Contacts of the helix formed by residues 72 - 96 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.4 36.3 - - + -
18A LYS* 4.9 1.3 - - + -
19A LYS* 3.7 34.1 - - + -
22A ILE* 3.9 15.2 - - + +
66A LEU* 3.5 7.3 - - - +
69A TYR* 2.9 24.4 + + + +
71A MET* 1.3 108.5 - - + +
73A TYR* 1.3 65.3 + - - +
74A SER 3.2 2.2 - - - -
75A ASN* 3.0 37.4 + - + +
76A GLY 3.4 7.3 + - - -
109B TRP* 3.9 35.0 - + - -
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Residues in contact with TYR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 3.9 33.4 - - + +
69A TYR 3.9 1.0 + - - -
70A PRO* 3.1 21.2 + - + +
71A MET 3.5 0.4 - - - -
72A PHE* 1.3 76.3 - - - +
74A SER* 1.3 66.2 + - - +
76A GLY* 3.1 12.6 + - - -
77A PHE* 3.1 37.6 + + - +
80A LEU* 5.9 1.1 - - + -
107A ASP* 2.7 36.7 + - - -
109A TRP* 5.0 0.7 - + - -
110A VAL* 3.6 14.0 + - + +
70B PRO* 3.8 24.5 - - + +
71B MET* 3.5 44.0 - - + +
73B TYR* 5.6 0.2 - - + -
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A MET 4.5 6.8 + - - -
73A TYR* 1.3 85.9 - - - +
75A ASN* 1.3 69.1 + - - +
76A GLY 3.4 0.7 + - - -
77A PHE* 3.5 16.8 + - - +
78A ILE* 4.8 5.2 + - - +
74B SER* 5.8 9.3 - - - -
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Residues in contact with ASN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LYS* 3.9 21.0 - - + +
22A ILE* 4.0 10.0 - - + +
23A VAL* 3.8 29.9 - - + +
26A SER* 3.7 17.8 + - - -
71A MET 4.4 1.4 + - - -
72A PHE* 3.0 42.2 + - + +
74A SER* 1.3 83.4 + - - +
76A GLY* 1.3 57.5 + - - +
77A PHE 3.5 0.2 - - - -
78A ILE* 5.2 0.7 + - - +
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Residues in contact with GLY 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 3.8 14.6 - - - +
26A SER* 3.9 4.2 + - - -
62A GLN* 3.8 14.3 + - - -
66A LEU* 4.3 11.7 - - - -
72A PHE 3.4 3.8 + - - -
73A TYR 3.1 7.1 + - - -
75A ASN* 1.3 77.7 - - - +
77A PHE* 1.3 67.0 + - - +
78A ILE 3.4 2.2 + - - -
79A GLY* 3.4 2.9 + - - -
80A LEU* 3.3 22.3 + - - +
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Residues in contact with PHE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A LEU* 5.4 0.4 - - - -
73A TYR* 3.1 37.1 + + - +
74A SER* 3.5 18.4 + - - +
75A ASN 3.5 0.2 - - - -
76A GLY* 1.3 77.2 - - - +
78A ILE* 1.3 64.1 + - + +
80A LEU* 3.1 7.2 + - - +
81A GLN* 2.9 48.3 + - + +
109A TRP* 3.7 17.3 - + - -
110A VAL* 3.3 30.0 - - + +
113A PHE* 3.7 43.1 - + + -
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Residues in contact with ILE 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A SER* 4.5 3.8 - - - +
30A SER* 5.6 3.6 - - - -
74A SER 4.8 3.9 + - - +
75A ASN 5.2 0.8 + - - +
76A GLY 3.4 0.6 - - - -
77A PHE* 1.3 81.0 - - + +
79A GLY* 1.3 59.2 + - - +
81A GLN* 3.3 18.8 + - + +
82A GLU* 2.9 48.5 + - + +
163F ARG* 6.0 7.6 - - - +
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Residues in contact with GLY 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER* 3.0 39.6 + - - -
29A MET* 3.4 23.5 - - - +
30A SER* 4.7 1.8 - - - -
76A GLY 3.4 1.8 + - - -
77A PHE 3.3 0.6 - - - -
78A ILE* 1.3 77.8 - - - +
80A LEU* 1.3 57.8 + - - +
82A GLU* 3.4 6.6 + - - +
83A TYR* 3.0 21.0 + - - +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A MET* 3.8 20.4 - - + -
59A ALA* 4.3 4.7 - - + +
62A GLN* 4.3 9.6 - - + -
63A ILE* 3.8 35.2 - - + -
66A LEU* 3.6 31.6 - - + -
