Contacts of the helix formed by residues 42 - 71 (chain I) 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 I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I ARG* 3.6 2.6 + - - +
40I LYS* 4.0 4.0 - - - +
41I TYR* 1.3 79.7 - - - +
43I ASP* 1.3 66.1 + - - +
44I GLU* 3.9 5.8 - - + +
45I SER* 3.0 34.4 + - - +
46I GLU* 3.1 10.4 + - - +
157I ASN* 3.8 32.5 - - + +
159I ASP* 4.9 0.8 + - + -
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Residues in contact with ASP 43 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I ARG* 3.0 25.4 + - - +
42I VAL* 1.3 73.1 - - - +
44I GLU* 1.3 56.9 + - - +
46I GLU* 3.3 11.5 + - - +
47I SER* 2.9 37.0 + - - +
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Residues in contact with GLU 44 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I VAL* 3.1 6.0 - - + +
43I ASP* 1.3 77.8 - - - +
45I SER* 1.3 58.5 + - - +
47I SER* 3.4 5.9 + - - -
48I ALA* 2.9 28.8 + - + +
153I VAL* 3.8 21.9 - - + +
156I LYS* 6.2 1.1 - - - +
157I ASN* 2.7 40.2 + - - +
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Residues in contact with SER 45 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I TYR* 3.9 17.5 - - - -
42I VAL* 3.0 19.9 + - - +
44I GLU* 1.3 75.9 - - - +
46I GLU* 1.3 65.3 + - - +
48I ALA* 3.1 6.6 + - - +
49I VAL* 2.9 27.7 + - - +
153I VAL* 4.7 1.6 - - - -
154I ALA* 4.7 2.1 - - - -
157I ASN* 3.5 20.8 + - - +
159I ASP* 4.1 8.4 + - - +
162I LEU* 3.8 25.8 - - - +
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Residues in contact with GLU 46 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I ARG* 3.6 24.1 + - - +
41I TYR* 3.7 22.9 - - + -
42I VAL 3.1 10.3 + - - +
43I ASP* 3.6 16.6 - - - +
45I SER* 1.3 77.1 - - - +
47I SER* 1.3 64.1 + - - +
49I VAL 3.3 0.3 + - - -
50I ASN* 3.1 16.5 + - - +
102I GLN* 3.0 37.0 + - - +
107I GLY* 3.4 6.9 - - - -
108I LYS* 2.7 34.9 + - - +
110I LYS* 5.6 1.9 + - - -
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Residues in contact with SER 47 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I ASP* 2.9 21.9 + - - +
44I GLU* 3.7 7.2 - - - -
46I GLU* 1.3 77.6 + - - +
48I ALA* 1.3 58.5 + - - +
50I ASN* 3.2 10.9 + - - +
51I GLU* 2.9 34.2 + - - +
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Residues in contact with ALA 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I GLU 2.9 17.9 + - - +
45I SER* 3.1 3.8 + - - +
47I SER* 1.3 76.7 - - - +
49I VAL* 1.3 62.4 + - - +
51I GLU* 3.3 11.0 + - - +
52I GLN* 3.0 22.5 + - - +
149I ASN* 6.1 0.9 - - - +
150I LEU* 3.5 25.4 - - + +
153I VAL* 4.0 23.3 - - + -
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Residues in contact with VAL 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41I TYR* 3.4 20.2 - - - +
45I SER 2.9 14.5 + - - +
46I GLU 3.7 4.5 - - - +
48I ALA* 1.3 75.8 - - - +
50I ASN* 1.3 59.3 + - - +
52I GLN* 3.2 7.0 + - - +
53I ILE* 2.9 30.9 + - + +
98I LEU* 3.9 32.1 - - + +
101I TYR* 4.6 4.9 - - + -
102I GLN* 3.8 20.4 - - + +
150I LEU* 4.2 12.1 - - + -
162I LEU* 3.9 27.1 - - + -
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Residues in contact with ASN 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I GLU* 3.1 17.2 + - - +
47I SER* 3.5 11.2 - - - +
49I VAL* 1.3 77.0 - - - +
51I GLU* 1.3 61.8 + - - +
53I ILE* 3.3 14.3 + - - +
54I ASN* 3.2 17.8 + - - +
