Contacts of the helix formed by residues 4 - 36 (chain U) 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 U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U GLY* 1.3 70.1 - - - -
5U LYS* 1.3 68.2 + - - +
6U LYS* 3.1 10.2 + - - +
7U VAL* 3.0 30.8 + - + +
8U ILE* 3.0 24.7 + - - +
65U LEU* 5.5 0.8 - - - +
107U HIS* 2.9 29.5 + - - -
111U VAL* 4.0 22.0 - - + +
113U ASP* 5.8 1.7 + - + +
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Residues in contact with LYS 5 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3U GLY 3.6 4.6 + - - +
4U ASP* 1.3 75.2 + - - +
6U LYS* 1.3 63.8 + - + +
8U ILE* 3.5 11.7 + - - +
9U GLN* 3.1 39.9 + - + +
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Residues in contact with LYS 6 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4U ASP* 3.1 13.1 + - - +
5U LYS* 1.3 85.5 - - + +
7U VAL* 1.3 59.5 + - - +
8U ILE 3.2 0.2 - - - -
9U GLN* 3.1 20.5 + - - +
10U HIS* 2.8 35.6 + - + -
107U HIS* 3.4 27.2 - - + +
110U GLN* 5.4 4.9 - - - +
111U VAL* 6.2 0.2 - - - +
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Residues in contact with VAL 7 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4U ASP* 3.0 39.0 + - + +
6U LYS* 1.3 70.3 - - - +
8U ILE* 1.3 55.4 + - + +
10U HIS* 3.0 6.5 + - - +
11U LEU* 2.7 54.7 + - + +
65U LEU* 4.3 4.5 - - + -
107U HIS* 3.7 17.6 - - + -
108U CYS* 4.1 19.3 - - - -
111U VAL* 3.9 12.3 - - + -
113U ASP* 3.5 24.9 - - + +
116U SER* 4.0 2.7 - - - +
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Residues in contact with ILE 8 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3U GLY 4.2 11.0 - - - +
4U ASP 3.0 15.4 + - - +
5U LYS* 3.6 11.7 - - - +
7U VAL* 1.3 74.7 - - - +
9U GLN* 1.3 59.4 + - + +
11U LEU* 3.2 7.7 + - + +
12U ASN* 2.9 43.3 + - - +
62U ILE* 4.4 9.4 - - + +
65U LEU* 3.9 40.8 - - + +
66U GLU 4.6 1.1 - - - -
67U GLY* 4.0 27.6 - - - +
68U LEU 4.8 1.3 - - - +
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Residues in contact with GLN 9 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5U LYS* 3.1 28.4 + - + +
6U LYS* 3.1 25.5 + - - +
8U ILE* 1.3 78.9 - - + +
10U HIS* 1.3 59.0 + - + +
12U ASN* 3.3 6.5 + - - +
13U LYS* 2.9 28.5 + - - +
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Residues in contact with HIS 10 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6U LYS* 2.8 25.3 + - + -
7U VAL* 3.0 8.9 + - + +
9U GLN* 1.3 79.1 - - + +
11U LEU* 1.3 57.9 + - + +
13U LYS* 3.1 14.7 + - + +
14U ILE* 2.8 36.3 + - - +
100U ASP 4.9 1.8 + - - -
103U GLU* 3.9 28.4 - - + +
104U ALA* 3.6 27.6 + - + +
107U HIS* 3.7 32.3 + + + +
108U CYS* 6.0 1.3 - - - -
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Residues in contact with LEU 11 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7U VAL* 2.7 40.9 + - + +
8U ILE* 3.7 5.2 - - - +
10U HIS* 1.3 73.4 - - + +
12U ASN* 1.3 56.5 + - - +
14U ILE* 3.4 4.7 + - - +
15U LEU* 2.9 28.6 + - - +
58U LEU* 4.0 16.0 - - + +
61U ARG* 3.9 27.4 - - + -
62U ILE* 3.7 25.3 - - + +
65U LEU* 4.0 9.6 - - + -
116U SER* 4.2 10.3 - - - +
119U LEU* 5.3 2.0 - - + -
120U LEU* 3.9 37.2 - - + -
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Residues in contact with ASN 12 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8U ILE* 2.9 30.2 + - - +
9U GLN* 3.7 7.0 - - - +
11U LEU* 1.3 76.8 - - - +
13U LYS* 1.3 58.0 + - - +
15U LEU* 3.4 8.1 + - - +
16U GLY* 2.9 24.3 + - - -
62U ILE* 3.7 9.1 - - - +
68U LEU 3.0 21.8 + - - -
69U PRO* 3.6 4.3 - - - +
70U ASN* 2.8 41.0 + - + +
