Contacts of the helix formed by residues 5 - 36 (chain A) in PDB entry 1NNQ
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 5 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 4.2 0.2 - - - +
4A LYS* 1.3 75.1 - - - +
6A THR* 1.3 66.9 + - - +
8A THR* 3.4 0.7 + - - -
9A LYS* 3.0 21.8 + - - +
97B PHE* 5.3 0.4 + - - -
98B GLN* 3.2 78.6 + - + +
100B GLU* 2.8 28.4 + - + +
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Residues in contact with THR 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A LYS 3.3 5.5 + - - -
5A ARG* 1.3 72.8 - - - +
7A MET* 1.3 66.6 + - - +
9A LYS* 3.5 6.0 - - - +
10A LYS* 2.9 35.3 + - + +
98B GLN* 5.1 1.0 - - - +
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Residues in contact with MET 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG 3.5 0.2 - - - -
6A THR* 1.3 83.1 - - - +
8A THR* 1.3 53.3 - - - +
10A LYS* 3.2 10.6 + - + +
11A PHE* 2.7 76.1 + - + -
94B ALA* 5.8 1.3 - - + -
98B GLN* 3.6 23.7 + - - +
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Residues in contact with THR 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 3.7 11.9 - - + -
5A ARG 3.4 4.7 + - - -
6A THR 3.4 0.2 - - - -
7A MET* 1.3 74.1 - - - +
9A LYS* 1.3 52.5 - - - +
11A PHE* 3.2 9.9 + - + +
12A LEU* 2.8 36.6 + - + +
94B ALA* 4.0 2.1 + - - +
95B ALA* 3.7 17.0 + - + -
98B GLN* 2.7 36.2 + - - +
100B GLU* 3.8 14.8 - - + +
103B ALA* 3.5 32.5 - - + -
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Residues in contact with LYS 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A VAL* 6.1 0.2 - - - +
3A VAL* 3.6 24.2 + - + +
4A LYS* 4.9 6.7 - - - +
5A ARG 3.0 18.8 + - - +
6A THR* 3.5 6.3 - - - +
8A THR* 1.3 74.9 - - - +
10A LYS* 1.3 57.5 + - - +
12A LEU* 3.2 2.6 + - - +
13A GLU* 2.9 54.2 + - - +
63A LEU* 3.6 37.8 + - + +
65A LYS* 4.7 6.5 - - - +
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Residues in contact with LYS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A THR* 2.9 23.3 + - + +
7A MET* 3.4 15.7 - - + +
9A LYS* 1.3 71.7 - - - +
11A PHE* 1.3 64.6 + - + +
13A GLU* 3.3 16.6 + - - +
14A GLU* 2.9 29.4 + - - +
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Residues in contact with PHE 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A MET* 2.7 58.0 + - + +
8A THR* 3.2 7.6 + - + +
10A LYS* 1.3 78.4 - - + +
12A LEU* 1.3 59.7 + - + +
14A GLU* 3.2 2.2 + - + +
15A ALA* 2.9 23.6 + - - +
90B VAL* 5.2 7.0 - - + -
91B TYR* 3.2 62.3 - + + +
94B ALA* 3.6 31.4 - - + -
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Residues in contact with LEU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A VAL* 4.0 15.5 - - + -
8A THR* 2.8 24.1 + - + +
9A LYS 3.8 3.1 - - - +
11A PHE* 1.3 73.2 - - + +
13A GLU* 1.3 56.7 + - - +
15A ALA* 3.6 6.1 - - + +
16A PHE* 2.8 35.0 + - - +
59A HIS* 4.1 28.1 - - + +
62A ALA* 4.0 19.1 - - + -
63A LEU* 4.0 16.1 - - + +
91B TYR* 5.5 1.3 - - + -
103B ALA* 4.0 26.9 - - + -
106B THR* 4.2 6.5 - - - +
107B THR* 4.0 26.5 - - + -
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Residues in contact with GLU 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LYS* 2.9 47.5 + - - +
10A LYS* 3.4 20.8 - - - +
12A LEU* 1.3 76.4 - - - +
