Contacts of the helix formed by residues 23 - 55 (chain E) in PDB entry 6XXD
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 ASN 23 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PRO 4.1 2.9 - - - -
106A ASP* 3.1 34.6 + - - +
22E PRO* 1.3 72.5 - - - +
24E LEU* 1.3 61.5 + - - +
25E LEU* 3.4 4.7 + - - +
26E ALA* 2.9 35.0 + - + +
27E ALA* 3.5 19.1 + - - +
42H ASP* 5.2 2.6 + - - -
46H PHE* 3.7 20.6 - - + -
68H GLY* 2.8 34.8 + - - -
70H LYS* 4.8 7.1 - - - +
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Residues in contact with LEU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.5 20.9 - - + -
48A GLU* 3.7 18.4 - - + +
57A TYR* 5.5 0.2 - - - +
88A TYR* 3.5 24.5 - - - +
104A THR 5.3 0.4 - - - +
105A PRO* 3.1 23.2 + - + +
108A GLY* 6.2 0.7 - - - -
4B ILE* 4.0 20.2 - - + -
8B ILE* 3.4 36.1 - - + +
21E ILE* 5.4 4.5 - - + -
22E PRO* 3.8 19.1 - - + +
23E ASN* 1.3 70.3 - - - +
25E LEU* 1.3 66.7 + - - +
27E ALA* 3.2 4.0 + - - +
28E ARG* 3.1 28.0 + - + +
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Residues in contact with LEU 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A TYR* 6.2 0.2 - - + -
86A ASN* 3.0 30.7 - - + +
87A SER* 4.9 6.5 - - - +
105A PRO* 3.7 16.9 + - + +
106A ASP* 3.8 39.5 - - + +
23E ASN* 3.4 0.8 + - - -
24E LEU* 1.3 79.2 - - - +
26E ALA* 1.3 62.0 + - - +
28E ARG* 3.5 9.6 + - + +
29E LYS* 3.3 46.9 + - + +
96E GLY* 5.9 2.2 - - - +
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Residues in contact with ALA 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23E ASN* 2.9 27.4 + - + +
25E LEU* 1.3 74.4 - - - +
27E ALA* 1.3 65.7 + - - +
29E LYS* 3.4 27.9 + - - +
30E ARG* 3.8 5.2 + - - +
46H PHE* 3.7 24.7 - - + -
49H MET* 3.8 23.1 - - + +
67H LEU 4.4 7.2 - - - +
68H GLY* 4.9 0.4 - - - -
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Residues in contact with ALA 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ILE* 4.2 18.2 - - + -
12B ILE* 4.8 6.0 - - + +
23E ASN 3.5 13.8 + - - +
24E LEU 3.2 9.5 + - - +
26E ALA* 1.3 80.1 - - - +
28E ARG* 1.3 60.6 + - - +
30E ARG* 3.8 6.8 + - - +
31E ALA* 3.6 17.0 + - - +
49H MET* 5.3 3.3 - - - -
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Residues in contact with ARG 28 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLU* 3.0 24.3 + - - -
51A GLN* 3.4 38.3 + - - +
52A ILE* 5.3 0.6 - - - +
57A TYR* 3.6 23.1 - - - -
86A ASN* 6.3 1.3 - - - +
8B ILE* 3.7 18.6 - - + +
11B ALA* 4.1 15.4 - - - +
12B ILE* 4.2 8.9 - - + +
15B ILE* 3.4 29.5 - - - +
24E LEU 3.1 17.5 + - - +
25E LEU* 3.9 8.7 - - + +
26E ALA 3.3 0.4 - - - -
27E ALA* 1.3 74.1 - - - +
29E LYS* 1.3 54.8 + - - +
31E ALA* 3.2 7.5 + - - +
32E ASN* 2.7 52.9 + - - +
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Residues in contact with LYS 29 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E LEU* 3.3 45.1 + - + +
26E ALA* 3.4 16.0 + - - +
28E ARG* 1.3 78.7 - - - +
30E ARG* 1.3 60.2 + - + +
32E ASN* 3.4 3.5 + - - +
33E ASP* 3.1 33.8 + - - +
96E GLY 3.6 22.7 - - - +
97E GLY* 3.6 18.9 - - - +
98E THR* 4.1 18.8 - - + +
49H MET* 5.9 1.8 - - + -
67H LEU 5.6 4.0 + - - +
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Residues in contact with ARG 30 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E ALA 3.8 10.9 + - - +
27E ALA* 3.8 7.0 + - - +
28E ARG 3.2 0.4 - - - -
29E LYS* 1.3 75.3 - - - +
31E ALA* 1.3 64.3 + - - +
33E ASP* 3.4 15.5 + - - +
34E THR* 2.9 26.1 + - - -
98E THR* 3.7 26.3 + - - +
111E LYS* 5.2 3.0 - - - +
