Contacts of the helix formed by residues 127 - 157 (chain P) in PDB entry 3A68
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 GLY 127 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123P HIS* 2.8 19.8 + - - -
125P ASP 3.5 1.4 - - - -
126P LYS* 1.3 82.0 - - - +
128P ASP* 1.3 67.4 + - - -
129P ALA 3.3 2.9 + - - -
130P LEU 3.6 0.8 + - - -
131P HIS* 3.1 19.2 + - - +
193P LYS* 3.8 18.9 - - - +
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Residues in contact with ASP 128 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190L ARG* 3.2 38.7 + - - -
69P TYR* 4.1 13.8 + - + +
70P PHE* 3.6 17.5 - - + -
75P VAL* 3.6 16.8 - - - +
77P LEU* 3.8 1.9 - - - +
121P PHE 3.6 21.7 - - - +
122P ASP* 4.2 3.8 - - + -
123P HIS 4.2 5.2 + - - +
127P GLY* 1.3 72.7 - - - +
129P ALA* 1.3 77.5 + - - +
131P HIS* 3.7 1.2 - - - +
132P ALA* 3.0 26.7 + - - +
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Residues in contact with ALA 129 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70P PHE* 4.3 0.4 - - - -
77P LEU* 4.2 2.7 - - + -
80P LEU* 3.7 27.7 - - + +
127P GLY 3.3 0.6 - - - -
128P ASP* 1.3 84.5 + - - +
130P LEU* 1.3 63.7 + - - +
132P ALA* 3.8 1.9 - - - +
133P MET* 3.1 27.9 + - - +
188P LEU* 3.9 15.3 - - + -
197P VAL* 3.7 33.0 - - + -
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Residues in contact with LEU 130 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126P LYS* 3.6 35.0 - - + +
127P GLY 3.6 1.4 + - - -
128P ASP 3.4 0.2 - - - -
129P ALA* 1.3 79.1 - - - +
131P HIS* 1.3 64.3 + - - +
133P MET 3.3 1.0 + - - -
134P GLU* 2.9 58.7 + - + +
185P VAL* 3.9 17.7 - - + +
188P LEU* 4.0 20.7 - - + +
189P ARG* 3.9 34.1 - - + +
197P VAL* 5.7 2.1 - - + +
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Residues in contact with HIS 131 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K LEU* 4.3 14.8 - - + +
118P LEU* 5.9 2.6 - - - +
120P ASP 5.5 0.8 + - - -
121P PHE* 3.4 30.9 - - + +
122P ASP 4.0 8.1 + - - -
123P HIS* 3.4 35.4 + + + -
126P LYS* 4.2 16.4 + - + +
127P GLY 3.1 19.1 + - - +
128P ASP 3.7 2.7 - - - +
130P LEU* 1.3 78.1 - - - +
132P ALA* 1.3 57.0 + - - +
134P GLU* 3.3 4.1 + - - +
135P LEU* 2.9 59.5 + - + +
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Residues in contact with ALA 132 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P MET* 3.2 33.8 - - + +
70P PHE* 3.4 33.7 - - + -
84P PHE* 4.1 6.3 - - + -
121P PHE* 4.7 5.4 - - + -
128P ASP 3.0 8.2 + - - +
129P ALA 3.8 3.1 - - - +
131P HIS* 1.3 78.0 - - - +
133P MET* 1.3 58.1 + - - +
135P LEU* 3.3 6.5 + - - +
136P ALA* 2.8 24.8 + - - +
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Residues in contact with MET 133 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80P LEU* 4.5 9.9 - - + -
83P PHE* 3.6 32.3 - - + -
84P PHE* 4.3 11.0 - - + -
129P ALA 3.1 13.6 + - - +
130P LEU* 3.3 3.8 + - - +
132P ALA* 1.3 73.8 - - - +
134P GLU* 1.3 61.4 + - - +
136P ALA* 3.3 2.2 + - - -
137P LEU* 2.9 24.6 + - - +
181P ILE* 3.4 19.7 - - - +
184P TYR* 3.4 39.3 - - + -
185P VAL* 3.8 16.8 - - + +
188P LEU* 3.6 24.9 - - + -
200P PHE* 4.8 1.6 - - + -
204P LEU* 3.9 16.6 - - + -
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Residues in contact with GLU 134 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25K LEU* 3.7 12.9 - - + +
28K VAL* 4.3 13.6 - - + +
126P LYS* 2.9 37.0 + - - +
130P LEU* 2.9 41.8 + - + +
131P HIS* 3.6 4.3 - - - +
133P MET* 1.3 72.8 - - - +
135P LEU* 1.3 61.6 + - - +
