Contacts of the helix formed by residues 4 - 35 (chain R) in PDB entry 3IS7
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 R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3R GLY* 1.3 72.1 - - - -
5R LYS* 1.3 66.8 + - - +
6R LYS* 3.0 6.5 + - - +
7R VAL* 2.9 32.5 + - + +
8R ILE* 3.0 21.0 + - - +
107R HIS* 2.8 30.2 + - - -
111R VAL* 3.9 22.0 - - + +
113R ASP* 5.7 2.8 + - + +
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Residues in contact with LYS 5 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3R GLY 3.4 4.9 + - - -
4R ASP* 1.3 75.9 + - - +
6R LYS* 1.3 67.5 + - + +
8R ILE* 3.3 11.4 + - - +
9R GLN* 3.0 50.0 + - + +
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Residues in contact with LYS 6 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4R ASP* 3.0 4.5 + - - +
5R LYS* 1.3 78.5 - - + +
7R VAL* 1.3 58.8 + - - +
9R GLN* 3.1 20.3 + - + +
10R HIS* 2.8 38.6 + - + +
107R HIS* 3.1 38.1 - - + +
110R GLN* 6.0 0.2 - - - +
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Residues in contact with VAL 7 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4R ASP* 2.9 37.9 + - + +
6R LYS* 1.3 75.4 - - - +
8R ILE* 1.3 59.6 + - - +
10R HIS* 3.0 7.1 + - - +
11R LEU* 2.7 51.2 + - + +
65R LEU* 4.1 7.4 - - + -
107R HIS* 3.6 17.2 - - + -
108R CYS* 4.4 13.0 - - - -
111R VAL* 3.8 12.8 - - + -
113R ASP* 3.5 24.9 - - + +
116R SER* 4.0 7.2 - - - +
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Residues in contact with ILE 8 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2R LYS* 5.5 5.2 - - + -
3R GLY 4.1 11.2 - - - +
4R ASP 3.0 14.3 + - - +
5R LYS* 3.6 9.6 - - - +
6R LYS 3.3 0.2 - - - -
7R VAL* 1.3 80.6 - - - +
9R GLN* 1.3 60.5 + - + +
11R LEU* 3.7 7.4 - - + +
12R ASN* 2.9 43.1 + - - +
62R ILE* 4.6 8.5 - - + +
65R LEU* 3.6 42.6 - - + +
66R GLU 4.5 1.3 - - - +
67R GLY* 3.9 27.1 - - - +
68R LEU 4.9 1.1 - - - +
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Residues in contact with GLN 9 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5R LYS* 3.0 44.1 + - + +
6R LYS* 3.1 26.7 + - - +
8R ILE* 1.3 80.2 - - + +
10R HIS* 1.3 63.1 + - + +
12R ASN* 3.4 6.9 + - - +
13R LYS* 2.9 22.7 + - - +
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Residues in contact with HIS 10 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6R LYS* 2.8 32.4 + - + +
7R VAL* 3.5 8.1 - - - +
9R GLN* 1.3 74.9 - - + +
11R LEU* 1.3 63.0 + - + +
13R LYS* 2.9 24.9 + - + +
14R ILE* 2.9 20.3 + - - +
100R ASP 4.9 1.8 + - - -
103R GLU* 3.9 28.7 - - + -
104R ALA* 3.5 28.0 + - + +
107R HIS* 3.9 32.3 + + + +
108R CYS* 6.2 1.3 - - - -
120R LEU* 5.8 0.2 - - + -
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Residues in contact with LEU 11 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7R VAL* 2.7 42.4 + - + +
8R ILE* 3.7 4.9 - - - +
10R HIS* 1.3 71.3 - - + +
12R ASN* 1.3 58.3 + - - +
14R ILE* 3.2 5.8 + - - +
15R LEU* 2.8 29.1 + - - +
58R LEU* 4.0 23.9 - - + +
61R ARG* 3.9 28.3 - - + -
62R ILE* 3.8 25.0 - - + +
65R LEU* 4.1 9.6 - - + -
116R SER* 4.3 6.7 - - - +
119R LEU* 5.5 1.8 - - + -
120R LEU* 4.0 29.6 - - + -
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Residues in contact with ASN 12 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8R ILE* 2.9 33.3 + - - +
9R GLN* 3.9 7.0 - - - +
11R LEU* 1.3 76.1 - - - +
13R LYS* 1.3 57.8 - - - +
15R LEU* 3.3 8.0 + - - +
16R GLY* 2.8 26.0 + - - -
62R ILE* 3.7 9.7 - - - +
68R LEU 3.1 20.4 + - - -
69R PRO* 3.4 6.1 - - - +
