* 3.8 27.9 - - + +
75C ASN* 5.6 2.2 - - - +
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Residues in contact with GLN 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MSE 4.0 20.9 - - + +
5C LYS 3.0 15.0 + - - +
6C GLN* 3.2 10.7 + - - +
8C LEU* 1.3 74.4 - - - +
10C MSE 1.3 58.4 + - - +
12C ALA* 3.3 4.5 + - - +
13C ASP* 2.9 56.8 + - - +
75C ASN* 2.9 25.3 + - - +
77C LYS* 2.6 41.5 + - + +
101C TYR* 4.7 1.3 - - - +
105C GLU* 4.2 15.0 - - - +
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Residues in contact with MSE 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLN* 3.0 35.9 + - + +
7C LEU* 3.7 7.9 - - - +
9C GLN* 1.3 73.4 - - - +
11C GLN* 1.3 61.2 + - - +
13C ASP* 3.9 6.9 - - + +
14C ALA* 2.9 31.9 + - - +
50C LEU* 4.4 5.8 - - + -
54C CYS* 3.7 15.3 - - - -
102C LEU* 3.8 23.6 - - + -
105C GLU* 4.0 31.9 - - + +
106C PHE* 3.6 47.3 - - + -
109C LEU* 4.1 12.6 - - + -
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Residues in contact with GLN 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TRP* 3.5 20.2 - - - -
7C LEU 2.8 13.6 + - - +
8C LEU* 3.5 16.3 - - - +
9C GLN 3.2 0.4 - - - -
10C MSE 1.3 77.5 - - - +
12C ALA* 1.3 62.1 + - - +
14C ALA* 3.4 2.8 + - - +
15C HIS* 3.2 17.8 + - - +
51C PHE* 3.4 39.7 - - + +
54C CYS* 4.0 12.0 - - + +
55C ALA* 3.9 12.2 - - + +
65C ALA* 3.8 4.9 - - - +
66C ILE* 3.0 57.2 + - + +
72C LEU* 4.1 1.1 - - + +
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Residues in contact with ALA 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C LEU 3.1 8.8 + - - +
9C GLN 3.6 8.1 - - - +
11C GLN* 1.3 77.7 - - - +
13C ASP* 1.3 57.6 + - - +
15C HIS* 3.2 5.5 + - - +
16C HIS* 3.0 26.7 + - - +
66C ILE* 4.4 6.5 - - + +
72C LEU* 3.8 27.4 - - - +
75C ASN* 3.7 37.2 - - + +
76C ALA* 4.1 3.2 - - - +
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Residues in contact with ASP 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLN* 2.9 33.0 + - - +
10C MSE 3.9 7.5 - - + +
12C ALA* 1.3 75.2 - - - +
14C ALA* 1.3 58.6 + - - +
16C HIS* 3.1 5.3 + - - +
17C LEU* 2.9 38.9 + - + +
76C ALA* 3.4 1.9 - - - +
77C LYS 2.8 28.6 + - - -
78C SER* 3.4 7.0 + - - -
101C TYR* 2.6 40.8 + - + -
102C LEU* 5.1 5.2 - - + -
105C GLU* 4.5 3.5 - - - +
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Residues in contact with ALA 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C MSE 2.9 17.4 + - - +
11C GLN 3.8 3.4 - - - +
13C ASP* 1.3 75.6 - - - +
15C HIS* 1.3 57.9 + - - +
17C LEU* 5.0 0.4 - - - -
18C TRP* 2.9 29.3 + - - +
47C MSE 3.6 23.8 - - - +
50C LEU* 3.8 18.6 - - + +
51C PHE* 3.6 30.5 - - - +
102C LEU* 5.6 0.8 - - - +
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Residues in contact with HIS 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A HIS* 2.9 34.8 + + - -
18A TRP* 3.7 26.5 - + - -
19A VAL* 4.3 1.5 - - + +
69A GLN* 3.3 33.4 + - + -
11C GLN 3.2 7.9 + - - +
12C ALA 3.5 9.3 + - - +
13C ASP 3.2 0.2 - - - -
14C ALA* 1.3 76.6 - - - +
16C HIS* 1.3 61.6 + - - +
18C TRP* 3.2 9.2 + + - +
19C VAL* 3.1 34.3 + - + +
51C PHE* 3.8 22.1 - + + -
69C GLN* 5.3 3.1 - - + -
72C LEU* 3.8 33.4 - - + +