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Residues in contact with LYS 13 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9U GLN 2.9 14.3 + - - +
10U HIS* 3.1 18.4 + - + +
12U ASN* 1.3 75.5 - - - +
14U ILE* 1.3 66.4 + - + +
16U GLY* 3.2 3.1 + - - -
17U ASN* 3.1 25.9 + - - +
96U LYS* 4.1 10.5 - - - +
100U ASP* 3.1 42.4 + - + +
103U GLU* 5.1 4.8 + - - -
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Residues in contact with ILE 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10U HIS* 2.8 26.0 + - - +
11U LEU* 3.7 5.6 - - - +
13U LYS* 1.3 72.6 - - + +
15U LEU* 1.3 62.9 + - - +
17U ASN* 3.0 10.7 + - + +
18U GLU* 3.0 30.4 + - - +
58U LEU* 3.7 20.0 - - + -
97U ALA 4.8 0.9 - - - +
100U ASP* 3.8 36.1 - - + +
101U LEU* 3.5 37.9 - - + +
104U ALA* 4.4 4.9 - - + -
120U LEU* 4.0 17.0 - - + -
123U ILE* 5.0 1.8 - - + -
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Residues in contact with LEU 15 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11U LEU 2.9 18.3 + - - +
12U ASN* 3.5 23.3 - - - +
14U ILE* 1.3 75.9 - - - +
16U GLY* 1.3 58.4 + - - +
18U GLU* 3.1 4.7 + - - +
19U LEU* 2.9 49.1 + - + +
55U ALA* 3.8 32.1 - - + +
58U LEU* 3.9 13.1 - - + +
59U ILE* 3.9 29.2 - - + +
62U ILE* 4.1 9.9 - - + -
69U PRO* 4.2 0.9 - - + -
70U ASN 3.8 18.6 - - - +
71U LEU* 4.1 5.2 - - + -
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Residues in contact with GLY 16 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12U ASN 2.9 15.7 + - - -
13U LYS* 3.2 4.9 + - - -
15U LEU* 1.3 74.2 - - - +
17U ASN* 1.3 63.3 + - - +
19U LEU* 3.3 13.7 + - - +
20U ILE* 3.2 29.3 + - - +
70U ASN 5.4 1.3 + - - -
73U ASP 4.9 9.0 - - - +
75U GLY 5.3 0.9 + - - -
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Residues in contact with ASN 17 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13U LYS* 3.1 15.9 + - - +
14U ILE* 3.0 13.8 + - + +
16U GLY* 1.3 76.7 - - - +
18U GLU* 1.3 66.5 + - + +
20U ILE* 3.3 17.4 + - - +
21U ALA* 3.1 21.8 + - - +
93U LEU* 4.9 4.1 - - + +
96U LYS* 4.5 10.1 + - - +
97U ALA* 3.9 27.9 + - + +
100U ASP* 2.9 39.7 + - - +
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Residues in contact with GLU 18 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14U ILE* 3.0 21.7 + - - +
15U LEU 3.4 7.4 - - - +
17U ASN* 1.3 77.6 - - - +
19U LEU* 1.3 58.0 + - - +
21U ALA* 3.1 4.3 + - - +
22U ILE* 2.8 34.5 + - - +
51U GLU* 2.6 48.4 - - - +
54U HIS* 3.8 11.7 - - + -
55U ALA* 4.3 11.0 - - + +
58U LEU* 3.9 19.3 - - + -
97U ALA* 5.9 1.7 - - - +
101U LEU* 5.4 1.2 - - - +
123U ILE* 3.5 16.8 - - - +
127U GLU* 3.0 19.9 - - - +
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Residues in contact with LEU 19 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U LEU* 2.9 39.5 + - + +
16U GLY* 3.3 8.9 + - - +
17U ASN 3.2 0.4 - - - -
18U GLU* 1.3 74.8 - - - +
20U ILE* 1.3 62.9 + - - +
22U ILE* 3.6 10.6 + - + +
23U ASN* 3.5 21.8 + - - +
55U ALA* 4.6 2.7 - - + -
70U ASN 3.7 23.1 - - - +
71U LEU* 4.0 23.3 - - + +
73U ASP 4.4 9.2 - - - +
74U LEU* 3.8 21.0 - - + +
23V ASN* 4.8 5.8 - - - +
159V HEM 3.8 28.9 - - + -
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Residues in contact with ILE 20 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16U GLY 3.2 16.4 + - - +
17U ASN* 3.6 18.8 - - - +
18U GLU 3.1 0.4 - - - -
19U LEU* 1.3 78.2 - - - +
21U ALA* 1.3 62.2 + - - +
23U ASN* 3.2 2.8 + - - -
24U GLN* 3.0 24.4 + - - +
74U LEU* 4.1 7.2 - - + -
75U GLY* 3.7 42.0 - - - +
76U LYS 3.6 21.5 - - - +
77U LEU* 4.0 13.0 - - + +
