Contacts of the helix formed by residues 13 - 42 (chain I) in PDB entry 5JKL
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 HIS 13 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ARG* 3.6 2.2 + - - -
11I ASN 3.9 3.8 + - - -
12I TYR* 1.3 77.3 - - - +
14I GLN* 1.3 72.4 + - + +
15I ASP* 2.9 48.2 + - - +
16I SER* 3.0 28.4 + - - +
17I GLU 3.0 10.2 + - - -
124I LYS* 3.6 41.8 + - + +
126I ASP* 4.7 1.0 + - - -
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Residues in contact with GLN 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ARG* 3.6 15.0 - - - +
12I TYR 3.7 0.4 + - - -
13I HIS* 1.3 80.9 + - + +
15I ASP* 1.3 67.0 + - - +
17I GLU* 3.3 9.9 + - - +
18I GLU* 3.0 46.7 + - + +
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Residues in contact with ASP 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I HIS* 2.9 23.5 + - + +
14I GLN* 1.3 80.7 - - - +
16I SER* 1.3 58.5 + - - +
18I GLU* 3.4 13.1 + - - +
19I ALA* 3.0 28.1 + - - +
22I ARG* 4.8 2.1 + - - -
120I LEU* 3.6 23.8 - - + +
124I LYS* 3.6 18.5 + - - -
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Residues in contact with SER 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I TYR* 4.2 11.9 - - - -
13I HIS* 3.0 24.8 + - - +
15I ASP* 1.3 77.1 - - - +
17I GLU* 1.3 65.9 + - - +
19I ALA* 3.1 2.0 + - - +
20I ILE* 2.9 28.2 + - - +
117I LEU* 4.8 0.8 - - - +
120I LEU* 4.0 19.6 - - - +
121I ALA* 4.8 2.6 - - - -
124I LYS* 4.3 8.7 - - - +
126I ASP* 4.6 2.9 + - - +
129I LEU* 3.9 26.7 - - - +
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Residues in contact with GLU 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I ARG* 2.8 31.3 + - - +
12I TYR* 3.7 22.6 - - + -
13I HIS 3.0 8.8 + - - +
14I GLN* 3.3 16.4 + - - +
16I SER* 1.3 77.8 - - - +
18I GLU* 1.3 64.1 + - + +
20I ILE 3.4 0.5 + - - -
21I ASN* 3.2 13.1 + - - +
73I GLN* 3.0 36.7 + - - +
78I GLY* 3.4 4.6 - - - -
79I ARG* 2.8 32.9 + - - +
81I PHE* 5.5 1.4 - - - -
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Residues in contact with GLU 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I GLN* 3.0 43.6 + - + +
15I ASP* 3.6 14.7 - - - +
17I GLU* 1.3 78.6 - - + +
19I ALA* 1.3 63.7 + - - +
21I ASN* 3.2 11.9 + - - +
22I ARG* 3.1 39.4 + - - +
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Residues in contact with ALA 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ASP 3.0 17.6 + - - +
16I SER 3.1 2.7 + - - +
18I GLU* 1.3 77.9 - - - +
20I ILE* 1.3 56.5 + - - +
22I ARG* 3.2 30.3 + - - +
23I GLN* 3.0 26.7 + - - +
117I LEU* 3.5 27.3 - - + +
120I LEU* 3.8 11.0 - - + -
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Residues in contact with ILE 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I TYR* 3.5 15.7 - - + +
16I SER 2.9 20.1 + - - +
17I GLU 3.6 4.7 - - - +
18I GLU 3.3 0.2 - - - -
19I ALA* 1.3 72.7 - - - +
21I ASN* 1.3 57.4 + - - +
23I GLN* 3.1 3.6 + - - +
24I ILE* 2.9 37.1 + - + +
69I LEU* 3.8 42.1 - - + +
72I LEU* 4.2 9.0 - - + -
73I GLN* 3.6 21.1 - - + +
117I LEU* 3.9 24.0 - - + -
129I LEU* 3.9 24.0 - - + -
132I PHE* 5.2 1.3 - - + -
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Residues in contact with ASN 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I GLU* 3.2 16.2 + - - +
