Contacts of the helix formed by residues 42 - 71 (chain V) in PDB entry 3A68
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 VAL 42 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38V ARG* 3.6 2.7 + - - +
40V LYS* 4.3 4.2 + - - +
41V TYR* 1.3 81.7 - - - +
43V ASP* 1.3 67.6 + - - +
44V GLU* 3.9 4.9 - - + +
45V SER* 3.0 34.7 + - - +
46V GLU* 3.1 10.4 + - - +
157V ASN* 3.7 34.3 - - + +
159V ASP* 4.9 0.6 + - + -
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Residues in contact with ASP 43 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38V ARG* 3.0 24.2 + - - +
42V VAL* 1.3 74.0 - - - +
44V GLU* 1.3 57.9 + - - +
46V GLU* 3.3 13.3 + - - +
47V SER* 2.9 35.9 + - - +
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Residues in contact with GLU 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42V VAL* 3.2 7.1 - - + +
43V ASP* 1.3 78.9 - - - +
45V SER* 1.3 58.3 + - - +
47V SER* 3.7 6.5 - - - -
48V ALA* 3.0 27.0 + - - +
153V VAL* 3.7 18.3 - - + +
156V LYS* 3.0 30.4 + - - +
157V ASN* 2.9 28.4 + - - +
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Residues in contact with SER 45 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41V TYR* 4.0 16.2 - - - -
42V VAL* 3.0 24.2 + - - +
44V GLU* 1.3 76.4 - - - +
46V GLU* 1.3 65.9 + - - +
48V ALA* 3.2 3.0 + - - +
49V VAL* 2.9 28.2 + - - +
153V VAL* 4.2 10.6 + - - +
154V ALA* 4.7 0.2 - - - -
157V ASN* 4.1 13.0 + - - +
159V ASP* 4.2 9.6 + - - +
162V LEU* 3.8 24.4 - - - +
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Residues in contact with GLU 46 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38V ARG* 3.6 25.4 + - - +
41V TYR* 3.7 21.4 - - + -
42V VAL 3.1 12.5 + - - +
43V ASP* 3.5 17.0 - - - +
45V SER* 1.3 75.5 - - - +
47V SER* 1.3 64.7 + - - +
49V VAL 3.3 1.2 + - - -
50V ASN* 3.1 16.6 + - - +
102V GLN* 3.0 36.3 + - - +
107V GLY* 3.5 4.2 - - - -
108V LYS* 2.8 35.6 + - - +
110V LYS* 5.5 1.5 + - - -
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Residues in contact with SER 47 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43V ASP* 2.9 21.3 + - - +
44V GLU* 3.7 8.2 - - - -
46V GLU* 1.3 79.1 + - - +
48V ALA* 1.3 57.4 + - - +
50V ASN* 3.3 10.2 + - - +
51V GLU* 2.9 27.9 + - - +
112V GLN* 5.4 0.7 + - - -
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Residues in contact with ALA 48 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44V GLU 3.0 19.1 + - - +
45V SER 3.2 3.8 + - - +
47V SER* 1.3 75.2 - - - +
49V VAL* 1.3 62.6 + - - +
51V GLU* 3.2 9.4 + - - +
52V GLN* 3.0 20.1 + - - +
150V LEU* 3.5 27.8 - - + +
153V VAL* 3.7 26.2 - - + -
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Residues in contact with VAL 49 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41V TYR* 3.3 19.1 - - - +
45V SER 2.9 12.7 + - - +
46V GLU 3.6 7.0 - - - +
47V SER 3.3 0.2 - - - -
48V ALA* 1.3 76.1 - - - +
50V ASN* 1.3 56.6 + - - +
52V GLN* 3.1 5.4 + - - +
53V ILE* 2.9 32.1 + - + +
98V LEU* 3.9 34.3 - - + +
101V TYR* 4.7 4.7 - - + -
102V GLN* 3.7 21.8 - - + +
150V LEU* 4.2 12.1 - - + -
162V LEU* 4.0 25.4 - - + -
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Residues in contact with ASN 50 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46V GLU* 3.1 16.7 + - - +
47V SER* 3.3 11.2 + - - +
49V VAL* 1.3 75.0 - - - +
51V GLU* 1.3 63.2 + - - +