102I GLN* 3.0 18.9 + - - +
108I LYS 3.1 20.4 + - - -
109I VAL* 3.4 4.2 - - - -
110I LYS* 3.0 47.5 + - + +
112I GLN* 3.8 14.3 - - - +
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Residues in contact with GLU 51 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 3.0 53.0 - - - +
15D PHE* 5.5 0.9 - - - +
47I SER* 2.9 22.0 + - - +
48I ALA* 3.5 11.2 - - - +
49I VAL 3.2 0.2 - - - -
50I ASN* 1.3 76.0 - - - +
52I GLN* 1.3 58.2 + - - +
54I ASN* 3.1 6.6 + - - +
55I VAL* 3.0 31.3 + - + +
112I GLN* 3.4 9.1 - - - +
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Residues in contact with GLN 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48I ALA 3.0 13.7 + - - +
49I VAL* 3.2 6.7 + - - +
51I GLU* 1.3 73.6 - - - +
53I ILE* 1.3 66.8 + - - +
55I VAL* 3.1 18.9 + - - +
56I GLU* 3.0 49.2 + - - +
98I LEU* 3.6 21.8 - - + -
143I THR* 4.0 5.9 + - - +
146I LYS* 3.3 29.0 - - - +
147I LEU* 3.5 29.2 - - + +
150I LEU* 3.9 17.7 - - + +
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Residues in contact with ILE 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49I VAL* 2.9 24.3 + - + +
50I ASN* 3.6 24.7 - - - +
51I GLU 3.3 0.2 - - - -
52I GLN* 1.3 75.2 - - - +
54I ASN* 1.3 58.4 - - - +
56I GLU* 3.4 2.6 + - - +
57I TYR* 3.0 29.6 + - + +
95I ALA* 3.9 12.3 - - + +
98I LEU* 3.6 28.0 - - + +
99I MET* 3.7 46.4 - - + +
102I GLN* 4.7 0.2 - - + -
109I VAL* 4.3 8.1 - - + -
110I LYS 6.0 0.9 - - - +
111I LEU* 3.8 21.5 - - + -
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Residues in contact with ASN 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ILE* 3.5 19.8 - - + +
15D PHE* 3.9 8.8 + - - +
61E TYR* 4.1 6.0 + - - -
50I ASN 3.2 5.8 + - - +
51I GLU 3.1 9.7 + - - +
53I ILE* 1.3 78.2 - - - +
55I VAL* 1.3 58.9 + - - +
57I TYR* 4.4 3.3 - - - +
58I ASN* 2.9 52.2 + - - +
112I GLN* 3.3 43.8 + - + +
113I SER 3.1 25.5 + - - +
114I ILE* 4.3 2.6 - - - +
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Residues in contact with VAL 55 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 4.0 33.5 - - + -
51I GLU* 3.0 20.7 + - + +
52I GLN* 3.1 28.5 + - - +
54I ASN* 1.3 77.4 - - - +
56I GLU* 1.3 63.2 + - - +
58I ASN* 3.3 2.6 + - - +
59I VAL* 3.0 24.1 + - + +
142I LEU* 5.8 0.4 - - + -
143I THR* 4.3 17.7 - - + +
146I LYS* 4.1 35.0 - - + +
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Residues in contact with GLU 56 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I GLN* 3.0 38.5 + - - +
55I VAL* 1.3 72.6 - - - +
57I TYR* 1.3 66.1 + - - +
59I VAL* 3.3 3.4 + - - +
60I SER* 2.9 23.9 + - - -
91I GLU* 3.2 17.4 - - - +
94I HIS* 3.6 13.0 - - + +
95I ALA* 3.8 24.0 - - + +
98I LEU* 4.0 15.5 - - + -
143I THR* 3.5 13.1 - - - +
147I LEU* 4.0 11.3 - - - +
170I TYR* 4.4 4.7 - - - -
214I CA 2.4 27.8 - - - -
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Residues in contact with TYR 57 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E TYR* 5.3 13.0 - + - -
60E SER* 4.9 2.4 + - - -
61E TYR* 3.6 40.0 - + - +
64E HIS* 2.7 40.8 + + - +
88E SER* 4.5 1.9 + - - -
53I ILE* 3.0 16.3 + - + +
54I ASN* 3.9 6.5 - - - +
56I GLU* 1.3 77.3 - - - +
58I ASN* 1.3 63.4 + - - +
60I SER* 3.3 13.3 + - - -
61I TYR* 3.1 22.3 + + + +
92I ARG* 3.7 26.1 + - + +
95I ALA* 3.8 21.9 - - + +
99I MET* 4.5 5.8 - - - -
111I LEU* 4.6 9.2 - - + -
114I ILE* 3.6 25.7 - - + +
