Contacts of the helix formed by residues 4 - 35 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I GLY* 1.3 70.9 - - - +
5I LYS* 1.3 65.7 + - - +
6I LYS* 2.9 26.2 + - - +
7I VAL* 3.0 22.7 + - + +
8I ILE* 3.2 21.3 + - - +
65I LEU* 5.3 1.0 - - - +
107I HIS* 3.0 24.0 + - - -
111I VAL* 3.6 23.5 - - + +
113I ASP* 5.8 1.9 + - + +
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Residues in contact with LYS 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I GLY 3.2 5.4 + - - -
4I ASP* 1.3 75.0 + - - +
6I LYS* 1.3 63.8 + - + +
8I ILE* 3.3 9.0 + - - +
9I GLN* 3.1 42.1 + - + +
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Residues in contact with LYS 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ASP* 2.9 4.2 + - - +
5I LYS* 1.3 81.3 - - + +
7I VAL* 1.3 59.8 + - - +
8I ILE 3.1 0.2 - - - -
9I GLN* 3.1 20.9 + - - +
10I HIS* 2.8 39.3 + - + +
107I HIS* 3.1 34.5 - - + +
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Residues in contact with VAL 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I ASP* 3.0 37.9 + - + +
6I LYS* 1.3 74.6 - - - +
8I ILE* 1.3 58.5 - - + +
10I HIS* 3.1 6.9 + - - +
11I LEU* 2.8 40.3 + - + +
65I LEU* 4.1 6.3 - - + -
107I HIS* 3.5 11.1 - - + -
108I CYS* 4.3 11.4 - - - -
111I VAL* 3.7 20.0 - - + -
113I ASP* 3.4 27.4 - - + +
116I SER* 3.8 14.8 - - - +
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Residues in contact with ILE 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I GLY 4.1 9.2 - - - +
4I ASP 3.2 14.2 + - - +
5I LYS* 3.6 11.2 - - - +
6I LYS 3.1 0.4 - - - -
7I VAL* 1.3 75.8 - - - +
9I GLN* 1.3 59.5 + - + +
11I LEU* 3.5 8.6 + - + +
12I ASN* 2.9 43.4 + - - +
62I ILE* 4.5 7.9 - - + +
65I LEU* 3.6 50.3 - - + +
66I GLU 4.5 0.7 - - - -
67I GLY* 3.9 26.7 - - - +
68I LEU 4.8 0.7 - - - +
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Residues in contact with GLN 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I LYS* 3.1 28.6 + - + +
6I LYS* 3.1 28.9 + - + +
8I ILE* 1.3 78.2 - - + +
10I HIS* 1.3 57.8 + - + +
12I ASN* 3.4 6.9 + - - +
13I LYS* 2.9 26.7 + - - +
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Residues in contact with HIS 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I LYS* 2.8 28.3 + - + +
7I VAL* 3.1 8.9 + - - +
9I GLN* 1.3 76.2 - - + +
11I LEU* 1.3 55.8 + - + +
13I LYS* 2.9 16.7 + - + +
14I ILE* 2.8 40.2 + - - +
100I ASP 4.9 1.4 + - - -
103I GLU* 4.0 25.1 - - + -
104I ALA* 3.6 27.3 + - + +
107I HIS* 3.7 32.9 - + + +
108I CYS* 5.9 2.0 - - - -
120I LEU* 5.8 0.2 - - + -
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Residues in contact with LEU 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I VAL* 2.8 32.7 + - + +
8I ILE* 3.6 4.5 - - - +
10I HIS* 1.3 71.7 - - + +
12I ASN* 1.3 50.7 + - - +
14I ILE* 3.2 6.5 + - - +
15I LEU* 2.7 35.3 + - - +
58I LEU* 4.1 21.1 - - + +
61I ARG* 3.9 26.5 - - + -
62I ILE* 3.4 31.9 - - + +
65I LEU* 4.0 19.3 - - + -
108I CYS* 5.5 0.2 - - - -
116I SER* 4.3 6.7 - - - +
119I LEU* 5.5 1.3 - - + -
120I LEU* 4.2 26.5 - - + -
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Residues in contact with ASN 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I ILE* 2.9 37.7 + - - +
9I GLN* 3.8 6.2 - - - +
11I LEU* 1.3 72.5 - - - +
13I LYS* 1.3 63.4 + - - +
15I LEU* 3.7 7.5 - - - +
16I GLY* 2.9 20.1 + - - -
62I ILE* 3.7 10.3 - - - +
68I LEU 3.1 20.4 + - - -
69I PRO* 3.5 4.7 - - - +
70I ASN* 2.7 41.7 + - + +
