Contacts of the helix formed by residues 4 - 36 (chain B) in PDB entry 1JGC
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLY* 1.3 71.4 - - - -
5B ALA* 1.3 69.0 + - - +
6B LYS* 3.0 20.1 + - - +
7B VAL* 2.9 32.3 + - + +
8B ILE* 3.2 11.4 + - - +
65B LEU* 5.3 0.2 - - - +
107B TYR* 2.9 33.6 + - - -
111B VAL* 3.8 24.6 - - + +
113B ASP* 5.5 2.9 + - + +
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Residues in contact with ALA 5 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LYS* 6.2 1.6 - - - +
3B GLY 3.2 6.9 + - - -
4B ASP* 1.3 72.7 - - - +
6B LYS* 1.3 60.7 + - - +
8B ILE* 3.3 13.3 + - - +
9B GLU* 3.1 26.1 + - - +
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Residues in contact with LYS 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASP* 3.0 12.1 + - - +
5B ALA* 1.3 76.9 - - - +
7B VAL* 1.3 64.9 + - - +
9B GLU* 3.2 23.6 + - + +
10B PHE* 3.0 45.8 + - + -
107B TYR* 3.5 34.5 - - + +
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Residues in contact with VAL 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASP* 2.9 29.9 + - + +
6B LYS* 1.3 76.0 - - - +
8B ILE* 1.3 58.8 + - - +
10B PHE* 3.1 7.6 + - - +
11B LEU* 2.9 38.5 + - + +
65B LEU* 4.0 4.7 - - + -
107B TYR* 3.8 20.9 - - + -
108B CYS* 4.0 17.0 - - - -
111B VAL* 4.6 3.4 - - + -
113B ASP* 3.6 31.6 - - + +
116B SER* 3.8 18.2 - - - +
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Residues in contact with ILE 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B LYS* 5.1 5.4 - - - -
3B GLY 4.4 9.2 - - - +
4B ASP 3.2 12.7 + - - +
5B ALA* 3.4 11.0 - - - +
7B VAL* 1.3 77.4 - - - +
9B GLU* 1.3 61.6 + - - +
11B LEU* 3.4 9.6 + - + +
12B ASN* 3.0 38.1 + - - +
62B ILE* 4.6 6.7 - - + +
65B LEU* 3.5 43.1 - - + +
66B GLU 4.5 0.9 - - - +
67B GLY* 3.7 28.3 - - - +
68B HIS 4.7 1.3 - - - +
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Residues in contact with GLU 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ALA* 3.1 16.6 + - - +
6B LYS* 3.4 28.5 - - + +
7B VAL 3.2 0.2 - - - -
8B ILE* 1.3 78.2 - - - +
10B PHE* 1.3 61.9 + - + +
12B ASN* 3.3 8.0 + - - +
13B ALA* 3.0 22.7 + - - +
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Residues in contact with PHE 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B LYS* 3.0 44.1 + - + -
7B VAL* 3.5 9.0 - - - +
9B GLU* 1.3 78.4 - - + +
11B LEU* 1.3 56.6 + - - +
13B ALA* 3.1 7.0 + - + +
14B ALA* 2.9 29.5 + - - +
100B LEU* 4.2 19.0 - - + +
103B GLU* 4.0 28.0 - - + -
104B ALA* 3.4 44.8 - - + +
107B TYR* 3.5 36.3 - + + -
108B CYS* 5.8 0.4 - - - -
120B PHE* 4.2 7.0 - - + -
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B VAL* 2.9 27.8 + - + +
8B ILE* 3.7 4.7 - - - +
9B GLU 3.3 0.2 - - - -
10B PHE* 1.3 75.2 - - - +
12B ASN* 1.3 57.5 + - - +
14B ALA* 3.2 2.1 + - - +
15B LEU* 2.8 28.6 + - - +
58B ILE* 3.5 24.0 - - + +
61B ARG* 3.9 22.0 - - + -
62B ILE* 3.5 27.4 - - + +
65B LEU* 3.8 28.9 - - + -
116B SER* 4.4 4.3 - - - +
119B ILE* 5.2 7.9 - - + -
120B PHE* 3.6 28.0 - - + -
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Residues in contact with ASN 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.0 32.3 + - - +
9B GLU* 3.7 6.9 - - - +
11B LEU* 1.3 74.2 - - - +
13B ALA* 1.3 59.9 + - - +
15B LEU* 3.5 8.3 + - - +
