Contacts of the helix formed by residues 4 - 35 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLY* 1.3 72.2 - - - -
5C THR* 1.3 64.7 + - - +
6C LYS* 3.0 6.5 + - - +
7C VAL* 2.9 43.9 + - + +
8C ILE* 3.2 20.3 + - - +
65C LEU* 5.4 0.4 - - - +
107C TYR* 2.9 26.7 + - - -
111C VAL* 3.8 19.2 - - + +
113C ASP* 5.5 3.4 + - + +
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Residues in contact with THR 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C LYS* 4.7 12.1 + - - -
3C GLY 3.5 4.1 + - - -
4C ASP* 1.3 73.8 - - - +
6C LYS* 1.3 58.0 + - - +
8C ILE* 3.2 14.9 + - + +
9C ASN* 2.9 40.6 + - - +
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Residues in contact with LYS 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ASP* 3.0 11.1 + - - +
5C THR* 1.3 77.0 - - - +
7C VAL* 1.3 61.0 + - - +
9C ASN* 3.2 19.6 + - + +
10C TYR* 2.9 57.0 + - + -
107C TYR* 3.4 32.4 - - + +
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Residues in contact with VAL 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ASP* 2.9 31.1 + - + +
6C LYS* 1.3 76.2 - - - +
8C ILE* 1.3 57.1 + - - +
10C TYR* 3.2 9.1 + - + +
11C LEU* 2.8 47.6 + - + +
65C LEU* 4.2 4.0 - - + -
107C TYR* 3.7 10.8 - - + -
108C ALA* 4.4 8.1 - - + -
111C VAL* 3.7 24.7 - - + -
113C ASP* 3.4 28.7 - - + +
116C SER* 4.1 7.9 - - - +
120C MET* 5.8 1.1 - - + -
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Residues in contact with ILE 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLY 4.4 9.0 - - - +
4C ASP 3.2 14.1 + - - +
5C THR* 3.2 12.0 + - + +
7C VAL* 1.3 77.5 - - - +
9C ASN* 1.3 59.2 + - - +
11C LEU* 3.2 8.0 + - - +
12C ASN* 2.9 37.2 + - - +
62C ILE* 4.0 25.1 - - + -
65C LEU* 3.7 43.3 - - + +
66C GLU 4.6 0.9 - - - +
67C GLY* 4.0 19.5 - - - +
68C LEU 4.7 1.1 - - - +
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Residues in contact with ASN 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C THR* 2.9 33.2 + - - +
6C LYS* 3.2 23.2 + - + +
8C ILE* 1.3 76.1 - - - +
10C TYR* 1.3 57.7 + - + +
12C ASN* 3.3 8.7 + - - +
13C LYS* 2.9 28.6 + - - +
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Residues in contact with TYR 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C LYS* 2.9 48.5 + - + -
7C VAL* 3.5 9.9 - - + +
9C ASN* 1.3 76.6 - - + +
11C LEU* 1.3 59.4 - - + +
13C LYS* 3.0 20.7 + - + +
14C LEU* 2.8 36.7 + - + +
100C ASN* 4.8 3.8 - - + -
103C GLU* 3.5 30.9 + - + +
104C ALA* 3.7 40.4 - - + -
107C TYR* 3.7 39.6 - + + +
120C MET* 5.7 0.2 - - - -
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Residues in contact with LEU 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C VAL* 2.8 34.5 + - + +
8C ILE* 3.5 5.6 - - - +
10C TYR* 1.3 74.6 - - + +
12C ASN* 1.3 57.4 + - - +
14C LEU* 3.4 4.2 + - - +
15C LEU* 2.8 29.8 + - - +
58C TYR* 4.1 25.5 - - + +
61C ARG* 3.8 28.5 - - + -
62C ILE* 3.6 24.2 - - + +
65C LEU* 3.9 19.1 - - + -
116C SER* 4.2 5.2 - - - +
119C MET* 5.6 1.3 - - - -
120C MET* 4.0 30.1 - - + -
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Residues in contact with ASN 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 2.9 28.7 + - - +
9C ASN* 3.7 7.8 + - - +
11C LEU* 1.3 73.8 - - - +
13C LYS* 1.3 60.5 + - - +
15C LEU* 3.3 6.7 + - - +
16C GLY* 2.8 26.0 + - - -
62C ILE* 3.3 16.7 - - - +
68C LEU 3.0 22.2 + - - -
69C PRO* 3.3 0.2 - - - +
70C ASN* 2.7 42.3 + - + +