49H MET* 3.5 46.2 + - + +
52H ILE* 4.3 26.5 - - + +
53H ASP* 2.7 42.5 + - - -
67H LEU* 4.2 10.5 + - - +
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Residues in contact with ALA 31 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 3.2 46.0 - - + -
15B ILE* 5.2 4.7 - - + -
16B LEU* 4.7 6.9 - - + +
27E ALA 3.6 7.5 + - - +
28E ARG* 3.2 7.5 + - - +
30E ARG* 1.3 78.5 - - - +
32E ASN* 1.3 62.8 + - - +
34E THR* 3.3 11.2 + - - -
35E VAL* 3.2 26.2 + - - +
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Residues in contact with ASN 32 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A ASN* 3.5 13.6 + - - +
15B ILE* 5.7 4.9 - - - +
28E ARG* 2.7 39.4 + - - +
29E LYS 3.5 5.6 - - - +
31E ALA* 1.3 71.4 - - - +
33E ASP* 1.3 64.3 + - - +
35E VAL* 3.4 9.6 + - - +
36E VAL* 3.2 26.2 + - - +
94E HIS* 3.2 43.1 + - + -
96E GLY 2.9 24.3 + - - +
97E GLY* 4.3 1.3 - - - -
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Residues in contact with ASP 33 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E LYS 3.1 18.7 + - - +
30E ARG* 3.6 19.3 + - - +
31E ALA 3.3 0.4 - - - -
32E ASN* 1.3 72.3 - - - +
34E THR* 1.3 56.3 + - - +
36E VAL* 3.3 3.5 + - - +
37E THR* 2.7 39.4 + - - +
94E HIS* 5.5 0.7 - - - +
97E GLY* 3.8 3.5 - - - -
98E THR* 2.7 49.7 + - - +
99E VAL 4.7 0.5 - - - +
101E PHE* 3.8 28.0 - - + -
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Residues in contact with THR 34 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 4.4 21.8 - - + +
19B VAL* 4.8 1.3 - - + -
20B LEU* 3.8 25.8 - - + -
30E ARG 2.9 16.4 + - - -
31E ALA* 3.3 12.6 + - - -
33E ASP* 1.3 77.2 - - - +
35E VAL* 1.3 55.5 + - - +
37E THR* 4.0 6.2 - - - -
38E ALA* 2.8 32.4 + - - +
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Residues in contact with VAL 35 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ILE* 3.3 33.9 - - + -
16B LEU* 5.6 0.2 - - + -
19B VAL* 4.0 25.7 - - + +
31E ALA 3.2 11.9 + - - +
32E ASN* 3.6 13.5 - - - +
33E ASP 3.3 0.2 - - - -
34E THR* 1.3 77.0 - - - +
36E VAL* 1.3 56.5 - - - +
38E ALA* 3.6 1.4 + - - +
39E TYR* 3.0 28.6 + - - +
73E PRO* 3.9 29.6 - - + -
76E VAL* 4.3 10.5 - - + -
94E HIS* 4.6 6.3 - - + +
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Residues in contact with VAL 36 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E ASN 3.2 14.4 + - - +
33E ASP* 3.3 8.0 + - - +
35E VAL* 1.3 75.4 - - - +
37E THR* 1.3 58.7 + - - +
39E TYR* 3.5 4.7 + - - +
40E LEU* 3.0 32.8 + - + +
76E VAL* 4.5 10.1 - - + -
92E ALA* 3.5 32.3 - - + +
93E GLY* 3.7 3.8 - - - +
94E HIS* 3.4 35.9 - - + +
101E PHE* 3.6 26.7 - - + -
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Residues in contact with THR 37 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ASP 2.7 28.2 + - - -
34E THR* 4.0 6.2 - - - -
36E VAL* 1.3 74.2 - - - +
38E ALA* 1.3 57.3 + - - +
40E LEU* 3.6 2.5 + - - +
41E ASN* 2.9 32.0 + - + +
101E PHE* 3.3 22.4 - - + -
109E VAL* 4.3 22.9 - - + +
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Residues in contact with ALA 38 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 3.9 33.4 - - + +
20B LEU* 4.0 14.4 - - + -
34E THR 2.8 19.9 + - - +
35E VAL 3.9 3.1 - - - +
36E VAL 3.3 0.2 - - - -
37E THR* 1.3 77.1 - - - +
39E TYR* 1.3 57.3 + - - +
41E ASN* 3.3 8.2 + - - +
42E ASP* 2.8 35.9 + - - +
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Residues in contact with TYR 39 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL* 5.7 0.4 - - - +
