Contacts of the helix formed by residues 82 - 113 (chain B) in PDB entry 3F8F
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 THR 82 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B GLY 2.6 29.0 + - - +
62B ILE 2.9 13.1 + - - -
63B ILE 3.7 2.0 - - - -
64B SER* 3.6 39.9 - - - +
80B ARG* 4.9 3.8 - - + +
81B LEU* 1.3 74.9 - - - +
83B GLU* 1.3 59.2 + - - +
84B ILE* 3.5 4.9 + - - +
85B GLY 3.0 8.0 + - - -
86B HIS* 2.9 30.7 + - - -
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Residues in contact with GLU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B THR* 1.3 74.3 - - - +
84B ILE* 1.3 64.6 + - + +
86B HIS* 3.2 16.0 + - - +
87B GLU* 2.9 23.2 + - + +
90B ARG* 3.1 30.0 + - - -
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Residues in contact with ILE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 3.6 13.7 - - - +
2A ALA* 3.5 32.7 - - + +
60B ASP 4.0 11.4 - - - +
61B GLY* 3.6 25.4 - - - +
62B ILE* 4.2 4.7 - - + -
82B THR* 3.3 2.1 + - - +
83B GLU* 1.3 77.6 - - + +
85B GLY* 1.3 57.9 + - - +
87B GLU* 3.5 4.9 + - - -
88B ASN* 3.0 26.3 + - - +
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Residues in contact with GLY 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B ILE* 3.4 33.5 + - - +
81B LEU* 3.9 9.8 - - - +
82B THR* 3.0 15.4 + - - -
84B ILE* 1.3 74.9 - - - +
86B HIS* 1.3 63.4 - - - +
88B ASN* 3.2 3.0 + - - +
89B MET* 3.1 28.2 + - - +
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Residues in contact with HIS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B LYS* 4.2 28.5 + - - +
81B LEU* 4.0 36.7 - - + +
82B THR 2.9 24.2 + - - -
83B GLU* 3.5 24.1 + - - +
85B GLY* 1.3 74.6 - - - +
87B GLU* 1.3 58.3 + - - +
89B MET* 3.2 7.8 + - - +
90B ARG* 2.9 42.9 + - - +
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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
----------------------------------------------------------
2A ALA* 3.9 16.6 - - + -
83B GLU* 2.9 13.2 + - + +
84B ILE* 3.7 9.9 - - - +
86B HIS* 1.3 76.1 - - - +
88B ASN* 1.3 57.9 + - - +
90B ARG* 2.6 49.0 + - - +
91B LEU* 2.8 52.5 + - + +
94B GLU* 5.3 2.6 - - - +
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Residues in contact with ASN 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 2.9 30.6 - - - +
3A GLU 3.7 8.7 - - - +
4A ILE* 4.4 5.4 - - - +
5A PRO* 4.7 6.2 - - - +
8A MET* 5.6 6.1 - - - +
18B LEU* 3.8 25.7 - - - +
57B LEU* 5.6 0.8 - - - +
62B ILE* 3.9 28.1 - - + +
84B ILE 3.0 18.0 + - - +
85B GLY 3.2 6.2 + - - +
87B GLU* 1.3 75.8 - - - +
89B MET* 1.3 57.1 + - - +
91B LEU* 3.4 2.6 + - - +
92B ALA* 2.9 31.6 + - - +
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Residues in contact with MET 89 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B LEU* 3.8 35.4 - - + +
19B ASN* 3.8 29.8 - - - +
22B LYS* 3.6 31.2 - - + +
81B LEU* 3.6 31.6 - - - -
85B GLY 3.1 10.2 + - - +
86B HIS* 3.5 8.5 - - - +
88B ASN* 1.3 75.6 - - - +
90B ARG* 1.3 65.3 + - - +
92B ALA* 3.7 5.8 - - - +
93B PHE* 3.1 23.7 + - - +
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLU* 3.1 25.3 + - - -
86B HIS* 2.9 28.3 + - - +
87B GLU* 2.6 51.3 + - - +
89B MET* 1.3 76.3 - - - +
91B LEU* 1.3 55.8 + - - +
93B PHE* 3.3 6.4 + - - +
94B GLU* 2.9 46.9 + - - +
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Residues in contact with LEU 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 3.6 27.6 - - + +
3A GLU* 4.2 11.0 - - + +
4A ILE* 3.6 16.8 - - + +
87B GLU* 2.8 42.2 + - + +
88B ASN 3.8 2.2 - - - +
90B ARG* 1.3 70.2 - - - +
92B ALA* 1.3 56.0 + - - +
94B GLU* 3.7 19.1 - - + +
95B SER* 2.8 38.6 + - - -
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Residues in contact with ALA 92 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.6 6.0 - - + +
