Contacts of the helix formed by residues 8 - 37 (chain A) in PDB entry 1B71
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 ARG 8 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLY 5.6 0.2 - - - +
7A SER* 1.3 71.2 - - - +
9A THR* 1.3 64.8 - - - +
10A GLU 3.1 0.4 - - - -
11A LYS* 3.1 12.7 + - - +
12A ASN* 3.0 28.2 + - - +
108A ILE* 4.1 34.5 - - + +
111A GLU* 4.9 7.9 + - - -
112A GLU* 2.8 21.5 + - + +
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Residues in contact with THR 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 5.4 1.6 - - + -
7A SER* 3.0 3.8 + - - -
8A ARG* 1.3 78.0 - - - +
10A GLU* 1.3 57.1 + - - +
12A ASN* 2.8 10.2 + - - +
13A ILE* 2.8 38.7 + - + +
105A PHE 5.2 0.2 - - - +
108A ILE* 3.7 0.7 - - - +
109A ALA* 3.2 29.0 + - + -
112A GLU* 2.5 29.1 + - - -
114A TYR* 3.4 12.3 - - + -
117A ILE* 3.9 31.2 - - + -
121A PHE* 4.3 5.4 - - + -
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Residues in contact with GLU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.3 34.3 - - + +
5A LYS* 2.8 41.2 + - - +
6A GLY* 2.6 30.7 + - - -
7A SER* 2.8 15.7 + - - +
8A ARG 3.1 0.2 - - - -
9A THR* 1.3 73.3 - - - +
11A LYS* 1.3 62.8 + - - +
13A ILE* 3.6 3.3 + - - +
14A LEU* 3.2 21.7 + - - +
64A LEU* 4.2 11.7 - - + +
65A GLU* 5.2 3.3 + - - +
66A GLY* 4.9 2.6 - - - -
69A LEU* 3.3 29.1 - - + +
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Residues in contact with LYS 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLY* 4.9 10.3 - - - -
7A SER 3.7 20.4 - - - +
8A ARG* 3.1 12.2 + - - +
10A GLU* 1.3 77.5 - - - +
12A ASN* 1.3 61.8 + - - +
14A LEU* 3.4 1.4 + - - +
15A THR* 2.8 34.7 + - - +
69A LEU* 3.7 35.8 - - + +
70A GLU* 4.2 15.4 + - - +
71A ILE* 4.1 6.3 - - + +
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Residues in contact with ASN 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 3.0 22.0 + - - +
9A THR* 2.8 16.7 + - - +
11A LYS* 1.3 77.2 - - - +
13A ILE* 1.3 55.1 + - - +
15A THR* 3.1 3.7 + - - -
16A ALA* 2.8 35.9 + - - +
105A PHE* 3.4 52.2 + - + +
108A ILE* 3.7 28.4 - - - +
121A PHE* 4.3 7.9 - - + -
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Residues in contact with ILE 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LEU* 3.5 31.0 - - + -
9A THR* 2.8 20.2 + - + +
10A GLU 3.9 0.4 - - - +
12A ASN* 1.3 73.1 - - - +
14A LEU* 1.3 60.0 + - - +
16A ALA* 3.2 3.6 + - - +
17A PHE* 2.8 29.3 + - + +
60A LEU* 3.5 30.9 - - + +
63A PHE* 3.5 16.4 - - + -
64A LEU* 3.3 25.4 - - + -
117A ILE* 3.7 18.8 - - + -
121A PHE* 3.9 22.2 - - + -
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Residues in contact with LEU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU 3.2 15.5 + - - +
11A LYS 4.0 1.8 - - - +
13A ILE* 1.3 81.0 - - - +
15A THR* 1.3 57.5 + - - +
17A PHE* 3.3 23.9 + - + -
18A ALA* 2.8 29.0 + - + +
61A PHE* 5.9 1.3 - - + -
64A LEU* 4.3 18.4 - - + +
69A LEU* 3.3 50.3 - - + +
71A ILE* 3.8 16.4 - - + -
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Residues in contact with THR 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 2.8 24.7 + - - +
12A ASN* 3.6 7.6 - - - -
13A ILE 3.1 0.2 - - - -
14A LEU* 1.3 79.1 - - - +
16A ALA* 1.3 57.7 + - - +
18A ALA* 3.2 2.6 + - - +
19A GLY* 2.9 24.8 + - - -
71A ILE* 3.7 26.3 - - - +
72A VAL 4.5 3.7 + - - +
73A ALA* 3.7 26.7 - - + -
75A PHE* 4.2 6.4 - - + -
101A MET* 5.5 5.0 - - - +
105A PHE* 4.6 14.1 - - + -
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Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ASN 2.8 17.0 + - - +
13A ILE 3.6 1.3 - - - +
15A THR* 1.3 75.1 - - - +
17A PHE* 1.3 56.4 + - - +
19A GLY* 3.0 1.8 + - - +
20A GLU* 2.6 42.0 + - - +
60A LEU* 3.5 22.0 - - + -
101A MET* 4.1 14.1 - - + -
102A TYR* 3.8 23.3 - - + +
105A PHE* 4.5 0.4 - - - -
121A PHE* 4.2 5.8 - - + -
