Contacts of the helix formed by residues 72 - 96 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A TRP* 3.8 34.5 - + - -
15B LEU* 3.3 36.3 - - + -
18B LYS* 4.8 0.9 - - + -
19B LYS* 3.8 36.8 - - + -
22B ILE* 3.9 15.0 - - + +
66B LEU* 3.4 7.6 - - - +
69B TYR* 2.9 24.6 + + + +
71B MET* 1.3 109.3 - - + +
73B TYR* 1.3 63.4 + - - +
74B SER 3.2 3.1 - - - -
75B ASN* 3.0 34.6 + - + +
76B GLY 3.4 6.9 + - - -
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Residues in contact with TYR 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A PRO* 3.8 28.7 - - + +
71A MET* 3.5 37.2 - - + +
73A TYR* 5.6 0.2 - - + -
66B LEU* 3.8 32.9 - - + +
69B TYR 3.9 0.8 + - - -
70B PRO* 3.1 21.9 + - + +
71B MET 3.6 0.6 - - - -
72B PHE* 1.3 75.2 - - - +
74B SER* 1.3 68.8 + - - +
76B GLY* 3.1 12.6 + - - -
77B PHE* 3.1 37.0 + + - +
80B LEU* 5.9 0.9 - - + -
107B ASP* 2.7 36.4 + - - -
109B TRP* 5.1 0.9 - + - -
110B VAL* 3.6 13.7 + - + +
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Residues in contact with SER 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A SER* 5.8 9.5 - - - -
71B MET 4.5 6.8 + - - -
73B TYR* 1.3 86.4 - - - +
75B ASN* 1.3 69.6 + - - +
76B GLY 3.4 0.7 + - - -
77B PHE* 3.5 17.2 + - - +
78B ILE* 4.8 4.7 + - - +
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Residues in contact with ASN 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B LYS* 3.7 25.3 - - + +
22B ILE* 4.0 11.0 - - + +
23B VAL* 3.8 25.8 - - + +
26B SER* 3.7 17.7 + - - -
71B MET 4.3 1.2 - - - +
72B PHE* 3.0 37.7 + - + +
74B SER* 1.3 84.8 + - - +
76B GLY* 1.3 57.1 + - - +
77B PHE 3.5 0.4 - - - -
78B ILE 5.3 0.4 + - - -
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Residues in contact with GLY 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ILE* 3.8 6.2 - - - +
26B SER* 3.9 3.7 + - - -
62B GLN* 3.8 23.1 + - - -
66B LEU* 4.3 11.4 - - - -
72B PHE 3.4 3.4 + - - -
73B TYR 3.1 8.4 + - - -
75B ASN* 1.3 78.2 - - - +
77B PHE* 1.3 66.0 + - - +
78B ILE 3.4 2.2 + - - -
79B GLY* 3.4 3.1 + - - -
80B LEU* 3.3 22.3 + - - +
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 5.5 0.2 - - - -
73B TYR* 3.1 37.6 + + + +
74B SER* 3.5 18.2 + - - +
75B ASN 3.5 0.2 - - - -
76B GLY* 1.3 77.3 - - - +
78B ILE* 1.3 64.8 + - + +
80B LEU* 3.1 8.7 + - - +
81B GLN* 2.9 49.9 + - + +
109B TRP* 3.7 17.3 - + - -
110B VAL* 3.4 28.3 - - + -
113B PHE* 3.7 42.0 - + + -
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Residues in contact with ILE 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER* 4.4 4.7 + - - +
30B SER* 5.6 3.6 - - - -
74B SER 4.8 1.0 + - - -
75B ASN 5.3 0.4 + - - -
76B GLY 3.4 0.6 - - - -
77B PHE* 1.3 83.8 - - + +
79B GLY* 1.3 59.2 + - - +
81B GLN* 3.3 17.5 + - + +
82B GLU* 2.9 47.9 + - + +
160D PHE* 6.4 1.8 - - + -
163D ARG* 6.0 6.3 - - - +
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Residues in contact with GLY 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B SER* 3.0 39.7 + - - -
29B MET* 3.4 24.3 - - - +
30B SER* 4.7 3.6 - - - -
76B GLY 3.4 1.8 + - - -
77B PHE 3.3 0.6 - - - -
78B ILE* 1.3 76.9 - - - +
80B LEU* 1.3 56.6 + - - +
82B GLU* 3.4 5.0 + - - +
83B TYR 3.0 21.0 + - - -
