Contacts of the helix formed by residues 4 - 35 (chain X) 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 X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X GLY* 1.3 71.7 - - - -
5X LYS* 1.3 65.9 + - - +
6X LYS* 3.1 6.8 + - - +
7X VAL* 3.0 30.5 + - + +
8X ILE* 3.1 21.0 + - - +
65X LEU* 5.7 0.2 - - - +
107X HIS* 2.9 30.6 + - - -
111X VAL* 4.0 24.3 - - + +
113X ASP* 6.0 0.6 + - + -
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Residues in contact with LYS 5 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X GLY 3.4 4.7 + - - -
4X ASP* 1.3 75.3 + - - +
6X LYS* 1.3 58.7 + - + +
8X ILE* 3.4 10.8 + - - +
9X GLN* 3.0 39.9 + - + +
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Residues in contact with LYS 6 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X ASP* 3.1 4.8 + - - +
5X LYS* 1.3 78.0 - - + +
7X VAL* 1.3 55.0 + - - +
9X GLN* 3.2 21.5 + - - +
10X HIS* 2.8 42.9 + - + +
107X HIS* 3.2 33.7 - - + +
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Residues in contact with VAL 7 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X ASP* 3.0 27.2 + - + +
6X LYS* 1.3 71.7 - - - +
8X ILE* 1.3 61.1 + - - +
10X HIS* 3.1 6.7 + - - +
11X LEU* 2.8 51.5 + - + +
65X LEU* 4.1 7.9 - - + -
107X HIS* 3.5 22.4 + - + -
108X CYS* 4.1 19.7 - - - -
111X VAL* 3.6 19.1 - - + -
113X ASP* 3.3 24.9 - - + +
116X SER* 4.1 1.8 - - - +
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Residues in contact with ILE 8 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X GLY 4.2 10.1 - - - +
4X ASP 3.1 14.7 + - - +
5X LYS* 3.7 10.5 - - - +
6X LYS 3.3 0.2 - - - -
7X VAL* 1.3 75.9 - - - +
9X GLN* 1.3 56.9 + - + +
11X LEU* 3.2 8.0 + - + +
12X ASN* 2.9 44.6 + - - +
62X ILE* 4.3 8.3 - - + -
65X LEU* 3.8 37.7 - - + +
66X GLU 4.5 1.3 - - - +
67X GLY* 3.8 33.9 - - - -
68X LEU 4.8 1.3 - - - +
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Residues in contact with GLN 9 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X LYS* 3.0 26.6 + - + +
6X LYS* 3.4 30.2 - - - +
8X ILE* 1.3 74.9 - - + +
10X HIS* 1.3 64.0 + - + +
12X ASN* 3.3 8.6 + - - +
13X LYS* 3.0 21.3 + - - +
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Residues in contact with HIS 10 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X LYS* 2.8 30.2 + - + +
7X VAL* 3.5 8.7 - - - +
9X GLN* 1.3 74.0 - - + +
11X LEU* 1.3 65.9 + - + +
13X LYS* 2.9 18.6 + - + +
14X ILE* 2.9 27.7 + - - +
100X ASP 4.7 2.2 + - - -
103X GLU* 3.7 29.8 - - + -
104X ALA* 3.5 27.9 + - + +
107X HIS* 3.8 33.0 - + + +
108X CYS* 6.0 1.8 - - - -
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Residues in contact with LEU 11 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X VAL* 2.8 42.0 + - + +
8X ILE* 3.2 6.0 + - - +
10X HIS* 1.3 73.1 - - + +
12X ASN* 1.3 58.5 + - - +
14X ILE* 3.4 4.9 + - - +
15X LEU* 2.9 28.6 + - - +
58X LEU* 4.2 14.6 - - + +
61X ARG* 3.9 28.3 - - + -
62X ILE* 3.7 25.1 - - + +
65X LEU* 4.0 9.4 - - + -
108X CYS* 5.3 0.7 - - - -
116X SER* 4.1 9.2 - - - +
119X LEU* 5.5 1.3 - - + -
120X LEU* 3.8 39.3 - - + -
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Residues in contact with ASN 12 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X ILE* 2.9 33.2 + - - +
9X GLN* 3.7 7.8 - - - +
10X HIS 3.1 0.4 - - - -
11X LEU* 1.3 78.2 - - - +
13X LYS* 1.3 57.9 + - - +
15X LEU* 3.7 8.2 - - - +
16X GLY* 2.9 23.0 + - - -
62X ILE* 3.6 9.8 - - - +
68X LEU 3.1 21.8 + - - -
69X PRO* 3.5 5.2 - - - +
