Contacts of the helix formed by residues 50 - 81 (chain P) 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 ASP 50 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P LYS* 4.7 0.2 - - - +
48P ASP* 3.1 9.5 + - - +
49P ALA* 1.3 80.7 - - - +
51P LYS* 1.3 63.2 + - - +
52P GLY 3.5 1.8 - - - -
53P ARG* 3.8 34.8 + - + -
54P SER* 3.0 26.5 + - - +
4T SER 5.4 0.2 - - - +
8T LYS* 2.8 45.2 + - + +
13T ARG* 4.2 17.6 + - + -
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Residues in contact with LYS 51 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P LYS* 4.0 6.3 - - + +
46P ASN* 3.8 16.4 - - - +
48P ASP* 2.9 33.0 + - + +
49P ALA 3.1 3.0 + - - -
50P ASP* 1.3 79.5 - - - +
52P GLY* 1.3 61.1 + - - +
54P SER* 3.9 3.0 + - - -
55P TYR* 3.1 57.3 + - + -
36S PRO* 3.9 15.8 - - + +
4T SER 4.4 16.5 + - - +
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Residues in contact with GLY 52 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286O TRP* 4.4 1.8 - - - -
290O PHE* 4.0 10.1 - - - -
44P LYS* 3.5 12.4 - - - +
51P LYS* 1.3 77.9 - - - +
53P ARG* 1.3 58.9 + - - +
54P SER 3.5 0.2 - - - -
55P TYR* 3.7 8.9 - - - +
56P ALA* 2.9 30.7 + - - +
32S TYR* 4.7 5.2 - - - -
34S GLN 4.6 10.1 - - - -
36S PRO* 4.6 12.0 - - - +
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Residues in contact with ARG 53 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427L ASP* 3.0 37.8 + - - -
428L GLN* 3.9 15.2 + - - +
429L ASP* 4.7 3.6 + - - +
448L ARG* 3.8 15.4 - - - +
44P LYS* 5.0 1.6 - - - +
50P ASP* 3.5 33.8 + - + +
51P LYS 3.3 0.6 - - - -
52P GLY* 1.3 74.9 - - - +
54P SER* 1.3 57.7 + - - +
56P ALA* 3.3 2.6 + - - +
57P TYR* 2.7 63.2 + - + -
32S TYR* 4.1 26.2 + - + +
7T TYR* 6.0 0.4 - - + -
13T ARG* 3.4 51.1 + - - +
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Residues in contact with SER 54 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50P ASP* 3.0 19.6 + - - +
51P LYS 4.3 2.9 - - - -
53P ARG* 1.3 76.8 - - - +
55P TYR* 1.3 61.7 + - - +
58P PHE* 2.9 31.5 + - - +
4T SER* 3.8 20.8 + - - -
7T TYR* 3.8 37.4 - - - -
8T LYS* 4.0 16.8 - - - +
13T ARG* 5.8 1.0 + - - -
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Residues in contact with TYR 55 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286O TRP* 3.8 21.8 - + + -
51P LYS* 3.1 50.7 + - + -
52P GLY* 3.7 9.2 - - - +
54P SER* 1.3 77.2 - - - +
56P ALA* 1.3 65.6 + - - +
58P PHE* 3.2 6.5 + - - +
59P MET* 2.9 40.4 + - + +
36S PRO* 3.5 25.6 - - + -
4T SER* 5.1 11.9 - - - -
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Residues in contact with ALA 56 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286O TRP* 3.4 14.1 - - + -
290O PHE* 3.5 39.3 - - + -
52P GLY 2.9 17.5 + - - +
53P ARG* 3.5 4.5 - - - +
55P TYR* 1.3 78.2 - - - +
57P TYR* 1.3 70.8 + - + +
59P MET* 2.9 6.9 + - - +
60P VAL* 2.9 27.0 + - + +
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Residues in contact with TYR 57 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427L ASP* 2.7 31.7 + - - -
290O PHE* 5.5 2.2 - + - -
53P ARG* 2.7 38.7 + - + +
56P ALA* 1.3 77.9 - - + +
58P PHE* 1.3 56.4 + - - +
60P VAL* 3.8 11.4 - - + +
61P GLY* 2.8 26.0 + - - -
32S TYR* 2.6 46.2 + + - -
7T TYR* 3.0 25.9 + + + +
13T ARG 3.8 10.1 - - - -
14T ASN* 3.6 20.2 - - - -
15T ALA* 3.6 21.4 - - + +
16T VAL* 4.2 3.5 + - - +
