Contacts of the helix formed by residues 72 - 96 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 3.3 37.5 - - + -
18C LYS* 4.9 0.9 - - + -
19C LYS* 3.7 36.6 - - + -
22C ILE* 3.9 15.0 - - + +
66C LEU* 3.4 7.7 - - - +
69C TYR* 2.9 24.6 + + + +
71C MET* 1.3 108.9 - - + +
73C TYR* 1.3 64.5 + - - +
74C SER 3.2 2.5 - - - -
75C ASN* 3.0 34.2 + - + +
76C GLY 3.4 7.3 + - - -
109D TRP* 3.8 35.2 - + - -
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Residues in contact with TYR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 3.9 32.6 - - + +
69C TYR 3.9 1.0 + - - -
70C PRO* 3.1 21.7 + - + +
71C MET 3.5 0.2 - - - -
72C PHE* 1.3 75.6 - - - +
74C SER* 1.3 67.6 + - - +
76C GLY* 3.1 12.1 + - - -
77C PHE* 3.1 37.1 + + - -
80C LEU* 5.9 0.7 - - + -
107C ASP* 2.6 36.3 + - - -
109C TRP* 4.3 0.4 - + - +
110C VAL* 3.6 14.2 + - + +
70D PRO* 3.8 28.7 - - + +
71D MET* 3.6 37.8 - - + +
73D TYR* 5.7 0.2 - - + -
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Residues in contact with SER 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C MET 4.6 6.8 + - - -
73C TYR* 1.3 85.6 - - - +
75C ASN* 1.3 70.9 + - - +
76C GLY 3.4 0.7 + - - -
77C PHE* 3.5 17.5 + - - +
78C ILE* 4.8 4.2 + - - +
74D SER* 6.2 3.6 - - - -
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Residues in contact with ASN 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LYS* 3.7 26.0 - - + +
22C ILE* 4.0 11.7 - - + +
23C VAL* 3.8 25.8 - - + +
26C SER* 3.7 17.8 + - - -
71C MET 4.3 0.9 - - - +
72C PHE* 3.0 37.7 + - + +
74C SER* 1.3 84.5 + - - +
76C GLY* 1.3 57.5 + - - +
77C PHE 3.5 0.2 - - - -
78C ILE 5.3 0.6 + - - -
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C ILE* 3.8 15.6 - - - +
26C SER* 3.9 3.7 + - - -
62C GLN* 3.8 13.5 + - - -
66C LEU* 4.3 11.9 - - - -
72C PHE 3.4 4.0 + - - -
73C TYR 3.1 7.3 + - - -
75C ASN* 1.3 77.7 - - - +
77C PHE* 1.3 65.4 + - - +
78C ILE 3.4 2.1 + - - -
79C GLY* 3.5 2.6 + - - -
80C LEU* 3.3 22.3 + - - +
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Residues in contact with PHE 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C LEU* 5.5 0.7 - - - -
73C TYR* 3.1 36.6 + + - +
74C SER* 3.5 18.7 + - - +
75C ASN 3.5 0.2 - - - -
76C GLY* 1.3 77.5 - - - +
78C ILE* 1.3 65.2 + - + +
80C LEU* 3.2 7.1 + - - +
81C GLN* 2.9 49.0 + - + +
109C TRP* 3.7 17.5 - + - -
110C VAL* 3.4 29.4 - - + -
113C PHE* 3.7 42.6 - + + -
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Residues in contact with ILE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A PHE* 5.9 7.0 - - + -
163A ARG* 5.7 11.0 - - - +
26C SER* 4.4 4.7 + - - +
30C SER* 4.1 7.2 - - - +
74C SER 4.8 3.7 + - - +
75C ASN 5.3 0.6 + - - -
76C GLY 3.5 0.6 - - - -
77C PHE* 1.3 82.1 - - + +
79C GLY* 1.3 57.7 + - - +
81C GLN* 3.3 18.1 + - - +
82C GLU* 2.9 48.1 + - + +
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Residues in contact with GLY 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C SER* 3.0 40.3 + - - -
29C MET* 3.4 22.8 - - - +
30C SER* 4.0 6.1 - - - -
76C GLY 3.5 1.5 + - - -
77C PHE 3.3 0.6 - - - -
78C ILE* 1.3 77.9 - - - +
80C LEU* 1.3 54.8 + - - +
82C GLU* 3.4 3.5 + - - +
83C TYR* 3.0 21.0 + - - +
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Residues in contact with LEU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET* 3.8 20.2 - - + -
59C ALA 4.3 4.9 - - - +
62C GLN* 4.3 9.0 - - + -
63C ILE* 3.8 36.1 - - + -
66C LEU* 3.6 31.9 - - + -
