Contacts of the helix formed by residues 66 - 94 (chain B) in PDB entry 2YGG
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 66 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 4.4 11.2 - - + -
13B PHE* 3.5 23.6 - - + -
14B LYS* 3.5 33.2 - - + -
17B PHE* 3.3 53.1 - + + -
26B GLY 3.8 7.6 + - - +
65B ASP* 1.3 72.4 - - - +
67B PRO* 1.3 70.9 - - + +
69B PHE* 3.0 13.4 + + - +
70B LEU* 2.9 48.8 + - + +
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Residues in contact with PRO 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ASP* 3.4 18.4 - - + +
66B PHE* 1.3 97.4 - - + +
68B GLU* 1.3 59.8 + - + +
70B LEU* 3.3 17.1 - - + +
71B THR* 3.1 26.9 + - - -
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Residues in contact with GLU 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B VAL* 3.9 15.5 - - - +
57B ASP* 3.9 1.1 - - - +
58B ALA* 3.3 25.1 + - + +
59B ASP* 3.0 29.5 + - - +
63B THR 3.4 0.5 - - - +
64B ILE* 3.3 10.7 - - + +
65B ASP* 2.9 39.5 + - - +
67B PRO* 1.3 75.4 - - + +
69B PHE* 1.3 65.7 + - - +
71B THR* 3.5 6.8 + - - -
72B MET* 3.2 24.1 + - - +
1152B CA 2.8 29.8 - - - -
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Residues in contact with PHE 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A TYR* 4.4 18.2 - + - -
662A ALA* 6.2 0.2 - - + -
13B PHE* 3.4 28.3 - + - -
16B ALA* 3.8 15.0 - - + -
17B PHE* 3.6 41.7 - + + -
20B PHE* 4.4 12.8 - + - -
28B ILE* 5.6 2.5 - - + -
56B VAL* 4.7 0.2 - - - -
64B ILE* 4.0 11.4 - - + +
65B ASP 3.1 12.4 + - - +
66B PHE* 3.0 22.3 + + - +
68B GLU* 1.3 74.7 - - - +
70B LEU* 1.3 66.2 + - - +
72B MET* 3.4 14.0 - - + +
73B MET* 3.0 59.7 + - + +
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 5.7 8.5 - - + -
13B PHE* 3.5 47.9 - - + -
66B PHE* 2.9 36.3 + - + +
67B PRO* 3.3 17.7 - - + +
69B PHE* 1.3 75.6 - - - +
71B THR* 1.3 55.6 + - - +
73B MET* 2.9 5.6 + - - +
74B ALA* 2.7 37.4 + - - +
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Residues in contact with THR 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B PRO 3.1 14.5 + - - -
68B GLU* 3.8 7.4 - - - -
70B LEU* 1.3 76.6 - - - +
72B MET* 1.3 59.4 + - + +
74B ALA* 3.5 7.5 + - - +
75B ARG* 3.1 27.3 + - + +
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Residues in contact with MET 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A TYR* 3.2 55.2 - - + -
55B GLU 5.9 0.7 - - - +
56B VAL* 3.6 37.2 - - + -
68B GLU 3.2 7.8 + - - +
69B PHE* 3.4 17.3 - - + +
70B LEU 3.2 0.6 - - - -
71B THR* 1.3 78.1 - - + +
73B MET* 1.3 69.2 + - - +
75B ARG* 3.5 7.8 + - - +
76B LYS* 3.1 45.0 + - - +
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Residues in contact with MET 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A TYR* 4.0 29.2 - - - +
662A ALA* 6.2 0.2 - - + -
663A TRP* 3.4 49.6 - - + -
13B PHE* 3.5 22.4 - - + -
16B ALA* 4.6 1.1 - - + -
69B PHE* 3.0 54.6 + - + +
70B LEU 2.9 2.3 + - - +
72B MET* 1.3 79.9 - - + +
74B ALA* 1.3 64.9 + - - +
75B ARG 3.0 1.6 - - - -
76B LYS* 3.0 11.5 + - - +
77B MET* 2.9 29.8 + - + +
1155B MRD 4.9 5.6 - - - +
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Residues in contact with ALA 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 4.9 5.2 - - + -
70B LEU 2.7 20.7 + - - +
71B THR* 3.8 7.0 - - - +
73B MET* 1.3 73.5 - - - +
75B ARG* 1.3 56.6 + - - +
77B MET* 3.6 13.8 + - - +
78B LYS* 2.9 27.9 + - - +
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B THR* 3.1 17.9 + - + +