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Residues in contact with ASN 58 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 3.6 29.5 + - + +
17D PRO* 3.8 8.9 - - + +
54I ASN* 2.9 47.4 + - - +
55I VAL 3.6 0.2 - - - +
56I GLU 3.2 0.2 - - - -
57I TYR* 1.3 78.6 - - - +
59I VAL* 1.3 57.3 + - - +
61I TYR* 3.1 7.5 + - - +
62I VAL* 3.0 32.7 + - - +
113I SER 4.0 3.8 - - - +
114I ILE* 3.6 11.0 - - - +
115I VAL* 3.5 41.6 + - - +
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Residues in contact with VAL 59 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D PHE* 5.0 8.3 - - + -
17D PRO* 5.9 0.9 - - + -
55I VAL* 3.0 21.1 + - + +
56I GLU* 3.3 1.7 + - - +
58I ASN* 1.3 72.2 - - - +
60I SER* 1.3 66.5 + - - +
62I VAL* 3.3 7.6 + - - +
63I TYR* 3.0 46.5 + - + -
91I GLU* 3.4 22.9 - - - +
139I LEU* 4.3 25.8 - - + +
140I GLU* 4.5 3.4 - - - +
142I LEU* 6.0 0.9 - - + -
143I THR* 3.5 23.8 - - - +
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Residues in contact with SER 60 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E TYR* 5.0 2.1 + - - -
92E ARG* 4.5 4.3 + - - -
56I GLU 2.9 14.4 + - - -
57I TYR* 3.3 16.4 + - - -
59I VAL* 1.3 77.4 - - - +
61I TYR* 1.3 57.4 + - - +
63I TYR 3.4 0.3 + - - -
64I HIS* 3.0 14.7 + - - +
88I SER* 2.7 51.5 + - - +
91I GLU* 3.6 16.0 - - - +
92I ARG* 3.7 17.8 - - - +
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Residues in contact with TYR 61 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54E ASN* 4.2 4.9 + - - -
57E TYR* 3.6 49.4 - + - +
111E LEU* 3.6 20.2 - - + +
112E GLN 2.6 38.1 + - - -
114E ILE* 3.8 18.3 - - + +
57I TYR* 3.1 12.5 + + + +
58I ASN 3.1 8.5 + - - +
60I SER* 1.3 75.5 - - - +
62I VAL* 1.3 60.5 + - + +
64I HIS* 3.1 6.6 + - + +
65I ALA* 3.0 26.9 + - - +
114I ILE* 3.4 30.7 - - + -
115I VAL 3.8 3.6 - - - -
117I PRO* 3.6 30.7 - - + -
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Residues in contact with VAL 62 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D PRO* 4.0 21.8 - - + -
18D PHE* 3.7 38.8 - - + -
58I ASN 3.0 20.0 + - - +
59I VAL* 3.3 7.6 + - - +
61I TYR* 1.3 77.1 - - + +
63I TYR* 1.3 55.8 + - - +
65I ALA* 3.0 5.0 + - - +
66I MET* 2.9 37.1 + - + +
117I PRO* 4.2 12.6 - - + -
121I PHE* 5.0 0.7 - - + -
139I LEU* 3.5 28.9 - - + -
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Residues in contact with TYR 63 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59I VAL* 3.0 36.4 + - + +
60I SER 3.7 4.7 - - - +
62I VAL* 1.3 76.0 - - - +
64I HIS* 1.3 57.6 + - - +
66I MET* 3.2 13.0 + - - +
67I PHE* 2.8 28.6 + - - +
83I PHE* 5.4 0.9 - + - -
84I PHE* 3.6 39.6 - + - +
87I SER* 3.7 20.9 - - - -
88I SER 3.7 4.5 - - - +
91I GLU* 3.6 20.6 - - + -
136I ALA* 3.7 29.9 + - + -
139I LEU* 4.6 6.8 - - + +
140I GLU* 2.4 41.6 + - - +
181I ILE* 3.9 7.6 - - + +
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Residues in contact with HIS 64 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E TYR* 2.7 34.7 + + - +
92E ARG* 3.7 17.5 + - + -
96E GLU* 2.7 42.0 + - + +
99E MET* 3.6 29.0 - - + +
111E LEU* 4.1 8.1 - - + -
60I SER 3.0 8.4 + - - +
61I TYR 3.1 9.2 + - - +
63I TYR* 1.3 76.9 - - - +
65I ALA* 1.3 61.9 + - - +
67I PHE* 3.3 19.8 + + + +
68I ALA 3.0 17.8 + - - -
85I LYS* 5.0 2.9 - - + -
88I SER* 3.5 20.3 + - - +
