Contacts of the helix formed by residues 43 - 74 (chain S) in PDB entry 6CP3
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 ILE 43 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36S GLY 4.2 5.6 - - - +
40S ASN* 3.3 44.6 - - + +
41S PRO 3.2 0.4 - - - -
42S SER* 1.3 79.6 - - - +
44S LYS* 1.3 60.9 + - - +
45S ASP* 3.3 2.7 - - - -
46S THR* 2.8 54.7 + - + +
47S VAL* 3.4 6.3 + - + +
37T VAL 3.3 26.2 - - - +
38T SER* 4.2 12.8 - - - -
41T PRO* 3.7 24.5 - - + -
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Residues in contact with LYS 44 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46R THR* 3.4 32.3 + - + +
50R MET* 5.1 16.3 - - - +
33S LEU* 5.4 0.6 - - + +
37S VAL* 3.7 28.5 - - + -
41S PRO 3.5 15.0 + - - +
42S SER 3.6 1.1 - - - -
43S ILE* 1.3 79.9 - - - +
45S ASP* 1.3 64.9 + - - +
47S VAL* 3.0 14.8 + - + +
48S PHE* 2.6 46.5 + - + +
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Residues in contact with ASP 45 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1727 VAL 5.3 8.8 - - - +
1737 MET* 5.2 6.7 - - - +
43S ILE 3.3 1.0 - - - -
44S LYS* 1.3 88.2 - - - +
46S THR* 1.3 61.2 - - - +
48S PHE* 3.1 20.3 + - - +
49S PRO* 3.2 15.1 - - - +
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Residues in contact with THR 46 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43S ILE* 2.8 34.5 + - + +
45S ASP* 1.3 79.1 - - - +
47S VAL* 1.3 60.4 + - + +
48S PHE 3.9 0.2 + - - -
49S PRO* 4.8 0.3 - - - +
50S MET* 3.3 25.9 - - - +
37T VAL* 4.0 21.5 - - + -
44T LYS* 3.6 41.9 + - + +
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Residues in contact with VAL 47 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33S LEU* 3.6 21.4 - - + +
36S GLY 5.2 11.4 - - - +
37S VAL* 5.8 0.4 - - + -
43S ILE* 4.0 4.3 - - + +
44S LYS* 3.3 22.0 - - + +
46S THR* 1.3 82.3 - - + +
48S PHE* 1.3 64.2 + - - +
49S PRO 3.5 1.8 - - - -
50S MET* 3.7 11.0 - - + -
51S ALA* 3.0 26.0 + - - +
34T ILE* 4.6 20.2 - - + -
37T VAL* 3.7 29.2 - - + -
38T SER* 4.9 8.1 - - - +
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Residues in contact with PHE 48 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1727 VAL* 5.9 5.6 - - + -
50R MET* 3.7 43.3 - - + -
53R LEU* 5.6 11.0 - - + -
33S LEU* 4.9 6.4 - - + +
44S LYS* 2.6 28.3 + - + +
45S ASP* 3.1 15.7 + - - +
47S VAL* 1.3 76.6 - - - +
49S PRO* 1.3 72.7 - - + +
51S ALA* 4.6 1.0 - - - +
52S ILE* 3.6 26.5 + - + +
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Residues in contact with PRO 49 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1727 VAL* 4.4 19.7 - - + +
1737 MET* 3.6 31.2 - - + -
45S ASP* 3.2 19.7 - - - +
46S THR 4.8 1.3 - - - +
48S PHE* 1.3 91.0 - - + +
50S MET* 1.3 58.5 + - + +
51S ALA 3.2 0.9 - - - -
52S ILE* 2.9 11.0 + - + +
53S LEU* 2.6 38.2 + - + +
232X TYR* 5.8 7.9 - - + -
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Residues in contact with MET 50 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1737 MET* 6.5 0.4 - - + -
46S THR* 3.3 25.8 - - - +
47S VAL* 3.6 7.5 + - + -
48S PHE 3.5 1.0 - - - -
49S PRO* 1.3 80.4 - - + +
51S ALA* 1.3 61.9 + - - +
53S LEU* 3.9 15.4 - - + +
54S GLY 3.9 3.1 + - - -
30T PHE* 4.1 16.3 - - - -
33T LEU* 3.9 20.2 - - + +
34T ILE* 5.5 3.5 - - + +
37T VAL* 5.5 7.4 - - + -
44T LYS* 3.6 31.9 - - + -
48T PHE* 3.6 40.2 - - + -
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Residues in contact with ALA 51 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S VAL* 3.6 16.6 - - + +
30S PHE* 5.9 1.1 - - + -
