Contacts of the helix formed by residues 46 - 76 (chain I) in PDB entry 1VEQ
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 46 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B ASN* 4.2 18.8 - - + +
155B HIS* 4.7 0.9 - - - -
45D PRO* 2.8 36.4 + - - +
46D ASN* 4.3 13.0 - - + +
45I PRO* 1.3 82.0 - - + +
47I PHE* 1.3 65.1 + - - +
48I ILE 3.7 0.7 - - - -
49I GLY* 3.6 10.8 + - - -
50I VAL* 3.8 9.8 + - - +
102I VAL* 3.6 32.7 - - - +
103I GLN* 4.7 3.9 + - - +
155I HIS* 4.4 4.0 - - - -
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Residues in contact with PHE 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TRP* 4.2 12.8 - + - -
151B PHE* 3.3 33.2 - + - -
154B ALA* 3.6 24.7 - - + +
155B HIS* 3.2 35.1 + + + +
39I HIS 5.0 0.9 - - - -
40I TRP 5.7 0.2 - - - -
42I VAL* 3.5 38.3 - - + +
44I GLY 3.7 17.1 + - - +
45I PRO 3.2 4.0 + - - -
46I ASN* 1.3 76.1 - - - +
48I ILE* 1.3 72.7 + - + +
49I GLY 3.1 0.7 + - - -
50I VAL* 3.1 3.5 + - - +
51I HIS* 3.0 53.9 + + + -
102I VAL* 4.7 7.2 - - - -
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Residues in contact with ILE 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY* 4.1 24.5 - - - +
53B MET* 3.2 42.8 - - + -
151B PHE* 4.1 27.4 - - + -
155B HIS* 3.5 14.1 + - + +
47I PHE* 1.3 82.6 - - + +
49I GLY* 1.3 71.7 + - - +
50I VAL 3.1 0.5 + - - -
51I HIS* 4.1 8.1 - - + -
52I GLU* 3.0 49.7 + - - +
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Residues in contact with GLY 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B GLY* 5.3 5.6 - - - -
48D ILE* 4.2 22.7 - - - +
49D GLY* 5.3 5.4 - - - -
46I ASN* 3.6 9.4 + - - -
47I PHE 3.1 1.8 + - - -
48I ILE* 1.3 85.4 - - - +
50I VAL* 1.3 60.7 + - - +
52I GLU* 3.7 2.5 + - - +
53I MET* 3.1 20.4 + - - +
155I HIS* 5.6 0.7 - - - -
----------------------------------------------------------
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Residues in contact with VAL 50 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I VAL* 5.4 0.4 - - + -
42I VAL* 4.5 13.5 - - + -
46I ASN* 3.8 5.7 + - - +
47I PHE 3.1 6.6 + - - +
49I GLY* 1.3 70.7 - - - +
51I HIS* 1.3 70.1 + - - +
53I MET* 2.7 30.7 + - + +
54I ILE* 3.1 30.7 + - + +
102I VAL* 3.2 35.2 - - + -
105I HIS* 6.5 0.4 - - + -
106I LEU* 3.9 22.2 - - + -
155I HIS* 4.0 17.9 - - + +
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Residues in contact with HIS 51 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B TRP* 4.3 13.5 - + - -
151B PHE* 3.7 27.3 - + - -
70C GLU* 3.3 20.0 + - + -
209C FE 4.1 0.6 - - - -
39I HIS* 2.7 82.6 + + - +
42I VAL* 5.4 2.9 - - - +
47I PHE* 3.0 32.2 + + + +
48I ILE* 3.5 15.9 - - + +
50I VAL* 1.3 80.5 - - - +
52I GLU* 1.3 68.3 + - + +
54I ILE* 3.6 11.3 + - - +
55I ASP 4.1 0.9 + - - -
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Residues in contact with GLU 52 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B MET* 6.1 1.4 - - - -
151B PHE* 6.1 0.5 - - - -
48I ILE* 3.0 40.4 + - + +
49I GLY 4.1 2.0 - - - +
51I HIS* 1.3 81.3 - - + +
53I MET* 1.3 65.1 + - - +
54I ILE 3.1 3.5 + - - -
55I ASP* 3.5 11.3 + - + +
56I PRO* 3.3 18.7 - - - +
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Residues in contact with MET 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D ILE* 3.3 39.0 - - + -
52D GLU* 6.2 0.4 - - - -
49I GLY 3.1 15.7 + - - +
50I VAL* 2.7 31.2 + - + +
52I GLU* 1.3 72.3 - - - +
54I ILE* 1.3 59.7 + - + +
56I PRO* 3.6 10.4 - - - +
57I GLN 4.5 2.1 + - - -
106I LEU* 4.1 26.0 - - + -
109I LEU* 6.4 0.2 - - + -
148I PHE* 4.0 29.5 - - + -
151I PHE* 4.1 21.3 - - + -