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Residues in contact with ALA 65 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E LEU* 3.6 13.1 - - + +
61I TYR 3.0 12.4 + - - +
62I VAL* 3.0 8.9 + - - +
64I HIS* 1.3 77.5 - - - +
66I MET* 1.3 61.3 + - - +
68I ALA* 3.2 7.3 + - - +
69I TYR* 3.1 17.5 + - - +
117I PRO* 3.9 16.6 - - + -
118I LEU 3.4 25.1 - - - +
119I SER* 4.5 4.6 - - - +
121I PHE* 3.8 9.8 - - + -
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Residues in contact with MET 66 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I VAL* 2.9 29.9 + - - +
63I TYR* 3.2 25.8 + - - +
65I ALA* 1.3 73.6 - - - +
67I PHE* 1.3 66.0 + - - +
69I TYR* 3.2 2.1 + - - +
70I PHE* 3.1 31.2 + - + -
84I PHE* 3.4 40.8 - - + -
121I PHE* 3.5 33.0 - - + -
132I ALA* 3.1 39.7 - - + +
135I LEU* 4.6 4.7 - - + -
136I ALA* 4.3 4.3 - - + +
139I LEU* 4.7 6.1 - - - -
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Residues in contact with PHE 67 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E GLU* 4.4 12.3 - - + -
99E MET* 4.1 13.5 - - + -
100E GLU* 4.0 20.9 - - + -
63I TYR 2.8 13.9 + - - +
64I HIS* 3.4 24.9 - + - +
66I MET* 1.3 77.1 - - - +
68I ALA* 1.3 69.7 + - - +
70I PHE* 3.2 1.4 + - - -
71I ASP* 3.0 47.0 + - + +
81I ALA* 3.3 28.8 - - + +
84I PHE* 3.7 7.9 - - - +
85I LYS* 3.6 54.3 - - + +
----------------------------------------------------------
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Residues in contact with ALA 68 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E MET* 4.0 10.1 - - + -
103E ASN* 3.0 26.8 + - - +
109E VAL* 3.7 39.4 - - + +
64I HIS 3.0 13.2 + - - +
65I ALA* 3.2 10.9 + - - +
67I PHE* 1.3 82.8 - - + +
69I TYR* 1.3 62.6 + - - +
72I ARG* 3.6 9.9 + - - +
----------------------------------------------------------
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Residues in contact with TYR 69 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65I ALA 3.1 6.0 + - - +
66I MET 3.6 6.7 - - - +
67I PHE 3.1 0.2 - - - -
68I ALA* 1.3 77.0 - - - +
70I PHE* 1.3 94.7 + + - +
71I ASP 3.1 0.2 - - - -
72I ARG* 3.2 62.8 + - - +
75I VAL* 3.6 29.1 - - + +
119I SER 3.6 10.0 + - - +
120I ASP* 3.5 8.4 + - - -
121I PHE* 3.5 45.8 - + + -
122I ASP* 3.2 32.6 - - - +
128I ASP* 4.1 7.1 + - + +
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Residues in contact with PHE 70 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66I MET* 3.1 30.1 + - + +
67I PHE 3.8 0.2 - - - -
69I TYR* 1.3 92.7 - + - +
71I ASP* 1.3 57.2 + - - +
72I ARG 3.3 2.0 + - - -
75I VAL* 3.6 17.0 - - + -
76I ALA* 3.8 5.0 + - - -
77I LEU* 3.5 40.1 + - + +
78I ARG* 5.2 0.3 - - - +
80I LEU* 3.7 19.1 - - + -
81I ALA* 3.9 24.8 - - - +
84I PHE* 3.7 16.8 - + - -
121I PHE* 4.4 6.7 - - + -
128I ASP* 3.6 34.8 - - + -
132I ALA* 3.4 35.0 - - + -
----------------------------------------------------------
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Residues in contact with ASP 71 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LYS* 3.0 33.4 + - - -
183B GLU* 4.5 2.0 - - - +
100E GLU* 4.1 12.5 - - - +
103E ASN* 2.9 33.6 + - - +
67I PHE* 3.0 44.5 + - + +
69I TYR 3.1 0.4 - - - -
70I PHE* 1.3 75.0 - - - +
72I ARG* 1.3 63.9 + - - +
76I ALA* 5.7 0.2 - - - -
81I ALA* 4.0 7.6 - - + +
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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