Contacts of the helix formed by residues 46 - 71 (chain F) in PDB entry 6RIN
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 ALA 46 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1105C SER* 3.6 14.6 + - - +
1106C ARG* 5.4 0.9 - - - -
1107C MET* 4.5 8.7 - - + +
736D GLN* 3.1 16.9 - - - +
45F ASN* 1.3 84.1 + - - +
47F ASP* 1.3 58.2 + - - -
48F TYR 3.4 2.0 - - - -
49F GLN* 3.6 11.4 - - - +
50F TYR* 2.9 55.6 + - + -
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Residues in contact with ASP 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732D GLY* 3.3 29.1 + - - +
733D SER* 3.2 13.5 + - - -
735D ALA* 5.0 2.9 - - - +
736D GLN* 2.8 17.1 - - - +
35F TRP* 3.2 29.0 - - + -
36F ALA* 4.6 2.9 - - + -
39F LEU* 5.6 2.2 - - + -
45F ASN* 2.6 20.0 + - - +
46F ALA* 1.3 68.5 - - - +
48F TYR* 1.3 63.8 + - - +
50F TYR* 4.1 1.4 - - - +
51F ASN* 2.4 65.8 + - - -
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Residues in contact with TYR 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929D GLN* 3.5 41.7 + - + +
33F VAL* 3.7 35.9 - - + -
36F ALA* 4.1 15.2 - - + +
37F ALA* 4.7 11.0 - - + -
42F ARG* 5.1 25.1 - - + +
45F ASN* 3.9 19.7 + - + +
47F ASP* 1.3 76.7 - - - +
49F GLN* 1.3 69.0 + - + +
51F ASN* 4.0 2.8 - - - +
52F LYS* 2.9 54.3 + - + +
13R U 4.7 24.8 + - - -
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Residues in contact with GLN 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677C ASN* 4.1 23.6 + - - +
779D ALA* 5.8 4.2 - - - +
42F ARG 5.9 0.9 - - - +
45F ASN 3.9 14.2 + - - +
46F ALA* 3.2 21.3 + - - +
48F TYR* 1.3 87.1 - - + +
50F TYR* 1.3 77.8 + - + +
52F LYS* 3.2 5.4 + - - +
53F LYS* 3.0 26.0 + - + +
13R U 2.5 50.0 + - + +
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Residues in contact with TYR 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675C ASP* 3.6 13.2 + - - -
677C ASN* 5.7 0.9 + - - -
1107C MET* 3.1 33.7 - - + +
735D ALA* 4.3 20.8 - - + +
736D GLN* 4.9 5.6 - - + -
739D GLN* 3.0 38.9 + - - -
744D ARG* 4.0 10.5 + - - -
46F ALA* 2.9 41.5 + - + +
47F ASP* 4.4 1.6 - - - +
49F GLN* 1.3 89.4 + - + +
51F ASN* 1.3 66.7 + - - +
53F LYS* 3.1 28.8 + - + +
54F ARG* 3.0 21.7 + - - +
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Residues in contact with ASN 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733D SER* 4.0 6.3 + - - -
735D ALA* 3.9 16.7 - - - +
29F VAL* 3.9 7.5 - - + +
32F LYS* 4.6 19.6 + - - +
33F VAL* 3.8 21.3 - - + +
35F TRP* 5.4 1.2 - - - -
36F ALA* 4.7 6.5 - - - +
47F ASP* 2.4 48.0 + - - +
48F TYR* 4.0 3.5 - - - +
50F TYR* 1.3 77.7 - - - +
52F LYS* 1.3 61.6 + - - +
54F ARG* 3.1 18.6 + - - +
55F LEU* 3.1 15.2 + - - +
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Residues in contact with LYS 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929D GLN* 3.9 11.7 + - - +
931D THR* 6.4 1.6 - - - -
1244D GLN* 2.2 45.5 + - - +
33F VAL* 4.2 17.8 - - + +
48F TYR* 2.9 56.2 + - + +
49F GLN* 3.4 6.3 - - - +
51F ASN* 1.3 76.0 - - - +
53F LYS* 1.3 62.5 + - - +
55F LEU* 3.0 18.3 + - + +
56F ARG* 3.0 43.1 + - + +
13R U 5.9 8.7 - - + -
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Residues in contact with LYS 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739D GLN* 5.0 5.0 - - - +
744D ARG* 5.6 2.2 + - - +
746D LEU 3.8 7.7 + - - -
747D MET* 3.8 30.3 - - - +
748D ALA 6.3 0.7 - - - +
49F GLN* 3.0 13.3 + - + +
50F TYR* 3.1 35.8 + - + +
52F LYS* 1.3 75.9 - - - +
54F ARG* 1.3 62.2 + - - +
56F ARG* 3.2 16.2 + - + +
57F GLU* 3.0 46.0 + - + +
13R U 5.9 7.6 - - + +
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Residues in contact with ARG 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D ASP* 5.1 15.5 + - - -
