Contacts of the helix formed by residues 23 - 55 (chain G) 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 G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C LEU* 5.1 1.9 - - - +
22G PRO* 1.3 72.5 - - - +
24G LEU* 1.3 63.3 + - - +
25G LEU* 3.4 4.5 + - - +
26G ALA* 2.9 36.7 + - + +
27G ALA* 3.5 18.7 + - - +
42I ASP* 5.2 2.6 + - - -
46I PHE* 3.7 20.4 - - + -
68I GLY* 2.8 35.2 + - - -
70I LYS* 4.8 7.5 - - - +
105J PRO 4.1 2.9 - - - -
106J ASP* 3.1 35.0 + - - +
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Residues in contact with LEU 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D ILE* 4.0 20.4 - - + -
8D ILE* 3.4 37.9 - - + -
21G ILE* 5.4 4.3 - - + -
22G PRO* 3.8 19.7 - - + +
23G ASN* 1.3 70.8 - - - +
25G LEU* 1.3 67.1 + - - +
27G ALA* 3.2 4.0 + - - +
28G ARG* 3.1 28.9 + - + +
44J VAL* 3.5 20.6 - - + -
48J GLU* 3.7 18.2 - - - +
88J TYR* 3.5 24.2 - - - +
104J THR 5.3 0.4 - - - +
105J PRO* 3.1 19.6 + - + +
108J GLY* 6.2 0.7 - - - -
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Residues in contact with LEU 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G ASN* 3.4 1.0 + - - -
24G LEU* 1.3 78.4 - - - +
26G ALA* 1.3 61.7 + - - +
28G ARG* 3.5 8.9 + - + +
29G LYS* 3.3 46.8 + - + +
96G GLY* 5.9 1.8 - - - +
57J TYR* 6.1 0.4 - - - -
86J ASN* 3.0 31.2 - - + +
87J SER* 4.9 6.1 - - - +
105J PRO* 3.7 17.1 + - + +
106J ASP* 3.8 40.2 - - + +
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Residues in contact with ALA 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G ASN* 2.9 25.9 + - + +
25G LEU* 1.3 74.2 - - - +
27G ALA* 1.3 65.4 + - - +
29G LYS* 3.4 26.6 + - - +
30G ARG* 3.8 5.5 + - - +
46I PHE* 3.7 24.7 - - + -
49I MET* 3.8 22.3 - - + +
67I LEU 4.4 7.4 - - - +
68I GLY* 4.9 0.4 - - - -
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Residues in contact with ALA 27 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C LEU* 4.4 27.4 - - + -
7C LEU* 5.5 7.3 - - + +
10C ILE* 5.2 3.6 - - - +
8D ILE* 4.2 14.8 - - + -
12D ILE* 4.7 5.2 - - + +
23G ASN 3.5 13.6 + - - +
24G LEU 3.2 9.9 + - - +
26G ALA* 1.3 79.4 - - - +
28G ARG* 1.3 59.2 + - - +
30G ARG* 3.8 6.6 + - - +
31G ALA* 3.6 17.0 + - - +
49I MET* 5.3 3.5 - - - -
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Residues in contact with ARG 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D ILE* 3.7 19.4 - - + +
11D ALA* 4.1 15.4 - - - +
12D ILE* 4.2 9.3 - - + +
15D ILE* 3.4 29.7 - - - +
24G LEU 3.1 17.5 + - - +
25G LEU* 3.9 9.6 - - + +
26G ALA 3.3 0.2 - - - -
27G ALA* 1.3 73.3 - - - +
29G LYS* 1.3 54.1 + - - +
31G ALA* 3.2 8.0 + - - +
32G ASN* 2.7 54.0 + - - +
48J GLU* 3.0 23.7 + - - -
51J GLN* 3.5 37.4 + - - +
52J ILE* 5.3 0.8 - - - +
57J TYR* 3.6 23.1 - - - -
86J ASN* 6.1 1.6 - - - +
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Residues in contact with LYS 29 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25G LEU* 3.3 45.7 + - + +
