Contacts of the helix formed by residues 5 - 35 (chain V) in PDB entry 1BFR
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 THR 5 (chain V).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3V GLY 3.4 4.9 + - - -
4V ASP* 1.3 72.1 - - - +
6V LYS* 1.3 58.4 + - + +
8V ILE* 3.4 10.2 + - - +
9V ASN* 3.0 41.1 + - - +
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Residues in contact with LYS 6 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4V ASP* 3.2 2.6 + - - +
5V THR* 1.3 76.1 - - + +
7V VAL* 1.3 60.4 + - - +
9V ASN* 3.3 11.4 + - + +
10V TYR* 3.0 60.6 + - + -
107V TYR* 3.3 43.3 - - + +
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Residues in contact with VAL 7 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4V ASP* 3.1 17.5 + - + +
6V LYS* 1.3 72.6 - - - +
8V ILE* 1.3 64.0 + - + +
10V TYR* 3.2 6.9 + - + +
11V LEU* 2.9 36.6 + - + +
65V LEU* 4.5 3.6 - - + -
107V TYR* 3.6 15.0 - - + -
108V ALA* 4.1 11.7 - - + -
111V VAL* 3.5 31.9 - - + -
113V ASP* 3.4 24.0 - - - +
116V SER* 4.0 14.8 - - - +
120V MET* 5.3 1.6 - - + -
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Residues in contact with ILE 8 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2V LYS* 5.9 2.0 - - + -
3V GLY* 4.4 8.7 - - - +
4V ASP 3.0 14.9 + - - +
5V THR* 3.4 10.7 + - - +
7V VAL* 1.3 73.1 - - - +
9V ASN* 1.3 60.8 + - - +
11V LEU* 3.5 7.5 + - + +
12V ASN* 3.0 34.4 + - - +
62V ILE* 4.0 14.8 - - + +
65V LEU* 3.4 45.1 - - + +
66V GLU 4.4 0.7 - - - -
67V GLY* 3.8 29.4 - - - +
68V LEU 4.7 1.1 - - - +
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Residues in contact with ASN 9 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5V THR* 3.0 29.3 + - - +
6V LYS* 3.3 14.0 + - + +
8V ILE* 1.3 80.3 + - - +
10V TYR* 1.3 59.1 + - + +
12V ASN* 3.2 10.5 + - - +
13V LYS* 2.9 29.4 + - - +
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Residues in contact with TYR 10 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6V LYS* 3.0 50.6 + - - -
7V VAL* 3.6 7.0 - - + +
9V ASN* 1.3 73.7 - - + +
11V LEU* 1.3 60.5 + - + +
13V LYS* 3.2 25.4 + - + +
14V LEU* 2.9 37.2 + - + +
103V GLU* 2.8 39.1 + - + +
104V ALA* 3.8 30.3 - - + -
107V TYR* 3.6 43.6 - + + +
120V MET* 5.7 1.1 - - + -
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Residues in contact with LEU 11 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7V VAL* 2.9 30.7 + - + +
8V ILE* 3.7 4.5 - - - +
10V TYR* 1.3 72.8 - - + +
12V ASN* 1.3 56.7 + - - +
14V LEU* 3.6 4.4 - - - +
15V LEU* 2.8 28.6 + - - +
58V TYR* 4.2 22.7 - - + -
61V ARG* 3.9 24.5 - - + -
62V ILE* 3.7 26.9 - - + +
65V LEU* 4.0 17.7 - - + -
116V SER* 4.3 3.4 - - - +
119V MET* 4.3 9.2 - - + -
120V MET* 3.9 33.7 - - + -
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Residues in contact with ASN 12 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8V ILE* 3.0 28.2 + - - +
9V ASN* 3.6 11.5 - - - +
11V LEU* 1.3 75.3 - - - +
13V LYS* 1.3 57.0 + - - +
15V LEU* 3.7 5.5 - - - +
16V GLY* 2.9 26.0 + - - -
62V ILE* 3.6 11.2 - - - +
68V LEU 3.0 22.2 + - - -
69V PRO* 3.5 4.5 - - - +
70V ASN* 2.7 42.4 + - + +
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Residues in contact with LYS 13 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9V ASN 2.9 16.8 + - - +
10V TYR* 3.5 31.6 - - + +
12V ASN* 1.3 69.9 - - - +
