Contacts of the helix formed by residues 42 - 71 (chain W) in PDB entry 3A68
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 VAL 42 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38W ARG* 3.5 3.3 + - - +
40W LYS* 4.3 3.3 + - - -
41W TYR* 1.3 81.2 - - - +
43W ASP* 1.3 67.6 + - - +
44W GLU* 3.9 8.7 - - + +
45W SER* 3.0 30.1 + - - +
46W GLU* 3.1 9.4 + - - +
157W ASN* 3.7 33.4 - - + +
159W ASP* 4.9 0.6 + - + -
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Residues in contact with ASP 43 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38W ARG* 3.0 25.1 + - - +
42W VAL* 1.3 74.2 - - - +
44W GLU* 1.3 56.7 + - - +
46W GLU* 3.2 14.4 + - - +
47W SER* 2.8 36.0 + - - +
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Residues in contact with GLU 44 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42W VAL* 3.1 4.2 - - + +
43W ASP* 1.3 78.2 - - - +
45W SER* 1.3 57.9 + - - +
47W SER* 3.6 7.0 + - - -
48W ALA* 3.0 27.4 + - - +
153W VAL* 3.8 15.7 - - + +
156W LYS* 2.9 29.8 + - - +
157W ASN* 2.8 35.1 + - - +
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Residues in contact with SER 45 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41W TYR* 4.0 17.3 - - - -
42W VAL* 3.0 22.7 + - - +
44W GLU* 1.3 76.7 - - - +
46W GLU* 1.3 65.0 + - - +
48W ALA* 3.2 5.8 + - - +
49W VAL* 2.9 28.4 + - - +
153W VAL* 4.4 2.9 - - - -
154W ALA* 4.6 2.6 - - - -
157W ASN* 4.1 14.4 + - - +
159W ASP* 4.1 9.1 + - - +
162W LEU* 3.8 25.3 - - - +
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Residues in contact with GLU 46 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38W ARG* 3.8 15.3 + - - +
41W TYR* 3.8 19.6 - - + -
42W VAL 3.1 11.2 + - - +
43W ASP* 3.5 26.7 - - - +
45W SER* 1.3 77.7 - - - +
47W SER* 1.3 63.2 + - - +
50W ASN* 3.1 21.5 + - - +
102W GLN* 3.1 27.6 + - - +
107W GLY* 3.4 7.0 - - - -
108W LYS* 2.7 38.1 + - - +
110W LYS* 6.3 3.1 - - - -
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Residues in contact with SER 47 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43W ASP* 2.8 25.4 + - - +
44W GLU* 3.8 7.6 - - - -
46W GLU* 1.3 75.6 + - - +
48W ALA* 1.3 56.9 + - - +
50W ASN* 3.2 11.6 + - - +
51W GLU* 2.9 26.9 + - - +
112W GLN* 5.4 0.3 - - - +
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Residues in contact with ALA 48 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44W GLU 3.0 18.6 + - - +
45W SER* 3.2 5.1 + - - +
47W SER* 1.3 74.2 - - - +
49W VAL* 1.3 66.1 + - - +
51W GLU* 3.3 8.8 + - - +
52W GLN* 3.0 23.0 + - - +
150W LEU* 3.6 23.5 - - + +
153W VAL* 3.9 25.4 - - + -
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Residues in contact with VAL 49 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41W TYR* 3.3 19.5 - - - +
45W SER 2.9 14.7 + - - +
46W GLU 3.6 7.4 - - - +
48W ALA* 1.3 76.8 - - - +
50W ASN* 1.3 62.3 + - - +
52W GLN* 3.2 6.1 + - - +
53W ILE* 2.9 26.3 + - + +
98W LEU* 3.9 30.9 - - + +
101W TYR* 4.8 4.0 - - + -
102W GLN* 3.6 23.8 - - + +
150W LEU* 4.2 11.2 - - + -
162W LEU* 3.9 26.2 - - + -
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Residues in contact with ASN 50 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46W GLU* 3.1 17.2 + - - +
47W SER* 3.2 11.8 + - - +
49W VAL* 1.3 77.4 - - - +
51W GLU* 1.3 60.1 - - - +
53W ILE* 3.4 15.4 + - - +
54W ASN* 3.2 17.7 + - - +
102W GLN* 3.1 17.9 + - - +
