Contacts of the helix formed by residues 81 - 109 (chain B) in PDB entry 4JF7
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 VAL 81 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B ILE* 6.1 0.4 - - + -
77B TYR* 3.0 44.6 + - + +
80B ALA* 1.3 86.2 - - + +
82B ALA* 1.3 65.8 + - - +
83B LEU 3.4 1.3 - - - -
84B PRO* 3.6 1.1 - - - +
85B LEU* 3.0 35.8 + - + +
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Residues in contact with ALA 82 (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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79A SER 5.4 2.2 - - - +
77B TYR* 2.9 29.2 + - + +
78B ASN* 3.5 24.2 - - + +
81B VAL* 1.3 74.0 - - - +
83B LEU* 1.3 64.7 + - + +
85B LEU* 3.9 6.4 - - - +
86B GLN* 3.3 23.6 + - - +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A SER* 3.7 34.5 - - - +
83A LEU* 4.4 21.8 - - + -
84A PRO* 3.9 22.0 - - + -
87A LEU* 4.5 12.1 - - + -
78B ASN 2.9 23.2 + - - +
79B SER* 4.3 10.3 - - - +
82B ALA* 1.3 76.2 - - + +
84B PRO* 1.4 65.5 - - + +
85B LEU 3.2 1.6 - - - -
86B GLN* 3.2 12.9 + - - +
87B LEU* 2.9 41.4 + - + +
83D LEU* 6.2 1.3 - - + -
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Residues in contact with PRO 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B SER 3.3 23.6 - - - +
80B ALA* 3.2 24.2 - - - +
81B VAL* 3.6 8.3 - - - +
83B LEU* 1.4 90.3 - - + +
85B LEU* 1.3 59.7 + - - +
87B LEU* 4.5 10.3 - - + -
88B ASP* 2.9 34.1 + - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 3.0 26.2 + - + +
82B ALA* 3.9 6.5 - - - +
84B PRO* 1.3 77.4 - - - +
86B GLN* 1.3 54.7 + - - +
88B ASP* 3.4 7.1 + - + +
89B THR* 2.5 41.5 + - - +
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Residues in contact with GLN 86 (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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84A PRO* 3.4 35.8 + - - +
87A LEU* 3.4 39.7 - - + +
88A ASP* 3.5 13.9 + - - -
82B ALA 3.3 15.0 + - - +
83B LEU* 3.2 10.9 + - - +
85B LEU* 1.3 78.4 - - - +
87B LEU* 1.3 59.9 + - - +
89B THR* 3.2 6.6 + - - -
90B LEU* 2.8 38.0 + - + +
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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
----------------------------------------------------------
87A LEU* 3.9 34.1 - - + -
83B LEU* 2.9 29.2 + - + +
84B PRO* 4.1 9.4 - - + +
86B GLN* 1.3 76.6 - - - +
88B ASP* 1.3 60.1 - - - +
90B LEU* 3.8 18.8 - - + +
91B GLU* 3.1 28.8 + - - +
87D LEU* 5.1 6.5 - - + -
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PRO* 2.9 24.5 + - - +
85B LEU* 3.6 10.3 - - + +
86B GLN 3.1 0.4 - - - -
87B LEU* 1.3 79.2 - - - +
89B THR* 1.3 63.0 + - - +
91B GLU* 3.4 15.0 + - - +
92B SER* 3.3 18.7 + - - -
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Residues in contact with THR 89 (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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85B LEU* 2.5 34.1 + - - +
86B GLN* 3.2 6.5 + - - -
88B ASP* 1.3 75.0 - - - +
90B LEU* 1.3 64.0 + - - +
92B SER* 3.0 19.5 + - - -
93B THR* 3.2 18.5 + - - +
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Residues in contact with LEU 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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87A LEU* 3.7 25.4 - - + +
88A ASP* 6.0 0.2 - - - +
90A LEU* 4.6 10.1 - - + -
91A GLU* 3.6 49.6 - - + +
86B GLN* 2.8 22.4 + - + +
87B LEU* 3.8 24.2 - - + +
89B THR* 1.3 75.7 - - - +
91B GLU* 1.3 68.0 + - + +
93B THR* 3.5 1.1 + - - -
94B LEU* 3.4 37.1 + - + +
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Residues in contact with GLU 91 (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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87B LEU 3.1 19.3 + - - +