26G ALA* 3.4 15.8 + - - +
28G ARG* 1.3 76.6 - - - +
30G ARG* 1.3 60.4 + - + +
32G ASN* 3.4 2.8 + - - +
33G ASP* 3.1 34.7 + - - +
96G GLY 3.6 22.9 + - - +
97G GLY* 3.6 19.1 - - - +
98G THR* 4.1 18.6 - - + +
49I MET* 5.8 1.8 - - + -
67I LEU 5.5 4.7 + - - +
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Residues in contact with ARG 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C LEU* 4.3 20.0 - - + -
10C ILE* 3.5 19.3 - - + +
26G ALA 4.0 10.7 + - - +
27G ALA 3.8 6.0 + - - +
28G ARG 3.2 0.6 - - - -
29G LYS* 1.3 75.7 - - - +
31G ALA* 1.3 62.7 + - - +
33G ASP* 3.4 15.1 + - - +
34G THR* 2.9 26.2 + - - -
98G THR* 3.7 25.7 + - - +
111G LYS* 5.2 3.6 - - - +
49I MET* 3.5 41.1 + - + +
52I ILE* 4.3 20.6 - - + +
53I ASP* 2.7 41.7 + - - -
67I LEU* 4.2 10.5 + - - +
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Residues in contact with ALA 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 4.5 6.6 - - + +
12D ILE* 3.2 46.4 - - + -
15D ILE* 5.2 4.9 - - + -
16D LEU* 4.6 5.5 - - + +
27G ALA 3.6 7.3 + - - +
28G ARG 3.2 7.1 + - - +
30G ARG* 1.3 79.9 - - - +
32G ASN* 1.3 61.4 + - - +
34G THR* 3.3 11.4 + - - -
35G VAL* 3.2 26.1 + - - +
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Residues in contact with ASN 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ILE* 5.7 4.9 - - - +
28G ARG* 2.7 40.0 + - - +
29G LYS 3.5 6.0 - - - +
31G ALA* 1.3 71.8 - - - +
33G ASP* 1.3 63.7 + - - +
35G VAL* 3.4 8.7 + - - +
36G VAL* 3.2 26.5 + - - +
94G HIS* 3.2 43.2 + - + -
96G GLY 2.9 23.9 + - - +
97G GLY* 4.3 0.9 - - - -
86J ASN* 3.5 14.0 + - - +
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Residues in contact with ASP 33 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G LYS 3.1 18.4 + - - +
30G ARG* 3.6 19.8 + - - +
31G ALA 3.3 0.4 - - - -
32G ASN* 1.3 73.1 - - - +
34G THR* 1.3 56.6 + - - +
36G VAL* 3.3 4.0 + - - +
37G THR* 2.7 39.2 + - - +
94G HIS* 5.5 0.7 - - - +
97G GLY* 3.8 3.8 - - - -
98G THR* 2.7 50.5 + - - +
99G VAL 4.7 0.2 - - - +
101G PHE* 3.8 27.6 - - + -
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Residues in contact with THR 34 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ILE* 3.2 20.5 + - + +
13C ILE* 4.3 20.4 - - + -
16D LEU* 4.3 19.5 - - + -
19D VAL* 4.8 1.6 - - + -
20D LEU* 3.8 25.6 - - + -
30G ARG 2.9 16.6 + - - -
31G ALA* 3.3 11.0 + - - -
33G ASP* 1.3 76.3 - - - +
35G VAL* 1.3 57.8 + - - +
37G THR* 4.0 6.0 - - - -
38G ALA* 2.8 32.6 + - - +
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Residues in contact with VAL 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ILE* 3.3 34.3 - - + -
16D LEU* 5.6 0.2 - - + -
19D VAL* 4.0 24.4 - - + +
31G ALA 3.2 11.4 + - - +
32G ASN* 3.6 13.5 - - - +
33G ASP 3.3 0.4 - - - -
34G THR* 1.3 77.8 - - - +
36G VAL* 1.3 57.4 + - - +