738D ARG* 6.1 3.4 - - - +
25F GLU* 4.3 21.0 + - - +
29F VAL* 4.2 24.0 - - + +
50F TYR 3.0 11.8 + - - +
51F ASN* 3.1 14.6 + - - +
53F LYS* 1.3 77.6 - - - +
55F LEU* 1.3 62.9 + - - +
57F GLU* 3.3 22.3 + - - +
58F ILE* 3.0 35.8 + - + +
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Residues in contact with LEU 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1243D LEU 5.1 3.1 - - - +
1244D GLN* 4.2 15.7 - - - +
26F ARG* 2.9 43.6 + - - +
29F VAL* 3.6 25.4 - - + +
30F THR* 4.6 9.6 - - - +
33F VAL* 3.8 24.7 - - + -
51F ASN 3.1 9.1 + - - +
52F LYS* 3.0 27.4 + - + +
54F ARG* 1.3 76.8 - - - +
56F ARG* 1.3 63.6 + - + +
58F ILE* 3.1 9.2 - - + +
59F ASP* 2.9 25.4 + - - +
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Residues in contact with ARG 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785D ASP* 5.6 2.2 + - - -
789D LYS* 4.8 0.2 - - - +
931D THR* 4.7 17.0 + - - -
934D THR* 5.4 12.4 - - + +
52F LYS* 3.0 31.6 + - + +
53F LYS* 3.6 15.2 - - + +
55F LEU* 1.3 75.2 - - + +
57F GLU* 1.3 65.3 + - + +
59F ASP* 3.2 8.2 + - - +
60F ARG* 3.0 32.8 + - - +
13R U 3.3 59.7 + - - +
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Residues in contact with GLU 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
746D LEU* 4.9 10.0 + - - +
53F LYS* 3.0 43.6 + - + +
54F ARG* 3.8 24.3 + - - +
56F ARG* 1.3 79.7 - - + +
58F ILE* 1.3 61.4 + - - +
60F ARG* 3.4 14.7 + - - +
61F ARG* 3.4 17.8 + - - +
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Residues in contact with ILE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU* 4.1 33.2 - - + +
25F GLU* 3.7 32.3 - - + -
26F ARG* 3.7 29.4 - - + +
29F VAL* 6.4 2.0 - - + -
54F ARG* 3.0 30.5 + - + +
55F LEU* 3.1 19.1 - - + +
57F GLU* 1.3 73.6 - - - +
59F ASP* 1.3 65.7 + - - +
61F ARG* 3.3 6.9 + - + +
62F VAL* 3.0 23.8 + - + +
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Residues in contact with ASP 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
934D THR* 5.0 11.1 + - - +
935D PHE 4.4 16.6 - - - +
937D ILE* 4.9 7.2 + - - +
1243D LEU* 5.2 9.9 - - - +
26F ARG* 4.7 11.4 + - - +
55F LEU 2.9 18.3 + - - +
56F ARG* 3.5 8.5 - - - +
58F ILE* 1.3 79.1 - - - +
60F ARG* 1.3 62.9 + - - +
62F VAL* 3.0 16.2 - - - +
63F ARG* 2.9 25.0 + - - +
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Residues in contact with ARG 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
752D GLY* 4.6 13.8 + - - -
754D ILE* 5.5 10.7 - - - +
56F ARG* 3.0 20.4 + - - +
57F GLU* 3.8 17.5 - - - +
58F ILE 3.3 0.2 - - - -
59F ASP* 1.3 76.9 - - - +
61F ARG* 1.3 63.1 + - - +
63F ARG* 3.2 10.2 + - - +
64F TYR* 3.0 24.4 + - + +
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Residues in contact with ARG 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684D ASP* 5.5 7.0 + - - -
14F LEU* 5.9 1.8 - - - +
17F GLU* 3.9 25.1 + - - -
21F LEU* 4.1 15.0 - - + +
57F GLU 3.4 8.9 + - - +
58F ILE* 3.3 10.9 + - + +
59F ASP 3.3 0.4 - - - -
60F ARG* 1.3 80.0 - - - +
62F VAL* 1.3 63.2 + - - +
64F TYR* 3.3 20.5 + - - +
65F LEU* 3.0 66.9 + - + +
112F PHE* 5.6 9.9 - - - -
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Residues in contact with VAL 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937D ILE* 6.0 5.8 - - + -
941D ALA* 5.5 6.3 - - + -
18F LEU* 3.6 25.4 - - + -
21F LEU* 5.4 9.8 - - + +
22F TRP* 4.6 28.3 - - + -
58F ILE* 3.0 13.4 + - + +
59F ASP* 3.0 41.7 - - - +
61F ARG* 1.3 78.0 - - - +
63F ARG* 1.3 54.7 + - - +
65F LEU* 3.4 6.0 + - - +
66F THR* 2.6 43.9 + - - +
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Residues in contact with ARG 63 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
