Contacts of the helix formed by residues 4 - 30 (chain C) in PDB entry 1JI5
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 GLN 4 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 1.3 92.6 + - - +
6C ILE* 3.2 34.0 - - + +
7C GLU* 3.5 26.6 + - + +
8C VAL* 3.7 10.6 + - - +
63C ILE* 5.8 2.2 + - - +
113C ILE* 4.1 9.0 - - - +
117C SER* 4.6 7.9 + - - -
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Residues in contact with VAL 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLN* 1.3 86.0 + - - +
6C ILE* 1.3 58.9 + - - +
7C GLU 3.0 2.2 - - - -
8C VAL* 2.8 26.7 + - + +
9C LEU* 3.0 18.0 + - + +
63C ILE* 4.7 6.7 - - + -
110C GLY 5.4 0.2 - - - +
113C ILE* 3.3 28.0 - - + -
114C ALA* 4.2 10.1 - - + -
117C SER* 3.8 21.3 - - - +
119C ASP* 4.1 16.2 - - + +
122C THR* 3.8 29.8 - - + -
126C LEU* 6.0 0.7 - - + -
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Residues in contact with ILE 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLN* 4.1 26.9 - - + +
5C VAL* 1.3 78.3 - - - +
7C GLU* 1.3 61.6 + - - +
9C LEU* 3.5 9.5 + - - +
10C ASN* 2.8 54.8 + - - +
60C ILE* 4.3 11.2 - - + -
63C ILE* 4.0 22.9 - - + +
64C GLY 4.5 2.9 - - - +
65C GLY* 3.4 31.6 - - - +
66C LYS 4.5 3.1 - - - +
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Residues in contact with GLU 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLN* 3.5 21.6 + - + +
5C VAL 3.0 0.8 - - - -
6C ILE* 1.3 85.4 - - - +
8C VAL* 1.3 66.2 + - + +
10C ASN* 3.9 17.4 + - - +
11C LYS* 3.1 23.4 + - - +
68C VAL* 5.6 2.1 - - - +
77C ILE* 4.3 12.6 - - - +
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Residues in contact with VAL 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C GLN 3.7 7.2 - - - +
5C VAL* 2.8 7.2 + - + +
7C GLU* 1.3 76.3 - - - +
9C LEU* 1.3 67.2 + - + +
11C LYS* 3.1 8.8 + - - +
12C GLN* 3.1 24.9 + - + +
106C GLU 4.8 4.9 - - - +
107C LEU* 6.1 0.9 - - + -
110C GLY* 3.7 24.9 - - - +
113C ILE* 3.7 39.7 - - + -
126C LEU* 4.3 14.4 - - + -
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Residues in contact with LEU 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C VAL* 3.0 15.4 + - + +
6C ILE 3.8 4.5 - - - +
8C VAL* 1.3 79.8 - - + +
10C ASN* 1.3 57.3 + - - +
12C GLN* 2.9 10.1 + - + +
13C VAL* 2.8 30.1 + - - +
56C ILE* 3.4 16.7 - - + +
59C ARG* 4.0 15.9 - - + -
60C ILE* 3.2 33.7 - - + -
63C ILE* 4.0 16.8 - - + -
122C THR* 3.5 34.3 - - + -
125C LEU* 5.6 0.2 - - + -
126C LEU* 3.7 23.6 - - + -
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Residues in contact with ASN 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 2.8 48.0 + - - +
7C GLU* 4.0 17.8 + - - +
9C LEU* 1.3 74.5 - - - +
11C LYS* 1.3 57.9 + - - +
13C VAL* 3.4 7.1 + - - +
14C ALA* 3.1 25.3 + - - +
60C ILE* 3.5 7.3 - - - +
66C LYS 3.5 12.3 + - - -
67C PRO* 3.2 6.9 - - - +
68C VAL* 2.7 51.0 + - + +
77C ILE* 3.6 3.9 - - + +
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Residues in contact with LYS 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C GLU 3.1 13.5 + - - +
