Contacts of the helix formed by residues 83 - 106 (chain B) in PDB entry 5GJQ
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 MET 83 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA* 3.8 25.8 - - + +
34B GLN* 5.5 4.3 - - + -
35B GLY* 5.8 2.0 - - - +
82B GLY* 1.3 69.5 - - - -
84B THR* 1.3 56.4 + - - +
85B ALA* 4.8 3.8 - - + +
86B ASP* 3.8 29.1 - - + +
87B SER* 2.7 35.5 + - - -
132B ARG* 4.6 4.3 - - - +
135B GLY* 2.6 35.2 + - - +
14X PHE* 4.2 9.6 - - - -
18X GLY 5.3 2.0 - - - +
19X ARG* 6.4 0.4 - - - -
20X VAL* 4.6 16.4 - - + +
23X VAL* 6.4 1.3 - - + -
154X SER* 6.2 4.7 - - - -
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Residues in contact with THR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B HIS* 4.7 11.3 - - + -
82B GLY 3.3 5.9 + - - -
83B MET* 1.3 70.3 - - - +
85B ALA* 1.3 64.2 + - - +
87B SER* 3.0 9.0 + - - -
88B ARG* 2.9 44.6 + - - +
156X VAL* 3.3 39.5 - - + +
158X TYR* 3.8 22.0 + - - +
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Residues in contact with ALA 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B MET* 3.5 4.2 - - + +
84B THR* 1.3 79.5 - - - +
86B ASP* 1.3 65.0 + - - +
88B ARG* 3.2 7.9 + - - +
89B SER* 3.0 22.3 + - - -
117X MET* 4.4 2.5 - - - +
120X HIS* 3.6 16.0 + - + -
154X SER* 3.2 31.6 - - - +
155X GLY 3.9 11.4 - - - -
156X VAL* 3.6 16.7 - - + +
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Residues in contact with ASP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B MET* 3.5 30.1 + - + +
84B THR 3.3 0.2 - - - -
85B ALA* 1.3 73.1 - - - +
87B SER* 1.3 66.9 + - - +
89B SER* 3.2 4.2 + - - -
90B GLN* 2.9 23.9 + - - +
132B ARG* 2.6 29.4 + - - -
134B LEU* 3.5 14.0 - - + +
135B GLY 3.1 26.2 + - - +
136B CYS* 3.8 9.3 - - + -
120X HIS* 2.7 28.4 + - - -
123X THR* 4.9 0.3 + - - -
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B HIS* 5.6 4.3 + - - -
70B PHE* 5.3 3.1 - - - -
80B MET* 3.6 35.3 - - - +
81B THR 4.5 1.4 + - - -
82B GLY 4.1 5.7 + - - -
83B MET 2.7 21.6 + - - -
84B THR* 3.0 11.4 + - - -
86B ASP* 1.3 76.3 - - - +
88B ARG* 1.3 59.8 + - - +
90B GLN* 3.2 3.1 + - - +
91B VAL* 2.9 33.9 + - - +
136B CYS* 3.4 14.0 - - - +
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B THR 4.4 4.4 + - - -
67B THR 5.5 3.4 + - - +
70B PHE* 4.1 31.0 - - + -
84B THR* 2.9 32.2 + - + +
85B ALA* 3.2 7.9 + - - +
87B SER* 1.3 73.7 - - - +
89B SER* 1.3 65.5 + - - +
91B VAL* 3.2 6.8 + - - +
92B GLN* 2.9 29.6 + - + +
113X ASP* 4.0 20.0 + - - -
117X MET* 4.1 11.9 - - + -
155X GLY 4.6 2.8 + - - -
156X VAL* 4.1 2.6 - - - +
157X SER* 2.8 50.7 + - - +
158X TYR* 3.3 29.3 + - - -
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA 3.0 7.3 + - - -
86B ASP* 3.3 9.6 - - - -
88B ARG* 1.3 75.8 - - - +
90B GLN* 1.3 65.0 + - - +
92B GLN* 3.2 6.1 + - - +
93B ARG* 3.0 22.9 + - - +
125B TYR* 5.3 3.8 + - - -
134B LEU* 4.2 11.6 - - - +
117X MET* 3.4 22.7 - - - +
120X HIS* 3.4 33.0 - - - -
124X LEU* 5.5 1.4 - - - +
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Residues in contact with GLN 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B MET* 3.4 20.2 - - + +
86B ASP 2.9 15.4 + - - +
87B SER 3.7 4.0 - - - +
89B SER* 1.3 78.6 - - - +
91B VAL* 1.3 57.6 + - - +
93B ARG* 3.4 6.6 + - + +
