Contacts of the helix formed by residues 58 - 88 (chain B) in PDB entry 3JTC
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 GLU 58 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PRO* 4.4 9.5 - - - +
56B LEU 4.2 2.6 + - - +
57B GLN* 1.3 75.8 - - - +
59B PRO* 1.3 83.8 - - + +
60B GLU* 3.2 3.8 + - + +
61B SER* 3.2 11.7 + - - +
62B TRP* 2.8 19.4 + - - +
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Residues in contact with PRO 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B GLN* 6.0 0.2 - - - +
57B GLN 4.5 1.3 - - - +
58B GLU* 1.3 96.6 - - + +
60B GLU* 1.3 58.2 + - - +
62B TRP* 3.8 7.7 - - + +
63B ALA* 2.9 29.3 + - - +
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Residues in contact with GLU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B GLU* 3.3 2.3 - - + +
59B PRO* 1.3 75.5 - - - +
61B SER* 1.3 66.1 + - - +
63B ALA* 3.2 7.5 + - - +
64B ARG* 3.0 50.8 + - - +
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Residues in contact with SER 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLN* 3.0 24.3 + - - +
58B GLU* 3.2 16.4 + - - +
60B GLU* 1.3 79.8 - - - +
62B TRP* 1.3 60.7 + - - +
64B ARG* 3.3 28.2 + - - +
65B THR* 3.1 23.6 + - - -
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Residues in contact with TRP 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B HIS* 3.6 30.7 - + - -
50B ILE* 3.6 33.2 + - + -
51B ILE* 3.9 1.7 - - - +
52B GLN* 3.8 40.8 - - + +
57B GLN* 3.3 43.2 - - + +
58B GLU 2.8 19.5 + - - +
59B PRO* 3.8 7.2 - - + +
61B SER* 1.3 69.3 - - - +
63B ALA* 1.3 62.0 + - + +
65B THR* 3.1 16.0 + - + -
66B GLN* 2.8 69.5 + - + +
69B LEU* 4.7 3.4 - - + -
607B PTY 4.6 1.8 - - + -
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B PRO 2.9 18.8 + - - +
60B GLU* 3.6 7.6 - - + +
61B SER 3.2 0.2 - - - -
62B TRP* 1.3 79.2 - - + +
64B ARG* 1.3 56.2 + - - +
66B GLN* 3.4 16.7 + - - +
67B SER* 3.0 27.4 + - - -
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Residues in contact with ARG 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLU* 3.0 49.3 + - - +
61B SER* 3.3 40.2 + - - +
63B ALA* 1.3 72.1 - - - +
65B THR* 1.3 65.1 + - - +
67B SER* 3.2 8.5 + - - -
68B GLY* 3.2 17.7 + - - -
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLN* 2.9 28.3 + - - +
61B SER 3.1 7.6 + - - -
62B TRP* 3.1 18.8 + - + -
64B ARG* 1.3 71.8 - - - +
66B GLN* 1.3 67.7 + - - +
68B GLY* 3.2 2.6 + - - -
69B LEU* 3.0 27.6 + - + +
172B TYR* 6.0 0.2 - - - -
607B PTY 3.8 37.0 - - + +
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Residues in contact with GLN 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 3.2 34.4 + - + +
62B TRP* 2.8 55.2 + - + +
63B ALA* 3.5 17.0 - - - +
65B THR* 1.3 77.5 - - - +
67B SER* 1.3 58.4 + - - +
69B LEU* 3.2 10.8 + - - +
70B GLN* 2.9 39.6 + - + +
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA 3.0 13.8 + - - -
64B ARG* 3.4 13.2 - - - -
65B THR 3.1 0.2 - - - -
66B GLN* 1.3 78.3 - - - +
68B GLY* 1.3 56.5 + - - +
70B GLN* 3.3 7.4 + - - +
71B SER* 3.0 33.1 + - - -
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Residues in contact with GLY 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ARG 3.2 9.8 + - - -
65B THR* 3.2 3.5 + - - -
67B SER* 1.3 77.7 - - - +
69B LEU* 1.3 65.0 + - - +
71B SER* 3.4 7.3 + - - -
72B TYR* 3.0 22.9 + - - +
156B ARG* 5.4 0.9 + - - -
607B PTY 4.4 16.5 + - - +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 5.3 2.9 - - + -
50B ILE* 3.7 29.6 - - + -
62B TRP* 4.7 1.6 - - + -
65B THR* 3.0 32.4 + - + +
66B GLN* 3.5 6.7 - - - +
68B GLY* 1.3 77.7 - - - +
70B GLN* 1.3 56.7 + - - +
72B TYR* 3.3 7.5 + - + +
73B LEU* 3.0 32.8 + - - +
164B PHE* 4.9 9.4 - - + -
607B PTY 3.7 80.1 - - + +