33S LEU* 3.8 25.8 - - + -
47S VAL* 3.0 20.9 + - - +
48S PHE 4.6 0.4 - - - +
50S MET* 1.3 76.7 - - - +
52S ILE* 1.3 59.0 + - - +
54S GLY* 3.0 20.6 + - - -
55S PHE 3.2 7.3 + - - -
30T PHE* 5.6 0.6 - - - +
34T ILE* 3.7 30.7 - - + +
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Residues in contact with ILE 52 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53R LEU* 4.0 26.9 - - + -
57R LEU* 5.8 3.6 - - + -
30S PHE* 4.7 10.1 - - + -
48S PHE* 3.6 25.3 + - + +
49S PRO* 2.9 19.6 + - + +
51S ALA* 1.3 76.9 - - + +
53S LEU* 1.3 61.9 + - - +
55S PHE* 2.7 45.9 - - + +
56S ALA* 3.1 7.6 + - - +
229X ILE* 4.4 24.9 - - + +
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Residues in contact with LEU 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49S PRO 2.6 21.8 + - - +
50S MET* 3.9 10.8 - - + +
52S ILE* 1.3 72.4 - - - +
54S GLY* 1.3 64.4 + - - +
56S ALA* 3.0 16.8 + - - +
57S LEU* 3.2 32.4 + - + +
30T PHE* 4.3 13.9 - - + -
48T PHE* 5.4 9.9 - - + -
52T ILE* 5.3 5.6 - - + -
229X ILE* 4.8 7.6 - - + -
232X TYR* 3.9 30.5 - - + -
233X VAL* 3.7 24.9 - - + -
236X ILE* 4.2 18.2 - - + -
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Residues in contact with GLY 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S VAL* 5.3 5.4 - - - -
50S MET 3.9 2.6 + - - -
51S ALA 3.0 10.0 + - - -
53S LEU* 1.3 77.2 - - - +
55S PHE* 1.3 58.3 + - - +
57S LEU* 3.0 8.3 + - - +
58S SER* 2.9 33.9 + - - -
27T ALA* 6.1 0.2 - - - -
30T PHE* 4.0 34.8 - - - -
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Residues in contact with PHE 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57R LEU* 3.3 55.2 - - + -
26S ILE* 3.6 34.3 - - + +
29S VAL* 4.9 5.6 - - + +
30S PHE* 3.6 27.1 - + + -
51S ALA 3.2 5.6 + - - +
52S ILE* 2.7 38.1 + - + +
54S GLY* 1.3 73.8 - - - +
56S ALA* 1.3 63.1 + - + +
58S SER* 3.0 4.0 + - - -
59S GLU* 2.7 54.5 + - + +
222X LEU* 5.7 2.0 - - + -
225X ALA* 5.4 7.2 - - + -
229X ILE* 5.4 4.5 - - + -
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Residues in contact with ALA 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52S ILE 3.1 1.0 + - - -
53S LEU 3.0 9.6 + - - +
55S PHE* 1.3 85.6 - - + +
57S LEU* 1.3 63.0 + - - +
59S GLU* 4.3 6.1 - - - -
60S ALA* 3.4 10.9 - - - +
176X ARG* 5.2 0.7 - - - -
225X ALA 5.8 0.7 - - - +
226X ILE* 6.2 0.9 - - + -
229X ILE* 3.7 31.9 - - + -
230X GLN* 3.1 32.1 + - + +
233X VAL* 4.0 8.3 - - + -
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Residues in contact with LEU 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53S LEU* 3.2 23.8 + - + +
54S GLY* 3.0 9.5 + - - +
56S ALA* 1.3 80.8 - - - +
58S SER* 1.3 62.3 + - - +
60S ALA* 4.3 1.6 - - - +
61S THR* 3.3 25.3 + - - +
26T ILE* 3.3 5.7 - - + +
30T PHE* 3.6 32.1 - - + -
52T ILE* 5.0 4.5 - - + -
55T PHE* 3.6 44.5 - - + -
59T GLU* 4.7 0.2 - - - +
176X ARG* 4.8 8.8 + - - +
233X VAL* 3.7 33.0 - - + -
237X LEU* 4.5 4.5 - - + -
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Residues in contact with SER 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22S ALA* 4.6 6.5 - - - +
26S ILE* 3.7 23.1 - - - -
29S VAL* 5.3 0.7 - - - +
54S GLY 2.9 14.9 + - - -
57S LEU* 1.3 76.0 - - - +
59S GLU* 1.3 65.2 + - - +
61S THR* 2.3 27.4 + - - -
62S GLY* 2.9 7.3 + - - -
23T GLY* 4.1 13.4 - - - -
26T ILE* 3.6 14.1 - - - +
27T ALA* 3.3 26.4 - - - +
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Residues in contact with GLU 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61R THR* 3.3 33.3 - - - +
64R PHE* 4.2 0.9 - - - -