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 3.8 20.4 - - + -
59B ALA 4.3 4.9 - - - +
62B GLN* 4.3 9.6 - - + -
63B ILE* 3.8 36.1 - - + +
66B LEU* 3.6 30.7 - - + -
73B TYR* 5.9 1.1 - - + -
76B GLY 3.3 9.2 + - - +
77B PHE* 3.1 8.3 + - - +
79B GLY* 1.3 73.8 - - - +
81B GLN* 1.3 65.1 + - - +
83B TYR* 3.2 15.0 + - + +
84B VAL* 3.0 27.2 + - - +
106B VAL* 4.4 4.7 - - + -
110B VAL* 4.1 25.6 - - + -
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Residues in contact with GLN 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 2.9 37.8 + - + +
78B ILE* 3.5 19.0 - - - +
80B LEU* 1.3 75.4 - - - +
82B GLU* 1.3 61.1 + - + +
84B VAL* 3.3 1.4 + - - -
85B GLU* 3.0 24.4 + - - +
110B VAL* 4.5 9.3 - - - +
113B PHE* 3.5 19.8 + - - +
114B GLY* 3.6 25.4 - - - +
117B ASP* 2.7 27.3 + - - +
165B LYS* 3.8 12.1 - - - +
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B SER* 3.3 18.9 + - - +
33B SER* 3.0 32.8 + - - +
34B LYS* 2.8 33.8 + - - +
78B ILE* 2.9 35.0 + - + +
79B GLY 3.8 4.7 - - - +
81B GLN* 1.3 76.8 - - + +
83B TYR* 1.3 61.4 + - - +
85B GLU* 3.5 16.5 + - - +
86B ALA* 3.0 24.6 + - - +
163D ARG* 5.6 0.9 + - - -
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Residues in contact with TYR 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 3.7 10.5 - - + -
33B SER* 4.4 0.6 - - - -
55B LEU* 3.8 22.0 - - + -
56B THR* 4.1 21.5 - - - +
59B ALA* 3.6 31.3 - - + +
63B ILE* 4.8 1.1 - - + -
79B GLY 3.0 14.9 + - - +
80B LEU* 3.2 20.6 + - + +
82B GLU* 1.3 76.1 - - - +
84B VAL* 1.3 64.6 + - + +
86B ALA* 3.4 0.3 + - - +
87B LEU* 3.0 54.1 + - + +
103B GLU 5.0 0.5 + - - -
104B LEU* 2.7 48.0 + - + +
106B VAL* 3.8 15.5 - - + -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B LEU 3.0 16.9 + - - +
81B GLN 3.3 7.2 + - - +
83B TYR* 1.3 77.9 - - + +
85B GLU* 1.3 59.1 + - - +
87B LEU* 3.9 0.5 - - - +
88B ALA* 2.9 29.3 + - - +
104B LEU* 3.9 23.6 - - + +
106B VAL* 3.9 21.5 - - + -
110B VAL* 3.9 23.1 - - + +
111B TYR* 3.9 26.5 - - + +
114B GLY* 4.1 2.9 - - - -
115B ILE* 4.0 19.1 - - + +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B SER* 5.7 0.4 - - - -
37B ILE* 3.9 12.4 - - + +
81B GLN* 3.0 15.9 + - - +
82B GLU* 3.7 19.6 - - - +
84B VAL* 1.3 76.5 - - - +
86B ALA* 1.3 61.7 + - - +
88B ALA* 3.5 2.6 + - - +
89B LEU* 3.1 22.7 + - - +
114B GLY* 3.8 14.5 + - - +
117B ASP* 3.8 38.3 - - + +
118B ILE* 3.9 9.4 - - + +
121B GLU* 3.1 28.8 - - + +
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B SER* 3.8 32.1 - - - +
36B LEU* 4.0 17.8 - - + +
37B ILE* 3.9 15.6 - - + +
40B MET* 5.9 0.2 - - - +
55B LEU* 4.2 2.9 - - + -
82B GLU 3.0 19.4 + - - +
83B TYR 3.9 2.9 - - - +
85B GLU* 1.3 74.7 - - - +
87B LEU* 1.3 60.9 + - - +
89B LEU* 3.3 3.8 + - - +
90B TYR* 2.9 26.9 + - - +
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 4.0 10.5 - - + -
52B LYS* 3.7 35.9 - - + -
55B LEU* 3.7 18.2 - - + -
56B THR* 4.5 9.0 - - - +
83B TYR* 3.0 51.1 + - + +
84B VAL 4.1 0.7 - - - +
86B ALA* 1.3 74.6 - - - +
88B ALA* 1.3 60.3 + - - +
90B TYR* 3.2 5.9 + - + +
91B TYR* 2.9 48.5 + - + -
99B PRO* 4.4 0.9 - - - -
104B LEU* 3.7 22.0 - - + -
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 2.9 19.9 + - + +
87B LEU* 1.3 78.1 - - - +