73C TYR* 5.9 1.3 - - + -
76C GLY 3.3 9.3 + - - +
77C PHE* 3.2 8.1 + - - +
79C GLY* 1.3 72.1 - - - +
81C GLN* 1.3 67.2 + - - +
83C TYR* 3.2 15.0 + - + +
84C VAL* 3.0 27.4 + - - +
106C VAL* 4.4 5.2 - - + -
110C VAL* 4.1 23.6 - - + -
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Residues in contact with GLN 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C PHE* 2.9 37.8 + - + +
78C ILE* 3.4 19.4 - - - +
80C LEU* 1.3 76.3 - - - +
82C GLU* 1.3 60.5 + - + +
84C VAL* 3.3 1.6 + - - -
85C GLU* 3.0 23.8 + - - +
110C VAL* 4.4 13.1 - - - +
113C PHE* 3.5 19.3 + - + +
114C GLY* 3.6 23.1 - - - +
117C ASP* 2.7 27.0 + - - +
165C LYS* 3.8 12.9 - - - +
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Residues in contact with GLU 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ARG* 5.5 1.0 + - - -
30C SER* 3.5 27.0 + - - +
33C SER* 3.0 24.7 + - - +
34C LYS* 2.8 34.0 + - - +
37C ILE* 5.3 0.2 - - - +
78C ILE* 2.9 33.2 + - + +
79C GLY 3.8 3.8 - - - +
81C GLN* 1.3 78.3 - - + +
83C TYR* 1.3 60.8 + - - +
85C GLU* 3.4 18.0 + - - +
86C ALA* 3.0 24.6 + - - +
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Residues in contact with TYR 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C MET* 3.7 11.2 - - + -
33C SER* 3.5 7.8 + - - -
55C LEU* 3.8 15.3 - - + -
56C THR* 4.1 13.1 - - - +
59C ALA* 3.6 30.1 - - + -
60C LYS* 4.3 10.9 - - - -
63C ILE* 4.8 1.1 - - + -
79C GLY 3.0 14.1 + - - +
80C LEU* 3.3 19.5 - - + +
82C GLU* 1.3 73.6 - - - +
84C VAL* 1.3 68.6 + - + +
86C ALA* 3.4 0.7 + - - +
87C LEU* 3.0 58.1 + - + +
103C GLU 5.0 0.3 + - - -
104C LEU* 2.8 45.7 + - + +
106C VAL* 3.9 15.7 - - + -
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Residues in contact with VAL 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU 3.0 17.3 + - - +
81C GLN 3.7 6.7 - - - +
83C TYR* 1.3 74.8 - - + +
85C GLU* 1.3 67.5 + - - +
87C LEU* 3.8 0.3 - - - +
88C ALA* 2.9 23.9 + - - +
104C LEU* 3.9 23.9 - - + +
106C VAL* 3.9 21.3 - - + -
110C VAL* 3.9 23.8 - - + +
111C TYR* 3.9 27.1 - - + +
114C GLY* 4.0 8.3 - - - -
115C ILE* 4.0 12.1 - - + +
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Residues in contact with GLU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 3.9 13.7 - - + +
81C GLN* 3.0 16.0 + - - +
82C GLU* 3.7 20.1 - - - +
83C TYR 3.3 0.2 - - - -
84C VAL* 1.3 78.5 - - - +
86C ALA* 1.3 63.6 + - - +
88C ALA* 3.6 2.1 - - - +
89C LEU* 3.1 22.3 + - - +
114C GLY 3.8 14.1 + - - +
117C ASP* 3.7 40.2 - - + +
118C ILE* 3.9 9.2 - - + +
121C GLU* 3.2 28.2 - - + +
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Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C SER* 3.9 33.2 - - - +
36C LEU* 4.0 18.0 - - + +
37C ILE* 4.0 15.9 - - + +
40C MET* 5.9 0.3 - - - +
55C LEU* 4.1 2.0 - - + -
82C GLU 3.0 18.1 + - - +
83C TYR 3.9 2.7 - - - +
84C VAL 3.2 0.2 - - - -
85C GLU* 1.3 77.4 - - - +
87C LEU* 1.3 58.2 + - - +
89C LEU* 3.3 4.7 + - - +
90C TYR* 2.9 26.5 + - - +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 4.0 11.2 - - + -
52C LYS* 4.5 15.5 - - + -
55C LEU* 3.8 18.2 - - + -
56C THR* 4.0 16.4 - - + +
83C TYR* 3.0 49.5 + - + +
84C VAL 4.1 0.9 - - - +
86C ALA* 1.3 73.1 - - - +
88C ALA* 1.3 58.8 + - - +
90C TYR* 3.2 5.1 + - + +
91C TYR* 2.9 47.9 + - + -
99C PRO* 4.4 1.1 - - - -
104C LEU* 3.6 32.8 - - + -
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Residues in contact with ALA 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C VAL 2.9 19.8 + - - +