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Residues in contact with LYS 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C ASN 2.9 14.2 + - - +
10C TYR* 3.0 23.3 + - + +
12C ASN* 1.3 77.7 - - - +
14C LEU* 1.3 64.3 + - + +
16C GLY* 3.1 4.7 + - - -
17C ASN* 3.0 23.2 + - - +
100C ASN* 3.5 42.4 + - + +
103C GLU* 5.7 2.5 - - - -
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C TYR* 2.8 25.9 + - + +
11C LEU* 3.7 2.9 - - + +
13C LYS* 1.3 73.4 - - + +
15C LEU* 1.3 62.1 + - - +
17C ASN* 2.9 21.6 + - - +
18C GLU* 3.0 15.9 + - - +
58C TYR* 3.6 33.9 - - + +
100C ASN* 3.6 33.2 - - + +
101C LEU* 3.8 25.1 - - + +
104C ALA* 3.9 11.4 - - + -
120C MET* 3.6 30.7 - - - -
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Residues in contact with LEU 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU 2.8 21.9 + - - +
12C ASN* 3.5 18.4 - - - +
14C LEU* 1.3 70.7 - - - +
16C GLY* 1.3 57.7 + - - +
18C GLU* 3.2 2.2 + - - +
19C LEU* 2.9 48.9 + - + +
55C ALA* 3.6 40.8 - - + +
58C TYR* 3.8 14.5 - - + -
59C ILE* 3.8 21.8 - - + -
62C ILE* 4.3 4.9 - - + -
69C PRO* 4.2 3.8 - - + -
70C ASN 3.8 22.7 - - - +
71C LEU* 4.1 5.6 - - + -
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Residues in contact with GLY 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ASN 2.8 14.7 + - - -
13C LYS* 3.1 6.0 + - - -
15C LEU* 1.3 77.4 - - - +
17C ASN* 1.3 61.0 + - - +
19C LEU* 3.3 14.8 + - - +
20C VAL* 3.1 27.9 + - - +
70C ASN 5.4 1.6 - - - -
73C ASP 5.1 6.0 - - - +
74C LEU* 5.1 0.7 - - - +
75C GLY 5.2 1.7 + - - -
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Residues in contact with ASN 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C LYS* 3.0 19.1 + - - +
14C LEU* 2.9 16.4 + - - +
16C GLY* 1.3 76.0 - - - +
18C GLU* 1.3 64.7 + - + +
20C VAL* 3.3 10.7 + - - +
21C ALA* 3.1 21.5 + - - +
93C LEU* 5.0 9.0 - - + +
96C ASP 5.5 0.2 - - - -
97C GLY* 3.6 23.9 - - - -
100C ASN* 2.9 35.5 + - - +
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Residues in contact with GLU 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU* 3.0 16.8 + - - +
15C LEU 3.7 4.9 - - - +
17C ASN* 1.3 78.0 - - - +
19C LEU* 1.3 59.5 + - - +
21C ALA* 3.2 4.4 + - - +
22C ILE* 2.8 34.4 + - - +
51C GLU* 2.9 47.8 - - - +
54C HIS* 3.3 19.3 + - + +
55C ALA* 4.3 7.6 - - + -
58C TYR* 3.7 20.3 + - + -
101C LEU* 5.2 2.8 - - - +
123C ILE* 3.7 11.3 - - - +
127C GLU* 2.7 20.5 - - - +
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Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 2.9 54.3 + - + +
16C GLY* 3.3 19.0 + - - +
17C ASN 3.2 0.4 - - - -
18C GLU* 1.3 80.0 - - - +
20C VAL* 1.3 62.0 + - - +
22C ILE* 3.8 11.3 - - + +
23C ASN* 3.6 18.1 + - - +
55C ALA* 4.7 4.9 - - + -
70C ASN 4.3 9.9 - - - +
71C LEU* 4.0 29.8 - - + +
73C ASP 4.5 11.4 - - - +
74C LEU* 3.8 18.7 - - + +
200C HEM 4.3 15.7 - - + -
23D ASN* 4.9 5.8 - - - +
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Residues in contact with VAL 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLY 3.1 18.9 + - - +
17C ASN* 3.9 7.6 - - - +
19C LEU* 1.3 73.4 - - - +
21C ALA* 1.3 64.7 + - - +
23C ASN* 3.2 5.4 + - - +
24C GLN* 2.9 22.1 + - - +
74C LEU* 3.8 8.4 - - + +
75C GLY* 3.9 27.6 - - - +
76C LYS 3.9 15.3 - - - +
77C LEU* 3.7 25.1 - - + +
93C LEU* 3.7 27.8 - - + -
----------------------------------------------------------
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Residues in contact with ALA 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C ASN 3.1 14.2 + - - +