18I GLU* 3.2 11.0 + - - +
20I ILE* 1.3 75.3 - - - +
22I ARG* 1.3 62.2 + - + +
24I ILE* 3.4 16.2 + - - +
25I ASN* 3.3 20.3 + - - +
73I GLN* 3.1 18.7 + - - +
79I ARG 3.0 21.2 + - - -
80I ILE* 3.5 5.9 - - - +
81I PHE* 3.3 45.6 + - + +
83I GLN* 6.1 0.5 - - - +
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Residues in contact with ARG 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ASP 4.8 2.0 + - - -
18I GLU* 3.1 37.1 + - - +
19I ALA* 3.2 32.1 + - - +
21I ASN* 1.3 79.2 - - + +
23I GLN* 1.3 61.6 + - - +
25I ASN* 3.2 7.8 + - - +
26I LEU* 3.1 21.0 + - - +
113I SER* 5.9 0.9 - - - -
120I LEU* 5.2 4.0 - - - +
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Residues in contact with GLN 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I ALA 3.0 15.5 + - - +
20I ILE* 3.1 6.2 + - - +
22I ARG* 1.3 73.9 - - - +
24I ILE* 1.3 67.4 + - - +
26I LEU* 3.2 20.4 + - - +
27I GLU* 2.9 51.7 + - - +
69I LEU* 3.7 20.9 - - + -
110I VAL* 3.9 4.2 + - - +
113I SER* 2.5 35.6 + - - +
114I LEU* 3.5 30.0 - - + +
117I LEU* 4.3 16.4 - - + +
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Residues in contact with ILE 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ILE* 2.9 26.4 + - + +
21I ASN* 3.6 24.9 - - - +
23I GLN* 1.3 76.5 - - - +
25I ASN* 1.4 63.2 + - - +
27I GLU* 3.2 3.7 + - - +
28I LEU* 3.0 40.3 + - + +
66I ALA* 4.1 5.0 - - + +
69I LEU* 3.6 40.4 - - + +
70I MET* 3.9 32.8 - - + +
73I GLN* 4.7 0.7 - - + -
80I ILE* 4.7 9.0 - - + -
81I PHE 6.1 0.2 - - - +
82I LEU* 4.1 14.6 - - + -
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Residues in contact with ASN 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ASN 3.3 9.0 + - - +
22I ARG* 3.2 10.9 + - - +
23I GLN 3.2 0.6 - - - -
24I ILE* 1.4 81.2 - - - +
26I LEU* 1.3 59.6 + - - +
28I LEU* 3.3 8.8 + - - +
29I TYR* 2.8 30.5 + - - +
83I GLN* 3.3 32.3 + - + +
84I ASP 2.9 28.7 + - - +
85I ILE* 4.3 8.1 - - - +
86I GLN* 5.3 5.0 + - - +
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Residues in contact with LEU 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I ARG 3.1 13.0 + - - +
23I GLN* 3.2 20.2 + - - +
25I ASN* 1.3 78.8 + - - +
27I GLU* 1.3 56.4 + - - +
29I TYR* 3.3 23.0 + - + +
30I ALA* 2.9 25.8 + - - +
106I LEU* 5.5 1.6 - - + -
109I ASN* 4.7 4.0 - - + +
110I VAL* 4.0 28.4 - - + +
113I SER* 3.5 36.1 - - - +
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Residues in contact with GLU 27 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I GLN* 2.9 45.5 + - - +
24I ILE 3.8 3.6 - - - +
26I LEU* 1.3 75.3 - - - +
28I LEU* 1.3 62.0 + - - +
30I ALA* 3.2 6.4 + - - +
31I SER* 3.0 22.5 + - - -
62I GLU* 2.9 13.6 - - - +
65I HIS* 3.3 12.0 - - + +
66I ALA* 3.8 19.1 - - + +
69I LEU* 3.6 18.4 - - + -
110I VAL* 3.6 10.8 - - - +
114I LEU* 4.3 0.7 - - - +
137I TYR* 4.1 12.7 - - - -
201I FE 2.0 32.5 - - - -
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Residues in contact with LEU 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I ILE* 3.0 35.0 + - + +
25I ASN* 3.6 10.5 - - - +
27I GLU* 1.3 75.4 - - - +
29I TYR* 1.3 62.1 + - - +
31I SER* 3.3 8.9 + - - -
32I TYR* 3.1 21.1 + - - +
63I ARG* 4.2 26.0 - - - +
66I ALA* 3.7 18.8 - - + -
