Contacts of the helix formed by residues 4 - 35 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H GLY* 1.3 71.1 - - - -
5H THR* 1.3 64.5 + - - +
6H LYS* 3.0 6.1 + - - +
7H VAL* 2.9 44.4 + - + +
8H ILE* 3.2 20.9 + - - +
65H LEU* 5.4 1.2 - - - +
107H TYR* 3.0 27.5 + - - -
111H VAL* 3.8 20.1 - - + +
113H ASP* 5.5 3.6 + - + +
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Residues in contact with THR 5 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LYS* 4.7 12.3 + - - -
3H GLY 3.5 3.9 + - - -
4H ASP* 1.3 74.5 + - - +
6H LYS* 1.3 58.0 + - + +
8H ILE* 3.1 12.9 + - + +
9H ASN* 2.9 39.9 + - - +
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Residues in contact with LYS 6 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ASP* 3.0 10.7 + - - +
5H THR* 1.3 76.7 - - - +
7H VAL* 1.3 64.4 + - - +
9H ASN* 3.2 18.7 + - + +
10H TYR* 2.9 50.5 + - + -
103H GLU* 5.2 1.0 + - - -
107H TYR* 3.4 33.5 - - + +
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Residues in contact with VAL 7 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H ASP* 2.9 30.7 + - + +
6H LYS* 1.3 76.8 - - - +
8H ILE* 1.3 57.8 + - - +
10H TYR* 3.2 8.5 + - + +
11H LEU* 2.8 47.8 + - + +
65H LEU* 4.3 4.0 - - + -
107H TYR* 3.7 19.0 - - + -
108H ALA* 4.4 7.9 - - + -
111H VAL* 3.7 17.3 - - + -
113H ASP* 3.4 29.4 - - + +
116H SER* 4.1 7.9 - - - +
120H MET* 5.8 1.1 - - + -
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Residues in contact with ILE 8 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H GLY 4.4 9.2 - - - +
4H ASP 3.2 15.3 + - - +
5H THR* 3.1 12.4 + - - +
7H VAL* 1.3 77.0 - - - +
9H ASN* 1.4 57.8 + - - +
11H LEU* 3.2 8.2 + - - +
12H ASN* 2.9 36.5 + - - +
62H ILE* 4.0 25.6 - - + -
65H LEU* 3.7 43.5 - - + +
66H GLU 4.6 0.4 - - - -
67H GLY* 4.1 19.7 - - - +
68H LEU 4.7 1.1 - - - +
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Residues in contact with ASN 9 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H THR* 2.9 33.3 + - - +
6H LYS* 3.2 22.3 + - + +
8H ILE* 1.4 76.9 - - - +
10H TYR* 1.3 57.4 + - + +
12H ASN* 3.2 8.9 + - - +
13H LYS* 2.9 29.0 + - - +
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Residues in contact with TYR 10 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6H LYS* 2.9 48.2 + - + -
7H VAL* 3.4 9.2 - - + +
9H ASN* 1.3 76.3 - - + +
11H LEU* 1.3 55.6 + - + +
13H LYS* 3.0 21.6 + - + +
14H LEU* 2.8 40.5 + - + +
100H ASN* 4.8 4.3 - - + -
103H GLU* 2.6 47.8 + - + +
104H ALA* 3.7 32.3 - - + -
107H TYR* 3.7 39.9 - + + +
120H MET* 5.7 0.4 - - + -
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Residues in contact with LEU 11 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7H VAL* 2.8 34.0 + - + +
8H ILE* 3.5 6.5 - - - +
10H TYR* 1.3 73.3 - - + +
12H ASN* 1.3 56.9 + - - +
14H LEU* 3.4 5.0 + - + +
15H LEU* 2.8 29.8 + - - +
58H TYR* 4.1 24.3 - - + +
61H ARG* 3.8 28.5 - - + -
62H ILE* 3.6 24.7 - - + -
65H LEU* 3.9 19.7 - - + -
116H SER* 4.2 5.6 - - - +
119H MET* 5.6 1.6 - - - -
120H MET* 4.0 29.8 - - + -
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Residues in contact with ASN 12 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8H ILE* 2.9 28.2 + - - +
9H ASN* 3.7 8.4 + - - +
11H LEU* 1.3 73.2 - - - +
13H LYS* 1.3 60.9 + - - +
15H LEU* 3.3 7.2 + - - +
16H GLY* 2.8 25.5 + - - -
62H ILE* 3.3 17.7 - - - +
68H LEU 3.0 23.2 + - - -
69H PRO* 3.3 0.2 - - - +
70H ASN* 2.7 42.6 + - + +