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Residues in contact with PHE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ILE* 2.8 23.2 + - + +
14A LEU* 3.5 24.5 - - + +
16A ALA* 1.3 71.1 - - - +
18A ALA* 1.3 58.8 + - - +
20A GLU* 4.1 3.1 - - - +
21A SER* 2.7 55.8 + - - -
57A ALA* 3.5 31.9 - - + -
58A LYS* 5.5 0.4 - - - -
60A LEU* 4.0 11.5 - - + +
61A PHE* 3.4 48.9 - + + +
64A LEU* 5.3 0.7 - - + -
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Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 2.8 19.6 + - + +
15A THR 3.6 4.7 - - - +
17A PHE* 1.3 81.4 - - + +
19A GLY* 1.3 61.5 + - - +
21A SER* 3.9 4.8 - - - -
22A GLN* 2.9 36.7 + - - +
71A ILE* 4.1 13.2 - - + -
75A PHE* 4.0 15.9 - - + -
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A THR 2.9 12.5 + - - -
16A ALA* 3.6 2.0 - - - -
18A ALA* 1.3 77.8 - - - +
20A GLU* 1.3 64.9 + - - +
22A GLN* 3.1 5.5 + - - +
23A ALA* 2.9 22.1 + - - +
26A ARG* 4.6 3.6 + - - -
75A PHE* 3.6 23.5 - - - -
97A GLU* 5.8 2.5 - - - -
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Residues in contact with GLU 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ALA 2.6 23.4 + - - +
17A PHE 4.1 2.0 - - - +
19A GLY* 1.3 73.6 - - - +
21A SER* 1.3 61.4 + - - +
23A ALA* 3.0 6.6 + - - +
24A ARG* 3.0 22.2 + - - +
53A GLU* 2.5 24.9 - - - +
56A HIS* 3.1 18.3 + - + +
57A ALA* 4.1 17.9 - - + -
60A LEU* 4.8 3.8 - - + -
97A GLU* 3.5 15.2 - - - +
102A TYR* 3.2 26.9 + - - +
124A ILE* 3.9 0.9 - - - +
128A GLU* 3.0 6.9 - - - +
194A ZN 2.1 29.0 - - - -
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A PHE* 2.7 55.6 + - - -
18A ALA* 3.9 6.5 - - - -
20A GLU* 1.3 71.5 - - - +
22A GLN* 1.4 66.4 + - - +
23A ALA 3.3 0.2 + - - -
24A ARG* 3.4 10.0 + - - +
25A ASN* 3.4 21.1 + - - +
57A ALA* 4.4 5.4 - - - +
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Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA* 2.9 22.1 + - - +
19A GLY 3.1 4.7 + - - +
21A SER* 1.4 82.5 - - - +
23A ALA* 1.3 55.7 + - - +
25A ASN* 3.3 8.3 + - - +
26A ARG* 2.9 48.0 + - + +
75A PHE* 3.3 53.0 - - - +
76A PRO 4.7 4.2 - - - +
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY 2.9 12.7 + - - +
20A GLU* 3.0 15.2 + - - +
22A GLN* 1.3 75.7 - - - +
24A ARG* 1.3 61.7 + - - +
26A ARG* 3.7 23.8 - - - +
27A TYR* 2.7 57.2 + - + +
53A GLU* 4.2 8.3 - - - +
97A GLU* 5.3 4.9 - - - +
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Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLU 3.0 11.2 + - - +
21A SER* 3.6 12.8 - - - +
23A ALA* 1.3 77.6 - - - +
25A ASN* 1.3 62.2 + - - +
27A TYR 3.3 0.2 + - - -
28A ASN* 2.8 46.2 + - - +
50A ALA* 3.5 27.4 + - - +
51A ASP* 4.9 4.8 + - - -
53A GLU* 4.2 6.8 - - + +
54A ARG* 3.7 54.4 - - - +
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Residues in contact with ASN 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER 3.4 8.6 + - - +
22A GLN* 3.3 11.4 + - - +
23A ALA 3.2 0.4 - - - -
24A ARG* 1.3 83.8 - - - +
26A ARG* 1.3 58.5 + - + +
28A ASN* 3.0 6.7 + - - +
29A TYR* 2.8 68.5 + - + +
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Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLY* 4.6 2.8 + - - -
22A GLN* 2.9 47.0 + - + +
23A ALA* 3.7 26.1 - - - +
25A ASN* 1.3 76.3 - - + +
27A TYR* 1.3 69.6 + - + +
29A TYR* 3.1 15.0 + - + -
30A PHE* 2.6 60.2 + - + -
75A PHE* 5.8 1.0 - - - -
76A PRO* 3.7 41.9 + - - +
78A GLY 4.7 13.2 - - - +
93A GLY* 6.1 3.2 - - - -
97A GLU* 5.2 6.7 + - - -
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Residues in contact with TYR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 2.7 36.8 + - + +
24A ARG 3.9 2.7 - - - +
26A ARG* 1.3 82.8 + - + +
28A ASN* 1.3 53.4 + - - +
30A PHE* 3.9 11.4 - + - -
31A GLY 2.6 32.2 + - - -
46A PHE* 3.5 33.9 - + + +
49A THR* 3.6 19.5 - - + -
50A ALA* 4.0 5.4 - - + -
53A GLU* 3.5 27.0 - - + -
90A SER* 3.4 34.9 + - - -
