Contacts of the helix formed by residues 21 - 54 (chain C) in PDB entry 2WP9
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 PRO 21 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B MET 4.6 0.4 - - - +
211B ASN* 2.9 30.3 - - - +
214B SER* 4.2 13.0 - - - +
19C ARG 4.0 4.7 - - - +
20C PHE* 1.3 91.8 - - + +
22C ILE* 1.3 68.0 + - - +
23C THR* 3.9 13.5 - - - +
24C ALA* 3.0 14.0 + - + -
25C ILE* 3.2 9.7 + - - +
103C PHE* 4.1 24.0 - - + -
107C LYS* 6.2 0.2 - - + -
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Residues in contact with ILE 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PRO* 1.3 73.4 - - - +
23C THR* 1.3 62.5 + - - +
25C ILE* 3.0 12.1 + - + +
26C ALA* 2.9 27.6 + - - +
107C LYS* 3.7 40.1 - - + +
110C ALA* 4.3 7.0 - - + -
111C LYS* 3.5 39.0 - - + -
114C PHE* 3.5 32.3 - - + -
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Residues in contact with THR 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B SER 5.0 1.4 - - - +
209B ILE 3.0 21.2 + - - +
210B MET* 3.4 24.1 + - + -
21C PRO* 3.9 9.2 - - - +
22C ILE* 1.3 78.6 - - + +
24C ALA* 1.3 63.3 + - - +
26C ALA* 3.5 9.1 - - - +
27C SER* 3.2 21.3 + - - -
90C ARG* 4.0 13.3 + - - +
103C PHE* 4.3 13.2 - - + -
106C GLY* 3.6 36.6 - - - +
107C LYS* 4.0 5.2 - - - +
110C ALA* 4.7 0.7 - - - -
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B PRO* 5.9 1.3 - - + -
209B ILE* 3.9 26.8 - - + +
211B ASN* 3.9 18.4 - - - +
20C PHE* 4.2 18.2 - - + -
21C PRO* 3.0 13.7 + - + +
23C THR* 1.3 79.2 + - - +
25C ILE* 1.3 66.7 + - - +
27C SER* 3.1 3.0 + - - -
28C ILE* 3.0 24.5 + - - +
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Residues in contact with ILE 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 4.2 25.6 - - + +
21C PRO 3.2 13.5 + - - +
22C ILE* 3.0 15.3 + - + +
24C ALA* 1.3 75.9 - - - +
26C ALA* 1.3 64.2 + - - +
27C SER 3.0 0.7 + - - -
28C ILE* 3.1 16.9 - - + +
29C LEU* 3.0 41.2 + - + +
114C PHE* 5.0 6.7 - - + -
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Residues in contact with ALA 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE 2.9 12.6 + - - +
23C THR* 3.5 11.0 - - - +
25C ILE* 1.3 77.6 - - - +
27C SER* 1.3 57.9 + - - +
29C LEU* 4.7 0.2 - - - -
30C HIS* 3.0 19.6 + - - +
83C TYR* 2.7 29.0 + - - +
87C VAL* 4.2 7.9 - - + +
90C ARG* 4.5 11.4 - - - +
110C ALA* 4.2 15.0 - - + -
114C PHE* 3.9 18.3 - - + -
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Residues in contact with SER 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207B THR* 4.0 12.5 + - - -
208B SER 4.5 1.5 + - - -
209B ILE* 3.5 36.7 - - - +
23C THR 3.2 9.8 + - - -
24C ALA 3.1 9.6 + - - -
25C ILE 3.1 0.8 - - - -
26C ALA* 1.3 77.9 - - - +
28C ILE* 1.3 65.6 + - - +
30C HIS* 3.1 9.8 + - - +
31C ARG* 3.1 20.3 + - - +
87C VAL* 5.6 1.1 - - - -
90C ARG* 5.7 2.0 - - - +
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Residues in contact with ILE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24C ALA 3.0 15.7 + - - +
25C ILE* 3.1 28.7 - - + +
27C SER* 1.3 75.2 - - - +
29C LEU* 1.3 66.6 + - + +
31C ARG* 3.2 16.1 + - + +
32C VAL* 3.0 33.2 + - + +
83D TYR* 4.3 17.9 - - + +
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ILE* 3.0 33.8 + - + +
28C ILE* 1.3 79.0 - - + +
30C HIS* 1.3 59.2 + - - +
32C VAL* 3.2 13.8 + - + +