70X ASN* 2.8 42.1 + - + +
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Residues in contact with LYS 13 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X GLN 3.0 12.9 + - - +
10X HIS* 2.9 22.6 + - + +
12X ASN* 1.3 76.3 - - - +
14X ILE* 1.3 67.3 + - + +
16X GLY* 3.2 2.3 + - - -
17X ASN* 3.0 23.8 + - - +
96X LYS* 4.6 8.3 - - - +
100X ASP* 3.7 40.6 + - + +
103X GLU* 4.9 7.1 + - - -
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Residues in contact with ILE 14 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X HIS* 2.9 17.6 + - - +
11X LEU* 3.7 6.3 - - - +
13X LYS* 1.3 78.3 - - + +
15X LEU* 1.3 64.3 + - - +
17X ASN* 2.9 10.4 + - + +
18X GLU* 2.9 31.0 + - - +
58X LEU* 3.8 17.3 - - + -
97X ALA 5.0 0.2 - - - +
100X ASP* 3.6 36.6 - - + +
101X LEU* 3.4 37.0 - - + -
104X ALA* 4.2 5.2 - - + -
120X LEU* 3.9 18.4 - - + -
123X ILE* 4.8 2.9 - - + -
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Residues in contact with LEU 15 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11X LEU 2.9 17.7 + - - +
12X ASN* 3.7 17.9 - - - +
14X ILE* 1.3 76.3 - - - +
16X GLY* 1.3 58.9 + - - +
18X GLU* 3.0 3.8 + - - +
19X LEU* 2.9 44.4 + - + +
55X ALA* 3.8 40.2 - - + +
58X LEU* 3.7 14.8 - - + +
59X ILE* 3.9 23.8 - - + -
62X ILE* 4.4 5.4 - - + -
69X PRO* 4.3 3.4 - - + -
70X ASN 3.5 28.0 - - - +
71X LEU* 4.1 5.4 - - + -
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Residues in contact with GLY 16 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12X ASN 2.9 16.0 + - - -
13X LYS* 3.6 4.7 - - - -
14X ILE 3.1 0.4 - - - -
15X LEU* 1.3 77.7 - - - +
17X ASN* 1.3 63.3 + - - +
19X LEU* 3.4 12.0 + - - +
20X ILE* 3.2 28.1 + - - +
70X ASN 5.5 1.6 - - - -
73X ASP 4.9 10.1 - - - +
74X LEU* 5.3 0.2 - - - +
75X GLY 5.3 0.3 + - - -
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Residues in contact with ASN 17 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13X LYS* 3.0 17.1 + - - +
14X ILE* 2.9 12.8 + - + +
16X GLY* 1.3 75.8 - - - +
18X GLU* 1.3 66.6 + - + +
20X ILE* 3.3 16.6 + - - +
21X ALA* 3.1 22.9 + - - +
93X LEU* 5.0 8.2 - - + +
96X LYS* 3.9 13.7 + - - +
97X ALA* 3.9 28.0 + - + +
100X ASP* 2.6 41.6 + - - +
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Residues in contact with GLU 18 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14X ILE* 2.9 22.6 + - - +
15X LEU* 3.0 6.9 + - - +
17X ASN* 1.3 76.7 - - - +
19X LEU* 1.3 59.7 + - - +
21X ALA* 3.2 4.0 + - - +
22X ILE* 2.9 34.8 + - - +
51X GLU* 2.7 51.4 - - - +
54X HIS* 3.8 13.5 - - + -
55X ALA* 4.3 9.9 - - + +
58X LEU* 3.9 17.9 - - + -
97X ALA* 6.0 1.4 - - - +
101X LEU* 5.4 0.7 - - - +
123X ILE* 3.5 18.5 - - - +
127X GLU* 3.2 16.0 - - - +
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Residues in contact with LEU 19 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23W ASN* 4.7 8.5 - - - +
15X LEU* 2.9 37.3 + - + +
16X GLY* 3.8 9.2 - - - +
17X ASN 3.2 0.2 - - - -
18X GLU* 1.3 77.1 - - - +
20X ILE* 1.3 61.4 + - - +
22X ILE* 3.6 9.2 + - + +
23X ASN* 3.4 23.0 + - - +
55X ALA* 4.7 2.9 - - + -
59X ILE* 5.9 0.2 - - + -
70X ASN 3.9 8.3 - - - +
71X LEU* 3.8 38.4 - - + +
73X ASP 4.7 7.9 - - - +
74X LEU* 3.7 19.1 - - + +
159X HEM 3.8 29.6 - - + -
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Residues in contact with ILE 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16X GLY 3.2 15.8 + - - +
17X ASN* 3.6 17.9 - - - +
19X LEU* 1.3 76.4 - - - +
21X ALA* 1.3 58.5 + - - +
