Contacts of the helix formed by residues 13 - 42 (chain G) in PDB entry 5JKL
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 HIS 13 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G ARG* 3.6 2.8 + - - -
11G ASN 4.0 2.6 + - - -
12G TYR* 1.3 77.2 - - - +
14G GLN* 1.3 71.0 + - + +
15G ASP* 3.0 47.6 + - - +
16G SER* 3.0 28.3 + - - +
17G GLU 3.1 9.4 + - - -
124G LYS* 3.5 42.6 + - + -
126G ASP* 4.8 1.2 + - - -
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Residues in contact with GLN 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G ARG* 3.6 15.2 - - - +
12G TYR 3.7 0.4 + - - -
13G HIS* 1.3 79.0 + - + +
15G ASP* 1.4 62.8 + - - +
17G GLU* 3.3 11.9 + - - +
18G GLU* 3.0 27.7 + - + +
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Residues in contact with ASP 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G HIS* 3.0 29.6 + - - +
14G GLN* 1.4 79.8 + - - +
16G SER* 1.3 61.7 + - - +
18G GLU* 3.3 16.9 + - - +
19G ALA* 2.9 28.9 + - - +
22G ARG* 4.5 2.6 + - - -
120G LEU* 3.6 23.0 - - + +
124G LYS* 3.8 11.5 + - - -
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Residues in contact with SER 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G TYR* 4.2 11.7 - - - -
13G HIS* 3.0 24.2 + - - +
15G ASP* 1.3 74.8 - - - +
17G GLU* 1.3 63.2 + - - +
19G ALA* 3.1 3.4 + - - +
20G ILE* 2.9 28.2 + - - +
117G LEU* 4.7 0.8 - - - +
120G LEU* 3.9 14.8 - - - +
121G ALA* 4.7 2.8 - - - -
124G LYS* 4.2 13.7 - - - +
126G ASP* 4.7 2.6 + - - -
129G LEU* 3.8 26.7 - - - +
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Residues in contact with GLU 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G ARG* 2.9 32.9 + - - +
12G TYR* 3.6 23.0 + - + -
13G HIS 3.1 9.2 + - - +
14G GLN* 3.3 17.6 + - - +
16G SER* 1.3 74.5 - - - +
18G GLU* 1.3 63.2 + - - +
20G ILE 3.4 0.3 + - - -
21G ASN* 3.1 12.3 + - - +
73G GLN* 3.1 36.9 + - - +
78G GLY* 3.5 4.9 - - - -
79G ARG* 2.9 33.9 + - - +
81G PHE* 5.3 2.4 - - - -
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Residues in contact with GLU 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS* 2.9 29.6 + - - +
14G GLN* 3.0 17.4 + - + +
15G ASP* 3.7 15.3 - - - +
16G SER 3.2 0.2 - - - -
17G GLU* 1.3 75.0 - - - +
19G ALA* 1.3 62.4 + - - +
21G ASN* 3.2 12.5 + - + +
22G ARG* 2.8 55.7 + - + +
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Residues in contact with ALA 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G ASP 2.9 17.9 + - - +
16G SER 3.1 2.7 + - - +
18G GLU* 1.3 77.4 - - - +
20G ILE* 1.3 55.8 + - - +
22G ARG* 3.3 24.5 + - - +
23G GLN* 2.9 27.5 + - - +
117G LEU* 3.3 28.4 - - + +
120G LEU* 3.7 13.2 - - + -
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Residues in contact with ILE 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G TYR* 3.5 15.5 - - - +
16G SER 2.9 20.6 + - - +
17G GLU 3.7 4.3 - - - +
19G ALA* 1.3 73.7 - - - +
21G ASN* 1.3 59.0 + - - +
23G GLN* 3.2 4.5 + - - +
24G ILE* 2.9 32.6 + - + +
69G LEU* 3.8 43.7 - - + +
72G LEU* 4.2 7.4 - - + -
73G GLN* 3.7 21.1 - - + +
117G LEU* 4.0 18.6 - - + -
129G LEU* 3.9 27.8 - - + -
132G PHE* 5.3 0.9 - - + -
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Residues in contact with ASN 21 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17G GLU* 3.1 17.0 + - - +
18G GLU* 3.2 11.5 + - + +
20G ILE* 1.3 75.1 - - - +
22G ARG* 1.3 61.4 + - + +
24G ILE* 3.4 15.8 + - - +