53V ILE* 3.3 15.1 + - - +
54V ASN* 3.2 20.1 + - - +
102V GLN* 3.1 18.4 + - - +
108V LYS 3.0 21.4 + - - -
109V VAL* 3.4 4.9 - - - +
110V LYS* 3.0 46.3 + - + +
112V GLN* 3.9 11.6 + - - +
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Residues in contact with GLU 51 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 3.4 32.5 - - - +
15B PHE* 3.8 13.3 - - - +
47V SER 2.9 13.7 + - - +
48V ALA* 3.5 12.6 - - - +
49V VAL 3.2 0.2 - - - -
50V ASN* 1.3 76.6 - - - +
52V GLN* 1.3 62.7 + - - +
54V ASN* 3.1 6.8 + - - +
55V VAL* 3.0 28.5 + - + +
112V GLN* 3.5 19.9 + - - +
146V LYS* 5.4 7.2 + - + +
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Residues in contact with GLN 52 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48V ALA 3.0 13.9 + - - +
49V VAL 3.1 6.5 + - - +
51V GLU* 1.3 74.4 - - - +
53V ILE* 1.3 66.7 + - - +
55V VAL* 3.1 19.1 + - - +
56V GLU* 2.8 49.6 + - - +
98V LEU* 3.6 19.7 - - + -
143V THR* 3.9 5.1 + - - +
146V LYS* 3.4 29.3 - - - +
147V LEU* 3.5 30.7 - - + +
150V LEU* 3.9 17.8 - - + +
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Residues in contact with ILE 53 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49V VAL* 2.9 23.6 + - + +
50V ASN* 3.5 26.9 - - - +
52V GLN* 1.3 76.1 - - - +
54V ASN* 1.3 59.1 + - - +
56V GLU* 3.4 2.3 + - - +
57V TYR* 3.0 29.4 + - + +
95V ALA* 3.8 11.1 - - + +
98V LEU* 3.6 29.6 - - + +
99V MET* 3.7 37.5 - - + +
102V GLN* 4.7 0.7 - - + -
109V VAL* 4.4 8.1 - - + -
110V LYS 5.9 0.9 - - - +
111V LEU* 3.7 29.8 - - + -
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Residues in contact with ASN 54 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 3.0 21.6 - - - +
15B PHE* 3.7 9.7 - - - +
61L TYR* 4.1 6.5 + - - -
50V ASN 3.2 6.1 + - - +
51V GLU* 3.1 9.7 + - - +
53V ILE* 1.3 78.8 - - - +
55V VAL* 1.3 59.8 + - - +
57V TYR* 3.8 3.5 - - - +
58V ASN* 2.9 52.5 + - - +
112V GLN* 3.4 43.0 + - + +
113V SER 3.1 22.4 + - - -
114V ILE* 4.3 2.2 - - - +
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Residues in contact with VAL 55 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 4.3 27.3 - - + -
51V GLU* 3.0 33.3 + - + +
52V GLN* 3.1 33.4 + - - +
54V ASN* 1.3 76.8 - - - +
56V GLU* 1.3 62.3 + - - +
58V ASN* 3.2 3.5 + - - +
59V VAL* 3.0 23.0 + - + +
143V THR* 4.2 20.4 - - + +
146V LYS* 4.2 27.1 - - + -
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Residues in contact with GLU 56 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52V GLN* 2.8 44.6 + - - +
55V VAL* 1.3 75.0 - - - +
57V TYR* 1.3 57.4 + - - +
59V VAL* 3.2 4.5 + - - +
60V SER* 2.9 28.2 + - - -
91V GLU* 3.1 17.6 - - - +
94V HIS* 3.6 13.9 - - + +
95V ALA* 3.8 23.3 - - + +
98V LEU* 4.0 16.2 - - + -
143V THR* 3.7 11.0 - - - +
147V LEU* 4.1 9.2 - - - +
170V TYR* 4.3 6.9 - - - -
222V CA 2.4 29.0 - - - -
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Residues in contact with TYR 57 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L TYR* 5.3 12.3 - + - -
60L SER* 5.0 2.1 + - - -
61L TYR* 3.6 39.2 - + - +
64L HIS* 2.7 40.8 + + - +
88L SER* 4.6 1.6 + - - -
53V ILE* 3.0 22.6 + - + +
54V ASN* 3.9 7.0 - - - +
56V GLU* 1.3 75.8 - - - +
58V ASN* 1.3 64.4 + - - +
60V SER* 3.2 13.5 + - - -
61V TYR* 3.1 21.3 + - + +
92V ARG* 3.7 25.5 + - + -
95V ALA* 3.7 22.8 - - + +
99V MET* 4.5 6.5 - - - -