89B LEU* 1.3 57.8 + - - +
91B TYR* 3.4 0.7 + - - -
92B TYR* 2.8 30.2 + - - +
97B ARG 4.0 3.3 - - - +
98B ILE* 4.1 8.4 - - + +
99B PRO* 3.7 18.8 - - + +
115B ILE* 4.1 16.8 - - + -
118B ILE* 3.6 25.4 - - + -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ILE* 3.7 44.4 - - + +
40B MET* 4.7 3.6 - - + -
41B ILE* 4.4 5.8 - - + -
85B GLU 3.1 13.3 + - - +
86B ALA* 3.6 7.9 - - - +
88B ALA* 1.3 75.2 - - - +
90B TYR* 1.3 67.0 + - - +
92B TYR* 3.6 5.1 - - + +
93B ILE* 3.0 50.2 + - + +
118B ILE* 4.9 4.6 - - + +
121B GLU* 3.9 37.2 - - + +
122B ILE* 4.2 16.6 - - + -
125B LYS* 5.0 1.6 - - + -
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Residues in contact with TYR 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 4.1 12.3 - - + -
40B MET* 3.6 43.5 - - + +
45B TYR* 6.5 0.2 - - + -
48B ALA* 4.6 2.9 - - + -
49B ASP* 2.7 29.4 + - - -
52B LYS* 3.4 43.5 + - + +
86B ALA 2.9 13.8 + - - +
87B LEU* 3.3 13.2 - - + +
89B LEU* 1.3 77.6 - - - +
91B TYR* 1.3 78.6 + + - +
94B LYS* 2.9 61.9 + - + +
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Residues in contact with TYR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B LYS* 3.4 24.3 + - - -
87B LEU* 2.9 45.6 + - + +
90B TYR* 1.3 90.2 - + - +
92B TYR* 1.3 62.7 + - - +
94B LYS* 5.3 0.2 - - + -
95B GLU* 2.9 51.7 + - + +
96B ASN 3.0 6.4 + - - -
97B ARG* 3.1 46.8 + - + +
99B PRO* 4.0 24.7 - - + -
103B GLU* 4.3 11.9 + - + +
104B LEU* 5.1 2.5 - - + -
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Residues in contact with TYR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.9 28.0 - - + -
88B ALA 2.8 19.7 + - - +
89B LEU* 3.2 9.2 + - + +
91B TYR* 1.3 77.4 - - - +
93B ILE* 1.3 64.2 + - + +
96B ASN* 3.1 31.7 + - - +
97B ARG 3.1 14.7 + - - +
98B ILE* 4.2 9.2 - - + -
122B ILE* 3.9 37.0 - - + -
125B LYS* 6.0 0.2 - - + -
137B TYR* 3.6 26.5 + + - -
140B LYS* 4.2 5.5 + - - +
141B ALA* 3.6 16.6 + - - +
144B ASP* 2.6 36.9 + - + +
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Residues in contact with ILE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 3.8 36.3 - - + +
41B ILE 4.7 0.7 - - - +
45B TYR* 3.8 22.9 - - + +
89B LEU* 3.0 45.5 + - + +
92B TYR* 1.3 80.9 - - + +
94B LYS* 1.3 64.5 + - - +
96B ASN 4.5 1.0 + - - -
125B LYS* 4.0 31.4 - - + -
137B TYR* 4.0 19.7 - - + +
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Residues in contact with LYS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B MET* 4.5 9.0 - - + -
45B TYR* 6.3 1.1 - - - -
90B TYR* 2.9 53.7 + - + +
91B TYR* 4.6 0.2 - - - -
93B ILE* 1.3 81.1 - - - +
95B GLU* 1.3 77.7 + - + +
96B ASN 3.7 0.2 - - - -
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B TYR* 2.9 32.0 + - + +
94B LYS* 1.3 96.5 - - + +
96B ASN* 1.3 72.5 + - - +
97B ARG* 2.8 45.1 + - - +
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Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.8 2.3 - - - +
91B TYR 3.0 3.2 + - - -
92B TYR* 3.1 24.7 + - - +
93B ILE 4.5 1.0 + - - +
94B LYS 3.7 1.0 - - - -
95B GLU* 1.3 79.4 - - - +
97B ARG* 1.3 59.4 + - - +
140B LYS* 2.6 38.8 + - - +
144B ASP* 4.2 3.1 - - - +
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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