14V LEU* 1.3 61.1 + - + +
16V GLY* 3.2 4.4 + - - -
17V ASN* 3.0 31.3 + - - +
100V ASN* 3.3 45.0 + - + +
103V GLU* 3.9 19.0 + - - -
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Residues in contact with LEU 14 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10V TYR* 2.9 22.9 + - + +
11V LEU* 3.6 4.0 - - - +
13V LYS* 1.3 78.1 - - + +
15V LEU* 1.4 64.9 + - - +
17V ASN* 3.0 22.5 + - - +
18V GLU* 3.1 14.2 + - - +
58V TYR* 3.8 30.1 - - + +
97V GLY 5.2 0.2 - - - +
100V ASN* 3.7 39.7 - - + +
101V LEU* 4.2 11.0 - - + +
104V ALA* 3.7 12.6 - - + -
120V MET* 3.6 30.3 - - - -
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Residues in contact with LEU 15 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11V LEU 2.8 21.0 + - - +
12V ASN* 3.3 18.4 + - - +
14V LEU* 1.4 69.2 - - - +
16V GLY* 1.3 63.2 + - - +
18V GLU* 3.0 6.8 + - - +
19V LEU* 3.0 27.5 + - + +
55V ALA* 3.8 38.6 - - + +
58V TYR* 4.0 15.7 - - + -
59V ILE* 4.0 13.0 - - + +
62V ILE* 4.2 5.6 - - + -
69V PRO* 4.2 5.4 - - + -
70V ASN 3.9 24.0 - - - +
71V LEU* 3.9 26.0 - - + -
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Residues in contact with GLY 16 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12V ASN 2.9 14.5 + - - -
13V LYS* 3.5 5.6 - - - -
14V LEU 3.2 0.4 - - - -
15V LEU* 1.3 76.2 - - - +
17V ASN* 1.3 62.1 + - - +
19V LEU* 3.4 21.2 + - - +
20V VAL* 3.5 16.1 + - - +
70V ASN 5.1 3.1 + - - -
73V ASP 4.7 11.0 - - - +
75V GLY 5.2 0.3 + - - -
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Residues in contact with ASN 17 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13V LYS* 3.0 22.5 + - - +
14V LEU* 3.0 15.0 + - - +
16V GLY* 1.3 74.2 - - - +
18V GLU* 1.3 64.5 + - + +
20V VAL* 3.2 11.4 + - - +
21V ALA* 3.2 20.5 + - - +
93V LEU* 4.9 10.5 - - + +
96V ASP* 6.5 0.2 - - - -
97V GLY* 4.1 15.5 - - - -
100V ASN* 2.9 37.4 + - - +
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Residues in contact with GLU 18 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14V LEU 3.1 13.1 + - - +
15V LEU 3.0 8.1 + - - +
17V ASN* 1.3 75.5 - - - +
19V LEU* 1.3 58.9 + - - +
21V ALA* 3.2 5.2 + - - +
22V ILE* 2.8 34.9 + - - +
51V GLU* 2.8 19.2 - - - +
54V HIS* 3.6 15.4 - - + +
55V ALA* 4.2 17.0 - - + +
58V TYR* 3.7 26.6 + - + -
101V LEU* 5.9 1.0 - - - +
123V ILE* 4.0 5.4 - - - +
127V GLU* 5.3 0.2 - - - +
202V MN 2.1 37.7 + - - -
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Residues in contact with LEU 19 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23U ASN* 4.6 5.6 - - - +
74U LEU* 5.8 0.9 - - + -
15V LEU* 3.0 27.4 + - + +
16V GLY* 3.7 9.0 - - - +
17V ASN 3.3 0.2 - - - -
18V GLU* 1.3 76.7 - - - +
20V VAL* 1.3 59.6 + - - +
22V ILE* 3.8 7.9 + - + +
23V ASN* 3.5 26.5 + - - +
55V ALA* 4.6 1.6 - - + -
70V ASN 4.1 6.3 - - - +
71V LEU* 3.9 44.9 - - + +
73V ASP 4.4 13.5 - - - +
74V LEU* 3.9 15.4 - - + +
200V HEM 3.9 32.5 - - + -
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Residues in contact with VAL 20 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16V GLY 3.8 11.9 - - - +
17V ASN* 3.2 7.3 + - - +
19V LEU* 1.3 72.5 - - - +
21V ALA* 1.3 64.6 + - - +
23V ASN* 3.2 2.9 + - - +
24V GLN* 2.8 34.8 + - - +
74V LEU* 3.8 11.2 - - + -
75V GLY* 3.5 36.8 - - - +
76V LYS 4.4 13.7 - - - +
77V LEU* 4.1 10.0 - - + +
93V LEU* 3.7 31.2 - - + -