108W LYS 3.1 20.4 + - - -
109W VAL* 3.5 4.7 - - - -
110W LYS* 3.0 47.0 + - + +
112W GLN* 3.9 13.5 - - - +
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Residues in contact with GLU 51 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ILE* 3.0 51.9 - - - +
15I PHE* 3.9 12.8 - - - +
47W SER 2.9 12.8 + - - +
48W ALA* 3.5 13.0 - - - +
49W VAL 3.2 0.2 - - - -
50W ASN* 1.3 76.5 - - - +
52W GLN* 1.3 61.0 + - - +
54W ASN* 3.1 4.4 + - - +
55W VAL* 3.0 31.9 + - + +
112W GLN* 3.9 7.6 + - - +
146W LYS* 5.4 7.4 + - + +
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Residues in contact with GLN 52 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48W ALA 3.0 14.3 + - - +
49W VAL 3.2 4.0 + - - +
51W GLU* 1.3 74.9 - - - +
53W ILE* 1.3 66.5 + - - +
55W VAL* 3.1 17.8 + - - +
56W GLU* 2.8 51.3 + - - +
98W LEU* 3.6 20.0 - - + -
143W THR* 4.0 4.9 + - - +
146W LYS* 3.4 28.2 - - - +
147W LEU* 3.5 25.6 - - + +
150W LEU* 3.9 24.1 - - + +
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Residues in contact with ILE 53 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49W VAL* 2.9 24.7 + - + +
50W ASN* 3.6 25.6 - - - +
51W GLU 3.3 0.2 - - - -
52W GLN* 1.3 76.9 - - - +
54W ASN* 1.3 56.9 + - - +
56W GLU* 3.4 2.4 + - - +
57W TYR* 3.0 29.3 + - + +
95W ALA* 3.9 10.9 - - + +
98W LEU* 3.5 29.1 - - + +
99W MET* 3.7 39.3 - - + +
102W GLN* 4.7 0.2 - - + -
109W VAL* 4.4 8.3 - - + -
110W LYS 5.9 1.1 - - - +
111W LEU* 3.7 28.7 - - + -
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Residues in contact with ASN 54 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I ILE* 3.2 20.4 - - - +
15I PHE* 3.8 5.5 + - - +
61K TYR* 4.2 6.2 + - - -
50W ASN 3.2 6.4 + - - +
51W GLU* 3.1 11.3 + - - +
53W ILE* 1.3 78.3 - - - +
55W VAL* 1.3 63.0 + - - +
57W TYR* 3.9 3.9 - - - +
58W ASN* 3.0 48.0 + - - +
111W LEU* 6.4 0.2 - - - -
112W GLN* 3.3 41.4 + - + +
113W SER 3.1 24.8 + - - +
114W ILE* 4.2 2.6 - - - +
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Residues in contact with VAL 55 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I PHE* 4.1 26.9 - - + -
51W GLU* 3.0 33.1 + - + +
52W GLN* 3.1 33.4 + - - +
54W ASN* 1.3 75.3 - - - +
56W GLU* 1.3 62.7 + - - +
58W ASN* 3.3 4.3 + - - +
59W VAL* 3.1 22.4 + - + +
143W THR* 4.3 18.4 - - + +
146W LYS* 4.2 30.7 - - + -
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Residues in contact with GLU 56 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52W GLN* 2.8 38.7 + - - +
55W VAL* 1.3 75.2 - - - +
57W TYR* 1.3 63.3 + - - +
59W VAL* 3.3 4.6 + - - +
60W SER* 3.0 22.7 + - - -
91W GLU* 3.2 13.3 - - - +
94W HIS* 3.5 13.6 - - + +
95W ALA* 3.7 22.7 - - + +
98W LEU* 3.9 16.8 - - + -
143W THR* 3.7 12.1 - - - +
147W LEU* 4.0 9.5 - - - +
170W TYR* 4.3 6.1 - - - -
232W CA 2.4 27.7 - - - -
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Residues in contact with TYR 57 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57K TYR* 5.3 13.2 - + - -
60K SER* 5.0 2.4 + - - -
61K TYR* 3.5 37.3 - + - +
64K HIS* 2.7 41.2 + + - +
88K SER* 4.6 1.4 + - - -
53W ILE* 3.0 22.2 + - + +
54W ASN* 3.9 7.2 - - - +
56W GLU* 1.3 77.1 - - - +
58W ASN* 1.3 61.9 + - - +
60W SER* 3.2 12.7 + - - -
61W TYR* 3.0 22.4 + + + +
92W ARG* 3.8 23.4 + - + -
95W ALA* 3.7 22.4 - - + +
99W MET* 4.5 6.5 - - - -
111W LEU* 4.6 2.0 - - + -
114W ILE* 3.5 26.9 - - + -