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Residues in contact with GLN 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP 5.6 1.0 - - - +
48B THR* 2.9 41.6 + - - -
50B ILE* 3.5 22.4 - - + +
66B GLN* 2.9 29.6 + - + +
67B SER* 3.8 7.0 - - - +
69B LEU* 1.3 72.2 - - - +
71B SER* 1.3 63.5 + - - +
73B LEU* 3.2 10.5 + - - +
74B LEU* 3.1 29.9 + - + +
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Residues in contact with SER 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B SER* 3.0 16.6 + - - -
68B GLY* 3.6 8.3 - - - -
70B GLN* 1.3 75.3 - - - +
72B TYR* 1.3 65.8 + - - +
74B LEU* 3.2 12.0 + - - +
75B GLN* 3.0 39.3 + - - +
156B ARG* 5.1 4.7 - - - -
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Residues in contact with TYR 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 2.7 31.6 + - - -
68B GLY 3.0 14.3 + - - +
69B LEU* 3.4 9.6 - - - +
71B SER* 1.3 74.9 - - - +
73B LEU* 1.4 77.4 + - + +
75B GLN* 3.2 7.3 + - - +
76B PHE* 2.9 45.3 + + + +
97B CYS* 4.1 0.9 - - - -
114B PHE* 3.6 21.2 - + - -
156B ARG* 4.6 6.9 - - - +
607B PTY 3.6 95.5 - - + +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 3.7 30.3 - - + +
27B TYR* 3.3 34.5 + - + +
41B LEU* 4.2 19.1 - - + -
48B THR* 3.8 37.0 - - + +
50B ILE* 4.7 2.9 - - + -
69B LEU* 3.0 20.1 + - + +
70B GLN* 3.2 17.6 + - - +
72B TYR* 1.4 85.1 - - + +
74B LEU* 1.3 60.6 - - + +
76B PHE* 3.3 3.0 + - - +
77B HIS* 2.9 27.1 + - - +
607B PTY 5.4 1.3 - - + -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 4.9 16.6 - - + +
70B GLN* 3.1 16.6 + - + +
71B SER* 3.6 11.7 - - - +
73B LEU* 1.3 77.2 - - + +
75B GLN* 1.3 59.6 + - + +
77B HIS* 3.4 8.8 + - + +
78B GLY* 2.9 24.6 + - - -
5D LEU* 5.2 0.3 - - - +
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Residues in contact with GLN 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B SER* 3.0 23.2 + - - +
72B TYR 3.7 3.4 - - - +
74B LEU* 1.3 74.8 - - + +
76B PHE* 1.4 59.3 + - - +
78B GLY* 3.2 1.2 + - - -
79B LEU* 2.8 30.3 + - - +
156B ARG* 2.9 42.4 + - - +
607B PTY 3.7 16.0 - - + +
4D PHE* 3.4 24.9 - - + -
5D LEU* 4.0 15.9 - - + +
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Residues in contact with PHE 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLN* 3.5 12.1 - - - -
17B SER* 3.3 33.9 - - - -
19B PHE* 3.8 13.2 - + - -
27B TYR* 3.8 12.3 - + - -
72B TYR* 2.9 42.8 + - + +
73B LEU* 3.4 5.8 - - - +
75B GLN* 1.4 70.7 - - - +
77B HIS* 1.4 66.4 + - - +
79B LEU* 3.3 5.8 + - - +
80B VAL* 3.1 29.3 + - + +
95B ILE* 4.0 25.8 - - + -
97B CYS* 3.8 21.1 - - - -
607B PTY 3.9 37.8 - - + +
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Residues in contact with HIS 77 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 3.6 18.2 - + - -
22B PRO 2.8 27.9 + - - -
23B TYR* 3.4 27.6 - - - -
24B HIS 4.0 2.1 + - - -
25B VAL* 4.0 12.4 - - + +
27B TYR* 3.8 9.4 - - - +
45B ASP* 4.2 17.8 + - - +
73B LEU 2.9 17.6 + - - +
74B LEU* 3.6 9.2 - - + +
76B PHE* 1.4 79.6 - - - +
78B GLY* 1.3 66.5 + - - +
80B VAL* 3.2 4.9 + - - +
81B ARG* 3.0 26.1 + - + +
----------------------------------------------------------
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU 2.9 16.2 + - - -
75B GLN 3.2 4.0 + - - -
77B HIS* 1.3 77.7 - - - +
79B LEU* 1.3 55.3 + - - +
81B ARG* 3.3 9.5 + - - +
82B LEU* 2.8 28.9 + - - +
5D LEU* 3.8 9.9 - - - -
8D LEU* 3.7 22.2 - - - +
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Residues in contact with LEU 79 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN 2.8 18.7 + - - +
76B PHE* 3.8 6.1 - - - +
77B HIS 3.3 0.2 - - - -
78B GLY* 1.3 69.8 - - - +
80B VAL* 1.3 65.7 + - - +
82B LEU* 3.2 17.3 + - + +
83B VAL* 3.0 27.9 + - + +
147B THR* 5.5 1.1 - - + +
150B GLN* 4.0 26.7 - - + +
151B LEU* 3.5 33.0 - - + -
154B TYR* 5.9 1.3 - - + -
157B THR* 5.0 5.4 - - + -
607B PTY 3.9 38.1 - - + -
