Contacts of the helix formed by residues 57 - 86 (chain A) in PDB entry 2Q1V
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 HIS 57 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 1.3 79.1 - - - +
58A LEU* 1.3 75.8 + - + +
59A ASP* 2.8 43.3 + - - +
60A ASP* 3.1 20.3 + - - +
61A GLN* 3.0 19.9 + - - +
150A LYS* 3.3 31.2 - - + +
151A SER* 3.0 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ARG* 5.8 5.2 - - - +
56A LEU 4.6 1.8 - - - +
57A HIS* 1.3 86.2 - - + +
59A ASP* 1.3 63.9 + - - +
61A GLN* 3.5 28.2 + - + +
62A MET* 3.1 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A HIS* 2.8 21.9 + - - +
58A LEU* 1.3 76.7 - - - +
60A ASP* 1.3 59.4 + - - +
62A MET* 3.5 21.5 + - + +
63A THR* 2.7 39.2 + - - +
150A LYS* 2.7 35.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A LEU* 4.3 12.3 - - + -
57A HIS* 3.1 19.1 + - - +
59A ASP* 1.3 77.2 - - - +
61A GLN* 1.3 65.1 + - - +
63A THR* 3.8 4.7 + - - -
64A LEU* 2.9 34.1 + - + +
149A LEU* 3.5 23.8 - - + +
150A LYS* 3.0 25.1 + - - +
151A SER* 2.8 39.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LYS* 4.9 6.6 - - - +
53A PHE* 3.4 57.7 - - + +
54A ARG* 3.7 25.1 + - - +
56A LEU* 2.9 25.5 + - + +
57A HIS 3.0 15.1 + - - +
58A LEU* 3.7 33.0 - - + +
60A ASP* 1.3 76.5 - - - +
62A MET* 1.3 61.7 + - - +
64A LEU* 3.6 0.4 + - - -
65A ILE* 3.2 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU 3.1 14.3 + - - +
59A ASP* 3.7 22.7 - - + +
61A GLN* 1.3 77.1 - - - +
63A THR* 1.3 66.7 + - - +
65A ILE* 3.4 6.7 + - - +
66A GLN* 3.0 44.4 + - - +
229A ASP* 6.0 3.4 - - + +
233A LYS* 4.6 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A ASP* 2.7 25.0 + - - +
60A ASP* 3.8 7.0 + - - -
62A MET* 1.3 77.8 - - - +
64A LEU* 1.3 63.2 + - - +
66A GLN* 3.2 14.3 - - + +
67A TYR* 3.0 54.1 + - + +
145A PRO* 3.5 22.8 - - + +
149A LEU* 5.0 2.9 - - + -
233A LYS* 4.5 11.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 4.0 12.1 - - + -
56A LEU* 3.8 27.8 - - + -
60A ASP* 2.9 24.7 + - + +
61A GLN 3.8 2.9 - - - +
63A THR* 1.3 78.3 - - - +
65A ILE* 1.3 61.0 + - - +
67A TYR* 3.4 1.4 + - - +
68A SER* 2.9 31.3 + - - -
140A LEU* 3.6 23.9 - - + +
141A LEU* 4.0 7.6 - - + -
143A THR 3.8 19.9 - - - +
144A VAL* 4.1 9.2 - - + -
145A PRO* 5.5 0.9 - - + -
149A LEU* 4.7 11.4 - - + -
155A PHE* 3.9 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 4.5 21.3 - - - -
43A VAL* 5.0 9.6 - - + -
44A VAL* 4.3 31.4 - - + -
47A ALA* 4.3 13.9 - - + -
48A LYS* 6.2 0.4 - - + -
53A PHE* 4.1 20.4 - - + -
61A GLN* 3.2 20.7 + - + +
62A MET* 3.8 6.3 - - - +
64A LEU* 1.3 76.6 - - - +
66A GLN* 1.3 60.1 + - - +
68A SER* 4.4 2.7 - - - -
69A TRP* 2.9 32.6 + - + +
72A LEU* 5.7 0.9 - - - -
140A LEU* 4.4 9.4 - - + -
226A ILE* 5.0 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A MET* 3.0 34.9 + - + +
63A THR* 3.2 19.1 - - - +
65A ILE* 1.3 78.2 - - - +
67A TYR* 1.3 62.5 + - + +
69A TRP* 3.2 14.6 - - - -
226A ILE* 3.8 23.0 + - + +
229A ASP* 4.3 15.8 + - - +
230A GLN* 2.9 42.4 + - + +
233A LYS* 2.9 45.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A THR* 3.0 43.8 + - + +
64A LEU 4.0 1.1 - - - +
66A GLN* 1.3 85.9 - - + +
68A SER* 1.3 59.4 + - - +
69A TRP 3.8 0.4 - - - -
70A MET* 5.3 1.6 + - - +
71A SER* 5.8 0.3 - - - -