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Residues in contact with ASN 58 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I PHE* 3.8 25.6 + - + -
17I PRO* 3.7 11.5 - - + +
54W ASN* 3.0 50.4 + - - +
55W VAL 3.3 5.1 + - - +
57W TYR* 1.3 77.2 - - - +
59W VAL* 1.3 57.4 + - - +
61W TYR* 3.1 4.3 + - - +
62W VAL* 2.9 33.2 + - - +
113W SER 4.2 6.3 + - - -
114W ILE* 3.5 24.3 - - - +
115W VAL* 3.6 22.7 + - - +
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Residues in contact with VAL 59 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I PHE* 5.1 7.6 - - + -
17I PRO* 5.9 0.9 - - + -
55W VAL* 3.1 19.9 + - + +
56W GLU* 3.3 4.2 + - - +
58W ASN* 1.3 75.0 - - - +
60W SER* 1.3 63.6 + - - +
62W VAL* 3.2 7.0 + - - +
63W TYR* 2.9 49.7 + - + +
91W GLU* 3.5 23.1 - - - +
139W LEU* 5.0 20.6 - - + +
140W GLU* 4.0 6.3 - - - +
143W THR* 3.5 23.8 - - - +
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Residues in contact with SER 60 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57K TYR* 4.8 3.0 + - - -
92K ARG* 4.4 4.3 + - - -
56W GLU 3.0 10.1 + - - -
57W TYR* 3.3 16.0 - - - -
59W VAL* 1.3 78.2 - - - +
61W TYR* 1.3 57.4 + - - +
63W TYR 3.3 0.5 + - - -
64W HIS* 3.0 16.0 + - - +
88W SER* 2.7 50.3 + - - +
91W GLU* 3.6 18.7 - - - +
92W ARG* 3.7 18.3 + - - +
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Residues in contact with TYR 61 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K ASN* 4.1 5.4 + - - -
57K TYR* 3.5 46.6 - + - +
111K LEU* 3.6 25.6 - - + +
112K GLN 2.7 31.7 + - - -
114K ILE* 3.7 23.8 - - + +
57W TYR* 3.0 13.2 + + - +
58W ASN 3.1 8.3 + - - +
60W SER* 1.3 74.9 - - - +
62W VAL* 1.3 64.5 + - + +
64W HIS* 3.1 6.2 + - - +
65W ALA* 3.0 21.5 + - - +
114W ILE* 3.6 25.8 - - + -
115W VAL 3.9 5.2 - - - -
117W PRO* 3.6 31.9 - - + -
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Residues in contact with VAL 62 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17I PRO* 4.2 22.0 - - + -
18I PHE* 3.6 39.7 - - + -
58W ASN* 2.9 20.7 + - - +
59W VAL* 3.7 7.9 - - - +
61W TYR* 1.3 75.7 - - + +
63W TYR* 1.3 58.7 + - - +
65W ALA* 3.1 4.0 + - - +
66W MET* 2.9 36.8 + - + +
117W PRO* 4.3 12.6 - - + -
121W PHE* 4.9 0.4 - - + -
139W LEU* 3.7 27.8 - - + -
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Residues in contact with TYR 63 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59W VAL* 2.9 27.5 + - + +
60W SER 3.6 4.3 - - - +
62W VAL* 1.3 76.7 - - - +
64W HIS* 1.3 57.3 + - - +
66W MET* 3.2 9.2 + - - +
67W PHE* 2.9 24.8 + - - +
83W PHE* 5.9 2.0 - + - -
84W PHE* 3.5 33.4 - + - +
87W SER* 3.6 23.3 - - - -
88W SER* 3.8 13.5 - - - -
91W GLU* 3.6 22.9 - - + -
136W ALA* 3.7 28.9 + - + +
139W LEU* 4.2 14.3 - - + +
140W GLU* 2.6 41.5 + - - +
181W ILE* 4.0 5.0 - - + +
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Residues in contact with HIS 64 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57K TYR* 2.6 36.0 + + - +
92K ARG* 3.5 23.9 + - + -
96K GLU* 2.8 38.7 + - + +
99K MET* 3.7 22.2 - - + +
111K LEU* 4.1 9.0 - - + -
60W SER 3.0 8.4 + - - +
61W TYR 3.1 9.2 + - - +
63W TYR* 1.3 77.1 - - - +
65W ALA* 1.3 58.5 + - - +
67W PHE* 3.3 20.5 + + + +
68W ALA* 3.0 28.1 + - - +
85W LYS* 5.1 2.2 - - - -
88W SER* 3.5 19.5 - - - +
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Residues in contact with ALA 65 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111K LEU* 3.7 12.7 - - + +