25G ASN* 3.2 19.8 + - - +
73G GLN* 2.9 19.6 + - - +
79G ARG 3.1 20.2 + - - -
80G ILE* 3.4 6.2 - - - +
81G PHE* 3.2 48.9 + - + +
83G GLN* 5.0 3.1 - - - +
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Residues in contact with ARG 22 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LYS* 4.3 6.8 - - - +
123A LYS* 3.2 31.3 - - - +
15G ASP 4.5 2.0 + - - -
18G GLU* 2.8 51.1 + - + +
19G ALA* 3.3 32.9 + - - +
21G ASN* 1.3 75.1 - - + +
23G GLN* 1.3 58.0 + - - +
25G ASN* 3.2 9.3 + - - +
26G LEU* 3.0 26.8 + - - +
83G GLN* 4.8 12.6 - - - +
113G SER* 5.9 0.7 - - - -
120G LEU* 5.4 2.4 - - - +
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Residues in contact with GLN 23 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G ALA 2.9 16.4 + - - +
20G ILE* 3.2 8.7 + - - +
22G ARG* 1.3 74.4 - - - +
24G ILE* 1.3 66.3 + - - +
26G LEU* 3.1 13.4 + - - +
27G GLU* 2.9 51.0 + - - +
69G LEU* 3.6 21.3 - - + -
110G VAL* 3.8 11.7 + - - +
113G SER* 2.7 35.0 + - - +
114G LEU* 3.5 29.6 + - + +
117G LEU* 4.4 13.4 - - + +
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Residues in contact with ILE 24 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G ILE* 2.9 25.9 + - + +
21G ASN* 3.6 25.1 - - - +
23G GLN* 1.3 76.8 - - - +
25G ASN* 1.4 62.8 + - - +
27G GLU* 3.3 3.8 + - - +
28G LEU* 3.1 40.4 + - + +
66G ALA* 4.1 4.0 - - + +
69G LEU* 3.6 30.9 - - + +
70G MET* 3.8 42.2 - - + +
73G GLN* 4.6 4.3 - - + -
80G ILE* 4.6 5.4 - - + -
81G PHE 6.0 0.4 - - - +
82G LEU* 4.1 15.0 - - + -
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Residues in contact with ASN 25 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21G ASN 3.2 9.1 + - - +
22G ARG* 3.2 9.9 + - - +
24G ILE* 1.4 79.8 - - - +
26G LEU* 1.3 57.3 + - - +
28G LEU* 3.2 7.7 + - - +
29G TYR* 2.8 31.5 + - - +
83G GLN* 3.3 41.5 + - + +
84G ASP 3.0 27.7 + - - +
85G ILE* 4.3 6.9 - - - +
86G GLN* 5.4 1.9 + - - +
32H TYR* 4.2 3.4 + - - -
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Residues in contact with LEU 26 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22G ARG 3.0 13.8 + - - +
23G GLN* 3.1 19.2 + - - +
25G ASN* 1.3 77.8 + - - +
27G GLU* 1.3 58.3 + - - +
29G TYR* 3.3 24.6 + - + +
30G ALA* 2.9 27.5 + - - +
106G LEU* 5.4 1.8 - - + -
109G ASN* 4.7 4.0 - - + +
110G VAL* 4.0 27.3 - - + +
113G SER* 3.5 35.7 - - - +
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Residues in contact with GLU 27 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23G GLN* 2.9 44.3 + - - +
24G ILE 3.8 0.2 - - - +
26G LEU* 1.3 75.6 - - - +
28G LEU* 1.3 63.6 + - - +
30G ALA* 3.3 5.4 + - - +
31G SER* 3.0 21.8 + - - -
62G GLU* 2.8 14.9 - - - +
65G HIS* 3.2 12.2 - - + +
66G ALA* 3.8 22.4 - - + +
69G LEU* 3.6 18.2 - - + -
110G VAL* 3.6 11.8 - - - +
114G LEU* 4.5 0.7 - - - +
137G TYR* 4.1 13.4 - - - -
201G FE 2.0 32.5 - - - -
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Residues in contact with LEU 28 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24G ILE* 3.1 35.1 + - + +
25G ASN* 3.6 9.0 - - - +
27G GLU* 1.3 74.4 - - - +
29G TYR* 1.3 63.5 + - - +
31G SER* 3.3 7.7 + - - -
32G TYR* 3.1 22.5 + - - +
63G ARG* 4.2 17.3 - - - +
66G ALA* 3.6 20.2 - - + -
82G LEU* 4.6 1.3 - - + -
85G ILE* 3.8 22.2 - - + +
32H TYR* 3.7 36.3 - - + +
35H LEU* 4.1 21.1 - - + -
