Contacts of the helix formed by residues 38 - 76 (chain A) in PDB entry 1AJ3
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 38 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 1.3 108.7 + - - +
39A LEU* 1.3 69.4 + - - +
40A THR 3.5 0.2 - - - -
41A GLY* 2.7 19.5 + - - +
42A VAL* 3.5 6.8 + - - +
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Residues in contact with LEU 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 3.0 23.0 + - - +
38A ASP* 1.3 84.8 + - - +
40A THR* 1.3 67.4 + - - +
42A VAL* 3.3 18.5 - - - +
43A GLN* 5.2 1.6 - - - +
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Residues in contact with THR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A GLY* 3.4 18.6 + - - +
37A ARG* 2.8 7.9 + - - +
39A LEU* 1.3 82.3 - - - +
41A GLY* 1.3 68.3 + - - +
42A VAL* 3.0 3.4 - - - -
43A GLN* 2.7 29.3 + - + +
44A ASN* 2.7 19.6 + - + +
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP 4.4 10.3 - - - -
36A GLY 4.3 1.0 + - - -
37A ARG 2.8 10.5 + - - -
38A ASP* 2.7 13.6 + - - -
40A THR* 1.3 74.6 - - - +
42A VAL* 1.3 54.5 + - - -
44A ASN* 2.9 11.7 + - - +
45A LEU* 2.8 38.0 + - - +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP 3.5 5.1 + - - +
39A LEU 3.3 23.1 - - - +
40A THR 2.8 3.4 + - - -
41A GLY* 1.3 72.0 - - - +
43A GLN* 1.3 89.4 + - + +
45A LEU* 3.1 24.5 + - + +
46A ARG* 3.2 13.1 + - + +
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Residues in contact with GLN 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A LEU 5.2 1.1 - - - +
40A THR* 2.7 22.4 + - + +
42A VAL* 1.3 99.6 + - + +
44A ASN* 1.3 56.4 + - - +
46A ARG* 2.8 50.1 + - - +
47A LYS* 2.9 27.1 + - - +
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Residues in contact with ASN 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU 2.9 10.3 + - - +
34A ASP* 2.7 37.1 + - - +
35A TYR 4.4 5.7 + - - -
36A GLY* 4.6 4.8 + - - +
40A THR* 2.7 19.5 + - + +
41A GLY* 2.9 17.2 + - - +
43A GLN* 1.3 76.0 - - - +
45A LEU* 1.3 59.2 + - + +
47A LYS* 2.8 41.9 + - - +
48A LYS* 2.8 28.5 + - - +
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Residues in contact with LEU 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ASP* 5.3 13.7 - - + +
41A GLY 2.8 21.4 + - - +
42A VAL* 3.1 15.0 + - + +
44A ASN* 1.3 76.3 - - + +
46A ARG* 1.3 63.2 + - - +
48A LYS* 3.0 9.5 + - + +
49A HIS* 2.9 23.8 + - - +
105A ARG* 4.6 38.9 - - - +
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.2 10.8 + - + +
43A GLN* 2.8 59.7 + - - +
45A LEU* 1.3 79.9 - - - +
47A LYS* 1.3 77.2 - - - +
49A HIS* 3.3 8.4 + - + +
50A LYS* 3.3 37.4 + - - +
105A ARG* 6.1 0.2 - - - +
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLU* 3.0 42.8 + - - +
43A GLN 2.9 17.1 + - - +
44A ASN* 2.8 47.1 + - - +
46A ARG* 1.3 85.5 - - - +
48A LYS* 1.3 72.8 + - - +
50A LYS* 3.4 8.1 + - - +
51A ARG* 3.2 25.1 + - + +
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Residues in contact with LYS 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A VAL* 3.3 44.0 - - + +
33A GLU* 3.0 54.1 + - + +
34A ASP* 6.2 0.9 - - + -