4D PHE* 5.3 7.4 - - + -
5D LEU* 3.7 12.6 - - + +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 3.8 36.6 - - + -
22B PRO* 6.1 0.9 - - + +
76B PHE* 3.1 19.1 + - + +
77B HIS 3.6 7.0 - - - +
79B LEU* 1.3 74.9 - - - +
81B ARG* 1.3 62.7 + - - +
83B VAL* 3.2 2.9 + - - -
84B HIS* 3.0 19.4 + - - +
89B LEU* 3.6 22.1 - - + +
91B PHE* 4.8 6.3 - - + -
93B LEU* 4.9 2.0 - - + -
95B ILE* 3.6 27.6 - - + -
607B PTY 4.0 22.2 - - + -
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Residues in contact with ARG 81 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 3.7 34.3 - - + +
23B TYR* 3.9 24.4 - - + +
77B HIS* 3.0 22.4 + - - +
78B GLY* 3.5 7.4 - - - +
80B VAL* 1.3 76.9 - - - +
82B LEU* 1.3 58.6 + - - +
84B HIS* 3.2 8.8 + - - +
85B GLN* 2.8 65.9 + - + +
91B PHE* 6.1 0.2 - - - -
8D LEU* 3.7 38.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B GLY 2.8 15.3 + - - +
79B LEU* 3.2 18.8 + - + +
81B ARG* 1.3 77.2 - - - +
83B VAL* 1.3 57.0 + - - +
85B GLN* 3.1 7.1 + - + +
86B GLU* 2.9 42.3 + - + +
146B PHE* 4.4 7.2 - - + -
150B GLN* 3.6 29.6 - - - +
5D LEU* 4.7 13.7 - - + +
7D CGU 3.6 50.0 - - + +
8D LEU* 3.8 12.5 - - + +
----------------------------------------------------------
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Residues in contact with VAL 83 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LEU* 3.0 25.5 + - + +
80B VAL 3.7 6.5 - - - +
82B LEU* 1.3 76.1 - - - +
84B HIS* 1.3 62.9 + - - +
87B ARG* 2.9 22.7 + - + +
88B THR 3.4 3.5 + - - -
89B LEU* 3.8 26.5 - - + -
143B VAL* 3.9 13.5 - - + +
146B PHE* 3.8 28.3 - - + -
147B THR* 3.6 30.1 - - - +
150B GLN* 5.2 0.2 - - + -
607B PTY 4.1 15.7 - - + -
----------------------------------------------------------
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Residues in contact with HIS 84 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B PRO* 3.3 27.9 - - + +
23B TYR* 5.7 3.1 - - - -
80B VAL 3.0 13.2 + - - +
81B ARG* 3.4 9.9 - - - +
83B VAL* 1.3 77.6 - - - +
85B GLN* 1.3 71.3 + - + +
88B THR* 2.7 38.7 + - + +
89B LEU* 3.0 51.8 + - + +
91B PHE* 3.6 17.1 - + + -
----------------------------------------------------------
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Residues in contact with GLN 85 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B TYR* 4.4 12.0 + - - +
81B ARG* 2.8 50.6 + - + +
82B LEU* 3.1 6.3 + - + +
84B HIS* 1.3 88.1 - - + +
86B GLU* 1.3 63.4 + - + +
7D CGU 4.5 9.7 + - - -
8D LEU* 3.8 25.7 + - - +
29D CGU 5.1 3.1 - - - -
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Residues in contact with GLU 86 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 2.9 28.6 + - + +
85B GLN* 1.3 81.4 - - + +
87B ARG* 1.4 84.5 + - - +
146B PHE* 3.5 29.8 - - + -
7D CGU 3.2 16.5 - - - +
25D CGU 3.0 5.2 - - - -
29D CGU 3.2 8.9 - - - +
34D MG 2.1 30.1 - - - -
35D CA 2.3 29.0 - - - -
----------------------------------------------------------
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Residues in contact with ARG 87 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 2.9 11.2 + - + +
86B GLU* 1.4 110.3 + - - +
88B THR* 1.3 74.2 + - - +
142B GLY* 4.0 15.7 + - - +
143B VAL* 4.1 20.1 - - + +
146B PHE* 3.6 49.3 - - + +
25D CGU 2.9 43.4 - - - +
34D MG 4.0 0.4 - - - -
----------------------------------------------------------
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Residues in contact with THR 88 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL 3.4 2.6 + - - -
84B HIS* 2.7 32.9 + - + -
87B ARG* 1.3 84.3 + - - +
89B LEU* 1.3 74.5 + - - +
90B ALA 4.3 0.2 + - - -
143B VAL* 3.7 14.7 - - - +
----------------------------------------------------------
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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