Contacts of the helix formed by residues 3 - 34 (chain U) in PDB entry 2JD6
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 SER 3 (chain U).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1U MET 4.0 1.4 + - - -
2U LEU* 1.3 77.5 - - - +
4U GLU* 1.3 64.0 + - - +
5U ARG* 3.4 4.5 + - - -
6U MET* 2.8 25.1 + - - +
7U LEU* 3.1 21.1 + - - +
111U GLU* 3.0 27.3 + - - -
113U ASP* 5.6 0.6 + - - -
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Residues in contact with GLU 4 (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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2U LEU 3.8 0.4 + - - -
3U SER* 1.3 74.7 - - - +
5U ARG* 1.3 59.0 + - + +
7U LEU* 3.7 12.3 - - + +
8U LYS* 3.1 27.8 + - + +
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Residues in contact with ARG 5 (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 SER* 3.1 7.3 - - - +
4U GLU* 1.3 79.0 - - - +
6U MET* 1.3 60.2 + - - +
8U LYS* 3.1 7.9 + - - +
9U ALA* 3.0 27.8 + - - +
107U LEU* 4.1 24.1 - - + +
110U GLU* 4.5 14.9 + - - -
111U GLU* 4.2 14.4 + - - +
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Residues in contact with MET 6 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2U LEU* 3.6 23.3 - - + -
3U SER* 2.8 26.5 + - - +
5U ARG* 1.3 73.9 - - - +
7U LEU* 1.3 64.4 + - - +
9U ALA* 3.0 1.9 + - - +
10U LEU* 2.9 25.6 + - + +
104U LEU* 3.6 22.9 - - + -
107U LEU* 3.7 19.9 - - + +
108U ALA* 3.4 44.2 - - + +
111U GLU* 3.6 9.6 + - - +
113U ASP* 3.7 10.3 - - + +
116U THR* 3.9 13.5 - - + +
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Residues in contact with LEU 7 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2U LEU* 4.3 19.4 - - + +
3U SER 3.1 18.1 + - - +
4U GLU* 3.7 11.2 - - + +
6U MET* 1.3 76.6 - - - +
8U LYS* 1.3 63.9 + - - +
10U LEU* 3.1 3.7 + - - +
11U ASN* 3.0 49.3 + - - +
61U ILE* 4.0 13.9 - - + -
66U GLY* 4.1 7.0 - - - -
67U ARG* 3.6 31.6 - - + +
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Residues in contact with LYS 8 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4U GLU* 3.1 16.4 + - + +
5U ARG* 3.1 10.3 + - - +
7U LEU* 1.3 77.8 - - - +
9U ALA* 1.3 57.6 + - - +
11U ASN* 3.5 7.0 + - + +
12U ASP* 2.9 58.1 + - - +
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Residues in contact with ALA 9 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5U ARG 3.0 13.5 + - - +
6U MET 3.0 8.5 + - - +
8U LYS* 1.3 79.2 - - - +
10U LEU* 1.3 57.0 + - - +
12U ASP* 3.3 10.0 + - - +
13U GLN* 3.0 28.1 + - - +
16U ARG* 4.7 2.1 + - - -
104U LEU* 3.8 26.0 - - + +
107U LEU* 3.8 15.3 - - + -
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Residues in contact with LEU 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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2U LEU* 3.8 38.6 - - + -
6U MET* 2.9 26.9 + - + +
7U LEU* 3.1 3.8 + - - +
9U ALA* 1.3 73.4 - - - +
11U ASN* 1.3 61.4 + - - +
13U GLN* 3.3 4.4 + - - +
14U LEU* 2.9 27.9 + - - +
57U PHE* 3.6 33.2 - - + -
60U TYR* 4.0 15.9 - - + -
61U ILE* 3.9 18.6 - - + -
104U LEU* 4.1 11.4 - - + -
116U THR* 4.1 13.7 - - + -
119U PHE* 4.1 11.9 - - + -
120U LEU* 4.9 0.4 - - + -
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Residues in contact with ASN 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 LEU* 3.0 38.3 + - - +
8U LYS* 3.8 7.2 - - + +
10U LEU* 1.3 72.7 - - - +
12U ASP* 1.3 67.6 + - - +
14U LEU* 3.2 9.3 + - - +
15U ASN* 3.0 21.8 + - - +
61U ILE* 3.7 9.0 - - - +
67U ARG 3.4 17.8 + - - -
68U VAL* 3.3 11.4 - - - +
69U GLU* 2.9 44.5 + - + +
71U ASP* 5.4 3.6 - - - +
