Contacts of the helix formed by residues 3 - 34 (chain P) in PDB entry 2X17
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 SER 3 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1P MET 3.8 2.0 + - - -
2P LEU* 1.3 76.1 - - - +
4P GLU* 1.3 64.8 + - - +
5P ARG* 3.8 2.4 + - - -
6P MET* 3.0 16.8 + - - +
7P LEU* 3.0 23.0 + - - +
111P GLU* 2.7 35.7 + - - -
113P ASP* 5.4 1.2 + - - -
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Residues in contact with GLU 4 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2P LEU 3.9 1.2 + - - -
3P SER* 1.3 73.4 - - - +
5P ARG* 1.3 59.4 + - - +
7P LEU* 3.8 9.9 + - + +
8P LYS* 3.6 19.8 + - - +
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Residues in contact with ARG 5 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P SER* 3.1 1.7 - - - +
4P GLU* 1.3 78.8 - - - +
6P MET* 1.3 62.8 - - - +
8P LYS* 3.6 6.2 + - - +
9P ALA* 3.3 20.6 + - - +
107P LEU* 4.4 20.3 - - + +
111P GLU* 3.7 22.2 - - - +
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Residues in contact with MET 6 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2P LEU* 3.9 15.3 - - + -
3P SER* 3.0 25.9 + - - +
5P ARG* 1.3 76.9 - - - +
7P LEU* 1.3 58.5 + - - +
9P ALA* 3.1 4.2 + - - +
10P LEU* 3.0 30.6 + - + +
104P LEU* 4.0 18.2 - - - +
107P LEU* 3.8 19.3 - - + -
108P ALA* 3.7 39.3 - - + +
111P GLU* 3.8 11.8 + - - +
113P ASP* 3.7 21.1 - - + +
116P THR* 3.8 18.4 - - - +
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Residues in contact with LEU 7 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2P LEU* 3.9 22.6 - - + +
3P SER 3.0 15.5 + - - +
4P GLU* 4.1 9.9 - - + +
5P ARG 3.4 0.2 - - - -
6P MET* 1.3 78.4 - - - +
8P LYS* 1.3 55.8 + - - +
10P LEU* 3.4 8.1 + - - +
11P ASN* 3.0 40.1 + - - +
61P ILE* 3.8 15.3 - - + -
66P GLY* 4.0 3.8 - - - -
67P ARG* 3.6 42.8 - - + +
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Residues in contact with LYS 8 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P GLU 3.6 11.2 + - - +
5P ARG* 3.6 9.5 + - - +
6P MET 3.3 0.2 - - - -
7P LEU* 1.3 78.5 - - - +
9P ALA* 1.3 58.2 + - - +
11P ASN* 3.8 7.1 - - + +
12P ASP* 3.0 61.0 + - - +
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Residues in contact with ALA 9 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P ARG 3.3 11.9 + - - +
6P MET 3.1 10.2 + - - +
8P LYS* 1.3 80.3 - - - +
10P LEU* 1.3 57.8 - - - +
12P ASP* 4.1 6.2 - - - +
13P GLN* 3.4 22.3 + - - +
16P ARG* 4.7 2.1 + - - -
104P LEU* 3.7 26.1 - - + +
107P LEU* 3.8 17.0 - - + -
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Residues in contact with LEU 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2P LEU* 3.9 38.4 - - + -
6P MET* 3.0 26.6 + - + +
7P LEU* 3.4 4.2 + - - +
9P ALA* 1.3 75.6 - - - +
11P ASN* 1.3 59.8 + - - +
12P ASP 3.3 0.4 - - - -
13P GLN* 4.6 0.7 - - - +
14P LEU* 3.0 27.2 + - - +
57P PHE* 3.7 35.4 - - + -
60P TYR* 4.0 16.2 - - + -
61P ILE* 3.8 18.8 - - + +
104P LEU* 4.2 8.3 - - + -
116P THR* 3.9 20.6 - - + -
119P PHE* 4.3 7.6 - - + -
120P LEU* 5.3 0.4 - - + -
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Residues in contact with ASN 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P LEU* 3.0 33.9 + - - +
8P LYS* 3.5 9.2 + - + +
10P LEU* 1.3 76.4 - - - +
12P ASP* 1.3 61.2 + - - +
14P LEU* 3.4 8.3 - - - +
15P ASN* 3.1 24.9 + - - +
61P ILE* 3.9 7.1 - - - +
67P ARG 3.3 20.0 + - - -
68P VAL* 3.3 13.9 - - - +
69P GLU* 2.9 44.9 + - + +
71P ASP* 4.7 2.8 - - - +
