Contacts of the helix formed by residues 72 - 101 (chain A) in PDB entry 2WY2
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 LEU 72 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A GLU* 5.4 0.4 + - - -
70A VAL* 3.2 9.4 + - + +
71A SER* 1.3 69.4 + - - +
73A VAL* 1.3 66.9 + - + +
74A LEU 3.0 6.5 + - - -
75A VAL* 3.1 24.3 + - + +
76A HIS 4.2 0.5 + - - -
72B LEU* 4.3 25.6 - - + -
68C MET 5.5 0.9 - - - +
69C LYS* 4.0 47.3 - - + +
70C VAL* 4.8 13.5 - - + +
72C LEU* 4.3 18.4 - - + -
75C VAL* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A ALA 5.2 11.2 - - - +
4A LEU* 4.4 11.9 - - + +
5A GLU* 5.3 7.9 - - + -
8A VAL* 3.4 33.4 - - + +
71A SER* 3.2 19.3 - - - +
72A LEU* 1.3 75.3 - - + +
74A LEU* 1.3 69.9 + - - +
75A VAL 2.9 3.1 - - - -
76A HIS* 2.8 23.0 + - + +
77A ALA* 3.1 12.1 + - - +
14D MET* 6.4 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 5.7 0.2 - - - -
55A GLN* 3.4 22.3 + - - +
58A LEU* 4.1 31.0 - - + +
59A ILE* 3.9 28.3 - - + -
62A ASP* 4.7 15.3 - - + +
70A VAL* 4.7 12.1 - - + -
71A SER* 3.2 23.5 + - - +
72A LEU 3.0 0.2 - - - -
73A VAL* 1.3 84.0 - - - +
75A VAL* 1.3 59.9 + - + +
77A ALA* 3.5 4.2 + - + +
78A GLN* 2.8 35.0 + - - +
76B HIS* 5.6 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A VAL* 6.6 0.4 - - + -
71A SER 5.3 0.9 - - - +
72A LEU* 3.5 14.1 - - - +
73A VAL 2.9 1.2 - - - -
74A LEU* 1.3 78.9 - - + +
76A HIS* 1.4 57.1 + - - +
77A ALA 3.1 1.3 - - - -
78A GLN* 4.1 12.1 - - - +
79A LEU* 2.6 45.2 + - + +
72B LEU 6.0 1.1 - - - +
75B VAL* 3.8 22.0 - - + -
76B HIS* 6.0 1.1 - - + +
79B LEU* 5.4 5.4 - - + -
75C VAL* 3.7 38.4 - - + -
78C GLN* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.5 23.6 - - + -
12A ILE* 3.1 35.3 - - + +
72A LEU 4.2 1.2 + - - -
73A VAL* 2.8 20.6 + - + +
75A VAL* 1.4 73.2 - - - +
77A ALA* 1.3 60.9 + - - +
79A LEU* 4.1 2.9 - - - +
80A HIS* 3.3 34.5 + - - -
59C ILE* 5.8 0.2 - - + -
75C VAL* 6.0 0.6 - - - +
78C GLN* 3.7 18.4 + - - +
12D ALA* 3.9 9.4 - - + -
14D MET* 3.5 34.8 - - + +
15D SER* 4.9 2.9 - - - -
200D PO3 3.4 23.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.4 9.4 - - + +
11A LEU* 3.8 32.3 - - + -
12A ILE* 4.2 8.7 - - - -
55A GLN* 4.1 7.9 - - - +
58A LEU* 5.6 2.7 - - + -
73A VAL 3.1 8.9 + - - +
74A LEU* 3.7 9.4 - - + +
76A HIS* 1.3 77.3 - - - +
78A GLN* 1.3 59.4 + - - +
80A HIS* 4.0 0.2 - - - +
81A LEU* 2.8 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLN* 3.3 22.6 - - - +
59A ILE* 5.2 7.1 - - - +
74A LEU* 2.8 25.5 + - - +
75A VAL* 3.7 13.1 - - - +
77A ALA* 1.3 75.6 - - - +
79A LEU* 1.3 55.0 + - - +
