Contacts of the helix formed by residues 3 - 34 (chain A) in PDB entry 1EUM
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 3 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 1.3 72.5 - - - +
4A PRO* 1.3 79.2 - - + +
5A GLU* 4.2 5.8 - - + +
6A MET* 2.7 25.0 + - + +
7A ILE* 3.0 11.0 + - - +
111A ASN* 3.0 59.2 + - + +
113A ASP* 5.3 1.9 + - + -
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Residues in contact with PRO 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU 3.6 3.9 - - - +
3A LYS* 1.3 90.9 - - + +
5A GLU* 1.3 62.6 + - - +
7A ILE* 3.2 17.4 + - + +
8A GLU* 3.1 22.7 + - - +
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Residues in contact with GLU 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LYS* 3.0 2.8 + - + -
4A PRO* 1.3 81.5 - - - +
6A MET* 1.3 66.8 + - - +
8A GLU* 3.5 15.1 + - - +
9A LYS* 3.2 46.2 + - + +
107A ALA* 4.4 7.7 - - - +
111A ASN* 3.6 33.4 + - - +
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Residues in contact with MET 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 4.7 7.0 - - + -
3A LYS* 2.7 26.4 + - + +
5A GLU* 1.3 76.0 - - - +
7A ILE* 1.3 66.5 + - - +
9A LYS* 3.2 3.3 + - + +
10A LEU* 2.9 32.0 + - + +
104A LEU* 3.4 35.9 - - + +
107A ALA* 4.1 16.2 - - + +
108A ALA* 3.8 35.7 - - + +
111A ASN* 4.6 10.8 - - + +
113A ASP* 3.2 25.1 - - + +
116A THR* 4.1 12.6 - - + +
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Residues in contact with ILE 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 3.6 39.0 - - + +
3A LYS 3.0 12.3 + - - +
4A PRO* 3.2 16.4 + - + +
6A MET* 1.3 78.0 - - - +
8A GLU* 1.3 59.8 + - + +
10A LEU* 3.4 1.9 + - - +
11A ASN* 3.0 31.8 + - + +
61A LEU* 4.3 15.3 - - + +
66A ASN* 3.5 33.0 - - + +
67A LEU 6.1 0.7 - - - +
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Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO 3.1 13.7 + - - +
5A GLU* 3.8 17.8 - - - +
6A MET 3.2 0.2 - - - -
7A ILE* 1.3 77.7 - - + +
9A LYS* 1.3 76.0 + - + +
11A ASN* 3.4 5.5 + - - +
12A GLU* 2.9 47.2 + - - +
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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
----------------------------------------------------------
5A GLU* 3.2 36.3 + - + +
6A MET* 3.2 3.3 + - + +
8A GLU* 1.3 90.6 - - + +
10A LEU* 1.3 58.1 + - - +
12A GLU* 3.3 13.7 + - - +
13A GLN* 2.9 28.4 + - - +
103A GLU* 5.0 16.0 + - + +
104A LEU* 3.7 27.8 - - + +
107A ALA* 4.8 16.5 - - + +
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Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A LEU* 3.8 18.6 - - + -
6A MET* 2.9 21.1 + - + +
7A ILE 3.8 3.4 - - - +
9A LYS* 1.3 77.4 - - - +
11A ASN* 1.3 57.3 + - - +
13A GLN* 3.0 6.1 + - - +
14A MET* 2.8 29.1 + - - +
57A LEU* 3.6 28.4 - - + +
60A TYR* 3.6 31.6 - - + -
61A LEU* 4.2 16.6 - - + -
104A LEU* 4.1 24.0 - - + -
116A THR* 4.2 17.7 - - + -
119A PHE* 4.5 8.1 - - + -
120A LEU* 4.5 3.1 - - + -
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Residues in contact with ASN 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 3.0 21.5 + - + +
8A GLU* 3.7 6.7 - - - +
9A LYS 3.3 0.2 - - - -
10A LEU* 1.3 75.7 - - - +
12A GLU* 1.3 63.5 + - - +
14A MET* 3.2 8.6 + - - +
15A ASN* 2.9 37.5 + - - +
61A LEU* 3.8 11.9 - - + +
67A LEU 4.6 0.5 - - - +
68A PRO* 3.4 10.0 - - - +