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Residues in contact with LYS 13 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9H ASN 2.9 13.4 + - - +
10H TYR* 3.0 24.4 + - + +
12H ASN* 1.3 78.3 - - - +
14H LEU* 1.3 62.5 + - + +
16H GLY* 3.1 3.7 + - - -
17H ASN* 3.0 23.7 + - - +
100H ASN* 3.5 44.2 + - + +
103H GLU* 5.6 2.2 - - - -
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Residues in contact with LEU 14 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H TYR* 2.8 24.8 + - + +
11H LEU* 3.7 3.1 - - + +
13H LYS* 1.3 71.1 - - + +
15H LEU* 1.3 65.8 + - - +
17H ASN* 2.9 21.4 + - - +
18H GLU* 3.0 15.5 + - - +
58H TYR* 3.5 33.4 - - + +
97H GLY 4.6 0.2 - - - +
100H ASN* 3.6 32.8 - - + +
101H LEU* 3.8 25.1 - - + +
104H ALA* 3.9 10.3 - - + -
120H MET* 3.6 32.1 - - - -
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Residues in contact with LEU 15 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H LEU 2.8 22.1 + - - +
12H ASN* 3.4 18.4 - - - +
14H LEU* 1.3 71.5 - - - +
16H GLY* 1.3 57.6 + - - +
18H GLU* 3.1 3.0 + - - +
19H LEU* 2.9 48.8 + - + +
55H ALA* 3.6 40.6 - - + +
58H TYR* 3.8 14.3 - - + -
59H ILE* 3.9 21.8 - - + -
62H ILE* 4.3 4.7 - - + -
69H PRO* 4.2 3.6 - - + -
70H ASN 3.8 22.7 - - - +
71H LEU* 4.1 5.8 - - + -
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Residues in contact with GLY 16 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12H ASN 2.8 14.5 + - - -
13H LYS* 3.1 6.2 + - - -
15H LEU* 1.3 76.7 - - - +
17H ASN* 1.3 61.0 + - - +
19H LEU* 3.3 14.5 + - - +
20H VAL* 3.2 26.9 + - - +
70H ASN 5.3 1.8 + - - -
73H ASP 5.1 6.0 - - - +
74H LEU* 5.1 0.7 - - - +
75H GLY 5.1 2.0 + - - -
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Residues in contact with ASN 17 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H LYS* 3.0 18.0 + - - +
14H LEU* 2.9 16.0 + - - +
16H GLY* 1.3 76.1 - - - +
18H GLU* 1.3 65.9 + - + +
20H VAL* 3.3 10.8 + - - +
21H ALA* 3.0 21.7 + - - +
93H LEU* 5.0 7.7 - - + +
96H ASP 5.5 0.2 - - - -
97H GLY* 3.6 23.7 - - - -
100H ASN* 2.9 35.9 + - - +
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Residues in contact with GLU 18 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 3.0 17.4 + - - +
15H LEU 3.7 5.2 - - - +
17H ASN* 1.3 77.6 - - - +
19H LEU* 1.3 59.3 + - - +
21H ALA* 3.2 4.2 + - - +
22H ILE* 2.8 35.1 + - - +
51H GLU* 2.9 47.9 - - - +
54H HIS* 3.3 19.0 + - + +
55H ALA* 4.3 8.3 - - + +
58H TYR* 3.7 21.4 + - + -
101H LEU* 5.2 2.6 - - - +
123H ILE* 3.8 10.7 - - - +
127H GLU* 2.7 20.8 - - - +
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Residues in contact with LEU 19 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G ASN* 4.8 4.5 - - - +
15H LEU* 2.9 54.5 + - + +
16H GLY* 3.3 18.4 + - - +
17H ASN 3.2 0.2 - - - -
18H GLU* 1.3 79.9 - - - +
20H VAL* 1.3 61.3 + - - +
22H ILE* 3.7 5.8 + - + +
23H ASN* 3.6 17.7 + - - -
55H ALA* 4.7 3.1 - - + -
70H ASN 4.3 11.0 - - - +
71H LEU* 4.0 24.5 - - + +
73H ASP 4.5 11.7 - - - +
74H LEU* 3.8 18.5 - - + +
200H HEM 3.7 33.4 - - + -
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Residues in contact with VAL 20 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H GLY 3.2 18.4 + - - +
17H ASN* 3.3 8.0 + - - +
19H LEU* 1.3 76.6 - - - +
21H ALA* 1.3 58.5 + - - +
23H ASN* 3.2 4.5 + - - +
24H GLN* 2.9 26.6 + - - +
74H LEU* 3.8 8.4 - - + +
75H GLY* 3.9 27.8 - - - +
76H LYS 3.8 15.3 - - - +
77H LEU* 3.7 25.0 - - + +
93H LEU* 3.7 26.7 - - + -