70R ASN* 2.7 41.8 + - + +
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Residues in contact with LYS 13 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9R GLN 2.9 13.3 + - - +
10R HIS* 2.9 23.3 + - + +
12R ASN* 1.3 75.5 - - - +
14R ILE* 1.3 69.6 + - + +
16R GLY* 3.1 4.4 + - - -
17R ASN* 3.0 23.5 + - - +
96R LYS* 4.1 10.3 - - - +
99R LYS* 5.4 2.6 - - - +
100R ASP* 3.8 36.5 + - + +
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Residues in contact with ILE 14 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10R HIS 2.9 20.0 + - - +
11R LEU* 3.8 6.7 - - - +
13R LYS* 1.3 72.7 - - + +
15R LEU* 1.3 61.4 + - - +
17R ASN* 3.0 12.2 + - + +
18R GLU* 3.0 35.4 + - + +
58R LEU* 3.8 17.9 - - + -
97R ALA 4.6 1.1 - - - +
100R ASP* 3.7 21.5 - - + +
101R LEU* 3.3 56.3 - - + +
104R ALA* 4.3 8.3 - - + -
120R LEU* 4.1 15.7 - - + -
123R ILE* 4.8 2.0 - - + -
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Residues in contact with LEU 15 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11R LEU 2.8 17.3 + - - +
12R ASN* 3.5 19.7 - - - +
14R ILE* 1.3 76.9 - - - +
16R GLY* 1.4 57.8 + - - +
18R GLU* 3.3 2.1 + - - +
19R LEU* 2.9 51.2 + - + +
55R ALA* 3.9 29.6 - - + +
58R LEU* 3.8 14.7 - - + +
59R ILE* 3.9 30.7 - - + -
62R ILE* 4.3 5.6 - - + -
69R PRO* 4.2 3.6 - - + -
70R ASN 3.6 23.1 - - - +
71R LEU* 4.1 5.4 - - + -
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Residues in contact with GLY 16 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12R ASN 2.8 15.0 + - - -
13R LYS* 3.1 5.3 + - - -
15R LEU* 1.4 77.3 - - - +
17R ASN* 1.3 61.6 + - - +
19R LEU* 3.4 12.9 + - - +
20R ILE* 3.3 28.1 + - - +
70R ASN 5.3 1.5 + - - -
73R ASP 4.8 9.3 - - - +
75R GLY 5.3 0.3 + - - -
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Residues in contact with ASN 17 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13R LYS* 3.0 16.4 + - - +
14R ILE* 3.0 16.4 + - + +
16R GLY* 1.3 77.5 - - - +
18R GLU* 1.3 59.0 + - + +
20R ILE* 3.3 15.6 + - - +
21R ALA* 3.0 27.2 + - - +
93R LEU* 4.8 7.4 - - + +
96R LYS* 4.1 16.1 + - - +
97R ALA* 3.7 27.5 - - + +
100R ASP* 2.8 40.7 + - - +
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Residues in contact with GLU 18 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14R ILE* 3.0 20.5 + - + +
15R LEU* 3.6 7.2 - - - +
17R ASN* 1.3 74.0 - - + +
19R LEU* 1.3 60.7 + - - +
21R ALA* 3.1 4.0 + - - +
22R ILE* 2.7 37.0 + - - +
51R GLU* 2.6 40.0 - - - +
54R HIS* 3.7 11.4 - - + -
55R ALA* 4.1 18.2 - - + +
58R LEU* 4.1 16.4 - - + -
97R ALA* 6.1 0.9 - - - +
101R LEU* 5.5 0.9 - - - +
123R ILE* 3.4 19.8 - - - +
127R GLU* 2.8 19.8 - - - +
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Residues in contact with LEU 19 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Q ASN* 4.5 8.7 - - - +
159Q HEM 3.9 31.4 - - + -
15R LEU* 2.9 34.8 + - + +
16R GLY* 3.4 9.6 + - - +
18R GLU* 1.3 76.1 - - - +
20R ILE* 1.3 61.4 - - - +
22R ILE* 3.5 7.5 + - + +
23R ASN* 3.3 25.1 + - - +
55R ALA* 4.9 1.6 - - + -
70R ASN 3.7 23.3 - - - +
71R LEU* 4.0 20.0 - - + +
73R ASP 4.6 9.2 - - - +
74R LEU* 3.7 19.4 - - + +
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Residues in contact with ILE 20 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R GLY 3.3 17.2 + - - +
17R ASN* 3.6 16.4 - - - +
18R GLU 3.1 0.4 - - - -
19R LEU* 1.3 75.4 - - - +
21R ALA* 1.3 67.3 + - - +
22R ILE 3.3 0.2 + - - -
23R ASN* 3.3 3.3 + - - +
24R GLN* 3.0 22.1 + - - +
74R LEU* 3.9 7.9 - - + -
