Contacts of the helix formed by residues 134 - 164 (chain B) in PDB entry 1C03
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 ASN 134 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LYS 5.6 3.0 + - - +
56B LEU* 4.1 20.8 - - + +
91B LYS* 2.7 35.9 + - - -
132B ASP* 3.1 16.7 + - - +
133B GLU* 1.3 78.8 - - - +
135B SER* 1.3 55.0 + - - +
136B ILE 3.1 2.7 - - - -
137B TYR* 2.8 32.7 + - - +
138B LEU* 3.1 21.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 5.3 7.0 + - - +
131B LYS* 3.3 18.5 - - - +
132B ASP* 3.2 41.0 + - - +
133B GLU 3.4 0.2 - - - -
134B ASN* 1.3 76.6 - - - +
136B ILE* 1.3 57.9 + - - +
138B LEU* 3.6 11.2 + - - +
139B ILE* 3.1 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 136 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B HIS 5.6 0.9 - - - +
132B ASP 4.8 0.2 + - - -
133B GLU 4.3 7.4 + - - +
135B SER* 1.3 79.8 - - - +
137B TYR* 1.3 86.3 + - + +
139B ILE* 3.5 17.4 + - + -
140B LEU* 3.1 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 137 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.5 12.1 - - + -
88B LEU* 3.4 32.2 - - + +
91B LYS* 3.7 41.9 - - + +
93B GLU 3.4 23.1 - - - -
94B HIS* 2.6 36.1 + + + -
133B GLU 4.3 7.4 - - - -
134B ASN 2.8 10.8 + - - +
136B ILE* 1.3 95.0 - - + +
138B LEU* 1.3 59.8 + - - +
140B LEU* 3.8 5.5 - - + +
141B ILE* 2.9 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B LEU* 4.0 14.8 - - + +
54B LYS* 3.5 50.7 - - + +
56B LEU* 3.5 26.9 - - + -
59B LEU* 3.9 18.6 - - + -
126B ILE* 5.0 10.8 - - + +
132B ASP* 5.5 2.0 - - - +
134B ASN* 3.1 23.4 + - + +
135B SER* 3.9 11.0 - - - +
137B TYR* 1.3 74.2 - - - +
139B ILE* 1.3 59.2 + - - +
141B ILE* 3.9 3.2 - - - +
142B ALA* 3.0 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 139 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 4.1 16.7 - - + +
126B ILE* 3.9 33.0 - - + +
135B SER* 3.1 24.8 + - - +
136B ILE* 3.7 20.9 - - + +
137B TYR 3.3 0.2 - - - -
138B LEU* 1.3 76.4 - - - +
140B LEU* 1.3 62.3 + - + +
142B ALA* 3.5 6.7 + - - +
143B LYS* 3.1 33.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B LEU* 3.4 27.5 - - + +
94B HIS 3.6 29.2 - - - +
95B PHE* 4.1 2.5 - - - -
96B PHE* 3.6 33.8 - - + +
136B ILE* 3.1 43.0 + - + +
137B TYR* 4.0 7.9 - - + +
139B ILE* 1.3 77.2 - - + +
141B ILE* 1.3 62.3 + - - +
143B LYS* 3.5 17.8 + - + +
144B ALA* 3.1 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B MET* 6.3 1.3 - - + -
50B LEU* 4.0 19.5 - - + -
56B LEU* 3.9 15.7 - - + -
59B LEU* 3.9 32.3 - - + -
85B ILE* 4.1 26.9 - - + +
88B LEU* 3.8 20.6 - - + -
89B GLY* 4.0 19.7 - - - +
137B TYR 2.9 22.1 + - - +
138B LEU* 3.9 4.7 - - - +
140B LEU* 1.3 75.3 - - - +
142B ALA* 1.3 60.1 + - - +
144B ALA* 2.8 8.2 + - - +
145B LEU* 2.8 28.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLN* 6.3 0.2 - - - +
50B LEU* 4.0 25.6 - - + -
124B ILE* 3.7 25.4 - - + +
126B ILE* 6.2 1.3 - - + -
138B LEU 3.0 20.1 + - - +
139B ILE 3.6 7.2 - - - +
141B ILE* 1.3 78.2 - - - +
143B LYS* 1.3 57.1 + - - +
145B LEU* 4.0 4.0 - - - +
146B ASN* 3.3 28.1 + - - -
149B ARG* 5.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B PHE* 2.6 36.1 + - + -
97B PRO 3.3 11.5 + - - -
98B ASN* 3.1 32.4 - - - +
99B LYS* 5.8 0.4 - - - +
124B ILE* 3.7 17.3 - - + -
139B ILE* 3.1 23.2 + - + +
140B LEU* 3.6 23.0 - - + +
141B ILE 3.1 0.2 - - - -
142B ALA* 1.3 76.5 - - - +
144B ALA* 1.3 63.0 + - - +
145B LEU 3.2 0.7 - - - -