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Residues in contact with PHE 58 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283O LEU* 5.6 1.3 - - + -
54P SER 2.9 20.2 + - - +
55P TYR* 3.4 5.6 - - + +
56P ALA 3.1 0.2 - - - -
57P TYR* 1.3 73.1 - - - +
59P MET* 1.3 84.9 + - + +
61P GLY* 3.0 2.1 + - - -
62P ALA* 2.7 53.8 + - + -
7T TYR* 3.8 22.4 - + + -
11T PHE* 6.0 2.7 - + - -
16T VAL* 5.4 1.6 - - - -
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Residues in contact with MET 59 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283O LEU* 3.9 23.2 - - + +
286O TRP* 3.3 56.3 - - + -
287O VAL* 4.0 13.9 - - + -
55P TYR* 2.9 30.8 + - + +
56P ALA 2.9 5.8 + - - +
58P PHE* 1.3 110.4 - - + +
60P VAL* 1.3 63.6 + - - +
62P ALA* 3.1 4.0 + - - +
63P MET* 2.9 24.8 + - - +
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Residues in contact with VAL 60 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227N PHE* 6.1 3.1 - - + -
286O TRP* 6.4 0.4 - - + -
287O VAL* 4.2 24.7 - - + +
290O PHE* 5.8 4.9 - - + -
291O LYS* 5.4 7.0 - - - +
56P ALA* 2.9 23.7 + - + +
57P TYR* 3.8 14.1 - - + +
59P MET* 1.3 75.6 - - - +
61P GLY* 1.3 59.5 + - - +
63P MET* 3.3 15.1 + - + +
64P GLY* 2.9 24.6 + - - -
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Residues in contact with GLY 61 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P TYR 2.8 19.4 + - - -
58P PHE 3.5 2.5 - - - -
60P VAL* 1.3 75.3 - - - +
62P ALA* 1.3 56.0 + - - +
64P GLY 3.3 0.7 + - - -
65P LEU* 2.9 27.6 + - - +
16T VAL* 4.2 15.7 - - - -
21T ILE* 3.4 23.6 - - - +
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Residues in contact with ALA 62 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283O LEU* 3.5 20.4 - - + -
58P PHE* 2.7 43.9 + - + +
59P MET 3.6 1.3 - - - +
61P GLY* 1.3 72.1 - - - +
63P MET* 1.3 62.9 + - - +
65P LEU* 3.4 7.4 + - - +
66P LEU* 3.0 30.3 + - + +
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Residues in contact with MET 63 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227N PHE* 3.6 32.3 - - + -
230N LEU* 4.2 14.8 - - + -
234N PHE* 4.6 4.5 - - + -
280O LEU* 3.7 16.9 - - + +
283O LEU* 3.3 14.3 - - + +
284O SER* 3.9 33.4 - - - -
287O VAL* 4.1 18.2 - - + -
59P MET 2.9 16.8 + - - +
60P VAL* 3.5 11.0 - - + +
62P ALA* 1.3 74.9 - - - +
64P GLY* 1.3 59.7 + - - +
66P LEU 3.4 0.2 + - - -
67P SER* 2.8 39.7 + - - +
----------------------------------------------------------
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Residues in contact with GLY 64 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60P VAL 2.9 14.5 + - - -
61P GLY 3.7 2.7 - - - -
63P MET* 1.3 77.0 - - - +
65P LEU* 1.3 62.9 + - - +
67P SER* 3.2 5.3 + - - -
68P SER* 2.9 27.9 + - - -
21T ILE* 3.6 13.5 - - - -
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Residues in contact with LEU 65 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P GLY 2.9 14.1 + - - +
62P ALA* 3.4 12.3 - - - +
64P GLY* 1.3 76.9 - - - +
66P LEU* 1.3 82.2 + - + +
68P SER* 3.2 3.6 + - - -
69P ALA* 3.1 18.1 + - + +
20T THR 5.0 0.4 - - - +
21T ILE* 3.3 38.3 - - + +
24T GLY* 3.3 11.9 - - - +
25T ALA* 3.3 17.1 - - - +
28T PHE* 4.1 25.6 - - + -
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Residues in contact with LEU 66 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276O ILE* 4.4 11.6 - - + +
279O SER* 3.6 31.2 - - - +