75R GLY* 3.6 43.3 - - - +
76R LYS 3.6 21.3 - - - +
77R LEU* 4.0 12.6 - - + +
93R LEU* 3.8 26.0 - - + -
96R LYS* 6.4 1.8 - - - -
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Residues in contact with ALA 21 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17R ASN 3.0 15.3 + - - +
18R GLU* 3.1 5.4 + - - +
20R ILE* 1.3 77.1 - - - +
22R ILE* 1.3 63.9 + - - +
24R GLN* 4.4 0.9 - - - -
25R TYR* 2.8 56.8 + - + +
51R GLU* 3.9 15.5 - - + +
93R LEU* 3.6 20.6 - - + +
94R GLU* 4.9 0.7 - - - +
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Residues in contact with ILE 22 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159Q HEM 3.8 49.6 - - + -
18R GLU 2.7 27.4 + - - +
19R LEU* 3.7 7.9 - - + +
20R ILE 3.2 0.2 - - - -
21R ALA* 1.3 71.8 - - - +
23R ASN* 1.3 67.9 + - - +
26R PHE* 3.0 18.0 + - - +
48R SER* 2.9 29.8 + - - +
51R GLU* 3.7 12.8 - - + +
52R MET* 3.6 41.5 - - + +
55R ALA* 3.9 11.9 - - + -
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Residues in contact with ASN 23 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Q LEU* 4.8 8.7 - - - +
71Q LEU* 3.1 53.2 + - + +
159Q HEM 3.6 18.0 - - - +
19R LEU 3.3 14.0 + - - +
20R ILE 3.3 3.8 + - - +
22R ILE* 1.3 88.3 - - - +
24R GLN* 1.3 64.9 + - - +
26R PHE* 3.3 1.1 + - - -
27R LEU* 3.0 25.6 + - - +
74R LEU* 3.8 12.5 - - - +
77R LEU* 4.2 11.9 - - + -
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Residues in contact with GLN 24 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20R ILE* 3.0 18.0 + - - +
21R ALA* 3.8 3.8 - - - +
23R ASN* 1.3 76.5 - - - +
25R TYR* 1.3 65.2 + - + +
27R LEU* 3.4 1.4 + - - +
28R HIS* 2.9 39.5 + - + +
77R LEU* 3.8 11.5 - - + +
78R LEU* 2.7 49.0 + - - +
79R ILE* 4.7 6.7 - - + -
89R CYS 3.2 25.1 + - - -
90R ASP* 3.0 27.6 + - - +
93R LEU* 3.8 16.2 - - - +
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Residues in contact with TYR 25 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21R ALA* 2.8 31.5 + - + +
24R GLN* 1.3 83.6 - - + +
26R PHE* 1.3 57.1 + - - +
28R HIS 3.4 0.2 + - - -
29R SER* 2.9 26.9 + - - -
44R GLU* 3.1 27.6 - - - +
47R GLU* 4.0 12.3 - - + -
48R SER* 3.8 20.4 - - - +
51R GLU* 3.6 33.9 - - + -
90R ASP* 3.3 41.0 + - + -
93R LEU* 4.0 8.9 - - + +
94R GLU* 2.6 32.1 + - - +
130R HIS* 3.4 16.4 - + - -
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Residues in contact with PHE 26 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Q ASP* 3.2 38.4 - - + -
59Q ILE* 4.1 14.6 - - + -
71Q LEU* 4.8 2.2 - - + -
159Q HEM 3.3 53.4 - + + -
22R ILE 3.0 21.7 + - - +
23R ASN* 4.0 4.0 - - - +
24R GLN 3.2 0.4 - - - -
25R TYR* 1.3 75.9 - - - +
27R LEU* 1.3 58.2 + - - +
29R SER* 3.3 4.6 + - - -
30R ARG* 3.0 40.7 + - + +
45R TYR* 3.7 28.5 - + - -
48R SER* 3.6 18.1 + - - +
52R MET* 4.1 8.3 - - + -
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Residues in contact with LEU 27 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59Q ILE* 4.4 8.5 - - + -
63Q LEU* 4.8 0.9 - - + -
69Q PRO* 3.7 50.9 - - + +
71Q LEU* 4.1 19.2 - - + +
23R ASN 3.0 17.6 + - - +
24R GLN 3.9 2.9 - - - +
26R PHE* 1.3 75.4 - - - +
28R HIS* 1.3 68.4 + - - +
30R ARG* 3.1 2.7 + - - +
31R MET* 2.9 41.0 + - + +
77R LEU* 5.7 0.9 - - + -
79R ILE* 3.3 37.9 - - + -
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Residues in contact with HIS 28 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24R GLN* 2.9 24.9 + - + +
25R TYR 3.9 0.2 - - - +
27R LEU* 1.3 72.7 - - - +
29R SER* 1.3 65.6 + - - +
31R MET* 3.2 11.6 + - - +
