Contacts of the helix formed by residues 33 - 66 (chain M) in PDB entry 7KHE
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 33 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M TYR* 4.0 2.2 + - - -
29M GLU* 3.0 47.3 + - - +
30M GLU* 3.8 8.9 + - + +
31M TYR 3.4 1.2 + - - -
32M MET* 1.3 74.5 - - - +
34M GLU* 1.3 75.0 + - - +
35M ALA* 3.0 11.3 + - - +
36M GLN* 2.7 47.2 + - - +
37M LEU* 3.3 22.9 + - - +
109M GLU* 6.1 0.2 - - - -
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Residues in contact with GLU 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33M ASN* 1.3 83.3 - - - +
35M ALA* 1.3 63.0 + - - +
37M LEU* 3.3 5.3 + - - +
38M ALA* 2.9 25.5 + - - +
109M GLU* 5.9 1.1 - - - -
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Residues in contact with ALA 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M TYR* 4.3 17.7 - - + +
29M GLU* 5.9 0.2 - - - +
33M ASN* 3.0 10.9 + - - +
34M GLU* 1.3 80.2 + - - +
36M GLN* 1.3 57.6 + - - +
38M ALA* 3.4 6.2 + - - +
39M HIS* 2.9 29.0 + - - +
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Residues in contact with GLN 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23M TYR* 3.6 35.1 - - + -
25M GLU* 4.8 8.9 + - - +
29M GLU* 4.4 4.8 - - - +
30M GLU 4.2 3.8 + - - -
31M TYR* 2.9 28.2 + - - +
32M MET* 3.2 18.4 - - + +
33M ASN* 2.7 36.6 + - - +
35M ALA* 1.3 71.5 - - - +
37M LEU* 1.3 68.4 + - + +
39M HIS* 3.2 11.4 + - - +
40M PHE* 2.9 33.5 + - + +
123M ILE* 3.9 19.1 - - + +
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Residues in contact with LEU 37 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M MET* 3.4 38.6 - - + -
33M ASN 3.3 16.7 + - - +
34M GLU* 3.7 8.7 - - - +
36M GLN* 1.3 76.0 - - + +
38M ALA* 1.3 62.7 + - - +
40M PHE* 3.3 4.2 + - + +
41M ARG* 2.9 24.4 + - - +
106M VAL* 3.4 40.4 - - + +
109M GLU* 3.2 37.5 - - - +
111M PHE* 4.4 17.5 - - + +
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Residues in contact with ALA 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34M GLU 2.9 17.8 + - - +
35M ALA* 3.6 7.2 - - - +
37M LEU* 1.3 75.1 - - - +
39M HIS* 1.3 63.6 + - - +
41M ARG* 3.2 18.3 + - - +
42M ARG* 2.9 24.5 + - - +
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Residues in contact with HIS 39 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M LEU* 4.0 1.8 - - - +
20M VAL* 3.4 32.1 - - + +
21M GLU 4.7 0.8 + - - -
23M TYR* 4.3 20.9 - + + +
35M ALA 2.9 14.3 + - - +
36M GLN* 3.2 13.5 + - - +
38M ALA* 1.3 75.2 - - - +
40M PHE* 1.3 80.0 + + - +
42M ARG* 3.2 19.2 + - - +
43M ILE* 3.0 53.8 + - + +
123M ILE* 5.8 1.6 - - - +
127M GLU* 3.2 30.0 + - + -
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Residues in contact with PHE 40 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32M MET* 5.1 8.1 - - + -
36M GLN* 2.9 22.3 + - + +
37M LEU* 3.8 5.6 - - - +
39M HIS* 1.3 101.3 - + - +
41M ARG* 1.3 63.6 + - - +
43M ILE* 3.2 11.5 + - + +
44M LEU* 2.9 37.9 + - + +
106M VAL* 4.9 4.5 - - + -
111M PHE* 3.2 28.5 - + + -
123M ILE* 3.5 25.8 - - + -
126M LEU* 3.4 58.6 - - + -
127M GLU* 4.1 6.3 - - + -
130M PRO* 5.2 6.7 - - + +
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Residues in contact with ARG 41 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37M LEU 2.9 13.8 + - - +
38M ALA* 3.5 18.8 + - - +
40M PHE* 1.3 77.6 - - - +
42M ARG* 1.3 63.4 + - - +
44M LEU* 3.3 2.6 + - - +
45M GLU* 2.9 54.2 + - + +
103M LEU* 3.8 24.7 - - + -
106M VAL* 4.6 10.2 - - + +
107M GLU* 3.1 32.6 + - - +