72B MET* 3.7 8.9 - - - +
73B MET 3.0 0.6 - - - -
74B ALA* 1.3 76.2 - - - +
76B LYS* 1.3 61.5 + - - +
78B LYS* 3.5 13.7 + - + +
79B ASP* 3.0 50.8 + - - +
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Residues in contact with LYS 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ASP* 3.7 36.6 + - - +
659A TYR* 4.3 16.6 - - + -
660A GLU* 5.2 9.5 + - + +
72B MET* 3.1 32.1 + - - +
73B MET* 3.0 13.7 + - - +
75B ARG* 1.3 76.5 - - + +
77B MET* 1.3 59.9 + - - +
79B ASP* 3.4 9.2 + - - +
80B THR* 3.0 22.7 + - - -
1155B MRD 3.3 31.7 + - + +
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Residues in contact with MET 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A TRP* 4.7 13.2 - - + -
13B PHE* 4.0 28.0 - - + -
73B MET* 2.9 15.9 + - + +
74B ALA* 3.7 11.7 - - - +
76B LYS* 1.3 74.7 - - - +
78B LYS* 1.3 59.5 + - - +
80B THR* 3.2 2.8 + - - -
81B ASP* 2.9 43.4 + - - +
1155B MRD 3.9 34.9 + - + +
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Residues in contact with LYS 78 (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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74B ALA 2.9 18.9 + - - +
75B ARG* 3.7 14.8 - - + +
76B LYS 3.4 0.2 - - - -
77B MET* 1.3 76.4 - - - +
79B ASP* 1.3 76.6 + - - +
81B ASP* 3.5 8.5 + - + +
82B SER* 2.9 56.3 + - - +
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B ARG* 3.0 40.2 + - - +
76B LYS* 3.8 8.4 - - - +
78B LYS* 1.3 91.8 + - - +
80B THR* 1.3 66.1 + - - +
82B SER* 3.4 5.9 + - - -
83B GLU* 3.1 23.7 + - - +
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Residues in contact with THR 80 (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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76B LYS 3.0 9.7 + - - -
77B MET 3.2 7.8 + - - -
79B ASP* 1.3 76.4 - - - +
81B ASP* 1.3 67.6 + - - +
83B GLU* 3.3 8.5 + - - +
84B GLU* 3.1 40.8 + - + +
1155B MRD 3.2 46.5 - - + +
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Residues in contact with ASP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B MET* 2.9 31.6 + - - +
78B LYS* 3.8 6.9 - - - +
80B THR* 1.3 80.4 - - - +
82B SER* 1.3 57.9 + - - +
84B GLU* 3.4 19.3 + - - +
85B GLU* 2.9 46.8 + - - +
1155B MRD 5.4 1.3 + - - -
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Residues in contact with SER 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B LYS* 2.9 44.8 + - - +
79B ASP* 3.7 6.7 - - - -
80B THR 3.2 0.2 - - - -
81B ASP* 1.3 74.7 - - - +
83B GLU* 1.3 59.4 + - - +
85B GLU* 3.1 14.1 + - - +
86B ILE* 2.8 45.7 + - - +
147B THR* 6.3 1.1 - - - -
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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
----------------------------------------------------------
647A ARG* 3.1 39.6 + - - -
651A ARG* 5.5 0.5 + - - -
79B ASP 3.1 13.7 + - - +
80B THR* 3.6 10.1 - - - +
82B SER* 1.3 75.5 - - - +
84B GLU* 1.3 64.3 + - + +
86B ILE* 3.4 8.0 + - - +
87B ARG* 3.0 43.1 + - - +
139B TYR* 2.9 26.0 + - - +
143B VAL* 5.0 3.5 - - - +
1156B TAM 5.5 0.5 + - - -
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Residues in contact with GLU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B THR* 3.1 30.1 + - + +
81B ASP* 3.5 20.2 - - - +
83B GLU* 1.3 79.1 - - + +
85B GLU* 1.3 62.4 + - + +
87B ARG* 3.3 12.6 + - - +
88B GLU* 3.0 23.3 + - - +
91B ARG* 4.9 1.7 + - - -
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ASP* 2.9 33.3 + - - +
82B SER* 3.1 16.6 + - - +