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Residues in contact with ALA 21 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17V ASN 3.2 12.2 + - - +
18V GLU* 3.2 10.3 + - - +
20V VAL* 1.3 77.0 - - - +
22V ILE* 1.3 56.8 + - - +
24V GLN 4.5 0.2 - - - +
25V TYR* 2.8 47.6 + - + -
51V GLU* 3.9 24.2 - - + +
93V LEU* 4.0 18.6 - - + -
94V GLU* 4.9 3.1 - - - +
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Residues in contact with ILE 22 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18V GLU 2.8 25.9 + - - +
19V LEU* 3.9 7.6 - - + +
21V ALA* 1.3 68.6 - - - +
23V ASN* 1.3 65.5 + - - +
26V PHE* 2.9 28.6 + - - +
48V SER* 3.2 12.0 + - - +
51V GLU* 3.6 13.2 - - + +
52V MET* 3.6 56.8 - - + +
55V ALA* 4.0 10.3 - - + -
200V HEM 3.8 46.7 - - + -
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Residues in contact with ASN 23 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19U LEU* 4.5 9.9 - - - +
71U LEU* 2.9 54.5 + - + +
19V LEU 3.5 12.8 + - - +
20V VAL 3.2 7.5 + - - +
22V ILE* 1.3 77.3 - - - +
24V GLN* 1.3 63.7 + - - +
26V PHE* 4.6 2.0 - - - -
27V LEU* 3.0 21.9 + - - +
74V LEU* 3.7 16.3 - - - +
77V LEU* 4.3 9.6 - - + -
200V HEM 3.8 20.9 - - - +
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Residues in contact with GLN 24 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20V VAL* 2.8 23.5 + - - +
21V ALA 4.0 1.3 - - - +
23V ASN* 1.3 72.5 - - - +
25V TYR* 1.3 61.7 + - - +
27V LEU* 4.1 3.6 - - - +
28V HIS* 3.0 37.2 + - + +
76V LYS 4.8 1.0 + - - -
77V LEU* 3.8 13.9 - - + +
78V ASN* 3.0 38.7 + - - +
79V ILE* 4.5 7.4 - - + -
89V SER* 3.4 20.7 + - - -
90V ASP* 3.0 23.4 - - - +
93V LEU* 3.6 26.0 - - + +
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Residues in contact with TYR 25 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21V ALA* 2.8 39.6 + - + +
24V GLN* 1.3 71.2 - - + +
26V PHE* 1.3 57.7 + - - +
28V HIS* 3.4 2.2 + - - +
29V ALA* 2.9 29.1 + - - +
44V GLU* 3.5 33.5 - - - +
47V GLU* 3.2 39.5 + - + -
48V SER* 3.9 18.8 - - - +
51V GLU* 3.6 20.6 - - + -
90V ASP* 3.8 20.9 - - + -
93V LEU* 5.9 3.4 - - + -
94V GLU* 3.0 44.1 + - + +
130V HIS* 3.6 7.1 + - - +
134V LEU* 3.8 3.7 - - + +
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Residues in contact with PHE 26 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56U ASP* 3.4 36.6 - - + -
59U ILE* 3.8 17.0 - - + -
71U LEU* 5.1 1.6 - - + -
22V ILE 2.9 20.2 + - - +
23V ASN* 3.9 4.0 - - - +
25V TYR* 1.3 75.7 - - - +
27V LEU* 1.3 62.7 + - - +
29V ALA* 3.2 7.0 + - + +
30V ARG* 3.1 36.8 + - + +
45V TYR* 3.6 27.4 - + - -
48V SER* 3.4 21.4 + - - +
52V MET* 4.1 4.9 - - + -
200V HEM 3.6 52.5 - + + -
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Residues in contact with LEU 27 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59U ILE* 4.0 11.9 - - + -
63U LEU* 4.5 1.3 - - + -
68U LEU* 5.5 3.6 - - + -
69U PRO* 3.7 50.7 - - + +
71U LEU* 3.8 19.4 - - + +
23V ASN 3.0 18.0 + - - +
24V GLN 4.1 2.0 - - - +
26V PHE* 1.3 77.0 - - - +
28V HIS* 1.3 62.3 + - - +
30V ARG* 3.3 3.1 + - - -
31V MET* 2.9 42.4 + - + +
77V LEU* 5.1 0.9 - - + -
79V ILE* 3.5 36.3 - - + -
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Residues in contact with HIS 28 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24V GLN* 3.0 33.1 + - + +
25V TYR 3.7 0.9 - - - +
27V LEU* 1.3 70.4 - - - +
