Contacts of the helix formed by residues 72 - 96 (chain F) in PDB entry 5JRE
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 PHE 72 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109E TRP* 3.9 34.3 - + - -
15F LEU* 3.3 37.7 - - + -
18F LYS* 4.8 1.1 - - + -
19F LYS* 3.8 36.8 - - + -
22F ILE* 3.9 15.2 - - + +
66F LEU* 3.5 7.3 - - - +
69F TYR* 2.9 24.6 + + + +
71F MET* 1.3 108.8 - - + +
73F TYR* 1.3 64.7 + - - +
74F SER 3.2 2.7 - - - +
75F ASN* 3.0 34.1 + - + +
76F GLY 3.4 6.6 + - - -
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Residues in contact with TYR 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E PRO* 3.8 23.3 - - + +
71E MET* 3.5 41.5 - - + +
73E TYR* 5.6 0.4 - - + -
66F LEU* 3.8 33.1 - - + +
69F TYR 3.9 0.8 + - - -
70F PRO* 3.1 21.9 + - + +
71F MET 3.5 0.2 - - - -
72F PHE* 1.3 77.8 - - - +
74F SER* 1.3 67.8 + - - +
76F GLY* 3.1 12.8 + - - -
77F PHE* 3.1 36.6 + + - -
80F LEU* 5.9 0.9 - - + -
107F ASP* 2.7 37.3 + - - -
109F TRP* 4.3 0.8 - + - +
110F VAL* 3.6 13.7 + - + +
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Residues in contact with SER 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E SER* 5.9 7.4 - - - -
71F MET 4.5 6.8 + - - -
73F TYR* 1.3 86.0 - - - +
75F ASN* 1.3 72.3 + - - +
76F GLY 3.4 0.3 + - - -
77F PHE* 3.5 16.8 + - - +
78F ILE* 4.8 5.2 + - - +
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Residues in contact with ASN 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19F LYS* 3.7 25.5 - - + +
22F ILE* 4.0 11.7 - - + +
23F VAL* 3.8 27.1 - - + +
26F SER* 3.7 17.7 + - - -
71F MET 4.3 0.9 - - - +
72F PHE* 3.0 38.7 + - + +
74F SER* 1.3 83.0 + - - +
76F GLY* 1.3 57.6 + - - +
77F PHE 3.5 0.2 - - - -
78F ILE* 5.3 0.6 + - - -
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Residues in contact with GLY 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F ILE* 3.8 15.5 - - - +
26F SER* 3.9 3.7 + - - -
62F GLN* 3.9 13.2 + - - -
66F LEU* 4.3 11.9 - - - -
72F PHE 3.4 3.8 + - - -
73F TYR 3.1 7.6 + - - -
75F ASN* 1.3 77.9 - - - +
77F PHE* 1.3 65.2 + - - +
78F ILE 3.4 2.1 + - - -
79F GLY* 3.4 2.9 + - - -
80F LEU* 3.3 22.9 + - - +
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Residues in contact with PHE 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66F LEU* 5.5 0.7 - - - -
73F TYR* 3.1 37.3 + + - +
74F SER* 3.5 18.2 + - - +
75F ASN 3.5 0.2 - - - -
76F GLY* 1.3 77.4 - - - +
78F ILE* 1.3 68.8 + - + +
80F LEU* 3.1 7.3 + - - +
81F GLN* 2.9 49.5 + - + +
109F TRP* 3.7 17.9 - + - -
110F VAL* 3.4 28.9 - - + +
113F PHE* 3.7 42.4 - + + -
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Residues in contact with ILE 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F SER* 4.4 5.3 + - - +
30F SER* 5.7 3.1 - - - -
74F SER 5.2 4.7 - - - +
75F ASN 5.3 0.6 + - - -
76F GLY 3.4 0.6 - - - -
77F PHE* 1.3 86.9 - - + +
79F GLY* 1.3 58.5 + - - +
81F GLN* 3.2 22.4 + - - +
82F GLU* 2.9 48.5 + - + +
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Residues in contact with GLY 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F SER* 3.0 39.2 + - - -
29F MET* 3.4 24.3 - - - +
30F SER* 4.7 1.8 - - - -
76F GLY 3.4 1.5 + - - -
77F PHE 3.3 0.6 - - - -
78F ILE* 1.3 78.4 - - - +
80F LEU* 1.3 56.5 + - - +
82F GLU* 3.4 6.3 + - - +
83F TYR* 3.0 21.7 + - - +
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Residues in contact with LEU 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F MET* 3.8 20.6 - - + -
59F ALA* 4.3 4.3 - - - +
62F GLN* 4.3 10.1 - - + -
63F ILE* 3.8 35.4 - - + -