38G ALA* 3.9 1.2 - - - +
39G TYR* 3.0 28.1 + - - +
73G PRO* 3.9 30.1 - - + -
76G VAL* 4.3 10.8 - - + -
94G HIS* 4.6 6.5 - - + +
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Residues in contact with VAL 36 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32G ASN 3.2 14.6 + - - +
33G ASP* 3.7 7.6 - - - +
35G VAL* 1.3 75.5 - - - +
37G THR* 1.3 60.0 + - - +
39G TYR* 3.5 4.0 + - - +
40G LEU* 3.0 32.2 + - + +
76G VAL* 4.5 11.2 - - + -
92G ALA* 3.5 32.7 - - + +
93G GLY* 3.7 3.4 - - - +
94G HIS* 3.4 35.7 - - + +
101G PHE* 3.6 26.5 - - + -
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Residues in contact with THR 37 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C ILE* 6.1 2.9 - - + -
14C ALA* 5.5 8.1 - - - +
17C ALA* 3.9 27.8 - - + -
33G ASP* 2.7 28.5 + - - +
34G THR* 4.0 6.5 - - - -
36G VAL* 1.3 74.5 - - - +
38G ALA* 1.3 56.4 + - - +
40G LEU* 3.9 2.2 - - - +
41G ASN* 2.9 30.7 + - + +
101G PHE* 3.3 23.3 - - + -
109G VAL* 4.3 22.5 - - + +
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Residues in contact with ALA 38 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 3.9 34.5 - - + +
20D LEU* 4.0 13.7 - - + -
34G THR 2.8 19.5 + - - +
35G VAL 3.9 3.4 - - - +
37G THR* 1.3 78.3 - - - +
39G TYR* 1.3 56.7 - - - +
41G ASN* 3.3 7.9 + - - +
42G ASP* 2.8 35.8 + - - +
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Residues in contact with TYR 39 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL* 5.7 0.6 - - + +
35G VAL 3.0 18.8 + - - +
36G VAL* 4.0 5.2 - - - +
37G THR 3.4 0.2 - - - -
38G ALA* 1.3 73.4 - - - +
40G LEU* 1.3 55.9 + - + +
42G ASP* 3.4 8.9 + - - +
43G ALA* 2.8 33.4 + - - +
61G GLN* 3.1 21.8 + - - -
69G LEU* 3.8 24.2 - - + +
70G LYS* 2.9 29.1 + - + -
71G SER 3.4 19.3 - - - -
72G THR* 3.5 6.6 + - - -
73G PRO* 3.7 25.6 - - + -
76G VAL* 5.4 3.4 - - + -
78G PHE* 3.6 44.2 - + + -
92G ALA* 5.7 1.6 - - + -
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Residues in contact with LEU 40 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36G VAL* 3.0 24.6 + - + +
37G THR 3.9 0.2 - - - +
39G TYR* 1.3 72.6 - - + +
41G ASN* 1.3 60.7 + - - +
43G ALA* 3.5 3.4 - - - +
44G VAL* 2.9 35.2 + - - +
78G PHE* 3.9 18.6 - - + -
90G MET* 3.8 20.3 - - + +
92G ALA* 3.6 22.7 - - + -
101G PHE* 3.3 44.9 - - + +
102G ALA 3.9 1.6 - - - +
103G ALA* 3.8 8.7 - - + -
109G VAL* 3.8 26.2 - - + -
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Residues in contact with ASN 41 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C ALA* 5.8 6.5 - - + +
21C ILE* 3.8 31.1 - - - +
37G THR* 2.9 22.3 + - + +
38G ALA* 3.5 9.2 + - - +
40G LEU* 1.3 76.6 - - - +
42G ASP* 1.3 61.1 + - - +
44G VAL* 3.7 7.1 + - - +
45G LYS* 3.5 48.9 + - - +
109G VAL* 4.0 12.5 - - + +
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Residues in contact with ASP 42 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D VAL 3.7 18.2 - - - +