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Residues in contact with ARG 42 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M ALA* 4.7 12.3 - - + -
19M GLY 5.7 2.8 - - - +
20M VAL* 3.4 42.0 - - - +
38M ALA 2.9 13.1 + - - +
39M HIS* 3.4 19.2 + - - +
41M ARG* 1.3 77.0 - - - +
43M ILE* 1.3 65.7 + - - +
45M GLU* 3.3 7.5 + - - +
46M ALA* 3.0 24.3 + - + +
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Residues in contact with ILE 43 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ILE* 4.5 19.6 - - + +
15M LEU* 3.2 32.5 - - + -
18M ALA* 4.8 4.5 - - + -
20M VAL* 4.0 14.4 - - + -
39M HIS* 3.0 39.0 + - + +
40M PHE* 3.2 19.3 + - + +
42M ARG* 1.3 77.0 - - + +
44M LEU* 1.3 65.4 + - - +
46M ALA* 3.7 4.4 - - - +
47M TRP* 3.0 22.7 + - + +
127M GLU* 5.5 4.3 - - + +
130M PRO* 4.3 26.9 - - + -
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Residues in contact with LEU 44 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M PHE* 2.9 34.0 + - + +
41M ARG* 3.9 2.9 - - - +
43M ILE* 1.3 77.0 - - - +
45M GLU* 1.3 63.3 - - - +
47M TRP* 3.3 6.2 + - + +
48M ARG* 2.9 25.5 + - - +
99M ILE* 3.5 42.7 - - + +
102M THR* 3.9 32.5 - - + +
103M LEU* 4.2 23.8 - - + +
106M VAL* 4.6 8.5 - - + -
111M PHE* 5.3 1.6 - - + -
130M PRO* 4.4 24.0 - - + +
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Residues in contact with GLU 45 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41M ARG* 2.9 45.9 + - + +
42M ARG* 3.8 7.2 - - - +
44M LEU* 1.3 77.3 - - - +
46M ALA* 1.3 63.2 + - - +
48M ARG* 3.4 25.7 + - - +
49M ASN* 3.0 38.5 + - - +
103M LEU* 4.6 13.7 - - + +
107M GLU* 5.7 0.2 - - - +
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Residues in contact with ALA 46 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M ILE* 4.0 14.1 - - + +
18M ALA* 3.9 25.4 - - + +
42M ARG* 3.0 18.3 + - + +
43M ILE 3.7 3.4 - - - +
45M GLU* 1.3 77.2 - - - +
47M TRP* 1.3 64.1 + - - +
49M ASN* 3.9 6.1 - - - +
50M GLN* 3.0 24.8 + - - +
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Residues in contact with TRP 47 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684D ASP* 4.7 8.6 + - - -
14M ILE* 3.6 48.0 - - + +
17M ILE* 4.3 19.9 - - + +
43M ILE* 3.0 17.1 + - + +
44M LEU* 3.3 6.7 + - + +
46M ALA* 1.3 76.0 - - - +
48M ARG* 1.3 65.1 + - - +
50M GLN* 3.2 4.8 + - - +
51M LEU* 3.0 47.5 + - + +
95M LEU* 3.9 28.7 - - + -
99M ILE* 3.5 32.8 - - + -
129M ARG* 5.3 5.6 - - - -
130M PRO* 3.7 26.2 - - + -
131M THR* 5.2 5.4 - - + -
202M G4P 4.5 11.7 - - - -
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Residues in contact with ARG 48 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
946D ALA* 6.0 3.6 - - - +
947D GLU* 4.2 20.6 + - - +
1131D THR* 5.9 2.4 - - - +
44M LEU 2.9 16.1 + - - +
45M GLU* 3.7 20.0 + - - +
47M TRP* 1.3 75.6 - - - +
49M ASN* 1.3 63.3 + - - +
51M LEU* 2.7 34.3 + - - +
52M ARG* 2.9 51.2 + - - +
96M ILE* 4.4 15.5 - - + -
99M ILE* 4.3 18.7 - - + +
100M GLU* 5.6 13.2 - - - +
103M LEU* 3.6 29.6 - - - +
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Residues in contact with ASN 49 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
945D ALA* 5.2 7.0 + - - +
45M GLU* 3.0 32.7 + - - +
46M ALA* 3.9 5.5 - - - +
48M ARG* 1.3 84.0 + - - +
50M GLN* 1.3 62.4 + - - +
52M ARG* 3.4 11.1 + - - +
53M ASP* 3.0 34.4 + - - +
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Residues in contact with GLN 50 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M ILE* 4.1 29.9 - - + +
46M ALA 3.0 14.6 + - - +
47M TRP* 3.4 10.5 - - + +