70I MET* 5.5 5.2 - - - -
82I LEU* 4.6 13.0 - - + -
83I GLN 5.7 1.3 - - - +
85I ILE* 3.9 36.0 - - + +
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Residues in contact with TYR 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I ASN* 2.8 21.2 + - - +
26I LEU* 3.5 24.7 - - + +
27I GLU 3.2 0.2 - - - -
28I LEU* 1.3 76.1 - - - +
30I ALA* 1.3 59.5 + - - +
32I TYR* 3.0 4.3 + - - +
33I VAL* 2.9 51.3 + - + +
85I ILE* 3.8 12.0 - - + +
86I GLN* 3.3 39.9 - - + +
87I LYS 3.8 10.8 - - - -
88I PRO* 4.2 0.4 - - + -
89I ASP* 3.9 27.2 + - - -
106I LEU* 4.0 15.7 - - + -
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Residues in contact with ALA 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I LEU 2.9 13.5 + - - +
27I GLU* 3.2 9.6 + - - +
29I TYR* 1.3 79.7 - - - +
31I SER* 1.3 63.4 + - - +
33I VAL* 3.3 2.6 + - - +
34I TYR* 3.1 28.0 + - + -
62I GLU* 3.9 23.3 - - + +
106I LEU* 4.1 29.2 - - + -
107I GLU* 5.6 1.1 - - - +
110I VAL* 4.6 9.6 - - + -
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Residues in contact with SER 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I GLU 3.0 8.7 + - - -
28I LEU* 3.4 15.7 - - - -
29I TYR 3.2 0.2 - - - -
30I ALA* 1.3 75.8 - - - +
32I TYR* 1.3 56.4 + - - +
34I TYR 3.4 0.5 + - - -
35I LEU* 3.0 15.1 + - - +
59I SER* 2.6 52.8 + - - +
62I GLU* 3.6 17.4 - - - +
63I ARG* 3.9 16.4 + - - +
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Residues in contact with TYR 32 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I LEU 3.1 11.8 + - - +
29I TYR* 3.0 10.2 + - - +
31I SER* 1.3 75.0 - - - +
33I VAL* 1.3 66.5 + - - +
35I LEU* 3.2 24.9 + - + -
36I SER* 3.0 23.8 + - - -
85I ILE* 3.9 21.5 - - + -
86I GLN 3.4 22.2 - - - +
87I LYS* 3.9 9.6 - - + +
88I PRO* 3.7 21.8 - - + -
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Residues in contact with VAL 33 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I TYR* 2.9 54.5 + - + +
30I ALA 3.7 6.1 - - - +
32I TYR* 1.3 77.1 - - - +
34I TYR* 1.3 58.5 + - - +
36I SER* 3.2 4.9 + - - -
37I MET* 2.9 52.3 + - + +
88I PRO* 3.7 16.8 - - + +
89I ASP 5.4 0.7 - - - +
93I TRP* 4.2 11.9 - - + -
106I LEU* 3.9 22.7 - - + -
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Residues in contact with TYR 34 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I ALA 3.1 21.4 + - - +
33I VAL* 1.3 76.8 - - - +
35I LEU* 1.3 56.5 + - - +
37I MET* 3.3 9.1 + - - -
38I SER* 2.9 29.6 + - - -
54I TYR* 5.8 0.2 - + - -
55I PHE* 3.5 43.9 - + - +
58I GLN* 3.8 27.4 + - + +
59I SER* 3.7 9.6 - - - +
62I GLU* 3.8 24.0 - - + -
103I ALA* 3.8 25.5 + - + +
106I LEU* 4.1 16.8 - - + -
107I GLU* 2.5 42.1 + - - +
148I LEU* 4.0 6.2 - - + +
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Residues in contact with LEU 35 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I SER 3.0 15.4 + - - +
32I TYR* 3.5 29.6 - - + +
34I TYR* 1.3 77.1 - - - +
36I SER* 1.3 62.5 + - - +
38I SER* 3.2 5.5 + - - -
39I TYR* 3.2 49.7 + - + +
56I LEU* 3.9 15.3 - - + -
59I SER* 3.7 10.7 - - - +
60I HIS* 5.9 1.3 - - + +
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Residues in contact with SER 36 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32I TYR* 3.0 15.1 + - - -
33I VAL 3.4 9.0 - - - -