93U LEU* 3.9 26.0 - - + -
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Residues in contact with ALA 21 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17U ASN 3.1 16.7 + - - +
18U GLU* 3.1 5.0 + - - +
20U ILE* 1.3 73.0 - - - +
22U ILE* 1.3 69.1 + - - +
24U GLN* 4.5 0.9 - - - -
25U TYR* 2.9 40.4 + - + +
51U GLU* 3.4 27.1 - - + +
93U LEU* 3.7 23.1 - - + -
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Residues in contact with ILE 22 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18U GLU 2.8 25.5 + - - +
19U LEU* 3.8 9.6 - - + +
20U ILE 3.3 0.2 - - - -
21U ALA* 1.3 74.8 - - - +
23U ASN* 1.3 69.3 + - - +
26U PHE* 3.0 13.9 + - + +
48U SER* 2.9 26.1 + - - +
51U GLU* 3.7 12.1 - - + +
52U MET* 3.5 49.6 - - + +
55U ALA* 4.2 13.9 - - + -
159V HEM 3.8 44.2 - - + -
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Residues in contact with ASN 23 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19U LEU 3.5 10.1 + - - +
20U ILE 3.2 7.1 + - - +
22U ILE* 1.3 84.2 - - - +
24U GLN* 1.3 63.3 + - - +
26U PHE* 3.2 2.9 + - - +
27U LEU* 3.0 25.1 + - - +
74U LEU* 3.8 14.5 - - - +
77U LEU* 4.3 12.3 - - + +
19V LEU* 4.8 7.9 - - - +
71V LEU* 3.1 45.6 + - + +
159V HEM 3.2 27.1 - - - +
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Residues in contact with GLN 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20U ILE* 3.0 17.3 + - - +
21U ALA* 4.0 2.2 - - - +
23U ASN* 1.3 78.2 - - - +
25U TYR* 1.3 64.5 + - + +
27U LEU* 3.9 0.5 - - - +
28U HIS* 2.9 34.1 + - + +
77U LEU* 3.9 7.6 - - + +
78U LEU* 2.9 46.8 + - - +
79U ILE* 4.2 17.5 - - + -
89U CYS* 3.4 21.0 + - - +
90U ASP* 2.9 29.5 + - - +
93U LEU* 3.6 23.8 - - - +
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Residues in contact with TYR 25 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21U ALA* 2.9 27.9 + - + +
24U GLN* 1.3 85.3 - - - +
26U PHE* 1.3 63.8 + - - +
29U SER* 2.9 21.3 + - - -
44U GLU* 3.1 29.2 - - - +
47U GLU* 3.8 18.2 - - + -
48U SER* 3.7 16.6 - - - -
51U GLU* 3.8 28.0 - - + -
90U ASP* 3.3 37.8 + - + -
93U LEU* 4.1 11.8 - - + +
94U GLU* 2.8 31.9 + - - +
130U HIS* 3.5 19.9 - + - -
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Residues in contact with PHE 26 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22U ILE 3.0 18.9 + - - +
23U ASN* 3.8 6.3 - - - +
24U GLN 3.2 0.4 - - - -
25U TYR* 1.3 78.6 - - - +
27U LEU* 1.3 62.1 + - - +
29U SER* 3.3 6.1 + - - -
30U ARG* 3.0 39.1 + - + +
45U TYR* 3.8 25.4 - + - -
48U SER* 3.6 18.8 + - - +
52U MET* 4.1 6.7 - - + -
56V ASP* 3.5 46.2 - - + -
59V ILE* 4.1 14.6 - - + -
71V LEU* 4.8 3.1 - - + -
159V HEM 3.6 46.7 - - + -
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Residues in contact with LEU 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23U ASN 3.0 16.3 + - - +
24U GLN 3.9 3.1 - - - +
26U PHE* 1.3 73.8 - - - +
28U HIS* 1.3 67.0 + - - +
30U ARG* 3.2 3.3 + - - +
31U MET* 2.9 44.5 + - + +
77U LEU* 5.9 1.6 - - + -
79U ILE* 3.8 39.7 - - + -
59V ILE* 4.3 10.3 - - + -
63V LEU* 4.6 1.6 - - + -
69V PRO* 3.8 48.7 - - + +
71V LEU* 4.2 17.9 - - + +
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Residues in contact with HIS 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24U GLN* 2.9 21.2 + - + +
25U TYR 3.6 0.4 - - - +
27U LEU* 1.3 79.0 - - - +
29U SER* 1.3 56.0 + - - +
31U MET* 3.3 12.0 + - - -
32U TRP* 2.9 38.8 + - + -
44U GLU* 3.3 17.6 + - + +
78U LEU 3.5 16.6 - - - -
79U ILE* 3.6 10.9 - - + +
80U GLY 3.2 22.7 + - - -
86U MET* 3.5 48.5 + - + +
89U CYS* 4.2 0.2 - - + -
