Contacts of the helix formed by residues 4 - 35 (chain A) in PDB entry 3E1J
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 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLY* 1.3 71.8 - - - -
5A THR* 1.3 65.5 + - - +
6A LYS* 3.0 5.6 + - - +
7A VAL* 2.9 43.7 + - + +
8A ILE* 3.2 21.8 + - - +
65A LEU* 5.4 0.6 - - - +
107A TYR* 2.9 27.2 + - - -
111A VAL* 3.8 19.5 - - + +
113A ASP* 5.5 3.3 + - + +
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Residues in contact with THR 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LYS* 4.7 12.5 + - - -
3A GLY 3.5 4.4 + - - -
4A ASP* 1.3 73.4 + - - +
6A LYS* 1.3 58.1 + - + +
8A ILE* 3.2 13.5 + - + +
9A ASN* 2.9 40.8 + - - +
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Residues in contact with LYS 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASP* 3.0 2.5 + - - +
5A THR* 1.3 77.6 - - - +
7A VAL* 1.3 66.4 + - - +
9A ASN* 3.2 18.9 + - + +
10A TYR* 2.9 51.2 + - + -
107A TYR* 3.4 41.4 - - + +
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Residues in contact with VAL 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ASP* 2.9 30.9 + - + +
6A LYS* 1.3 76.2 - - - +
8A ILE* 1.3 57.2 + - - +
10A TYR* 3.2 8.8 + - + +
11A LEU* 2.8 47.7 + - + +
65A LEU* 4.2 4.9 - - + -
107A TYR* 3.7 10.5 - - + -
108A ALA* 4.4 8.3 - - + -
111A VAL* 3.7 24.7 - - + -
113A ASP* 3.4 28.7 - - + +
116A SER* 4.1 7.4 - - - +
120A MET* 5.8 1.1 - - + -
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Residues in contact with ILE 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLY 4.4 8.3 - - - +
4A ASP 3.2 14.3 + - - +
5A THR* 3.2 11.8 + - + +
7A VAL* 1.3 79.1 - - - +
9A ASN* 1.3 58.3 + - - +
11A LEU* 3.2 7.8 + - + +
12A ASN* 2.9 37.6 + - - +
62A ILE* 4.0 24.2 - - + +
65A LEU* 3.7 44.4 - - + +
66A GLU 4.6 0.9 - - - +
67A GLY* 4.1 20.0 - - - +
68A LEU 4.7 0.7 - - - +
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Residues in contact with ASN 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A THR* 2.9 32.7 + - - +
6A LYS* 3.2 23.4 + - + +
8A ILE* 1.3 75.9 - - - +
10A TYR* 1.3 56.4 + - + +
12A ASN* 3.3 8.8 + - - +
13A LYS* 2.9 28.8 + - - +
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Residues in contact with TYR 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LYS* 2.9 48.3 + - + -
7A VAL* 3.4 8.3 - - + +
9A ASN* 1.3 77.4 - - + +
11A LEU* 1.3 56.0 + - + +
13A LYS* 3.0 20.2 + - + +
14A LEU* 2.8 41.2 + - + +
100A ASN* 4.8 3.4 - - + -
103A GLU* 4.2 24.4 + - + +
104A ALA* 3.7 40.8 - - + -
107A TYR* 3.7 38.1 - + + +
120A MET* 5.7 0.2 - - - -
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Residues in contact with LEU 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 2.8 33.4 + - + +
8A ILE* 3.2 6.7 + - - +
10A TYR* 1.3 73.1 - - + +
12A ASN* 1.3 55.9 + - - +
14A LEU* 3.4 4.5 + - + +
15A LEU* 2.8 30.5 + - - +
58A TYR* 4.1 25.5 - - + +
61A ARG* 3.8 28.7 - - + -
62A ILE* 3.6 25.4 - - + +
65A LEU* 3.9 19.5 - - + -
116A SER* 4.2 5.2 - - - +
119A MET* 5.6 1.8 - - - -
120A MET* 4.0 29.8 - - + -
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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 ILE* 2.9 28.6 + - - +
9A ASN* 3.7 7.1 + - - +
11A LEU* 1.3 73.2 - - - +
13A LYS* 1.3 61.4 + - - +
15A LEU* 3.3 7.3 + - - +