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Residues in contact with ASP 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 LYS* 2.9 51.4 + - - +
9U ALA* 3.5 9.5 - - - +
10U LEU 3.2 0.2 - - - -
11U ASN* 1.3 75.9 - - - +
13U GLN* 1.3 52.3 + - - +
15U ASN* 2.9 11.7 + - - +
16U ARG* 2.7 57.8 + - - +
71U ASP* 4.4 10.5 - - - +
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Residues in contact with GLN 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 ALA 3.0 15.6 + - - +
10U LEU 3.6 5.2 - - - +
12U ASP* 1.3 74.3 - - - +
14U LEU* 1.3 56.1 + - - +
16U ARG* 2.8 41.6 + - - +
17U GLU* 2.8 63.9 + - - +
57U PHE* 3.4 26.9 - - + -
97U ILE* 4.2 9.7 - - - +
100U SER* 3.2 17.4 - - - +
101U ILE* 3.5 19.7 - - + +
104U LEU* 3.8 15.0 - - + +
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Residues in contact with LEU 14 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PHE* 4.6 4.3 - - + -
10U LEU 2.9 13.6 + - - +
11U ASN* 3.4 11.9 - - - +
13U GLN* 1.3 74.8 - - - +
15U ASN* 1.3 63.9 + - + +
17U GLU* 3.2 9.5 + - - +
18U LEU* 3.1 40.6 + - + +
54U ALA* 3.9 19.0 - - + +
57U PHE* 4.0 11.7 - - + -
58U TYR* 3.8 34.5 - - + +
61U ILE* 4.2 7.4 - - + -
68U VAL* 4.0 22.7 - - + -
69U GLU 5.9 1.1 - - - +
70U LEU* 3.9 16.2 - - + -
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Residues in contact with ASN 15 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C TYR* 4.1 5.4 + - - +
11U ASN 3.0 10.4 + - - +
12U ASP* 2.9 11.4 + - - +
14U LEU* 1.3 75.9 - - + +
16U ARG* 1.3 64.8 + - - +
18U LEU* 3.2 6.1 + - - +
19U TYR* 2.9 31.1 + - - +
69U GLU 5.9 0.7 - - - +
70U LEU* 6.2 0.4 - - - -
71U ASP* 3.5 36.5 + - + +
72U GLU 2.9 29.8 + - - +
73U ILE* 4.2 6.7 - - - +
74U PRO* 5.0 4.0 - - - +
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Residues in contact with ARG 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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9U ALA 4.7 1.6 + - - -
12U ASP* 2.7 36.8 + - - +
13U GLN* 2.8 53.8 + - - +
15U ASN* 1.3 74.1 - - - +
17U GLU* 1.3 66.5 + - - +
19U TYR* 3.2 8.1 + - - +
20U SER* 3.0 25.8 + - - -
93U HIS* 4.9 0.3 + - - -
96U PHE* 4.1 24.5 - - + -
97U ILE* 4.2 11.2 - - + +
100U SER* 3.4 29.2 + - - +
104U LEU* 5.7 2.0 - - - +
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Residues in contact with GLU 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 GLN* 2.8 47.6 + - - +
14U LEU 3.2 7.8 + - - +
16U ARG* 1.3 72.4 - - - +
18U LEU* 1.3 56.8 + - - +
20U SER* 3.1 10.0 + - - -
21U ALA 3.0 21.7 + - - -
50U GLU* 2.9 18.6 - - - +
53U HIS* 3.4 16.7 - - + +
54U ALA* 3.7 21.1 - - - +
57U PHE* 4.2 15.2 - - + -
97U ILE* 4.2 9.0 - - - +
101U ILE* 4.6 0.7 - - - +
123U PHE* 4.4 5.9 - - - -
127U GLN* 5.3 0.2 + - - -
201U FE 2.3 31.5 - - - -
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Residues in contact with LEU 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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22C TYR* 3.8 36.8 - - + +
25C PHE* 4.4 13.2 - - + -
14U LEU* 3.1 39.1 + - + +
15U ASN* 3.8 6.5 - - - +
16U ARG 3.2 0.2 - - - -
17U GLU* 1.3 73.6 - - - +
19U TYR* 1.3 67.0 + - - +
21U ALA* 3.1 9.1 + - + +
22U TYR* 3.0 21.7 + - - +
50U GLU 5.5 0.2 - - - -
51U ILE* 4.5 19.7 - - + -
54U ALA* 3.8 17.7 - - + -
73U ILE* 4.2 17.4 - - + +
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Residues in contact with TYR 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 ASN* 2.9 18.6 + - - +
16U ARG* 3.7 7.6 - - - +
18U LEU* 1.3 77.4 - - - +
20U SER* 1.3 52.0 + - - +
22U TYR* 3.0 2.1 + - + -
23U LEU* 2.7 46.2 + - + +
73U ILE* 4.0 13.3 - - + +