35E VAL 3.0 19.0 + - - +
36E VAL* 4.0 5.2 - - - +
37E THR 3.4 0.2 - - - -
38E ALA* 1.3 72.7 - - - +
40E LEU* 1.3 56.1 + - + +
42E ASP* 3.4 8.2 + - - +
43E ALA* 2.8 33.4 + - - +
61E GLN* 3.1 20.8 + - - -
69E LEU* 3.8 24.0 - - + +
70E LYS* 2.9 29.2 + - + -
71E SER 3.4 20.0 - - - -
72E THR* 3.5 6.0 + - - -
73E PRO* 3.7 27.1 - - + -
76E VAL* 5.4 3.8 - - + -
78E PHE* 3.6 44.0 - + + -
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Residues in contact with LEU 40 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E VAL* 3.0 25.0 + - + +
37E THR 3.9 0.2 - - - +
39E TYR* 1.3 73.9 - - + +
41E ASN* 1.3 61.1 + - - +
43E ALA* 3.5 3.1 - - - +
44E VAL* 2.9 34.7 + - - +
78E PHE* 3.9 18.2 - - + -
90E MET* 3.8 21.0 - - + +
92E ALA* 3.6 22.2 - - + -
101E PHE* 3.3 43.7 - - + +
102E ALA 3.9 1.6 - - - +
103E ALA* 3.8 7.4 - - + -
109E VAL* 3.8 26.5 - - + -
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Residues in contact with ASN 41 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37E THR* 2.9 22.9 + - + +
38E ALA* 3.3 8.9 + - - +
40E LEU* 1.3 75.0 - - - +
42E ASP* 1.3 62.9 + - - +
44E VAL* 3.7 6.4 + - - +
45E LYS* 3.5 48.6 + - - +
109E VAL* 4.0 12.4 - - + +
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Residues in contact with ASP 42 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B VAL 3.7 18.1 - - - +
20B LEU 5.8 0.2 - - - +
21B ILE 5.3 0.9 - - - +
22B PRO* 4.4 15.0 - - - +
23B ASN 5.2 1.9 + - - -
38E ALA 2.8 22.9 + - - +
39E TYR* 3.6 9.9 - - + +
41E ASN* 1.3 76.0 + - - +
43E ALA* 1.3 63.9 + - - +
45E LYS* 3.2 34.2 + - - +
46E PHE* 3.2 24.8 + - + -
69E LEU* 3.7 18.4 - - + -
70E LYS* 5.4 5.4 + - - -
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Residues in contact with ALA 43 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39E TYR 2.8 22.3 + - - +
40E LEU* 3.3 9.4 + - - +
42E ASP* 1.3 74.2 - - - +
44E VAL* 1.3 57.2 + - - +
46E PHE* 3.6 2.2 + - - +
47E GLN* 3.1 33.1 + - - +
64E LEU* 4.5 2.7 - - + +
69E LEU* 4.0 18.1 - - + +
78E PHE* 4.0 21.5 - - + -
90E MET* 3.6 18.2 - - + -
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Residues in contact with VAL 44 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E LEU 2.9 20.6 + - - +
41E ASN* 3.8 9.4 - - - +
42E ASP 3.3 0.2 - - - -
43E ALA* 1.3 74.7 - - - +
45E LYS* 1.3 65.9 + - + +
47E GLN* 3.5 6.1 + - - +
48E GLU* 3.2 28.3 + - + +
88E TYR* 3.4 24.6 + - + +
90E MET* 4.0 14.4 - - + -
103E ALA* 4.3 5.8 - - + -
104E THR 5.3 2.5 - - - +
108E GLY* 5.6 2.2 - - - -
109E VAL* 3.9 21.1 - - + +
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Residues in contact with LYS 45 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B PRO* 4.2 19.5 - - + +
41E ASN* 3.5 40.5 + - - +
42E ASP* 3.2 26.0 + - - +
44E VAL* 1.3 79.6 - - + +
46E PHE* 1.3 64.4 + - + +
48E GLU* 3.1 10.2 + - - +
49E MET* 3.0 32.5 + - - +
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Residues in contact with PHE 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASN* 3.7 28.5 - - + -
26B ALA* 3.7 10.1 - - + -
42E ASP* 3.2 27.9 + - + +
43E ALA 4.3 2.2 - - - +
45E LYS* 1.3 81.8 - - + +
47E GLN* 1.3 59.9 + - - +
49E MET* 3.5 27.9 - - - +
50E TYR* 3.2 20.8 + - - +
64E LEU* 3.4 28.4 - - + +
67E LEU* 3.9 19.9 - - + +
68E GLY* 3.3 23.8 - - - -
69E LEU* 3.3 42.8 - - + -
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Residues in contact with GLN 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ALA 3.1 24.2 + - - +
44E VAL* 3.6 7.6 - - - +
