Contacts of the helix formed by residues 38 - 64 (chain S) in PDB entry 1BFR
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 LYS 38 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K ARG* 5.1 9.3 - - - +
157K GLU* 3.0 28.5 + - - +
33S LYS* 5.5 6.3 - - + +
36S GLY* 2.9 18.1 + - - +
37S LEU* 1.3 70.5 - - - +
39S ARG* 1.3 63.9 + - - +
41S ASN* 3.2 8.8 + - - +
42S ASP* 3.0 30.0 + - - +
153S GLN 3.1 5.7 + - - +
154S ILE 3.0 23.3 + - - +
156S GLU* 3.6 33.9 - - - +
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Residues in contact with ARG 39 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S LYS* 1.3 70.8 - - - +
40S LEU* 1.3 65.6 + - - +
42S ASP* 3.3 4.5 + - - +
43S VAL* 3.1 36.9 + - + +
133S TRP* 4.0 14.1 - - - +
137S GLU* 3.1 39.4 + - - -
152S ALA* 4.1 2.5 - - - -
153S GLN* 2.6 56.8 + - - +
155S ARG 3.8 12.2 + - - +
156S GLU* 4.6 7.4 - - - +
157S GLU* 4.2 24.6 - - + +
38U LYS* 5.2 8.5 - - - +
154U ILE* 5.9 7.6 - - - +
155U ARG* 3.4 23.7 - - - +
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Residues in contact with LEU 40 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32S PHE* 3.7 33.4 - - + -
37S LEU* 3.1 17.4 + - + +
39S ARG* 1.3 85.2 - - - +
41S ASN* 1.3 64.8 + - - +
43S VAL* 4.2 1.3 - - - +
44S GLU* 3.1 30.0 + - - +
83S VAL* 4.2 22.2 - - + -
87S LEU* 5.0 3.1 - - + -
133S TRP* 4.1 20.0 - - + -
149S TYR* 3.6 21.8 - - + +
150S LEU* 5.7 0.2 - - + -
153S GLN* 3.5 38.3 + - + +
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Residues in contact with ASN 41 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S ALA* 3.1 32.5 - - - +
30S ARG* 2.9 28.2 + - - +
32S PHE* 3.7 1.4 - - - +
33S LYS* 3.4 38.7 - - + +
37S LEU 3.1 8.6 + - - +
38S LYS* 3.2 10.8 + - - +
40S LEU* 1.3 75.8 - - - +
42S ASP* 1.3 77.0 + - - +
45S TYR* 2.9 25.6 + - - +
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Residues in contact with ASP 42 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38S LYS* 3.0 16.5 + - - +
39S ARG* 3.3 5.1 + - - +
41S ASN* 1.3 88.3 + - - +
43S VAL* 1.3 62.1 + - + +
45S TYR* 3.8 3.6 - - - +
46S HIS* 2.7 43.9 + - + +
156S GLU* 3.3 38.0 - - - +
157S GLU 5.5 0.2 - - - +
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Residues in contact with VAL 43 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S ARG* 3.1 29.1 + - + +
40S LEU 4.4 0.7 - - - +
42S ASP* 1.3 74.1 - - + +
44S GLU* 1.3 63.1 + - - +
46S HIS* 3.2 8.3 + - + +
47S GLU* 3.0 30.3 + - + +
133S TRP* 3.5 56.5 - - + +
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Residues in contact with GLU 44 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25S TYR* 3.5 25.3 - - - +
28S HIS* 3.3 20.6 - - - +
29S ALA* 3.9 19.1 - - + +
32S PHE* 3.8 17.4 - - + -
40S LEU 3.1 19.0 + - - +
43S VAL* 1.3 73.4 - - - +
45S TYR* 1.3 62.7 + - - +
47S GLU* 3.2 7.7 + - - +
48S SER* 2.9 22.2 + - - -
87S LEU* 4.4 3.1 - - - +
90S ASP* 2.7 27.8 - - - +
133S TRP* 3.6 26.2 - - + -
134S LEU* 4.1 2.9 - - - +
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Residues in contact with TYR 45 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26S PHE* 3.6 32.5 - + - -
29S ALA* 3.4 11.6 - - + +
30S ARG* 3.7 28.3 - - - +
41S ASN* 2.9 20.3 + - - +
42S ASP* 3.8 4.0 - - - +
44S GLU* 1.3 75.7 - - - +
46S HIS* 1.3 84.3 + + - +
48S SER* 3.2 8.2 - - - -
49S ILE* 3.0 44.3 + - + +
200T HEM 3.6 29.2 - - + +
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Residues in contact with HIS 46 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S ASP* 2.7 35.6 + - + +
43S VAL* 3.6 8.4 - - + +
45S TYR* 1.3 96.8 - + - +
47S GLU* 1.3 65.5 + - + +
49S ILE* 3.2 10.1 + - + +
50S ASP* 2.9 28.4 + - - +
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Residues in contact with GLU 47 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25S TYR* 3.2 39.0 + - + -
43S VAL* 3.0 20.7 + - + +
44S GLU* 3.2 14.3 + - - +