22S ALA* 4.8 5.4 - - - +
26S ILE* 3.4 18.8 - - + +
55S PHE* 2.7 46.5 + - + +
56S ALA* 4.4 3.1 - - - -
58S SER* 1.3 72.0 - - - +
60S ALA* 1.3 51.3 + - - +
62S GLY* 3.0 4.9 + - - +
63S LEU* 2.6 60.5 + - + +
222X LEU* 3.9 23.9 - - + +
226X ILE* 5.2 8.1 - - + -
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Residues in contact with ALA 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56S ALA 3.4 18.8 + - - +
57S LEU 4.3 2.5 - - - +
58S SER 3.3 0.6 - - - -
59S GLU* 1.3 79.1 - - - +
61S THR* 1.3 52.3 + - + +
63S LEU* 3.0 6.8 - - - -
64S PHE* 2.5 39.6 + - + -
176X ARG* 4.1 13.0 - - + +
180X ASN* 3.5 23.4 - - - +
226X ILE* 4.8 2.0 - - + -
230X GLN* 3.4 17.7 - - - +
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Residues in contact with THR 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57S LEU 3.3 13.7 + - - +
58S SER* 2.3 31.7 + - - -
60S ALA* 1.3 74.0 - - + +
62S GLY* 1.3 62.1 + - - +
64S PHE* 3.0 48.8 - - + +
19T LEU* 3.4 20.1 - - - +
22T ALA* 5.5 2.7 - - + +
23T GLY* 4.0 18.7 - - - -
26T ILE* 4.1 3.0 - - + +
59T GLU* 3.3 27.6 - - - +
176X ARG* 5.8 3.1 - - - +
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Residues in contact with GLY 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18S GLY 4.6 4.3 - - - -
19S LEU* 4.2 12.7 - - - +
22S ALA* 3.8 23.0 - - - +
58S SER 2.9 11.5 + - - -
59S GLU 3.3 4.5 - - - -
61S THR* 1.3 74.7 + - - +
63S LEU* 1.3 61.0 + - - +
65S CYS* 3.0 31.4 + - - -
66S LEU* 3.5 5.5 - - - +
19T LEU* 4.6 1.1 - - - +
23T GLY* 5.6 0.6 - - - -
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Residues in contact with LEU 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61R THR* 5.5 0.7 - - + -
64R PHE* 3.7 28.5 - - + -
19S LEU* 6.4 0.4 - - + -
59S GLU* 2.6 47.3 + - + +
60S ALA* 3.0 14.3 + - - +
62S GLY* 1.3 70.7 - - - +
64S PHE* 1.3 66.3 + - - +
66S LEU* 3.7 21.3 - - + -
67S MET* 3.7 15.4 + - - +
179X SER 4.6 1.0 - - - +
180X ASN* 3.9 13.2 - - - +
183X ALA* 4.2 25.5 - - + +
187X LEU* 5.8 3.1 - - + -
222X LEU* 5.4 5.8 - - + -
226X ILE* 5.3 7.9 - - + -
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Residues in contact with PHE 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60S ALA 2.5 22.5 + - - -
61S THR* 3.0 38.8 + - + +
63S LEU* 1.3 74.7 - - - +
65S CYS* 1.3 65.1 + - - +
67S MET* 3.1 26.7 + - - +
68S VAL* 3.3 8.5 + - + +
19T LEU* 3.8 15.5 - - + -
59T GLU* 4.4 10.3 - - - -
62T GLY 5.6 2.2 - - - -
63T LEU* 4.5 9.6 - - + -
66T LEU* 3.7 29.2 - - + -
172X SER* 4.6 8.5 - - - -
175X LEU* 4.1 9.2 - - + -
176X ARG* 3.6 48.5 - - + -
179X SER* 5.2 6.1 - - - -
180X ASN* 4.9 2.9 - - - -
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Residues in contact with CYS 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S SER 3.8 8.8 - - - +
16S THR 3.9 8.7 - - - -
18S GLY* 3.5 6.7 - - - -
19S LEU* 3.2 35.9 - - - -
62S GLY 3.0 18.3 + - - +
64S PHE* 1.3 78.0 - - - +
66S LEU* 1.3 71.1 + - - +
68S VAL* 3.0 12.7 + - - +
69S SER 3.0 19.8 + - - -
16T THR* 3.6 24.5 - - + +
19T LEU* 4.0 20.9 - - + -
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Residues in contact with LEU 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64R PHE* 4.1 21.3 - - + -
67R MET* 3.9 27.8 - - + -
68R VAL* 4.7 8.3 - - + -
15S SER 4.4 2.2 - - - +
16S THR* 5.4 3.4 - - - +
19S LEU* 4.3 17.3 - - + -
62S GLY 3.5 19.5 - - - +
63S LEU* 3.7 32.5 - - + -
65S CYS* 1.3 83.3 - - - +
67S MET* 1.3 63.4 + - + +
69S SER* 2.8 30.7 - - - -
70S PHE* 2.9 25.8 + - + -
183X ALA* 5.7 0.9 - - + -
187X LEU* 5.5 2.2 - - + -