8A MET* 4.0 24.7 - - + -
127A DM1 4.2 16.4 - - + -
88B ASN* 2.9 20.4 + - - +
89B MET* 3.7 7.6 - - - +
91B LEU* 1.3 75.8 - - - +
93B PHE* 1.3 63.1 + - - +
95B SER* 3.1 7.0 + - - -
96B TRP* 3.0 31.2 + - - -
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Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A DM1 5.0 5.0 - - - -
89B MET 3.1 13.3 + - - +
90B ARG* 3.6 8.5 - - - +
92B ALA* 1.3 77.0 - - - +
94B GLU* 1.3 65.2 + - + +
96B TRP* 4.3 3.9 - - + +
97B SER* 2.7 57.0 + - - -
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 5.3 2.3 - - - +
90B ARG* 2.9 40.6 + - - +
91B LEU* 3.8 20.7 - - + +
92B ALA 3.2 0.2 - - - -
93B PHE* 1.3 90.6 - - + +
95B SER* 1.3 58.3 + - - +
97B SER* 3.5 6.5 + - - -
98B ARG* 3.1 25.3 + - - +
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Residues in contact with SER 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ILE* 3.8 14.6 - - - +
9A LEU* 6.2 0.7 - - - -
12A GLN* 3.1 29.0 + - - +
91B LEU 2.8 26.8 + - - -
92B ALA* 3.1 9.5 + - - -
94B GLU* 1.3 74.0 - - - +
96B TRP* 1.3 56.9 + - - +
98B ARG* 3.2 9.7 + - - +
99B VAL* 3.0 29.1 + - - +
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Residues in contact with TRP 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A MET* 3.6 8.6 - - + +
11A ALA* 4.0 11.4 - - + -
12A GLN* 3.4 36.8 - - + +
15A VAL* 3.8 31.9 - - + -
127A DM1 3.1 97.1 - + + +
92B ALA 3.0 25.1 + - - +
93B PHE* 4.3 4.0 - - - +
95B SER* 1.3 74.9 + - - +
97B SER* 1.3 64.7 + - - +
98B ARG 3.1 0.2 - - - -
99B VAL* 3.4 23.4 + - + +
100B ASP* 3.0 36.1 + - - +
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Residues in contact with SER 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PHE* 2.7 49.8 + - - -
94B GLU* 3.5 8.3 - - - -
96B TRP* 1.3 76.0 - - - +
98B ARG* 1.3 62.1 + - - +
100B ASP* 3.2 11.3 + - - +
101B LYS* 3.1 22.3 + - - +
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Residues in contact with ARG 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A SER* 4.0 14.1 + - - +
40A ASN* 5.3 5.1 - - - +
42A GLU* 3.0 43.6 + - - +
43A MET* 4.9 2.2 - - - +
94B GLU 3.1 13.7 + - - +
95B SER* 3.2 13.5 - - - +
96B TRP 3.1 0.2 - - - -
97B SER* 1.3 74.2 - - - +
99B VAL* 1.3 66.3 + - + +
101B LYS* 3.4 11.0 + - - +
102B ILE* 3.2 43.4 + - + +
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Residues in contact with VAL 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN* 3.8 35.0 - - + +
15A VAL* 4.3 4.9 - - + -
16A ILE* 3.9 21.8 - - + -
95B SER 3.0 19.0 + - - +
96B TRP* 3.5 28.5 - - + +
98B ARG* 1.3 78.9 - - + +
100B ASP* 1.3 64.8 + - - +
102B ILE* 3.3 10.4 + - + +
103B ILE* 3.0 40.7 + - + +
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Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 6.0 0.3 - - - +
127A DM1 4.0 37.4 + - - +
96B TRP* 3.0 26.4 + - - +
97B SER* 3.2 12.8 + - - +
99B VAL* 1.3 80.7 - - - +
101B LYS* 1.3 53.1 + - - +
103B ILE* 3.3 10.5 + - - +
104B GLU* 2.7 35.5 + - - +
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Residues in contact with LYS 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B SER 3.1 12.7 + - - +
98B ARG* 3.7 15.7 - - - +
99B VAL 3.3 0.2 - - - -
100B ASP* 1.3 71.4 - - - +
102B ILE* 1.3 57.4 + - + +
104B GLU* 3.1 36.3 + - - +
105B ASN* 2.6 56.0 + - - +
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.4 24.2 - - + -
35A VAL* 4.5 10.1 - - + -
38A ALA* 3.6 31.3 - - + +
39A SER* 4.1 16.8 - - - -
43A MET* 4.4 16.8 - - + -
98B ARG* 3.2 44.9 + - + +
99B VAL* 3.6 7.2 - - + +
101B LYS* 1.3 77.6 - - + +
103B ILE* 1.3 56.6 + - - +
105B ASN* 3.2 3.3 + - - +
106B LEU* 2.8 37.3 + - + +
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A VAL* 3.6 34.1 - - + +
16A ILE* 4.5 11.0 - - + -