20D LEU 5.8 0.3 - - - +
21D ILE 5.3 0.7 - - - +
22D PRO* 4.4 15.0 - - - +
23D ASN 5.2 1.9 + - - -
38G ALA* 2.8 22.9 + - - +
39G TYR* 3.6 10.8 - - + +
41G ASN* 1.3 76.6 + - - +
43G ALA* 1.3 64.2 + - - +
45G LYS* 3.1 34.7 + - - +
46G PHE* 3.2 25.3 + - + -
69G LEU* 3.7 18.4 - - + -
70G LYS* 5.4 5.8 + - - -
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Residues in contact with ALA 43 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39G TYR 2.8 20.8 + - - +
40G LEU* 3.3 9.8 + - - +
42G ASP* 1.3 74.0 - - - +
44G VAL* 1.3 56.0 + - - +
46G PHE* 3.6 2.0 + - - +
47G GLN* 3.1 33.3 + - - +
64G LEU* 4.5 2.7 - - + +
69G LEU* 4.0 18.6 - - + +
78G PHE* 3.9 21.3 - - + -
90G MET* 3.6 19.5 - - + -
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Residues in contact with VAL 44 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ILE* 5.5 8.5 - - + -
24C LEU* 3.5 20.4 - - + -
40G LEU 2.9 20.4 + - - +
41G ASN* 3.8 9.4 - - - +
42G ASP 3.3 0.2 - - - -
43G ALA* 1.3 74.3 - - - +
45G LYS* 1.3 64.7 + - + +
47G GLN* 3.5 6.5 + - - +
48G GLU* 3.2 23.4 + - + +
88G TYR* 3.4 25.1 + - + +
90G MET* 4.0 14.4 - - + -
103G ALA* 4.3 6.7 - - + -
104G THR 5.3 2.5 - - - +
108G GLY* 5.6 1.6 - - - -
109G VAL* 3.9 19.5 - - + +
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Residues in contact with LYS 45 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D PRO* 4.2 19.1 - - + +
41G ASN* 3.5 43.1 + - - +
42G ASP* 3.1 25.3 + - - +
44G VAL* 1.3 79.2 - - + +
46G PHE* 1.3 65.1 + - + +
48G GLU* 3.1 10.6 + - - +
49G MET* 3.0 32.9 + - - +
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Residues in contact with PHE 46 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D ASN* 3.7 28.7 - - + -
26D ALA* 3.7 9.9 - - + -
42G ASP* 3.2 28.3 + - + +
43G ALA 4.3 2.2 - - - +
45G LYS* 1.3 80.6 - - + +
47G GLN* 1.3 59.6 + - - +
49G MET* 3.5 28.8 - - - +
50G TYR* 3.2 21.3 + - - +
64G LEU* 3.4 27.2 - - + +
67G LEU* 3.9 19.9 - - + +
68G GLY* 3.4 23.8 - - - -
69G LEU* 3.3 43.5 - - + -
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Residues in contact with GLN 47 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43G ALA 3.1 24.6 + - - +
44G VAL* 3.6 7.9 - - - +
45G LYS 3.2 0.2 - - - -
46G PHE* 1.3 77.4 - - - +
48G GLU* 1.3 57.8 + - - +
50G TYR* 3.5 4.2 + - - +
51G GLN* 3.1 25.5 + - - +
57G TYR* 3.5 30.3 - - + -
58G THR* 2.9 52.4 + - - +
64G LEU* 3.8 5.9 - - + +
80G ILE* 4.3 3.4 - - - +
88G TYR* 4.0 22.3 - - + +
90G MET* 3.4 33.1 - - + +
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Residues in contact with GLU 48 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C LEU* 3.7 40.8 - - + +
28C ARG* 3.0 30.3 + - - +
44G VAL* 3.2 13.9 + - + +
45G LYS* 3.1 11.0 + - - +
47G GLN* 1.3 75.2 - - + +
49G MET* 1.3 62.5 + - + +
51G GLN* 3.4 6.8 + - - +