69A ARG* 2.8 53.3 + - - +
71A ASN* 4.3 7.7 - - - +
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Residues in contact with GLU 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU* 2.9 36.7 + - - +
9A LYS* 3.5 12.9 - - - +
11A ASN* 1.3 77.8 - - - +
13A GLN* 1.3 56.0 - - - +
15A ASN* 3.1 9.2 + - - +
16A LEU* 2.9 27.9 + - - +
71A ASN* 6.0 3.1 - - - +
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Residues in contact with GLN 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 13.8 + - - +
10A LEU* 3.5 8.1 - - - +
12A GLU* 1.3 75.8 - - - +
14A MET* 1.3 63.7 + - - +
16A LEU* 3.2 14.7 + - - +
17A GLU* 3.0 50.8 + - - +
57A LEU* 3.6 18.8 - - + -
97A ILE* 4.1 11.3 - - - +
100A LYS* 3.3 29.2 - - - +
101A ILE* 3.6 24.4 - - + +
104A LEU* 3.7 21.1 - - + +
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Residues in contact with MET 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU 2.8 12.1 + - - +
11A ASN* 3.4 16.8 - - - +
13A GLN* 1.3 77.0 - - - +
15A ASN* 1.3 86.7 + - - +
17A GLU* 3.3 3.1 + - - +
18A LEU* 3.1 18.6 + - + +
54A MET* 3.4 36.5 - - + +
57A LEU* 3.7 17.8 - - + +
58A PHE* 3.5 37.9 - - - +
61A LEU* 4.6 4.3 - - + -
68A PRO* 3.9 7.6 - - + -
69A ARG 3.6 22.0 - - - +
70A ILE* 4.2 11.4 - - + +
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Residues in contact with ASN 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASN* 2.9 32.5 + - - +
12A GLU* 3.5 9.3 - - - +
14A MET* 1.3 80.3 - - - +
16A LEU* 1.3 60.6 + - - +
18A LEU* 3.3 11.5 + - - +
19A TYR* 2.9 28.6 + - - +
69A ARG 3.1 21.0 + - - -
70A ILE* 3.6 7.3 - - - +
71A ASN* 2.9 44.4 + - + +
73A VAL* 5.6 1.9 - - - +
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Residues in contact with LEU 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLU 2.9 13.8 + - - +
13A GLN* 3.2 24.9 + - - +
15A ASN* 1.3 77.7 - - - +
17A GLU* 1.3 49.8 + - - +
19A TYR* 3.4 12.6 + - + +
20A SER* 2.7 51.3 + - - +
93A HIS* 4.2 13.9 - - + -
96A LEU* 4.6 13.0 - - + -
97A ILE* 4.5 14.4 - - + -
100A LYS* 3.9 30.1 - - + -
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Residues in contact with GLU 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 3.0 39.9 + - - +
14A MET 3.6 6.7 - - - +
15A ASN 3.3 0.2 - - - -
16A LEU* 1.3 73.2 - - - +
18A LEU* 1.3 60.8 + - - +
20A SER* 3.1 5.2 + - - -
21A SER* 2.8 30.1 + - - -
50A GLU* 2.5 35.5 - - - +
53A HIS* 3.4 18.4 + - + +
54A MET* 3.8 19.1 - - + +
57A LEU* 4.1 15.0 - - + -
97A ILE* 3.8 16.5 - - - +
101A ILE* 4.7 0.2 - - - +
123A TYR* 4.4 12.4 - - - -
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Residues in contact with LEU 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 3.1 13.2 + - + +
15A ASN* 3.5 14.4 - - - +
16A LEU 3.3 0.2 - - - -
17A GLU* 1.3 76.5 - - - +
19A TYR* 1.3 63.2 + - - +
21A SER* 3.1 14.2 + - - -
22A LEU* 3.1 29.5 + - + +
51A MET* 4.1 14.8 - - - -
54A MET* 3.8 33.3 - - + +
70A ILE* 3.7 31.0 - - + -
73A VAL* 4.1 20.2 - - + -
18F LEU* 5.9 0.2 - - + -
22F LEU* 3.8 21.1 - - + -
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Residues in contact with TYR 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ASN 2.9 13.2 + - - +
16A LEU* 3.5 15.9 - - + +
18A LEU* 1.3 77.8 - - - +
20A SER* 1.3 67.0 + - - +
22A LEU* 3.1 4.9 + - + +
23A LEU* 2.8 49.2 + - + +
73A VAL* 3.9 20.2 - - + +
