Contacts of the helix formed by residues 2 - 27 (chain I) in PDB entry 1JI4
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 2 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 1.3 85.3 - - - +
3I THR* 1.3 67.0 + - - +
4I PHE* 3.3 26.9 - - + -
5I GLU* 3.0 41.8 + - - +
6I ILE* 3.1 12.6 + - - +
116I GLU* 3.8 10.5 - - - +
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Residues in contact with THR 3 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I LYS* 1.3 72.3 - - - +
4I PHE* 1.3 58.7 + - - +
6I ILE* 3.1 7.7 + - - +
7I LEU* 3.0 43.8 + - + +
61I LEU* 4.3 4.7 - - + -
109I LEU* 3.8 16.4 - - + -
112I THR* 3.5 10.0 + - - -
113I ALA* 3.4 17.5 - - + -
116I GLU* 2.7 34.8 + - - -
118I ASP* 4.0 11.8 + - - +
121I THR* 3.8 11.4 - - + -
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Residues in contact with PHE 4 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I LYS* 3.8 26.5 - - + -
3I THR* 1.3 79.3 - - - +
5I GLU* 1.3 82.9 + - + +
7I LEU* 3.5 14.1 - - + +
8I LYS* 3.0 49.9 + - + +
58I ILE* 4.4 5.3 - - + +
61I LEU* 5.0 6.7 - - + +
63I HIS* 3.5 63.0 - + + -
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Residues in contact with GLU 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 3.4 21.7 - - + +
2I LYS* 3.0 53.9 + - + +
4I PHE* 1.3 103.2 - - + +
6I ILE* 1.3 64.9 + - - +
8I LYS* 3.4 8.6 + - - +
9I HIS* 2.9 33.9 + - + +
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Residues in contact with ILE 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 3.8 32.3 - - + +
2I LYS 3.1 12.5 + - - +
3I THR* 3.5 6.5 - - - +
5I GLU* 1.3 76.9 - - - +
7I LEU* 1.3 57.5 + - - +
9I HIS* 3.3 4.1 + - + +
10I LEU* 3.0 45.5 + - + +
105I GLU* 4.0 17.5 - - - +
108I GLU* 4.2 6.5 - - + -
109I LEU* 3.9 26.9 - - + +
112I THR* 3.5 40.6 - - + +
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Residues in contact with LEU 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I THR* 3.0 24.4 + - + +
4I PHE* 3.5 11.7 - - - +
6I ILE* 1.3 76.9 - - - +
8I LYS* 1.3 56.7 + - - +
10I LEU* 3.3 5.6 + - + +
11I GLN* 2.8 28.9 + - - +
54I LEU* 3.9 26.4 - - + +
57I ARG* 4.2 13.7 - - + -
58I ILE* 3.5 20.4 - - + +
61I LEU* 3.6 31.9 - - + -
109I LEU* 3.7 34.3 - - + -
121I THR* 4.4 4.5 - - + -
124I TYR* 5.4 2.2 - - + -
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Residues in contact with LYS 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I PHE* 3.0 42.4 + - + +
5I GLU* 3.8 7.9 - - - +
6I ILE 3.3 0.2 - - - -
7I LEU* 1.3 73.3 - - - +
9I HIS* 1.3 61.3 + - - +
11I GLN* 3.3 5.7 + - - +
12I ALA* 3.0 21.8 + - - +
58I ILE* 3.7 15.5 - - + -
64I HIS* 2.9 31.0 + - - +
65I PRO* 4.4 5.1 + - + -
66I LEU* 3.6 32.4 - - + +
71I GLU* 4.6 6.5 + - - -
75I LEU* 4.0 16.9 - - + +
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Residues in contact with HIS 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1I MET* 3.4 23.2 - - + -