35I LEU* 1.3 77.8 - - - +
37I MET* 1.3 62.3 + - - +
39I TYR* 3.5 3.0 + - - +
40I TYR* 3.1 21.7 + - - +
88I PRO* 3.7 17.0 - - - +
90I GLU 3.6 10.6 + - - -
91I ASP* 4.4 6.4 + - - +
93I TRP* 3.0 18.5 + - - -
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Residues in contact with MET 37 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I VAL* 2.9 30.6 + - + +
34I TYR* 3.7 16.6 - - + +
36I SER* 1.3 74.5 - - - +
38I SER* 1.3 64.3 + - - +
40I TYR* 3.1 8.8 + - - +
41I PHE* 3.1 24.3 + - + -
55I PHE* 3.9 35.0 - - + -
93I TRP* 3.7 41.5 - - + +
99I ALA* 3.5 29.2 - - + +
102I GLU* 3.7 21.5 - - + -
103I ALA* 3.8 9.6 - - - +
----------------------------------------------------------
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Residues in contact with SER 38 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I TYR 2.9 18.1 + - - -
35I LEU 3.5 5.8 - - - -
36I SER 3.2 0.4 - - - -
37I MET* 1.3 77.0 - - - +
39I TYR* 1.3 67.6 + - - +
41I PHE 3.2 15.4 + - - -
42I ASP* 3.3 1.6 + - - +
52I ALA* 2.6 47.3 + - - +
55I PHE* 3.8 7.4 - - - +
56I LEU* 3.4 27.6 - - - +
----------------------------------------------------------
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Residues in contact with TYR 39 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I LEU* 3.2 41.3 + - + +
36I SER* 4.4 2.5 - - - +
38I SER* 1.3 80.5 - - - +
40I TYR* 1.3 64.9 + - - +
42I ASP* 3.4 37.2 + - + +
43I ARG* 3.5 13.3 + - - +
56I LEU* 4.3 23.5 - - + +
----------------------------------------------------------
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Residues in contact with TYR 40 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36I SER 3.1 13.8 + - - +
37I MET 3.4 8.1 - - - +
39I TYR* 1.3 77.0 - - - +
41I PHE* 1.3 96.6 + + - +
43I ARG* 3.1 47.8 + - - +
46I VAL* 3.5 33.9 - - + +
91I ASP 4.1 5.2 - - - +
92I ASP* 3.4 31.0 + - - -
93I TRP* 3.6 27.6 - - + -
94I GLU* 3.2 38.3 + - - -
95I SER* 4.2 3.3 - - - -
----------------------------------------------------------
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Residues in contact with PHE 41 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37I MET* 3.1 23.7 + - + -
38I SER 3.2 8.1 + - - +
40I TYR* 1.3 97.4 - + - +
42I ASP* 1.3 56.4 + - - +
43I ARG 3.3 0.7 - - - -
46I VAL* 3.5 17.7 - - + -
47I ALA* 3.3 7.7 + - - -
48I LEU* 3.0 54.1 + - + +
49I LYS* 4.9 0.3 - - - -
51I PHE* 3.5 17.9 - + + -
52I ALA* 3.7 8.1 - - - +
55I PHE* 3.6 21.5 - + - -
93I TRP* 5.0 0.2 - - + -
95I SER* 3.6 4.7 - - - -
96I GLY* 3.6 29.4 - - - -
99I ALA* 3.6 34.1 - - + -
----------------------------------------------------------
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Residues in contact with ASP 42 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I SER 3.3 5.7 + - - +
39I TYR* 3.5 42.5 - - + +
40I TYR 3.2 1.0 - - - -
41I PHE* 1.3 75.3 - - - +
43I ARG* 1.3 60.0 + - - +
47I ALA* 4.9 1.1 - - - +
49I LYS* 6.1 2.1 - - - +
52I ALA* 4.1 9.3 - - + +
146K LYS* 2.9 34.0 + - - -
----------------------------------------------------------
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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).
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