19A ASN* 3.6 40.2 - - + +
23A GLN* 4.7 1.8 - - - +
127A DM1 6.0 6.5 - - + -
99B VAL* 3.0 28.1 + - + +
100B ASP* 3.6 13.7 - - - +
102B ILE* 1.3 70.9 - - - +
104B GLU* 1.3 64.8 + - - +
106B LEU* 3.2 12.4 + - + +
107B GLU* 3.1 35.7 + - - +
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Residues in contact with GLU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100B ASP 2.7 20.1 + - - +
101B LYS* 3.3 40.2 + - - +
103B ILE* 1.3 73.8 - - - +
105B ASN* 1.3 59.9 + - - +
107B GLU* 3.4 14.9 + - - +
108B ALA* 3.1 28.5 + - + +
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Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 2.7 39.1 + - + +
40A ASN* 4.1 18.8 + - - +
101B LYS* 2.6 43.3 + - - +
102B ILE* 3.4 2.7 - - - +
104B GLU* 1.3 74.8 - - - +
106B LEU* 1.3 60.3 + - - +
108B ALA* 3.8 5.8 - - - +
109B ASN* 2.9 38.8 + - - +
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Residues in contact with LEU 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ILE* 4.3 13.2 - - + +
19A ASN* 5.0 1.6 - - + -
20A VAL* 3.7 32.1 - - + +
23A GLN* 4.5 12.4 - - + +
34A GLN* 3.9 57.1 + - + +
35A VAL* 4.3 2.0 - - + +
38A ALA* 3.8 8.3 - - + -
102B ILE* 2.8 28.1 + - + +
103B ILE* 3.2 19.0 + - + +
105B ASN* 1.3 75.7 - - - +
107B GLU* 1.3 58.9 - - - +
109B ASN* 4.1 3.6 - - + +
110B LYS* 3.0 29.3 + - - +
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASN* 4.7 4.2 + - - -
22A LYS* 5.7 2.9 + - - -
23A GLN* 3.6 26.5 + - - +
103B ILE* 3.1 33.0 + - - +
104B GLU* 3.7 15.3 - - - +
106B LEU* 1.3 77.5 - - - +
108B ALA* 1.3 56.6 + - - +
110B LYS* 3.5 9.0 - - - +
111B LYS* 2.9 27.5 + - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B GLU* 3.1 18.4 + - + +
105B ASN* 3.8 8.1 - - - +
107B GLU* 1.3 75.4 - - - +
109B ASN* 1.3 58.4 + - - +
111B LYS* 3.0 10.0 + - - +
112B SER* 2.7 35.0 + - - -
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Residues in contact with ASN 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A GLN* 5.1 4.7 + - + -
37A GLU* 3.8 36.0 + - - +
38A ALA* 3.8 12.1 - - - +
105B ASN* 2.9 23.7 + - - +
106B LEU* 4.1 4.5 - - + +
108B ALA* 1.3 76.1 - - - +
110B LYS* 1.3 65.1 + - - +
112B SER* 3.2 13.5 + - - -
113B GLU* 3.2 23.4 + - - +
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Residues in contact with LYS 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LYS 5.2 0.4 + - - -
23A GLN* 3.2 56.2 + - + +
34A GLN* 5.6 6.3 - - - +
106B LEU 3.0 21.1 + - - +
107B GLU* 3.5 7.2 - - - +
109B ASN* 1.3 75.0 - - - +
111B LYS* 1.3 59.9 + - - +
113B GLU* 3.1 20.5 + - - +
114B ALA* 3.2 12.4 + - + +
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Residues in contact with LYS 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B GLU 2.9 18.6 + - - +
108B ALA* 3.0 10.0 + - - +
110B LYS* 1.3 73.6 - - - +
112B SER* 1.3 61.5 + - - +
113B GLU 3.1 1.8 - - - -
114B ALA* 3.4 6.8 + - + +
115B ILE* 2.9 50.1 + - + +
----------------------------------------------------------
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Residues in contact with SER 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 2.7 17.3 + - - -
109B ASN* 3.2 18.2 + - - -
111B LYS* 1.3 74.0 - - - +
113B GLU* 1.3 67.1 + - - +
114B ALA 3.3 0.9 - - - -
115B ILE* 3.0 27.6 - - - +
----------------------------------------------------------
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Residues in contact with GLU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASN 3.2 14.2 + - - +
110B LYS* 3.1 10.7 + - - +
112B SER* 1.3 87.7 - - - +
114B ALA* 1.3 59.0 + - - +
115B ILE 4.5 1.7 - - - +
----------------------------------------------------------
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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