85C GLU 3.6 0.2 - - - +
87C LEU* 1.3 77.3 - - - +
89C LEU* 1.3 56.7 + - - +
91C TYR* 3.8 0.3 - - - -
92C TYR* 2.8 30.2 + - - +
97C ARG 4.0 3.6 - - - +
98C ILE* 4.1 9.2 - - + +
99C PRO* 3.6 22.1 - - + +
115C ILE* 4.1 14.8 - - + -
118C ILE* 3.6 25.1 - - + -
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Residues in contact with LEU 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 3.7 42.4 - - + +
40C MET* 4.7 3.4 - - + -
41C ILE* 4.5 7.0 - - + -
85C GLU 3.1 14.0 + - - +
86C ALA* 3.6 8.1 - - - +
88C ALA* 1.3 73.8 - - - +
90C TYR* 1.3 67.6 + - - +
92C TYR* 3.2 5.9 + - + +
93C ILE* 3.0 50.7 + - + +
118C ILE* 4.9 4.8 - - + +
121C GLU* 3.9 38.6 - - + +
122C ILE* 4.2 16.8 - - + -
125C LYS* 5.0 1.6 - - + -
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Residues in contact with TYR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 4.0 16.6 - - + -
40C MET* 3.7 41.3 - - + +
48C ALA* 4.7 1.8 - - + -
49C ASP* 2.7 28.9 + - - -
52C LYS* 3.4 44.6 + - + +
86C ALA 2.9 14.3 + - - +
87C LEU* 3.3 12.6 - - - +
89C LEU* 1.3 76.5 - - - +
91C TYR* 1.3 81.6 + + - +
93C ILE 3.4 0.2 + - - -
94C LYS* 2.9 50.2 + - + +
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Residues in contact with TYR 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C LYS* 3.4 34.5 + - - -
87C LEU* 2.9 38.0 + - + +
90C TYR* 1.3 87.5 - + - +
92C TYR* 1.3 61.8 + - - +
95C GLU* 2.9 51.7 + - + +
96C ASN 3.0 5.9 + - - -
97C ARG* 3.1 46.2 + - + +
99C PRO* 4.0 25.4 - - + -
103C GLU* 4.4 11.5 + - + +
104C LEU* 5.1 2.2 - - + -
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Residues in contact with TYR 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ALA 2.8 19.7 + - - +
89C LEU* 3.2 8.7 + - + +
91C TYR* 1.3 77.9 - - - +
93C ILE* 1.3 64.1 + - + +
96C ASN* 3.1 30.0 + - - +
97C ARG 3.0 15.4 + - - +
98C ILE* 4.2 8.5 - - + -
122C ILE* 4.0 35.9 - - + -
125C LYS* 5.9 0.7 - - + -
137C TYR* 3.6 26.0 + + - -
140C LYS* 4.2 5.3 + - - +
141C ALA* 3.6 17.2 + - - +
144C ASP* 2.6 36.4 + - + +
1D MET* 3.6 30.3 - - + -
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C MET* 3.8 35.0 - - + +
41C ILE 4.7 0.4 - - - +
45C TYR* 3.8 23.8 - - + +
89C LEU* 3.0 46.2 + - + +
92C TYR* 1.3 80.7 - - + +
94C LYS* 1.3 65.2 + - - +
96C ASN* 4.5 1.0 + - - +
125C LYS* 4.1 30.3 - - + -
137C TYR* 4.0 20.1 - - + +
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Residues in contact with LYS 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C MET* 4.5 7.2 - - + -
45C TYR* 6.4 0.9 - - - -
90C TYR* 2.9 41.2 + - + +
91C TYR* 4.6 0.2 - - - -
93C ILE* 1.3 81.0 - - - +
95C GLU* 1.3 73.3 + - + +
96C ASN 3.7 0.4 - - - -
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Residues in contact with GLU 95 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C TYR* 5.8 0.2 - - - -
91C TYR* 2.9 32.0 + - + +
94C LYS* 1.3 91.8 - - + +
96C ASN* 1.3 71.8 + - - +
97C ARG* 2.8 46.3 + - - +
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Residues in contact with ASN 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91C TYR 3.0 2.8 + - - -
92C TYR* 3.1 24.8 + - - +
93C ILE 4.5 1.0 + - - +
94C LYS 3.7 1.0 - - - -
95C GLU* 1.3 80.3 - - - +
97C ARG* 1.3 58.5 + - - +
140C LYS* 2.6 40.5 + - - +
144C ASP* 4.2 2.6 - - - +
1D MET* 5.9 2.8 - - - +
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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