Contacts of the helix formed by residues 58 - 88 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A PRO 6.0 0.4 - - - +
56A LEU 5.6 1.3 - - - +
57A GLN* 1.4 77.5 - - - +
59A PRO* 1.4 71.3 - - + +
60A GLU* 3.3 3.3 + - + +
61A SER* 3.3 10.4 + - - +
62A TRP* 2.9 21.3 + - - +
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Residues in contact with PRO 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A GLN* 6.1 0.2 - - - +
57A GLN 4.8 0.2 - - - +
58A GLU* 1.4 86.2 - - + +
60A GLU* 1.3 66.2 + - + +
62A TRP* 3.5 7.6 + - + +
63A ALA* 3.0 25.1 + - - +
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Residues in contact with GLU 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A GLU* 3.3 2.3 - - + +
59A PRO* 1.3 81.7 - - + +
61A SER* 1.3 58.5 + - - +
63A ALA* 3.3 7.7 + - - +
64A ARG* 3.0 47.2 + - - +
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 2.8 30.2 + - - +
58A GLU* 3.3 14.6 + - - +
60A GLU* 1.3 79.2 - - - +
62A TRP* 1.3 57.5 + - - +
64A ARG* 3.3 28.1 + - - +
65A THR* 3.1 22.7 + - - -
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Residues in contact with TRP 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A HIS* 3.7 33.2 - + - -
50A ILE* 3.4 35.3 + - + -
51A ILE* 3.7 0.8 - - - +
52A GLN* 3.4 49.1 - - + +
57A GLN* 3.4 29.9 - - + +
58A GLU 2.9 17.9 + - - +
59A PRO* 3.8 7.9 - - + +
61A SER* 1.3 73.0 - - - +
63A ALA* 1.3 60.7 + - + +
65A THR* 3.2 18.8 + - + -
66A GLN* 2.8 62.5 + - + +
606A PTY 4.7 2.2 - - + -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO 3.0 18.3 + - - +
60A GLU* 3.6 7.0 - - - +
62A TRP* 1.3 76.8 - - + +
64A ARG* 1.3 58.0 + - - +
66A GLN* 3.4 17.1 + - - +
67A SER* 2.9 28.6 + - - -
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Residues in contact with ARG 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A GLU* 3.0 41.0 + - - +
61A SER* 3.6 31.1 + - - +
62A TRP 3.2 0.4 - - - -
63A ALA* 1.3 74.1 - - + +
65A THR* 1.4 66.3 + - - +
67A SER* 3.1 10.3 + - - -
68A GLY* 3.0 18.5 + - - -
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 2.9 28.3 + - - +
61A SER 3.1 6.8 + - - -
62A TRP* 3.5 22.2 - - + -
64A ARG* 1.4 76.4 - - - +
66A GLN* 1.3 61.4 + - - +
68A GLY* 3.2 2.7 + - - -
69A LEU* 3.0 37.8 + - + +
606A PTY 3.8 29.9 - - + +
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Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ILE* 3.0 35.2 + - + +
62A TRP* 2.8 59.1 + - + +
63A ALA* 3.6 16.8 - - - +
65A THR* 1.3 71.3 - - - +
67A SER* 1.3 64.7 + - - +
69A LEU* 3.1 10.9 + - - +
70A GLN* 2.9 32.5 + - + +
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Residues in contact with SER 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ALA 2.9 15.1 + - - -
64A ARG* 3.1 12.8 + - - -
66A GLN* 1.3 77.6 - - - +
68A GLY* 1.3 60.7 + - - +
70A GLN* 3.3 7.3 + - - +
71A SER* 3.0 27.0 + - - -
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Residues in contact with GLY 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A ARG 3.0 12.3 + - - -
65A THR* 3.2 2.9 + - - -
67A SER* 1.3 76.9 - - - +
69A LEU* 1.3 58.9 + - - +
71A SER* 3.4 6.9 + - - -
72A TYR* 2.9 29.1 + - - +
156A ARG* 5.2 1.9 + - - -
606A PTY 4.4 14.8 + - - +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 5.3 3.4 - - + -
50A ILE* 3.7 27.4 - - + -
62A TRP* 5.1 0.4 - - + -
65A THR* 3.0 36.2 + - + +
66A GLN* 3.1 6.5 + - - +
68A GLY* 1.3 76.8 - - - +
70A GLN* 1.3 56.4 + - - +
72A TYR* 3.3 6.1 + - + +
73A LEU* 3.0 32.8 + - - +
164A PHE* 5.2 5.8 - - + -
606A PTY 3.6 81.7 - - + +
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Residues in contact with GLN 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP 5.4 2.6 - - - +
48A THR* 3.0 33.9 + - - +
50A ILE* 3.5 19.8 - - + +
66A GLN* 2.9 25.8 + - + +