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Residues in contact with MET 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63S LEU 3.7 9.6 - - - +
64S PHE* 3.1 20.6 + - - +
66S LEU* 1.3 79.5 - - - +
68S VAL* 1.3 77.5 + - - +
70S PHE* 2.9 24.5 + - + +
71S LEU* 3.0 35.7 + - + +
70T PHE* 5.3 7.4 - - + -
115X LEU* 5.3 0.2 - - + -
179X SER* 3.7 39.0 - - - +
182X LEU* 3.7 31.6 - - + +
183X ALA* 3.8 22.4 - - + +
186X LEU* 6.6 0.2 - - + -
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Residues in contact with VAL 68 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15S SER* 4.7 2.0 - - - -
64S PHE* 3.3 15.2 + - - +
65S CYS* 3.0 9.6 + - - +
67S MET* 1.3 86.6 - - - +
69S SER* 1.3 64.0 + - - +
71S LEU* 4.2 14.0 - - + +
72S LEU* 3.2 24.3 + - + +
12T ALA* 5.2 2.2 - - + +
16T THR* 4.7 12.1 - - + +
66T LEU* 3.9 23.8 - - + -
69T SER* 3.3 27.4 - - - +
70T PHE* 4.6 15.7 - - + -
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Residues in contact with SER 69 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68R VAL* 5.0 5.6 - - - +
12S ALA* 3.4 28.4 + - - +
15S SER* 3.3 23.9 + - - -
16S THR* 4.8 1.9 + - - -
65S CYS 3.0 5.5 + - - -
66S LEU* 2.8 25.9 + - - -
68S VAL* 1.3 77.4 - - - +
70S PHE* 1.3 59.8 + - - +
72S LEU* 3.0 6.9 + - - +
73S LEU* 2.4 34.3 + - - +
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Residues in contact with PHE 70 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67R MET* 3.7 29.2 - - + -
68R VAL* 4.3 16.2 - - + -
71R LEU* 4.6 9.9 - - + -
66S LEU* 2.9 30.1 + - + -
67S MET* 2.9 17.4 + - + +
69S SER* 1.3 84.9 - - - +
71S LEU* 1.3 57.1 + - - +
73S LEU* 2.9 29.1 + - + +
74S PHE* 2.8 32.1 + - + +
183X ALA* 5.3 9.9 - - + -
186X LEU* 4.4 29.2 - - + -
187X LEU* 4.6 15.9 - - + -
190X ILE* 5.2 10.3 - - + -
191X LEU* 6.3 0.2 - - + -
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Residues in contact with LEU 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S LYS* 6.0 0.2 - - - +
67S MET* 3.0 43.1 + - + +
68S VAL* 4.2 14.6 - - + +
70S PHE* 1.3 74.6 - - - +
72S LEU* 1.3 60.7 + - + +
74S PHE* 3.3 23.7 - - - +
70T PHE* 4.9 15.0 - - + -
73T LEU* 3.8 35.9 - - + +
182X LEU* 5.3 7.2 - - + -
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Residues in contact with LEU 72 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8S LYS* 3.5 42.1 - - + +
11S GLY* 3.5 32.8 - - - +
12S ALA 4.0 0.4 - - - +
15S SER* 4.7 2.7 - - - +
68S VAL* 3.2 22.1 + - + +
69S SER 3.0 6.1 + - - +
71S LEU* 1.3 77.2 - - + +
73S LEU* 1.3 63.1 + - - +
74S PHE* 3.2 1.1 - - - -
9T TYR* 3.6 55.6 - - + +
12T ALA* 4.9 4.0 - - + -
13T GLY* 4.0 10.1 - - - +
73T LEU* 5.0 8.5 - - + -
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Residues in contact with LEU 73 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R LEU* 3.8 29.2 - - + -
72R LEU* 4.4 9.9 - - + -
8S LYS* 5.7 1.0 - - - +
9S TYR* 3.6 47.5 + - + -
12S ALA* 4.4 12.3 - - + -
69S SER* 2.4 25.7 + - - +
70S PHE* 2.9 33.6 + - + +
72S LEU* 1.3 71.3 - - - +
74S PHE* 1.3 88.8 + - + +
190X ILE* 5.1 6.1 - - + -
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Residues in contact with PHE 74 (chain S).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8S LYS* 4.7 14.3 + - - +
9S TYR* 5.3 6.3 - - - -
70S PHE* 2.8 18.4 + - + +
71S LEU* 3.3 21.3 - - - -
72S LEU 4.6 1.8 - - - -
73S LEU* 1.3 107.8 - - + +
186X LEU* 5.9 5.6 - - + -
190X ILE* 4.4 19.5 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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