280O LEU* 3.6 29.2 - - + +
283O LEU* 4.6 9.4 - - + -
62P ALA* 3.0 19.0 + - + +
65P LEU* 1.3 93.9 - - + +
67P SER* 1.3 62.5 + - - +
69P ALA* 3.2 4.6 + - - +
70P GLY* 2.9 20.8 + - - -
28T PHE* 3.9 35.0 - - + -
----------------------------------------------------------
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Residues in contact with SER 67 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234N PHE* 4.1 12.6 - - - -
280O LEU* 3.3 19.9 - - - +
63P MET* 2.8 29.6 + - - +
64P GLY* 3.6 5.8 - - - -
66P LEU* 1.3 72.4 - - - +
68P SER* 1.3 52.9 + - - +
70P GLY* 3.2 2.5 + - - -
71P ALA* 2.7 38.4 + - - +
----------------------------------------------------------
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Residues in contact with SER 68 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64P GLY* 2.9 14.5 + - - -
65P LEU 3.4 9.2 - - - -
67P SER* 1.3 74.8 - - - +
69P ALA* 1.3 56.6 + - - +
71P ALA* 3.2 7.2 + - - +
72P LYS* 2.8 31.9 + - - +
21T ILE* 3.8 7.9 - - - +
22T PHE* 3.7 30.1 - - - -
25T ALA* 3.8 17.0 - - - -
----------------------------------------------------------
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Residues in contact with ALA 69 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276O ILE* 5.7 4.0 - - + -
65P LEU 3.1 9.9 + - - +
66P LEU* 3.2 10.5 + - - +
68P SER* 1.3 78.2 - - - +
70P GLY* 1.3 58.7 + - - +
72P LYS* 3.2 7.4 + - - +
73P SER* 2.9 31.5 + - - -
25T ALA* 4.0 20.8 - - + +
28T PHE* 4.2 27.4 - - + -
29T GLN* 3.8 8.2 - - + +
----------------------------------------------------------
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Residues in contact with GLY 70 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276O ILE* 5.2 12.7 - - - +
66P LEU 2.9 14.0 + - - -
67P SER* 3.6 2.5 - - - -
69P ALA* 1.3 75.8 - - - +
71P ALA* 1.3 57.0 + - - +
73P SER* 3.3 8.0 + - - -
74P THR* 2.8 34.7 + - - -
----------------------------------------------------------
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Residues in contact with ALA 71 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P SER 2.7 22.3 + - - +
68P SER* 3.4 8.5 - - - +
70P GLY* 1.3 68.8 - - - +
72P LYS* 1.3 68.1 + - - +
74P THR* 3.1 15.7 + - - -
75P VAL* 3.1 20.4 + - + +
----------------------------------------------------------
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Residues in contact with LYS 72 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68P SER 2.8 16.1 + - - +
69P ALA* 3.4 10.8 - - - +
71P ALA* 1.3 75.2 - - - +
73P SER* 1.3 64.4 + - - +
75P VAL* 3.3 6.3 + - - +
76P GLU* 2.9 54.8 + - - +
25T ALA* 5.5 4.0 - - + +
26T PHE* 3.6 48.3 - - + +
29T GLN* 2.6 36.8 - - - +
----------------------------------------------------------
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Residues in contact with SER 73 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272O LYS* 5.9 0.7 + - - -
69P ALA 2.9 15.2 + - - -
70P GLY* 3.5 8.5 - - - -
71P ALA 3.2 0.2 - - - -
72P LYS* 1.3 77.3 - - - +
74P THR* 1.3 55.1 - - - +
76P GLU* 3.5 9.8 + - - +
77P THR* 2.6 36.1 + - - -
29T GLN* 3.2 21.5 + - - +
----------------------------------------------------------
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Residues in contact with THR 74 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70P GLY 2.8 20.9 + - - -