82A MET* 2.6 48.0 + - + +
75B VAL* 6.1 0.2 - - - +
76B HIS* 3.4 44.2 + - - -
79B LEU* 3.4 19.1 - - + +
80B HIS* 3.4 20.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 2.6 28.6 + - + +
76A HIS* 4.1 3.8 - - - +
78A GLN* 1.3 74.2 - - - +
80A HIS* 1.3 53.5 + - + +
82A MET* 4.0 0.3 - - - +
83A THR* 2.6 53.0 + - + +
79B LEU* 3.6 17.2 - - + +
75C VAL* 5.0 5.6 - - + +
78C GLN* 3.4 48.9 - - + +
79C LEU* 3.6 39.9 - - + +
82C MET* 4.1 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 5.3 0.2 - - - +
12A ILE* 3.2 36.7 + - + +
15A SER* 3.5 21.8 + - - +
16A GLY* 5.4 1.4 + - - -
76A HIS* 3.3 38.2 + - - +
77A ALA 4.0 1.3 - - - +
78A GLN 3.3 0.4 - - - -
79A LEU* 1.3 81.9 - - + +
81A LEU* 1.3 58.6 + - + +
83A THR* 2.6 19.4 + - - -
84A SER* 2.9 21.9 + - - -
78C GLN* 3.4 17.3 + - - -
82C MET* 4.1 25.2 - - + +
11D SER* 5.5 1.6 - - - -
12D ALA* 3.9 12.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.4 13.9 - - + +
15A SER* 4.1 18.6 - - - -
48A LEU* 5.0 8.4 - - + +
51A ALA* 3.5 36.1 - - + +
52A HIS* 4.7 6.5 - - + +
55A GLN* 2.8 46.7 - - + +
77A ALA* 2.8 33.5 + - + +
78A GLN 3.8 0.2 - - - +
80A HIS* 1.3 74.3 - - + +
82A MET* 1.3 57.0 + - + +
84A SER* 3.8 1.6 - - - -
85A MET* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A HIS* 6.4 1.8 - - - -
55A GLN* 5.6 0.4 - - - +
78A GLN* 2.6 46.7 + - + +
79A LEU 4.0 2.5 - - - +
81A LEU* 1.3 73.6 - - + +
83A THR* 1.3 63.0 + - - +
85A MET* 3.9 20.0 - - - +
86A LEU* 3.0 27.0 + - + +
19B ARG* 5.3 10.3 - - - +
79B LEU* 4.1 9.9 - - + -
80B HIS* 4.1 31.2 - - + +
83B THR* 3.9 38.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 6.4 0.2 - - - -
79A LEU* 2.6 39.3 + - + +
80A HIS* 2.6 26.7 + - - -
82A MET* 1.3 76.5 - - + +
84A SER* 1.3 56.0 + - - -
86A LEU* 3.7 3.4 - - - +
87A ALA* 2.9 32.0 + - - +
83B THR* 5.4 8.1 - - + -
82C MET* 3.9 34.3 - - + +
83C THR* 5.2 5.6 - - + +
86C LEU* 3.7 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 2.9 35.6 + - - -
16A GLY* 4.8 0.2 - - - -
18A ALA* 4.7 2.1 - - - +
19A ARG* 4.2 16.0 + - - +
48A LEU* 4.0 16.7 - - - +
80A HIS* 2.9 20.3 + - - -
81A LEU 3.8 2.9 - - - -
83A THR* 1.3 79.0 + - - +
85A MET* 1.3 61.9 + - - +
87A ALA* 3.3 7.4 + - - +
88A ARG* 2.9 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.1 25.9 - - + +
52A HIS* 4.8 22.7 - - + -
81A LEU 2.8 21.1 + - - +
82A MET* 3.9 22.2 - - - +
84A SER* 1.3 74.7 - - - +
86A LEU* 1.3 64.2 + - + +
88A ARG* 3.3 2.6 + - - +
89A GLU* 3.0 26.4 + - + +
19B ARG* 3.9 29.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A MET* 3.0 20.0 + - + +