143A THR* 3.5 43.1 + - + +
144A VAL 4.5 2.5 - - - -
145A PRO* 4.0 13.9 - - + +
198A VAL* 5.6 4.5 - - - +
202A LEU* 5.2 5.7 - - - +
230A GLN* 4.3 9.0 + - + +
233A LYS* 3.6 32.3 - - + +
234A VAL* 4.0 25.8 - - + -
238A MET* 3.6 22.0 + - - +
239A ALA* 3.5 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A LEU 2.9 20.0 + - - -
65A ILE 4.1 0.3 + - - -
67A TYR* 1.3 79.2 - - - +
69A TRP* 1.3 66.7 + - - +
70A MET 3.2 3.1 - - - -
71A SER* 3.1 11.3 + - - +
72A LEU* 3.0 29.6 + - - +
139A LEU 3.5 23.6 - - - -
140A LEU* 3.5 20.5 - - - +
143A THR* 4.7 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A MET* 3.6 31.2 - - + -
43A VAL* 5.5 2.2 - - + -
65A ILE* 2.9 16.8 + - + +
66A GLN 3.2 24.2 + - - -
67A TYR 3.8 0.2 - - - -
68A SER* 1.3 76.7 - - - +
70A MET* 1.3 103.7 + - + +
72A LEU* 3.3 11.2 + - + +
73A MET* 3.0 45.1 + - + +
202A LEU* 4.5 3.1 - - + -
205A CYS* 4.1 12.3 - - - -
223A LEU* 4.4 21.5 - - + -
226A ILE* 3.9 14.9 - - + +
227A ILE* 4.0 20.4 - - + -
230A GLN* 2.9 25.4 + - - +
248A PDN 4.0 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR 5.3 1.5 + - - +
68A SER 3.2 0.6 - - - -
69A TRP* 1.3 114.0 - - + +
71A SER* 1.3 63.3 + - - +
73A MET* 4.0 1.0 - - - -
74A ALA* 3.0 27.0 + - - +
198A VAL* 4.0 15.5 - - + -
201A LEU* 3.8 31.0 - - + +
202A LEU* 3.8 24.2 - - + -
205A CYS* 3.9 15.7 - - + -
230A GLN* 5.8 0.4 - - - +
248A PDN 3.7 51.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 71 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A SER* 3.1 17.0 + - - +
70A MET* 1.3 78.8 - - - +
72A LEU* 1.3 59.4 + - - +
75A PHE* 2.9 32.4 + - - +
139A LEU* 3.7 30.1 - - - +
143A THR* 5.9 2.2 - - - -
194A MET* 3.6 18.7 - - - +
198A VAL* 3.6 23.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 3.9 31.6 - - + -
46A TRP* 4.0 18.2 - - + -
65A ILE* 5.4 2.0 - - - +
68A SER* 3.0 35.5 + - - +
69A TRP* 3.6 8.7 - - - +
71A SER* 1.3 78.3 - - - +
73A MET* 1.3 60.0 + - + +
75A PHE* 3.4 4.5 + - - +
76A SER* 3.0 33.3 + - - -
136A LYS* 3.4 42.0 - - + +
139A LEU* 4.1 4.7 - - + -
140A LEU* 4.0 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 3.6 11.7 - - - +
39A GLN* 3.3 31.0 - - + +
40A MET* 3.5 46.2 - - + +
43A VAL* 4.1 14.1 - - + -
69A TRP* 3.0 44.7 + - + +
70A MET* 4.1 2.9 - - - +
72A LEU* 1.3 73.0 - - - +
74A ALA* 1.3 61.6 + - - +
76A SER* 3.8 5.5 - - - +
77A LEU* 2.9 28.9 + - - +
80A ARG* 4.6 0.5 + - - -
248A PDN 3.9 32.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A MET 3.0 18.2 + - - +
71A SER* 3.9 3.1 - - - +
73A MET* 1.3 76.7 - - - +
75A PHE* 1.3 58.0 + - - +
77A LEU* 3.3 10.3 + - - +
78A GLY* 3.0 23.7 + - - -
115A MET* 4.8 7.3 - - + +
118A ILE* 4.8 5.0 - - - +
194A MET* 4.1 14.4 - - + -
197A LEU* 4.7 5.8 - - + -
201A LEU* 3.8 25.1 - - + -
248A PDN 4.5 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER 2.9 18.4 + - - +
72A LEU 3.7 3.6 - - - +
74A ALA* 1.3 75.4 - - - +
76A SER* 1.3 64.7 + - - +
78A GLY* 3.2 3.3 + - - -
79A TRP* 3.1 18.2 + - - +
118A ILE* 4.5 4.9 - - + -
122A PHE* 3.4 38.7 - + - -
132A PHE* 3.6 36.3 - + - -
135A MET* 3.7 40.2 - - + -
136A LYS* 3.8 12.3 - - + -
139A LEU* 3.2 24.0 - - + -
190A LEU* 4.4 14.4 - - + -
191A LEU* 4.6 6.1 - - + -
194A MET* 4.0 20.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU* 5.0 2.0 + - - -