146B ASN* 3.4 6.1 + - - +
147B GLN* 3.2 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 144 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 3.2 9.0 - - + +
85B ILE* 3.6 24.2 - - + +
88B LEU* 4.5 4.3 - - + -
96B PHE* 3.7 31.4 - - + -
140B LEU 3.1 11.2 + - - +
141B ILE* 2.8 10.4 + - - +
143B LYS* 1.3 79.4 - - - +
145B LEU* 1.3 59.0 + - - +
147B GLN 3.3 1.0 + - - -
148B SER* 2.9 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 145 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.4 42.8 - - + +
46B MET* 3.9 27.4 - - + -
47B GLN* 3.7 21.8 - - - +
50B LEU* 3.7 25.8 - - + -
85B ILE* 4.3 6.0 - - + +
141B ILE* 2.8 15.9 + - + +
142B ALA* 4.0 7.6 - - - +
143B LYS 3.2 0.2 - - - -
144B ALA* 1.3 77.9 - - - +
146B ASN* 1.3 56.6 + - - +
148B SER* 3.0 7.2 + - - -
149B ARG* 2.9 40.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 146 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LYS* 4.3 8.1 + - - +
120B ASP* 5.9 0.2 - - - +
121B ASP* 3.3 35.7 + - - +
122B GLU 3.0 41.6 + - - +
124B ILE* 4.1 11.3 - - - +
142B ALA 3.3 16.6 + - - -
143B LYS* 3.4 8.8 + - - +
144B ALA 3.4 0.2 - - - -
145B LEU* 1.3 76.8 - - - +
147B GLN* 1.3 59.6 + - - +
149B ARG* 3.1 24.0 + - - +
150B LEU* 3.5 18.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 5.5 0.2 - - + -
81B VAL* 4.1 17.3 - - + -
96B PHE* 3.9 11.3 - - + -
99B LYS* 3.3 42.6 - - - +
102B LEU* 3.6 33.8 - - + +
103B VAL* 4.6 2.9 - - - +
143B LYS 3.2 12.2 + - - +
144B ALA 3.5 8.3 - - - +
145B LEU 3.2 0.6 - - - -
146B ASN* 1.3 76.3 - - - +
148B SER* 1.3 59.9 + - - +
150B LEU* 3.4 10.2 + - - +
151B GLU* 2.7 57.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 148 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 3.6 27.2 - - - -
78B ILE* 5.0 7.2 + - - +
81B VAL* 3.1 22.2 - - - +
82B CYS* 4.7 5.2 + - - -
85B ILE* 4.0 10.5 - - - +
144B ALA 2.9 14.5 + - - -
145B LEU* 3.0 13.4 + - - -
147B GLN* 1.3 76.0 - - - +
149B ARG* 1.3 60.8 + - - +
151B GLU* 3.8 5.7 - - - +
152B PHE* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 149 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B PHE* 4.2 30.6 + - + +
44B ALA* 5.7 0.4 - - - +
47B GLN* 2.7 39.4 - - - +
120B ASP* 3.3 43.3 + - + +
122B GLU* 3.0 25.7 + - - +
142B ALA 5.4 0.6 + - - -
145B LEU* 2.9 36.0 + - + +
146B ASN* 3.1 26.0 + - - +
148B SER* 1.3 75.5 - - - +
150B LEU* 1.3 60.8 + - - +
152B PHE* 3.5 9.1 - - - +
153B LYS* 3.2 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LYS* 3.8 22.9 - - + -
103B VAL* 3.7 30.3 - - + -
112B ILE* 5.4 0.2 - - + -
115B ILE* 4.7 5.6 - - + -
117B ILE* 4.1 31.6 - - + +
119B GLU* 4.7 7.6 - - - +
120B ASP* 5.0 4.4 - - - +
146B ASN 3.5 11.6 + - - +
147B GLN* 3.4 16.7 + - - +
148B SER 3.2 0.6 - - - -
149B ARG* 1.3 76.5 - - - +
151B GLU* 1.3 66.7 + - - +
153B LYS* 3.4 4.7 + - + +
154B LEU* 3.1 46.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 151 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ILE* 4.2 3.6 - - - +
8B ILE* 5.3 3.1 - - - +
77B ARG* 2.6 52.1 + - + +
78B ILE* 3.9 21.9 - - + +
81B VAL* 4.2 15.9 - - + -
102B LEU 5.4 0.2 - - - -
103B VAL* 5.4 1.2 - - - +
147B GLN* 2.7 44.3 + - - +
148B SER* 3.8 5.6 - - - +
149B ARG 3.4 0.2 - - - -
150B LEU* 1.3 77.7 - - - +
152B PHE* 1.3 59.7 + - - +
154B LEU* 3.4 13.8 + - - +
155B ALA* 3.0 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 152 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B PHE* 3.8 23.3 - + - -