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Residues in contact with LYS 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I GLN 2.9 15.1 + - - +
10I HIS* 2.9 17.7 + - + +
12I ASN* 1.3 76.1 - - - +
14I ILE* 1.3 67.8 + - + +
16I GLY* 3.2 3.0 + - - -
17I ASN* 3.1 24.2 + - - +
96I LYS* 4.3 9.0 - - - +
100I ASP* 3.4 42.4 + - + +
103I GLU* 5.1 6.7 + - - -
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Residues in contact with ILE 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10I HIS 2.8 21.9 + - - +
11I LEU* 3.6 4.9 - - - +
13I LYS* 1.3 72.8 - - + +
15I LEU* 1.3 64.3 + - - +
17I ASN* 3.0 19.5 + - + +
18I GLU* 3.0 23.1 + - - +
58I LEU* 3.9 16.6 - - + -
97I ALA 5.0 0.7 - - - +
100I ASP* 3.6 35.2 - - + +
101I LEU* 3.5 38.4 - - + +
104I ALA* 4.0 6.5 - - + -
120I LEU* 4.0 18.4 - - + -
123I ILE* 4.9 2.5 - - + -
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Residues in contact with LEU 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I LEU 2.7 21.1 + - - +
12I ASN* 3.7 18.6 - - - +
13I LYS 3.2 0.4 - - - -
14I ILE* 1.3 72.5 - - - +
16I GLY* 1.3 63.5 + - - +
18I GLU* 3.2 2.4 + - - +
19I LEU* 3.0 35.6 + - + +
55I ALA* 3.6 35.7 - - + +
58I LEU* 3.8 15.0 - - + +
59I ILE* 3.9 28.0 - - + -
62I ILE* 4.3 6.7 - - + -
69I PRO* 4.4 0.7 - - + -
70I ASN 3.5 26.5 - - - +
71I LEU* 4.2 5.2 - - + -
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Residues in contact with GLY 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I ASN 2.9 15.3 + - - -
13I LYS* 3.2 3.8 + - - -
14I ILE 3.2 0.4 - - - -
15I LEU* 1.3 78.2 - - - +
17I ASN* 1.3 64.7 + - - +
19I LEU* 3.4 13.5 + - - +
20I ILE* 3.2 28.1 + - - +
70I ASN 5.4 1.5 + - - -
73I ASP 4.8 8.6 - - - +
74I LEU* 5.2 0.3 - - - +
75I GLY 5.3 0.7 + - - -
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Residues in contact with ASN 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I LYS* 3.1 15.4 + - - +
14I ILE* 3.0 14.9 + - + +
16I GLY* 1.3 79.3 - - - +
18I GLU* 1.3 63.2 + - + +
20I ILE* 3.2 18.0 + - - +
21I ALA* 3.0 22.8 + - - +
93I LEU* 5.0 5.1 - - + +
96I LYS* 3.7 16.5 + - - +
97I ALA* 4.0 26.1 + - + +
100I ASP* 2.9 36.8 + - - +
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Residues in contact with GLU 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ILE* 3.0 20.9 + - + +
15I LEU* 3.2 8.5 + - - +
17I ASN* 1.3 74.5 - - - +
19I LEU* 1.3 58.7 + - - +
21I ALA* 3.1 3.9 + - - +
22I ILE* 2.8 35.1 + - - +
51I GLU* 2.9 39.0 - - - +
54I HIS* 3.8 13.9 - - + -
55I ALA* 4.2 18.2 - - + +
58I LEU* 4.1 18.2 - - + -
97I ALA* 5.8 2.1 - - - +
101I LEU* 5.3 1.6 - - - +
123I ILE* 3.6 15.2 - - - +
127I GLU* 2.8 22.2 - - - +
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Residues in contact with LEU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LEU* 3.0 35.7 + - + +
16I GLY* 3.8 10.8 - - - +
17I ASN 3.3 0.4 - - - -
18I GLU* 1.3 76.2 - - - +
20I ILE* 1.3 62.6 + - - +
22I ILE* 3.7 9.4 + - + +
23I ASN* 3.4 27.2 + - - +
55I ALA* 4.8 2.5 - - + -
59I ILE* 6.0 0.2 - - + -
70I ASN 3.8 21.1 - - - +
71I LEU* 4.0 21.5 - - + +
73I ASP 4.5 8.5 - - - +
74I LEU* 3.8 14.9 - - + +
23J ASN* 4.5 11.2 - - - +
159J HEM 3.9 28.5 - - + -
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Residues in contact with ILE 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I GLY 3.2 17.4 + - - +
17I ASN* 3.4 18.6 - - - +
18I GLU 3.2 0.6 - - - -
19I LEU* 1.3 77.9 - - - +
21I ALA* 1.3 57.2 + - - +
23I ASN* 3.4 3.3 + - - +
24I GLN* 3.0 27.5 + - - +
74I LEU* 3.9 9.0 - - + -
75I GLY* 3.6 40.2 - - - +