84B GLU* 1.3 75.7 - - + +
86B ILE* 1.3 58.4 + - + +
88B GLU* 3.3 7.7 + - - +
89B ALA* 2.9 30.0 + - - +
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Residues in contact with ILE 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B SER* 2.8 33.2 + - - +
83B GLU* 3.7 10.8 - - - +
85B GLU* 1.3 70.5 - - + +
87B ARG* 1.3 60.1 + - - +
89B ALA* 3.5 4.0 + - - -
90B PHE* 3.0 25.1 + - - +
139B TYR* 3.9 3.4 - - + +
142B PHE* 3.4 28.2 - - + -
143B VAL* 3.9 30.5 - - + -
146B MET* 4.4 15.7 - - + -
147B THR* 3.7 30.5 - - + -
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B GLU* 3.0 31.8 + - - +
84B GLU* 3.3 10.5 + - - +
86B ILE* 1.3 75.5 - - - +
88B GLU* 1.3 64.2 + - - +
90B PHE* 3.4 3.5 + - - +
91B ARG* 3.2 49.6 + - - +
139B TYR* 2.9 42.0 - - + +
1156B TAM 4.6 22.7 + - - +
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Residues in contact with GLU 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU 3.0 14.2 + - - +
85B GLU* 3.7 10.1 - - - +
87B ARG* 1.3 73.4 - - - +
89B ALA* 1.3 66.2 + - - +
91B ARG* 2.6 44.9 + - - +
92B VAL* 3.1 35.1 + - + +
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLU 2.9 17.5 + - - +
86B ILE* 3.9 5.8 - - - +
88B GLU* 1.3 74.1 - - - +
90B PHE* 1.3 67.0 + - - +
92B VAL* 3.1 8.3 + - - +
93B PHE* 2.9 42.1 + - + -
142B PHE* 4.1 15.0 - - + -
146B MET* 5.8 4.0 - - + -
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Residues in contact with PHE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ILE 3.0 18.3 + - - +
87B ARG 3.8 5.4 - - - +
89B ALA* 1.3 76.2 - - - +
91B ARG* 1.3 55.1 + - - +
93B PHE* 3.3 3.0 + - - +
94B ASP* 2.8 51.5 + - + +
99B GLY* 3.3 33.7 - - - -
100B TYR 4.1 1.3 - - - -
101B ILE* 3.5 34.8 - - + -
137B VAL 3.6 11.2 - - - -
138B ASN 3.7 2.5 - - - -
139B TYR* 3.6 39.0 - + + -
142B PHE* 3.7 24.1 - + + -
1156B TAM 5.9 2.2 - - - -
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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
----------------------------------------------------------
84B GLU 4.9 1.6 + - - -
87B ARG* 3.2 41.4 + - - +
88B GLU* 2.6 53.0 + - - +
90B PHE* 1.3 83.2 - - - +
92B VAL* 1.3 61.1 + - - +
94B ASP* 3.4 18.9 - - - +
95B LYS* 4.9 0.7 - - - -
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU* 3.1 27.2 + - + +
89B ALA* 3.1 10.6 + - - +
91B ARG* 1.3 78.1 - - + +
93B PHE* 1.3 80.8 + - + +
94B ASP 3.5 0.2 + - - -
95B LYS* 3.7 18.4 + - - +
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Residues in contact with PHE 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B ALA* 2.9 29.1 + - + +
90B PHE 3.8 2.5 - - - +
92B VAL* 1.3 94.7 - - + +
94B ASP* 1.3 55.4 + - - +
95B LYS* 3.0 11.5 + - - +
101B ILE* 4.1 17.9 - - + -
105B GLU* 3.6 23.2 - - - +
106B LEU* 6.3 1.1 - - + -
109B VAL* 3.4 46.8 - - + +
113B LEU* 5.1 10.5 - - + -
142B PHE* 3.7 35.4 - + - -
146B MET* 5.4 5.4 - - + -
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Residues in contact with ASP 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PHE* 2.8 36.4 + - + +
91B ARG* 3.4 14.2 - - - +
92B VAL 3.4 0.4 - - - -
93B PHE* 1.3 69.9 - - - +
95B LYS* 1.3 60.2 + - - +
96B ASP* 3.0 9.4 - - - +
97B GLY* 3.0 17.9 + - - -
98B ASN* 3.2 0.7 - - - +
99B GLY* 2.7 28.7 + - - -
100B TYR 3.0 12.1 - - - +
101B ILE* 4.3 4.4 - - + +
105B GLU* 3.9 5.4 - - - -
1151B CA 2.2 31.6 - - - -
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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