33C SER* 2.8 33.6 + - - -
83C TYR* 3.3 36.3 - - + +
114C PHE* 4.9 6.5 - - + -
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Residues in contact with HIS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C ALA 3.0 14.0 + - - +
27C SER* 3.1 12.3 + - - +
29C LEU* 1.3 77.6 - - - +
31C ARG* 1.3 61.8 + - - +
33C SER* 2.8 18.9 + - - -
34C GLY 3.1 6.4 + - - -
83C TYR* 3.4 4.2 - - - -
84C HIS* 3.0 68.1 + + - -
87C VAL* 3.7 22.2 - - + +
88C GLY* 3.5 19.4 - - - -
91C HIS* 5.1 15.7 - + - -
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Residues in contact with ARG 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B TRP* 4.7 1.2 - - - -
205B ARG* 5.1 0.6 - - - +
207B THR* 6.0 4.2 - - - +
27C SER 3.1 11.7 + - - +
28C ILE* 3.5 18.6 - - + +
29C LEU 3.2 0.2 - - - -
30C HIS* 1.3 80.7 - - - +
32C VAL* 1.3 65.5 + - + +
34C GLY* 3.2 10.7 + - - -
35C VAL* 3.2 18.3 + - + +
78D GLN* 4.2 12.5 + - - +
79D VAL* 3.8 35.4 - - + +
82D ASP* 2.9 31.5 + - - +
83D TYR* 3.0 47.5 + - - -
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Residues in contact with VAL 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 3.0 33.3 + - + +
29C LEU* 3.8 15.3 - - + +
31C ARG* 1.3 76.8 - - + +
33C SER* 1.3 64.4 + - - +
35C VAL* 3.2 7.9 + - - +
36C ILE* 3.0 41.9 + - + +
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Residues in contact with SER 33 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU 2.8 17.8 + - - -
30C HIS* 2.8 20.1 + - - -
32C VAL* 1.3 75.2 - - - +
34C GLY* 1.3 55.9 + - - +
36C ILE* 3.5 8.3 + - - +
37C THR* 2.8 34.3 + - - -
80C ALA* 3.4 30.6 - - - +
83C TYR* 3.8 10.0 - - - -
84C HIS* 3.2 19.4 + - - +
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Residues in contact with GLY 34 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C HIS 3.1 5.5 + - - -
31C ARG* 3.2 4.2 + - - -
32C VAL 3.2 0.4 - - - -
33C SER* 1.3 79.5 + - - +
35C VAL* 1.3 64.3 + - - +
37C THR* 3.3 5.5 + - - -
38C PHE* 3.1 22.2 + - - +
84C HIS* 3.3 27.1 - - - -
76D MET* 5.1 2.5 - - - +
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Residues in contact with VAL 35 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ARG* 3.2 18.4 + - + +
32C VAL* 3.2 7.6 + - - +
34C GLY* 1.3 71.6 - - - +
36C ILE* 1.3 70.2 + - + +
38C PHE* 3.1 14.2 + - + +
39C VAL* 3.3 15.9 + - + +
76D MET* 4.3 32.1 - - + -
79D VAL* 4.3 24.9 - - + -
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Residues in contact with ILE 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C VAL* 3.0 38.9 + - + +
33C SER* 3.6 5.4 - - - +
35C VAL* 1.3 77.8 - - + +
37C THR* 1.3 58.6 + - - +
39C VAL* 3.0 11.2 + - - +
40C ALA* 2.8 31.4 + - + +
76C GLY 5.4 0.7 - - - +
77C ILE* 5.3 9.2 - - + -
80C ALA* 3.9 26.7 - - + -
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Residues in contact with THR 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C SER 2.8 23.3 + - - -
34C GLY* 3.7 8.0 - - - -
35C VAL 3.2 0.6 - - - -
36C ILE* 1.3 75.9 - - - +
38C PHE* 1.3 63.3 + - - +
40C ALA* 3.6 9.4 - - + +
41C VAL* 3.0 33.2 + - + +
77C ILE 5.3 0.2 + - - -
80C ALA* 4.3 1.9 + - - +
81C LEU* 3.9 45.0 + - + +
84C HIS* 4.5 7.1 - - + +
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Residues in contact with PHE 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C GLY 3.1 12.4 + - - +