52G ILE* 3.2 28.9 + - + +
57G TYR* 3.0 27.3 + - - -
88G TYR* 4.5 2.1 - - - -
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Residues in contact with MET 49 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ALA* 3.8 36.3 - - + +
27D ALA* 5.2 2.2 - - - -
29D LYS* 5.8 2.0 - - + -
30D ARG* 3.5 39.5 + - + +
45G LYS* 3.0 19.3 + - + +
46G PHE* 3.5 33.9 - - + +
47G GLN 3.3 0.2 - - - -
48G GLU* 1.3 75.7 - - + +
50G TYR* 1.3 62.2 + - - +
52G ILE* 3.4 13.0 + - + +
53G ASP* 3.2 27.5 + - - +
67G LEU* 3.6 19.3 - - + +
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Residues in contact with TYR 50 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G PHE 3.2 17.8 + - - +
47G GLN* 3.7 6.7 - - - +
49G MET* 1.3 73.9 - - - +
51G GLN* 1.3 59.2 + - - +
53G ASP* 4.5 2.2 - - - +
54G ASN* 2.8 68.4 + - + +
56G SER* 3.5 19.9 - - - +
57G TYR 4.8 2.0 - - - -
58G THR* 3.3 37.5 - - + -
63G ALA* 3.8 18.0 - - + +
64G LEU* 4.7 0.9 - - + -
67G LEU* 3.4 27.9 - - + +
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Residues in contact with GLN 51 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ARG* 3.4 39.3 + - - +
75C ASN* 4.7 3.0 - - - +
47G GLN 3.1 14.1 + - - +
48G GLU* 3.4 15.0 - - - +
49G MET 3.3 0.2 - - - -
50G TYR* 1.3 74.7 - - - +
52G ILE* 1.3 61.9 + - - +
55G ASN* 3.2 54.0 + - - +
56G SER 3.0 27.6 + - - +
57G TYR* 3.2 26.6 - - + +
85G ALA 3.4 8.6 + - - +
86G ASN* 5.6 3.4 - - - +
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Residues in contact with ILE 52 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ARG* 5.6 7.9 - - - +
30D ARG* 4.3 27.8 - - + +
111D LYS* 3.7 14.4 + - - +
48G GLU* 3.2 18.4 + - + +
49G MET* 3.5 16.8 - - + +
50G TYR 3.3 0.2 - - - -
51G GLN* 1.3 79.9 - - + +
53G ASP* 1.3 69.4 + - - +
55G ASN* 4.0 8.2 + - - +
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Residues in contact with ASP 53 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D ARG* 2.7 40.1 + - - -
111D LYS* 3.9 18.8 + - - +
49G MET 3.2 12.3 + - - +
50G TYR* 3.3 5.0 + - - +
52G ILE* 1.3 82.5 - - - +
54G ASN* 1.3 77.1 + - - +
55G ASN* 3.6 5.2 + - - +
67G LEU* 4.6 9.7 - - - +
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Residues in contact with ASN 54 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA* 5.4 0.3 - - - +
50G TYR* 2.8 65.1 + - + +
53G ASP* 1.3 88.2 + - - +
55G ASN* 1.3 73.4 + - - +
56G SER* 3.5 6.8 + - - +
67G LEU* 5.7 0.4 - - - +
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Residues in contact with ASN 55 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C ALA* 3.3 32.9 - - + +
75C ASN* 2.7 33.6 + - - +
50G TYR 3.9 0.2 + - - -
51G GLN* 3.2 34.6 + - - +
52G ILE 4.0 10.7 + - - -
53G ASP 4.5 4.3 + - - +
54G ASN* 1.3 81.0 - - - +
56G SER* 1.3 57.4 + - - +
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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