18C GLU* 3.2 9.6 + - - +
20C VAL* 1.3 76.8 - - - +
22C ILE* 1.3 53.2 + - - +
24C GLN* 4.4 0.4 - - - +
25C TYR* 2.8 49.4 + - + +
51C GLU* 3.8 25.4 - - + +
93C LEU* 3.8 20.4 - - + -
94C GLU* 5.6 1.6 - - - +
----------------------------------------------------------
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU 2.8 24.1 + - - +
19C LEU* 3.8 11.2 - - + +
20C VAL 3.3 0.2 - - - -
21C ALA* 1.3 71.3 - - - +
23C ASN* 1.3 64.6 - - - +
26C PHE* 3.1 16.1 + - - +
48C SER* 2.8 31.7 + - - +
51C GLU* 3.6 13.0 - - + +
52C MET* 3.6 45.5 - - + +
55C ALA* 4.1 13.9 - - + -
200C HEM 3.5 44.4 - - + -
----------------------------------------------------------
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Residues in contact with ASN 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.6 10.9 + - - +
20C VAL 3.2 7.2 + - - +
22C ILE* 1.3 79.7 - - - +
24C GLN* 1.3 67.6 + - - +
26C PHE* 3.3 2.5 + - - +
27C LEU* 3.0 26.7 + - - +
74C LEU* 3.8 12.5 - - - +
77C LEU* 4.4 10.5 - - + -
200C HEM 3.2 35.4 - - - +
19D LEU* 4.8 3.8 - - - +
71D LEU* 3.5 46.4 - - + +
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Residues in contact with GLN 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C VAL* 2.9 19.1 + - - +
21C ALA 4.0 2.2 - - - +
23C ASN* 1.3 77.8 - - - +
25C TYR* 1.3 62.6 + - + +
27C LEU* 3.6 0.9 + - - +
28C HIS* 3.0 41.4 + - + +
76C LYS 4.8 0.3 - - - +
77C LEU* 3.8 15.3 - - + +
78C ASN* 3.0 33.4 + - - +
79C ILE* 4.5 8.3 - - + -
89C SER* 3.1 24.5 + - - -
90C ASP* 2.9 34.7 + - - +
93C LEU* 4.0 19.5 - - + +
----------------------------------------------------------
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Residues in contact with TYR 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA* 2.8 29.3 + - + +
24C GLN* 1.3 77.6 - - - +
26C PHE* 1.3 56.5 + - - +
28C HIS* 3.4 1.8 + - - +
29C ALA* 2.8 30.1 + - - +
44C GLU* 3.4 39.0 - - - +
47C GLU* 3.6 34.0 + - + -
48C SER* 3.8 9.0 - - - +
51C GLU* 3.9 25.6 - - + -
90C ASP* 3.5 29.3 - - + +
93C LEU* 6.1 1.8 - - + -
94C GLU* 2.4 39.4 + - + +
130C HIS* 4.0 4.3 - - - +
134C LEU* 3.6 13.0 - - + +
----------------------------------------------------------
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Residues in contact with PHE 26 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE 3.1 19.0 + - - +
23C ASN* 3.3 4.9 + - - +
25C TYR* 1.3 74.1 - - - +
27C LEU* 1.3 66.1 + - - +
29C ALA* 3.3 6.2 + - + +
30C ARG* 3.0 39.2 + - + +
45C TYR* 3.5 26.5 - + - -
48C SER* 3.6 20.1 + - - +
52C MET* 4.6 0.4 - - + -
200C HEM 3.5 55.4 - + + -
56D ASP* 3.4 41.1 - - + -
59D ILE* 4.0 13.2 - - + -
71D LEU* 5.2 1.6 - - + -
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Residues in contact with LEU 27 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASN 3.0 16.3 + - - +
24C GLN 4.0 2.9 - - - +
26C PHE* 1.3 76.6 - - - +
28C HIS* 1.3 65.7 + - + +
30C ARG 3.2 1.6 + - - -
31C MET* 2.9 39.8 + - + +
77C LEU* 5.6 0.2 - - + -
79C ILE* 3.6 44.6 - - + -
59D ILE* 4.4 7.2 - - + -
63D LEU* 4.3 6.7 - - + -
69D PRO* 3.8 43.1 - - + +
71D LEU* 4.0 23.4 - - + +
----------------------------------------------------------
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Residues in contact with HIS 28 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C GLN* 3.0 32.2 + - + +
25C TYR 3.7 0.7 - - - +
27C LEU* 1.3 74.5 - - - +
29C ALA* 1.3 65.1 + - - +
31C MET* 3.1 4.6 + - - +
32C PHE* 2.9 32.2 + + + -