8C VAL* 3.5 9.6 - - - +
10C ASN* 1.3 74.7 - - - +
12C GLN* 1.3 57.4 + - - +
14C ALA* 3.3 0.7 + - - +
15C ASP* 2.7 50.0 + - - +
77C ILE* 2.9 33.9 + - + +
79C SER* 2.9 42.9 - - - +
106C GLU* 2.8 44.4 - - - +
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Residues in contact with GLN 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 3.1 20.0 + - + +
9C LEU* 2.9 21.5 + - + +
11C LYS* 1.3 77.3 - - - +
13C VAL* 1.3 51.5 + - - +
15C ASP* 3.2 6.6 + - - -
16C TRP* 2.7 63.4 + - - -
56C ILE* 3.7 14.4 - - + -
103C MET* 2.9 38.1 + - - +
106C GLU* 5.4 6.5 - - - +
107C LEU* 3.9 18.6 - - + +
126C LEU* 5.4 3.6 - - + -
129C ILE* 3.8 14.2 - - - +
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Residues in contact with VAL 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LEU 2.8 19.3 + - - +
10C ASN* 3.6 17.7 - - - +
11C LYS 3.2 0.2 - - - -
12C GLN* 1.3 75.7 - - - +
14C ALA* 1.3 57.6 + - - +
16C TRP* 3.4 5.0 + - - +
17C SER* 2.8 35.8 + - - +
53C ILE* 4.4 16.7 - - + +
56C ILE* 3.6 19.7 - - + -
57C ALA* 4.1 16.8 - - + +
60C ILE* 5.3 0.9 - - + -
67C PRO* 5.3 2.0 - - + -
68C VAL* 4.0 9.0 - - + +
74C TYR* 3.6 29.6 - - + +
28D TRP* 4.4 6.1 - - + -
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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 ASN 3.1 10.9 + - - +
11C LYS 3.6 7.2 - - - +
12C GLN 3.2 0.2 - - - -
13C VAL* 1.3 79.8 - - - +
15C ASP* 1.3 63.2 + - - +
17C SER* 3.2 3.1 + - - -
18C VAL* 3.0 26.9 + - - +
68C VAL* 5.0 0.4 - - + -
74C TYR* 3.4 43.0 - - + +
77C ILE* 3.9 17.9 - - + -
78C SER* 3.9 5.2 - - - +
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Residues in contact with ASP 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LYS* 2.7 46.8 + - - +
12C GLN* 3.6 11.6 + - - +
14C ALA* 1.3 72.6 - - - +
16C TRP* 1.3 64.4 + - - +
18C VAL* 3.0 5.9 + - - +
19C LEU* 2.9 26.0 + - - +
78C SER* 3.0 12.0 + - - -
79C SER* 3.0 31.0 + - - -
80C ILE* 3.7 16.0 - - + +
103C MET* 4.5 15.9 - - - +
106C GLU* 3.4 8.0 - - - +
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Residues in contact with TRP 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLN* 2.7 49.6 + - - +
13C VAL 3.8 0.9 - - - +
15C ASP* 1.3 73.0 - - - +
17C SER* 1.3 57.3 + - - +
19C LEU* 3.1 23.2 + - + +
20C PHE* 2.8 30.0 + - - +
23C LEU* 5.7 0.7 - - + -
45C LEU 5.5 0.9 - - - -
48C GLU* 6.2 0.4 - - + -
49C SER* 3.6 29.8 + - - +
52C HIS* 3.5 36.4 - + + +
53C ILE* 3.7 22.0 - - + +
56C ILE* 3.4 23.1 - - + +
100C TYR* 4.3 14.6 - + - -
103C MET* 3.4 23.6 - - + +
129C ILE* 3.6 13.9 - - + +
132C GLU* 4.6 0.2 - - - -
133C LEU* 3.7 25.1 - - + -
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Residues in contact with SER 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C VAL* 2.8 26.0 + - - +
14C ALA 3.5 5.2 - - - -
16C TRP* 1.3 75.5 - - - +
18C VAL* 1.3 63.8 + - - +
20C PHE* 3.3 15.8 - - - +
21C THR* 3.5 10.9 + - - -
53C ILE* 3.8 21.9 - - - +
74C TYR* 3.5 40.1 + - - -
71D MET* 4.0 7.2 - - - +
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Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C ALA 3.0 15.9 - - - +