39A GLN* 5.7 1.1 - - - -
72A LEU 3.0 17.7 + - - -
73A MET* 3.9 5.4 - - - -
75A PHE* 1.3 73.4 - - - +
77A LEU* 1.3 66.2 + - - +
79A TRP* 3.1 2.4 + - - +
80A ARG* 2.9 45.6 + - - +
132A PHE* 4.0 13.2 - - - -
136A LYS* 3.3 24.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET 2.9 19.2 + - - +
74A ALA* 3.4 5.8 - - - +
75A PHE 3.2 0.2 - - - -
76A SER* 1.3 78.1 - - - +
78A GLY* 1.3 58.2 + - - +
80A ARG* 3.6 13.3 - - - +
81A SER* 2.8 48.7 + - - +
90A LEU* 4.2 9.6 - - + -
91A TYR 3.6 26.5 - - - +
92A PHE* 3.5 39.9 - - + +
115A MET* 3.6 35.4 - - + -
248A PDN 4.2 5.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ALA 3.0 14.4 + - - -
75A PHE 3.2 4.6 + - - -
77A LEU* 1.3 78.7 - - - +
79A TRP* 1.3 56.6 + - - +
81A SER* 4.5 0.4 - - - -
82A TYR* 3.0 26.9 + - - +
90A LEU* 6.2 0.2 - - - -
115A MET 4.8 3.8 - - - -
118A ILE* 4.4 4.5 - - - -
119A SER* 3.0 28.0 + - - -
122A PHE* 3.4 12.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PHE 3.1 5.1 + - - -
76A SER 3.1 6.3 + - - +
78A GLY* 1.3 73.3 - - - +
80A ARG* 1.3 73.7 - - + +
82A TYR* 3.0 25.0 + + - +
83A LYS* 2.9 62.8 + - + +
122A PHE* 3.2 16.3 - + + -
127A VAL* 3.4 28.0 - - + -
128A THR 4.0 0.2 - - - -
129A TYR* 3.5 54.0 - + + -
132A PHE* 3.4 58.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A VAL* 5.4 10.8 - - - +
39A GLN* 3.5 13.4 + - - +
73A MET 4.6 0.2 + - - -
76A SER* 2.9 37.2 + - - +
77A LEU* 3.6 18.9 - - - +
79A TRP* 1.3 84.4 - - + +
81A SER* 1.3 58.0 + - - +
83A LYS* 4.8 0.7 - - - -
84A HIS* 2.9 47.4 + - + +
91A TYR* 3.0 40.5 + - + +
92A PHE* 3.0 24.0 + - - +
93A ALA* 5.1 1.1 - - - +
248A PDN 3.1 22.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A LEU* 2.8 24.3 + - - +
78A GLY* 3.8 0.7 - - - -
80A ARG* 1.3 76.9 - - - +
82A TYR* 1.3 57.3 + - - +
85A THR* 2.7 32.4 + - - +
87A GLY 3.0 5.2 + - - -
89A MET 3.2 19.8 + - - -
90A LEU* 3.4 8.9 - - - +
91A TYR* 2.9 28.2 + - - -
119A SER* 3.2 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLY 3.0 19.0 + - - +
79A TRP* 3.3 31.2 - + - +
81A SER* 1.3 76.9 - - - +
83A LYS* 1.3 86.9 + - + +
86A ASN* 3.0 32.0 + - - +
87A GLY 3.8 4.5 - - - +
119A SER* 3.1 9.1 + - - +
122A PHE* 3.6 27.8 - - + -
123A VAL* 3.5 33.9 - - + -
126A GLN* 3.5 36.3 + - - -
127A VAL 3.6 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A TRP* 2.9 61.5 + - + +
80A ARG* 4.2 2.9 - - - +
82A TYR* 1.3 105.1 + - + +
84A HIS* 1.3 70.3 + - + +
86A ASN 4.7 0.4 + - - -
127A VAL 5.3 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ARG* 2.9 35.6 + - + +
83A LYS* 1.3 87.2 + - + +
85A THR* 1.3 60.6 + - + +
86A ASN 3.7 0.4 - - - -
91A TYR* 3.6 56.9 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A SER 2.7 19.2 + - - +
84A HIS* 1.3 89.1 - - + +
86A ASN* 1.3 70.9 + - - +
88A GLN* 3.0 21.8 + - - +
89A MET* 3.0 60.7 + - + +
91A TYR* 4.4 14.4 - - + -
97A ILE* 5.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 3.0 24.8 + - - +
83A LYS 4.7 0.2 - - - -
84A HIS 3.7 0.6 - - - -
85A THR* 1.3 80.4 - - - +
87A GLY* 1.3 58.3 + - - +
88A GLN* 3.6 11.4 + - + +
120A GLN* 5.7 0.5 - - - +
123A VAL* 3.5 35.3 - - - +
126A GLN* 5.5 1.6 + - - -
----------------------------------------------------------
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