Contacts of the helix formed by residues 83 - 113 (chain A) in PDB entry 5G49
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 SER 83 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE* 1.3 76.5 - - - +
84A ASP* 1.3 64.7 + - - +
85A ASP 3.6 2.2 + - - -
86A SER* 3.1 17.2 + - - -
87A LYS* 3.1 21.4 + - - +
123B THR* 4.0 12.4 - - - +
124B LEU 3.1 13.4 + - - -
125B GLN* 4.7 0.7 - - - -
1152B ACT 2.7 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ILE 3.8 0.7 + - - +
83A SER* 1.3 73.4 - - - +
85A ASP* 1.3 65.1 + - - +
87A LYS* 3.2 24.2 + - - +
88A GLU* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A SER* 3.3 2.3 + - - +
84A ASP* 1.3 77.1 - - - +
86A SER* 1.3 58.0 + - - +
88A GLU* 3.2 10.9 + - - +
89A THR* 2.8 34.4 + - - +
126B LYS* 4.3 18.5 - - + +
1152B ACT 3.3 28.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A MET* 5.3 0.7 - - - -
82A ILE* 3.8 11.2 - - - -
83A SER* 3.1 17.1 + - - -
85A ASP* 1.3 78.0 - - - +
87A LYS* 1.3 63.3 + - - +
89A THR* 3.1 1.2 + - - -
90A ILE* 2.9 30.5 + - - +
124B LEU* 2.9 36.3 + - - +
125B GLN 3.1 20.1 - - - -
126B LYS* 3.9 1.5 - - - +
129B ILE* 4.0 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 3.7 20.1 - - + +
68A VAL* 5.0 1.6 - - - +
69A ILE* 3.4 33.6 - - + +
72A MET* 5.0 5.2 - - - -
73A ARG* 3.7 19.7 - - - +
82A ILE* 3.4 38.9 + - + -
83A SER 3.1 11.1 + - - +
84A ASP* 3.2 22.1 + - - +
86A SER* 1.3 74.9 - - - +
88A GLU* 1.3 63.4 + - - +
90A ILE* 3.5 5.3 + - - +
91A GLN* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 3.4 44.3 + - - +
65A ILE* 4.4 1.3 - - + +
84A ASP 3.1 9.4 + - - +
85A ASP* 3.6 12.3 - - - +
87A LYS* 1.3 78.5 - - - +
89A THR* 1.3 57.3 + - - +
91A GLN* 3.2 11.0 + - - +
92A GLU* 2.9 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASP* 2.8 26.1 + - - +
86A SER* 3.1 4.2 + - - -
88A GLU* 1.3 73.8 - - - +
90A ILE* 1.3 63.3 + - - +
92A GLU* 3.1 11.9 + - - +
93A CYS* 2.9 28.4 + - - -
126B LYS* 3.2 30.3 + - + +
129B ILE* 3.9 22.0 - - + -
145B ILE* 5.4 2.0 - - + +
146B VAL* 3.6 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 3.6 22.9 - - + -
72A MET* 3.6 29.6 - - + -
86A SER 2.9 19.8 + - - +
87A LYS 3.9 3.4 - - - +
89A THR* 1.3 74.6 - - - +
91A GLN* 1.3 63.4 + - - +
93A CYS* 3.2 4.4 + - - +
94A VAL* 3.1 29.7 + - + +
104B PHE* 6.0 0.4 - - + -
105B ILE* 4.4 14.1 - - + -
108B LEU* 3.5 35.9 - - + -
109B THR* 4.6 9.0 - - - +
112B SER* 5.2 0.4 - - - +
124B LEU* 6.3 0.2 - - + -
129B ILE* 3.6 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 2.8 36.2 + - - +
62A PHE* 3.6 20.4 - - + +
63A MET 2.6 31.0 + - - +
64A PRO* 4.6 0.4 - - - +
65A ILE* 3.6 34.6 - - + +
68A VAL* 4.7 10.8 - - + -
87A LYS 3.1 17.2 + - - +
88A GLU* 3.5 6.5 - - - +
90A ILE* 1.3 78.4 - - - +
92A GLU* 1.3 60.7 + - - +
94A VAL* 3.4 15.8 + - - +
95A SER* 3.6 13.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ARG* 3.2 26.4 + - - +
62A PHE* 3.6 26.5 - - + -
88A GLU* 2.9 26.2 + - - +
89A THR* 3.1 14.3 + - - +
91A GLN* 1.3 75.5 - - - +
93A CYS* 1.3 66.2 + - - +
95A SER* 3.2 5.7 + - - -
96A GLU* 3.1 21.4 + - - +
126B LYS* 5.3 3.8 + - - -
145B ILE* 4.4 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A THR* 2.9 26.6 + - - -
90A ILE 3.2 7.2 + - - +