73A TYR* 5.9 1.6 - - + -
76A GLY 3.3 8.7 + - - +
77A PHE* 3.1 8.5 + - - +
79A GLY* 1.3 73.4 - - - +
81A GLN* 1.3 65.9 + - - +
83A TYR* 3.2 15.1 + - + +
84A VAL* 3.0 26.9 + - - +
106A VAL* 4.4 4.7 - - + -
110A VAL* 4.1 24.0 - - + -
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Residues in contact with GLN 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 2.9 37.1 + - + +
78A ILE* 3.4 19.8 - - - +
80A LEU* 1.3 77.6 - - - +
82A GLU* 1.3 60.8 + - + +
84A VAL* 3.3 1.6 + - - -
85A GLU* 3.1 24.0 + - - +
110A VAL* 4.5 9.5 - - - +
113A PHE* 3.5 18.6 + - - +
114A GLY* 3.6 25.5 - - - +
117A ASP* 2.6 28.3 + - - +
165A LYS* 3.8 12.1 - - - +
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Residues in contact with GLU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 3.3 24.4 + - - +
33A SER* 3.0 25.5 + - - +
34A LYS* 2.8 34.5 + - - +
37A ILE* 5.2 0.2 - - - +
78A ILE* 2.9 35.8 + - + +
79A GLY 3.8 3.8 - - - +
80A LEU 3.2 0.2 - - - -
81A GLN* 1.3 76.8 - - + +
83A TYR* 1.3 60.4 + - - +
85A GLU* 3.6 18.4 - - - +
86A ALA* 3.0 24.8 + - - +
163F ARG* 5.8 0.3 + - - -
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Residues in contact with TYR 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A MET* 3.7 10.8 - - + -
33A SER* 3.5 7.8 + - - -
55A LEU* 3.8 15.3 - - + -
56A THR* 4.1 19.0 - - - +
59A ALA* 3.6 30.6 - - + +
63A ILE* 4.8 0.7 - - + -
79A GLY 3.0 15.1 + - - +
80A LEU* 3.2 19.3 + - + +
82A GLU* 1.3 74.1 - - - +
84A VAL* 1.3 67.4 + - + +
86A ALA* 3.4 0.5 + - - +
87A LEU* 3.0 57.2 + - + +
103A GLU 5.0 0.3 + - - -
104A LEU* 2.7 45.3 + - + +
106A VAL* 3.8 15.9 - - + -
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Residues in contact with VAL 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A LEU 3.0 18.0 + - - +
81A GLN 3.3 6.9 + - - +
83A TYR* 1.3 76.0 - - + +
85A GLU* 1.3 58.6 + - - +
87A LEU* 4.2 0.3 - - - +
88A ALA* 2.9 29.6 + - - +
104A LEU* 3.9 24.5 - - + +
106A VAL* 3.9 22.2 - - + -
110A VAL* 3.9 21.8 - - + +
111A TYR* 3.9 28.5 - - + +
114A GLY* 4.0 3.4 - - - -
115A ILE* 4.0 17.9 - - + +
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.9 9.9 - - + +
81A GLN* 3.1 16.8 + - - +
82A GLU* 3.6 21.4 - - - +
84A VAL* 1.3 77.8 - - - +
86A ALA* 1.3 61.6 + - - +
88A ALA* 3.7 2.3 - - - +
89A LEU* 3.1 22.5 + - - +
114A GLY 3.8 14.3 + - - +
117A ASP* 3.7 39.3 - - + +
118A ILE* 3.9 8.5 - - + +
121A GLU* 2.9 40.1 - - + +
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Residues in contact with ALA 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A SER* 3.8 32.8 - - - +
36A LEU* 4.0 17.6 - - + +
37A ILE* 3.9 15.9 - - + +
40A MET* 5.9 0.2 - - - +
55A LEU* 4.1 2.2 - - + -
82A GLU 3.0 17.7 + - - +
83A TYR 3.9 2.5 - - - +
84A VAL 3.3 0.2 - - - -
85A GLU* 1.3 75.3 - - - +
87A LEU* 1.3 61.7 + - - +
89A LEU* 3.3 4.3 + - - +
90A TYR* 2.9 26.7 + - - +
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A LEU* 4.0 11.2 - - + -
52A LYS* 4.5 17.3 - - + -
55A LEU* 3.8 18.4 - - + -
56A THR* 4.0 15.9 - - + +
83A TYR* 3.0 48.9 + - + +
84A VAL 4.2 0.4 - - - +
86A ALA* 1.3 73.9 - - - +
88A ALA* 1.3 61.4 + - - +
90A TYR* 3.2 4.6 + - + +
91A TYR* 2.9 47.7 + - + -
99A PRO* 4.4 0.9 - - - -
104A LEU* 3.5 32.8 - - + -
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Residues in contact with ALA 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 2.9 19.5 + - + +