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Residues in contact with TYR 29 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G ASN* 2.8 18.7 + - - +
26G LEU* 3.4 27.4 - - + +
28G LEU* 1.3 73.4 - - - +
30G ALA* 1.3 62.5 + - - +
32G TYR* 3.0 5.1 + - + +
33G VAL* 2.9 52.8 + - + +
85G ILE* 3.7 11.1 - - + +
86G GLN* 3.3 57.2 + - + +
87G LYS 3.9 6.5 - - - -
88G PRO* 4.2 0.9 - - + -
89G ASP* 3.7 24.6 + - - -
106G LEU* 3.9 17.9 - - + +
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Residues in contact with ALA 30 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LEU 2.9 16.7 + - - +
27G GLU* 3.6 6.7 - - - +
28G LEU 3.3 0.2 - - - -
29G TYR* 1.3 79.0 - - - +
31G SER* 1.3 62.1 + - - +
33G VAL* 3.3 3.5 + - - +
34G TYR* 3.0 29.0 + - + -
62G GLU* 3.9 24.9 - - + +
106G LEU* 4.0 26.2 - - + -
107G GLU* 5.2 0.4 - - - +
110G VAL* 4.6 10.5 - - + -
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Residues in contact with SER 31 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27G GLU 3.0 13.1 + - - -
28G LEU* 3.4 14.1 - - - -
29G TYR 3.2 0.2 - - - -
30G ALA* 1.3 75.2 - - - +
32G TYR* 1.3 58.9 + - - +
34G TYR 3.4 0.9 + - - -
35G LEU* 3.0 15.6 + - - +
59G SER* 2.8 46.6 + - - +
62G GLU* 3.6 13.3 - - - +
63G ARG* 3.9 10.8 + - - +
63H ARG* 2.9 22.7 + - - -
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Residues in contact with TYR 32 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G LEU 3.1 11.6 + - - +
29G TYR 3.0 9.7 + - - +
31G SER* 1.3 75.8 - - - +
33G VAL* 1.3 65.2 + - - +
35G LEU* 3.2 18.4 + - + +
36G SER* 2.9 22.7 + - - -
85G ILE* 4.0 10.8 - - + -
86G GLN 3.6 21.8 - - - +
87G LYS* 4.1 1.3 - - - -
88G PRO* 3.7 15.2 - - + +
25H ASN* 4.2 2.8 + - - -
28H LEU* 3.7 21.7 - - + +
63H ARG* 4.8 4.4 - - - +
82H LEU* 3.5 36.5 - - + +
83H GLN 2.6 30.4 + - - -
85H ILE* 3.6 33.9 - - + +
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Residues in contact with VAL 33 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29G TYR* 2.9 55.7 + - + +
30G ALA 3.6 7.0 - - - +
32G TYR* 1.3 74.0 - - - +
34G TYR* 1.4 58.5 + - + +
36G SER* 3.2 5.2 + - - -
37G MET* 2.9 53.0 + - + +
88G PRO* 3.7 15.7 - - + -
89G ASP 5.3 0.4 - - - +
93G TRP* 4.2 11.9 - - + -
106G LEU* 4.0 20.6 - - + -
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Residues in contact with TYR 34 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30G ALA 3.0 23.4 + - - +
32G TYR 3.3 0.2 - - - -
33G VAL* 1.4 73.0 - - - +
35G LEU* 1.3 61.1 + - - +
37G MET* 4.2 8.5 - - - -
38G SER* 2.8 31.0 + - - -
55G PHE* 3.4 49.9 - + - +
58G GLN* 3.7 27.6 + - + +
59G SER* 3.6 9.4 - - - +
62G GLU* 3.7 22.7 - - + -
103G ALA* 3.9 18.5 + - + +
106G LEU* 4.2 14.1 - - + -
107G GLU* 2.6 42.7 + - - +
148G LEU* 3.9 11.8 - - + +
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Residues in contact with LEU 35 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31G SER 3.0 15.0 + - - +
32G TYR* 3.4 24.5 - - + +
33G VAL 3.2 0.2 - - - -
34G TYR* 1.3 77.6 - - - +
36G SER* 1.3 62.3 + - - +
38G SER* 3.3 6.0 + - - -
39G TYR* 3.2 53.0 + - + +
56G LEU* 3.8 15.5 - - + -
59G SER* 3.7 7.8 - - - +
28H LEU* 4.1 20.6 - - + -
63H ARG* 4.0 19.7 - - - +
66H ALA* 5.7 0.2 - - + -
67H GLU* 3.9 15.3 - - + +
70H MET* 4.0 21.7 - - + +
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Residues in contact with SER 36 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32G TYR 2.9 13.1 + - - -
33G VAL 3.4 8.7 - - - -