83A THR* 3.7 4.3 - - - +
85A MET* 1.3 77.2 - - - +
87A ALA* 1.3 65.1 + - - +
89A GLU* 3.2 11.6 + - + +
90A LEU* 3.0 44.3 + - + +
19B ARG* 4.3 26.5 - - - +
83B THR* 3.7 35.4 - - + +
86B LEU* 4.8 8.3 - - + -
87B ALA* 3.6 28.9 - - + +
86C LEU* 4.8 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 4.8 10.5 - - + -
83A THR 2.9 19.0 + - - +
84A SER* 3.3 7.8 + - - +
86A LEU* 1.3 77.2 - - - +
88A ARG* 1.3 57.0 + - - +
90A LEU* 3.3 5.3 + - - +
91A ILE* 2.8 45.6 + - + +
86C LEU* 3.6 30.4 - - + +
90C LEU* 4.6 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 5.8 0.9 - - - +
19A ARG* 6.3 0.2 - - - -
22A ALA* 4.1 23.0 - - + +
41A MET* 3.6 34.2 + - + +
44A SER* 4.1 7.2 - - - +
45A ARG* 3.9 27.8 - - - +
48A LEU* 3.7 26.2 - - + -
84A SER 2.9 17.1 + - - +
85A MET 3.6 4.5 + - - +
86A LEU 3.2 0.2 - - - -
87A ALA* 1.3 77.6 - - - +
89A GLU* 1.3 63.5 + - - +
91A ILE* 3.1 6.4 + - + +
92A THR* 2.4 71.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A MET* 3.0 18.1 + - + +
86A LEU* 3.2 14.8 + - + +
88A ARG* 1.3 87.2 - - - +
90A LEU* 1.3 66.9 + - + +
92A THR* 3.2 5.9 + - - -
93A GLU* 3.1 33.4 + - + +
19B ARG* 4.4 23.0 + - - +
23B TYR* 3.7 29.0 - - + +
91B ILE* 6.2 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LEU* 3.0 37.7 + - + +
87A ALA 3.7 3.6 - - - +
89A GLU* 1.3 75.5 - - + +
91A ILE* 1.3 61.0 + - - +
93A GLU* 3.0 10.3 + - + +
94A LEU* 2.8 34.6 + - + +
87B ALA* 4.5 5.4 - - + +
90B LEU* 3.8 33.4 - - + -
91B ILE* 4.0 21.8 - - + -
94B LEU* 3.9 24.5 - - + +
90C LEU* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 5.1 4.7 - - + +
22A ALA* 3.6 48.5 - - + +
23A TYR* 4.2 9.2 - - + +
26A LEU* 3.9 22.7 - - + -
41A MET* 5.6 0.9 - - + -
87A ALA* 2.8 39.8 + - + +
88A ARG* 3.5 5.4 - - + +
90A LEU* 1.3 72.3 - - - +
92A THR* 1.3 58.3 + - - +
94A LEU* 3.0 11.0 + - + +
95A ILE* 2.8 36.5 + - + +
90C LEU* 4.0 18.6 - - + -
93C GLU* 6.4 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A MET* 3.3 33.5 - - + +
88A ARG* 2.4 55.9 + - - +
89A GLU* 3.3 12.3 - - + +
90A LEU 3.2 0.2 - - - -
91A ILE* 1.3 73.7 - - - +
93A GLU* 1.3 66.5 + - + +
95A ILE* 3.1 4.9 + - - +
96A GLU* 2.9 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A GLU* 3.1 21.3 + - + +
90A LEU* 3.0 12.3 + - + +
92A THR* 1.3 79.5 - - - +
94A LEU* 1.3 63.3 + - - +
96A GLU* 3.1 7.4 + - - +
97A LEU* 2.9 27.2 + - + +
23B TYR* 3.3 30.5 + - + -
26B LEU* 3.2 24.8 - - + +
30B LYS* 2.9 29.4 + - - -
94B LEU* 4.3 18.8 - - + -
98B HIS* 5.5 2.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 4.5 7.0 - - + -
90A LEU* 2.8 19.9 + - + +