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Residues in contact with ASP 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P LYS* 3.0 51.5 + - - +
9P ALA* 4.1 7.1 - - - +
10P LEU 3.3 0.2 - - - -
11P ASN* 1.3 77.7 - - - +
13P GLN* 1.3 59.2 + - - +
15P ASN* 3.3 9.2 + - - +
16P ARG* 3.0 48.7 + - - +
71P ASP* 3.6 17.5 - - - +
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Residues in contact with GLN 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P ALA 3.4 16.8 + - - +
10P LEU 4.1 3.4 - - - +
11P ASN 3.4 0.2 - - - -
12P ASP* 1.3 74.9 - - - +
14P LEU* 1.3 61.2 + - - +
15P ASN 3.2 0.2 - - - -
16P ARG* 3.0 27.4 + - - +
17P GLU* 3.0 60.6 + - - +
57P PHE* 3.4 28.7 - - + -
97P ILE* 4.0 12.9 - - - +
100P SER* 3.0 23.9 + - - +
101P ILE* 3.8 15.1 - - + +
104P LEU* 3.6 13.9 - - + -
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Residues in contact with LEU 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257 PHE* 4.3 8.3 - - + -
10P LEU 3.0 16.3 + - - +
11P ASN* 3.4 10.1 - - - +
13P GLN* 1.3 78.0 - - - +
15P ASN* 1.3 60.2 + - - +
17P GLU* 3.5 6.2 + - - +
18P LEU* 3.2 39.7 + - + +
54P ALA* 3.5 19.0 - - + +
57P PHE* 4.0 12.7 - - + -
58P TYR* 3.6 33.7 - - + +
61P ILE* 4.0 14.6 - - + -
68P VAL* 4.0 15.3 - - + -
70P LEU* 3.9 18.2 - - + -
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Residues in contact with ASN 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227 TYR* 3.4 10.3 + - - -
11P ASN 3.1 13.9 + - - +
12P ASP* 3.4 11.9 - - - +
13P GLN 3.2 0.2 - - - -
14P LEU* 1.3 76.6 - - - +
16P ARG* 1.3 60.9 + - - +
18P LEU* 3.4 8.0 + - - +
19P TYR* 3.0 26.2 + - - +
70P LEU* 5.9 0.6 - - - +
71P ASP* 3.1 46.5 + - + +
72P GLU 3.4 18.8 + - - +
73P ILE* 4.1 5.9 - - - +
74P PRO* 4.6 7.4 - - - +
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Residues in contact with ARG 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9P ALA 4.7 2.4 + - - -
12P ASP* 3.0 33.5 + - - +
13P GLN* 3.0 54.6 + - - +
15P ASN* 1.3 77.2 - - + +
17P GLU* 1.3 58.9 + - - +
19P TYR* 3.4 9.5 + - - +
20P SER* 2.9 31.4 + - - -
93P HIS* 5.1 0.2 - - - -
96P PHE* 4.1 28.3 - - + -
97P ILE* 4.1 8.4 - - + +
100P SER* 4.0 22.4 + - - -
103P GLU* 5.9 0.4 + - - -
104P LEU* 5.4 1.2 - - - +
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Residues in contact with GLU 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13P GLN* 3.0 40.6 + - - +
14P LEU 3.8 5.6 - - - +
15P ASN 3.3 0.2 - - - -
16P ARG* 1.3 75.7 - - - +
18P LEU* 1.3 58.2 + - - +
20P SER* 3.4 3.8 + - - -
21P ALA* 3.2 20.1 + - - +
50P GLU* 3.0 52.4 - - - +
53P HIS* 3.4 22.5 + - + +
54P ALA* 4.0 7.9 - - + +
57P PHE* 4.3 12.9 - - + -
97P ILE* 3.9 14.8 - - - +
101P ILE* 4.4 1.6 - - - +
123P PHE* 4.1 16.7 - - - -
127P GLN* 4.8 2.6 + - - -
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Residues in contact with LEU 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227 TYR* 3.6 38.1 - - + +
257 PHE* 4.3 10.3 - - + -
14P LEU* 3.2 34.7 + - + +
15P ASN* 3.4 9.2 + - - +
16P ARG 3.3 0.2 - - - -
17P GLU* 1.3 75.7 - - - +
19P TYR* 1.3 59.1 + - - +
21P ALA* 3.4 6.9 + - + +
22P TYR* 3.1 24.1 + - - +
51P ILE* 5.0 20.2 - - + -
54P ALA* 3.8 17.3 - - + -
70P LEU* 4.2 2.9 - - + -
73P ILE* 4.0 18.1 - - + +
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Residues in contact with TYR 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15P ASN* 3.0 17.0 + - - +
16P ARG* 3.7 7.6 - - - +
17P GLU 3.4 0.2 - - - -
18P LEU* 1.3 73.5 - - - +
20P SER* 1.3 55.4 + - - +
22P TYR* 3.0 3.2 + - + -