66F LEU* 3.6 31.9 - - + -
73F TYR* 5.9 1.3 - - + -
76F GLY 3.3 8.9 + - - +
77F PHE* 3.1 8.3 + - - +
79F GLY* 1.3 73.6 - - - +
81F GLN* 1.3 65.7 + - - +
83F TYR* 3.2 15.5 + - + +
84F VAL* 3.0 26.9 + - - +
106F VAL* 4.4 3.8 - - + -
110F VAL* 4.1 24.0 - - + -
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Residues in contact with GLN 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77F PHE* 2.9 37.7 + - + +
78F ILE* 3.2 23.5 + - - +
80F LEU* 1.3 77.5 - - - +
82F GLU* 1.3 59.9 + - + +
84F VAL 3.3 1.8 + - - +
85F GLU* 3.1 24.6 + - - +
110F VAL* 4.5 9.7 - - + +
113F PHE* 3.5 19.1 + - - +
114F GLY* 3.6 24.8 - - - +
117F ASP* 2.7 27.2 + - - +
165F LYS* 3.8 12.1 - - - +
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Residues in contact with GLU 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F SER* 3.3 18.9 + - - +
33F SER* 3.0 32.5 + - - +
34F LYS* 2.8 34.7 + - - +
78F ILE* 2.9 36.4 + - + +
79F GLY 3.8 4.7 - - - +
80F LEU 3.3 0.2 - - - -
81F GLN* 1.3 75.8 - - + +
83F TYR* 1.3 59.3 + - - +
85F GLU* 3.4 16.6 + - - +
86F ALA* 3.0 24.8 + - - +
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Residues in contact with TYR 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F MET* 3.7 11.4 - - + -
33F SER* 4.4 0.6 - - - -
55F LEU* 3.8 21.8 - - + -
56F THR* 4.1 22.0 + - - +
59F ALA* 3.6 32.0 - - + +
63F ILE* 4.8 1.1 - - + +
79F GLY 3.0 14.1 + - - +
80F LEU* 3.3 20.2 - - + +
82F GLU* 1.3 73.4 - - - +
84F VAL* 1.3 67.8 + - + +
86F ALA* 3.4 0.7 + - - +
87F LEU* 3.0 52.3 + - + +
103F GLU 4.9 0.2 + - - -
104F LEU* 2.7 49.3 + - + +
106F VAL* 3.8 15.3 - - + -
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Residues in contact with VAL 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80F LEU 3.0 17.5 + - - +
81F GLN 3.3 7.6 + - - +
83F TYR* 1.3 77.2 - - + +
85F GLU* 1.3 57.8 + - - +
87F LEU* 3.9 0.5 - - - +
88F ALA* 2.9 29.9 + - + +
104F LEU* 3.9 25.1 - - + +
106F VAL* 3.9 20.9 - - + -
110F VAL* 3.9 22.0 - - + -
111F TYR* 3.9 28.3 - - + +
114F GLY* 4.1 2.7 - - - -
115F ILE* 4.0 17.5 - - + +
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Residues in contact with GLU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F SER* 5.7 0.7 - - - -
37F ILE* 3.9 9.8 - - + +
81F GLN* 3.1 16.4 + - - +
82F GLU* 3.7 20.2 - - - +
83F TYR 3.3 0.2 - - - -
84F VAL* 1.3 78.4 - - - +
86F ALA* 1.3 61.0 + - - +
88F ALA* 3.5 2.4 + - - +
89F LEU* 3.1 21.8 + - - +
114F GLY 3.8 13.4 + - - +
117F ASP* 3.8 38.7 - - + +
118F ILE* 3.9 8.9 - - + +
121F GLU* 2.9 40.6 - - + +
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Residues in contact with ALA 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F SER* 3.8 32.8 - - - +
36F LEU* 4.0 18.3 - - + +
37F ILE* 3.9 15.7 - - + +
40F MET* 5.9 0.2 - - - +
55F LEU* 4.2 2.7 - - + -
82F GLU 3.0 19.0 + - - +
83F TYR 3.9 3.1 - - - +
85F GLU* 1.3 75.1 - - - +
87F LEU* 1.3 60.1 + - - +
89F LEU* 3.3 3.6 + - - +
90F TYR* 2.9 27.7 + - - +
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Residues in contact with LEU 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LEU* 4.0 9.9 - - + -
52F LYS* 3.7 35.9 - - + -
55F LEU* 3.7 18.8 - - + -
56F THR* 4.5 8.3 - - - +
83F TYR* 3.0 50.6 + - + +
84F VAL 4.1 1.1 - - - +
86F ALA* 1.3 73.8 - - - +
88F ALA* 1.3 60.2 + - - +
90F TYR* 3.2 5.8 + - + +
91F TYR* 2.9 48.9 + - + -
99F PRO* 4.4 0.9 - - - -
104F LEU* 3.7 22.2 - - + -
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Residues in contact with ALA 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84F VAL* 2.9 19.7 + - + +