152I VAL* 4.7 2.9 - - - -
155I HIS* 3.9 15.3 - - + -
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Residues in contact with ILE 54 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I LEU* 3.5 30.7 - - + +
38I VAL* 3.2 32.3 - - + -
39I HIS* 4.0 16.4 - - + -
42I VAL* 4.9 0.4 - - + -
50I VAL* 3.4 30.3 - - + +
51I HIS* 3.8 7.2 - - - +
52I GLU 3.1 1.0 - - - -
53I MET* 1.3 85.6 - - + +
55I ASP* 1.3 69.1 + - - +
56I PRO 3.3 0.4 - - - -
57I GLN* 3.0 14.0 + - - +
58I VAL* 3.1 26.0 + - + -
106I LEU* 6.1 1.1 - - + -
109I LEU* 5.5 3.4 - - + -
148I PHE* 4.6 9.0 - - + -
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Residues in contact with ASP 55 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209C FE 3.9 4.3 - - - -
36I LYS* 3.2 28.4 + - - +
39I HIS* 3.2 25.7 + - - -
51I HIS 4.1 2.7 + - - +
52I GLU* 3.5 11.2 + - + +
54I ILE* 1.3 76.2 - - - +
56I PRO* 1.3 65.4 - - + +
58I VAL* 2.9 10.6 + - - +
59I GLU* 2.8 36.8 + - + +
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Residues in contact with PRO 56 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I GLU 3.3 14.6 - - - +
53I MET* 3.6 8.1 - - - +
54I ILE 3.5 3.4 - - - -
55I ASP* 1.3 93.9 - - + +
57I GLN* 1.3 55.8 + - - +
59I GLU* 3.3 7.7 + - + +
60I LEU* 2.9 33.4 + - - +
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Residues in contact with GLN 57 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I LEU* 4.6 4.9 - - + -
53I MET 4.5 1.2 + - - +
54I ILE 3.0 6.8 + - - +
56I PRO* 1.3 78.9 - - - +
58I VAL* 1.3 56.6 + - - +
60I LEU* 3.4 20.0 - - - +
61I VAL* 2.9 43.4 + - + +
64I TYR* 5.6 0.8 - - - -
113I TYR* 3.1 28.5 + - - +
144I GLU* 4.3 4.6 + - - +
145I LEU* 3.6 26.9 - - - +
148I PHE* 3.0 59.7 - - + +
----------------------------------------------------------
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Residues in contact with VAL 58 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C ARG* 2.8 37.8 + - - +
32I HIS* 4.2 6.9 - - + +
35I LEU* 3.3 31.0 - - + -
36I LYS* 3.6 25.4 - - + +
54I ILE* 3.1 24.0 - - + +
55I ASP* 2.9 11.6 + - - +
57I GLN* 1.3 74.2 - - - +
59I GLU* 1.3 56.3 + - + +
60I LEU 2.7 14.0 + - - -
61I VAL* 3.0 5.7 + - - +
62I ARG* 2.9 25.3 + - - +
----------------------------------------------------------
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Residues in contact with GLU 59 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU* 3.7 29.4 - - - +
62C ARG* 3.7 19.4 + - - +
55I ASP* 2.8 23.3 + - + +
56I PRO* 3.7 7.9 - - + +
58I VAL* 1.3 73.5 - - + +
60I LEU* 1.3 57.0 + - - +
62I ARG* 4.4 3.8 - - - +
63I GLY* 3.5 14.6 + - - -
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Residues in contact with LEU 60 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56I PRO 2.9 17.3 + - - +
57I GLN* 3.4 20.2 - - - +
58I VAL 2.7 1.2 - - - -
59I GLU* 1.3 77.6 - - - +
61I VAL* 1.3 60.1 + - - +
62I ARG 3.2 0.9 - - - -
63I GLY* 2.8 17.9 + - - -
64I TYR* 3.0 43.5 + - + +
144I GLU* 3.5 33.2 - - + +
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Residues in contact with VAL 61 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I TYR* 3.7 29.4 - - + +
31I LEU* 3.6 31.0 - - + -
32I HIS* 3.5 26.2 - - + -
35I LEU* 5.1 1.6 - - + -
57I GLN* 2.9 43.5 + - + +
58I VAL* 3.8 0.7 - - - +
60I LEU* 1.3 69.8 - - - +
62I ARG* 1.3 61.1 + - - +
63I GLY 2.9 1.6 - - - -
64I TYR* 2.8 28.2 + - + +
65I ALA* 3.1 10.2 + - - +
113I TYR* 4.4 1.8 - - - +
145I LEU* 4.6 4.7 - - + -
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Residues in contact with ARG 62 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C HIS* 3.3 29.1 + - - -