111V LEU* 4.6 2.5 - - + -
114V ILE* 3.6 25.3 - - + +
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Residues in contact with ASN 58 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 3.8 27.7 + - + +
17B PRO* 4.0 8.4 - - + +
54V ASN* 2.9 52.2 + - - +
55V VAL 3.2 4.5 + - - +
57V TYR* 1.3 78.0 - - - +
59V VAL* 1.3 56.6 + - - +
61V TYR* 3.1 3.5 + - - +
62V VAL* 3.0 32.5 + - - +
113V SER 4.1 6.9 + - - -
114V ILE* 3.3 25.0 - - - +
115V VAL* 3.6 21.3 + - - +
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Residues in contact with VAL 59 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B PHE* 5.4 3.4 - - + -
55V VAL* 3.0 18.8 + - + +
56V GLU* 3.2 2.9 + - - +
58V ASN* 1.3 74.1 - - + +
60V SER* 1.3 66.0 + - - +
62V VAL* 3.2 2.1 + - - +
63V TYR* 3.0 39.7 + - + -
91V GLU* 3.2 31.9 - - - +
139V LEU* 4.0 32.3 - - + -
140V GLU* 4.1 6.5 - - - +
143V THR* 3.4 26.0 - - - +
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Residues in contact with SER 60 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L TYR* 4.9 3.0 + - - -
92L ARG* 4.4 4.2 + - - -
56V GLU 2.9 10.2 + - - -
57V TYR* 3.2 17.2 + - - -
59V VAL* 1.3 78.0 - - - +
61V TYR* 1.3 56.2 + - - +
63V TYR 3.4 0.2 + - - -
64V HIS* 3.0 15.1 + - - +
88V SER* 2.7 50.9 + - - +
91V GLU* 3.5 20.3 - - - +
92V ARG* 3.7 18.8 + - - +
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Residues in contact with TYR 61 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L ASN* 4.2 5.2 + - - -
57L TYR* 3.5 49.5 - + - +
111L LEU* 3.5 20.4 - - + +
112L GLN 2.6 37.9 + - - -
114L ILE* 3.8 18.4 - - + +
57V TYR* 3.1 13.3 + + + +
58V ASN 3.1 8.0 + - - +
60V SER* 1.3 73.8 - - - +
62V VAL* 1.3 67.9 + - + +
64V HIS* 3.1 6.6 + - + +
65V ALA* 3.0 20.8 + - - +
114V ILE* 3.6 26.9 - - + -
115V VAL 3.9 4.5 - - - -
117V PRO* 3.6 32.0 - - + +
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Residues in contact with VAL 62 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 4.1 22.9 - - + -
18B PHE* 3.9 38.1 - - + -
58V ASN 3.0 18.3 + - - +
59V VAL 3.7 6.1 - - - +
61V TYR* 1.3 77.9 - - + +
63V TYR* 1.3 62.3 + - - +
65V ALA* 3.0 10.0 + - - +
66V MET* 2.9 34.9 + - + +
117V PRO* 4.3 7.9 - - + -
121V PHE* 5.2 0.4 - - + -
139V LEU* 3.6 24.7 - - + -
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Residues in contact with TYR 63 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59V VAL* 3.0 33.7 + - + +
60V SER 3.7 4.5 - - - +
62V VAL* 1.3 77.3 - - + +
64V HIS* 1.3 58.0 + - - +
66V MET* 3.1 11.0 + - - +
67V PHE* 2.9 26.0 + - - +
83V PHE* 5.2 1.8 - + - -
84V PHE* 3.5 50.9 - + - +
87V SER* 3.7 21.3 - - - -
88V SER 3.8 4.5 - - - +
91V GLU* 3.6 20.9 - - + -
136V ALA* 3.9 20.3 + - + +
139V LEU* 5.2 4.9 - - + +
140V GLU* 2.5 40.2 + - - +
181V ILE* 3.7 11.9 - - + +
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Residues in contact with HIS 64 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57L TYR* 2.6 36.0 + + - +
92L ARG* 3.5 22.4 + - + -
96L GLU* 2.7 38.5 + - + +
99L MET* 3.6 26.3 - - + +
111L LEU* 4.2 9.9 - - + -
60V SER 3.0 8.6 + - - +
61V TYR 3.1 9.1 + - - +
63V TYR* 1.3 77.1 - - - +
65V ALA* 1.3 62.4 + - - +
67V PHE* 3.4 24.9 + + + +
68V ALA 3.0 18.4 + - - -
85V LYS* 5.0 2.0 - - - -
88V SER* 3.4 19.4 + - - +
