Contacts of the helix formed by residues 4 - 35 (chain P) 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 P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P GLY* 1.3 71.0 - - - -
5P LYS* 1.3 66.2 + - - +
6P LYS* 3.3 8.9 + - - +
7P VAL* 2.8 45.0 + - + +
8P ILE* 3.1 13.7 + - - +
107P HIS* 2.8 30.9 + - - -
111P VAL* 3.8 25.0 - - + +
113P ASP* 5.6 2.1 + - + +
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Residues in contact with LYS 5 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P GLY 3.4 4.8 + - - -
4P ASP* 1.3 75.2 + - - +
6P LYS* 1.3 64.5 + - + +
8P ILE* 3.3 13.2 + - - +
9P GLN* 3.1 36.5 + - + +
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Residues in contact with LYS 6 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P ASP* 3.2 7.0 + - - +
5P LYS* 1.3 77.4 - - + +
7P VAL* 1.3 67.9 + - - +
9P GLN* 3.3 23.1 + - - +
10P HIS* 2.9 30.4 + - + +
107P HIS* 3.2 34.8 - - + +
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Residues in contact with VAL 7 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4P ASP* 2.8 39.6 + - + +
6P LYS* 1.3 75.2 - - - +
8P ILE* 1.3 58.3 + - - +
10P HIS* 3.1 7.5 + - - +
11P LEU* 2.8 35.4 + - + +
65P LEU* 4.1 12.3 - - + -
107P HIS* 3.7 11.9 - - + -
108P CYS* 4.2 18.2 - - - -
111P VAL* 3.7 17.7 - - + -
113P ASP* 3.5 24.5 - - + +
116P SER* 4.0 8.7 - - - +
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Residues in contact with ILE 8 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P GLY 4.1 10.1 - - - +
4P ASP 3.1 15.3 + - - +
5P LYS* 3.5 11.0 - - - +
7P VAL* 1.3 77.0 - - - +
9P GLN* 1.3 56.1 + - + +
11P LEU* 3.5 7.7 + - + +
12P ASN* 2.9 41.2 + - - +
62P ILE* 4.5 7.6 - - + +
65P LEU* 3.8 43.5 - - + +
66P GLU 4.6 0.7 - - - +
67P GLY* 4.0 28.7 - - - +
68P LEU 4.6 1.3 - - - +
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Residues in contact with GLN 9 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5P LYS* 3.1 26.6 + - + +
6P LYS* 3.3 38.1 + - - +
8P ILE* 1.3 71.2 - - + +
10P HIS* 1.3 62.7 + - + +
12P ASN* 3.3 6.4 + - - +
13P LYS* 2.8 28.6 + - - +
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Residues in contact with HIS 10 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6P LYS* 2.9 25.5 + - + +
7P VAL* 3.4 8.3 - - + +
9P GLN* 1.3 78.9 - - + +
11P LEU* 1.3 58.9 + - + +
13P LYS* 3.0 14.6 + - + +
14P ILE* 2.9 36.2 + - - +
100P ASP 5.0 1.4 + - - -
103P GLU* 3.9 27.5 + - + +
104P ALA* 3.7 27.1 + - + +
107P HIS* 3.7 35.4 + + + +
108P CYS* 6.0 1.8 - - - -
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Residues in contact with LEU 11 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7P VAL* 2.8 30.1 + - + +
8P ILE* 3.8 4.3 - - - +
10P HIS* 1.3 71.4 - - + +
12P ASN* 1.3 58.2 + - - +
14P ILE* 3.3 5.2 + - - +
15P LEU* 3.0 28.8 + - - +
58P LEU* 4.2 14.7 - - + +
61P ARG* 4.0 19.5 - - + -
62P ILE* 3.6 27.8 - - + +
65P LEU* 3.8 29.4 - - + -
116P SER* 4.2 9.9 - - - +
119P LEU* 5.7 1.8 - - + -
120P LEU* 4.1 35.7 - - + -
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Residues in contact with ASN 12 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8P ILE* 2.9 32.2 + - - +
9P GLN* 3.8 7.1 - - - +
11P LEU* 1.3 74.1 - - - +
13P LYS* 1.3 60.4 + - - +
15P LEU* 3.6 7.7 - - - +
16P GLY* 2.9 25.8 + - - -
62P ILE* 3.5 13.9 - - - +
68P LEU 3.0 23.6 + - - -
69P PRO* 4.2 0.2 - - - +
70P ASN* 2.9 39.6 + - + +