16A GLY* 2.8 24.9 + - - -
62A ILE* 3.2 18.3 - - - +
68A LEU 3.0 22.2 + - - +
69A PRO* 3.3 0.2 - - - +
70A ASN* 2.7 42.2 + - + +
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Residues in contact with LYS 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ASN 2.9 14.3 + - - +
10A TYR* 3.4 23.3 - - + +
12A ASN* 1.3 77.2 - - - +
14A LEU* 1.3 64.9 + - + +
16A GLY* 3.0 4.4 + - - -
17A ASN* 3.0 23.8 + - - +
100A ASN* 3.5 43.0 + - + +
103A GLU* 5.3 1.8 - - - -
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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 TYR* 2.8 26.0 + - + +
11A LEU* 3.7 3.1 - - + +
13A LYS* 1.3 70.7 - - + +
15A LEU* 1.3 65.1 + - - +
17A ASN* 2.9 22.3 + - - +
18A GLU* 3.0 15.8 + - - +
58A TYR* 3.6 35.2 - - + +
97A GLY 4.6 0.4 - - - +
100A ASN* 3.6 33.7 - - + +
101A LEU* 3.8 24.9 - - + +
104A ALA* 3.9 10.1 - - + -
120A MET* 3.6 29.6 - - - -
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Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 2.8 22.7 + - - +
12A ASN* 3.5 18.4 - - - +
14A LEU* 1.3 70.5 - - - +
16A GLY* 1.3 58.1 + - - +
18A GLU* 3.2 1.9 + - - +
19A LEU* 2.9 47.9 + - + +
55A ALA* 3.6 40.6 - - + +
58A TYR* 3.8 14.4 - - + -
59A ILE* 3.9 22.4 - - + -
62A ILE* 4.3 5.2 - - + -
69A PRO* 4.2 3.4 - - + -
70A ASN 3.8 22.9 - - - +
71A LEU* 4.1 5.2 - - + -
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Residues in contact with GLY 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 14.6 + - - -
13A LYS* 3.0 5.8 + - - -
15A LEU* 1.3 77.8 - - - +
17A ASN* 1.3 61.9 + - - +
19A LEU* 3.3 14.9 + - - +
20A VAL* 3.1 27.2 + - - +
70A ASN 5.4 1.6 - - - -
73A ASP 5.1 6.2 - - - +
74A LEU* 5.1 0.7 - - - +
75A GLY 5.2 1.4 + - - -
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Residues in contact with ASN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 3.0 19.8 + - - +
14A LEU* 2.9 17.0 + - - +
16A GLY* 1.3 76.3 - - - +
18A GLU* 1.4 65.0 + - + +
20A VAL* 3.3 10.0 + - - +
21A ALA* 3.0 22.2 + - - +
93A LEU* 5.0 7.8 - - + +
96A ASP* 5.5 0.4 - - - -
97A GLY* 3.7 23.7 + - - -
100A ASN* 2.9 36.5 + - - +
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Residues in contact with GLU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 3.0 17.4 + - - +
15A LEU 3.7 5.2 - - - +
17A ASN* 1.4 77.7 - - - +
19A LEU* 1.3 60.0 + - - +
21A ALA* 3.2 4.8 + - - +
22A ILE* 2.8 34.3 + - - +
51A GLU* 2.9 48.0 - - - +
54A HIS* 3.2 18.3 + - + +
55A ALA* 4.3 8.1 - - + +
58A TYR* 3.7 21.4 + - + -
101A LEU* 5.2 2.8 - - - +
123A ILE* 3.7 11.3 - - - +
127A GLU* 2.7 20.7 - - - +
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Residues in contact with LEU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 2.9 54.3 + - + +
16A GLY* 3.5 19.3 - - - +
17A ASN 3.2 0.2 - - - -
18A GLU* 1.3 80.4 - - - +
20A VAL* 1.3 61.9 + - - +
22A ILE* 3.8 11.3 - - + +
23A ASN* 3.6 18.5 + - - +
55A ALA* 4.7 4.5 - - + -
70A ASN 4.3 10.3 - - - +
71A LEU* 4.0 29.4 - - + +
73A ASP 4.5 11.2 - - - +
74A LEU* 3.8 18.3 - - + +
23B ASN* 4.8 7.0 - - - +
200B HEM 4.4 15.3 - - + -
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Residues in contact with VAL 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLY 3.1 18.8 + - - +
17A ASN* 3.9 7.4 - - - +
19A LEU* 1.3 76.9 - - - +