35C VAL* 3.1 11.4 + - + +
37C THR* 1.3 80.0 - - - +
39C VAL* 1.3 74.1 + - + +
41C VAL* 3.6 7.3 + - - +
68D ILE* 6.1 0.7 - - + -
72D ALA* 4.4 14.1 - - + -
76D MET* 4.0 28.9 - - + -
97D ILE* 3.9 33.7 - - + -
100D ALA* 4.3 16.2 - - + -
101D LEU* 3.9 35.9 - - + -
104D TYR* 3.2 32.2 + + - -
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Residues in contact with VAL 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C VAL* 3.3 13.4 + - + +
36C ILE* 3.0 9.7 + - - +
38C PHE* 1.3 90.6 - - + +
40C ALA* 1.3 65.9 + - - +
41C VAL 3.0 1.4 + - - -
42C GLY* 3.1 13.2 + - - -
43C ILE* 3.5 25.2 + - + +
104D TYR* 3.9 3.7 + - - -
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Residues in contact with ALA 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ILE* 2.8 19.7 + - + +
37C THR* 3.3 13.4 + - + +
39C VAL* 1.3 79.3 - - - +
41C VAL* 1.3 56.5 + - - +
43C ILE* 3.1 7.4 + - - +
44C LEU* 2.9 34.0 + - + +
77C ILE* 3.7 44.0 - - + +
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Residues in contact with VAL 41 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C THR* 3.0 31.7 + - + +
38C PHE* 3.8 9.6 - - - +
39C VAL 3.0 0.8 + - - -
40C ALA* 1.3 76.6 - - + +
42C GLY* 1.3 57.6 + - - +
44C LEU* 3.4 10.9 + - + +
45C LEU* 2.8 41.4 + - + +
65D LEU* 5.0 2.5 - - + -
68D ILE* 4.7 33.9 - - + -
104D TYR* 3.6 23.8 - - + -
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Residues in contact with GLY 42 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL 3.1 6.6 + - - -
41C VAL* 1.3 78.3 - - - +
43C ILE* 1.3 55.6 + - - +
45C LEU* 3.1 5.4 + - - +
46C TRP* 2.8 31.5 + - - +
104D TYR* 3.2 33.7 + - - -
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Residues in contact with ILE 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C VAL* 3.5 28.3 + - + +
40C ALA* 3.1 13.0 + - - +
42C GLY* 1.3 74.6 - - - +
44C LEU* 1.3 67.1 + - + +
46C TRP* 3.1 15.8 + - + +
47C LEU* 2.9 23.9 + - + +
73C ILE* 5.9 6.3 - - + -
74C MET* 5.5 6.3 - - + -
77C ILE* 4.3 19.5 - - + -
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Residues in contact with LEU 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ALA* 2.9 25.5 + - + +
41C VAL* 3.8 9.2 - - + +
43C ILE* 1.3 73.2 - - - +
45C LEU* 1.3 58.2 + - + +
47C LEU* 3.3 10.0 + - + +
48C LEU* 2.8 30.2 + - - +
74C MET* 3.9 33.4 - - + -
77C ILE* 4.4 22.9 - - + -
78C LEU* 5.6 7.4 - - + -
81C LEU* 5.8 6.7 - - + -
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Residues in contact with LEU 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C VAL* 2.8 28.0 + - + +
42C GLY* 3.1 5.8 + - - +
44C LEU* 1.3 70.7 - - + +
46C TRP* 1.3 66.5 + - - +
48C LEU* 3.7 21.8 - - + +
49C GLY 2.9 21.7 + - - -
61D THR* 6.4 1.3 - - + -
65D LEU* 3.8 31.9 - - + -
104D TYR* 3.8 36.6 - - + +
107D TYR* 3.5 28.7 - - + -
108D GLY* 4.9 9.2 - - - -
111D VAL* 5.3 2.9 - - + +
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Residues in contact with TRP 46 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLY 2.8 17.2 + - - +
43C ILE* 3.4 17.0 - - + +
45C LEU* 1.3 72.9 - - - +
47C LEU* 1.3 96.8 + - + +
49C GLY* 4.2 0.7 - - - -
50C THR* 3.2 39.5 + - + -
60C GLN* 6.0 2.9 - - - -
64C ILE* 3.7 28.5 - - + -
107D TYR* 4.5 10.9 + + - -
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Residues in contact with LEU 47 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C ILE* 2.9 17.8 + - + +