85F GLU 3.6 0.2 - - - +
87F LEU* 1.3 79.4 - - - +
89F LEU* 1.3 56.4 + - - +
91F TYR* 3.4 0.9 + - - -
92F TYR* 2.8 29.8 + - - +
97F ARG 4.0 3.5 - - - +
98F ILE* 4.1 8.9 - - + +
99F PRO* 3.7 22.1 - - + +
115F ILE* 4.1 14.1 - - + -
118F ILE* 3.6 25.1 - - + -
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Residues in contact with LEU 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37F ILE* 3.7 43.7 - - + +
40F MET* 4.7 2.9 - - + -
41F ILE* 4.4 6.7 - - + -
85F GLU 3.1 14.4 + - - +
86F ALA* 3.6 8.3 - - - +
87F LEU 3.3 0.2 - - - -
88F ALA* 1.3 71.9 - - - +
90F TYR* 1.3 67.9 + - - +
92F TYR* 3.6 6.0 - - + +
93F ILE* 3.0 50.7 + - + +
118F ILE* 4.9 4.4 - - + +
121F GLU* 3.9 37.9 - - + +
122F ILE* 4.2 17.0 - - + -
125F LYS* 5.0 1.6 - - + -
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Residues in contact with TYR 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36F LEU* 4.1 12.8 - - + -
40F MET* 3.6 42.1 - - + +
48F ALA* 4.6 4.3 - - + -
49F ASP* 2.7 28.3 + - - -
52F LYS* 3.4 43.4 + - + +
86F ALA 2.9 14.0 + - - +
87F LEU* 3.3 13.7 - - + +
89F LEU* 1.3 78.0 - - - +
91F TYR* 1.3 77.6 + + - +
94F LYS* 2.9 72.5 + - + +
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Residues in contact with TYR 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F LYS* 3.4 25.1 + - - -
87F LEU* 2.9 45.6 + - + +
90F TYR* 1.3 90.8 - + - +
92F TYR* 1.3 62.9 + - - +
94F LYS* 4.6 1.1 - - - -
95F GLU* 2.9 50.2 + - + +
96F ASN 3.0 6.4 + - - -
97F ARG* 3.1 45.9 + - + +
99F PRO* 4.0 25.4 - - + -
103F GLU* 4.3 11.9 + - + +
104F LEU* 5.1 2.9 - - + -
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Residues in contact with TYR 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 3.9 27.6 - - + -
88F ALA 2.8 19.6 + - - +
89F LEU* 3.2 9.2 + - + +
91F TYR* 1.3 77.6 - - - +
93F ILE* 1.3 64.9 + - + +
96F ASN* 3.1 30.5 + - - +
97F ARG 3.1 15.0 + - - +
98F ILE* 4.2 9.0 - - + -
118F ILE* 6.1 0.2 - - + -
122F ILE* 3.9 36.8 - - + -
125F LYS* 5.9 0.7 - - + -
137F TYR* 3.6 26.4 + + - -
140F LYS* 4.2 5.7 + - - +
141F ALA* 3.6 16.5 + - - +
144F ASP* 2.6 37.3 + - + +
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Residues in contact with ILE 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F MET* 3.8 36.1 - - + +
41F ILE* 4.7 0.7 - - - +
45F TYR* 3.8 23.3 - - + +
89F LEU* 3.0 46.2 + - + +
92F TYR* 1.3 82.6 - - + +
94F LYS* 1.3 63.6 + - - +
96F ASN* 4.5 1.0 + - - -
125F LYS* 4.0 30.3 - - + -
137F TYR* 4.0 20.6 - - + +
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Residues in contact with LYS 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40F MET* 4.5 8.3 - - + -
45F TYR* 6.3 0.9 - - - -
49F ASP* 5.0 2.5 + - - -
90F TYR* 2.9 57.2 + - + +
91F TYR* 5.6 0.6 - - - -
93F ILE* 1.3 81.9 - - - +
95F GLU* 1.3 81.1 + - + +
96F ASN 3.7 0.4 - - - -
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Residues in contact with GLU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91F TYR* 2.9 34.2 + - + +
94F LYS* 1.3 101.9 + - + +
96F ASN* 1.3 72.9 + - - +
97F ARG* 2.8 46.5 + - - +
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Residues in contact with ASN 96 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1E MET* 5.8 2.3 - - - +
91F TYR 3.0 2.6 + - - -
92F TYR* 3.1 25.3 + - - +
93F ILE 4.5 0.8 + - - -
94F LYS 3.7 1.2 - - - -
95F GLU* 1.3 80.2 - - - +
97F ARG* 1.3 58.9 + - - +
140F LYS* 2.6 39.3 + - - +
144F ASP* 4.2 2.6 - - - +
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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