23X ASN* 3.3 3.8 + - - +
24X GLN* 2.9 28.0 + - - +
74X LEU* 4.1 6.5 - - + -
75X GLY* 3.7 40.8 - - - +
76X LYS 3.6 22.2 - - - +
77X LEU* 3.9 15.2 - - + +
93X LEU* 3.8 26.2 - - + -
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Residues in contact with ALA 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17X ASN 3.1 10.6 + - - +
18X GLU 3.2 6.9 + - - +
20X ILE* 1.3 75.8 - - - +
22X ILE* 1.3 68.1 + - - +
24X GLN* 4.4 1.1 - - - +
25X TYR* 2.8 45.2 + - + +
51X GLU* 3.2 28.0 - - + +
93X LEU* 3.7 19.7 - - + +
94X GLU* 6.1 0.2 - - - -
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Residues in contact with ILE 22 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18X GLU 2.9 22.9 + - - +
19X LEU* 3.8 8.5 - - + +
20X ILE 3.2 0.2 - - - -
21X ALA* 1.3 75.0 - - - +
23X ASN* 1.3 68.2 + - - +
26X PHE* 2.9 18.4 + - - +
48X SER* 2.8 28.0 + - - +
51X GLU* 3.5 24.0 - - + +
52X MET* 3.6 36.1 - - + +
55X ALA* 4.1 13.5 - - + -
159X HEM 3.8 42.2 - - + -
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Residues in contact with ASN 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19W LEU* 4.7 10.5 - - - +
71W LEU* 3.0 50.4 + - + +
74W LEU* 6.4 0.4 - - - +
19X LEU 3.4 10.6 + - - +
20X ILE 3.3 6.6 + - - +
21X ALA 3.3 0.2 - - - -
22X ILE* 1.3 78.2 - - - +
24X GLN* 1.3 61.6 + - - +
26X PHE* 4.5 1.3 - - - -
27X LEU* 2.9 32.6 + - - +
74X LEU* 3.8 14.1 - - - +
77X LEU* 4.2 12.3 - - + -
159X HEM 3.5 20.9 - - - +
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Residues in contact with GLN 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20X ILE* 2.9 18.2 + - + +
21X ALA* 4.1 2.2 - - - +
23X ASN* 1.3 76.0 - - - +
25X TYR* 1.3 63.2 + - + +
27X LEU* 3.4 1.4 + - - +
28X HIS* 2.9 34.8 + - + -
77X LEU* 4.2 6.6 - - + +
78X LEU* 2.9 46.9 + - - +
79X ILE* 4.1 15.5 - - + -
89X CYS 3.2 23.0 + - - -
90X ASP* 2.8 31.7 + - - +
93X LEU* 3.6 19.6 - - - +
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Residues in contact with TYR 25 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21X ALA* 2.8 40.0 + - + +
24X GLN* 1.3 78.4 - - + +
26X PHE* 1.3 63.6 + - - +
29X SER* 2.9 22.0 + - - -
44X GLU* 3.2 26.7 - - - +
47X GLU* 4.0 13.5 - - + -
48X SER* 3.8 18.4 - - - +
51X GLU* 3.9 20.0 - - + -
90X ASP* 3.2 38.0 + - + -
93X LEU* 3.9 12.4 - - + +
94X GLU* 2.8 35.5 + - - +
130X HIS* 3.4 18.9 - + - -
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Residues in contact with PHE 26 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56W ASP* 3.5 43.3 - - + -
59W ILE* 4.0 19.7 - - + -
71W LEU* 4.8 2.5 - - + -
22X ILE 2.9 19.1 + - - +
23X ASN* 3.8 5.2 - - - +
24X GLN 3.3 0.2 - - - -
25X TYR* 1.3 78.7 - - - +
27X LEU* 1.3 64.0 + - - +
29X SER* 3.3 5.5 + - - -
30X ARG* 3.0 34.3 + - + +
45X TYR* 3.9 25.8 - + - -
48X SER* 3.6 18.6 + - - -
52X MET* 4.1 5.8 - - + -
159X HEM 3.7 47.3 - + + -
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Residues in contact with LEU 27 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59W ILE* 4.4 9.4 - - + -
63W LEU* 4.6 1.3 - - + -
69W PRO* 4.0 48.2 - - + +
71W LEU* 4.2 20.1 - - + +
23X ASN 2.9 17.6 + - - +
24X GLN 4.0 2.7 - - - +
26X PHE* 1.3 79.9 - - - +
28X HIS* 1.3 57.4 + - - +
30X ARG* 3.1 3.3 + - - -
31X MET* 2.9 51.6 + - + +
77X LEU* 5.5 1.6 - - + -
79X ILE* 3.8 37.5 - - + -
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Residues in contact with HIS 28 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24X GLN* 2.9 18.9 + - + +