14A GLU* 1.3 61.1 + - - +
16A PHE* 3.4 7.9 + - + +
17A ALA* 3.0 23.6 + - - +
63A LEU* 4.0 14.9 - - + +
65A LYS* 3.8 19.6 + - - +
21B MET* 5.1 1.2 - - - +
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Residues in contact with GLU 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LYS 2.9 13.6 + - - +
11A PHE* 3.2 4.9 + - + +
13A GLU* 1.3 75.7 - - - +
15A ALA* 1.3 57.4 + - - +
17A ALA* 3.3 12.7 + - - +
18A GLY* 2.8 28.9 + - - -
21A MET* 5.1 5.9 - - - +
87B MET* 4.5 13.7 - - + +
91B TYR* 3.4 24.7 - - - +
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Residues in contact with ALA 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A PHE 2.9 16.9 + - - +
12A LEU* 3.3 9.4 + - + +
14A GLU* 1.3 73.1 - - - +
16A PHE* 1.3 60.5 + - - +
18A GLY* 3.1 1.6 + - - +
19A GLU* 2.8 35.0 + - - +
59A HIS* 3.7 24.2 - - + +
87B MET* 4.6 7.2 - - - -
88B TYR* 3.9 18.8 - - + +
91B TYR* 4.1 12.4 - - + -
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Residues in contact with PHE 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LEU 2.8 20.3 + - - +
13A GLU* 3.5 8.7 - - + +
15A ALA* 1.3 73.8 - - - +
17A ALA* 1.3 55.3 + - - +
19A GLU* 3.4 2.4 + - - +
20A SER* 2.8 44.3 + - - -
56A ALA* 3.4 26.7 - - + -
59A HIS* 4.0 12.2 - - + -
60A PHE* 3.4 37.9 - + + -
63A LEU* 4.9 5.6 - - + -
65A LYS* 6.5 0.2 - - + -
21B MET* 3.8 34.8 - - + -
24B MET* 3.8 25.1 - - + -
25B ARG* 3.9 20.4 - - + -
28B ILE* 4.0 2.0 - - + -
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Residues in contact with ALA 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLU 3.0 13.8 + - - +
14A GLU* 3.5 20.4 - - - +
16A PHE* 1.3 74.6 - - - +
18A GLY* 1.3 64.4 + - - +
20A SER* 3.2 3.6 + - - -
21A MET* 3.0 37.2 + - + +
17B ALA* 5.7 1.1 - - + -
21B MET* 3.7 32.8 - - + -
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Residues in contact with GLY 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 2.8 18.9 + - - -
15A ALA* 3.1 4.7 + - - -
17A ALA* 1.3 77.1 - - - +
19A GLU* 1.3 57.3 + - - +
21A MET* 3.5 12.3 + - - +
22A ALA* 3.1 27.9 + - - +
25A ARG* 4.7 2.4 + - - -
83B GLU* 4.8 6.0 - - - +
87B MET* 5.2 9.0 - - - -
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Residues in contact with GLU 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ALA 2.8 22.7 + - - +
16A PHE 3.9 0.7 - - - +
18A GLY* 1.3 70.5 - - - +
20A SER* 1.3 61.1 + - - +
22A ALA* 4.5 2.4 - - - +
23A HIS* 2.9 31.9 + - - +
52A GLU* 2.9 24.3 - - - +
55A HIS* 3.4 14.7 - - + +
56A ALA* 3.7 20.0 - - + -
59A HIS* 4.1 7.2 - - + -
202A ZN 2.3 37.3 - - - -
24B MET* 4.1 2.2 - - - +
83B GLU* 3.5 6.3 - - - +
88B TYR* 2.5 29.9 + - - +
114B GLU* 3.0 3.8 - - - +
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 2.8 26.8 + - - -
17A ALA 3.5 4.3 - - - -
19A GLU* 1.3 78.4 - - - +
21A MET* 1.3 57.4 + - - +
23A HIS* 3.4 3.3 + - - +
24A MET* 2.9 30.0 + - - +
20B SER* 3.6 29.3 - - - +
21B MET* 3.8 13.4 - - - +
24B MET* 3.3 32.5 - - - +
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Residues in contact with MET 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 5.1 5.6 - - - +
17A ALA* 3.0 32.7 + - + +
18A GLY* 3.8 9.2 - - - +
20A SER* 1.3 73.7 - - - +
22A ALA* 1.3 54.1 + - - +
24A MET* 3.2 2.4 + - - +