44A ASN 2.8 18.6 + - - +
45A LEU* 3.3 10.1 - - + +
47A LYS* 1.3 84.3 - - - +
49A HIS* 1.3 50.5 + - - +
51A ARG* 3.0 6.9 + - - +
52A LEU* 2.7 49.5 + - + +
55A GLU* 3.0 19.4 + - - -
105A ARG* 6.3 1.3 - - + -
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Residues in contact with HIS 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU 2.9 12.0 + - - +
46A ARG* 3.5 11.9 - - + +
48A LYS* 1.3 75.8 - - - +
50A LYS* 1.3 76.3 + - - +
52A LEU* 2.8 31.8 + - - +
53A GLU* 2.7 53.8 + - + +
102A ALA* 3.9 18.6 + - + +
103A ALA* 5.8 0.4 - - - -
105A ARG* 4.0 17.6 - - + +
106A GLY* 3.2 36.4 + - - -
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Residues in contact with LYS 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ARG* 3.3 29.6 + - - +
47A LYS* 3.6 8.7 - - - +
48A LYS 3.3 0.2 - - - -
49A HIS* 1.3 101.8 + - - +
51A ARG* 1.3 62.3 + - - +
52A LEU 3.3 0.2 + - - -
53A GLU* 2.7 51.6 + - - +
54A ALA* 3.3 12.6 + - - +
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 4.1 22.0 - - - +
30A VAL* 5.0 0.4 - - - +
33A GLU* 2.8 42.2 + - - +
47A LYS* 3.2 13.5 + - + +
48A LYS* 3.0 10.5 + - - +
50A LYS* 1.3 79.1 - - - +
52A LEU* 1.3 57.9 + - - +
54A ALA* 3.5 6.9 + - + +
55A GLU* 2.8 73.2 + - + +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 4.3 15.9 - - - +
30A VAL* 4.7 9.9 - - + -
48A LYS* 2.7 38.7 + - + +
49A HIS* 2.8 21.2 + - - +
51A ARG* 1.3 71.3 - - - +
53A GLU* 1.3 58.3 + - - +
55A GLU* 3.1 9.7 + - - +
56A LEU* 2.8 35.4 + - + +
95A TRP* 5.6 3.4 - - + -
98A LEU* 5.3 13.7 - - + +
101A LEU* 6.2 2.0 - - + -
102A ALA* 3.8 38.4 - - + +
105A ARG* 5.6 4.9 - - + -
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Residues in contact with GLU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A HIS* 2.7 53.5 + - + +
50A LYS* 2.7 41.0 + - - +
52A LEU* 1.3 78.5 - - - +
54A ALA* 1.3 63.7 + - - +
56A LEU* 3.2 16.4 + - + +
57A ALA* 3.2 18.0 + - - +
102A ALA* 6.2 2.2 - - + -
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LYS 3.3 8.6 + - - +
51A ARG* 3.7 11.4 - - + +
52A LEU 3.3 0.2 - - - -
53A GLU* 1.3 77.2 - - - +
55A GLU* 1.3 65.7 + - - +
57A ALA* 3.0 23.5 + - - +
58A ALA* 3.5 4.3 + - - +
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 3.0 41.2 + - - +
29A LEU* 4.9 2.4 - - - +
48A LYS* 3.0 21.0 + - - -
51A ARG* 2.8 62.2 + - + +
52A LEU* 3.2 5.9 - - - +
54A ALA* 1.3 75.8 - - - +
56A LEU* 1.3 62.7 + - - +
58A ALA* 2.8 15.1 + - - +
59A HIS* 2.7 31.6 + - + -
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS* 4.5 0.4 - - - +
52A LEU* 2.8 21.7 + - + +
53A GLU* 3.2 20.2 + - + +
55A GLU* 1.3 72.9 - - - +
57A ALA* 1.3 76.6 + - + +
59A HIS* 3.6 0.8 - - - -
60A GLU* 2.9 58.4 + - - +
95A TRP* 3.8 21.1 - - + -
99A LYS* 3.2 36.1 - - + +
102A ALA* 6.0 3.8 - - + -
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLU 3.2 9.7 + - - +
54A ALA* 3.0 18.4 + - - +
55A GLU 3.0 0.2 + - - -
56A LEU* 1.3 82.3 - - + +
58A ALA* 1.3 50.1 + - - +
60A GLU* 3.9 4.5 - - - +
61A PRO* 2.7 32.1 - - - +
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TRP* 5.6 0.4 - - - -
54A ALA 3.5 3.8 + - - +