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Residues in contact with LYS 13 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9P GLN 2.8 14.0 + - - +
10P HIS* 3.0 20.6 + - + +
12P ASN* 1.3 78.2 - - - +
14P ILE* 1.3 65.7 + - + +
16P GLY* 3.3 2.2 + - - -
17P ASN* 3.2 24.0 + - - +
96P LYS* 4.1 10.5 - - - +
100P ASP* 3.7 39.6 + - + +
103P GLU* 5.2 5.9 + - - -
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Residues in contact with ILE 14 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P HIS* 2.9 19.5 + - - +
11P LEU* 3.7 4.7 - - - +
13P LYS* 1.3 77.6 - - + +
15P LEU* 1.3 63.6 + - - +
17P ASN* 3.1 12.3 + - + +
18P GLU* 3.0 31.0 + - - +
58P LEU* 4.0 17.0 - - + -
97P ALA 5.1 0.9 - - - +
100P ASP* 3.7 37.0 - - + +
101P LEU* 3.3 34.3 - - + +
104P ALA* 4.2 6.5 - - + -
120P LEU* 3.9 18.8 - - + -
123P ILE* 4.9 1.6 - - + -
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Residues in contact with LEU 15 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11P LEU 3.0 18.0 + - - +
12P ASN* 3.6 22.7 - - - +
14P ILE* 1.3 74.0 - - - +
16P GLY* 1.3 64.2 + - - +
18P GLU* 3.0 4.7 + - - +
19P LEU* 2.9 36.2 + - + +
55P ALA* 3.8 40.6 - - + +
58P LEU* 3.8 14.0 - - + +
59P ILE* 3.8 24.5 - - + -
62P ILE* 4.1 8.5 - - + -
69P PRO* 4.2 0.4 - - + -
70P ASN 3.7 22.9 - - - +
71P LEU* 4.1 4.9 - - + -
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Residues in contact with GLY 16 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12P ASN 2.9 16.9 + - - -
13P LYS 3.3 2.2 + - - -
14P ILE 3.3 0.4 - - - -
15P LEU* 1.3 76.7 - - - +
17P ASN* 1.3 62.3 + - - +
19P LEU* 3.4 13.0 + - - +
20P ILE* 3.3 27.2 + - - +
70P ASN 5.2 2.6 + - - -
73P ASP 4.8 10.3 - - - +
74P LEU* 5.1 0.2 - - - +
75P GLY 5.2 0.5 + - - -
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Residues in contact with ASN 17 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P LYS* 3.2 17.6 + - - +
14P ILE* 3.1 14.4 + - + +
16P GLY* 1.3 75.6 - - - +
18P GLU* 1.3 65.9 + - + +
20P ILE* 3.4 16.3 + - - +
21P ALA* 3.2 22.2 + - - +
93P LEU* 5.0 7.2 - - + +
96P LYS* 4.4 13.1 + - - +
97P ALA* 4.1 25.4 + - + +
100P ASP* 2.9 40.6 + - - +
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Residues in contact with GLU 18 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14P ILE* 3.0 24.3 + - - +
15P LEU* 3.0 6.5 + - - +
17P ASN* 1.3 77.8 - - - +
19P LEU* 1.3 53.8 + - - +
21P ALA* 3.1 4.5 + - - +
22P ILE* 2.8 40.1 + - - +
51P GLU* 3.0 40.0 - - - +
54P HIS* 3.9 12.7 - - + +
55P ALA* 4.2 17.9 - - + +
58P LEU* 3.9 17.7 - - + +
97P ALA* 6.0 1.4 - - - +
101P LEU* 5.3 1.2 - - - +
123P ILE* 3.6 17.0 - - - +
127P GLU* 3.1 19.4 - - - +
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Residues in contact with LEU 19 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23O ASN* 4.7 6.5 - - - +
15P LEU* 2.9 31.8 + - + +
16P GLY* 3.7 10.1 - - - +
18P GLU* 1.3 77.3 - - - +
20P ILE* 1.3 60.4 + - - +
22P ILE* 3.7 9.5 - - + +
23P ASN* 3.4 28.2 + - - +
55P ALA* 4.6 2.2 - - + -
59P ILE* 5.8 0.2 - - + -
70P ASN 3.9 8.7 - - - +
71P LEU* 3.8 37.2 - - + +
73P ASP 4.4 10.3 - - - +
74P LEU* 3.8 16.2 - - + +
159P HEM 3.6 36.1 - - + -
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Residues in contact with ILE 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P GLY 3.3 16.7 + - - +
17P ASN* 3.7 18.6 - - - +
18P GLU 3.2 0.4 - - - -
19P LEU* 1.3 74.3 - - - +
21P ALA* 1.3 60.9 + - - +
23P ASN* 3.4 1.4 + - - -
24P GLN* 2.9 27.1 + - - +
