Contacts of the helix formed by residues 51 - 80 (chain E) in PDB entry 1KYO
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 LYS 51 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E LYS* 3.7 9.6 - - + +
48E ASP* 3.2 36.1 + - + +
49E ALA 3.2 3.8 + - - -
50E ASP* 1.3 75.4 - - - +
52E GLY* 1.3 69.1 - - - +
53E ARG 3.1 0.9 - - - -
54E SER* 3.2 1.4 + - - -
55E TYR* 3.0 64.4 + - + +
36H PRO* 5.1 12.7 - - + +
4I SER* 3.4 28.7 - - - +
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Residues in contact with GLY 52 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D TRP* 4.8 1.0 - - - -
290D PHE* 4.0 12.3 - - - -
44E LYS* 2.7 24.6 - - - +
51E LYS* 1.3 71.9 - - - +
53E ARG* 1.3 55.6 + - - +
55E TYR* 3.5 1.7 + - - +
56E ALA* 3.0 30.9 + - - +
32H TYR* 4.0 9.9 - - - -
34H GLN 4.5 9.2 - - - -
36H PRO* 4.7 13.2 - - - +
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Residues in contact with ARG 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ASP* 2.9 46.4 + - - +
428A GLN* 4.2 10.0 + - - +
429A ASP* 4.8 3.6 + - - +
448A ARG* 3.5 22.0 - - - +
44E LYS* 4.7 0.2 - - - +
50E ASP* 4.2 22.8 + - - +
51E LYS 3.1 0.8 - - - +
52E GLY* 1.3 73.9 - - - +
54E SER* 1.3 63.3 + - - +
56E ALA* 4.5 2.5 - - - -
57E TYR* 3.0 48.9 + - + -
32H TYR* 3.9 28.4 + - + +
7I TYR* 5.6 0.2 - - + -
13I ARG* 3.4 54.8 + - - +
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Residues in contact with SER 54 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E ASP* 2.6 30.7 + - - +
51E LYS 3.2 4.0 + - - -
53E ARG* 1.3 78.9 - - - +
55E TYR* 1.3 62.4 + - - +
58E PHE* 3.3 24.1 + - - +
4I SER* 3.7 32.8 + - - -
7I TYR* 3.9 28.1 - - - +
8I LYS* 4.3 7.1 - - - +
13I ARG* 5.8 1.0 - - - -
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Residues in contact with TYR 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D TRP* 3.9 20.9 - + + -
51E LYS* 3.0 48.7 + - + +
52E GLY 3.8 3.8 - - - +
54E SER* 1.3 79.2 - - - +
56E ALA* 1.3 61.7 + - - +
58E PHE* 3.4 8.6 + + + +
59E MET* 2.9 33.5 + - + +
36H PRO* 3.4 33.4 - - + -
4I SER* 5.1 10.1 - - - -
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Residues in contact with ALA 56 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286D TRP* 3.5 12.9 - - - -
290D PHE* 3.3 48.5 - - + -
52E GLY 3.0 11.2 + - - +
53E ARG* 3.8 3.4 - - - +
55E TYR* 1.3 75.9 - - - +
57E TYR* 1.3 68.1 + - + +
59E MET* 3.1 4.0 + - - +
60E VAL* 2.8 35.6 + - + +
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Residues in contact with TYR 57 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ASP* 2.8 31.9 + - - -
290D PHE* 5.2 2.5 - + - -
53E ARG* 3.0 30.2 + - + +
56E ALA* 1.3 85.1 - - + +
58E PHE* 1.3 56.5 + - - +
60E VAL* 4.0 10.4 - - + +
61E GLY* 2.8 25.5 + - - -
32H TYR* 2.6 46.9 + + - -
7I TYR* 2.9 28.5 + + + +
13I ARG 4.0 4.9 - - - -
14I ASN 3.9 2.7 - - - -
15I ALA* 3.5 37.5 - - + +
16I VAL* 4.4 4.2 + - - +
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Residues in contact with PHE 58 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D LEU* 5.7 0.4 - - + -
54E SER 3.3 20.4 + - - +
55E TYR* 3.7 8.3 - + + +
56E ALA 3.2 1.0 - - - -
57E TYR* 1.3 72.3 - - - +
59E MET* 1.3 83.8 + - + +
61E GLY* 3.2 0.9 + - - -
62E ALA* 2.6 55.6 + - + +
7I TYR* 3.8 18.3 - + + -
11I PHE* 6.4 1.8 - + - -
16I VAL* 5.5 1.8 - - - -
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Residues in contact with MET 59 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D LEU* 3.6 30.4 - - + +
286D TRP* 3.2 53.4 - - + -
287D VAL* 4.1 12.6 - - + -
55E TYR* 2.9 23.1 - - + +
56E ALA 3.3 6.1 - - - +
58E PHE* 1.3 107.7 - - + +
60E VAL* 1.3 55.0 + - - +
62E ALA* 2.9 3.3 + - - +
63E MET* 2.7 35.5 + - - +
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Residues in contact with VAL 60 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C PHE* 5.9 5.4 - - + -
286D TRP* 6.1 0.7 - - + -
287D VAL* 4.3 22.2 - - + +
290D PHE* 6.0 3.8 - - + -
291D LYS* 6.1 4.7 - - - +
56E ALA* 2.8 32.4 + - + +