49M ASN* 1.3 77.9 - - - +
51M LEU* 1.3 87.1 + - - +
53M ASP* 3.2 8.6 + - + +
54M GLU* 2.9 36.7 + - - +
57M ARG* 5.2 3.6 + - - +
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Residues in contact with LEU 51 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684D ASP* 6.1 0.4 - - - +
47M TRP* 3.0 40.0 + - + +
48M ARG* 2.7 14.5 + - - +
50M GLN* 1.3 90.3 + - - +
52M ARG* 1.3 56.8 + - - +
54M GLU* 3.1 7.9 + - - +
55M VAL* 3.0 31.5 + - + +
89M ARG* 5.4 0.2 + - - -
92M GLU* 3.1 33.9 - - + +
95M LEU* 4.1 26.2 - - + -
96M ILE* 3.4 33.4 - - + -
99M ILE* 5.2 3.4 - - + -
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Residues in contact with ARG 52 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
939D GLY* 4.0 17.5 + - - +
940D ALA* 3.7 13.7 + - - +
941D ALA* 3.8 26.4 + - - +
943D ARG* 3.1 32.9 - - - +
947D GLU* 5.5 2.6 + - - -
1130D GLY 5.1 1.6 + - - -
1131D THR* 3.6 32.1 - - - +
48M ARG* 2.9 52.6 + - - +
49M ASN* 3.9 13.3 + - - +
51M LEU* 1.3 77.0 - - - +
53M ASP* 1.3 64.5 + - - +
55M VAL* 3.1 12.9 + - + +
56M ASP 3.0 17.5 + - - -
96M ILE* 4.2 22.4 - - + +
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Residues in contact with ASP 53 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941D ALA* 5.9 1.0 - - - +
49M ASN* 3.0 26.7 + - - +
50M GLN* 3.2 7.1 + - + +
52M ARG* 1.3 77.4 - - - +
54M GLU* 1.3 57.4 + - - +
56M ASP* 3.2 10.8 + - - +
57M ARG* 3.0 43.9 + - - +
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Residues in contact with GLU 54 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D ASP* 4.9 16.1 - - - +
50M GLN* 2.9 26.6 + - - +
51M LEU* 3.1 12.5 + - - +
53M ASP* 1.3 74.9 - - - +
55M VAL* 1.3 65.2 + - - +
57M ARG* 3.2 36.8 + - - +
58M THR* 3.0 30.0 + - - -
89M ARG* 3.7 31.5 + - - +
92M GLU* 4.9 2.7 - - - +
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Residues in contact with VAL 55 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937D ILE* 4.4 24.2 - - + +
939D GLY* 3.9 30.3 - - - +
940D ALA 4.6 3.8 - - - +
941D ALA* 4.9 5.2 - - + +
51M LEU* 3.0 20.7 + - + +
52M ARG* 3.1 10.9 + - + +
54M GLU* 1.3 77.9 - - - +
56M ASP* 1.3 57.1 + - - +
58M THR* 3.4 2.7 + - - -
59M VAL* 2.9 29.3 + - + +
89M ARG* 3.8 30.7 - - + +
92M GLU* 5.9 4.0 - - + -
93M ARG* 6.1 2.2 - - + +
96M ILE* 6.4 2.2 - - + -
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Residues in contact with ASP 56 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
941D ALA* 3.6 25.6 - - + +
942D SER* 5.2 1.7 + - - -
52M ARG 3.0 8.0 + - - +
53M ASP* 3.2 13.4 + - - +
55M VAL* 1.3 74.5 - - - +
57M ARG* 1.3 68.0 + - + +
59M VAL* 2.9 22.1 - - - +
60M THR* 2.9 28.5 + - - -
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Residues in contact with ARG 57 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691D ASP* 5.9 4.6 + - - -
50M GLN* 5.2 4.6 + - - +
53M ASP* 3.0 25.8 + - - +
54M GLU* 3.2 53.9 + - - +
56M ASP* 1.3 76.1 - - + +
58M THR* 1.3 65.4 + - - +
60M THR* 2.9 17.7 + - - -
61M HIS* 3.0 14.3 + - - +
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Residues in contact with THR 58 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937D ILE* 5.8 3.4 - - + -
54M GLU* 3.0 10.0 + - - -
55M VAL* 3.5 9.2 - - + +
57M ARG* 1.3 78.0 - - - +
59M VAL* 1.3 59.6 + - - +
61M HIS* 3.2 6.3 + - - +
62M MET* 2.9 42.9 + - + +
85M GLU* 3.3 27.2 + - + +
86M LEU* 5.7 1.3 - - + -
89M ARG* 3.0 47.2 + - + -
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Residues in contact with VAL 59 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