25A ARG* 2.7 58.3 + - - +
13B GLU 5.1 1.6 - - - +
16B PHE* 3.8 23.6 - - + -
17B ALA* 3.8 31.4 - - + -
20B SER* 3.9 15.9 - - - +
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Residues in contact with ALA 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 3.1 17.0 + - - +
19A GLU* 3.8 6.3 - - - +
20A SER 3.3 0.2 - - - -
21A MET* 1.3 71.6 - - - +
23A HIS* 1.3 66.4 + - - +
25A ARG* 3.3 22.2 + - - +
26A TYR* 2.9 50.9 + - + +
52A GLU* 4.3 10.5 - - + +
80B GLU* 5.6 0.4 - - - +
83B GLU* 4.9 9.2 - - - +
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Residues in contact with HIS 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU 2.9 18.4 + - - +
20A SER 3.6 2.2 - - - +
22A ALA* 1.3 77.2 - - - +
24A MET* 1.3 64.1 + - - +
26A TYR* 3.3 2.9 + - - +
27A LEU* 3.1 39.0 + - + +
49A ALA* 2.6 40.1 + - + +
50A TYR* 4.7 1.6 - - - -
52A GLU* 3.9 13.5 - - + +
53A PHE* 4.0 9.3 - - + +
23B HIS* 3.1 39.1 + + - -
24B MET* 3.4 22.0 - - + +
27B LEU* 3.7 15.4 - - + +
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Residues in contact with MET 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER 2.9 17.2 + - - +
21A MET 3.5 2.9 - - - +
23A HIS* 1.3 77.4 - - + +
25A ARG* 1.3 66.4 + - - +
27A LEU* 3.2 5.6 + - - +
28A ILE* 3.1 30.9 + - + +
16B PHE* 3.8 10.1 - - + -
20B SER* 3.5 24.9 - - - +
23B HIS* 3.5 42.8 - - + +
52B GLU 4.3 0.7 - - - +
53B PHE* 3.5 46.9 - - - +
56B ALA* 3.8 22.7 - - + -
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Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLY 4.7 2.2 + - - -
21A MET* 2.7 39.4 + - - +
22A ALA* 3.7 31.3 - - - +
24A MET* 1.3 71.7 - - - +
26A TYR* 1.3 65.9 + - + +
28A ILE* 3.2 10.1 + - - +
29A PHE* 2.8 52.2 + - + -
16B PHE* 4.0 9.5 - - + -
60B PHE* 3.5 35.0 - - + -
65B LYS* 6.1 0.2 - - - -
75B MET* 5.7 8.6 + - - +
76B GLY* 6.3 0.8 - - - -
79B GLY* 5.2 12.1 - - - -
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Residues in contact with TYR 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ALA* 2.9 32.6 + - + +
23A HIS 3.7 3.6 - - - +
24A MET 3.2 0.2 - - - -
25A ARG* 1.3 86.9 + - + +
27A LEU* 1.3 56.7 + - - +
29A PHE* 3.7 13.2 - + - -
30A ALA* 2.9 29.5 + - - +
45A PHE* 3.5 33.4 - + + +
48A ILE* 3.8 9.6 - - + -
49A ALA* 3.9 6.1 - - + -
52A GLU* 3.4 30.3 - - + -
76B GLY* 3.7 20.4 + - - -
79B GLY* 5.4 0.9 - - - -
80B GLU* 2.6 28.4 + - - +
121B TYR* 3.4 35.7 - + - -
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Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A HIS* 3.1 44.7 + - + +
24A MET* 3.2 7.8 + - - +
26A TYR* 1.3 73.5 - - - +
28A ILE* 1.3 64.7 + - - +
30A ALA* 3.8 4.9 - - - +
31A GLU* 3.3 22.0 + - - +
46A ARG* 4.8 22.0 + - + +
49A ALA* 4.0 17.5 - - + -
23B HIS* 3.7 19.5 - - + +
53B PHE* 4.0 25.4 - - + -
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Residues in contact with ILE 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A MET* 3.1 32.8 + - + +
25A ARG* 3.5 8.5 - - - +
27A LEU* 1.3 75.7 - - - +
29A PHE* 1.3 64.8 + - + +
31A GLU* 3.6 8.5 + - - +
32A LYS* 3.2 20.3 + - - +
16B PHE* 4.1 13.0 - - + -
53B PHE* 3.8 20.4 - - + -
57B LYS* 3.8 37.7 - - + +
60B PHE* 4.1 21.8 - - + -
66B LEU* 4.0 29.0 - - + +