44C LEU* 3.6 11.9 - - + +
46C TRP* 1.3 97.7 - - + +
48C LEU* 1.3 64.8 + - - +
50C THR* 3.3 6.9 + - - -
51C SER* 3.0 23.6 + - - -
61C ALA* 4.5 21.7 - - + +
64C ILE* 4.3 20.2 - - + -
65C MET* 4.3 14.4 - - + -
70C VAL* 6.4 0.2 - - + -
74C MET* 4.2 26.7 - - + -
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Residues in contact with LEU 48 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C LEU 2.8 21.7 + - - +
45C LEU* 3.7 23.1 - - + +
47C LEU* 1.3 74.2 - - - +
49C GLY* 1.3 62.4 + - - +
51C SER* 2.8 20.9 + - - +
52C LEU* 3.1 19.9 + - + +
48D TRP* 3.5 31.2 - - + -
52D PHE* 3.6 31.4 - - + -
61D THR* 5.5 8.1 - - + -
111D VAL* 4.7 12.3 - - + -
112D VAL* 5.7 2.9 - - + -
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Residues in contact with GLY 49 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C LEU 2.9 10.9 + - - -
48C LEU* 1.3 72.5 - - - +
50C THR* 1.3 64.4 + - - +
52C LEU* 3.4 1.6 + - - +
53C SER* 3.3 24.9 + - - -
107D TYR* 3.5 22.0 - - - -
111D VAL* 3.6 24.6 - - - +
----------------------------------------------------------
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Residues in contact with THR 50 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C TRP* 3.2 33.9 + - + -
47C LEU* 3.5 10.3 - - + +
49C GLY* 1.3 75.5 - - - +
51C SER* 1.3 58.8 + - - +
52C LEU 3.0 6.1 + - - -
53C SER* 3.2 20.0 + - - +
57C GLY* 3.4 27.0 - - - +
60C GLN* 3.9 26.7 + - + +
61C ALA* 4.5 8.3 - - + +
64C ILE* 5.6 4.7 - - + -
107D TYR* 4.5 0.8 + - - -
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Residues in contact with SER 51 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C LEU* 3.0 15.7 + - - -
48C LEU* 2.8 18.8 + - - -
50C THR* 1.3 75.0 - - - +
52C LEU* 1.3 56.8 + - - +
53C SER 3.8 0.2 - - - -
57C GLY 3.9 10.3 - - - -
58C PHE* 3.7 30.7 + - - +
61C ALA* 3.7 17.5 - - - -
45D TYR* 4.3 4.7 - - - -
48D TRP* 3.0 33.2 + - - -
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Residues in contact with LEU 52 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C LEU* 3.1 24.8 + - + +
49C GLY 3.4 3.3 + - - +
50C THR 3.0 1.2 - - - -
51C SER* 1.3 81.2 - - - +
53C SER* 1.3 64.8 + - - +
54C SER* 3.3 4.0 + - - -
45D TYR* 4.7 2.6 + - + -
48D TRP* 3.4 30.7 - - + +
49D ILE* 4.5 29.5 - - + +
52D PHE* 4.0 36.3 - - + -
111D VAL* 3.9 26.7 - - + +
112D VAL* 5.4 1.6 - - + -
114D GLY 5.4 2.3 - - - +
115D VAL* 4.3 21.9 - - + +
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Residues in contact with SER 53 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C GLY 3.3 13.2 + - - -
50C THR* 3.2 16.4 + - - -
52C LEU* 1.3 77.9 - - - +
54C SER* 1.3 68.9 + - - +
57C GLY* 4.3 3.5 - - - -
----------------------------------------------------------
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Residues in contact with SER 54 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C SER 4.5 0.7 - - - +
52C LEU 3.3 1.8 - - - -
53C SER* 1.3 85.9 + - - +
55C PRO* 1.3 77.3 - - - +
56C GLU* 3.8 7.9 + - - +
57C GLY 3.1 22.5 + - - -
58C PHE 3.2 8.8 + - - -
45D TYR* 3.7 17.2 - - - -
----------------------------------------------------------
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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