35G LEU* 1.3 76.3 - - - +
37G MET* 1.3 62.7 + - - +
39G TYR* 3.4 2.8 + - - +
40G TYR* 3.1 22.2 + - - +
88G PRO* 3.9 10.1 - - - -
90G GLU 3.4 11.3 + - - -
91G ASP* 4.3 6.2 + - - +
93G TRP* 2.9 18.6 + - - -
70H MET* 5.0 3.6 - - - -
80H ILE* 6.4 0.2 - - - -
82H LEU* 3.7 27.0 - - - +
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Residues in contact with MET 37 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33G VAL* 2.9 35.8 + - + +
34G TYR* 3.7 17.9 - - + +
36G SER* 1.3 74.8 - - - +
38G SER* 1.3 63.6 + - - +
40G TYR* 3.1 9.0 + - - +
41G PHE* 3.1 25.4 + - + -
55G PHE* 3.9 34.3 - - + -
93G TRP* 3.7 46.2 - - + -
99G ALA* 3.7 27.6 - - + +
102G GLU* 3.8 10.1 - - + -
103G ALA* 4.0 9.2 - - - +
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Residues in contact with SER 38 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34G TYR 2.8 21.0 + - - -
35G LEU 3.5 6.5 - - - -
36G SER 3.3 0.2 - - - -
37G MET* 1.3 73.7 - - - +
39G TYR* 1.3 67.6 + - - +
41G PHE 3.1 15.1 + - - -
42G ASP 3.4 1.4 + - - -
52G ALA* 2.7 47.3 + - - +
55G PHE* 3.7 7.8 - - - +
56G LEU* 3.4 27.4 - - - +
----------------------------------------------------------
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Residues in contact with TYR 39 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35G LEU* 3.2 35.5 + - + +
36G SER 3.4 2.0 + - - +
37G MET 3.3 0.2 - - - -
38G SER* 1.3 81.7 - - - +
40G TYR* 1.3 66.0 + - - +
41G PHE 3.3 0.2 - - - -
42G ASP* 3.4 26.6 + - + -
43G ARG* 3.5 3.8 + - - +
56G LEU* 4.2 20.6 - - + +
67H GLU* 3.4 29.7 + - + +
70H MET* 3.6 34.5 - - + -
71H LYS* 3.7 23.9 - - + +
74H ASN* 2.9 23.9 + - - +
80H ILE* 3.6 19.9 - - + +
----------------------------------------------------------
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Residues in contact with TYR 40 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36G SER 3.1 14.2 + - - +
37G MET 3.1 8.5 + - - +
39G TYR* 1.3 77.9 - - - +
41G PHE* 1.3 93.2 + + - +
42G ASP 3.1 0.2 - - - -
43G ARG* 3.1 46.5 + - - +
46G VAL* 3.5 31.6 - - + +
91G ASP 3.9 10.3 - - - +
92G ASP* 3.4 24.7 + - - -
93G TRP* 3.5 27.1 - - + -
94G GLU* 3.2 38.9 + - - -
95G SER* 4.1 3.8 - - - -
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Residues in contact with PHE 41 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37G MET* 3.1 23.3 + - + -
38G SER 3.1 4.6 + - - +
40G TYR* 1.3 95.3 - + - +
42G ASP* 1.3 56.5 + - - +
43G ARG 3.3 0.2 - - - -
46G VAL* 3.5 19.1 - - + -
47G ALA* 3.3 7.8 + - - -
48G LEU* 3.0 54.7 + - + +
49G LYS* 5.0 0.5 - - - -
51G PHE* 3.5 22.2 - + + -
52G ALA* 3.7 11.7 - - - +
55G PHE* 3.7 16.2 - + - -
93G TRP* 5.0 0.2 - - + -
95G SER 3.5 22.7 - - - -
96G GLY* 3.7 24.5 - - - -
99G ALA* 3.6 22.9 - - + -
----------------------------------------------------------
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Residues in contact with ASP 42 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38G SER 3.4 5.9 + - - +
39G TYR* 3.6 28.0 - - + +
40G TYR 3.1 0.4 - - - -
41G PHE* 1.3 75.5 - - - +
43G ARG* 1.3 63.3 + - - +
44G ASP* 3.6 1.6 + - - -
47G ALA* 5.1 1.7 - - - +
49G LYS* 5.6 6.7 - - - +
52G ALA* 4.2 8.3 - - + +
71H LYS* 4.1 17.2 + - - +
74H ASN* 2.9 37.6 + - - +
----------------------------------------------------------
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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