92A GLU* 1.3 76.4 - - - +
94A VAL* 1.3 56.6 + - - +
96A GLU* 3.3 3.0 + - - +
97A TYR* 2.9 29.8 + - - +
104B PHE* 3.7 6.9 - - + -
108B LEU* 3.9 29.8 - - + -
129B ILE* 4.8 1.1 - - - -
133B VAL* 5.5 0.2 - - - -
142B LEU* 3.8 26.7 - - + +
145B ILE* 4.5 3.8 - - - -
146B VAL* 3.7 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A MET* 3.8 28.9 - - + -
68A VAL* 4.9 2.5 - - + -
90A ILE* 3.1 18.5 + - + +
91A GLN* 3.6 10.1 - - - +
92A GLU 3.1 0.8 - - - -
93A CYS* 1.3 76.2 - - - +
95A SER* 1.3 61.6 + - - +
97A TYR* 3.2 5.4 + - - +
98A ILE* 3.1 23.7 + - + +
101B CYS* 4.1 26.5 - - + -
104B PHE* 3.9 13.7 - - + -
105B ILE* 3.5 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ARG 2.9 26.5 + - - -
62A PHE* 3.4 22.0 - - - -
63A MET 4.5 0.9 + - - -
91A GLN 3.6 2.2 + - - -
92A GLU 3.2 8.1 + - - -
94A VAL* 1.3 78.4 - - - +
96A GLU* 1.3 62.8 + - - +
98A ILE* 3.2 5.9 + - - +
99A SER* 3.0 27.0 + - - -
79B ILE* 3.4 26.1 - - - +
----------------------------------------------------------
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 GLU 3.1 12.3 + - - +
93A CYS* 3.6 8.5 - - - +
94A VAL 3.3 0.2 - - - -
95A SER* 1.3 76.9 - - - +
97A TYR* 1.3 57.8 + - - +
99A SER* 3.7 10.1 - - - +
100A PHE* 2.8 35.0 + - - +
141B PHE* 3.9 23.6 - - + +
142B LEU* 3.9 8.1 - - + -
145B ILE* 3.7 34.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A CYS 2.9 18.2 + - - +
94A VAL 3.4 4.5 - - - +
96A GLU* 1.3 76.2 - - - +
98A ILE* 1.3 65.7 + - + +
100A PHE* 3.7 0.5 - - - +
101A ILE* 3.1 51.9 + - + +
126A MET* 3.1 26.2 - - - +
131A PHE* 3.7 22.0 - + - -
134A TYR* 3.6 6.5 - + - -
97B PHE* 4.5 4.0 - + - -
100B ALA* 3.3 33.4 + - + +
101B CYS* 4.0 18.8 - - - -
104B PHE* 3.5 41.7 - + + -
141B PHE* 3.7 21.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A MET* 4.3 12.8 - - + -
94A VAL* 3.1 17.7 + - + +
95A SER 3.2 5.6 + - - +
97A TYR* 1.3 75.7 - - - +
99A SER* 1.3 58.2 + - - +
101A ILE 3.9 0.2 - - - -
102A THR* 2.7 36.1 + - - +
76B ILE* 4.4 11.0 - - + +
79B ILE* 4.0 35.9 - - + -
80B MET* 3.6 33.9 - - + +
97B PHE* 3.9 19.4 - - + -
101B CYS* 3.7 28.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER 3.0 16.8 + - - -
96A GLU* 3.8 11.9 - - - -
98A ILE* 1.3 77.0 - - - +
100A PHE* 1.3 58.4 + - - +
102A THR* 3.9 4.9 - - - -
103A GLY* 2.9 28.2 + - - -
79B ILE* 4.2 17.7 + - - +
80B MET* 6.1 0.4 - - - +
83B ASP* 5.4 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLU* 2.8 24.6 + - + +
97A TYR 3.7 3.6 - - - +
99A SER* 1.3 74.9 - - - +
101A ILE* 1.3 63.5 + - + +
103A GLY* 3.5 0.9 + - - -
104A GLU* 3.3 19.8 + - - +
129A LEU* 3.8 39.0 - - + +
131A PHE* 4.1 18.4 - + - -
138B ILE 5.0 1.1 - - - -
141B PHE* 3.5 56.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A TYR* 3.1 55.8 + - + +
100A PHE* 1.3 77.3 - - + +
102A THR* 1.3 65.2 + - - +
104A GLU 3.4 1.6 + - - -
105A ALA* 3.1 20.6 + - - +
122A VAL* 4.1 14.8 - - + +
125A ALA* 3.7 8.4 - - + +
126A MET* 3.7 35.0 - - + -
129A LEU* 4.1 11.0 - - + -
131A PHE* 4.1 17.0 - - + -
97B PHE* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A ILE 2.7 21.8 + - - -
99A SER* 3.9 4.5 - - - -
101A ILE* 1.3 77.7 - - - +
103A GLY* 1.3 51.6 + - - +
105A ALA* 3.2 6.0 + - - +
106A ASN* 2.7 34.0 + - - +