93A GLY 5.5 0.3 - - - -
94A GLU* 2.7 42.1 + - - +
97A GLU* 5.2 3.1 + - - -
135A PHE* 4.3 4.5 - + - -
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Residues in contact with ASN 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 2.8 34.2 + - - +
25A ASN* 3.5 8.1 - - - +
27A TYR* 1.3 76.7 - - - +
29A TYR* 1.3 71.3 + - + +
31A GLY* 3.2 3.0 + - - -
32A GLY* 3.0 18.9 + - - -
47A ALA* 4.2 17.7 + - - +
50A ALA* 3.5 20.5 - - - +
51A ASP* 5.2 4.1 + - - +
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Residues in contact with TYR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASN* 2.8 64.2 + - + -
26A ARG* 3.7 13.9 - - + +
28A ASN* 1.3 77.0 - - + +
30A PHE* 1.3 58.9 + - - +
32A GLY* 3.3 2.2 + - - -
33A GLN* 3.0 27.4 + - - +
80A ILE* 3.6 37.3 - - + +
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Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 2.6 51.7 + - + +
27A TYR* 3.5 11.2 - + - +
29A TYR* 1.3 72.1 - - - +
31A GLY* 1.3 58.9 + - - +
33A GLN* 3.3 3.9 + - - +
34A ALA* 2.8 28.1 + - - +
46A PHE* 3.6 26.1 - + + -
79A ILE 3.5 22.0 - - - -
80A ILE* 4.0 16.2 - - + -
83A THR* 4.9 0.3 + - - -
86A ASN* 3.4 44.1 + - + +
89A ALA* 5.2 8.1 - - + -
90A SER* 3.2 30.5 - - - -
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Residues in contact with GLY 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR 2.6 17.0 + - - -
28A ASN* 3.2 3.3 + - - -
30A PHE* 1.3 73.6 - - - +
32A GLY* 1.3 59.2 + - - +
34A ALA 3.1 0.9 + - - -
35A LYS 3.0 9.5 + - - -
43A SER* 2.7 32.5 + - - -
46A PHE* 3.3 24.8 - - - +
47A ALA* 4.7 2.7 - - - -
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Residues in contact with GLY 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ASN 3.0 13.5 + - - -
29A TYR* 3.3 3.7 + - - -
31A GLY* 1.3 72.9 - - - +
33A GLN* 1.3 62.2 + - - +
35A LYS* 3.3 8.3 + - - +
36A LYS* 3.1 28.9 + - - +
43A SER* 4.8 0.2 - - - -
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Residues in contact with GLN 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A TYR 3.0 13.1 + - - +
30A PHE 3.5 7.6 - - - +
32A GLY* 1.3 77.5 - - - +
34A ALA* 1.3 63.3 + - - +
36A LYS* 3.2 18.4 + - - +
37A ASP* 2.8 55.6 + - - +
80A ILE* 4.2 13.2 - - + +
81A ALA 3.3 25.8 - - - +
82A ASP* 5.4 1.8 - - - +
83A THR* 4.0 0.2 - - - -
86A ASN* 3.8 9.9 - - - +
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Residues in contact with ALA 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE 2.8 18.8 + - - +
31A GLY 3.1 5.8 + - - +
33A GLN* 1.3 72.5 - - - +
35A LYS* 1.3 64.1 + - - +
37A ASP* 2.9 10.8 + - - +
38A GLY 3.1 0.2 + - - -
39A PHE* 3.0 24.7 + - + +
42A ILE* 3.9 15.9 - - + -
43A SER* 3.7 22.7 - - - +
46A PHE* 4.2 3.6 - - + -
83A THR* 3.2 20.6 + - + +
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Residues in contact with LYS 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY 3.0 7.9 + - - +
32A GLY* 3.5 11.0 - - - +
33A GLN 3.3 0.2 - - - -
34A ALA* 1.3 77.2 - - - +
36A LYS* 1.3 77.9 + - + +
38A GLY* 3.3 12.1 + - - -
39A PHE 4.4 4.0 - - - -
40A VAL* 4.7 18.3 - - + +
43A SER* 3.5 21.4 + - - +
183A HIS* 6.1 3.4 - - - -
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Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLY 3.1 19.1 + - - +
33A GLN* 3.6 20.9 - - - +
35A LYS* 1.3 94.1 + - + +
37A ASP* 1.3 62.0 + - - +
38A GLY* 3.3 1.4 + - - -
----------------------------------------------------------
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Residues in contact with ASP 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 2.8 37.5 + - - +
34A ALA 2.9 5.4 + - - +
36A LYS* 1.3 77.7 - - - +
38A GLY* 1.3 58.2 + - - +
39A PHE* 3.5 23.3 - - + -
82A ASP* 3.9 4.4 - - - +
83A THR* 2.4 45.5 + - - +
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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