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Residues in contact with ALA 65 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109L VAL* 6.2 0.2 - - - -
111L LEU* 3.7 12.2 - - + +
61V TYR 3.0 12.0 + - - +
62V VAL 3.3 9.0 - - - +
64V HIS* 1.3 77.1 - - - +
66V MET* 1.3 61.2 + - - +
68V ALA* 3.3 6.1 + - - +
69V TYR* 3.1 18.0 + - - +
117V PRO* 3.9 16.4 - - + -
118V LEU 3.5 24.7 - - - +
119V SER* 4.5 4.6 - - - +
121V PHE* 3.8 11.2 - - + -
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Residues in contact with MET 66 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62V VAL* 2.9 26.2 + - + +
63V TYR* 3.1 21.5 + - - +
65V ALA* 1.3 75.2 - - - +
67V PHE* 1.3 66.2 + - - +
69V TYR* 3.2 2.4 + - - +
70V PHE* 3.1 31.1 + - + -
84V PHE* 3.4 33.2 - - + -
121V PHE* 3.5 32.3 - - + -
132V ALA* 3.1 52.3 - - + +
135V LEU* 4.8 4.3 - - + -
136V ALA* 4.7 6.5 - - - +
139V LEU* 5.9 0.2 - - - -
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Residues in contact with PHE 67 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96L GLU* 4.4 16.8 - - + -
99L MET* 4.1 14.4 - - + -
100L GLU* 3.9 26.5 - - + -
103L ASN* 5.5 0.2 - - - -
63V TYR 2.9 13.5 + - - +
64V HIS* 3.5 24.2 - + - +
66V MET* 1.3 75.4 - - - +
68V ALA* 1.3 64.1 + - - +
70V PHE* 3.2 2.3 + - - +
71V ASP* 2.9 55.4 + - + +
81V ALA* 3.3 28.5 - - + +
84V PHE* 3.6 7.7 - - - +
85V LYS* 3.6 43.7 - - + +
----------------------------------------------------------
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Residues in contact with ALA 68 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99L MET* 3.8 10.8 - - + -
103L ASN* 2.9 31.9 + - - +
109L VAL* 3.7 39.1 - - + +
64V HIS 3.0 16.7 + - - +
65V ALA* 3.7 6.7 - - - +
66V MET 3.2 0.2 - - - -
67V PHE* 1.3 82.8 - - + +
69V TYR* 1.3 62.7 + - - +
71V ASP 3.8 0.7 + - - -
72V ARG* 3.7 4.3 + - - +
----------------------------------------------------------
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Residues in contact with TYR 69 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65V ALA 3.1 6.5 + - - +
66V MET 3.6 7.2 - - - +
67V PHE 3.2 0.4 - - - -
68V ALA* 1.3 77.5 - - - +
70V PHE* 1.3 84.9 + + - +
71V ASP 3.1 0.4 - - - -
72V ARG* 3.1 65.3 + - - +
75V VAL* 3.6 32.9 - - + +
119V SER 3.6 15.7 + - - +
120V ASP* 3.8 5.2 - - + -
121V PHE* 3.5 34.5 - + + -
122V ASP* 3.5 32.6 + - + +
128V ASP* 4.1 13.0 + - + +
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Residues in contact with PHE 70 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66V MET* 3.1 30.6 + - + +
69V TYR* 1.3 92.1 - + - +
71V ASP* 1.3 57.4 + - - +
72V ARG 3.2 2.1 + - - -
75V VAL* 3.6 16.6 - - + -
76V ALA* 3.8 5.2 + - - -
77V LEU* 3.5 48.2 + - + +
78V ARG* 5.2 0.2 - - - -
80V LEU* 3.7 19.1 - - + -
81V ALA* 3.9 24.5 - - - +
84V PHE* 3.7 17.5 - + - -
121V PHE* 4.5 6.1 - - + -
128V ASP* 3.6 26.5 - - + -
132V ALA* 3.3 35.2 - - + -
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Residues in contact with ASP 71 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100L GLU* 4.0 16.7 - - - +
103L ASN* 3.0 33.9 + - - +
179M LYS* 3.0 32.8 + - - -
183M GLU* 4.5 1.7 - - - +
67V PHE* 2.9 41.2 + - + +
69V TYR 3.1 0.4 - - - -
70V PHE* 1.3 76.6 - - - +
72V ARG* 1.3 60.5 + - - +
76V ALA* 5.7 0.2 - - - -
81V ALA* 4.2 7.7 - - + +
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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