88B ASP* 3.4 15.5 - - - +
89B THR 3.2 0.2 - - - -
90B LEU* 1.3 83.1 - - + +
92B SER* 1.3 61.5 + - - +
94B LEU* 3.3 8.8 + - - +
95B LEU* 3.0 44.7 + - + +
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ASP 3.3 7.9 + - - -
89B THR* 3.0 13.9 + - - -
91B GLU* 1.3 78.8 - - - +
93B THR* 1.3 53.2 + - - +
95B LEU* 3.7 8.3 - - - +
96B THR* 2.8 47.5 + - - -
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Residues in contact with THR 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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91A GLU* 3.2 28.1 + - - +
95A LEU* 3.7 24.0 - - + -
89B THR* 3.2 15.2 + - - +
90B LEU 3.7 2.9 - - - -
91B GLU 3.3 0.4 - - - -
92B SER* 1.3 76.6 - - - +
94B LEU* 1.3 58.6 + - - +
96B THR* 3.6 6.4 + - - -
97B ALA* 3.1 26.9 + - - +
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Residues in contact with LEU 94 (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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90A LEU* 5.4 2.7 - - + -
91A GLU* 3.7 26.9 - - + +
94A LEU* 3.5 36.3 - - + -
95A LEU* 4.0 10.1 - - + -
98A ILE* 4.1 7.9 - - + +
90B LEU* 3.4 31.2 + - + +
91B GLU* 3.3 9.6 + - - +
92B SER 3.3 0.4 - - - -
93B THR* 1.3 83.9 - - - +
95B LEU* 1.3 58.1 + - + +
97B ALA* 3.3 7.2 + - - +
98B ILE* 2.8 38.8 + - + +
94D LEU* 5.7 5.2 - - + -
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Residues in contact with LEU 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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91B GLU* 3.0 49.5 + - + +
92B SER* 3.9 6.1 - - - +
94B LEU* 1.3 74.8 - - + +
96B THR* 1.3 56.5 + - - +
98B ILE* 3.7 20.7 - - + +
99B LYS* 2.8 37.1 + - - +
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Residues in contact with THR 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 SER* 2.8 33.4 + - - -
93B THR* 3.7 8.0 - - - -
95B LEU* 1.3 72.2 - - - +
97B ALA* 1.3 57.8 + - - +
99B LYS* 3.8 20.6 + - - +
100B SER* 2.9 28.3 + - - -
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Residues in contact with ALA 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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95A LEU* 3.5 24.5 - - + -
98A ILE* 3.7 20.4 - - + +
99A LYS* 4.4 17.2 + - - +
93B THR 3.1 18.3 + - - +
94B LEU 3.6 4.3 - - - +
96B THR* 1.3 76.3 - - - +
98B ILE* 1.3 62.3 + - - +
100B SER* 3.2 19.2 - - - -
101B LEU* 3.5 8.3 + - - +
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Residues in contact with ILE 98 (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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98A ILE* 3.7 26.0 - - + -
94B LEU* 2.8 33.4 + - + +
95B LEU* 3.3 23.3 + - + +
97B ALA* 1.3 73.9 - - - +
99B LYS* 1.3 65.8 + - - +
100B SER 3.1 0.9 - - - -
101B LEU* 3.1 17.5 + - - +
102B GLN* 3.1 12.2 + - + +
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Residues in contact with LYS 99 (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 LEU 2.8 19.5 + - - +
96B THR* 3.9 20.4 + - - +
98B ILE* 1.3 74.5 - - - +
100B SER* 1.3 51.8 + - - +
102B GLN* 3.2 29.0 + - - +
103B THR* 2.7 49.3 + - - +
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Residues in contact with SER 100 (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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99A LYS* 3.6 17.8 + - - -
96B THR* 2.9 19.7 + - - -
97B ALA* 3.2 14.4 - - - -
98B ILE 3.1 0.4 - - - -
99B LYS* 1.3 79.6 - - - +
101B LEU* 1.3 60.4 + - - +
103B THR* 3.6 6.6 + - - -
104B SER* 3.2 25.6 + - - -
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Residues in contact with LEU 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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98A ILE* 3.1 36.3 - - + +
