Contacts of the helix formed by residues 86 - 113 (chain B) in PDB entry 5NJ8
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 LYS 86 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B ASP* 1.3 81.6 - - - +
87B GLU* 1.3 53.4 + - - +
88B ARG* 3.0 6.1 - - - -
89B LEU* 2.6 59.7 + - + +
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASP* 3.3 8.9 - - - +
86B LYS* 1.3 76.0 - - - +
88B ARG* 1.3 78.2 + - + +
89B LEU* 5.2 0.2 - - - -
90B ALA* 2.9 11.4 + - - +
91B ARG* 2.8 51.7 + - + +
84D ALA* 4.7 15.9 - - - +
85D ASP* 5.0 4.0 - - - -
86D LYS* 4.6 10.0 + - - +
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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
----------------------------------------------------------
85B ASP 5.0 1.5 + - - +
86B LYS* 3.0 3.1 - - - +
87B GLU* 1.3 91.3 - - + +
89B LEU* 1.3 50.5 + - - +
91B ARG* 3.2 45.3 - - - +
92B GLU* 2.5 37.9 + - - +
8F T 3.2 47.9 + - - -
9F G 2.7 29.9 + - - -
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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
----------------------------------------------------------
86B LYS* 2.6 47.9 + - + +
87B GLU* 5.2 0.2 - - - -
88B ARG* 1.3 72.5 - - - +
90B ALA* 1.3 65.8 + - + +
92B GLU* 2.8 24.8 + - - +
93B ASN* 2.7 34.8 + - + +
84D ALA* 6.3 3.4 - - + -
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Residues in contact with ALA 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 2.9 9.0 + - - +
89B LEU* 1.3 92.1 - - + +
91B ARG* 1.3 58.5 + - - +
93B ASN* 3.3 10.5 + - - +
94B HIS* 3.0 21.3 + - - +
84D ALA* 4.6 13.5 - - + +
85D ASP* 4.1 30.4 - - + +
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Residues in contact with ARG 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 2.8 35.7 + - + +
88B ARG* 3.2 47.5 - - - +
90B ALA* 1.3 74.2 - - - +
92B GLU* 1.3 59.5 + - - +
93B ASN 3.3 0.2 - - - -
94B HIS* 3.3 33.1 - - + +
95B SER* 3.3 7.3 + - - -
85D ASP* 3.8 16.7 + - + +
86D LYS* 3.1 40.0 - - - +
8F T 4.0 11.8 + - - +
9F G 3.9 13.7 + - - +
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Residues in contact with GLU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ARG 2.5 25.7 + - - +
89B LEU* 2.8 20.7 + - - +
91B ARG* 1.3 72.0 - - - +
93B ASN* 1.3 59.5 + - + +
95B SER* 2.1 31.1 + - - +
96B GLU* 3.3 22.6 + - + +
8F T 4.9 4.7 - - - +
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Residues in contact with ASN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B LEU* 2.7 17.5 + - + +
90B ALA* 3.3 14.3 + - - +
92B GLU* 1.3 71.3 - - + +
94B HIS* 1.3 65.4 + - - +
96B GLU* 3.1 28.6 + - - +
97B ILE* 3.2 34.1 + - - +
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Residues in contact with HIS 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ALA 3.0 9.0 + - - +
91B ARG* 3.3 31.6 - - + +
92B GLU 3.2 0.4 - - - -
93B ASN* 1.3 73.9 - - - +
95B SER* 1.3 66.0 + - - +
97B ILE* 3.2 15.3 + - - +
98B GLU* 3.0 24.7 + - + +
2E G 5.0 10.8 + - - -
3E T 3.3 32.6 + + + -
8F T 4.5 9.3 + + + -
9F G 3.2 39.1 + + - -
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG 3.3 6.6 + - - -
92B GLU* 2.1 39.3 + - - +
94B HIS* 1.3 76.7 - - - +
96B GLU* 1.3 55.9 + - - +
97B ILE 3.1 0.3 + - - -
98B GLU* 3.1 3.3 + - - +
99B ARG* 2.8 33.1 + - - +
102B ARG* 4.6 2.6 + - - -
7F G 4.2 26.9 + - - -
8F T 4.0 29.5 + - - +
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Residues in contact with GLU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B GLU* 3.5 26.7 - - + +
93B ASN* 3.1 29.6 + - - +