16B ARG* 3.1 29.9 + - - +
62B ILE* 3.7 11.9 - - - +
68B HIS 3.1 20.7 + - - -
69B PRO* 3.6 4.0 - - - +
70B ASN* 2.9 39.1 + - + +
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Residues in contact with ALA 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU 3.0 13.6 + - - +
10B PHE* 3.1 11.0 + - + +
12B ASN* 1.3 74.3 - - - +
14B ALA* 1.3 62.9 + - - +
16B ARG* 3.2 15.6 + - - +
17B SER* 2.9 27.4 + - - -
75B ASP* 4.7 1.7 - - - +
100B LEU* 3.8 23.4 - - + +
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Residues in contact with ALA 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B PHE 2.9 12.8 + - - +
11B LEU* 3.5 8.5 - - - +
13B ALA* 1.3 77.8 - - - +
15B LEU* 1.3 55.7 + - - +
17B SER* 3.1 3.3 + - - -
18B GLU* 2.9 34.1 + - - +
58B ILE* 3.9 12.8 - - + -
100B LEU* 3.9 11.8 - - + +
101B TYR* 3.6 24.2 + - + -
120B PHE* 3.8 17.3 - - + -
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Residues in contact with LEU 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B LEU 2.8 16.8 + - - +
12B ASN* 3.5 17.3 - - - +
13B ALA 3.2 0.2 - - - -
14B ALA* 1.3 77.7 - - - +
16B ARG* 1.3 57.4 + - - +
18B GLU* 3.1 6.3 + - - +
19B LEU* 2.8 51.3 + - + +
55B ALA* 4.0 22.0 - - + +
58B ILE* 4.0 10.9 - - + +
59B ILE* 3.9 27.8 - - + -
62B ILE* 4.5 3.6 - - + -
69B PRO* 4.4 3.6 - - + -
70B ASN 3.8 11.9 - - - +
71B LEU* 3.2 29.6 - - + -
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Residues in contact with ARG 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASN 3.1 18.2 + - - +
13B ALA* 3.5 15.3 - - - +
15B LEU* 1.3 76.9 - - - +
17B SER* 1.3 54.9 + - - +
19B LEU* 3.5 7.9 + - - +
20B THR* 2.7 34.5 + - - -
70B ASN* 3.9 29.2 + - - +
73B LYS* 3.6 48.5 + - - +
74B LEU* 4.2 1.3 - - - -
75B ASP* 2.8 40.4 - - - +
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Residues in contact with SER 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B ALA 2.9 13.6 + - - -
14B ALA* 3.1 13.9 + - - -
16B ARG* 1.3 77.4 - - - +
18B GLU* 1.3 58.5 + - - +
20B THR* 3.3 7.1 - - - -
21B ALA* 3.0 25.3 + - - +
75B ASP* 3.7 13.6 + - - -
93B GLY 5.3 0.5 + - - -
97B ALA* 3.7 27.7 + - - +
100B LEU* 4.2 11.4 - - - -
101B TYR* 4.2 5.0 + - - -
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ALA 2.9 19.5 + - - +
15B LEU 3.1 6.9 + - - +
17B SER* 1.3 76.2 + - - +
19B LEU* 1.3 59.6 + - - +
20B THR 3.0 2.0 - - - -
21B ALA* 3.0 7.4 + - - +
22B ILE* 2.8 35.0 + - - +
51B GLU* 2.4 31.9 - - - +
54B HIS* 3.0 31.3 + - + +
55B ALA* 4.3 17.7 - - + +
58B ILE* 4.4 10.3 - - + -
97B ALA* 5.3 1.6 - - - +
101B TYR* 2.9 24.3 + - - +
123B LEU* 4.0 3.8 - - - +
127B GLU* 3.7 5.9 - - - +
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 2.8 42.0 + - + +
16B ARG* 3.9 4.0 - - - +
18B GLU* 1.3 73.5 - - - +
20B THR* 1.3 62.0 + - - +
22B ILE* 3.5 11.8 + - + +
23B SER* 3.3 24.6 + - - -
55B ALA* 4.6 2.5 - - + -
70B ASN 4.6 0.7 - - - +
71B LEU* 3.5 45.8 - - + +
73B LYS 4.3 5.8 - - - +
74B LEU* 3.3 25.3 - - + +
200B HEM 3.3 36.8 - - + -
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Residues in contact with THR 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ARG 2.7 18.5 + - - -
17B SER* 3.3 10.5 - - - -
18B GLU 3.0 0.6 - - - -
19B LEU* 1.3 75.5 - - - +
21B ALA* 1.3 65.2 + - - +