5I GLU* 2.9 27.3 + - + +
6I ILE* 3.7 8.5 - - + +
7I LEU 3.3 0.2 - - - -
8I LYS* 1.3 73.2 - - - +
10I LEU* 1.3 61.9 + - + +
12I ALA* 3.1 8.1 + - - +
13I ASP* 3.0 34.8 + - - +
75I LEU* 3.0 46.6 + - + +
77I ARG* 3.4 37.2 + - + +
105I GLU* 5.8 1.1 - - - +
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Residues in contact with LEU 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I ILE* 3.0 38.6 + - + +
7I LEU* 3.5 6.7 - - - +
9I HIS* 1.3 78.3 - - + +
11I GLN* 1.3 55.9 + - - +
13I ASP* 3.3 8.0 + - - +
14I ALA* 3.0 24.3 + - - +
50I MET* 3.9 3.6 - - + +
54I LEU* 3.5 18.7 - - + +
101I TYR* 5.1 0.2 - - - +
102I LEU* 4.1 22.7 - - + -
105I GLU* 3.5 35.9 - - + +
106I PHE* 4.0 29.2 - - + -
109I LEU* 4.2 16.2 - - + -
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Residues in contact with GLN 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I LEU 2.8 17.4 + - - +
8I LYS 3.5 3.8 - - - +
9I HIS 3.2 0.2 - - - -
10I LEU* 1.3 75.2 - - - +
12I ALA* 1.3 63.0 + - - +
14I ALA* 3.3 9.1 + - - +
15I ILE* 3.4 9.5 + - - +
51I PHE* 3.5 37.1 - - + +
54I LEU* 3.5 17.2 - - + +
55I ALA* 3.7 9.8 - - - +
58I ILE* 3.7 7.8 - - + +
65I PRO* 3.6 6.9 - - - +
66I LEU* 2.9 56.1 + - - +
26L TRP* 3.3 23.6 - - - -
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Residues in contact with ALA 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I LYS 3.0 8.5 + - - +
9I HIS 3.3 9.6 - - - +
11I GLN* 1.3 77.6 - - - +
13I ASP* 1.3 61.6 + - - +
15I ILE* 3.1 23.4 - - - +
16I VAL* 3.2 12.0 + - - +
66I LEU* 3.4 26.4 - - + +
72I ALA 3.6 18.6 - - - +
75I LEU* 3.8 6.5 - - + -
76I THR* 3.5 13.9 - - - +
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Residues in contact with ASP 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I HIS 3.0 19.2 + - - +
10I LEU* 3.6 13.4 - - - +
12I ALA* 1.3 74.8 - - - +
14I ALA* 1.3 53.5 + - - +
16I VAL* 3.7 0.5 - - - +
17I LEU* 2.8 47.2 + - + +
76I THR* 2.9 27.5 - - - +
77I ARG* 3.0 15.3 + - - +
78I VAL* 3.6 11.2 - - + +
101I TYR* 2.5 38.5 + - - -
102I LEU* 4.2 7.9 - - + -
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Residues in contact with ALA 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I LEU 3.0 8.7 + - - +
11I GLN* 3.5 10.5 - - - +
12I ALA 3.2 0.4 - - - -
13I ASP* 1.3 77.3 - - - +
15I ILE* 1.3 57.1 + - - +
17I LEU* 3.4 1.9 + - - +
18I PHE* 2.9 29.0 + - - +
47I PHE* 3.8 15.3 - - - +
50I MET* 3.4 29.1 - - + +
51I PHE* 3.8 28.7 - - + +
54I LEU* 4.4 0.4 - - + -
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Residues in contact with ILE 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I GLN 3.4 7.2 + - - +
12I ALA 3.1 16.4 - - - +
14I ALA* 1.3 77.1 - - - +
16I VAL* 1.3 65.9 + - - +
18I PHE* 3.4 15.7 + - + +
19I MET* 3.2 21.0 + - - +
51I PHE* 3.6 30.2 - - + -
66I LEU* 5.8 0.2 - - + -
69I LEU* 4.3 20.4 - - + -
72I ALA* 3.6 26.2 - - + -
15L ILE* 4.5 7.4 - - + -
18L PHE* 3.8 33.7 - - + -
19L MET* 4.5 1.3 - - + -