91A ILE* 3.3 14.6 - - + +
93A GLU* 1.3 77.0 - - - +
95A ILE* 1.3 55.8 + - - +
97A LEU* 3.1 8.1 + - - +
98A HIS* 2.5 41.5 + - + -
94B LEU* 3.9 21.3 - - + -
90C LEU* 3.9 29.8 - - + +
93C GLU* 4.3 18.8 - - + -
94C LEU* 3.9 14.6 - - + -
97C LEU* 3.3 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 4.0 5.6 - - + +
26A LEU* 3.9 39.3 - - + +
29A ALA* 4.0 14.6 - - + -
34A PHE* 4.7 7.4 - - + -
37A ALA* 4.2 13.2 - - + -
38A LYS* 5.7 0.4 - - - +
41A MET* 3.3 39.5 - - + -
91A ILE* 2.8 27.1 + - + +
92A THR 3.5 6.5 - - - +
94A LEU* 1.3 72.7 - - - +
96A GLU* 1.3 64.7 + - - +
98A HIS* 3.0 18.5 + - - +
99A GLU* 3.0 11.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A THR* 2.9 15.9 + - + +
93A GLU* 3.4 13.7 - - - +
95A ILE* 1.3 77.7 - - - +
97A LEU* 1.3 62.5 + - + +
99A GLU* 3.0 21.8 + - - +
100A LYS* 2.9 43.0 + - + +
30B LYS* 3.5 27.5 + - - +
98B HIS* 6.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU 2.9 16.0 + - - +
94A LEU* 3.1 11.4 + - - +
96A GLU* 1.3 73.1 - - + +
98A HIS* 1.3 54.8 + - - +
100A LYS* 2.9 9.5 + - + +
101A LEU* 2.7 40.3 + - + +
94B LEU* 3.3 33.9 - - + -
97B LEU* 4.6 16.2 - - + -
98B HIS* 3.2 39.7 - - + +
101B LEU* 3.4 29.8 - - + +
97C LEU* 4.6 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LEU* 3.5 24.5 - - + +
29A ALA* 4.3 17.0 - - + +
30A LYS* 4.3 17.4 - - + +
34A PHE* 4.1 5.6 - - + -
94A LEU* 2.5 39.4 + - + -
95A ILE* 3.0 12.2 + - - +
97A LEU* 1.3 74.7 - - - +
99A GLU* 1.3 63.6 + - - +
101A LEU* 3.2 22.7 + - + +
102A LYS 3.5 3.8 + - - -
103A ALA* 3.7 14.2 - - + +
93C GLU* 5.6 2.0 - - + -
96C GLU* 6.0 0.6 - - - +
97C LEU* 3.2 37.1 - - + +
100C LYS* 4.0 26.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A PHE* 3.4 37.6 - - + +
38A LYS* 5.7 3.5 + - - -
95A ILE* 3.0 9.4 + - + +
96A GLU* 3.0 25.2 + - - +
98A HIS* 1.3 78.4 - - - +
100A LYS* 1.3 58.7 + - + +
102A LYS* 2.9 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU* 2.9 36.6 + - + +
97A LEU* 2.9 14.9 + - + +
99A GLU* 1.3 72.3 - - + +
101A LEU* 1.3 55.1 + - - +
102A LYS* 2.7 17.6 + - - +
30B LYS* 3.6 40.6 + - - +
98B HIS* 4.0 20.9 + - + -
101B LEU* 4.6 17.3 - - + +
103B ALA* 6.2 4.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A LEU* 2.7 21.2 + - + +
98A HIS* 3.2 16.3 + - + +
100A LYS* 1.3 69.1 - - - +
102A LYS* 1.3 64.7 + - - +
103A ALA* 2.9 16.3 + - + +
101B LEU* 3.7 16.2 - - + -
97C LEU* 3.4 35.2 - - + +
100C LYS* 4.6 16.4 - - + +
101C LEU* 3.7 40.6 - - + +
----------------------------------------------------------
Back to top of page
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