95B SER* 1.3 76.8 - - - +
97B ILE* 1.3 63.0 + - + +
99B ARG* 3.3 23.6 + - - +
100B ARG* 3.2 45.0 + - - +
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Residues in contact with ILE 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ASN* 3.3 29.4 - - - +
94B HIS* 3.2 15.9 + - - +
95B SER 3.1 0.8 - - - -
96B GLU* 1.3 74.3 - - + +
98B GLU* 1.3 66.1 + - - +
99B ARG 3.0 0.9 + - - -
100B ARG* 3.1 18.6 + - - +
101B ARG* 3.3 12.6 + - + +
1E G 4.3 23.6 - - + +
2E G 3.9 36.6 - - + +
3E T 4.4 17.5 - - + +
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B HIS* 3.0 19.7 + - + +
95B SER 3.7 6.1 - - - +
97B ILE* 1.3 76.4 - - - +
99B ARG* 1.3 62.8 + - - +
101B ARG* 3.1 40.1 + - - +
102B ARG* 3.5 31.6 + - - +
3E T 3.8 2.6 - - - +
4E C 2.8 27.8 + - - -
5E A 3.1 16.2 + - - +
8F T 3.5 26.0 - - + +
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Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B SER* 2.8 11.3 + - - +
96B GLU* 3.3 32.4 - - - +
98B GLU* 1.3 74.1 - - - +
100B ARG* 1.3 64.9 + - - +
102B ARG* 2.7 43.7 + - - +
103B ASN* 3.0 28.8 + - - +
6F C 3.9 32.7 + - - +
7F G 4.1 21.7 + - - +
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Residues in contact with ARG 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLU* 3.2 37.3 + - - +
97B ILE* 3.1 10.8 + - - +
99B ARG* 1.3 84.9 - - - +
101B ARG* 1.3 54.4 + - - +
103B ASN* 4.3 15.0 - - + +
104B LYS* 2.6 59.8 + - + +
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Residues in contact with ARG 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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66A LYS* 5.9 1.8 - - - +
67A LEU* 3.1 37.4 - - + +
97B ILE* 3.3 8.9 + - + +
98B GLU* 3.1 38.5 + - - +
99B ARG 3.1 0.2 - - - -
100B ARG* 1.3 77.8 - - - +
102B ARG* 1.3 57.5 + - - +
104B LYS* 4.0 8.2 - - + +
105B MET* 2.8 36.0 + - - +
2E G 5.3 0.2 - - + -
3E T 2.9 78.4 + - - +
4E C 3.6 28.6 + - - +
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Residues in contact with ARG 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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95B SER 4.6 2.2 + - - -
98B GLU* 3.5 30.6 + - - +
99B ARG* 2.7 35.4 + - - +
101B ARG* 1.3 68.3 - - - +
103B ASN* 1.3 58.8 + - - +
105B MET* 2.7 11.5 + - - +
106B THR* 2.4 46.6 + - + +
5F G 4.8 7.2 - - - +
6F C 3.4 52.1 + - - +
7F G 3.4 59.9 + - - -
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Residues in contact with ASN 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 ARG* 3.0 32.1 + - - +
100B ARG* 3.7 16.5 - - + +
102B ARG* 1.3 76.0 - - - +
104B LYS* 1.3 55.4 + - + +
106B THR* 3.1 8.8 + - - +
107B ALA* 2.5 41.4 + - + +
6F C 4.5 4.9 + - - -
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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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67A LEU* 5.2 9.6 - - + -
100B ARG* 2.6 43.7 + - + +
101B ARG* 4.0 7.0 - - + +
103B ASN* 1.3 73.4 - - + +
105B MET* 1.3 62.3 + - - +
107B ALA* 4.3 4.7 - - - -
108B TYR* 3.1 50.8 + - + +
2E G 5.1 8.5 + - - -
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Residues in contact with MET 105 (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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43A LEU* 6.0 5.8 - - + -
47A LEU* 5.0 10.5 - - + -
66A LYS* 4.9 14.8 - - + -
67A LEU* 3.3 27.5 - - + +
70A LEU* 3.4 30.0 - - + +
101B ARG* 2.8 29.2 + - - +
102B ARG* 2.7 13.2 + - - +
104B LYS* 1.3 75.2 - - - +
106B THR* 1.3 69.0 + - + +
108B TYR* 3.2 10.1 + - - +