94B ALA* 2.9 28.9 + - - +
118B ILE* 3.7 28.1 - - + +
122B SER* 3.6 22.6 + - - -
134B LEU* 3.8 21.5 - - + +
136B CYS* 3.5 16.2 + - - -
137B CYS 4.9 0.2 + - - -
138B MET* 3.5 21.3 + - + +
154B CYS* 4.4 4.3 - - - -
155B ASP 5.3 3.8 + - - -
156B PRO* 6.4 0.2 - - - +
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Residues in contact with VAL 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B PHE* 3.6 36.3 - - + -
72B ILE* 4.0 8.7 - - + -
78B CYS* 3.9 9.2 - - - -
80B MET* 3.7 19.1 - - + -
87B SER 2.9 20.2 + - - +
88B ARG* 3.5 8.5 - - + +
89B SER 3.2 0.2 - - - -
90B GLN* 1.3 75.1 - - - +
92B GLN* 1.3 66.9 + - - +
94B ALA* 3.1 3.3 + - - +
95B ARG* 2.9 53.5 + - - +
138B MET* 4.3 4.7 - - + -
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Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ARG* 2.9 19.8 + - + +
89B SER* 3.5 7.6 - - - +
91B VAL* 1.3 74.2 - - - +
93B ARG* 1.3 65.7 + - - +
95B ARG* 3.2 35.9 + - - +
96B TYR* 3.0 22.9 + - - +
113X ASP* 5.3 12.4 + - - +
114X ARG* 5.7 2.3 + - - -
117X MET* 4.3 25.6 - - + -
65a PHE* 4.0 21.1 - - - -
69a GLU* 3.8 24.4 + - - +
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Residues in contact with ARG 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B SER* 3.0 10.6 + - - +
90B GLN* 3.7 10.5 - - + +
92B GLN* 1.3 80.9 - - - +
94B ALA* 1.3 61.8 + - - +
96B TYR* 3.3 20.6 + - - +
97B GLU* 3.0 50.2 + - - +
117B ARG* 4.1 7.3 - - - +
118B ILE* 4.1 5.2 - - + -
121B ILE* 3.4 48.5 - - + +
125B TYR* 4.7 6.5 + - - -
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Residues in contact with ALA 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 3.9 20.6 - - + +
90B GLN 2.9 17.6 + - - +
91B VAL 3.1 4.9 + - - +
93B ARG* 1.3 76.4 - - - +
95B ARG* 1.3 64.1 + - - +
97B GLU 3.3 1.4 + - - +
98B ALA* 3.0 24.6 + - - +
114B LEU* 3.7 22.8 - - + +
118B ILE* 3.7 13.9 - - + +
138B MET* 4.0 13.0 - - + -
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Residues in contact with ARG 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B PHE* 4.3 15.2 - - - -
71B LYS* 2.8 33.9 + - - +
72B ILE* 3.8 30.5 - - + +
91B VAL* 2.9 32.5 + - - +
92B GLN* 3.3 34.1 - - - +
94B ALA* 1.3 77.0 - - - +
96B TYR* 1.3 62.4 + - - +
98B ALA* 3.3 2.4 + - - +
99B ALA* 3.0 25.8 + - - +
65a PHE* 3.8 18.5 - - + -
68a ILE* 3.6 26.4 + - + +
69a GLU* 4.0 18.8 + - - +
71a ASN* 6.2 0.2 - - - +
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Residues in contact with TYR 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B GLN 3.0 12.0 + - - +
93B ARG* 3.4 24.7 - - - +
95B ARG* 1.3 78.1 - - - +
97B GLU* 1.3 76.0 + - - +
99B ALA* 3.4 0.5 + - - +
100B ASN* 2.6 61.7 + - - -
61a TYR* 3.3 20.9 + + - -
65a PHE* 3.7 21.2 - + + -
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Residues in contact with GLU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ARG* 3.0 48.6 + - - +
94B ALA* 3.7 5.8 - - - +
96B TYR* 1.3 87.1 - - - +
98B ALA* 1.3 57.6 + - - +
100B ASN* 3.7 8.3 - - - +
101B TRP* 2.9 28.2 + - - +
104B LYS* 5.9 0.5 + - - -
109B ILE* 5.1 3.0 - - + +
114B LEU* 4.6 7.0 - - + -
117B ARG* 2.9 57.2 + - + +
118B ILE* 4.3 7.6 - - + -
121B ILE* 3.9 1.1 - - + +
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Residues in contact with ALA 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ILE* 4.4 7.9 - - + +