117A ILE* 4.1 6.7 - - + -
122A VAL* 6.3 0.7 - - - -
80B MET* 3.6 37.3 - - + +
83B ASP* 5.5 3.1 - - + +
86B VAL* 3.8 26.7 - - + -
97B PHE* 3.4 21.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A SER 2.9 18.2 + - - -
100A PHE 4.0 0.9 - - - -
102A THR* 1.3 77.1 - - - +
104A GLU* 1.3 56.2 + - - +
106A ASN* 3.8 3.5 - - - +
107A GLU* 2.9 42.5 + - - +
83B ASP* 4.3 16.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A PHE* 3.3 7.8 + - + +
101A ILE 3.8 4.0 - - - +
103A GLY* 1.3 76.2 - - - +
105A ALA* 1.3 61.2 + - - +
107A GLU* 3.5 15.8 + - - +
108A ARG 3.5 14.0 + - - -
111A ARG* 5.4 1.6 + - - -
124A TRP* 3.7 19.5 - - + -
125A ALA* 3.7 16.4 - - + +
128A LYS* 3.4 22.3 - - + +
129A LEU* 3.7 45.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ILE 3.1 16.6 + - - +
102A THR* 3.7 5.4 - - - +
104A GLU* 1.3 73.8 - - - +
106A ASN* 1.3 66.6 + - - +
108A ARG* 3.3 5.5 + - - +
109A CYS* 3.3 25.4 + - - -
117A ILE* 4.2 12.6 - - + -
121A ASP* 3.6 37.0 - - + +
122A VAL* 4.4 4.5 - - + +
124A TRP* 4.5 4.7 - - - -
125A ALA* 3.7 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR 2.7 22.3 + - - +
103A GLY* 4.0 5.2 - - - +
105A ALA* 1.3 73.3 - - - +
107A GLU* 1.3 61.8 + - - +
109A CYS* 3.2 10.2 + - - +
110A GLN* 3.0 38.0 + - - +
115A LYS 5.7 1.0 - - - +
117A ILE* 3.5 27.5 - - + +
83B ASP* 5.1 2.7 + - - +
85B ASP* 3.0 33.2 + - - +
86B VAL* 3.7 21.1 - - + +
87B ARG 4.3 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A GLY* 2.9 27.3 + - - +
104A GLU* 3.8 16.3 - - - +
105A ALA 3.2 0.4 - - - -
106A ASN* 1.3 77.2 - - + +
108A ARG* 1.3 61.8 + - - +
110A GLN* 3.3 21.4 + - - +
111A ARG* 3.1 40.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU 3.5 1.8 + - - -
105A ALA 3.3 7.9 + - - +
106A ASN 3.3 0.4 - - - -
107A GLU* 1.3 76.9 - - - +
109A CYS* 1.3 66.9 + - - +
111A ARG* 2.9 28.8 + - - +
112A GLU* 2.8 47.1 + - + +
114A ARG* 3.9 9.5 - - - +
120A GLU* 4.6 2.6 + - - +
121A ASP* 3.1 27.1 + - - +
124A TRP* 3.3 75.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA 3.3 14.8 + - - -
106A ASN* 3.2 13.2 + - - +
108A ARG* 1.3 76.4 - - - +
110A GLN* 1.3 57.9 + - + +
112A GLU 3.0 3.2 + - - +
113A GLN 2.8 25.8 + - - -
114A ARG* 2.9 49.7 + - + +
115A LYS 5.5 0.7 - - - -
116A THR 4.0 10.5 - - - +
117A ILE* 4.2 14.4 - - - -
121A ASP* 3.5 25.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ASN* 3.0 24.0 + - - +
107A GLU* 3.6 25.2 - - - +
108A ARG 3.2 0.2 - - - -
109A CYS* 1.3 74.8 - - + +
111A ARG* 1.3 63.3 + - + +
113A GLN* 3.2 17.0 + - - +
114A ARG 4.8 3.1 - - - +
85B ASP* 3.6 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A GLU* 5.4 2.0 + - - -
107A GLU* 3.1 33.5 + - - +
108A ARG* 2.9 36.9 + - - +
110A GLN* 1.3 77.5 - - + +
112A GLU* 1.3 63.6 + - + +
113A GLN* 3.3 6.5 + - - +
124A TRP* 4.1 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 2.8 46.9 + - + +
109A CYS 3.8 2.5 - - - +
111A ARG* 1.3 78.8 - - + +
113A GLN* 1.3 71.5 + - - +
114A ARG* 2.9 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A CYS 2.8 6.9 + - - -
110A GLN* 3.2 13.4 + - - +
111A ARG 4.3 5.6 - - - +
112A GLU* 1.3 82.4 - - - +
114A ARG* 1.3 58.9 + - - +
115A LYS* 5.6 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