44C GLU* 3.1 15.9 - - - +
78C ASN 4.4 0.7 - - - -
79C ILE* 2.7 43.2 + - + -
86C MET* 3.2 48.5 + - + +
90C ASP* 2.7 36.2 + - - -
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Residues in contact with ALA 29 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C TYR 2.8 17.9 + - - +
26C PHE* 3.4 7.9 - - - +
28C HIS* 1.3 76.1 - - - +
30C ARG* 1.3 61.0 + - + +
32C PHE* 3.3 4.4 + - - +
33C LYS 2.9 21.8 + - - -
41C ASN* 3.0 26.9 - - - +
44C GLU* 3.9 8.4 - - + +
45C TYR* 3.6 32.3 - - + +
----------------------------------------------------------
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Residues in contact with ARG 30 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 3.0 34.6 + - + +
27C LEU 4.1 0.9 - - - +
29C ALA* 1.3 73.2 - - + +
31C MET* 1.3 61.2 + - - +
33C LYS* 3.5 13.3 - - + +
34C ASN* 2.9 28.9 + - - +
41C ASN* 3.4 30.5 + - - +
45C TYR* 3.3 34.5 - - - -
56D ASP* 2.7 46.4 + - - -
59D ILE* 4.1 9.6 - - + -
60D GLU* 3.0 33.2 + - + +
63D LEU* 3.7 19.3 - - + +
----------------------------------------------------------
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Residues in contact with MET 31 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C LEU* 2.9 34.4 + - + +
28C HIS* 3.4 7.4 - - - +
30C ARG* 1.3 74.7 - - - +
32C PHE* 1.3 66.5 + - - +
34C ASN* 3.1 6.5 + - - +
35C TRP* 2.9 50.0 + - + -
79C ILE* 3.7 22.0 - - + -
80C GLY 3.8 16.6 - - - +
81C GLU* 4.9 2.2 - - - +
86C MET* 3.7 33.9 - - + -
63D LEU* 4.2 16.6 - - + -
69D PRO* 6.3 0.2 - - - -
----------------------------------------------------------
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Residues in contact with PHE 32 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C HIS* 2.9 24.8 + - + -
29C ALA 3.4 6.7 - - - +
31C MET* 1.3 74.3 - - - +
33C LYS* 1.3 61.6 + - - +
35C TRP* 3.2 13.8 + + - -
36C GLY 3.0 4.2 + - - -
37C LEU* 2.8 37.2 + - + +
40C LEU* 3.6 38.8 - - + -
41C ASN 3.9 12.3 - - - +
44C GLU* 3.9 26.7 - - + -
83C VAL* 4.0 20.4 - - + -
86C MET* 3.4 39.3 - - + -
87C LEU* 3.9 17.7 - - + -
----------------------------------------------------------
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Residues in contact with LYS 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ALA 2.9 7.3 + - - +
30C ARG* 3.5 19.7 - - + +
31C MET 3.2 0.2 - - - -
32C PHE* 1.3 72.5 - - - +
34C ASN* 1.3 68.0 + - - +
36C GLY* 2.9 15.1 + - - +
37C LEU 4.8 2.9 - - - +
38C LYS* 5.3 3.3 - - + +
41C ASN* 3.5 42.0 - - - +
60D GLU* 3.4 29.8 - - + +
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Residues in contact with ASN 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ARG 2.9 18.0 + - - +
31C MET* 3.1 5.6 + - - +
33C LYS* 1.3 79.1 - - - +
35C TRP* 1.3 68.8 + - + +
36C GLY* 3.2 4.0 + - - -
60D GLU 5.1 1.2 + - - -
63D LEU* 4.2 24.3 - - + +
64D PHE* 4.0 30.1 - - - +
----------------------------------------------------------
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Residues in contact with TRP 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C MET* 2.9 34.5 + - + -
32C PHE* 3.2 22.4 + + - +
34C ASN* 1.3 87.5 + - - +
36C GLY* 1.3 59.1 + - - +
37C LEU* 3.2 26.1 + - + +
81C GLU 3.4 26.0 - - - -
82C ASP* 4.3 2.2 - - - -
83C VAL* 4.4 10.3 - - + -
86C MET* 3.7 33.7 - - + -
----------------------------------------------------------
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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