23B SER 3.3 1.9 + - - -
24B GLN* 3.0 27.1 + - - +
74B LEU* 3.5 9.6 - - + +
75B ASP* 2.7 47.0 + - + +
76B PRO 3.9 13.0 - - - +
77B LEU* 3.6 14.1 - - + +
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Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B SER 3.0 12.6 + - - +
18B GLU* 3.0 9.8 + - - +
20B THR* 1.3 77.4 - - - +
22B ILE* 1.3 63.9 + - - +
24B GLN* 3.7 6.9 - - - +
25B TYR* 2.8 42.9 + - + -
51B GLU* 3.8 25.1 - - + +
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Residues in contact with ILE 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLU 2.8 24.5 + - - +
19B LEU* 3.7 15.0 - - + +
21B ALA* 1.3 72.3 - - - +
23B SER* 1.3 57.1 + - - +
26B TRP* 3.0 17.7 + - - +
48B SER* 3.0 33.2 + - - +
51B GLU* 3.5 24.2 - - + +
52B MET* 3.5 44.6 - - + +
55B ALA* 4.1 12.8 - - + -
200B HEM 4.2 34.5 - - + -
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Residues in contact with SER 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LEU 3.3 10.4 + - - -
20B THR 3.3 6.8 + - - -
21B ALA 3.3 0.2 - - - -
22B ILE* 1.3 76.4 - - - +
24B GLN* 1.3 66.3 + - - +
26B TRP* 4.4 5.2 - - - -
27B VAL* 3.0 34.1 + - - +
74B LEU* 3.8 17.9 - - - +
77B LEU* 4.1 11.2 - - - -
200B HEM 4.5 15.1 - - - +
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Residues in contact with GLN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B THR* 3.0 22.0 + - - +
21B ALA* 3.2 7.8 + - - +
23B SER* 1.3 77.2 - - - +
25B TYR* 1.3 63.2 + - + +
27B VAL* 4.0 1.4 - - - +
28B HIS* 3.1 32.0 + - + +
76B PRO 4.8 1.2 - - - +
77B LEU* 3.8 12.5 - - + +
78B ARG* 2.9 50.0 + - - +
79B ILE* 4.5 6.3 - - + -
89B CYS 3.2 24.9 + - - -
90B ASP* 3.0 27.8 + - - +
93B GLY* 5.0 5.4 - - - -
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Residues in contact with TYR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 2.8 37.6 + - + +
24B GLN* 1.3 75.6 - - + +
26B TRP* 1.3 61.5 + - - +
28B HIS* 3.3 5.2 + - - +
29B PHE* 2.9 28.4 + - - +
44B SER* 3.7 12.2 - - - +
47B GLU* 3.5 41.9 + - + -
48B SER* 3.5 22.4 - - - -
51B GLU* 3.9 27.6 - - + -
90B ASP* 3.5 37.9 + - + +
94B GLU* 2.5 36.8 + - - +
130B HIS* 4.3 1.7 + - - -
134B LEU* 4.8 1.9 - - + +
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Residues in contact with TRP 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE 3.0 17.7 + - - +
23B SER* 3.9 5.6 - - - +
24B GLN 3.3 0.2 - - - -
25B TYR* 1.3 74.7 - - - +
27B VAL* 1.3 65.8 + - + +
29B PHE* 3.2 27.6 + + - +
30B ARG* 3.1 32.5 + - + +
45B ARG* 3.5 39.7 - - + -
48B SER* 3.3 26.0 + - - +
49B ILE* 4.1 10.3 - - + -
52B MET* 3.8 20.4 - - + -
200B HEM 3.5 65.6 - + + +
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B SER* 3.0 26.7 + - - +
24B GLN 4.0 3.6 - - - +
26B TRP* 1.3 77.7 - - + +
28B HIS* 1.3 57.2 + - - +
30B ARG* 3.2 7.1 + - + +
31B LEU* 2.8 49.2 + - + +
77B LEU* 5.8 4.7 - - + -
79B ILE* 4.0 26.2 - - + -
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Residues in contact with HIS 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLN* 3.1 20.3 + - + +
25B TYR* 3.5 6.0 - - - +
27B VAL* 1.3 77.7 - - - +
29B PHE* 1.3 56.3 + - - +
31B LEU* 4.2 5.2 - - + -
32B GLN* 2.8 43.6 + - - +
44B SER* 4.1 11.0 - - - +
78B ARG 3.4 18.7 + - - -
79B ILE* 3.7 14.5 - - + -