73B THR* 4.0 20.9 - - + +
94B ALA 3.0 16.8 + - - +
95B ARG 3.7 3.6 - - - +
97B GLU* 1.3 76.0 - - - +
99B ALA* 1.3 61.4 + - - +
101B TRP* 2.9 17.8 + - - +
102B LYS* 3.0 20.0 + - + +
109B ILE* 3.3 30.6 - - + +
114B LEU* 4.5 4.2 - - + +
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ARG 3.0 17.5 + - - +
96B TYR 3.7 3.4 - - - +
98B ALA* 1.3 75.0 - - - +
100B ASN* 1.3 58.0 + - - +
102B LYS* 3.1 19.0 + - + +
103B TYR* 2.9 28.6 + - - +
61a TYR* 3.9 23.8 - - + +
65a PHE* 4.4 19.3 - - + +
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Residues in contact with ASN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR* 2.6 56.9 + - - +
97B GLU* 3.7 11.3 - - - +
99B ALA* 1.3 75.5 - - - +
101B TRP* 1.3 53.7 + - - +
103B TYR* 4.1 6.2 - - - +
104B LYS* 2.8 58.3 + - - +
61a TYR* 2.7 36.2 + - - -
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Residues in contact with TRP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU 2.9 15.1 + - - +
98B ALA 2.9 13.7 + - - +
100B ASN* 1.3 78.2 - - - +
102B LYS* 1.3 56.5 + - - +
104B LYS* 5.5 0.4 - - - -
105B TYR* 3.2 36.7 + + + +
107B TYR* 2.2 59.9 - + + -
108B GLU 4.3 0.7 - - - -
109B ILE* 3.4 39.1 - - + +
110B PRO* 4.1 16.4 - - + -
113B MET* 4.1 14.5 - - + +
66b HIS* 3.7 33.1 - + - -
70b THR* 4.8 8.5 - - + -
78b THR* 5.6 3.1 - - - -
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Residues in contact with LYS 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B THR* 3.8 18.3 - - + +
74B GLU* 5.8 2.2 - - - +
98B ALA 3.0 17.3 - - - +
99B ALA* 3.1 17.8 + - + +
101B TRP* 1.3 73.6 - - - +
103B TYR* 1.3 61.9 + - - +
106B GLY* 2.7 30.4 + - - +
107B TYR 3.9 13.9 - - - +
108B GLU* 2.7 58.9 + - + +
109B ILE 4.6 0.7 - - - +
64a GLY* 6.1 3.4 - - - -
68a ILE* 6.0 3.4 - - - +
81b ARG* 3.3 5.4 + - - -
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Residues in contact with TYR 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B ALA 2.9 16.8 + - - +
100B ASN* 3.7 9.6 - - - +
102B LYS* 1.3 73.9 - - - +
104B LYS* 1.3 68.5 + - + +
54a ALA 5.3 0.7 + - - -
57a ASP* 4.3 5.8 - - + -
58a ALA* 3.8 27.5 + - - +
61a TYR* 3.0 57.2 - + + -
81b ARG* 2.9 22.8 + - - +
85b GLN* 3.0 31.4 + - - -
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B GLU* 5.9 0.4 + - - -
100B ASN* 2.8 34.2 + - + +
101B TRP* 5.5 0.4 - - - -
103B TYR* 1.3 85.6 - - + +
105B TYR* 1.3 92.0 + - + +
81b ARG* 3.7 14.1 - - - +
82b MET* 4.4 8.0 + - - +
85b GLN* 3.8 14.0 - - - +
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Residues in contact with TYR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TRP* 3.2 39.6 + + + +
104B LYS* 1.3 111.2 - - + +
106B GLY* 1.3 60.4 + - - +
107B TYR* 3.7 0.7 + - - +
62b ASN* 5.5 2.1 + - - +
66b HIS* 3.4 38.6 + + - +
77b VAL* 4.0 3.1 - - - +
78b THR* 3.1 53.6 + - + +
81b ARG* 4.2 8.5 - - - -
82b MET* 2.9 28.9 - - + +
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LYS* 2.7 25.2 + - - -
104B LYS 3.9 0.4 - - - -
105B TYR* 1.3 73.1 - - - +
107B TYR* 1.3 63.9 + - - +
77b VAL* 4.8 15.4 - - - +
81b ARG* 4.2 15.3 - - - +
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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