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 2.8 33.4 + - + +
26A TYR* 3.7 13.9 - + - +
28A ILE* 1.3 77.7 - - + +
30A ALA* 1.3 58.6 + - - +
32A LYS* 3.3 5.2 + - - +
33A ALA* 2.8 29.5 + - - +
45A PHE* 3.6 33.6 - + + -
60B PHE* 3.8 35.7 - + - -
65B LYS 4.4 3.6 - - - -
66B LEU* 3.9 8.1 - - + -
69B THR* 5.2 0.3 + - - -
72B ASN* 3.3 60.9 + - + +
75B MET* 4.5 11.2 - - + -
76B GLY* 4.6 7.2 - - - -
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Residues in contact with ALA 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR 2.9 18.1 + - - +
27A LEU* 3.8 7.4 - - - +
28A ILE 3.3 0.4 - - - -
29A PHE* 1.3 76.4 - - - +
31A GLU* 1.3 56.5 + - - +
33A ALA 3.2 1.2 + - - -
34A GLU* 3.0 26.7 + - - +
42A ALA* 3.4 33.2 - - - +
45A PHE* 3.7 13.2 - - + -
46A ARG* 3.7 26.0 - - + +
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Residues in contact with GLU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU 3.3 12.6 + - - +
28A ILE 3.7 4.9 - - - +
30A ALA* 1.3 78.4 - - - +
32A LYS* 1.3 61.6 + - - +
34A GLU* 3.4 6.3 + - - +
35A GLN* 3.2 46.5 + - - +
46A ARG* 3.7 12.7 - - - +
50B TYR* 5.2 3.5 + - - -
53B PHE* 3.3 18.1 - - + -
57B LYS* 2.9 44.2 + - - +
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Residues in contact with LYS 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE 3.2 14.6 + - - +
29A PHE 3.7 6.7 - - - +
31A GLU* 1.3 73.2 - - - +
33A ALA* 1.3 65.3 + - - +
35A GLN* 3.3 21.1 + - + +
36A GLU* 3.1 46.6 + - + +
66B LEU* 4.1 24.2 + - + +
67B GLY 3.3 31.2 - - - +
68B LYS* 4.6 2.2 - - - +
69B THR* 4.3 0.4 - - - +
72B ASN* 3.8 13.0 - - - +
----------------------------------------------------------
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Residues in contact with ALA 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE 2.8 17.4 + - - +
30A ALA* 3.2 5.6 + - - +
32A LYS* 1.3 76.1 - - - +
34A GLU* 1.3 60.6 + - - +
36A GLU* 3.4 2.3 + - - +
37A GLY 3.2 4.9 + - - -
38A PHE* 2.8 33.3 + - + +
41A ILE* 3.9 14.1 - - + -
42A ALA* 3.9 22.2 - - - +
45A PHE* 4.4 1.6 - - + -
69B THR* 3.5 21.0 + - + +
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ALA 3.0 11.4 + - - +
31A GLU* 3.6 11.4 - - + +
32A LYS 3.3 0.2 - - - -
33A ALA* 1.3 75.6 - - - +
35A GLN* 1.3 60.8 + - + +
37A GLY* 3.1 18.7 + - - -
38A PHE 4.7 3.1 - - - +
39A PRO* 4.9 10.7 - - + -
42A ALA* 4.0 16.3 - - + +
46A ARG* 4.4 12.1 - - - +
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Residues in contact with GLN 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLU* 3.2 37.6 + - + +
32A LYS* 3.6 27.1 + - + +
33A ALA 3.3 0.2 - - - -
34A GLU* 1.3 78.3 - - + +
36A GLU* 1.3 58.9 + - + +
37A GLY 3.3 0.8 + - - -
57B LYS* 5.7 0.8 - - - +
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Residues in contact with GLU 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LYS* 3.1 29.1 + - + +
33A ALA 3.4 0.4 + - - -
34A GLU 3.2 0.4 - - - -
35A GLN* 1.3 75.7 - - + +
37A GLY* 1.3 61.4 + - - +
38A PHE* 3.6 26.6 - - + -
68B LYS* 3.3 31.6 - - - +
69B THR* 2.5 44.1 + - - -
70B PRO* 5.5 0.4 - - - -
----------------------------------------------------------
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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