36C LYS* 4.7 16.9 - - + +
58C VAL* 2.8 37.8 + - - +
59C GLU* 3.7 23.6 + - - +
62C ARG* 3.3 66.8 - - - +
32I HIS* 4.2 16.9 - - + +
58I VAL 2.9 9.2 + - - +
59I GLU* 4.4 6.1 - - - +
61I VAL* 1.3 78.1 - - - +
63I GLY* 1.3 62.7 + - - +
65I ALA* 3.1 22.6 + - + +
66I ASP* 3.4 8.3 + - - +
----------------------------------------------------------
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Residues in contact with GLY 63 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I GLU 3.5 9.5 + - - -
60I LEU* 2.8 15.6 + - - -
62I ARG* 1.3 81.4 - - - +
64I TYR* 1.3 62.4 + - - +
66I ASP* 3.8 4.5 + - - +
67I GLU* 3.4 23.3 + - - +
----------------------------------------------------------
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Residues in contact with TYR 64 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28I TYR* 3.6 14.5 - + + -
57I GLN* 5.6 0.7 - - - -
60I LEU* 3.0 46.5 + - + +
61I VAL* 2.8 20.0 + - + +
63I GLY* 1.3 76.4 - - - +
65I ALA* 1.3 59.3 + - - +
67I GLU* 3.5 14.4 - - - -
68I VAL* 3.0 35.7 + - - +
140I ALA* 4.6 2.9 + - + -
141I HIS* 3.2 51.9 - + + -
144I GLU* 3.4 25.7 + - + +
145I LEU* 4.1 22.9 - - + -
----------------------------------------------------------
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Residues in contact with ALA 65 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 6.1 1.1 - - + -
40C TRP* 4.1 13.9 - - + -
25I LEU* 4.3 6.0 - - + +
28I TYR* 4.5 12.6 - - + -
29I ASN* 4.2 19.1 - - - +
32I HIS* 5.1 1.8 - - + +
61I VAL 3.1 7.5 + - - +
62I ARG* 3.1 22.0 + - + +
64I TYR* 1.3 74.5 - - - +
66I ASP* 1.3 67.5 + - - +
67I GLU 3.0 1.4 + - - -
68I VAL* 3.1 3.5 + - - +
69I ALA* 2.9 25.5 + - - +
----------------------------------------------------------
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Residues in contact with ASP 66 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LYS* 2.9 27.5 + - - +
39C HIS* 3.1 8.1 + - - -
40C TRP* 3.3 13.2 + - - +
62I ARG 3.4 7.3 + - - +
63I GLY* 4.3 6.3 - - - +
65I ALA* 1.3 78.0 - - - +
67I GLU* 1.3 56.4 + - - +
70I GLU* 2.7 57.2 + - - +
203I FE 2.5 30.5 - - - -
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Residues in contact with GLU 67 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H LYS* 5.1 8.0 + - - +
63I GLY 3.4 16.0 + - - +
64I TYR* 3.5 17.1 - - - +
65I ALA 3.0 1.0 - - - -
66I ASP* 1.3 80.3 + - - +
68I VAL* 1.3 62.1 + - - +
70I GLU* 4.0 4.3 - - - +
71I ARG* 3.2 20.6 + - - +
137I LEU* 4.7 19.3 - - + +
141I HIS* 3.0 28.5 + - + +
----------------------------------------------------------
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Residues in contact with VAL 68 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I LEU* 3.6 43.3 - - + +
24I GLN* 4.8 5.6 - - + -
25I LEU* 4.3 14.4 - - + +
28I TYR* 3.7 21.1 - - + -
64I TYR 3.0 19.3 + - - +
65I ALA* 3.8 2.5 - - - +
67I GLU* 1.3 73.1 - - - +
69I ALA* 1.3 58.7 + - - +
71I ARG* 2.7 32.2 + - - +
72I ILE* 2.9 8.6 + - + +
137I LEU* 4.5 9.4 - - + -
138I LEU* 4.9 3.1 - - + -
141I HIS* 3.9 12.6 - - + -
----------------------------------------------------------
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Residues in contact with ALA 69 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TRP* 3.1 42.4 - - + +
25I LEU* 3.2 27.1 - - + +
65I ALA 2.9 10.2 + - - +
68I VAL* 1.3 68.6 - - - +
70I GLU* 1.3 58.7 + - - +
71I ARG 2.8 4.3 - - - -
72I ILE* 2.7 23.7 + - - +
73I ALA* 3.0 11.3 + - - +
79I PRO* 3.4 12.5 - - + +
----------------------------------------------------------