46S HIS* 1.3 73.2 - - + +
48S SER* 1.3 63.6 + - - +
50S ASP* 3.1 7.4 + - - +
51S GLU* 3.1 27.4 + - - +
130S HIS* 3.5 44.4 - - + +
133S TRP* 3.8 27.1 - - - +
134S LEU* 4.6 1.6 - - - +
----------------------------------------------------------
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Residues in contact with SER 48 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S ILE* 3.3 19.7 + - - +
25S TYR* 3.9 8.6 - - - +
26S PHE* 3.4 29.5 - - - -
44S GLU 2.9 11.5 + - - -
45S TYR* 3.2 11.4 - - - -
47S GLU* 1.3 74.3 - - - +
49S ILE* 1.3 62.3 + - - -
51S GLU* 3.1 8.9 + - - +
52S MET* 3.0 41.6 + - - +
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Residues in contact with ILE 49 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45S TYR* 3.0 51.0 + - + +
46S HIS* 3.2 12.1 + - + +
48S SER* 1.3 73.7 - - - +
50S ASP* 1.3 62.2 + - - +
52S MET* 3.2 15.5 - - + +
53S LYS* 2.9 32.4 + - - +
200T HEM 3.8 60.3 - - + +
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Residues in contact with ASP 50 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46S HIS* 2.9 22.6 + - - +
47S GLU* 3.4 9.0 - - - +
49S ILE* 1.3 71.8 - - - +
51S GLU* 1.3 59.1 + - - +
53S LYS* 3.4 16.6 + - - +
54S HIS* 2.9 41.6 + - + +
126S ASP* 5.1 6.9 - - - +
130S HIS* 2.8 34.1 + - + -
----------------------------------------------------------
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Residues in contact with GLU 51 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S GLU* 2.8 11.2 - - - +
21S ALA* 3.9 15.1 - - + +
22S ILE* 3.6 24.6 - - + +
25S TYR* 3.6 10.4 - - + -
47S GLU 3.1 13.1 + - - +
48S SER 3.1 3.3 + - - +
50S ASP* 1.3 71.3 - - - +
52S MET* 1.3 56.5 + - - +
54S HIS* 2.8 15.1 + - - +
55S ALA* 2.8 35.0 + - - +
94S GLU* 3.2 5.7 - - - +
127S GLU* 2.9 2.3 - - - +
130S HIS* 3.4 6.2 + - - -
201S MN 2.1 35.1 + - - -
202S MN 2.0 34.7 + - - -
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Residues in contact with MET 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S ILE* 3.5 22.2 - - + +
26S PHE* 4.1 3.6 - - + -
48S SER* 3.0 38.6 + - - +
49S ILE* 3.2 20.2 - - + +
51S GLU* 1.3 74.5 - - - +
53S LYS* 1.3 61.9 + - - +
55S ALA* 3.2 2.9 + - - +
56S ASP* 3.0 21.0 + - - +
200T HEM 2.2 101.3 - - + +
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Residues in contact with LYS 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49S ILE* 2.9 25.4 + - - +
50S ASP* 3.6 17.7 + - - +
52S MET* 1.3 75.4 - - - +
54S HIS* 1.3 65.2 + - + +
56S ASP* 3.4 8.8 + - - +
57S ARG* 3.1 26.3 + - - +
200T HEM 3.5 41.7 - - + +
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Residues in contact with HIS 54 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S GLU* 3.6 14.8 - - - +
50S ASP* 2.9 29.1 + - + +
51S GLU* 2.8 12.3 + - - +
53S LYS* 1.3 72.8 - - + +
55S ALA* 1.3 64.5 + - - +
57S ARG* 2.9 24.0 + - - +
58S TYR* 3.1 17.9 + - + -
123S ILE* 3.6 30.6 - - + +
126S ASP* 2.8 38.5 + - + -
127S GLU* 3.1 18.4 - - - -
130S HIS* 4.9 0.4 - + - -
202S MN 2.5 24.4 + - - -
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Residues in contact with ALA 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S LEU* 3.8 21.5 - - + +
18S GLU* 4.2 8.6 - - + +
19S LEU* 4.6 3.4 - - + -
22S ILE* 4.0 13.9 - - + -
51S GLU 2.8 15.2 + - - +
52S MET 3.4 3.6 - - - +
54S HIS* 1.3 69.6 - - - +
56S ASP* 1.3 62.8 + - - +
58S TYR* 3.2 8.4 + - - +
59S ILE* 2.9 27.8 + - - +
200T HEM 3.4 22.9 - - + -
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Residues in contact with ASP 56 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52S MET 3.0 13.5 + - - +
53S LYS* 3.6 12.5 - - - +
54S HIS 3.2 0.2 - - - -
55S ALA* 1.3 76.0 - - - +
57S ARG* 1.3 60.5 + - + +
59S ILE* 3.5 2.1 + - - +
60S GLU* 3.0 34.5 + - - +
26T PHE* 3.4 20.9 - - + -
30T ARG* 2.9 45.7 + - - +
200T HEM 3.6 13.2 - - + +
----------------------------------------------------------