21A ALA* 1.3 57.2 + - - +
23A ASN* 3.2 4.7 + - - +
24A GLN* 2.9 27.2 + - - +
74A LEU* 3.9 6.7 - - + +
75A GLY* 3.9 30.1 - - - +
76A LYS 3.8 15.3 - - - +
77A LEU* 3.7 25.3 - - + +
93A LEU* 3.7 26.7 - - + -
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Residues in contact with ALA 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ASN 3.0 14.3 + - - +
18A GLU* 3.2 8.7 + - - +
20A VAL* 1.3 77.9 - - - +
22A ILE* 1.3 55.3 + - - +
24A GLN* 4.0 0.6 - - - +
25A TYR* 2.8 48.6 + - + +
51A GLU* 3.8 24.7 - - + +
93A LEU* 3.8 21.5 - - + -
94A GLU* 5.6 2.0 - - - +
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Residues in contact with ILE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLU 2.8 24.9 + - - +
19A LEU* 3.8 10.8 - - + +
21A ALA* 1.3 70.7 - - - +
23A ASN* 1.3 67.4 + - - +
26A PHE* 3.1 16.6 + - - +
48A SER* 2.8 30.3 + - - +
51A GLU* 3.6 13.4 - - + +
52A MET* 3.6 44.9 - - + +
55A ALA* 4.1 13.7 - - + -
200B HEM 3.5 44.2 - - + -
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Residues in contact with ASN 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 3.6 10.3 + - - +
20A VAL 3.2 7.6 + - - +
22A ILE* 1.3 79.9 - - - +
24A GLN* 1.3 67.8 + - - +
26A PHE* 3.3 2.3 + - - +
27A LEU* 3.0 26.5 + - - +
74A LEU* 3.8 12.4 - - - +
77A LEU* 4.4 10.5 - - + -
19B LEU* 4.8 4.7 - - - +
71B LEU* 3.4 45.5 - - + +
200B HEM 3.3 35.3 - - - +
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Residues in contact with GLN 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 2.9 19.3 + - - +
21A ALA 4.0 2.0 - - - +
23A ASN* 1.3 76.5 - - - +
25A TYR* 1.3 62.8 + - - +
27A LEU* 4.0 0.7 - - - +
28A HIS* 3.0 40.3 + - + +
76A LYS 4.8 0.5 - - - +
77A LEU* 3.8 15.3 - - + +
78A ASN* 3.0 33.7 + - - +
79A ILE* 4.5 8.7 - - + -
89A SER* 3.1 24.7 + - - -
90A ASP* 2.9 34.1 + - - +
93A LEU* 4.0 18.8 - - + +
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Residues in contact with TYR 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ALA* 2.8 29.1 + - + +
24A GLN* 1.3 77.7 - - + +
26A PHE* 1.3 56.5 + - - +
28A HIS* 3.7 1.8 - - - +
29A ALA* 2.8 29.6 + - - +
44A GLU* 3.4 38.2 - - - +
47A GLU* 3.6 33.3 + - + -
48A SER* 3.8 9.2 - - - +
51A GLU* 3.9 25.8 - - + -
90A ASP* 3.5 29.3 - - + +
93A LEU* 6.1 1.8 - - + -
94A GLU* 2.4 39.9 + - + +
130A HIS* 4.0 3.9 - - - +
134A LEU* 3.6 12.7 - - + +
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE 3.1 19.6 + - - +
23A ASN* 3.3 6.0 + - - +
25A TYR* 1.3 74.7 - - - +
27A LEU* 1.3 65.3 + - - +
29A ALA* 3.3 6.7 + - + +
30A ARG* 3.0 38.6 + - + +
45A TYR* 3.6 25.8 - + - -
48A SER* 3.6 20.1 + - - +
52A MET* 4.6 0.7 - - + -
56B ASP* 3.3 44.0 - - + -
59B ILE* 3.9 14.1 - - + -
71B LEU* 5.2 1.6 - - + -
200B HEM 3.5 53.6 - + + -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ASN 3.0 16.1 + - - +
24A GLN 4.0 2.5 - - - +
26A PHE* 1.3 78.0 - - - +
28A HIS* 1.3 64.9 + - - +
30A ARG 3.2 1.6 + - - -
31A MET* 2.9 40.2 + - + +
77A LEU* 5.6 0.4 - - + -
79A ILE* 3.6 44.9 - - + -
59B ILE* 4.4 6.5 - - + -
63B LEU* 4.3 6.5 - - + -
69B PRO* 3.8 44.2 - - + +
71B LEU* 4.0 24.3 - - + +
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Residues in contact with HIS 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 3.0 31.9 + - + +
25A TYR 3.7 0.4 - - - +
27A LEU* 1.3 75.4 - - - +