74U PRO* 3.5 54.1 - - + -
75U LYS 4.5 1.4 + - - -
76U PRO* 3.5 13.1 - - + +
77U PRO* 3.4 27.9 - - - +
93U HIS* 3.9 26.5 - + - -
96U PHE* 6.2 0.7 - + - -
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Residues in contact with SER 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 ARG 3.0 13.7 + - - -
17U GLU* 3.2 10.3 + - - -
19U TYR* 1.3 74.0 - - - +
21U ALA* 1.3 68.0 + - - +
22U TYR 3.1 0.2 + - - -
23U LEU* 3.1 4.3 + - - +
24U TYR* 3.0 34.5 + - - -
50U GLU* 3.8 22.6 + - - -
93U HIS* 2.7 32.4 + - - -
94U GLU* 5.4 0.2 - - - -
97U ILE* 3.5 10.6 - - - +
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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 GLU 3.0 9.6 + - - +
18U LEU* 3.3 12.8 - - + +
20U SER* 1.3 76.4 - - - +
22U TYR* 1.3 58.2 + - - +
24U TYR* 3.4 0.5 + - - -
25U PHE* 3.0 24.4 + - - +
47U ALA* 3.4 36.2 - - + +
50U GLU* 3.5 14.2 - - + +
51U ILE* 3.8 23.3 - - + +
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Residues in contact with TYR 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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15C ASN* 4.2 2.9 + - - +
18C LEU* 3.8 22.7 - - + +
70C LEU* 3.4 26.3 - - + +
71C ASP 2.6 41.0 + - - -
73C ILE* 3.6 26.8 - - + +
18U LEU 3.0 12.8 + - - +
19U TYR* 3.0 8.2 + + + +
21U ALA* 1.3 74.3 - - - +
23U LEU* 1.3 60.3 + - - +
25U PHE* 3.0 12.7 + + + +
26U ALA* 2.8 28.8 + - - +
73U ILE* 3.7 25.6 - - + -
74U PRO 3.8 4.5 - - - -
76U PRO* 3.3 31.4 - - + +
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Residues in contact with LEU 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 TYR* 2.7 33.2 + - + +
20U SER* 3.1 4.9 + - - +
22U TYR* 1.3 71.5 - - - +
24U TYR* 1.3 62.4 - - + +
26U ALA* 2.9 22.1 + - - +
27U MET* 2.9 31.0 + - + +
76U PRO* 4.3 5.0 - - + +
77U PRO* 3.7 31.0 - - + -
80U TRP* 3.9 19.1 - - + -
89U ALA* 5.0 2.2 - - + +
93U HIS* 3.6 43.5 - - + +
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Residues in contact with TYR 24 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20U SER* 3.0 27.0 + - - +
21U ALA 3.9 3.1 - - - +
23U LEU* 1.3 79.1 - - + +
25U PHE* 1.3 60.9 + - - +
27U MET* 3.7 9.8 - - - +
28U ALA* 2.8 23.9 + - - +
42U TRP* 6.1 0.2 - + - -
43U MET* 3.4 48.0 - - + +
46U GLN* 3.6 22.0 - - + -
47U ALA 3.9 3.1 - - - +
50U GLU* 3.6 32.1 - - + -
90U ALA* 3.9 26.6 + - + -
93U HIS* 3.6 14.1 - + - -
94U GLU* 2.4 33.3 + - - +
134U VAL* 5.4 2.9 - - + +
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Residues in contact with PHE 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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14C LEU* 4.4 5.6 - - + -
18C LEU* 4.4 19.7 - - + -
51C ILE* 6.6 0.7 - - + -
54C ALA* 5.5 2.0 - - + -
55C LEU* 4.0 28.0 - - + -
58C TYR* 3.7 39.0 - + + -
70C LEU* 3.6 33.2 - - + +
21U ALA 3.0 14.7 + - - +
22U TYR* 3.0 20.6 + + - +
24U TYR* 1.3 75.7 - - - +
26U ALA* 1.3 63.9 + - - +
28U ALA* 3.1 11.8 + - + +
29U ALA* 3.0 21.7 + - - +
44U LYS* 4.7 10.8 - - + -
47U ALA* 4.2 11.6 - - + +
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Residues in contact with ALA 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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70C LEU* 3.5 15.2 - - + +
22U TYR 2.8 13.1 + - - +
23U LEU 2.9 12.3 + - - +
25U PHE* 1.3 77.6 - - - +
27U MET* 1.3 59.9 + - - +
29U ALA* 3.2 7.5 + - - +
30U TYR* 3.0 20.6 + - - +
76U PRO* 3.8 14.8 - - + -
77U PRO 3.5 24.5 - - - +
78U LYS* 4.4 4.4 - - - +
80U TRP* 4.2 5.9 - - + -
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Residues in contact with MET 27 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U LEU* 2.9 29.5 + - + +