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Residues in contact with ALA 21 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H ASN 3.0 14.4 + - - +
18H GLU* 3.6 8.7 - - - +
20H VAL* 1.3 75.4 - - - +
22H ILE* 1.3 56.2 + - - +
24H GLN* 4.4 0.9 - - - +
25H TYR* 2.8 47.7 + - + +
51H GLU* 3.8 24.9 - - + +
93H LEU* 3.8 22.0 - - + -
94H GLU* 5.6 1.8 - - - +
----------------------------------------------------------
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Residues in contact with ILE 22 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H GLU 2.8 23.9 + - - +
19H LEU* 3.8 7.4 - - - +
20H VAL 3.3 0.2 - - - -
21H ALA* 1.3 72.6 - - - +
23H ASN* 1.3 69.8 + - - +
26H PHE* 3.1 16.8 + - - +
48H SER* 2.8 31.5 + - - +
51H GLU* 3.6 12.5 - - + +
52H MET* 3.6 45.5 - - + +
55H ALA* 4.1 11.2 - - + -
200H HEM 3.8 47.3 - - + -
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Residues in contact with ASN 23 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G LEU* 4.8 6.4 - - - +
71G LEU* 3.5 45.6 - - + +
19H LEU 3.6 9.5 + - - +
20H VAL 3.2 7.2 + - - +
22H ILE* 1.3 78.5 - - - +
24H GLN* 1.3 67.0 + - - +
26H PHE* 3.3 2.9 + - - +
27H LEU* 3.0 26.5 + - - +
74H LEU* 3.8 12.3 - - - +
77H LEU* 4.4 11.0 - - + -
200H HEM 3.0 36.0 - - - +
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Residues in contact with GLN 24 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H VAL* 2.9 19.7 + - - +
21H ALA 4.0 1.8 - - - +
23H ASN* 1.3 77.3 - - - +
25H TYR* 1.3 63.5 + - - +
27H LEU* 3.5 0.7 + - - +
28H HIS* 3.0 40.6 + - + +
76H LYS 4.8 0.5 - - - +
77H LEU* 3.8 14.8 - - + -
78H ASN* 3.0 33.9 + - - +
79H ILE* 4.5 8.7 - - + -
89H SER* 3.1 33.0 + - - -
90H ASP* 2.9 27.1 + - - +
93H LEU* 4.0 18.2 - - + +
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Residues in contact with TYR 25 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ALA* 2.8 29.5 + - + +
24H GLN* 1.3 78.4 - - - +
26H PHE* 1.3 56.9 + - - +
28H HIS* 3.4 1.7 + - - +
29H ALA* 2.8 30.0 + - - +
44H GLU* 3.4 38.5 - - - +
47H GLU* 3.6 33.8 + - + -
48H SER* 3.8 9.4 - - - +
51H GLU* 3.9 25.6 - - + -
90H ASP* 3.5 29.1 - - + +
93H LEU* 6.1 1.8 - - + -
94H GLU* 2.4 40.1 + - + +
130H HIS* 4.0 3.5 - - - +
134H LEU* 3.6 12.8 - - + +
----------------------------------------------------------
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Residues in contact with PHE 26 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G ASP* 3.3 44.4 - - + -
59G ILE* 3.9 13.9 - - + -
71G LEU* 5.2 1.6 - - + -
22H ILE 3.1 18.8 + - - +
23H ASN* 3.8 5.2 - - - +
25H TYR* 1.3 75.2 - - - +
27H LEU* 1.3 65.3 + - - +
29H ALA* 3.3 5.2 + - + +
30H ARG* 3.0 39.6 + - + +
45H TYR* 3.6 27.4 - + - -
48H SER* 3.6 19.9 + - - +
52H MET* 5.0 0.2 - - + -
200H HEM 3.5 52.7 - - + -
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Residues in contact with LEU 27 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G ILE* 4.4 6.7 - - + -
63G LEU* 4.3 6.5 - - + -
69G PRO* 3.8 43.5 - - + +
71G LEU* 4.0 24.3 - - + +
23H ASN 3.0 17.1 + - - +
24H GLN 4.0 2.9 - - - +
26H PHE* 1.3 76.7 - - - +
28H HIS* 1.3 64.1 + - - +
30H ARG 3.2 1.6 + - - -
31H MET* 2.9 40.2 + - + +
77H LEU* 5.6 0.2 - - + -
79H ILE* 3.6 44.0 - - + -
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Residues in contact with HIS 28 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H GLN* 3.0 33.2 + - + +
25H TYR 3.7 0.4 - - - +
27H LEU* 1.3 76.6 - - - +
29H ALA* 1.3 63.3 + - - +
31H MET* 3.1 3.9 + - - +
32H PHE* 2.9 31.9 + + + -