15C ASP 3.0 5.8 + - - +
17C SER* 1.3 74.1 - - - +
19C LEU* 1.3 66.8 + - - +
21C THR* 3.1 4.9 + - - -
22C LYS* 2.8 23.7 + - + +
74C TYR* 4.8 5.8 - - + +
75C LEU* 4.9 7.4 - - + -
78C SER* 3.2 26.9 - - - +
80C ILE* 3.9 30.1 - - + +
81C GLN 5.0 0.2 - - - +
82C GLU* 4.2 26.7 - - + +
71D MET* 4.1 15.5 - - - -
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ASP 2.9 30.2 + - - +
16C TRP* 3.4 35.4 - - + +
18C VAL* 1.3 75.2 - - - +
20C PHE* 1.3 54.7 + - - +
22C LYS* 3.1 9.0 + - + -
23C LEU* 2.7 54.0 + - + +
49C SER* 4.6 0.2 - - - -
80C ILE* 4.0 25.1 - - + -
96C ILE* 5.2 6.3 - - + -
99C ASP* 4.1 28.3 - - + +
100C TYR* 4.7 13.0 - - + -
103C MET* 4.4 11.2 - - - -
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Residues in contact with PHE 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP 2.8 11.7 + - - +
17C SER* 3.3 15.3 - - - +
19C LEU* 1.3 76.7 - - - +
21C THR* 1.3 65.4 + - - +
23C LEU 3.6 0.2 + - - -
24C HIS* 2.6 64.7 + + - -
46C TYR* 3.6 18.8 - + - +
49C SER* 3.4 24.6 + - - +
50C ALA* 3.9 17.3 - - + -
53C ILE* 4.3 3.4 - - + -
20D PHE* 3.4 52.9 - + - -
50D ALA* 4.7 9.9 - - + -
53D ILE* 4.7 10.5 - - + -
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Residues in contact with THR 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C SER 3.5 7.1 + - - -
18C VAL 3.1 6.5 + - - -
20C PHE* 1.3 83.3 - - - +
22C LYS* 1.3 67.3 + - - +
24C HIS* 3.0 10.5 + - + +
25C ASN* 2.9 21.4 + - - +
28C TRP* 6.0 0.2 - - + -
71C MET* 5.2 0.9 - - - +
82C GLU* 4.6 3.1 - - - +
69D ALA* 3.9 20.8 - - - +
70D THR* 4.0 6.5 - - - +
71D MET* 3.5 22.7 - - - +
74D TYR* 3.5 33.7 - - + +
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Residues in contact with LYS 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C VAL* 2.8 19.2 + - + +
19C LEU* 3.6 11.0 - - + +
21C THR* 1.3 78.1 - - - +
23C LEU* 1.3 56.9 + - + +
25C ASN* 3.3 9.4 - - - +
26C PHE* 3.1 53.3 + - + -
80C ILE* 4.2 8.5 - - + +
81C GLN* 2.6 43.3 + - - +
82C GLU* 4.6 3.7 + - + +
83C ALA* 3.8 26.7 - - + +
87C GLU* 5.6 0.4 - - - -
95C ALA* 4.8 8.5 + - - +
96C ILE* 5.1 3.1 - - + -
99C ASP* 2.7 28.9 + - - +
69D ALA 5.3 1.6 - - - -
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C TRP* 5.7 0.2 - - + -
19C LEU* 2.7 38.8 + - + +
22C LYS* 1.3 70.5 - - + +
24C HIS* 1.3 60.4 + - - +
26C PHE* 3.8 2.9 - - + +
27C HIS* 2.8 28.6 + - - +
42C PHE* 3.7 23.9 - - + +
45C LEU* 3.5 30.1 - - + +
46C TYR* 3.4 43.1 - - + +
49C SER* 4.2 6.7 - - - -
96C ILE* 4.1 25.8 - - + -
100C TYR* 4.5 7.2 - - + +
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Residues in contact with HIS 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 2.6 62.8 + + - -
21C THR* 3.0 12.4 + - + +
23C LEU* 1.3 72.7 - - - +
25C ASN* 1.3 56.2 + - - +
27C HIS* 3.0 9.0 + - - +
28C TRP* 2.6 78.0 + + + -
46C TYR* 3.4 41.4 + + - -
50D ALA* 5.1 5.5 + - - +
53D ILE* 4.2 13.8 - - + +
54D ASP* 4.5 6.7 - - + +
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Residues in contact with ASN 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C THR 2.9 9.4 + - - +