69L LEU* 4.0 10.1 - - + +
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Residues in contact with VAL 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ALA 3.2 6.4 + - - +
13I ASP* 3.7 2.0 - - - +
15I ILE* 1.3 80.5 - - + +
17I LEU* 1.3 56.9 - - - +
19I MET* 3.3 5.2 + - - +
20I LYS* 2.9 25.6 + - + +
72I ALA 4.6 3.4 - - - +
73I ILE* 4.3 9.9 - - + -
76I THR* 3.2 36.6 - - + +
78I VAL* 3.8 32.8 - - + +
79I LYS 5.0 0.2 - - - +
80I GLU* 4.2 21.3 - - + +
69L LEU* 3.7 23.1 - - + -
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Residues in contact with LEU 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I ASP* 2.8 30.1 + - + +
14I ALA 3.7 3.4 - - - +
16I VAL* 1.3 74.3 - - - +
18I PHE* 1.3 66.1 + - - +
20I LYS* 3.9 11.2 - - + -
21I VAL* 2.9 34.8 + - + +
47I PHE* 3.9 37.5 - - + -
78I VAL* 3.5 38.4 - - + -
98I ASP* 3.8 26.2 - - + +
99I TYR* 6.1 0.2 - - + -
102I LEU* 4.1 18.2 - - + -
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Residues in contact with PHE 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ALA 2.9 18.8 + - - +
15I ILE* 3.4 19.3 - - + +
17I LEU* 1.3 79.0 - - - +
19I MET* 1.3 58.3 + - - +
21I VAL* 3.9 2.4 - - - +
22I HIS* 2.8 59.0 + + - -
44I TYR* 3.3 37.7 - + + -
45I GLU* 5.8 0.7 - - - -
47I PHE* 4.2 10.5 - - + +
48I ALA* 3.8 23.1 - - + -
51I PHE* 6.3 0.4 - - + -
15L ILE* 3.8 29.6 - - + -
18L PHE* 4.0 22.4 - + - -
48L ALA* 4.4 13.0 - - + -
51L PHE* 4.3 6.5 - + - -
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Residues in contact with MET 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I ILE 3.2 3.2 + - - +
16I VAL* 3.6 8.1 - - - +
17I LEU 3.2 0.2 - - - -
18I PHE* 1.3 86.6 - - + +
20I LYS* 1.3 62.5 + - - +
22I HIS* 3.2 16.7 + - - +
23I ASN* 3.2 10.9 + - - +
26I TRP* 4.6 2.2 - - - -
80I GLU* 4.3 4.5 - - + +
15L ILE* 4.5 9.4 - - + -
51L PHE* 3.7 34.3 - - + -
66L LEU* 4.4 7.9 - - + +
67L VAL* 3.6 29.8 - - - +
68L THR* 3.6 23.3 - - - +
69L LEU* 3.3 43.3 - - + +
72L ALA* 4.7 2.2 - - + -
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Residues in contact with LYS 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I VAL* 2.9 17.7 + - + +
17I LEU* 3.2 15.9 + - + +
19I MET* 1.3 78.7 - - - +
21I VAL* 1.3 63.7 + - + +
23I ASN* 3.2 22.0 + - - +
24I PHE* 3.3 24.3 + - + -
78I VAL* 3.7 4.5 - - + +
79I LYS* 2.8 31.0 + - - +
80I GLU* 5.5 2.5 - - + -
81I GLU* 4.1 23.1 - - + +
94I GLU* 2.7 30.5 + - - +
98I ASP* 2.9 32.5 + - - +
67L VAL 5.1 2.5 - - - -
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Residues in contact with VAL 21 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I LEU* 2.9 24.1 + - + +
20I LYS* 1.3 72.9 - - + +
22I HIS* 1.3 60.0 + - - +
23I ASN 3.2 0.2 - - - -
24I PHE* 3.7 20.2 - - + +
25I HIS* 2.9 27.9 + - - +
40I THR* 3.7 15.6 - - + +
43I ILE* 4.1 19.3 - - + -
44I TYR* 3.0 46.0 - - + +
47I PHE* 4.2 9.0 - - + -
95I ILE* 4.8 10.1 - - + -