74A GLU* 3.6 41.5 + - + -
75A SER 4.5 2.5 + - - -
76A PRO* 4.0 27.5 + - + +
93A HIS* 4.3 9.6 - + - -
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Residues in contact with SER 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A LEU* 2.7 27.7 + - - +
17A GLU* 3.1 6.7 + - - -
19A TYR* 1.3 78.4 - - - +
21A SER* 1.3 61.8 + - - +
23A LEU* 3.4 3.9 + - - +
24A TYR* 3.1 28.9 + - - -
50A GLU* 3.8 19.1 - - - -
93A HIS* 2.5 39.1 + - - -
97A ILE* 3.8 8.7 - - - +
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Residues in contact with SER 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLU 2.8 12.5 + - - -
18A LEU 3.4 9.2 - - - -
20A SER* 1.3 76.8 - - - +
22A LEU* 1.3 65.7 + - - +
24A TYR 3.4 1.7 + - - -
25A GLN* 3.1 18.2 + - - +
47A ALA* 2.8 36.2 + - - +
50A GLU* 4.0 9.1 - - - +
51A MET* 3.8 31.6 - - - +
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Residues in contact with LEU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 3.1 26.8 + - + +
19A TYR* 3.1 7.0 + - + +
21A SER* 1.3 78.8 - - - +
23A LEU* 1.3 60.7 + - - +
25A GLN* 3.3 7.8 + - + +
26A GLN* 2.9 30.7 + - - +
51A MET* 6.3 0.9 - - - -
73A VAL* 4.0 28.5 - - + -
76A PRO* 3.8 11.2 - - + +
18F LEU* 4.0 41.3 - - + -
22F LEU* 5.3 1.6 - - + -
51F MET* 5.7 2.7 - - + -
54F MET* 5.1 7.0 - - + -
70F ILE* 3.7 22.2 - - + +
73F VAL* 4.8 3.4 - - + -
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Residues in contact with LEU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 2.8 34.5 + - + +
20A SER* 3.5 5.2 - - - +
21A SER 3.3 0.2 - - - -
22A LEU* 1.3 77.8 - - - +
24A TYR* 1.3 64.2 + - + +
26A GLN* 3.3 2.3 + - - +
27A MET* 2.9 53.8 + - + +
76A PRO* 3.7 29.3 - - + +
80A TYR* 4.2 6.1 - - - +
93A HIS* 3.8 42.6 - - + +
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A SER 3.1 15.9 + - - +
21A SER 3.9 3.8 - - - +
23A LEU* 1.3 82.7 - - + +
25A GLN* 1.3 65.1 + - - +
27A MET* 3.8 20.6 - - - +
28A SER* 3.1 23.4 + - - -
43A LEU* 3.8 33.3 - - + +
46A HIS* 4.0 26.2 - - + -
47A ALA* 4.0 5.4 - - - -
50A GLU* 4.2 18.2 - - + -
90A THR* 4.1 14.7 + - - -
93A HIS* 3.0 34.6 - + - -
94A GLU* 2.9 34.7 + - + +
97A ILE* 4.2 0.5 - - - +
134A PHE* 5.2 5.6 - + - -
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Residues in contact with GLN 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A SER 3.1 14.1 + - - +
22A LEU* 3.3 14.1 + - + +
24A TYR* 1.3 76.2 - - - +
26A GLN* 1.3 60.6 + - - +
28A SER* 2.6 23.6 + - - -
29A ALA 3.3 4.2 + - - -
43A LEU 5.3 0.2 - - - -
44A ARG* 4.5 11.5 - - - +
47A ALA* 3.8 16.0 - - + +
54F MET* 4.7 10.6 - - + +
55F GLN* 3.1 40.8 + - - -
58F PHE* 3.3 51.4 - - + +
70F ILE* 3.9 12.1 - - + -
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Residues in contact with GLN 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU 2.9 17.1 + - - +
23A LEU 3.5 5.4 - - - +
25A GLN* 1.3 79.3 - - - +
27A MET* 1.3 62.7 + - + +
29A ALA* 3.2 18.5 + - - +
30A TRP* 3.3 11.1 + - - +
76A PRO* 3.9 14.0 - - + +
77A PHE* 3.9 38.8 - - + +
78A ALA 4.9 2.0 - - - +
80A TYR* 6.2 2.2 - - + -
58F PHE* 5.1 1.5 - - - -
67F LEU* 4.7 3.5 - - - +
68F PRO 3.0 19.1 + - - +
69F ARG* 3.7 2.2 - - - +
70F ILE* 2.8 49.3 + - + +
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Residues in contact with MET 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 2.9 39.4 + - + +