90U ASP* 2.9 30.5 + - - -
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Residues in contact with SER 29 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25U TYR 2.9 13.6 + - - -
26U PHE* 3.3 12.8 - - - -
28U HIS* 1.3 79.0 - - - +
30U ARG* 1.3 86.6 + - - +
32U TRP* 3.2 3.5 + - - +
33U ASN* 3.0 28.2 + - - -
41U GLY* 2.7 27.7 + - - -
44U GLU* 3.7 9.8 - - - +
45U TYR* 3.5 15.1 - - - +
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Residues in contact with ARG 30 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26U PHE* 3.0 25.3 + - + +
27U LEU 3.2 2.9 + - - +
29U SER* 1.3 103.3 + - - +
31U MET* 1.3 56.9 - - - +
33U ASN* 3.5 22.8 + - + +
34U ASP* 3.0 28.2 + - - +
41U GLY 4.4 0.4 + - - -
42U ALA* 5.9 0.4 - - - +
45U TYR* 3.6 34.8 - - - +
56V ASP* 3.1 39.4 + - - +
59V ILE* 3.8 29.4 - - + -
60V GLU* 3.8 23.5 + - + +
63V LEU* 4.6 7.5 - - + +
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Residues in contact with MET 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27U LEU* 2.9 44.6 + - + +
28U HIS* 3.6 13.5 - - - +
30U ARG* 1.3 74.1 - - - +
32U TRP* 1.3 64.6 + - - +
34U ASP* 3.3 8.0 + - - +
35U TRP* 3.0 59.1 + - + -
79U ILE* 4.1 13.7 - - + -
80U GLY 3.4 24.0 - - - +
81U GLU* 4.6 2.2 - - - -
86U MET* 3.9 11.2 - - + -
63V LEU* 4.4 17.0 - - + -
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Residues in contact with TRP 32 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28U HIS* 2.9 26.2 + - + -
29U SER 3.5 5.4 - - - +
31U MET* 1.3 76.1 - - - +
33U ASN* 1.3 61.5 + - - +
35U TRP* 3.0 17.8 + + - -
37U LEU* 2.8 60.8 + - + +
40U LEU* 3.5 36.4 - - + +
41U GLY 3.7 5.2 - - - +
44U GLU* 3.8 33.0 - - + -
83U THR* 3.0 37.2 + - + -
86U MET* 3.5 38.4 - - + +
87U LEU* 4.1 22.0 - - + -
90U ASP* 4.8 0.9 - - - -
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Residues in contact with ASN 33 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136S THR* 5.0 1.4 + - - +
29U SER* 3.0 13.1 + - - +
30U ARG* 3.5 36.8 + - + +
32U TRP* 1.3 76.0 - - - +
34U ASP* 1.3 63.5 + - - +
36U GLY* 3.1 12.2 + - - +
37U LEU 4.8 1.1 - - - +
38U LYS* 3.8 28.5 + - + +
41U GLY* 3.5 22.7 - - - -
42U ALA 4.3 0.2 - - - +
60V GLU* 5.1 4.7 - - + +
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Residues in contact with ASP 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132S ASP* 4.0 16.0 - - - +
136S THR* 3.0 26.0 + - - +
30U ARG 3.0 18.0 + - - +
31U MET* 3.5 7.0 - - - +
33U ASN* 1.3 75.9 - - - +
35U TRP* 1.3 75.9 + - - +
36U GLY 3.2 0.3 + - - -
63V LEU* 3.7 44.8 - - + +
64V PHE* 4.2 3.3 + - - -
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Residues in contact with TRP 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136S THR* 3.7 7.5 - - - +
139S GLY 5.5 0.2 - - - -
140S LEU* 3.3 23.9 + - - +
143S LYS* 3.8 38.5 + - - +
31U MET* 3.0 38.2 + - + -
32U TRP* 3.0 25.5 + + - +
34U ASP* 1.3 93.6 + - - +
36U GLY* 1.3 61.7 + - - +
37U LEU* 4.2 10.5 - - + -
81U GLU 3.5 25.4 - - - -
82U ASN* 4.1 7.2 - - - -
83U THR* 4.4 3.4 - - - -
86U MET* 3.6 25.8 - - + -
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Residues in contact with GLY 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136S THR* 3.6 15.5 - - - -
140S LEU* 4.1 8.4 - - - +
32U TRP 3.0 2.2 + - - -
33U ASN 3.1 12.0 + - - -
34U ASP 3.1 1.8 + - - -
35U TRP* 1.3 79.3 - - - +
37U LEU* 1.3 59.9 + - - +
38U LYS* 3.3 17.0 - - - +
154U MET* 3.3 28.4 - - - +
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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