55A GLU* 2.8 13.4 + - - +
57A ALA* 1.3 74.2 - - - +
59A HIS* 1.3 68.8 + - + +
60A GLU 3.3 0.7 - - - -
61A PRO* 3.5 5.8 - - - +
62A ALA* 3.4 22.2 + - - +
----------------------------------------------------------
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Residues in contact with HIS 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TRP* 2.9 45.5 + + + -
26A LYS* 3.0 49.5 + - + +
55A GLU* 2.7 36.2 + - + -
56A LEU 3.0 2.0 + - - +
58A ALA* 1.3 80.4 - - + +
60A GLU* 1.3 64.2 + - - +
62A ALA* 3.7 1.7 - - - +
63A ILE* 2.8 32.7 + - + +
95A TRP* 3.3 31.2 - + + -
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 2.9 41.4 + - - +
57A ALA* 3.9 4.2 - - - +
59A HIS* 1.3 77.9 - - - +
61A PRO* 1.3 73.1 - - + +
64A GLN* 2.9 39.3 + - + +
95A TRP* 2.8 32.0 + - - +
99A LYS* 2.9 16.0 + - - -
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Residues in contact with PRO 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA 2.7 30.1 - - - +
58A ALA* 3.5 10.8 - - - +
60A GLU* 1.3 87.1 - - + +
62A ALA* 1.3 55.5 + - - +
64A GLN* 3.7 6.8 - - + +
65A GLY* 2.8 29.5 + - - -
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLU* 2.9 17.5 - - + +
22A TRP* 4.6 16.2 - - + -
58A ALA 3.4 17.2 + - - +
59A HIS* 3.7 8.1 - - - +
61A PRO* 1.3 81.9 - - - +
63A ILE* 1.3 62.1 + - - +
65A GLY* 3.3 7.3 + - - -
66A VAL 3.6 4.0 + - - -
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Residues in contact with ILE 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TRP* 3.8 19.1 - - + -
23A ILE* 4.8 0.7 - - + -
59A HIS 2.8 26.7 + - - +
60A GLU 4.0 2.0 - - - +
62A ALA* 1.3 76.3 - - - +
64A GLN* 1.3 79.0 + - - +
66A VAL* 3.1 16.1 + - - +
67A LEU* 3.2 18.5 + - + +
88A LEU* 5.6 0.2 - - - +
91A PHE* 2.9 51.6 - - + -
92A VAL* 5.4 7.4 - - + -
95A TRP* 3.8 41.7 - - + -
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Residues in contact with GLN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 2.9 29.5 + - + +
61A PRO* 3.7 7.6 - - + +
63A ILE* 1.3 86.8 - - - +
65A GLY* 1.3 66.5 + - - +
67A LEU* 2.8 29.5 + - + +
68A ASP* 2.8 23.9 + - - +
95A TRP* 5.5 4.6 - - - -
----------------------------------------------------------
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Residues in contact with GLY 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A PRO 2.8 20.5 + - - -
62A ALA 3.7 3.4 - - - -
63A ILE 3.2 0.6 - - - -
64A GLN* 1.3 72.7 - - - +
66A VAL* 1.3 60.4 + - - +
68A ASP* 3.3 7.7 + - - +
69A THR* 2.9 27.6 + - - -
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Residues in contact with VAL 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.7 19.7 - - + -
15A ASP* 5.1 5.4 - - + -
16A MET* 3.9 25.6 - - + +
19A GLU* 3.1 37.5 - - + +
62A ALA 3.6 4.0 + - - -
63A ILE 3.1 7.1 + - - +
65A GLY* 1.3 73.9 - - - +
67A LEU* 1.3 67.4 + - - +
69A THR* 3.0 9.2 + - - +
70A GLY* 2.8 20.4 + - - -
88A LEU* 3.2 26.7 - - + -
91A PHE* 4.6 1.3 - - + -
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.2 10.6 + - + +
64A GLN* 2.8 37.8 + - + +
66A VAL* 1.3 83.5 - - - +
68A ASP* 1.3 64.2 + - - +