24A TYR* 3.3 19.0 + - - +
25A GLN 3.3 0.2 - - - -
26A GLN* 1.3 75.0 - - + +
28A SER* 1.3 64.2 + - - +
30A TRP* 3.1 9.0 + - - +
31A CYS* 3.0 23.4 + - - -
43A LEU* 4.0 13.9 - - + -
80A TYR* 3.1 39.5 - - + +
86A LEU* 3.8 17.1 - - + +
89A GLU* 4.1 12.3 - - + -
90A THR* 3.2 36.6 - - + +
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Residues in contact with SER 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A TYR 3.1 11.9 + - - -
25A GLN* 2.6 25.0 + - - -
27A MET* 1.3 75.3 - - - +
29A ALA* 1.3 55.6 + - - +
31A CYS* 3.0 5.6 + - - +
32A SER* 2.8 27.9 + - - -
40A ALA* 3.2 39.1 - - - +
43A LEU* 3.8 10.5 - - - +
44A ARG* 4.0 13.0 - - - +
58F PHE* 3.9 11.2 - - - -
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Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN 3.3 0.6 + - - +
26A GLN* 3.2 19.2 + - - +
27A MET 3.2 0.4 - - - -
28A SER* 1.3 81.2 + - - +
30A TRP* 1.3 62.8 + - - +
32A SER* 3.2 8.6 + - - -
33A TYR* 2.9 24.9 + - - +
58F PHE* 3.5 27.4 - - + -
62F THR* 4.7 2.8 - - - +
66F ASN 5.4 0.2 - - - +
67F LEU* 3.6 17.6 - - + +
68F PRO* 3.9 13.7 - - + -
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Residues in contact with TRP 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A GLN 3.3 6.9 + - - +
27A MET* 3.1 12.2 + - - +
29A ALA* 1.3 78.2 - - - +
31A CYS* 1.3 62.2 + - - +
33A TYR 3.5 0.2 + - - -
34A HIS* 2.8 80.1 + + + -
36A PHE* 4.2 15.3 - + - -
78A ALA 4.5 3.6 - - - -
79A GLU* 2.6 36.1 + - - -
80A TYR* 3.2 43.2 + + + +
81A SER 4.5 1.3 - - - -
82A SER* 3.6 25.1 - - - -
83A LEU* 3.9 13.5 - - + -
86A LEU* 3.6 21.1 - - + -
67F LEU* 3.9 15.4 - - + +
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Residues in contact with CYS 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A MET 3.0 15.8 + - - -
28A SER 3.0 9.3 + - - +
30A TRP* 1.3 80.1 - - - +
32A SER* 1.3 61.0 + - - +
34A HIS 3.1 2.4 + - - -
35A THR 3.0 5.2 + - - -
36A PHE* 2.7 49.3 + - + +
39A ALA* 3.8 20.2 - - - -
40A ALA* 3.7 8.3 - - + +
43A LEU* 3.8 16.6 - - - -
83A LEU* 3.9 17.9 - - - -
86A LEU* 3.9 11.0 - - - -
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Residues in contact with SER 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A SER 2.8 13.4 + - - -
29A ALA* 3.5 7.4 - - - -
31A CYS* 1.3 71.5 - - - +
33A TYR* 1.3 63.9 + - - +
35A THR* 2.9 13.3 + - - +
37A GLU* 3.4 33.3 + - - +
40A ALA* 3.4 17.7 - - - +
44A ARG* 4.3 7.6 + - - -
58F PHE* 5.9 0.9 - - - -
62F THR* 4.0 30.0 + - - +
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Residues in contact with TYR 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ALA 2.9 16.2 + - - +
30A TRP 3.7 4.0 - - - +
32A SER* 1.3 78.3 - - - +
34A HIS* 1.3 78.6 + + - +
35A THR* 3.2 9.2 + - - +
62F THR* 5.8 0.2 - - - -
65F GLY* 3.4 28.0 - - - -
66F ASN* 4.0 22.1 + - - +
67F LEU* 3.9 30.1 - - + -
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Residues in contact with HIS 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A TRP* 2.8 86.6 + + + +
31A CYS 4.0 1.8 - - - +
32A SER 3.1 0.4 - - - -
33A TYR* 1.3 98.4 + + + +
35A THR* 1.3 80.3 + - - +
36A PHE* 3.4 18.6 + - + -
79A GLU* 4.2 6.4 + - - -
80A TYR 5.1 0.7 - - - -
67F LEU* 6.0 0.2 - - - +
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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