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Residues in contact with ARG 57 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53S LYS* 3.1 14.7 + - - +
54S HIS* 2.9 19.2 + - - +
56S ASP* 1.3 72.2 - - + +
58S TYR* 1.3 61.0 + - - +
60S GLU* 3.5 5.5 + - - +
61S ARG* 3.0 24.3 + - - +
119S MET* 3.7 37.9 - - - +
122S GLU* 3.0 48.6 + - - +
123S ILE* 4.1 19.1 - - + +
126S ASP* 5.8 1.4 + - - -
----------------------------------------------------------
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Residues in contact with TYR 58 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S LEU* 4.2 20.2 - - + +
14S LEU* 3.8 31.1 - - + +
15S LEU* 4.0 26.7 - - + -
18S GLU* 3.8 26.8 + - + -
54S HIS 3.1 20.5 + - - -
55S ALA* 3.7 4.5 - - - +
57S ARG* 1.3 75.4 - - - +
59S ILE* 1.4 61.8 + - - +
61S ARG* 3.1 4.9 + - - +
62S ILE* 2.9 32.8 + - + +
101S LEU* 3.7 23.7 - - - +
119S MET* 3.5 26.9 - - + -
120S MET* 4.4 3.1 - - + -
123S ILE* 3.6 27.1 - - + +
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Residues in contact with ILE 59 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S LEU* 4.0 17.5 - - + -
55S ALA 2.9 24.9 + - - +
56S ASP* 3.8 4.7 - - - +
58S TYR* 1.4 70.0 - - - +
60S GLU* 1.3 63.9 + - - +
62S ILE* 4.8 0.7 - - - -
63S LEU* 3.1 41.0 + - + +
69S PRO* 3.8 19.1 - - + +
71S LEU* 3.8 27.1 - - + -
26T PHE* 3.8 27.6 - - + -
27T LEU* 4.0 8.7 - - + -
30T ARG* 3.9 18.6 - - + -
200T HEM 4.0 9.4 - - + -
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Residues in contact with GLU 60 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S ASP* 3.0 42.2 + - - +
57S ARG* 3.9 5.2 - - - +
59S ILE* 1.3 77.0 - - - +
61S ARG* 1.3 60.0 + - - +
63S LEU* 3.5 7.0 + - + +
64S PHE* 3.1 23.0 + - - +
30T ARG* 3.2 24.7 + - + +
33T LYS* 3.4 31.2 + - - -
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Residues in contact with ARG 61 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128R GLU* 2.8 34.1 + - - +
1S MET* 5.0 0.8 - - - +
11S LEU* 4.0 20.9 - - + -
57S ARG 3.0 17.8 + - - +
58S TYR 3.7 2.5 - - - +
60S GLU* 1.3 70.5 - - - +
62S ILE* 1.3 66.9 + - - +
64S PHE* 3.2 26.3 + - - +
65S LEU* 2.9 43.4 + - + +
113S ASP* 3.1 25.1 + - - -
115S VAL* 3.7 16.3 - - - +
116S SER* 3.0 21.4 + - - +
119S MET* 4.0 24.5 - - + -
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Residues in contact with ILE 62 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S ILE* 4.0 12.3 - - + +
11S LEU* 3.7 28.9 - - + +
12S ASN* 3.6 38.4 - - - +
15S LEU* 4.2 10.3 - - + -
58S TYR 2.9 29.5 + - - +
59S ILE 4.0 2.9 - - - +
61S ARG* 1.3 72.0 - - - +
63S LEU* 1.3 59.4 + - - +
65S LEU* 3.3 6.2 + - - +
66S GLU 3.1 4.5 + - - -
67S GLY* 2.9 49.4 + - - -
68S LEU 3.7 6.7 - - - +
69S PRO* 3.7 15.3 - - + -
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Residues in contact with LEU 63 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59S ILE* 3.1 40.8 + - + +
60S GLU* 3.7 6.7 - - - +
61S ARG 3.3 0.2 - - - -
62S ILE* 1.3 75.2 - - - +
64S PHE* 1.3 62.6 + - - +
66S GLU* 3.0 16.3 + - - +
67S GLY 4.0 9.0 - - - +
68S LEU* 5.8 1.8 - - + -
69S PRO* 3.4 27.8 - - + -
27T LEU* 4.5 1.1 - - + -
30T ARG* 3.9 27.1 - - + +
31T MET* 4.1 19.3 - - + +
34T ASN* 3.9 33.8 + - + +
----------------------------------------------------------
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Residues in contact with PHE 64 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128R GLU* 3.7 22.9 - - + -
131R ILE* 4.6 1.6 - - + -
132R ASP* 3.6 47.3 - - + +
135R GLU* 4.0 5.4 - - - -
1S MET* 2.9 76.8 + - + +
60S GLU 3.1 15.0 + - - +
61S ARG* 3.2 38.6 + - - +
63S LEU* 1.3 74.2 - - - +
65S LEU* 1.3 63.3 + - + +
66S GLU* 3.1 4.7 + - - +
34T ASN* 4.2 10.2 + - - +
----------------------------------------------------------
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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