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Residues in contact with GLU 70 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C HIS* 3.2 6.9 + - - -
40C TRP* 3.6 13.5 - - + -
51C HIS* 3.3 16.9 + - - -
147H LYS* 2.8 45.4 + - - +
150H TRP* 4.3 22.2 - - + -
151H PHE* 5.1 0.9 - - - -
66I ASP* 2.7 45.6 + - - +
67I GLU 4.0 1.1 - - - +
69I ALA* 1.3 73.4 - - - +
71I ARG* 1.3 50.4 + - - +
73I ALA* 4.2 3.6 - - - +
74I THR* 2.5 31.5 + - - -
203I FE 2.3 27.0 - - - -
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Residues in contact with ARG 71 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H ARG* 3.9 2.2 - - - +
143H GLY* 4.3 9.9 + - - -
146H GLU* 3.0 38.7 + - - +
147H LYS* 5.2 1.0 - - - +
6I ILE* 5.3 0.4 - - - -
21I LEU* 3.8 19.1 - - + -
67I GLU 3.2 13.2 + - - +
68I VAL* 2.7 18.2 + - - +
69I ALA 2.7 1.0 + - - -
70I GLU* 1.3 77.3 - - - +
72I ILE* 1.3 63.2 + - - +
74I THR* 3.1 24.8 + - - +
75I LEU* 3.1 26.2 + - + +
131I ASP* 2.8 28.3 + - - -
133I VAL* 3.4 24.9 - - - +
134I SER* 3.0 14.8 + - - +
137I LEU* 4.7 18.2 - - + -
----------------------------------------------------------
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Residues in contact with ILE 72 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I ALA* 4.4 10.5 - - + +
21I LEU* 3.6 20.4 - - + -
22I GLN* 3.5 44.4 - - + +
25I LEU* 4.5 3.6 - - + -
68I VAL* 2.9 22.2 + - + +
69I ALA* 2.7 18.0 + - - +
71I ARG* 1.3 72.0 - - - +
73I ALA* 1.3 64.8 + - - +
75I LEU* 2.8 26.3 + - - +
76I GLY 3.2 4.9 + - - -
77I LYS* 3.7 21.1 + - + +
78I SER 4.4 0.7 - - - -
79I PRO* 3.5 24.5 - - + -
----------------------------------------------------------
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Residues in contact with ALA 73 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TRP* 4.3 7.9 - - + +
99C ARG* 3.7 16.9 + - - +
150H TRP* 3.5 38.0 + - + +
4I PHE* 4.0 1.2 - - - -
69I ALA 3.0 8.2 + - - +
70I GLU* 4.2 3.1 - - - +
72I ILE* 1.3 78.2 - - - +
74I THR* 1.3 64.4 + - - +
76I GLY* 3.1 10.7 + - - -
77I LYS 3.5 12.6 - - - -
79I PRO* 3.7 15.4 - - + +
----------------------------------------------------------
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Residues in contact with THR 74 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146H GLU* 3.5 35.2 - - + +
147H LYS* 4.1 9.1 - - - +
149H GLN* 5.9 0.9 - - - +
150H TRP* 3.7 24.7 - - + +
153H ARG* 5.1 1.6 + - - -
4I PHE* 3.5 14.9 - - - -
6I ILE* 3.2 20.9 - - + +
70I GLU 2.5 23.4 + - - -
71I ARG* 3.1 19.6 + - - +
72I ILE 3.0 0.4 - - - -
73I ALA* 1.3 80.8 - - - +
75I LEU* 1.3 59.9 + - - +
----------------------------------------------------------
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Residues in contact with LEU 75 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I PHE* 3.9 1.2 - - - +
5I THR* 3.5 26.7 + - - -
6I ILE* 3.3 22.2 - - + -
9I LEU* 4.0 23.3 - - + -
14I ALA* 3.8 24.5 - - + +
17I VAL* 3.7 30.5 - - + -
18I ALA* 3.9 13.7 - - + +
21I LEU* 4.5 8.7 - - + -
71I ARG* 3.1 27.0 + - - +
72I ILE* 2.8 12.3 + - - +
74I THR* 1.3 81.2 - - - +
76I GLY* 1.3 54.7 + - - +
77I LYS 3.8 3.1 - - - +
134I SER* 4.8 2.9 - - - +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ARG* 3.1 24.5 + - - -
4I PHE* 4.1 22.4 - - - -
72I ILE 3.2 0.8 + - - -
73I ALA 3.1 11.4 + - - -
74I THR 3.3 0.2 - - - -
75I LEU* 1.3 79.3 - - - +
77I LYS* 1.3 64.7 + - - +
----------------------------------------------------------
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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