137P LEU* 3.3 5.8 + - - +
138P SER* 2.9 31.2 + - - -
185P VAL* 4.1 15.0 - - + -
189P ARG* 2.8 35.6 + - - +
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Residues in contact with LEU 135 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18K PHE* 4.8 16.2 - - + -
21K VAL* 3.9 19.9 - - + +
25K LEU* 3.5 29.4 - - + +
66P MET* 4.8 5.4 - - + -
118P LEU* 5.2 4.7 - - + -
121P PHE* 3.9 27.8 - - + -
131P HIS* 2.9 45.1 + - + +
132P ALA* 3.5 7.6 - - - +
134P GLU* 1.3 74.1 - - - +
136P ALA* 1.3 59.8 + - - +
138P SER* 3.1 3.9 + - - -
139P LEU* 2.8 36.6 + - + +
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Residues in contact with ALA 136 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63P TYR* 3.7 28.0 + - + +
66P MET* 4.7 1.1 - - + +
83P PHE* 5.3 0.4 - - + -
84P PHE* 4.1 13.2 - - + -
132P ALA 2.8 17.8 + - - +
133P MET* 3.5 10.1 - - - +
135P LEU* 1.3 76.5 - - - +
137P LEU* 1.3 62.3 + - - +
139P LEU* 3.2 7.5 + - - +
140P GLU* 2.9 28.9 + - - +
181P ILE* 4.2 13.5 - - + -
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Residues in contact with LEU 137 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28K VAL* 4.5 22.0 - - + -
36K LEU* 3.9 27.4 - - + +
133P MET 2.9 14.4 + - - +
134P GLU* 3.5 9.2 - - - +
136P ALA* 1.3 74.9 - - - +
138P SER* 1.3 64.5 + - - +
140P GLU* 3.2 3.3 + - - -
141P LYS* 2.9 36.8 + - + +
178P ILE* 3.9 26.7 - - + +
181P ILE* 3.6 12.7 - - + +
182P SER* 3.4 27.6 - - - +
185P VAL* 4.4 14.8 - - + -
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Residues in contact with SER 138 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21K VAL* 3.9 16.4 - - - -
24K GLU* 3.4 19.0 + - - +
25K LEU* 3.0 38.7 + - - +
28K VAL* 3.5 8.9 - - - +
134P GLU 2.9 14.9 + - - -
135P LEU 3.1 8.0 + - - -
137P LEU* 1.3 76.0 - - - +
139P LEU* 1.3 57.8 + - - +
141P LYS* 3.3 3.4 + - - -
142P LEU* 2.9 26.9 + - - +
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Residues in contact with LEU 139 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K PHE* 5.7 0.4 - - + -
17K PRO* 4.1 22.4 - - + -
18K PHE* 5.6 5.2 - - + -
21K VAL* 3.5 24.9 - - + -
59P VAL* 4.7 20.6 - - + -
62P VAL* 3.5 33.9 - - + -
63P TYR* 4.2 23.1 - - + +
66P MET* 4.8 3.1 - - - -
135P LEU* 2.8 20.7 + - + +
136P ALA* 3.2 10.1 + - - +
138P SER* 1.3 77.1 - - - +
140P GLU* 1.3 57.4 + - - +
142P LEU* 3.3 7.6 + - + +
143P THR* 2.9 33.1 + - - -
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Residues in contact with GLU 140 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59P VAL* 4.4 2.6 - - - +
63P TYR* 2.5 33.7 + - - +
91P GLU* 3.7 15.7 - - - +
136P ALA 2.9 20.3 + - - +
137P LEU* 3.2 4.7 + - - +
139P LEU* 1.3 74.4 - - - +
141P LYS* 1.3 61.3 + - - +
143P THR* 3.4 7.1 + - - +
144P ASN* 2.9 18.2 + - - +
174P GLN* 2.7 51.8 + - - +
177P ALA* 4.2 11.9 - - + +
178P ILE* 4.0 14.1 - - + -
181P ILE* 3.5 22.0 - - + +
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Residues in contact with LYS 141 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K GLU* 3.8 21.8 - - + +
27K LEU 5.7 1.2 + - - -
28K VAL* 5.8 5.5 - - + +
29K PRO* 5.0 9.5 - - - +
35K SER 5.5 0.2 + - - -
36K LEU 2.7 28.9 + - - -
37K ALA* 3.6 14.6 - - - +
38K ARG 3.3 19.2 + - - -
39K GLN* 2.9 46.0 + - + +
137P LEU* 2.9 36.4 + - + +
138P SER* 3.8 4.5 - - - +
140P GLU* 1.3 74.5 - - - +
142P LEU* 1.3 64.4 + - - +
144P ASN* 3.2 1.2 + - - +
145P GLU* 3.0 11.8 + - - +
178P ILE* 4.1 9.2 - - + -