937D ILE* 4.9 13.0 - - + -
941D ALA* 5.9 1.1 - - + -
1134D ILE* 5.9 2.5 - - + -
1243D LEU* 3.5 36.1 - - + +
55M VAL* 2.9 20.1 + - + +
56M ASP* 2.9 35.2 - - - +
58M THR* 1.3 75.0 - - - +
60M THR* 1.3 65.7 + - - +
62M MET* 3.3 8.5 + - + +
63M GLN* 2.9 28.9 + - + +
----------------------------------------------------------
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Residues in contact with THR 60 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M ASP* 2.9 23.8 + - - -
57M ARG* 2.9 9.5 + - - -
59M VAL* 1.3 80.2 - - - +
61M HIS* 1.3 62.7 + - - +
63M GLN* 3.3 12.4 + - - +
64M ASP* 3.0 26.5 + - + +
----------------------------------------------------------
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Residues in contact with HIS 61 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733D SER* 4.8 10.1 + - - -
734D ALA* 5.7 5.6 - - + +
735D ALA* 4.2 24.4 + - + +
57M ARG 3.0 11.7 + - - +
58M THR* 3.4 11.4 - - - +
60M THR* 1.3 77.0 - - - +
62M MET* 1.3 65.1 + - - +
64M ASP* 3.2 5.4 + - - +
65M GLU* 2.9 34.4 + - + +
81M GLU* 4.5 11.9 - - - -
82M PHE* 4.2 20.4 - + - -
85M GLU* 4.2 16.9 + - - +
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Residues in contact with MET 62 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
931D THR* 6.3 1.1 - - - -
935D PHE* 4.8 5.6 - - - -
937D ILE* 5.5 3.8 - - + -
1243D LEU* 4.2 10.8 - - - +
1244D GLN* 3.2 37.4 - - - +
58M THR* 2.9 32.7 + - + +
59M VAL* 3.6 9.2 - - - +
61M HIS* 1.3 76.6 + - - +
63M GLN* 1.3 61.4 + - - +
66M ALA* 3.5 25.6 + - - +
82M PHE* 3.6 32.5 - - + -
85M GLU* 4.3 2.7 - - - +
86M LEU* 3.1 46.4 - - + -
----------------------------------------------------------
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Residues in contact with GLN 63 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1242D ARG* 3.4 29.1 + - - +
1243D LEU* 4.1 14.7 + - - +
1244D GLN 3.9 11.8 - - - +
1245D GLY* 4.0 13.1 - - - +
59M VAL* 2.9 21.8 + - + +
60M THR* 3.8 12.1 - - - +
62M MET* 1.3 78.9 - - - +
64M ASP* 1.3 61.6 + - - +
66M ALA* 4.5 2.4 + - - +
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Residues in contact with ASP 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599D LYS* 5.0 14.1 + - - -
60M THR* 3.0 19.5 + - + +
61M HIS* 3.8 4.9 - - - +
63M GLN* 1.3 78.8 - - - +
65M GLU* 1.3 67.9 + - - +
66M ALA 4.3 2.9 - - - +
----------------------------------------------------------
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Residues in contact with GLU 65 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
732D GLY 5.5 1.0 - - - -
733D SER* 3.4 31.6 + - - +
736D GLN* 4.9 7.9 + - - -
61M HIS* 2.9 27.8 + - + +
64M ASP* 1.3 81.5 - - - +
66M ALA* 1.3 68.8 + - - +
67M ALA* 3.1 11.3 + - - +
69M PHE* 4.1 19.4 - - - -
78M GLN* 4.2 10.2 - - + +
82M PHE* 4.0 25.6 - - + -
----------------------------------------------------------
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Residues in contact with ALA 66 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
929D GLN* 4.3 23.0 - - + +
1244D GLN* 3.1 35.6 - - + +
1245D GLY 5.0 5.4 - - - +
1246D VAL* 6.0 0.3 - - - +
62M MET* 3.5 12.6 + - + +
63M GLN 4.5 2.0 + - - +
64M ASP 3.5 3.7 - - - +
65M GLU* 1.3 78.2 - - - +
67M ALA* 1.3 59.0 + - - +
78M GLN* 4.1 13.7 - - - +
82M PHE* 4.9 2.2 - - + -
----------------------------------------------------------
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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