74P LEU* 4.0 7.0 - - + -
75P GLY* 3.5 43.5 - - - +
76P LYS 3.7 21.3 - - - +
77P LEU* 3.9 15.3 - - + +
93P LEU* 3.8 26.5 - - + -
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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
----------------------------------------------------------
17P ASN 3.2 11.0 + - - +
18P GLU 3.1 3.5 + - - +
20P ILE* 1.3 76.1 - - - +
22P ILE* 1.3 67.9 + - - +
24P GLN* 4.4 0.7 - - - -
25P TYR* 2.9 45.5 + - + +
51P GLU* 3.3 27.1 - - - +
93P LEU* 3.6 22.9 - - + +
94P GLU* 5.0 0.7 - - - +
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Residues in contact with ILE 22 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18P GLU 2.8 26.3 + - - +
19P LEU* 3.7 17.5 - - + +
21P ALA* 1.3 72.6 - - - +
23P ASN* 1.3 65.1 + - - +
26P PHE* 3.0 18.4 + - - +
48P SER* 2.9 26.6 + - - +
51P GLU* 3.7 23.1 - - + +
52P MET* 3.8 30.5 - - + +
55P ALA* 4.3 4.3 - - + -
159P HEM 3.6 54.1 - - + -
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Residues in contact with ASN 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19O LEU* 4.4 12.5 - - - +
71O LEU* 3.2 51.1 + - + +
19P LEU 3.4 17.3 + - - +
20P ILE 4.1 2.7 - - - +
21P ALA 3.3 0.2 - - - -
22P ILE* 1.3 77.6 - - - +
24P GLN* 1.3 66.2 + - - +
26P PHE* 4.4 1.3 - - - -
27P LEU* 2.9 26.3 + - - +
74P LEU* 3.8 12.1 - - - +
77P LEU* 4.2 12.1 - - + -
159P HEM 3.4 20.7 - - - +
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Residues in contact with GLN 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P ILE* 2.9 18.5 + - - +
21P ALA* 4.0 2.9 - - - +
23P ASN* 1.3 79.1 - - - +
25P TYR* 1.3 60.5 + - + +
27P LEU* 3.6 1.2 + - - +
28P HIS* 2.9 38.0 + - + +
77P LEU* 3.8 7.1 - - + +
78P LEU* 2.8 49.9 + - - +
79P ILE* 4.1 15.0 - - + -
89P CYS 3.3 22.8 + - - -
90P ASP* 3.0 23.1 + - - +
93P LEU* 3.7 20.4 - - - +
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Residues in contact with TYR 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P ALA* 2.9 36.8 + - + +
24P GLN* 1.3 80.2 - - + +
26P PHE* 1.3 57.4 + - - +
29P SER* 2.7 32.9 + - - -
44P GLU* 3.1 37.8 - - - +
47P GLU* 3.9 13.9 - - + -
48P SER* 3.9 9.4 - - - -
51P GLU* 3.8 20.6 - - + -
90P ASP* 3.5 36.3 + - + -
93P LEU* 4.0 13.2 - - + +
94P GLU* 2.6 42.1 + - - +
130P HIS* 3.6 13.6 - + - -
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Residues in contact with PHE 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56O ASP* 3.5 36.6 - - + -
59O ILE* 4.2 13.2 - - + -
71O LEU* 4.8 1.6 - - + -
22P ILE 3.0 21.7 + - - +
23P ASN* 3.8 4.5 - - - +
25P TYR* 1.3 78.1 - - - +
27P LEU* 1.3 62.4 + - - +
29P SER* 3.2 5.9 + - - -
30P ARG* 3.0 38.4 + - + +
45P TYR* 3.9 24.5 - + - -
48P SER* 3.6 17.9 + - - -
52P MET* 4.0 3.8 - - + -
159P HEM 3.4 58.8 - + + -
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Residues in contact with LEU 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59O ILE* 4.4 8.3 - - + -
63O LEU* 4.5 1.6 - - + -
69O PRO* 3.9 49.4 - - + +
71O LEU* 4.2 19.2 - - + +
23P ASN 2.9 17.7 + - - +
24P GLN 4.0 2.9 - - - +
26P PHE* 1.3 78.6 - - - +
28P HIS* 1.3 63.3 + - - +
30P ARG* 3.1 3.3 + - - +
31P MET* 2.9 44.7 + - + +
77P LEU* 5.6 1.1 - - + -
79P ILE* 3.9 36.1 - - + -
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Residues in contact with HIS 28 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24P GLN* 2.9 25.5 + - + +
25P TYR 3.7 0.4 - - - +
27P LEU* 1.3 72.5 - - - +
29P SER* 1.3 64.4 + - - +