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Residues in contact with LEU 142 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K PHE* 3.5 33.2 - - + -
17K PRO* 4.2 1.6 - - + +
20K GLU* 3.7 33.9 - - + +
21K VAL* 3.9 19.5 - - + -
24K GLU* 4.5 12.5 - - + +
59P VAL* 6.5 0.2 - - + -
138P SER 2.9 17.2 + - - +
139P LEU* 3.5 8.3 - - + +
141P LYS* 1.3 74.9 - - - +
143P THR* 1.3 65.2 + - - +
145P GLU* 3.2 20.8 + - - +
146P LYS* 3.0 48.1 + - - +
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Residues in contact with THR 143 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K PHE* 6.0 0.3 - - - -
52P GLN* 4.0 6.1 - - - +
55P VAL* 4.4 6.4 - - + +
56P GLU* 3.8 25.1 - - - +
59P VAL* 3.5 24.5 - - + +
139P LEU 2.9 20.4 + - - -
140P GLU* 3.6 9.1 + - - -
142P LEU* 1.3 78.2 - - - +
144P ASN* 1.3 56.3 + - - +
146P LYS* 3.1 9.4 + - - +
147P LEU* 2.8 30.4 + - + +
174P GLN* 3.5 20.4 - - - +
214P CA 4.1 9.0 - - - -
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Residues in contact with ASN 144 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K GLN* 2.9 31.7 + - - +
40K LYS* 6.0 0.2 - - - +
140P GLU 2.9 14.6 + - - +
141P LYS 3.4 9.2 - - - +
143P THR* 1.3 75.7 - - - +
145P GLU* 1.3 63.0 + - - +
147P LEU* 3.2 3.6 + - - +
148P LEU* 2.9 44.2 + - - +
171P LEU* 4.3 13.5 - - - +
174P GLN* 3.3 30.1 - - + +
175P VAL* 5.2 9.1 + - - +
178P ILE* 3.9 7.6 - - + +
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Residues in contact with GLU 145 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24K GLU* 4.2 14.4 - - - +
39K GLN* 4.2 6.6 + - - +
40K LYS* 4.5 25.5 - - - +
141P LYS 3.0 12.6 + - - +
142P LEU* 3.2 21.4 + - - +
144P ASN* 1.3 75.1 - - - +
146P LYS* 1.3 64.3 + - + +
148P LEU* 3.3 4.1 + - - +
149P ASN* 2.9 28.7 + - + +
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Residues in contact with LYS 146 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15K PHE* 3.2 30.3 - - + -
20K GLU* 2.9 30.8 + - - -
52P GLN* 3.4 24.5 - - - +
55P VAL* 4.2 20.4 - - + -
142P LEU* 3.0 28.1 + - - +
143P THR 3.4 7.9 - - - +
145P GLU* 1.3 79.7 - - + +
147P LEU* 1.3 59.9 + - - +
149P ASN* 3.2 12.1 + - + +
150P LEU* 2.9 24.6 + - - +
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Residues in contact with LEU 147 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52P GLN* 3.4 30.1 - - + +
56P GLU* 3.8 7.9 - - - +
98P LEU* 5.4 0.2 - - + -
143P THR* 2.8 25.7 + - + +
144P ASN* 3.6 4.5 - - - +
146P LYS* 1.3 73.2 - - - +
148P LEU* 1.3 59.1 + - - +
150P LEU* 3.2 8.8 + - + +
151P HIS* 2.9 27.4 + - - +
166P VAL* 3.8 11.9 - - + +
170P TYR* 3.8 38.4 - - + +
171P LEU* 3.8 15.0 - - + -
174P GLN* 3.6 38.6 - - + +
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Residues in contact with LEU 148 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40K LYS* 3.7 34.3 - - + -
160K VAL* 4.0 24.2 - - + +
161K GLN* 5.2 4.5 - - + +
144P ASN* 2.9 38.1 + - - +
145P GLU* 3.7 4.9 - - - +
147P LEU* 1.3 74.2 - - - +
149P ASN* 1.3 60.4 + - - +
151P HIS* 3.3 4.8 + - + +
152P SER* 2.9 27.7 + - - -
171P LEU* 3.9 30.1 - - + -
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Residues in contact with ASN 149 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51P GLU* 5.3 4.2 - - - +
145P GLU* 2.9 16.4 + - + +
146P LYS* 3.4 16.9 - - + +
148P LEU* 1.3 74.5 - - - +
150P LEU* 1.3 65.6 + - - +
152P SER* 2.6 30.1 + - - -
153P VAL* 2.9 20.2 + - - +