70A GLY* 3.1 3.5 + - - -
71A LYS* 3.0 20.9 + - + +
85A GLN* 6.1 2.9 - - - +
88A LEU* 4.0 24.2 - - + -
91A PHE* 6.3 0.2 - - + -
92A VAL* 4.4 24.0 - - + -
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Residues in contact with ASP 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN 2.8 14.4 + - - +
65A GLY* 3.6 10.5 - - - +
67A LEU* 1.3 72.3 - - - +
69A THR* 1.3 65.5 + - - +
71A LYS* 2.9 47.8 + - - +
72A LYS* 3.1 14.9 + - - +
----------------------------------------------------------
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Residues in contact with THR 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.8 23.6 - - + -
65A GLY 2.9 17.1 + - - -
66A VAL* 3.0 10.7 + - - -
68A ASP* 1.3 76.2 + - - +
70A GLY* 1.3 63.9 - - - +
72A LYS* 2.9 20.3 + - + +
73A LEU* 3.0 25.2 + - + +
----------------------------------------------------------
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.8 22.3 - - - -
66A VAL 2.8 14.9 + - - -
67A LEU* 3.1 4.2 + - - -
69A THR* 1.3 72.8 - - - +
71A LYS* 1.3 62.6 + - - +
73A LEU* 3.0 17.9 + - - +
74A SER* 2.8 16.0 + - - -
81A LYS* 3.6 10.7 - - - +
88A LEU* 5.9 2.2 - - - -
----------------------------------------------------------
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Residues in contact with LYS 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.0 11.7 + - + +
68A ASP* 2.9 53.1 + - - +
70A GLY* 1.3 74.3 - - - +
72A LYS* 1.3 69.9 + - + +
74A SER* 2.9 17.2 + - - -
75A ASP* 3.0 36.1 - - - +
----------------------------------------------------------
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Residues in contact with LYS 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 3.1 13.8 + - - +
69A THR* 2.9 15.1 + - + +
71A LYS* 1.3 80.0 - - + +
73A LEU* 1.3 69.1 + - + +
75A ASP* 2.8 51.9 + - - +
76A ASP* 2.9 49.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A PHE* 3.0 44.9 - - + -
69A THR* 3.0 42.2 + - + +
70A GLY* 3.2 8.7 - - - +
72A LYS* 1.3 75.6 - - + +
74A SER* 1.3 52.4 + - - +
76A ASP* 2.9 11.2 + - - +
77A ASN* 2.6 37.5 + - + +
78A THR 3.4 3.4 + - - -
81A LYS* 4.1 13.2 - - + -
84A ILE* 4.3 13.2 - - + -
----------------------------------------------------------
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A GLY 2.8 16.5 + - - -
71A LYS* 2.9 14.8 + - - -
73A LEU* 1.3 75.9 - - - +
75A ASP* 1.3 65.5 + - - +
78A THR* 2.7 51.3 + - - +
81A LYS* 2.9 30.6 + - - +
----------------------------------------------------------
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A LYS* 3.0 32.7 - - - +
72A LYS* 2.8 34.5 + - - +
74A SER* 1.3 76.1 - - - +
76A ASP* 1.3 60.7 + - - +
77A ASN 3.4 0.2 - - - -
78A THR* 5.0 0.7 + - - -
----------------------------------------------------------
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Residues in contact with ASP 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 2.9 55.0 + - - +
73A LEU* 3.5 12.3 + - - +
75A ASP* 1.3 80.5 - - - +
77A ASN* 1.3 60.7 + - + +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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