57E TYR* 4.0 10.8 - - + +
59E MET* 1.3 71.3 - - - +
61E GLY* 1.3 58.6 + - - +
63E MET* 3.2 16.3 + - + +
64E GLY* 2.9 25.8 + - - -
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Residues in contact with GLY 61 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E TYR 2.8 18.9 + - - -
58E PHE 3.6 0.7 - - - -
60E VAL* 1.3 76.9 - - - +
62E ALA* 1.3 56.6 + - - +
64E GLY 3.2 0.3 + - - -
65E LEU* 2.9 25.9 + - - +
16I VAL* 4.2 15.9 - - - -
21I ILE* 3.2 24.4 - - - +
----------------------------------------------------------
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Residues in contact with ALA 62 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283D LEU* 4.6 14.4 - - + -
58E PHE* 2.6 46.3 + - + +
59E MET* 3.4 5.4 - - - +
61E GLY* 1.3 69.1 - - - +
63E MET* 1.3 66.7 + - - +
65E LEU* 3.3 8.4 + - - +
66E LEU* 3.2 28.0 + - + +
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Residues in contact with MET 63 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227C PHE* 3.7 31.4 - - + -
230C LEU* 4.3 9.2 - - + -
234C PHE* 4.6 12.6 - - + -
280D LEU* 4.2 7.3 - - + +
283D LEU* 4.2 17.0 - - + +
284D SER* 4.0 33.4 - - - -
287D VAL* 4.1 17.5 - - + -
59E MET 2.7 16.5 + - - +
60E VAL* 3.4 15.3 - - + +
62E ALA* 1.3 74.0 - - - +
64E GLY* 1.3 64.0 + - - +
66E LEU* 3.4 2.6 + - - +
67E SER* 3.1 34.0 + - - +
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Residues in contact with GLY 64 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E VAL 2.9 14.8 + - - -
61E GLY 3.2 3.6 + - - -
63E MET* 1.3 77.6 - - - +
65E LEU* 1.3 64.9 + - - +
67E SER* 3.3 6.9 + - - -
68E SER* 3.1 25.1 + - - -
21I ILE* 3.7 13.6 - - - +
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Residues in contact with LEU 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLY 2.9 12.7 + - - +
62E ALA* 3.4 12.8 - - - +
63E MET 3.3 0.2 - - - -
64E GLY* 1.3 78.0 - - - +
66E LEU* 1.3 72.2 + - + +
67E SER 3.2 0.2 + - - -
68E SER* 3.3 4.0 + - - -
69E ALA* 3.3 16.6 + - - +
20I THR 5.2 0.2 - - - +
21I ILE* 3.5 22.1 - - + +
24I GLY* 3.4 11.0 - - - -
25I ALA* 3.4 30.6 - - - +
28I PHE* 4.1 33.9 - - + -
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Residues in contact with LEU 66 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D ILE* 4.2 22.1 - - + +
279D SER* 3.7 24.5 - - - -
280D LEU* 3.2 35.2 - - + +
283D LEU* 4.5 7.6 - - + -
62E ALA* 3.2 13.4 + - + +
65E LEU* 1.3 86.5 - - + +
67E SER* 1.3 55.5 + - - +
69E ALA* 3.5 3.5 - - - +
70E GLY* 2.9 24.8 + - - -
28I PHE* 3.4 43.3 - - + -
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Residues in contact with SER 67 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C PHE* 4.0 22.3 - - - -
280D LEU* 4.1 9.6 - - - +
63E MET* 3.1 22.4 + - - +
64E GLY* 3.7 6.5 - - - -
65E LEU 3.2 0.2 - - - -
66E LEU* 1.3 75.0 - - - +
68E SER* 1.3 60.0 + - - +
70E GLY* 3.3 1.8 + - - +
71E ALA* 2.8 30.9 + - - +
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Residues in contact with SER 68 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E GLY 3.1 13.8 + - - -
65E LEU 3.3 7.4 + - - -
67E SER* 1.3 75.5 - - - +
69E ALA* 1.3 54.3 + - - +
71E ALA* 3.2 5.9 + - - +
72E LYS* 2.7 38.3 + - - +
21I ILE* 3.6 6.7 - - - +
22I PHE* 3.3 33.5 - - - -
25I ALA* 3.8 17.7 - - - -
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Residues in contact with ALA 69 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D ILE* 5.4 3.1 - - + -
65E LEU 3.3 10.1 + - - +
66E LEU* 3.5 11.4 - - - +
67E SER 3.2 0.2 - - - -
68E SER* 1.3 80.6 - - - +
70E GLY* 1.3 57.6 + - - +
72E LYS* 3.3 7.0 + - - +
73E SER* 2.8 31.8 + - - -
25I ALA* 4.2 16.1 - - + +
28I PHE* 3.9 29.8 - - + -
29I GLN* 4.0 11.8 - - - +
----------------------------------------------------------
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Residues in contact with GLY 70 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276D ILE* 5.4 10.2 - - - +
280D LEU* 5.9 2.2 - - - -
66E LEU 2.9 16.3 + - - -
67E SER* 3.3 3.8 + - - -