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Residues in contact with HIS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLN* 3.2 25.1 - - - +
155A ACY 3.0 30.3 + - + +
12C ALA 3.0 13.7 + - - +
13C ASP* 3.4 8.3 - - - +
15C HIS* 1.3 82.0 + - - +
17C LEU* 1.3 56.5 + - - +
19C VAL* 3.3 5.9 + - - +
20C LYS* 3.0 40.5 + - + +
76C ALA* 3.6 17.8 - - + +
78C SER* 2.6 44.9 + - - -
79C PRO 3.6 5.2 - - - -
80C LYS* 3.9 17.0 + - - -
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Residues in contact with LEU 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ASP* 2.9 20.0 + - + +
14C ALA 4.0 0.2 - - - +
16C HIS* 1.3 73.0 - - - +
18C TRP* 1.3 60.9 + - - +
20C LYS* 3.6 10.8 - - - +
21C PHE* 2.8 44.6 + - + -
47C MSE 3.7 24.7 - - + -
78C SER* 3.5 29.2 - - - +
98C ASP* 3.5 38.6 - - + +
101C TYR* 5.0 0.9 - - + -
102C LEU* 3.8 37.5 - - + -
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Residues in contact with TRP 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A HIS* 3.7 26.5 - + - -
18A TRP* 4.1 37.4 - + + +
48A ALA* 4.1 24.6 - - + +
51A PHE* 3.6 37.7 - + + -
14C ALA 2.9 19.3 + - - +
15C HIS* 3.4 9.2 - + - +
17C LEU* 1.3 77.7 - - - +
19C VAL* 1.3 78.9 + - + +
22C HIS* 2.7 49.8 + + - -
44C TYR* 3.1 40.0 + - + +
47C MSE 3.8 8.6 - - + +
48C ALA* 3.7 22.4 - - + +
----------------------------------------------------------
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Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A HIS* 4.5 4.5 - - - +
51A PHE* 5.3 5.6 - - + -
66A ILE 5.8 0.2 - - - +
67A THR* 3.7 28.5 - - - +
69A GLN* 4.6 7.6 - - + +
72A LEU* 4.5 17.3 - - + -
155A ACY 3.8 11.0 - - + -
15C HIS* 3.1 33.9 + - + +
16C HIS* 3.6 7.6 - - - +
18C TRP* 1.3 96.9 - - + +
20C LYS* 1.3 63.7 + - - +
22C HIS* 3.1 17.5 + - - +
23C ASN* 3.3 9.7 + - - +
26C TRP* 5.3 1.8 - - + -
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Residues in contact with LYS 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ACY 3.7 19.5 - - + +
16C HIS* 3.0 41.2 + - + +
17C LEU* 3.3 14.5 + - + +
19C VAL* 1.3 77.4 - - - +
21C PHE* 1.3 65.9 + - + +
23C ASN* 3.0 21.9 + - - +
24C TYR* 3.1 38.7 + - + +
78C SER* 3.7 2.2 + - - -
79C PRO* 2.7 26.8 + - - +
81C VAL* 4.0 17.8 - - + +
98C ASP* 2.5 32.3 + - - -
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Residues in contact with PHE 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C LEU* 2.8 38.9 + - + +
20C LYS* 1.3 73.8 - - + +
22C HIS* 1.3 58.2 + - - +
24C TYR* 3.4 25.4 + + + +
25C HIS* 3.0 27.9 + - - +
40C THR* 3.8 10.6 - - + +
43C ALA* 3.6 31.2 - - + -
44C TYR* 3.9 16.6 - - + -
47C MSE 3.4 35.4 - - + -
95C ILE* 4.7 6.1 - - + -
98C ASP* 3.3 27.6 - - + -
99C TYR* 3.8 27.4 - + - -
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Residues in contact with HIS 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ALA* 4.9 2.0 + - - +
51A PHE* 3.7 18.6 - + + -
52A ASP* 3.5 27.3 + - - +
18C TRP* 2.7 55.3 + + - -
19C VAL 3.1 10.0 + - - +
21C PHE* 1.3 75.9 - - - +
23C ASN* 1.3 60.2 + - - +
25C HIS* 3.1 5.6 + - - +
26C TRP* 2.8 62.1 + + + -
44C TYR* 3.3 41.1 + + - -
----------------------------------------------------------