99A LYS* 4.9 9.4 - - + +
101A LEU* 3.8 25.1 - - + -
102A GLN* 4.6 26.9 - - + +
97B ALA 3.8 11.2 - - - +
98B ILE* 3.1 9.7 + - + +
100B SER* 1.3 80.9 - - - +
102B GLN* 1.3 64.7 + - - +
103B THR 3.2 2.0 - - - -
104B SER* 3.4 6.5 + - - +
105B ASP* 3.1 36.5 + - - +
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Residues in contact with GLN 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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98B ILE* 3.1 13.8 + - + +
99B LYS* 3.4 29.2 - - - +
101B LEU* 1.3 77.1 - - - +
103B THR* 1.3 62.0 + - - +
105B ASP* 4.0 3.8 + - - +
106B LYS* 3.4 35.8 + - - +
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Residues in contact with THR 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 LYS* 2.7 36.9 + - - +
100B SER* 3.9 7.6 - - - -
101B LEU 3.2 0.2 - - - -
102B GLN* 1.3 80.4 + - - +
104B SER* 1.3 61.4 + - - +
105B ASP 3.4 0.2 - - - -
106B LYS* 3.4 12.3 + - + +
107B LEU* 3.3 32.5 + - + +
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Residues in contact with SER 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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102A GLN* 4.4 14.4 - - - +
100B SER 3.2 18.5 + - - -
101B LEU* 3.4 12.5 + - - -
103B THR* 1.3 78.5 - - - +
105B ASP* 1.3 65.7 + - - +
107B LEU* 3.4 29.0 + - - +
108B GLU* 3.7 11.4 + - - +
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Residues in contact with ASP 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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102A GLN* 5.0 12.1 + - - +
101B LEU* 3.1 22.3 + - - +
102B GLN* 4.5 4.3 - - - +
104B SER* 1.3 82.0 + - - +
106B LYS* 1.3 60.3 + - - +
107B LEU 3.3 0.9 - - - -
108B GLU* 3.6 26.3 + - - +
109B GLN* 3.6 22.6 + - - +
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Residues in contact with LYS 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 GLN* 3.4 34.6 + - - +
103B THR* 3.4 12.5 + - + +
104B SER 3.2 0.2 - - - -
105B ASP* 1.3 76.3 - - - +
107B LEU* 1.3 63.7 + - - +
108B GLU 3.3 0.7 - - - -
109B GLN* 3.5 35.9 + - + +
110B ASN* 3.6 14.1 + - - +
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Residues in contact with LEU 107 (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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108A GLU* 5.6 6.7 - - - +
113A TRP* 4.8 22.7 - - + +
103B THR* 3.3 25.9 + - + +
104B SER* 3.4 20.2 - - - +
105B ASP 3.3 0.2 - - - -
106B LYS* 1.3 76.2 - - - +
108B GLU* 1.3 58.3 + - + +
109B GLN 3.2 0.4 - - - -
110B ASN* 3.1 22.5 + - + +
111B CYS* 3.2 18.0 - - - -
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Residues in contact with GLU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A GLN* 4.3 17.7 + - - +
107A LEU* 6.0 5.3 - - + +
267A ASN* 5.3 0.5 - - - +
104B SER* 3.9 14.8 + - - +
105B ASP* 3.6 23.4 + - - +
106B LYS 3.3 0.2 - - - -
107B LEU* 1.3 75.0 - - + +
109B GLN* 1.3 61.1 + - + +
110B ASN 3.1 2.2 - - - -
111B CYS* 3.3 21.7 + - - +
113B TRP* 3.9 34.1 + - + -
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Residues in contact with GLN 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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267A ASN* 3.0 31.9 + - - +
105B ASP* 3.6 20.6 + - - +
106B LYS* 3.5 29.3 + - + +
107B LEU 3.2 0.4 - - - -
108B GLU* 1.3 76.9 - - + +
110B ASN* 1.3 60.0 + - - +
111B CYS 3.3 1.9 + - - -
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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
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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) + - + + + + + -
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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