44H GLU* 3.1 16.4 - - - +
78H ASN 4.4 0.9 - - - -
79H ILE* 2.7 43.9 + - + -
86H MET* 3.2 48.0 + - + +
90H ASP* 2.7 36.8 + - - -
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Residues in contact with ALA 29 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H TYR 2.8 18.7 + - - +
26H PHE* 3.4 8.3 - - + +
28H HIS* 1.3 76.1 - - - +
30H ARG* 1.3 60.7 + - + +
32H PHE* 3.3 4.2 + - - +
33H LYS 2.9 22.0 + - - -
41H ASN* 3.0 26.0 - - - +
44H GLU* 3.9 8.6 - - + +
45H TYR* 3.6 32.8 - - + +
----------------------------------------------------------
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Residues in contact with ARG 30 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56G ASP* 2.6 47.3 + - - +
59G ILE* 4.1 9.9 - - + -
60G GLU* 2.9 32.2 + - + +
63G LEU* 3.7 20.7 - - + +
26H PHE* 3.0 34.8 + - + +
27H LEU 3.2 0.9 + - - +
29H ALA* 1.3 72.8 - - - +
31H MET* 1.3 60.1 + - - +
33H LYS* 3.5 13.5 - - - +
34H ASN* 2.9 28.1 + - - +
41H ASN* 3.4 30.3 + - - +
45H TYR* 3.3 34.6 - - - -
----------------------------------------------------------
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Residues in contact with MET 31 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G LEU* 4.2 17.0 - - + -
69G PRO* 6.2 0.2 - - - -
27H LEU* 2.9 34.8 + - + +
28H HIS* 3.3 7.6 - - - +
30H ARG* 1.3 73.8 - - - +
32H PHE* 1.3 65.4 + - - +
34H ASN* 3.1 6.5 + - - +
35H TRP* 2.9 48.9 + - + -
79H ILE* 3.7 22.2 - - + -
80H GLY 3.8 15.9 - - - +
81H GLU* 4.9 2.0 - - - +
86H MET* 3.7 33.4 - - + -
----------------------------------------------------------
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Residues in contact with PHE 32 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H HIS* 2.9 25.6 + - + -
29H ALA 3.4 6.1 - - - +
31H MET* 1.3 74.0 - - - +
33H LYS* 1.3 60.3 + - - +
35H TRP* 3.2 13.4 + + - -
36H GLY 3.0 4.2 + - - -
37H LEU* 2.8 36.4 + - + +
40H LEU* 3.6 39.7 - - + -
41H ASN 3.8 12.3 - - - +
44H GLU* 3.9 26.7 - - + -
83H VAL* 4.0 21.1 - - + -
86H MET* 3.4 39.9 - - + -
87H LEU* 3.9 18.6 - - + -
----------------------------------------------------------
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Residues in contact with LYS 33 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G GLU* 3.4 29.6 - - + -
29H ALA 2.9 7.1 + - - +
30H ARG* 3.5 20.2 - - + +
32H PHE* 1.3 72.3 - - - +
34H ASN* 1.3 69.1 + - - +
36H GLY* 2.9 14.8 + - - +
37H LEU 4.8 2.9 - - - +
38H LYS* 5.3 3.0 - - + +
41H ASN* 3.5 39.9 - - - +
----------------------------------------------------------
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Residues in contact with ASN 34 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G GLU 5.1 0.8 + - - -
63G LEU* 4.2 24.0 - - + +
64G PHE* 3.9 30.9 - - - +
30H ARG 2.9 17.6 + - - +
31H MET* 3.1 6.0 + - - +
33H LYS* 1.3 78.8 - - - +
35H TRP* 1.3 72.5 + - + +
36H GLY* 3.2 1.7 + - - -
----------------------------------------------------------
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Residues in contact with TRP 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H MET* 2.9 34.5 + - + -
32H PHE* 3.2 24.0 + + - +
34H ASN* 1.3 85.6 + - - +
36H GLY* 1.3 61.0 + - - +
37H LEU* 3.2 26.1 + - + +
81H GLU 3.4 26.0 - - - -
82H ASP* 4.3 2.5 - - - -
83H VAL* 4.4 10.5 - - + -
86H MET* 3.7 33.4 - - + -
----------------------------------------------------------
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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