67A SER* 3.8 6.5 - - - +
69A LEU* 1.3 74.4 - - - +
71A SER* 1.3 64.7 + - - +
73A LEU* 3.3 16.1 + - - +
74A LEU* 3.2 29.3 + - + +
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Residues in contact with SER 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A SER* 3.0 17.3 + - - -
68A GLY* 3.7 9.9 - - - -
70A GLN* 1.3 72.9 - - - +
72A TYR* 1.3 69.6 + - - +
74A LEU* 3.2 10.9 + - - +
75A GLN* 3.1 33.9 + - - +
156A ARG* 5.0 8.3 - - - -
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Residues in contact with TYR 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 2.7 38.7 + - - -
68A GLY 2.9 15.5 + - - +
69A LEU* 3.4 11.2 - - + +
71A SER* 1.3 77.5 - - - +
73A LEU* 1.3 68.6 + - + +
75A GLN* 3.1 10.6 + - - +
76A PHE* 2.8 45.4 + - + +
97A CYS* 4.1 0.9 - - - -
114A PHE* 3.8 19.4 - + - -
156A ARG* 4.7 3.7 - - - +
161A LEU* 5.8 0.2 - - + -
606A PTY 3.5 100.4 - - + +
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Residues in contact with LEU 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 3.6 29.4 - - + +
27A TYR* 3.2 38.3 + - + -
41A LEU* 4.3 20.2 - - + -
48A THR* 3.8 34.1 - - + +
50A ILE* 4.6 4.3 - - + -
69A LEU* 3.0 21.0 + - + +
70A GLN* 3.8 17.0 - - - +
71A SER 3.3 0.4 - - - -
72A TYR* 1.3 85.5 - - + +
74A LEU* 1.3 64.6 + - + +
76A PHE* 3.3 2.3 + - - +
77A HIS* 3.0 19.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ASP* 5.0 13.5 - - + +
70A GLN* 3.2 18.1 + - + +
71A SER* 3.8 11.2 - - - +
72A TYR 3.2 0.2 - - - -
73A LEU* 1.3 81.9 - - + +
75A GLN* 1.3 59.3 + - + +
77A HIS* 3.5 9.4 + - + +
78A GLY* 2.8 25.1 + - - -
81A ARG* 4.9 2.3 + - - -
5C LEU* 5.2 0.5 - - - +
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 3.1 23.3 + - - +
72A TYR* 3.6 3.5 - - - +
74A LEU* 1.3 76.1 - - + +
76A PHE* 1.4 58.5 + - - +
78A GLY* 3.2 1.4 + - - -
79A LEU* 2.9 29.5 + - - +
156A ARG* 2.9 42.2 + - - +
606A PTY 3.7 15.7 - - + +
4C PHE* 3.6 22.0 - - + -
5C LEU* 4.0 21.6 - - + +
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Residues in contact with PHE 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 3.6 12.1 - - - -
17A SER* 3.3 33.4 - - - -
19A PHE* 3.7 15.0 - + - -
27A TYR* 3.9 10.1 - + - -
72A TYR* 2.8 40.2 + + + +
73A LEU* 3.5 6.1 - - - +
75A GLN* 1.4 74.0 - - - +
77A HIS* 1.3 68.0 + - - +
79A LEU* 3.1 6.7 + - - +
80A VAL* 3.0 27.0 + - + +
95A ILE* 3.9 26.5 - - + -
97A CYS* 3.7 16.4 - - - -
606A PTY 3.6 44.8 - - + +
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Residues in contact with HIS 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.6 20.9 - + - -
22A PRO 2.8 28.4 + - - -
23A TYR* 3.5 26.4 - - - -
24A HIS 4.2 0.2 + - - -
25A VAL* 4.0 17.1 - - + +
27A TYR* 3.5 17.0 - - - +
45A ASP* 4.2 14.0 + - - +
73A LEU 3.0 10.9 + - - +
74A LEU* 3.7 10.3 - - + +
76A PHE* 1.3 81.4 - - - +
78A GLY* 1.3 64.0 + - - +
80A VAL* 3.1 2.3 + - - +
81A ARG* 2.9 41.2 + - + +
----------------------------------------------------------
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU 2.8 17.0 + - - -
75A GLN* 3.2 4.6 + - - -
77A HIS* 1.3 75.9 - - - +
79A LEU* 1.3 57.1 + - - +
81A ARG* 3.3 15.2 + - - +
82A LEU* 2.9 28.1 + - - +
5C LEU* 4.0 9.9 - - - -
8C LEU* 3.8 21.1 - - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A GLN 2.9 13.8 + - - +
76A PHE* 3.1 10.1 + - - +
78A GLY* 1.3 74.6 - - - +
80A VAL* 1.3 64.0 + - - +
82A LEU* 3.1 18.3 + - + +
83A VAL* 2.9 34.0 + - + +
147A THR* 5.5 1.1 - - + -
150A GLN* 4.3 25.6 - - + +
151A LEU* 3.5 34.1 - - + -
154A TYR* 5.8 0.4 - - + -
157A THR* 5.0 4.0 - - + -
606A PTY 3.9 36.1 - - + -
4C PHE* 4.9 8.5 - - + -
5C LEU* 3.9 11.6 - - + +
----------------------------------------------------------
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PHE* 3.7 38.4 - - + -
22A PRO 5.7 0.4 - - - +