80B GLY 3.1 23.9 + - - -
86B THR* 3.5 37.0 - - + +
89B CYS* 4.0 2.2 - - + -
90B ASP* 3.0 35.0 + - - +
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Residues in contact with PHE 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B TYR 2.9 13.6 + - - +
26B TRP* 3.4 35.7 - + - +
27B VAL 3.2 0.2 - - - -
28B HIS* 1.3 76.2 - - - +
30B ARG* 1.3 98.7 + - + +
32B GLN* 3.3 2.6 + - - -
33B GLU* 2.9 48.2 + - + +
41B ALA* 3.3 23.7 - - + +
42B LYS* 5.0 2.9 - - + -
44B SER* 3.8 17.4 - - - -
45B ARG* 3.3 46.4 - - + +
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Residues in contact with ARG 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B TRP* 3.1 24.6 + - + +
27B VAL* 3.6 9.9 - - + +
29B PHE* 1.3 109.3 - - + +
31B LEU* 1.3 63.4 + - + +
33B GLU* 3.2 27.2 + - - +
34B ASP* 3.0 23.2 + - - +
45B ARG* 5.9 1.2 - - - +
----------------------------------------------------------
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B VAL* 2.8 33.0 + - + +
28B HIS* 3.7 9.6 - - + +
30B ARG* 1.3 74.0 - - + +
32B GLN* 1.3 63.2 + - - +
34B ASP* 3.1 11.1 + - + +
35B TRP* 3.1 55.0 + - + +
79B ILE* 3.6 31.2 - - + -
80B GLY 4.1 8.3 - - - +
----------------------------------------------------------
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Residues in contact with GLN 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 2.8 30.3 + - - +
29B PHE 3.7 2.7 - - - +
31B LEU* 1.3 71.2 - - - +
33B GLU* 1.3 62.9 + - - +
35B TRP* 3.2 29.8 + - + +
37B LEU* 3.0 30.6 + - + +
40B MET* 3.2 40.0 - - + +
41B ALA* 3.4 14.5 - - + +
44B SER* 2.7 30.2 + - - -
86B THR* 3.3 27.7 + - + -
87B LEU* 5.6 1.0 - - - +
90B ASP* 5.3 2.4 + - - -
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Residues in contact with GLU 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B PHE* 2.9 31.6 + - + +
30B ARG* 3.4 28.9 - - - +
32B GLN* 1.3 77.2 - - - +
34B ASP* 1.3 57.4 + - - +
36B GLY* 3.0 18.9 + - - -
37B LEU 4.9 1.3 - - - +
38B ALA* 3.8 20.8 - - - +
41B ALA* 3.5 20.0 - - - +
42B LYS* 5.3 4.2 - - - +
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Residues in contact with ASP 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ARG 3.0 11.7 + - - +
31B LEU* 3.1 12.5 + - + +
33B GLU* 1.3 77.2 - - - +
35B TRP* 1.3 66.7 + - + +
36B GLY* 3.1 1.4 + - - -
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Residues in contact with TRP 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.1 37.6 + - + +
32B GLN* 3.6 37.5 - - + +
33B GLU 3.2 0.4 - - - -
34B ASP* 1.3 86.2 + - + +
36B GLY* 1.3 60.6 + - - +
37B LEU* 3.3 17.7 + - + +
80B GLY 4.2 1.1 - - - -
81B GLU* 3.6 20.4 + - - -
82B GLY* 3.5 37.2 - - - -
83B PRO* 3.7 17.5 - - + -
86B THR* 4.0 12.3 - - + -
----------------------------------------------------------
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Residues in contact with GLY 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLU 3.0 14.2 + - - -
34B ASP 3.1 2.0 - - - -
35B TRP* 1.3 80.0 - - - +
37B LEU* 1.3 61.3 - - - +
38B ALA* 3.3 7.5 + - - -
154B ALA* 3.5 7.3 - - - +
155B ALA* 3.3 22.7 + - - +
----------------------------------------------------------
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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