87A LEU* 1.3 77.5 - - - +
89A LEU* 1.3 58.8 + - - +
91A TYR 3.5 0.5 + - - -
92A TYR* 2.8 29.9 + - - +
97A ARG 4.0 3.5 - - - +
98A ILE* 4.1 8.2 - - + +
99A PRO* 3.6 21.9 - - + +
115A ILE* 4.1 14.4 - - + -
118A ILE* 3.6 25.8 - - + -
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ILE* 3.7 43.3 - - + +
40A MET* 4.7 3.1 - - + -
41A ILE* 4.4 7.2 - - + -
85A GLU 3.1 15.1 + - - +
86A ALA* 3.6 7.4 - - - +
87A LEU 3.3 0.2 - - - -
88A ALA* 1.3 72.7 - - - +
90A TYR* 1.3 69.0 + - - +
92A TYR* 3.2 5.3 + - + +
93A ILE* 3.0 50.7 + - + +
118A ILE* 4.9 4.2 - - + +
121A GLU* 3.9 37.2 - - + +
122A ILE* 4.2 17.0 - - + +
125A LYS* 4.9 1.6 - - + -
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Residues in contact with TYR 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.0 16.6 - - + -
40A MET* 3.7 40.5 - - + +
45A TYR* 5.9 1.3 - + - -
48A ALA* 4.7 1.6 - - + -
49A ASP* 2.7 28.5 + - - -
52A LYS* 3.4 45.2 + - + +
86A ALA 2.9 14.8 + - - +
87A LEU* 3.3 12.8 - - - +
89A LEU* 1.3 76.8 - - - +
91A TYR* 1.3 77.5 + + - +
94A LYS* 2.9 72.9 + - + +
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Residues in contact with TYR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A LYS* 3.4 34.9 + - - -
87A LEU* 2.9 37.5 + - + +
90A TYR* 1.3 87.2 - + - +
92A TYR* 1.3 61.5 + - - +
94A LYS* 5.6 0.9 - - - -
95A GLU* 2.9 51.4 + - + +
96A ASN 3.1 6.6 + - - -
97A ARG* 3.1 45.8 + - + +
99A PRO* 4.0 25.6 - - + -
103A GLU* 4.3 12.4 + - + +
104A LEU* 5.1 2.0 - - + -
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Residues in contact with TYR 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ALA 2.8 19.1 + - - +
89A LEU* 3.6 9.2 - - + +
91A TYR* 1.3 76.0 - - - +
93A ILE* 1.3 64.2 + - + +
96A ASN* 3.1 31.9 + - - +
97A ARG 3.0 15.6 + - - +
98A ILE* 4.2 18.2 - - + -
122A ILE* 4.0 38.8 - - + -
125A LYS* 5.9 0.4 - - + -
137A TYR* 3.6 25.7 - + - -
140A LYS* 4.2 5.5 + - - +
141A ALA* 3.6 16.6 + - - +
144A ASP* 2.6 44.8 + - + +
1B MET* 4.5 8.5 - - - -
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Residues in contact with ILE 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 3.8 35.2 - - + +
41A ILE* 4.7 0.7 - - - +
45A TYR* 3.8 24.0 - - + +
89A LEU* 3.0 47.4 + - + +
92A TYR* 1.3 79.2 - - + +
94A LYS* 1.3 64.0 + - - +
96A ASN 4.5 1.0 + - - -
125A LYS* 4.0 31.2 - - + -
137A TYR* 4.0 20.0 - - + +
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Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 4.5 8.3 - - + -
45A TYR* 5.5 9.6 - - + -
49A ASP* 5.1 1.9 + - - -
90A TYR* 2.9 56.9 + - + +
91A TYR* 4.6 1.4 - - - +
93A ILE* 1.3 82.7 - - - +
95A GLU* 1.3 83.5 + - + +
96A ASN 3.7 0.4 - - - -
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR* 2.9 32.9 + - + +
94A LYS* 1.3 102.3 + - + +
96A ASN* 1.3 72.9 + - - +
97A ARG* 2.8 44.9 + - - +
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Residues in contact with ASN 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A TYR 3.1 3.0 + - - -
92A TYR* 3.1 24.6 + - - +
93A ILE 4.5 0.8 - - - +
94A LYS 3.7 1.0 - - - -
95A GLU* 1.3 78.7 - - - +
97A ARG* 1.3 60.2 + - - +
140A LYS* 2.6 39.1 + - - +
144A ASP* 4.2 2.8 - - - +
1B MET* 5.7 4.5 - - - +
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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