935D PHE* 3.5 49.1 - - - +
937D ILE* 3.3 32.1 - - + +
1133D ASP* 3.0 23.8 + - - -
59F ASP* 2.9 15.3 + - - +
60F ARG* 3.5 13.0 - - + +
62F VAL* 1.3 77.7 - - - +
64F TYR* 1.3 64.6 + - - +
66F THR* 3.2 5.4 + - - -
67F LYS* 2.7 65.8 + - + +
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Residues in contact with TYR 64 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2F LYS* 4.9 3.1 + - - -
60F ARG* 3.0 13.8 + - + +
61F ARG* 3.7 21.1 - - - +
63F ARG* 1.3 79.4 - - - +
65F LEU* 1.3 80.3 + - + +
67F LYS* 3.3 8.1 + - + +
68F CYS* 3.0 49.5 + - - -
108F TYR* 3.5 28.7 - + - -
109F ASP* 3.6 12.6 + - - -
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Residues in contact with LEU 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LEU* 4.3 33.2 - - + +
17F GLU* 5.1 7.0 - - + -
18F LEU* 4.5 24.2 - - + +
21F LEU* 4.5 13.2 - - + -
61F ARG* 3.0 67.7 + - + +
62F VAL* 4.0 3.1 - - - +
64F TYR* 1.3 90.3 - - + +
66F THR* 1.3 57.8 + - - +
68F CYS* 3.4 5.4 + - - +
69F MET* 2.9 35.3 + - - +
109F ASP* 6.2 0.4 - - - -
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Residues in contact with THR 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937D ILE* 4.8 19.1 - - + +
940D ALA* 4.9 8.7 - - + +
941D ALA* 5.4 5.5 - - - -
944D ALA* 4.4 16.6 - - + -
18F LEU* 4.7 10.6 - - + +
62F VAL* 2.6 33.1 + - - +
63F ARG* 3.4 7.1 - - - -
65F LEU* 1.3 73.7 - - - +
67F LYS* 1.3 68.0 + - + +
68F CYS 3.2 0.2 + - - -
69F MET* 3.3 7.6 + - - +
70F GLU* 2.9 40.3 + - - +
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Residues in contact with LYS 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1133D ASP* 3.7 19.4 + - - -
63F ARG* 2.7 68.3 + - + +
64F TYR* 3.8 10.5 - - + +
66F THR* 1.3 76.7 - - + +
68F CYS* 1.3 67.5 + - - +
70F GLU* 3.1 20.5 + - - +
71F ASN* 3.0 27.6 + - - +
----------------------------------------------------------
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Residues in contact with CYS 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14F LEU* 5.3 2.7 - - + -
64F TYR* 3.0 62.9 + - - -
65F LEU* 3.4 13.2 - - + +
67F LYS* 1.3 74.1 - - - +
69F MET* 1.3 55.8 + - + +
71F ASN* 2.5 30.6 + - - +
72F LEU* 3.0 29.7 + - + +
109F ASP* 4.3 12.3 - - - +
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Residues in contact with MET 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
944D ALA* 5.5 15.7 - - + +
945D ALA* 6.1 2.0 - - - -
11F TYR* 3.4 48.6 + - + +
14F LEU* 3.5 27.6 - - + -
15F LYS* 3.8 31.4 - - + -
18F LEU* 4.8 14.1 - - + -
65F LEU 2.9 23.5 + - - +
66F THR* 3.7 6.1 - - - +
68F CYS* 1.3 73.3 - - - +
70F GLU* 1.3 61.1 + - - +
72F LEU* 3.6 24.4 + - - +
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Residues in contact with GLU 70 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
940D ALA* 5.6 4.5 - - - +
944D ALA* 4.6 16.7 - - + +
1023D HIS* 3.7 24.6 + - - -
1130D GLY* 4.0 32.2 + - - +
66F THR* 2.9 29.3 + - - +
67F LYS* 3.3 20.4 - - - +
68F CYS 2.8 0.8 + - - -
69F MET* 1.3 79.5 - - - +
71F ASN* 1.3 69.4 + - - +
72F LEU 3.5 2.6 + - - +
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Residues in contact with ASN 71 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023D HIS* 6.1 0.3 - - - -
1127D GLU* 5.6 1.9 - - - +
1128D SER 5.3 4.3 - - - +
4F PRO* 3.5 22.3 - - + +
67F LYS* 3.0 20.7 + - - +
68F CYS* 2.5 19.3 + - - +
70F GLU* 1.3 83.3 + - - +
72F LEU* 1.3 61.1 + - - +
73F LYS 3.9 0.7 - - - -
----------------------------------------------------------
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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