24U TYR* 3.8 16.8 - - - +
26U ALA* 1.3 72.0 - - - +
28U ALA* 1.3 66.8 + - - +
30U TYR* 2.9 4.8 + - + +
31U PHE* 2.8 33.2 + - + -
43U MET* 3.7 33.2 - - + -
80U TRP* 3.5 44.0 - - + -
86U ALA* 3.6 29.4 - - + +
89U ALA* 3.9 6.1 - - + -
90U ALA* 3.8 18.6 - - - +
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Residues in contact with ALA 28 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C TYR* 3.5 11.6 + - - +
24U TYR 2.8 15.2 + - - +
25U PHE* 3.3 14.4 - - + +
27U MET* 1.3 76.4 - - - +
29U ALA* 1.3 58.7 + - - +
31U PHE 3.1 0.5 + - - -
32U GLU* 2.8 25.5 + - - +
40U ALA* 3.5 29.6 - - - +
43U MET* 3.6 11.5 - - + +
44U LYS* 3.8 18.2 - - + +
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Residues in contact with ALA 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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58C TYR* 3.4 23.8 + - + -
62C TYR* 2.7 28.9 + - - +
67C ARG* 3.5 13.5 + - - +
68C VAL* 4.2 14.1 - - + +
70C LEU* 5.4 3.6 - - + -
25U PHE 3.0 11.9 + - - +
26U ALA* 3.4 11.9 - - - +
28U ALA* 1.3 75.1 - - - +
30U TYR* 1.3 61.6 + - - +
32U GLU 3.3 0.3 + - - -
33U ASP* 3.2 12.3 + - - +
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Residues in contact with TYR 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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67C ARG* 3.8 25.1 - - - +
26U ALA 3.0 11.9 + - - +
27U MET* 2.9 10.8 + - - +
29U ALA* 1.3 76.2 - - - +
31U PHE* 1.3 93.2 + + - +
33U ASP* 3.2 15.0 + - - +
34U LEU* 3.3 37.6 + - + +
78U LYS 4.0 5.2 - - - +
79U GLU* 4.4 4.9 - - + -
80U TRP* 3.3 44.9 + + + -
81U GLU 3.8 1.2 + - - -
82U SER* 3.0 35.4 + - - -
83U PRO 3.3 1.6 - - - -
86U ALA* 3.9 15.0 - - + -
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Residues in contact with PHE 31 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27U MET* 2.8 30.6 + - + +
28U ALA 3.9 0.9 - - - +
30U TYR* 1.3 83.5 - + - +
32U GLU* 1.3 63.2 + - - +
34U LEU* 3.0 9.7 + - + +
36U LEU* 2.9 39.5 + - + +
39U PHE* 3.4 28.7 - + + -
40U ALA 3.7 17.9 - - - +
43U MET* 4.0 23.6 - - + -
83U PRO* 3.6 29.8 - - + -
86U ALA* 3.7 26.7 - - + -
87U PHE* 3.8 31.4 - + - -
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Residues in contact with GLU 32 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C TYR* 2.5 44.7 + - - +
62C TYR* 3.7 31.7 - - + -
28U ALA 2.8 8.0 + - - +
29U ALA 3.5 5.2 - - - +
30U TYR 3.2 0.2 - - - -
31U PHE* 1.3 78.0 - - - +
33U ASP* 1.3 58.8 + - - +
35U GLY* 3.0 20.4 + - - -
36U LEU 4.8 1.6 - - - +
37U GLU* 4.1 23.1 - - - +
40U ALA* 3.5 15.2 - - - +
44U LYS* 3.0 19.1 + - - -
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Residues in contact with ASP 33 (chain U).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C TYR* 3.6 13.4 - - + -
66C GLY 4.5 3.3 - - - +
67C ARG* 3.5 39.2 + - - +
29U ALA 3.2 9.6 + - - +
30U TYR* 3.2 10.8 + - - +
31U PHE 3.2 0.6 - - - -
32U GLU* 1.3 80.3 - - - +
34U LEU* 1.3 65.5 + - - +
35U GLY 3.0 4.0 + - - -
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Residues in contact with LEU 34 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PHE* 5.6 5.4 - - - -
30U TYR* 3.4 52.7 - - + +
31U PHE* 3.0 12.1 + - + +
33U ASP* 1.3 85.1 - - - +
35U GLY* 1.3 61.0 + - - +
36U LEU* 3.5 23.5 + - + +
83U PRO* 4.2 14.4 - - + -
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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
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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