23P LEU* 2.7 49.4 + - + +
73P ILE* 4.0 13.8 - - + +
74P PRO* 3.5 51.1 - - + -
75P LYS 4.5 2.1 + - - -
76P PRO* 3.8 14.9 - - + +
77P PRO* 3.8 23.9 - - - +
93P HIS* 3.8 28.3 - + - -
96P PHE* 5.9 2.9 - + - -
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Residues in contact with SER 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P ARG 2.9 19.1 + - - -
17P GLU* 3.4 12.5 + - - -
19P TYR* 1.3 77.1 - - - +
21P ALA* 1.3 60.8 + - - +
23P LEU* 3.3 2.6 + - - +
24P TYR* 3.1 31.4 + - - -
50P GLU* 3.5 25.5 + - - -
93P HIS* 2.9 31.1 + - - -
97P ILE* 3.4 13.3 - - - +
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Residues in contact with ALA 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P GLU 3.2 6.3 + - - +
18P LEU* 3.5 12.1 - - + +
19P TYR 3.2 0.2 - - - -
20P SER* 1.3 78.4 - - - +
22P TYR* 1.3 58.1 + - - +
25P PHE* 3.1 27.2 + - - +
47P ALA* 3.4 32.1 - - + +
50P GLU* 3.5 14.7 - - + +
51P ILE* 3.7 21.1 - - + -
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Residues in contact with TYR 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157 ASN* 3.7 9.5 + - - +
187 LEU* 3.6 28.8 - - + +
707 LEU* 3.4 33.5 - - + +
717 ASP 2.6 32.0 + - - -
727 GLU* 4.7 0.4 - - - -
737 ILE* 3.7 22.2 - - + -
18P LEU 3.1 13.2 + - - +
19P TYR* 3.0 8.8 + - + +
21P ALA* 1.3 74.9 - - - +
23P LEU* 1.3 60.3 + - - +
25P PHE* 3.5 9.9 + + - +
26P ALA* 3.0 25.5 + - - +
73P ILE* 3.7 24.2 - - + -
74P PRO 3.9 4.3 - - - -
76P PRO* 3.7 29.8 - - + +
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Residues in contact with LEU 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19P TYR* 2.7 34.5 + - + +
20P SER* 3.7 4.3 - - - +
22P TYR* 1.3 73.2 - - - +
24P TYR* 1.3 63.2 + - + +
26P ALA* 3.1 6.4 + - - +
27P MET* 2.9 49.8 + - + +
76P PRO* 4.2 5.3 - - + +
77P PRO* 3.8 28.7 - - + -
80P TRP* 4.3 7.0 - - + -
89P ALA 5.3 0.7 - - - +
93P HIS* 3.5 47.8 - - + +
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Residues in contact with TYR 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P SER* 3.1 25.9 + - - +
23P LEU* 1.3 77.6 - - + +
25P PHE* 1.3 61.4 + - - +
27P MET* 3.8 12.1 - - + +
28P ALA* 2.9 27.7 + - - +
42P TRP* 5.9 0.7 - + - -
43P MET* 3.4 43.7 - - + +
46P GLN* 3.7 21.3 - - + -
47P ALA* 4.1 6.3 - - + -
50P GLU* 3.5 31.9 - - + -
90P ALA* 3.9 27.7 + - + +
93P HIS* 4.0 10.9 - + - -
94P GLU* 2.5 34.9 + - - +
134P VAL* 4.8 4.6 - - + +
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Residues in contact with PHE 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147 LEU* 4.2 11.4 - - + -
187 LEU* 4.2 14.8 - - + -
547 ALA* 5.1 2.7 - - + -
557 LEU* 3.7 30.1 - - + -
587 TYR* 3.6 38.9 - + + -
707 LEU* 3.6 37.8 - - + +
21P ALA 3.1 18.3 + - - +
22P TYR* 3.6 15.9 - + + +
23P LEU 3.2 0.2 - - - -
24P TYR* 1.3 76.9 - - - +
26P ALA* 1.3 60.4 + - - +
28P ALA* 3.7 8.5 - - + +
29P ALA* 3.3 20.1 + - - +
44P LYS* 4.9 7.9 - - + -
47P ALA* 4.2 9.3 - - + +
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Residues in contact with ALA 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677 ARG* 5.0 0.2 + - - -
707 LEU* 3.6 10.8 - - + -
22P TYR 3.0 13.4 + - - +
23P LEU 3.1 9.8 + - - +
25P PHE* 1.3 77.1 - - - +
27P MET* 1.3 63.6 + - - +
28P ALA 3.3 0.2 - - - -
29P ALA* 3.3 7.4 + - - +
30P TYR* 3.2 19.8 + - - +
76P PRO* 3.7 25.1 - - + -
77P PRO 3.8 15.5 - - - +
78P LYS* 4.5 4.2 - - - +
80P TRP* 4.0 6.1 - - + -
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Residues in contact with MET 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23P LEU* 2.9 35.9 + - + +