32R TRP* 2.9 36.6 + - + -
44R GLU* 3.4 18.1 + - - +
78R LEU 3.5 20.7 + - - -
79R ILE* 3.5 8.4 - - + -
80R GLY 3.2 22.5 + - - -
86R MET* 3.5 44.6 + - + +
89R CYS* 4.2 0.2 - - + -
90R ASP* 2.8 30.8 + - - -
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Residues in contact with SER 29 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25R TYR 2.9 18.4 + - - -
26R PHE* 3.5 6.7 - - - -
28R HIS* 1.3 76.7 - - - +
30R ARG* 1.3 81.0 + - - +
32R TRP 3.2 0.5 + - - -
33R ASN* 2.9 28.4 + - - -
41R GLY* 2.6 33.2 + - - -
44R GLU* 3.6 9.4 - - - +
45R TYR* 3.5 17.4 - - - +
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Residues in contact with ARG 30 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56Q ASP* 2.9 40.5 + - - +
59Q ILE* 3.8 15.5 - - + -
60Q GLU* 3.6 27.6 + - + +
63Q LEU* 3.6 19.0 - - + +
159Q HEM 5.5 0.2 - - - +
26R PHE* 3.0 33.9 + - + +
27R LEU 3.9 2.7 - - - +
29R SER* 1.3 94.8 + - - +
31R MET* 1.3 58.9 + - - +
33R ASN* 3.4 21.0 + - + +
34R ASP* 2.8 28.4 + - - +
41R GLY 4.6 0.4 + - - -
45R TYR* 3.4 32.3 - - - +
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Residues in contact with MET 31 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q LEU* 4.1 19.1 - - + -
27R LEU* 2.9 43.3 + - + +
28R HIS* 3.7 11.0 - - - +
30R ARG* 1.3 73.0 - - - +
32R TRP* 1.3 66.5 + - - +
34R ASP* 3.2 5.9 + - - +
35R TRP* 3.1 52.7 + - + -
79R ILE* 4.1 15.7 - - + -
80R GLY 3.4 23.3 - - - +
81R GLU* 4.7 1.8 - - - -
86R MET* 3.8 15.9 - - + -
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Residues in contact with TRP 32 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28R HIS* 2.9 27.3 + - + -
29R SER* 3.6 5.2 - - - +
31R MET* 1.3 77.2 - - - +
33R ASN* 1.3 60.3 + - - +
35R TRP* 3.2 16.8 + + - +
37R LEU* 2.9 54.7 + - + +
40R LEU* 3.6 34.8 - - + +
41R GLY 3.6 13.0 - - - +
44R GLU* 3.5 37.0 - - + -
83R THR* 3.0 37.2 + - + -
86R MET* 3.5 36.0 - - + +
87R LEU* 3.9 21.8 - - + -
90R ASP* 4.6 1.8 - - - -
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Residues in contact with ASN 33 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136P THR* 5.1 0.7 - - - +
60Q GLU* 5.1 3.9 - - + +
29R SER* 2.9 13.4 + - - +
30R ARG* 3.6 37.8 + - + +
32R TRP* 1.3 70.9 - - - +
34R ASP* 1.3 67.8 + - - +
36R GLY* 3.0 14.0 + - - +
37R LEU 4.8 2.5 - - - +
38R LYS* 3.8 22.4 + - + +
41R GLY* 3.2 25.3 - - - -
42R ALA 4.2 0.4 - - - +
156R GLU* 6.0 0.2 + - - -
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Residues in contact with ASP 34 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132P ASP* 4.7 9.7 - - - +
136P THR* 3.3 22.9 + - - +
63Q LEU* 3.6 43.3 - - + +
64Q PHE* 4.3 4.7 + - - -
30R ARG 2.8 21.4 + - - +
31R MET* 3.4 6.8 - - - +
33R ASN* 1.3 72.7 - - - +
35R TRP* 1.3 81.2 + - - +
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Residues in contact with TRP 35 (chain R).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136P THR* 3.6 8.9 - - - +
140P LEU* 3.2 27.2 + - - +
143P LYS* 3.8 34.6 + - - +
31R MET* 3.1 36.4 + - + +
32R TRP* 3.6 21.5 - + - +
33R ASN 3.1 1.0 - - - -
34R ASP* 1.3 96.6 + - - +
36R GLY* 1.3 58.2 + - - +
37R LEU* 4.2 15.2 - - + +
81R GLU 3.6 24.0 - - - -
82R ASN* 4.0 7.2 - - - -
83R THR* 4.4 3.1 - - - -
86R MET* 3.5 35.7 - - + -
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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) + - + + + + + -
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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