29A ALA* 1.3 63.8 + - - +
31A MET* 3.1 4.4 + - - +
32A PHE* 2.9 32.4 + + + -
44A GLU* 3.1 16.4 - - - +
78A ASN 4.4 0.7 - - - -
79A ILE* 2.8 43.4 + - + -
86A MET* 3.2 48.9 + - + +
90A ASP* 2.7 35.8 + - - -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR 2.8 18.9 + - - +
26A PHE* 3.4 9.0 - - + +
28A HIS* 1.3 76.3 - - - +
30A ARG* 1.3 60.2 + - + +
32A PHE* 3.3 2.5 + - - +
33A LYS 2.9 21.8 + - - -
41A ASN* 3.0 29.7 - - - +
44A GLU* 3.9 8.6 - - + +
45A TYR* 3.6 31.9 - - + +
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A PHE* 3.0 34.9 + - + +
27A LEU 4.1 0.7 - - - +
29A ALA* 1.3 73.5 - - + +
31A MET* 1.3 60.7 + - - +
33A LYS* 3.5 14.5 - - + +
34A ASN* 2.9 28.8 + - - +
41A ASN* 3.4 29.3 + - - +
45A TYR* 3.3 34.8 - - - -
56B ASP* 2.7 46.7 + - - +
59B ILE* 4.1 9.6 - - + -
60B GLU* 2.9 32.1 + - + +
63B LEU* 3.7 19.8 - - + +
200B HEM 5.3 0.2 - - - +
----------------------------------------------------------
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Residues in contact with MET 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 2.9 33.2 + - + +
28A HIS* 3.3 9.4 - - - +
30A ARG* 1.3 73.4 - - - +
32A PHE* 1.3 66.6 + - - +
34A ASN* 3.1 6.1 + - - +
35A TRP* 2.9 50.6 + - + -
79A ILE* 3.7 22.9 - - + -
80A GLY 3.8 16.2 - - - +
81A GLU* 4.9 2.2 - - - +
86A MET* 3.7 32.8 - - + -
63B LEU* 4.2 17.0 - - + -
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Residues in contact with PHE 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A HIS* 2.9 29.7 + - + -
29A ALA 3.5 6.3 - - - +
31A MET* 1.3 71.6 - - - +
33A LYS* 1.3 60.7 + - - +
35A TRP* 3.2 13.4 + + - -
36A GLY 3.0 4.2 + - - -
37A LEU* 2.8 36.2 + - + +
40A LEU* 3.6 41.5 - - + -
41A ASN 3.9 12.8 - - - +
44A GLU* 3.9 26.0 - - + -
83A VAL* 4.0 20.2 - - + -
86A MET* 3.4 38.8 - - + -
87A LEU* 3.9 19.1 - - + -
----------------------------------------------------------
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Residues in contact with LYS 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA 2.9 7.1 + - - +
30A ARG* 3.5 19.7 - - - +
31A MET 3.2 0.4 - - - -
32A PHE* 1.3 72.6 - - - +
34A ASN* 1.3 68.6 + - - +
36A GLY* 2.9 15.0 + - - +
37A LEU 4.8 2.7 - - - +
38A LYS* 5.3 4.6 - - + +
41A ASN* 3.5 40.1 - - - +
60B GLU* 3.5 28.3 - - + -
136C THR* 5.2 0.2 - - - +
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Residues in contact with ASN 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG 2.9 17.8 + - - +
31A MET* 3.5 6.3 - - - +
33A LYS* 1.3 78.4 - - - +
35A TRP* 1.3 72.3 + - + +
36A GLY 3.2 1.4 + - - -
60B GLU 5.2 1.4 + - - -
63B LEU* 4.1 23.4 + - + +
64B PHE* 4.0 24.9 - - - +
132C ASP* 3.9 19.9 + - - +
136C THR* 3.4 20.1 + - - +
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Residues in contact with TRP 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A MET* 2.9 34.1 + - + -
32A PHE* 3.2 23.8 + + - +
34A ASN* 1.3 86.5 + - + +
36A GLY* 1.3 60.0 + - - +
37A LEU* 3.5 17.2 + - + +
81A GLU 3.4 26.2 - - - -
82A ASP* 4.3 2.2 - - - -
83A VAL* 4.4 11.0 - - + -
86A MET* 3.7 32.3 - - + -
136C THR* 3.4 12.6 - - - +
139C ASP* 5.6 4.0 - - - +
140C LEU* 3.5 18.5 - - - +
143C LYS* 3.8 33.1 + - + +
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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