24P TYR* 3.9 12.3 - - + +
26P ALA* 1.3 72.4 - - - +
28P ALA* 1.3 60.4 + - - +
30P TYR* 3.1 3.3 + - - +
31P PHE* 3.0 39.5 + - + -
43P MET* 3.8 30.3 - - + -
80P TRP* 3.4 39.5 - - + -
86P ALA* 3.4 28.9 - - + +
89P ALA* 4.2 5.4 - - + -
90P ALA* 3.8 24.0 - - + +
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Residues in contact with ALA 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587 TYR* 3.1 13.1 + - - +
24P TYR 2.9 18.2 + - - +
25P PHE* 3.7 11.0 - - + +
26P ALA 3.3 0.2 - - - -
27P MET* 1.3 77.2 - - - +
29P ALA* 1.3 56.6 + - - +
31P PHE 3.4 0.5 + - - -
32P GLU* 3.0 24.8 + - - +
40P ALA* 3.5 29.9 - - - +
43P MET* 3.7 9.8 - - + +
44P LYS* 3.9 16.2 - - + +
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Residues in contact with ALA 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587 TYR* 3.5 18.1 + - + -
627 TYR* 2.5 30.8 + - - +
677 ARG* 3.5 13.8 + - - +
687 VAL* 4.1 13.7 - - + +
707 LEU* 5.5 1.8 - - + -
25P PHE 3.3 12.2 + - - +
26P ALA* 3.4 12.3 - - - +
27P MET 3.2 0.2 - - - -
28P ALA* 1.3 79.2 - - - +
30P TYR* 1.3 60.5 + - - +
33P ASP* 3.3 13.2 + - - +
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Residues in contact with TYR 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677 ARG* 3.8 22.9 - - - +
26P ALA 3.2 11.3 + - - +
27P MET* 3.1 10.8 + - - +
29P ALA* 1.3 77.5 - - - +
31P PHE* 1.3 72.0 + + - +
33P ASP* 3.4 13.7 + - + +
34P LEU* 3.4 43.4 + - + +
79P GLU* 4.3 6.5 - - + -
80P TRP* 3.0 59.8 + + + -
81P GLU 3.6 2.8 + - - -
82P SER* 3.4 24.4 + - - -
83P PRO* 3.7 2.9 - - - +
86P ALA* 4.0 24.0 - - + -
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Residues in contact with PHE 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P MET* 3.0 31.2 + - + +
28P ALA 4.0 1.8 - - - +
30P TYR* 1.3 81.8 - + - +
32P GLU* 1.3 63.5 + - - +
34P LEU* 3.3 8.1 + - + +
36P LEU* 3.0 44.3 + - + +
39P PHE* 3.5 39.5 - + + -
40P ALA 3.8 9.4 - - - +
43P MET* 4.0 31.9 - - + -
83P PRO* 3.8 26.5 - - + -
86P ALA* 3.9 22.9 - - + -
87P PHE* 3.8 22.4 - + - -
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Residues in contact with GLU 32 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587 TYR* 3.1 16.2 + - - +
597 ASN* 5.8 0.9 - - - -
627 TYR* 3.6 35.4 - - + -
28P ALA 3.0 16.8 + - - +
29P ALA 3.8 4.9 - - - +
30P TYR 3.3 0.2 - - - -
31P PHE* 1.3 76.4 - - - +
33P ASP* 1.3 61.8 + - - +
35P GLY* 3.2 12.9 + - - +
36P LEU 4.6 2.0 - - - +
37P GLU* 3.6 28.9 - - - +
40P ALA* 3.5 13.7 - - - +
41P ASN* 5.1 0.3 - - - +
44P LYS* 3.0 29.3 + - - -
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Residues in contact with ASP 33 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627 TYR* 3.7 7.4 - - + -
667 GLY 4.3 9.9 - - - +
677 ARG* 3.5 34.3 + - - +
29P ALA 3.3 12.2 + - - +
30P TYR* 3.5 13.3 - - + +
31P PHE 3.2 0.2 - - - -
32P GLU* 1.3 79.2 - - - +
34P LEU* 1.3 61.3 + - - +
35P GLY* 3.1 2.2 + - - -
79P GLU* 5.2 3.5 - - - +
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Residues in contact with LEU 34 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30P TYR* 3.4 50.9 + - + +
31P PHE* 3.3 10.8 + - + +
33P ASP* 1.3 80.7 - - + +
35P GLY* 1.3 59.8 + - - +
36P LEU* 3.2 28.4 + - + +
83P PRO* 4.1 12.1 - - + -
139Z ASP* 5.9 2.3 - - - +
143Z PHE* 5.4 9.4 - - - -
----------------------------------------------------------
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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