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Residues in contact with ASN 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A THR* 3.6 30.4 + - + +
19C VAL 3.3 5.3 + - - +
20C LYS* 3.0 19.4 + - - +
22C HIS* 1.3 78.1 - - - +
24C TYR* 1.3 59.6 + - + +
26C TRP* 4.0 10.1 - - - -
27C ASN* 2.8 48.3 + - - +
81C VAL* 3.9 11.9 + - - +
83C LYS 2.9 23.8 + - - -
84C ASP* 3.6 4.2 - - - -
86C PHE* 3.3 20.0 - - - -
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Residues in contact with TYR 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C LYS* 3.1 28.2 + - + -
21C PHE* 3.6 30.3 - + - +
22C HIS 3.3 0.2 - - - -
23C ASN* 1.3 73.0 - - + +
25C HIS* 1.3 62.5 + - - +
28C VAL* 3.3 30.5 + - - +
36C ILE* 4.6 0.9 - - - +
40C THR* 3.8 14.4 - - + -
81C VAL* 3.6 14.7 - - + +
86C PHE* 3.9 28.0 - + - -
91C VAL* 3.9 14.9 - - + +
94C LEU* 3.5 33.9 - - + +
95C ILE* 3.8 25.1 - - + -
98C ASP* 2.8 30.0 + - - -
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Residues in contact with HIS 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ASP* 3.4 11.9 + - - -
56A GLU* 2.9 8.6 + - - -
156A ZN 2.0 38.1 - - - -
21C PHE 3.0 16.8 + - - +
22C HIS* 3.3 5.8 - - - +
24C TYR* 1.3 78.6 - - - +
26C TRP* 1.3 70.8 + + - +
28C VAL* 4.2 5.0 - - - +
33C PHE* 4.4 0.9 - - - -
37C HIS* 2.7 76.1 + + - +
40C THR* 3.1 17.6 + - - +
41C GLU* 3.5 24.2 + - + +
44C TYR* 3.6 11.6 + + + -
----------------------------------------------------------
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Residues in contact with TRP 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A GLN* 3.5 20.9 - - - -
51A PHE* 3.7 16.4 - + - -
52A ASP* 2.8 21.1 + - - -
55A ALA* 3.2 19.8 - - + +
56A GLU* 3.5 34.3 + - + +
59A LEU* 3.5 23.5 - - + +
65A ALA* 4.0 12.8 - - + -
66A ILE 3.4 19.7 - - - -
67A THR* 4.0 17.0 - - + -
19C VAL* 5.3 1.8 - - + -
22C HIS* 2.8 52.5 + + + +
23C ASN* 4.0 2.9 - - - -
25C HIS* 1.3 81.0 - + - +
27C ASN* 1.3 72.8 + - - +
28C VAL* 3.6 5.2 + - - +
29C LYS* 5.0 1.9 + - - -
33C PHE* 4.6 7.3 - - - -
37C HIS* 4.9 1.8 - - - -
----------------------------------------------------------
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Residues in contact with ASN 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A LEU* 3.9 23.0 - - - +
64A LYS* 5.7 3.4 - - - +
65A ALA* 5.8 1.1 - - - +
67A THR* 3.8 14.7 - - - +
23C ASN* 2.8 33.5 + - - +
26C TRP* 1.3 89.4 + - - +
28C VAL* 1.3 62.8 + - - +
29C LYS* 3.0 26.6 + - - +
84C ASP* 3.1 30.8 + - - +
85C CYS* 3.5 0.2 - - - -
86C PHE* 3.2 20.0 + - + -
----------------------------------------------------------
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Residues in contact with VAL 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C TYR 3.3 19.3 + - - +
25C HIS 4.2 5.4 - - - +
26C TRP 4.5 0.9 - - - +
27C ASN* 1.3 81.0 - - - +
29C LYS* 1.3 69.4 + - - +
33C PHE* 3.4 46.7 - - + +
36C ILE* 4.0 25.1 - - + -
37C HIS 4.6 1.3 - - - +
86C PHE* 3.4 14.5 - - - +
87C THR 4.0 1.6 - - - -
88C PRO* 3.9 33.7 - - + -
91C VAL* 4.1 5.6 - - + -
----------------------------------------------------------
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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