71P ALA* 3.1 10.4 + - - -
73P SER* 1.3 72.0 - - - +
75P VAL* 1.3 67.0 + - + +
77P THR* 3.2 8.1 + - - -
78P PHE* 3.1 52.4 + - + -
----------------------------------------------------------
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Residues in contact with VAL 75 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P ALA* 3.1 15.4 + - + +
72P LYS* 3.5 8.3 - - - +
74P THR* 1.3 78.5 - - + +
76P GLU* 1.3 54.5 + - + +
78P PHE* 3.0 8.9 + - - +
79P ILE* 2.7 56.4 + - + +
----------------------------------------------------------
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Residues in contact with GLU 76 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72P LYS* 2.9 56.0 + - - +
73P SER* 3.7 7.5 + - - +
75P VAL* 1.3 78.6 - - + +
77P THR* 1.3 53.3 + - - +
79P ILE* 4.4 7.0 - - + -
80P SER* 2.6 43.2 + - - -
29T GLN* 3.6 12.6 + - - +
----------------------------------------------------------
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Residues in contact with THR 77 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74N ASN* 3.4 35.7 - - + +
77N ILE* 4.6 19.3 - - + -
78N LEU* 5.5 4.0 - - + -
73P SER* 2.6 23.4 + - - -
74P THR* 3.3 9.8 - - - -
75P VAL 3.2 0.2 - - - -
76P GLU* 1.3 75.6 - - - +
78P PHE* 1.3 69.2 + - + +
80P SER* 3.1 16.0 + - - -
81P SER* 3.3 10.7 + - - -
----------------------------------------------------------
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Residues in contact with PHE 78 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45N VAL* 4.0 23.8 - - + -
46N THR* 4.1 21.8 - - + -
49N PHE* 3.6 40.6 - + + -
78N LEU* 3.3 31.6 - - + -
81N LEU* 4.8 11.7 - - + -
74P THR* 3.1 42.9 + - + -
75P VAL* 3.0 7.8 + - - +
77P THR* 1.3 81.9 - - + +
79P ILE* 1.3 66.5 + - + +
81P SER* 2.9 25.3 + - - -
82P MET 4.0 0.2 + - - -
----------------------------------------------------------
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Residues in contact with ILE 79 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164C TRP* 3.4 42.0 + - + +
49N PHE* 4.8 7.4 - - + -
75P VAL* 2.7 40.2 + - + +
76P GLU* 3.7 6.7 - - + +
78P PHE* 1.3 71.6 - - + +
80P SER* 1.3 61.4 - - - +
81P SER 2.8 7.3 + - - -
82P MET* 2.9 16.1 + - - +
83P THR* 5.6 0.2 - - + -
----------------------------------------------------------
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Residues in contact with SER 80 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73N HIS* 3.9 12.2 + - - +
74N ASN* 3.4 12.4 + - - -
76P GLU* 2.6 30.8 + - - -
77P THR* 3.1 8.8 + - - -
79P ILE* 1.3 74.5 - - - +
81P SER* 1.3 54.6 + - - +
82P MET 3.0 4.2 + - - -
83P THR* 3.1 37.2 + - - -
----------------------------------------------------------
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Residues in contact with SER 81 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49N PHE* 3.7 12.5 + - - +
53N HIS* 3.3 22.3 + - - -
72N VAL* 3.5 9.5 - - - +
73N HIS* 3.2 27.8 + - - -
74N ASN* 4.8 0.4 - - - -
78N LEU* 3.6 27.7 - - - +
77P THR 3.3 9.7 + - - -
78P PHE* 2.9 18.2 + - - -
79P ILE 2.8 1.2 + - - -
80P SER* 1.3 76.1 - - - +
82P MET* 1.3 58.2 + - - +
83P THR 4.3 3.4 - - - +
85P THR* 5.6 0.3 - - - +
----------------------------------------------------------
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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