29V ALA* 1.3 63.0 + - - +
31V MET* 3.3 1.2 + - - +
32V PHE* 2.9 35.4 + + + -
44V GLU* 3.3 13.7 - - - +
78V ASN 4.2 1.7 + - - -
79V ILE* 2.7 49.1 + - + +
86V MET* 3.3 38.6 + - + +
90V ASP* 3.0 40.7 + - - -
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Residues in contact with ALA 29 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25V TYR 2.9 15.1 + - - +
26V PHE* 3.2 10.3 + - + +
28V HIS* 1.3 71.2 - - - +
30V ARG* 1.3 62.7 + - + +
32V PHE* 3.2 3.6 + - - +
33V LYS 2.8 24.6 + - - -
41V ASN* 3.1 24.4 - - - +
44V GLU* 3.9 9.7 - - + +
45V TYR* 3.5 36.3 - - + +
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Residues in contact with ARG 30 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56U ASP* 2.9 38.2 + - - +
59U ILE* 3.9 24.0 - - + -
60U GLU* 3.2 21.8 + - + +
63U LEU* 3.9 9.9 - - + +
26V PHE* 3.1 30.0 + - + +
27V LEU 4.1 0.9 - - - +
29V ALA* 1.3 77.7 - - - +
31V MET* 1.3 55.4 + - - +
33V LYS* 3.5 13.1 - - - +
34V ASN* 2.9 29.6 + - - +
41V ASN* 2.9 29.8 + - - +
45V TYR* 3.7 39.7 - - - +
200V HEM 5.2 0.2 - - - +
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Residues in contact with MET 31 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63U LEU* 4.2 23.1 - - + -
68U LEU* 5.6 8.5 - - + -
27V LEU* 2.9 34.2 + - + +
28V HIS* 3.5 3.8 - - - +
30V ARG* 1.3 72.0 - - - +
32V PHE* 1.3 65.5 + - - +
34V ASN* 3.2 7.3 + - - +
35V TRP* 3.1 50.7 + - + -
79V ILE* 3.8 22.4 - - + -
80V GLY 4.2 14.1 - - - +
81V GLU* 5.5 1.3 - - - +
86V MET* 3.6 27.6 - - + -
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Residues in contact with PHE 32 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28V HIS* 2.9 28.5 + - + -
29V ALA* 3.6 4.7 - - - +
31V MET* 1.3 70.7 - - - +
33V LYS* 1.3 60.9 + - - +
35V TRP* 3.2 20.7 + + - -
37V LEU* 2.9 39.2 + - + +
40V LEU* 3.7 34.1 - - + -
41V ASN 3.7 12.8 - - - +
44V GLU* 3.8 28.0 - - + -
83V VAL* 4.1 19.5 - - + -
86V MET* 3.7 34.1 - - + -
87V LEU* 3.7 22.7 - - + -
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Residues in contact with LYS 33 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60U GLU* 3.4 37.3 + - - -
29V ALA 2.8 11.0 + - - +
30V ARG* 3.5 19.5 - - - +
31V MET 3.2 0.2 - - - -
32V PHE* 1.3 71.9 - - - +
34V ASN* 1.3 63.3 + - - +
36V GLY* 2.9 16.3 + - - -
37V LEU 4.8 2.5 - - - +
38V LYS* 5.4 6.4 - - + +
41V ASN* 3.4 42.5 - - + +
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Residues in contact with ASN 34 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132E ASP* 4.4 11.1 - - - +
136E THR* 3.7 17.0 + - - +
63U LEU* 3.9 33.8 + - + +
64U PHE* 4.2 16.7 + - - +
30V ARG 2.9 17.6 + - - +
31V MET* 3.2 5.8 + - - +
33V LYS* 1.3 75.8 - - - +
35V TRP* 1.3 72.5 + - - +
36V GLY 3.2 1.3 + - - -
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Residues in contact with TRP 35 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E THR* 3.8 7.1 - - - +
139E ASP* 5.8 2.2 - - - +
140E LEU* 3.3 24.1 - - - +
143E LYS* 3.5 27.8 + - - +
31V MET* 3.1 33.1 + - + -
32V PHE* 3.7 15.0 - + - +
33V LYS 3.2 0.6 + - - -
34V ASN* 1.3 88.3 - - - +
36V GLY* 1.3 58.4 + - - +
37V LEU* 3.6 27.0 + - + +
81V GLU 3.9 19.3 - - - -
82V ASP* 4.6 2.0 - - - -
83V VAL* 4.1 16.4 - - + -
86V MET* 3.4 37.5 - - + -
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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