76I LYS 3.7 17.7 - - - +
77I LEU* 4.3 12.5 - - + +
93I LEU* 3.7 29.6 - - + -
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Residues in contact with ALA 21 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I ASN 3.0 13.6 + - - +
18I GLU* 3.1 7.8 + - - +
20I ILE* 1.3 73.8 - - - +
22I ILE* 1.3 66.3 + - - +
24I GLN* 4.5 0.2 - - - -
25I TYR* 2.8 48.3 + - + +
51I GLU* 3.5 26.9 - - + +
93I LEU* 3.6 20.4 - - + -
94I GLU* 5.0 0.4 - - - +
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Residues in contact with ILE 22 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I GLU 2.8 26.5 + - - +
19I LEU* 3.8 14.6 - - + +
20I ILE 3.3 0.2 - - - -
21I ALA* 1.3 72.8 - - - +
23I ASN* 1.3 68.7 + - - +
26I PHE* 3.0 24.8 + - + +
48I SER* 3.0 15.3 + - - +
51I GLU* 3.8 22.4 - - + +
52I MET* 3.8 41.5 - - + +
55I ALA* 4.3 9.0 - - + -
159J HEM 3.7 43.1 - - + -
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Residues in contact with ASN 23 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19I LEU 3.4 16.1 + - - +
20I ILE 3.4 4.2 + - - +
21I ALA 3.3 0.6 - - - -
22I ILE* 1.3 81.8 - - - +
24I GLN* 1.3 61.5 + - - +
26I PHE* 4.4 1.3 - - - -
27I LEU* 2.9 31.5 + - - +
74I LEU* 3.8 13.3 - - - +
77I LEU* 4.2 11.2 - - + +
19J LEU* 4.8 7.1 - - - +
71J LEU* 3.1 46.4 + - + +
159J HEM 3.5 27.1 - - - +
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Residues in contact with GLN 24 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ILE* 3.0 18.4 + - - +
21I ALA* 3.9 2.7 - - - +
23I ASN* 1.3 77.8 - - - +
25I TYR* 1.3 54.9 + - + +
27I LEU* 3.7 1.9 - - - +
28I HIS* 2.8 46.4 + - + +
77I LEU* 4.3 8.7 - - + +
78I LEU* 3.0 47.8 + - - +
79I ILE* 4.2 14.3 - - + +
89I CYS 3.2 24.7 + - - -
90I ASP* 2.9 24.5 + - - +
93I LEU* 3.5 21.1 - - - +
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Residues in contact with TYR 25 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I ALA* 2.8 37.9 + - + +
24I GLN* 1.3 77.0 - - + +
26I PHE* 1.3 59.8 + - - +
28I HIS 3.3 0.2 + - - -
29I SER* 2.8 27.4 + - - -
44I GLU* 3.0 29.0 - - - +
47I GLU* 3.9 15.0 - - + -
48I SER* 3.8 16.4 - - - -
51I GLU* 3.8 20.0 - - + -
90I ASP* 3.2 37.4 + - + -
93I LEU* 4.0 11.2 - - + +
94I GLU* 2.3 39.5 + - - +
130I HIS* 3.4 18.1 - + - -
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Residues in contact with PHE 26 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22I ILE 3.0 21.9 + - - +
23I ASN* 3.9 5.2 - - - +
24I GLN 3.2 0.2 - - - -
25I TYR* 1.3 75.9 - - - +
27I LEU* 1.3 64.3 + - - +
29I SER* 3.2 7.3 + - - -
30I ARG* 3.1 36.7 + - + -
45I TYR* 3.9 25.8 - + - -
48I SER* 3.6 17.7 + - - +
52I MET* 4.1 9.2 - - + -
56J ASP* 3.5 41.5 - - + -
59J ILE* 4.0 19.1 - - + -
71J LEU* 4.9 2.0 - - + -
159J HEM 3.6 45.3 - + + -
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Residues in contact with LEU 27 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23I ASN 2.9 18.3 + - - +
24I GLN 3.9 2.5 - - - +
26I PHE* 1.3 80.9 - - - +
28I HIS* 1.3 63.5 + - - +
30I ARG* 3.2 2.9 + - - -
31I MET* 2.9 42.1 + - + +
77I LEU* 5.8 1.6 - - + -
79I ILE* 3.7 36.6 - - + -
59J ILE* 4.5 5.4 - - + -
63J LEU* 4.5 6.3 - - + -
69J PRO* 3.9 46.7 - - + +
71J LEU* 4.4 18.3 - - + +
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Residues in contact with HIS 28 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24I GLN* 2.8 22.0 + - + +
25I TYR 3.6 0.4 - - - +
27I LEU* 1.3 77.3 - - - +
29I SER* 1.3 62.1 + - - +
31I MET* 3.2 14.4 + - - +