45E LYS 3.2 0.2 - - - -
46E PHE* 1.3 76.8 - - - +
48E GLU* 1.3 57.2 + - - +
50E TYR* 3.5 4.1 + - - +
51E GLN* 3.1 24.9 + - - +
57E TYR* 3.5 30.0 - - + -
58E THR* 3.0 52.9 + - - +
64E LEU* 3.8 7.0 - - + +
80E ILE* 4.3 3.0 - - - +
88E TYR* 4.0 22.9 - - + +
90E MET* 3.4 32.2 - - + +
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Residues in contact with GLU 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E VAL* 3.2 19.2 + - + +
45E LYS* 3.1 10.6 + - - +
47E GLN* 1.3 74.3 - - - +
49E MET* 1.3 64.9 + - + +
51E GLN* 3.4 11.4 + - - +
52E ILE* 3.2 29.5 + - + +
57E TYR* 3.0 28.8 + - + -
88E TYR* 4.5 7.8 + - - -
105E PRO* 5.2 3.1 - - - +
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Residues in contact with MET 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA* 3.8 35.9 - - + +
27B ALA* 5.3 2.2 - - - -
29B LYS* 5.9 1.8 - - + -
30B ARG* 3.5 39.1 + - + +
45E LYS* 3.0 19.0 + - - +
46E PHE* 3.5 34.1 - - + +
47E GLN 3.3 0.4 - - - -
48E GLU* 1.3 75.9 - - + +
50E TYR* 1.3 60.9 + - - +
52E ILE* 3.4 12.4 + - + +
53E ASP* 3.2 27.9 + - - +
67E LEU* 3.6 19.1 - - + +
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Residues in contact with TYR 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E PHE 3.2 17.2 + - - +
47E GLN* 3.7 7.0 - - - +
48E GLU 3.4 0.2 - - - -
49E MET* 1.3 72.8 - - - +
51E GLN* 1.3 59.7 + - - +
53E ASP* 4.5 2.0 - - - +
54E ASN* 2.8 70.4 + - + +
56E SER* 3.5 20.6 - - - +
57E TYR 4.8 1.8 - - - -
58E THR* 3.3 38.8 - - + -
63E ALA* 3.8 17.0 - - + +
64E LEU* 4.7 0.2 - - + -
67E LEU* 3.4 27.7 - - + +
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Residues in contact with GLN 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E GLN 3.1 13.7 + - - +
48E GLU* 3.4 19.1 - - - +
49E MET 3.3 0.2 - - - -
50E TYR* 1.3 74.7 - - - +
52E ILE* 1.3 62.7 + - - +
55E ASN* 3.2 53.1 + - - +
56E SER 3.0 27.0 + - - +
57E TYR* 3.2 31.9 - - + +
85E ALA 3.4 8.7 + - - +
86E ASN* 5.6 4.0 - - - +
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Residues in contact with ILE 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ARG* 4.3 30.1 - - + +
111B LYS* 3.7 15.4 + - - +
48E GLU* 3.2 19.5 + - + +
49E MET* 3.5 16.6 - - + +
50E TYR 3.3 0.4 - - - -
51E GLN* 1.3 80.1 - - - +
53E ASP* 1.3 68.3 + - - +
55E ASN* 4.0 8.5 + - - +
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Residues in contact with ASP 53 (chain E).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ARG* 2.7 40.0 + - - -
111B LYS* 3.9 17.2 + - - +
49E MET 3.2 12.2 + - - +
50E TYR* 3.3 5.5 + - + +
52E ILE* 1.3 82.7 - - - +
54E ASN* 1.3 76.4 + - - +
55E ASN* 3.6 5.4 + - - +
67E LEU* 4.6 10.2 - - - +
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Residues in contact with ASN 54 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E TYR* 2.8 62.1 + - + +
53E ASP* 1.3 88.2 + - - +
55E ASN* 1.3 73.9 + - - +
56E SER* 3.5 6.6 + - - +
67E LEU* 5.7 0.6 - - - +
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Residues in contact with ASN 55 (chain E).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50E TYR 3.9 0.2 + - - -
51E GLN* 3.2 39.1 + - - +
52E ILE* 4.0 10.5 + - - +
53E ASP 4.5 4.6 + - - +
54E ASN* 1.3 79.6 - - - +
56E SER* 1.3 60.6 + - - +
85E ALA* 4.2 8.3 - - - +
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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) + - + + + + + -
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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