61W TYR 3.0 11.9 + - - +
62W VAL 3.1 8.7 + - - +
64W HIS* 1.3 78.1 - - - +
66W MET* 1.3 60.2 + - - +
68W ALA* 3.2 7.2 + - - +
69W TYR* 3.1 18.0 + - - +
117W PRO* 3.9 17.3 - - + -
118W LEU 3.4 24.9 - - - +
119W SER* 4.6 4.2 - - - +
121W PHE* 3.8 9.6 - - + -
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Residues in contact with MET 66 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62W VAL* 2.9 23.7 + - - +
63W TYR* 3.2 24.2 + - - +
65W ALA* 1.3 74.0 - - - +
67W PHE* 1.3 65.5 + - - +
69W TYR* 3.3 1.9 + - - +
70W PHE* 3.1 31.6 + - + -
84W PHE* 3.4 31.9 - - + -
121W PHE* 3.4 37.5 - - + -
132W ALA* 3.1 52.9 - - + +
135W LEU* 4.6 4.5 - - + -
136W ALA* 5.0 0.7 - - - -
139W LEU* 4.7 5.8 - - - -
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Residues in contact with PHE 67 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96K GLU* 4.3 11.7 - - + -
99K MET* 4.1 14.4 - - + -
100K GLU* 3.9 22.4 - - + -
63W TYR 2.9 13.5 + - - +
64W HIS* 3.4 25.4 - + - +
66W MET* 1.3 75.0 - - - +
68W ALA* 1.3 70.1 + - - +
69W TYR 3.2 0.2 + - - -
70W PHE 3.2 1.7 + - - -
71W ASP* 3.0 47.7 + - + +
81W ALA* 3.3 28.8 - - + +
82W LYS* 5.8 0.2 - - - -
84W PHE* 3.6 6.8 - - - +
85W LYS* 3.6 54.5 - - + +
----------------------------------------------------------
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Residues in contact with ALA 68 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99K MET* 3.8 15.3 - - + -
103K ASN* 2.9 32.0 + - - +
109K VAL* 3.7 34.0 - - + +
64W HIS 3.0 13.6 + - - +
65W ALA* 3.2 11.6 + - - +
67W PHE* 1.3 83.0 - - - +
69W TYR* 1.3 61.6 + - - +
72W ARG* 3.7 4.9 + - - +
----------------------------------------------------------
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Residues in contact with TYR 69 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33K GLN* 6.0 0.5 - - - +
65W ALA 3.1 6.2 + - - +
66W MET 3.7 6.5 - - - +
67W PHE 3.2 0.2 - - - -
68W ALA* 1.3 77.2 - - - +
70W PHE* 1.3 83.4 + + - +
71W ASP 3.2 0.2 - - - -
72W ARG* 3.1 61.6 + - - +
75W VAL* 3.6 33.3 - - + +
119W SER 3.7 9.8 + - - +
120W ASP* 4.1 4.7 - - + -
121W PHE* 3.5 53.2 - - + -
122W ASP* 3.3 30.6 + - - +
128W ASP* 4.1 7.6 + - + +
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Residues in contact with PHE 70 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66W MET* 3.1 29.4 + - + +
69W TYR* 1.3 90.7 - + - +
71W ASP* 1.3 58.3 + - - +
72W ARG 3.2 1.9 + - - -
75W VAL* 3.6 17.3 - - + -
76W ALA* 3.7 5.7 + - - -
77W LEU* 3.5 44.4 + - + +
78W ARG* 5.2 0.3 - - - -
80W LEU* 3.7 16.6 - - + -
81W ALA* 3.8 24.6 - - - +
84W PHE* 3.7 18.8 - + - -
121W PHE* 4.5 5.8 - - + -
128W ASP* 3.6 30.7 - - + -
132W ALA* 3.4 35.4 - - + -
----------------------------------------------------------
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Residues in contact with ASP 71 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100K GLU* 4.1 16.9 - - - +
103K ASN* 2.9 34.5 + - - +
179P LYS* 2.9 33.4 + - - -
183P GLU* 4.6 1.8 - - - +
67W PHE* 3.0 42.5 + - + +
69W TYR 3.2 0.2 - - - -
70W PHE* 1.3 73.5 - - - +
72W ARG* 1.3 63.9 + - - +
76W ALA* 5.7 0.2 - - - -
81W ALA* 3.9 7.3 - - + +
----------------------------------------------------------
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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