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Residues in contact with HIS 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I PHE* 2.8 54.3 + + - -
19I MET 3.2 10.5 + - - +
20I LYS 3.1 0.2 - - - -
21I VAL* 1.3 76.1 - - - +
23I ASN* 1.3 67.7 + - - +
25I HIS* 3.0 7.9 + - - +
26I TRP* 2.8 56.6 + - + -
44I TYR* 3.5 44.2 - + - -
48L ALA* 4.7 3.6 - - + -
51L PHE* 3.8 20.0 - + + -
52L ASP* 3.6 17.9 + - + -
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Residues in contact with ASN 23 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I MET 3.2 8.6 + - - +
20I LYS* 3.2 12.5 + - - +
22I HIS* 1.3 80.4 - - - +
24I PHE* 1.3 57.3 + - + +
26I TRP* 3.3 10.4 + - - -
27I ASN* 2.7 56.3 + - - +
81I GLU* 3.5 24.2 + - - +
83I LYS 2.9 22.2 + - - +
86I PHE* 3.3 21.7 - - - -
67L VAL* 3.4 23.3 - - + +
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Residues in contact with PHE 24 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I LYS* 3.3 34.4 + - + -
21I VAL* 3.7 14.8 - - + +
22I HIS 3.3 0.2 - - - -
23I ASN* 1.3 76.4 - - - +
25I HIS* 1.3 53.8 + - - +
28I VAL* 2.7 41.1 + - - +
40I THR* 4.0 7.0 - - + -
81I GLU* 4.3 3.8 - - + -
86I PHE* 3.9 32.3 - + - -
90I ASP 5.6 0.2 - - - -
91I ILE* 3.7 46.6 - - + +
94I GLU* 3.6 41.3 - - + -
95I ILE* 3.8 25.8 - - + -
98I ASP* 5.7 0.4 - - - -
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Residues in contact with HIS 25 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I VAL 2.9 15.8 + - - +
22I HIS* 3.1 12.8 - - - +
24I PHE* 1.3 78.4 - - - +
26I TRP* 1.3 67.5 + + - +
28I VAL* 3.8 7.0 - - - +
33I PHE* 4.8 0.9 - - - -
37I HIS* 2.8 71.5 + + - -
40I THR* 3.1 16.4 + - - +
41I GLU* 3.8 21.6 + - + -
44I TYR* 3.7 13.0 + + + -
52L ASP* 3.3 16.5 + - - -
56L GLU* 3.1 8.5 + - - -
817L FE 2.2 31.0 - - - -
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Residues in contact with TRP 26 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C TRP* 3.9 27.0 + - + -
19I MET* 4.6 2.0 - - - -
22I HIS* 2.8 42.4 + - + -
23I ASN* 3.8 17.5 - - - -
25I HIS* 1.3 82.0 - + - +
27I ASN* 1.3 75.7 + - - +
28I VAL* 3.6 3.5 + - - +
29I LYS* 5.0 1.9 + - - -
33I PHE* 4.9 1.4 - - - -
11L GLN* 3.3 18.8 - - - -
51L PHE* 3.6 25.1 - + - -
52L ASP* 2.7 28.2 + - - -
55L ALA* 3.2 23.2 - - + +
56L GLU* 3.5 21.1 - - + -
59L VAL* 4.4 13.0 - - + +
65L PRO* 3.8 14.6 - - + -
66L LEU 3.2 22.7 - - - -
67L VAL* 4.3 4.5 - - + -
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Residues in contact with ASN 27 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I ASN* 2.7 36.3 + - - +
24I PHE 4.0 1.1 - - - -
26I TRP* 1.3 88.8 + - - +
28I VAL* 1.3 63.9 + - - +
29I LYS* 3.1 22.7 - - - +
84I THR* 3.2 33.7 + - - +
86I PHE* 3.1 18.1 + - + -
59L VAL* 4.0 19.8 - - - +
64L HIS* 5.7 1.6 + - - -
65L PRO* 4.3 8.0 - - - +
67L VAL* 3.9 11.6 - - - +
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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