27X LEU* 1.3 76.1 - - - +
29X SER* 1.3 65.6 + - - +
31X MET* 3.3 11.8 + - - -
32X TRP* 2.9 32.3 + - + -
44X GLU* 3.4 18.6 + - + +
78X LEU 3.4 17.7 - - - -
79X ILE* 3.4 12.3 - - + +
80X GLY 3.1 22.5 + - - -
86X MET* 3.6 51.3 - - + +
90X ASP* 2.9 30.7 + - - -
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Residues in contact with SER 29 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25X TYR 2.9 14.4 + - - -
26X PHE* 3.4 10.8 - - - -
28X HIS* 1.3 78.0 - - - +
30X ARG* 1.3 87.9 + - - +
32X TRP 3.3 0.5 + - - -
33X ASN* 3.0 29.3 + - - -
41X GLY* 2.9 27.1 + - - -
44X GLU* 3.4 8.1 - - - +
45X TYR* 3.5 17.0 - - - +
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Residues in contact with ARG 30 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56W ASP* 3.1 40.3 + - - +
59W ILE* 3.8 28.5 - - + -
60W GLU* 3.8 20.9 + - + +
63W LEU* 3.9 9.0 - - + +
26X PHE* 3.0 26.8 + - + +
27X LEU 3.1 2.9 + - - +
29X SER* 1.3 104.4 + - - +
31X MET* 1.3 56.9 + - - +
33X ASN* 3.4 21.1 + - + +
34X ASP* 2.9 30.3 + - - +
41X GLY 4.5 0.6 + - - -
42X ALA* 5.9 0.4 - - - +
45X TYR* 3.5 36.9 - - - +
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Residues in contact with MET 31 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63W LEU* 4.2 22.2 - - + -
27X LEU* 2.9 37.5 + - + +
28X HIS* 3.6 13.0 - - - +
30X ARG* 1.3 78.0 - - - +
32X TRP* 1.3 63.0 + - - +
34X ASP* 3.2 9.3 + - - +
35X TRP* 3.0 59.1 + - + -
79X ILE* 4.0 14.6 - - + -
80X GLY 3.5 22.7 - - - +
81X GLU* 4.8 1.6 - - - -
86X MET* 3.9 10.8 - - + -
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Residues in contact with TRP 32 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28X HIS* 2.9 26.8 + - + +
29X SER 3.7 4.0 - - - +
31X MET* 1.3 73.4 - - - +
33X ASN* 1.3 64.8 + - - +
35X TRP* 3.1 14.7 + + - +
36X GLY 3.1 4.5 + - - -
37X LEU* 2.8 52.9 + - + +
40X LEU* 3.7 36.7 - - + +
41X GLY 3.7 13.5 - - - +
44X GLU* 3.7 33.4 - - + -
83X THR* 2.9 38.0 + - + -
86X MET* 3.5 38.5 - - + +
87X LEU* 4.1 22.9 - - + -
90X ASP* 4.8 0.7 - - - -
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Residues in contact with ASN 33 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A THR* 5.2 1.0 + - - +
60W GLU* 5.3 2.2 - - - +
29X SER* 3.0 12.8 + - - +
30X ARG* 3.5 38.2 + - + +
32X TRP* 1.3 73.3 - - - +
34X ASP* 1.3 64.0 + - - +
36X GLY* 3.0 13.4 + - - +
37X LEU 4.7 1.6 - - - +
38X LYS* 3.8 25.9 + - + +
41X GLY* 3.3 23.9 - - - -
42X ALA 4.3 0.4 - - - +
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Residues in contact with ASP 34 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASP* 4.4 10.8 - - - +
136A THR* 3.1 24.1 + - - -
63W LEU* 3.8 41.7 - - + +
64W PHE* 4.3 6.2 - - - +
30X ARG 2.9 19.2 + - - +
31X MET* 3.5 7.5 - - - +
32X TRP 3.2 0.2 - - - -
33X ASN* 1.3 77.4 - - - +
35X TRP* 1.3 70.9 + - - +
36X GLY 3.2 0.2 - - - -
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Residues in contact with TRP 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A THR* 3.7 7.0 - - - +
140A LEU* 3.3 27.5 + - - +
143A LYS* 3.8 36.8 + - - +
31X MET* 3.0 43.6 + - + +
32X TRP* 3.1 23.5 + + - +
34X ASP* 1.3 90.7 + - - +
36X GLY* 1.3 58.0 + - - +
37X LEU* 3.3 12.0 + - + +
81X GLU* 3.5 25.8 - - - -
82X ASN* 4.1 6.5 - - + -
83X THR* 4.4 3.6 - - - -
86X MET* 3.4 28.5 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
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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