31P MET* 3.4 10.3 + - - -
32P TRP* 3.0 32.0 + - + -
44P GLU* 3.5 15.9 + - + +
78P LEU 3.5 18.6 - - - -
79P ILE* 3.5 9.3 - - + +
80P GLY 2.9 26.6 + - - -
86P MET* 3.6 44.4 + - + +
89P CYS* 4.1 0.7 - - + -
90P ASP* 2.8 30.2 + - - -
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Residues in contact with SER 29 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P TYR 2.7 22.6 + - - -
26P PHE* 3.3 7.9 - - - -
27P LEU 3.2 0.2 - - - -
28P HIS* 1.3 74.3 - - - +
30P ARG* 1.3 86.2 + - - -
32P TRP* 3.2 3.6 + - - +
33P ASN* 3.0 23.2 + - - -
41P GLY* 2.8 28.5 + - - -
44P GLU* 3.5 8.4 - - - +
45P TYR* 3.6 16.2 - - - +
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Residues in contact with ARG 30 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56O ASP* 2.8 41.3 + - - +
59O ILE* 3.9 15.5 - - + -
60O GLU* 3.5 25.8 + - + -
63O LEU* 3.8 20.0 - - + +
26P PHE* 3.0 29.1 + - + +
27P LEU 3.1 1.8 + - - +
29P SER* 1.3 100.9 + - - +
31P MET* 1.3 57.2 + - - +
33P ASN* 3.4 21.7 + - + +
34P ASP* 2.9 29.8 + - - +
41P GLY 4.5 0.4 + - - -
45P TYR* 3.5 31.5 - - - +
159P HEM 5.2 0.2 - - - +
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Residues in contact with MET 31 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63O LEU* 4.2 17.0 - - + -
27P LEU* 2.9 44.7 + - + +
28P HIS* 3.7 13.0 - - - +
30P ARG* 1.3 74.7 - - - +
32P TRP* 1.3 65.9 + - - +
34P ASP* 3.2 9.4 + - - +
35P TRP* 3.1 58.5 + - + -
79P ILE* 4.1 14.6 - - + -
80P GLY 3.6 21.3 - - - +
81P GLU* 5.0 2.0 - - - -
86P MET* 4.0 9.6 - - + -
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Residues in contact with TRP 32 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28P HIS* 3.0 29.0 + - + -
29P SER* 3.6 5.2 - - - +
31P MET* 1.3 77.0 - - - +
33P ASN* 1.3 61.1 + - - +
35P TRP* 3.1 23.1 + + - +
36P GLY 3.0 4.0 + - - -
37P LEU* 2.9 39.6 + - + +
40P LEU* 3.7 29.5 - - + +
41P GLY 3.7 13.2 - - - +
44P GLU* 3.6 44.4 - - + -
83P THR* 2.9 41.1 + - + +
86P MET* 3.6 36.3 - - + +
87P LEU* 4.1 20.9 - - + -
90P ASP* 4.6 1.3 - - - -
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Residues in contact with ASN 33 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136N THR* 4.9 1.0 - - - +
60O GLU* 5.3 2.5 - - + +
29P SER* 3.0 13.4 + - - +
30P ARG* 3.5 37.7 + - + +
32P TRP* 1.3 74.3 - - - +
34P ASP* 1.3 64.4 + - - +
36P GLY* 2.9 14.8 + - - +
37P LEU 4.7 2.2 - - - +
38P LYS* 3.7 25.7 + - + +
41P GLY* 3.4 23.9 - - - -
42P ALA* 4.2 0.4 - - - +
156P GLU* 6.2 0.2 - - - -
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Residues in contact with ASP 34 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132N ASP* 4.4 11.8 - - - +
136N THR* 3.2 21.8 + - - -
63O LEU* 4.0 39.8 - - + +
64O PHE* 4.5 5.2 - - - -
30P ARG 2.9 19.3 + - - +
31P MET* 3.2 8.3 + - - +
33P ASN* 1.3 76.5 - - - +
35P TRP* 1.3 72.1 + - - +
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Residues in contact with TRP 35 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136N THR* 3.5 10.6 - - - +
139N GLY 5.6 0.3 - - - -
140N LEU* 3.3 21.3 + - - +
143N LYS* 3.7 41.1 + - - +
31P MET* 3.1 33.5 + - + -
32P TRP* 3.6 28.5 - + - +
33P ASN 3.0 0.4 - - - -
34P ASP* 1.3 91.3 + - - +
36P GLY* 1.3 61.4 + - - +
37P LEU* 3.5 11.6 + - + -
81P GLU 3.7 22.4 - - - -
82P ASN* 4.0 8.3 - - + -
83P THR* 4.4 3.4 - - - -
86P MET* 3.4 35.9 - - + -
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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