76A PHE* 3.0 17.4 + - + +
77A HIS 3.6 5.8 - - - +
79A LEU* 1.3 77.2 - - - +
81A ARG* 1.3 62.5 + - - +
83A VAL* 3.3 3.0 + - - +
84A HIS* 3.0 22.2 + - - +
89A LEU* 3.7 18.1 - - + +
91A PHE* 4.6 8.5 - - + -
93A LEU* 5.0 1.1 - - + -
95A ILE* 3.6 28.7 - - + -
606A PTY 3.8 22.0 - - + -
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Residues in contact with ARG 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO* 3.1 33.4 - - + +
23A TYR* 4.0 23.8 - - - +
74A LEU 4.9 2.0 + - - -
77A HIS* 2.9 42.1 + - + +
78A GLY* 3.6 18.4 - - - +
80A VAL* 1.3 74.6 - - - +
82A LEU* 1.3 57.8 + - - +
84A HIS* 3.3 8.1 + - - +
85A GLN* 2.9 42.6 + - - +
91A PHE* 6.2 0.2 - - - -
8C LEU* 3.8 31.6 - - + +
----------------------------------------------------------
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLY 2.9 18.2 + - - +
79A LEU* 3.5 16.4 - - + +
81A ARG* 1.3 73.8 - - - +
83A VAL* 1.3 65.3 + - - +
85A GLN* 3.1 6.1 + - + +
86A GLU* 2.9 39.2 + - + +
146A PHE* 4.2 6.7 - - + -
150A GLN* 3.6 31.9 - - - +
5C LEU* 5.0 11.4 - - + +
7C CGU 3.4 49.8 - - + +
8C LEU* 3.8 12.7 - - + +
----------------------------------------------------------
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Residues in contact with VAL 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A LEU* 2.9 28.3 + - + +
80A VAL 3.7 4.0 - - - +
82A LEU* 1.3 74.4 - - - +
84A HIS* 1.3 60.2 + - - +
87A ARG* 2.8 29.1 + - + +
88A THR 3.4 3.1 + - - -
89A LEU* 3.9 25.8 - - + -
143A VAL* 4.0 12.6 - - + +
146A PHE* 3.8 28.0 - - + -
147A THR* 3.6 30.7 - - - +
606A PTY 4.0 15.3 - - + -
----------------------------------------------------------
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Residues in contact with HIS 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO* 3.3 27.6 - - + +
23A TYR* 5.1 5.8 + - - -
80A VAL 3.0 13.5 + - - +
81A ARG* 3.5 8.5 - - - +
83A VAL* 1.3 78.4 - - - +
85A GLN* 1.3 72.8 + - + +
88A THR* 2.9 34.5 + - + -
89A LEU* 3.2 51.4 + - + +
91A PHE* 3.6 16.2 - + + -
----------------------------------------------------------
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Residues in contact with GLN 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A TYR* 4.9 12.2 + - - +
81A ARG* 2.9 38.6 + - - +
82A LEU* 3.1 5.7 + - + +
84A HIS* 1.3 84.0 - - + +
86A GLU* 1.3 63.5 + - + +
7C CGU 4.6 8.9 + - - -
8C LEU* 4.0 26.5 + - - +
29C CGU 5.2 3.1 - - - -
----------------------------------------------------------
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Residues in contact with GLU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 2.9 32.2 + - + +
85A GLN* 1.3 84.0 - - + +
87A ARG* 1.3 77.7 + - + +
88A THR 4.0 0.2 - - - -
146A PHE* 3.5 33.2 - - + -
7C CGU 3.2 10.6 - - - +
25C CGU 2.8 5.9 - - - -
29C CGU 3.0 10.9 - - - +
34C MG 2.1 31.4 - - - -
35C CA 2.3 27.5 - - - -
----------------------------------------------------------
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Residues in contact with ARG 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 2.8 16.9 + - + +
86A GLU* 1.3 93.9 + - - +
88A THR* 1.3 74.6 + - - +
142A GLY* 4.1 15.8 + - - +
143A VAL* 4.1 22.8 - - + +
146A PHE* 3.6 47.6 - - + +
25C CGU 2.9 43.6 - - - +
34C MG 4.0 0.4 - - - -
----------------------------------------------------------
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Residues in contact with THR 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL 3.4 1.4 + - - -
84A HIS* 2.9 26.5 + - + +
86A GLU 4.0 0.2 - - - -
87A ARG* 1.3 87.1 + - - +
89A LEU* 1.3 74.6 + - - +
143A VAL* 3.6 14.1 - - - +
----------------------------------------------------------
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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