109B ILE* 3.2 21.5 + - + +
128B LYS* 5.8 2.9 - - + +
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Residues in contact with THR 106 (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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102B ARG* 2.4 36.3 + - + +
103B ASN* 3.1 13.5 + - - +
105B MET* 1.3 75.2 - - + +
107B ALA* 1.3 73.1 + - - +
109B ILE* 2.8 23.5 + - - +
110B THR* 3.0 15.2 + - - -
128B LYS* 3.2 32.1 - - - +
5F G 3.3 21.0 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ASN* 2.5 26.3 + - + +
104B LYS* 4.0 5.4 - - - +
106B THR* 1.3 73.5 + - - +
108B TYR* 1.3 63.6 + - + +
110B THR* 3.4 8.5 + - - -
111B GLU* 2.9 36.2 + - - +
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Residues in contact with TYR 108 (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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67A LEU* 3.5 19.0 - - + +
70A LEU* 3.6 22.9 - - + -
71A ARG* 3.1 45.9 - - + +
74A VAL* 4.3 2.9 - - + +
155A HIS* 4.0 16.8 - + - -
156A GLN* 5.6 3.3 + - - -
104B LYS* 3.1 35.6 + - + +
105B MET* 3.5 7.9 - - - +
106B THR 3.1 0.8 - - - -
107B ALA* 1.3 80.0 - - + +
109B ILE* 1.3 53.8 + - - +
111B GLU* 3.1 25.6 + - - +
112B LEU* 2.4 40.4 + - - +
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Residues in contact with ILE 109 (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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70A LEU* 3.8 17.7 - - + -
105B MET* 3.4 19.3 - - + +
106B THR* 2.8 14.1 + - - +
108B TYR* 1.3 75.9 - - - +
110B THR* 1.3 53.2 + - - +
112B LEU* 3.1 6.5 + - + +
113B SER* 2.7 36.3 + - - -
128B LYS* 3.9 31.9 - - + -
131B ILE* 3.8 30.4 - - + +
132B LEU* 3.5 37.9 - - + -
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Residues in contact with THR 110 (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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106B THR* 3.0 12.3 + - - -
107B ALA* 3.6 10.7 - - - -
109B ILE* 1.3 76.8 - - - +
111B GLU* 1.3 63.9 + - + +
113B SER* 2.6 28.1 + - - +
114B ASP* 3.1 22.0 - - - +
131B ILE* 5.8 0.7 - - - -
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Residues in contact with GLU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ARG* 5.8 0.2 - - - -
74A VAL* 3.9 27.4 - - + +
155A HIS* 4.3 15.3 + - - -
107B ALA* 2.9 23.0 + - + +
108B TYR* 3.4 29.9 - - - +
110B THR* 1.3 76.0 - - + +
112B LEU* 1.3 58.0 + - - +
114B ASP* 3.0 30.9 + - - +
115B MET* 3.7 17.0 + - + +
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Residues in contact with LEU 112 (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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50A LEU* 4.4 7.2 - - + -
70A LEU* 3.7 29.4 - - + -
73A SER* 4.5 9.4 - - - +
74A VAL* 4.0 21.9 - - + +
77A LEU* 3.6 28.9 - - + -
108B TYR 2.4 28.2 + - - +
109B ILE* 3.3 6.5 - - + +
111B GLU* 1.3 72.0 - - - +
113B SER* 1.3 55.6 + - - +
114B ASP 3.5 0.7 - - - -
115B MET* 4.3 2.2 + - - +
116B VAL* 3.1 22.7 - - - +
131B ILE* 4.0 7.7 - - + +
132B LEU* 4.1 11.7 - - + -
135B ALA* 3.8 27.6 - - + -
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Residues in contact with SER 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE 2.7 12.2 + - - -
110B THR* 2.6 24.5 + - - +
112B LEU* 1.3 76.6 - - - +
114B ASP* 1.3 58.5 + - - +
116B VAL* 3.1 23.2 - - - +
118B THR* 3.3 5.2 + - - -
119B CYS 2.8 24.6 + - - +
126B PRO* 5.6 4.0 - - - +
131B ILE* 3.8 28.8 - - - +
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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