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Residues in contact with LEU 150 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48P ALA* 3.6 35.9 - - + +
49P VAL* 4.0 14.4 - - + +
52P GLN* 3.9 31.9 - - + +
98P LEU* 4.5 13.0 - - + -
146P LYS 2.9 13.7 + - - +
147P LEU* 3.2 11.2 + - + +
149P ASN* 1.3 76.5 + - - +
151P HIS* 1.3 62.5 + - - +
153P VAL* 3.2 6.7 + - - +
154P ALA* 3.1 20.3 + - - +
162P LEU* 4.5 10.1 - - + -
166P VAL* 3.6 29.2 - - + -
170P TYR* 6.4 0.2 - - + -
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Residues in contact with HIS 151 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160K VAL* 3.5 31.4 - - + +
147P LEU 2.9 13.4 + - - +
148P LEU* 3.5 13.2 + - + +
149P ASN 3.2 0.2 - - - -
150P LEU* 1.3 79.1 - - - +
152P SER* 1.3 58.2 + - - +
154P ALA* 3.3 6.8 + - - +
155P THR* 3.0 55.6 + - + +
163P ALA* 3.5 20.9 - - - +
166P VAL* 4.2 12.3 - - + -
167P GLU* 2.5 47.0 + - + +
171P LEU* 4.4 4.3 - - + -
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Residues in contact with SER 152 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148P LEU 2.9 13.6 + - - -
149P ASN* 2.6 32.9 + - - -
151P HIS* 1.3 76.4 + - - +
153P VAL* 1.3 60.7 + - - +
155P THR* 2.8 22.3 + - - -
156P LYS* 2.9 31.4 + - - +
----------------------------------------------------------
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Residues in contact with VAL 153 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P GLU* 3.7 28.5 - - + +
45P SER* 4.3 5.4 - - - -
48P ALA* 3.9 27.1 - - + -
149P ASN* 2.9 29.2 + - - +
150P LEU* 3.2 8.5 + - + +
152P SER* 1.3 80.9 + - - +
154P ALA* 1.3 63.0 + - - +
156P LYS* 3.9 3.5 - - - +
157P ASN* 2.9 45.0 + - - +
162P LEU* 5.8 0.2 - - + -
----------------------------------------------------------
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Residues in contact with ALA 154 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45P SER* 4.7 2.0 - - - -
150P LEU 3.1 10.0 + - - +
151P HIS* 3.6 9.0 - - - +
153P VAL* 1.3 78.1 - - - +
155P THR* 1.3 57.0 + - - +
157P ASN 3.3 1.9 + - - -
158P GLY 2.9 8.0 + - - -
159P ASP* 2.8 36.7 + - - +
162P LEU* 3.7 37.0 - - + -
163P ALA* 3.8 19.1 - - - +
166P VAL* 5.9 0.2 - - + -
----------------------------------------------------------
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Residues in contact with THR 155 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151P HIS* 3.0 42.1 + - + +
152P SER* 2.8 25.3 + - - -
154P ALA* 1.3 75.3 - - - +
156P LYS* 1.3 69.4 + - - +
158P GLY* 3.1 14.1 + - - -
159P ASP 5.0 0.7 - - - +
163P ALA* 4.2 10.1 - - + -
----------------------------------------------------------
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Residues in contact with LYS 156 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44P GLU* 5.6 2.2 - - - +
152P SER* 2.9 32.4 + - - +
153P VAL* 3.9 5.4 - - - +
155P THR* 1.3 83.7 + - - +
157P ASN* 1.3 63.3 + - - +
158P GLY 3.3 0.7 + - - -
----------------------------------------------------------
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Residues in contact with ASN 157 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P VAL* 3.7 31.1 - - + +
44P GLU* 3.1 43.8 + - - +
45P SER* 4.2 7.9 + - - +
153P VAL* 2.9 29.4 + - - +
154P ALA 4.0 2.5 - - - +
156P LYS* 1.3 80.2 - - - +
158P GLY* 1.3 61.7 + - - +
159P ASP* 3.3 3.3 + - + +
----------------------------------------------------------
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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