69E ALA* 1.3 76.3 - - - +
71E ALA* 1.3 56.8 + - - +
73E SER* 3.4 6.9 + - - -
74E THR* 2.9 34.0 + - - -
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Residues in contact with ALA 71 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E SER 2.8 21.3 + - - +
68E SER* 3.5 7.4 - - - +
70E GLY* 1.3 71.8 - - - +
72E LYS* 1.3 66.6 + - - +
74E THR* 3.1 5.8 + - - -
75E VAL* 2.9 34.8 + - + +
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Residues in contact with LYS 72 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E SER 2.7 21.2 + - - +
69E ALA* 3.6 6.5 - - - +
71E ALA* 1.3 70.6 - - - +
73E SER* 1.3 62.4 + - - +
75E VAL* 3.7 4.9 - - - +
76E GLU* 3.0 56.5 + - + +
25I ALA* 5.7 3.1 - - + +
26I PHE* 4.3 40.6 - - + +
29I GLN* 2.7 37.9 - - - +
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Residues in contact with SER 73 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272D LYS* 5.5 4.2 + - - -
69E ALA 2.8 16.0 + - - -
70E GLY* 3.6 7.4 - - - -
72E LYS* 1.3 76.0 - - - +
74E THR* 1.3 63.1 + - - +
76E GLU* 4.0 8.0 + - - +
77E THR* 2.9 29.2 + - - -
29I GLN* 3.4 22.5 + - - -
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Residues in contact with THR 74 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E GLY 2.9 23.5 + - - -
71E ALA* 3.1 6.2 + - - -
73E SER* 1.3 71.3 - - - +
75E VAL* 1.3 68.3 + - + +
77E THR* 3.1 16.2 + - - -
78E PHE* 3.2 42.7 + - + -
----------------------------------------------------------
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Residues in contact with VAL 75 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E ALA* 2.9 23.8 + - + +
72E LYS* 3.7 6.3 - - - +
74E THR* 1.3 80.1 - - + +
76E GLU* 1.3 66.4 + - + +
78E PHE* 3.2 8.3 + - - +
79E ILE* 3.0 44.8 + - + +
----------------------------------------------------------
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Residues in contact with GLU 76 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LYS* 3.0 66.8 + - + +
73E SER* 4.0 5.6 + - - +
74E THR 3.3 0.2 - - - -
75E VAL* 1.3 80.5 - - + +
77E THR* 1.3 54.0 + - - +
79E ILE* 4.5 6.3 - - + -
80E SER* 2.7 39.1 + - - -
29I GLN* 3.7 4.9 + - - -
----------------------------------------------------------
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Residues in contact with THR 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ASN* 3.1 39.2 + - + +
77C ILE* 4.7 18.5 - - + +
78C LEU* 5.2 8.3 - - + -
73E SER 2.9 16.1 + - - -
74E THR* 3.1 12.6 + - - -
76E GLU* 1.3 76.6 - - - +
78E PHE* 1.3 69.1 + - + +
80E SER* 3.2 12.3 + - - -
81E SER* 3.3 11.3 + - - -
----------------------------------------------------------
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Residues in contact with PHE 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C VAL* 4.3 18.4 - - + -
46C THR* 4.1 24.7 - - + -
49C PHE* 3.6 41.6 - + + -
78C LEU* 3.2 32.8 - - + -
81C LEU* 5.1 7.4 - - + -
74E THR* 3.2 44.6 + - + -
75E VAL* 3.2 7.6 + - - +
77E THR* 1.3 81.4 - - + +
79E ILE* 1.3 69.3 + - + +
81E SER* 2.7 26.4 + - - -
82E MET 3.9 0.2 + - - -
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Residues in contact with ILE 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C PHE* 4.8 5.2 - - + -
75E VAL* 3.0 38.7 + - + +
76E GLU* 3.9 6.5 - - + +
78E PHE* 1.3 77.9 - - + +
80E SER* 1.3 59.9 + - - +
81E SER 2.9 6.8 + - - -
82E MET* 3.0 13.5 + - - +
83E THR* 5.5 0.4 - - + -
164N TRP* 3.1 48.7 + - + +
----------------------------------------------------------
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Residues in contact with SER 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C HIS* 4.0 15.0 - - - +
74C ASN* 4.1 8.1 + - - -
76E GLU* 2.7 26.8 + - - -
77E THR* 3.2 9.9 + - - -
79E ILE* 1.3 78.4 - - - +
81E SER* 1.3 55.0 + - - +
82E MET 3.1 3.6 + - - -
83E THR* 2.8 37.2 + - - +
----------------------------------------------------------
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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