32I TRP* 2.9 31.5 + - + -
44I GLU* 3.4 17.7 + - + +
78I LEU 3.5 20.2 + - - -
79I ILE* 3.7 7.2 - - + -
80I GLY 3.2 23.3 + - - -
86I MET* 3.6 47.5 - - + +
89I CYS* 4.1 0.7 - - + -
90I ASP* 2.8 29.3 + - - -
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Residues in contact with SER 29 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I TYR 2.8 16.3 + - - -
26I PHE* 3.2 12.3 + - - -
28I HIS* 1.3 71.1 - - - +
30I ARG* 1.3 80.8 + - - +
32I TRP* 3.2 5.2 + - - +
33I ASN* 2.9 29.1 + - - -
41I GLY* 2.7 27.8 + - - -
44I GLU* 3.5 10.1 - - - +
45I TYR* 3.5 16.4 - - - +
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Residues in contact with ARG 30 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26I PHE* 3.1 35.2 + - + +
27I LEU 4.0 1.6 - - - +
29I SER* 1.3 100.6 + - - +
31I MET* 1.3 61.6 + - - +
33I ASN* 3.5 20.5 + - + +
34I ASP* 2.9 30.0 + - - +
41I GLY 4.5 0.2 + - - -
45I TYR* 3.6 29.6 - - - +
56J ASP* 2.7 43.4 + - - +
59J ILE* 3.9 25.4 - - + -
60J GLU* 3.6 26.8 + - + +
63J LEU* 3.9 10.2 - - + +
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Residues in contact with MET 31 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27I LEU* 2.9 46.7 + - + +
28I HIS* 3.6 18.8 - - - +
30I ARG* 1.3 78.3 - - - +
32I TRP* 1.3 62.8 + - - +
34I ASP* 3.3 8.2 + - - +
35I TRP* 3.0 58.0 + - + -
79I ILE* 4.2 9.2 - - + -
80I GLY 3.5 22.9 - - - +
81I GLU* 4.7 2.7 - - - -
86I MET* 4.2 8.7 - - + -
63J LEU* 4.5 14.8 - - + -
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Residues in contact with TRP 32 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I HIS* 2.9 26.7 + - + -
29I SER 3.5 5.8 - - - +
31I MET* 1.3 77.2 - - - +
33I ASN* 1.3 59.5 + - - +
35I TRP* 3.1 12.5 + + - -
36I GLY 3.1 4.5 + - - -
37I LEU* 2.9 52.1 + - + +
40I LEU* 3.6 32.0 - - + +
41I GLY 3.6 13.9 - - - +
44I GLU* 3.6 43.3 - - + -
83I THR* 3.1 36.3 + - + -
86I MET* 3.5 36.2 - - + +
87I LEU* 4.1 20.6 - - + -
90I ASP* 4.8 1.8 - - - -
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Residues in contact with ASN 33 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G THR* 4.8 1.7 + - - +
29I SER* 2.9 19.5 + - - +
30I ARG* 3.5 35.4 + - + +
32I TRP* 1.3 70.6 - - - +
34I ASP* 1.3 64.3 + - - +
36I GLY* 2.9 15.2 + - - +
37I LEU 4.8 1.3 - - - +
38I LYS* 3.7 30.1 + - + +
41I GLY* 3.5 21.0 - - - -
42I ALA 4.3 0.4 - - - +
60J GLU* 5.1 5.8 - - + +
----------------------------------------------------------
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Residues in contact with ASP 34 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G ASP* 4.4 12.0 - - - +
136G THR* 3.4 19.2 + - - +
30I ARG 2.9 18.2 + - - +
31I MET* 3.6 5.0 - - - +
32I TRP 3.3 0.2 - - - -
33I ASN* 1.3 75.3 - - - +
35I TRP* 1.3 77.0 + - - +
36I GLY 3.4 0.2 + - - -
63J LEU* 4.1 42.4 - - + +
64J PHE* 4.6 3.9 - - - +
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Residues in contact with TRP 35 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G THR* 3.6 8.0 - - - +
139G GLY 5.6 0.2 - - - -
140G LEU* 3.4 24.1 + - - +
143G LYS* 3.8 38.8 + - - +
31I MET* 3.0 40.2 + - + +
32I TRP* 3.1 20.8 + + - +
34I ASP* 1.3 92.8 + - - +
36I GLY* 1.3 60.3 + - - +
37I LEU* 3.4 11.2 - - + -
81I GLU 3.5 25.1 - - - -
82I ASN* 4.1 6.5 - - - -
83I THR* 4.4 3.6 - - - -
86I MET* 3.5 32.8 - - + -
----------------------------------------------------------
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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