22C LYS* 3.3 13.5 - - - +
24C HIS* 1.3 75.5 - - - +
26C PHE* 1.3 65.4 + - + +
28C TRP* 3.0 5.9 + - - -
29C TYR* 2.7 47.8 + - - +
83C ALA* 3.9 17.1 - - + +
84C ALA 5.3 0.2 + - - -
85C TYR* 3.6 23.5 - - - -
87C GLU* 4.8 3.8 - - - +
92C MET* 4.4 1.7 - - - +
69D ALA* 2.9 46.2 + - + +
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Residues in contact with PHE 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C LYS* 3.1 33.7 + - + +
23C LEU* 3.9 3.6 - - - +
25C ASN* 1.3 79.6 - - - +
27C HIS* 1.3 66.5 + - - +
30C VAL* 3.1 29.8 + - - +
42C PHE* 3.5 25.8 - + + -
83C ALA* 3.7 23.3 - - + -
87C GLU* 3.9 16.6 - - - -
92C MET* 3.2 49.6 - - + -
95C ALA* 3.9 11.2 - - + -
96C ILE* 3.4 34.1 - - + -
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Residues in contact with HIS 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU 2.8 17.0 + - - +
24C HIS* 3.0 12.8 - - - +
26C PHE* 1.3 78.9 - - - +
28C TRP* 1.3 71.4 + + - +
30C VAL* 3.7 6.5 - - - +
35C PHE* 5.0 0.2 - - - -
39C HIS* 2.7 74.8 + + - -
42C PHE* 3.8 11.6 - - + -
43C GLU* 3.7 24.6 + - + +
46C TYR* 3.6 17.3 + + + -
54D ASP* 3.2 14.1 - - - -
58D GLU* 3.2 3.5 + - - -
153D FE 2.0 32.1 - - - -
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Residues in contact with TRP 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C THR 5.4 0.2 - - - -
24C HIS* 2.6 53.8 + + + +
25C ASN* 3.6 7.2 - - - +
27C HIS* 1.3 88.7 - + - +
29C TYR* 1.3 63.9 + + + +
30C VAL* 3.8 3.5 + - - +
31C LYS* 4.9 3.5 + - - -
35C PHE* 5.3 3.8 - - - -
39C HIS* 5.2 1.1 - - - -
13D VAL* 4.4 2.9 - - + -
53D ILE* 3.4 27.1 - - + -
54D ASP* 2.7 22.5 + - - -
57D ALA* 3.2 33.5 - - + +
58D GLU* 3.9 16.4 - - + +
61D LEU* 3.2 35.5 - - + +
67D PRO* 4.2 15.3 - - + -
68D VAL 3.8 10.8 - - - -
69D ALA* 4.1 10.8 - - + -
74D TYR* 3.8 20.4 - - - -
----------------------------------------------------------
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Residues in contact with TYR 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASN* 2.7 44.4 + - - +
28C TRP* 1.3 75.1 - - + +
30C VAL* 1.3 66.9 + - - +
31C LYS* 3.4 27.4 + - - +
85C TYR* 3.7 29.1 - + - -
86C GLY 6.3 1.6 - - - +
87C GLU 5.7 0.9 - - - +
92C MET* 3.9 17.1 - - + +
61D LEU* 4.8 5.4 - - + -
66D LYS* 2.9 32.3 - - + +
67D PRO* 2.6 58.3 + - + -
69D ALA* 4.3 2.5 - - + -
----------------------------------------------------------
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Residues in contact with VAL 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE 3.1 19.5 + - - +
27C HIS 3.7 12.1 - - - +
28C TRP 3.6 1.6 - - - +
29C TYR* 1.3 78.7 - - - +
31C LYS* 1.3 73.4 + - - +
34C GLN 5.1 0.2 - - - +
35C PHE* 3.4 35.0 - - + +
38C LEU* 4.0 21.8 - - + -
39C HIS* 4.1 17.0 - - - +
42C PHE* 4.1 4.9 - - + -
89C ALA* 4.0 24.7 - - + +
92C MET* 3.8 14.9 - - - +
----------------------------------------------------------
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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