36B ILE* 3.5 42.0 - - + -
39B ALA* 3.5 22.0 - - + -
40B GLN* 3.7 23.6 - - + -
43B PHE* 3.8 20.9 - + + -
78B ILE* 3.8 11.2 - - + +
148B SER 2.9 18.6 + - - +
149B ARG* 3.5 8.1 - - - +
151B GLU* 1.3 73.9 - - - +
153B LYS* 1.3 63.0 + - - +
155B ALA* 3.0 16.3 + - + +
156B ARG* 3.0 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 153 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B ILE* 4.1 26.1 - - + +
119B GLU* 3.0 49.1 + - - +
120B ASP* 3.7 9.1 + - - +
149B ARG 3.2 10.3 + - - +
150B LEU* 3.7 9.9 - - + +
152B PHE* 1.3 82.2 - - + +
154B LEU* 1.3 60.1 + - + +
156B ARG* 3.2 13.1 + - - +
157B ILE* 3.0 38.3 + - + +
168B HIS* 4.3 19.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 154 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.4 18.9 - - + +
103B VAL* 5.9 1.3 - - + -
106B LEU* 3.8 29.6 - - + -
111B ILE* 4.4 13.5 - - + +
112B ILE* 3.7 14.6 - - + -
115B ILE* 3.7 30.3 - - + -
150B LEU* 3.1 32.4 + - + +
151B GLU* 3.8 19.7 - - - +
152B PHE 3.3 0.2 - - - -
153B LYS* 1.3 74.8 - - + +
155B ALA* 1.3 60.4 + - - +
157B ILE* 3.9 8.4 - - + +
158B GLU* 3.1 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.8 15.9 - - + +
75B LEU* 4.2 22.2 - - + -
78B ILE* 4.0 17.5 - - + -
151B GLU 3.0 13.3 + - - +
152B PHE* 3.0 12.7 + - + +
154B LEU* 1.3 78.4 - - - +
156B ARG* 1.3 57.9 - - + +
158B GLU* 3.5 1.6 + - - +
159B LEU* 3.0 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B ILE* 3.5 33.9 - - + +
40B GLN* 3.2 23.4 + - - +
152B PHE* 3.0 39.6 + - + +
153B LYS* 3.4 9.4 - - - +
155B ALA* 1.3 74.5 - - + +
157B ILE* 1.3 65.7 + - - +
159B LEU* 3.3 5.4 + - + -
160B SER* 3.0 27.0 + - - -
167B LEU* 2.9 36.0 + - - +
168B HIS* 3.3 33.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B ILE* 3.6 37.5 - - + +
115B ILE* 4.3 17.5 - - + -
153B LYS* 3.0 39.1 + - + +
154B LEU* 4.1 8.7 - - + +
156B ARG* 1.3 76.1 - - - +
158B GLU* 1.3 63.8 + - - +
160B SER* 3.3 19.7 - - - -
161B LYS* 3.8 7.6 + - - +
168B HIS* 3.5 29.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 4.0 18.3 - - + +
9B ILE* 3.6 27.4 - - + +
11B TRP* 4.9 3.8 + - - -
111B ILE* 3.3 12.5 - - + +
154B LEU 3.1 21.0 + - - +
155B ALA 3.8 3.6 - - - +
156B ARG 3.2 0.2 - - - -
157B ILE* 1.3 78.9 - - - +
159B LEU* 1.3 59.5 + - - +
161B LYS* 2.9 38.3 + - - +
162B TYR* 3.2 39.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.6 25.8 - - + -
14B LEU* 4.1 15.7 - - + -
32B ILE* 4.1 39.3 - - + -
35B PHE* 6.3 0.2 - - + -
36B ILE* 6.2 0.9 - - + -
75B LEU* 4.1 23.6 - - + -
155B ALA* 3.0 29.2 + - + +
156B ARG* 4.0 3.6 - - + +
157B ILE 3.3 0.4 - - - -
158B GLU* 1.3 74.6 - - - +
160B SER* 1.3 65.2 + - - +
162B TYR* 3.0 16.5 + - + -
163B TYR* 3.1 25.6 + - + -
167B LEU* 3.6 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B ARG 3.0 12.3 + - - -
157B ILE* 3.3 12.7 - - - -
159B LEU* 1.3 71.6 - - - +
161B LYS* 1.3 60.8 + - - +
162B TYR 3.0 5.9 + - - -
163B TYR 4.4 1.1 - - - +
164B ASN* 3.2 21.5 + - - -
165B THR 3.2 16.4 + - - +
166B ASN* 3.7 11.2 + - - -
167B LEU* 2.9 31.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASP* 4.9 9.7 + - - -
111B ILE* 3.7 19.7 - - - +
157B ILE* 4.1 5.8 - - + +
158B GLU* 2.9 44.6 + - - +
159B LEU 3.2 0.8 - - - -
160B SER* 1.3 77.2 - - - +
162B TYR* 1.3 78.0 + - + +
164B ASN* 4.6 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 5.0 0.4 - - + -
11B TRP* 3.6 42.1 + + + -
18B ILE* 6.4 0.4 - - + -
158B GLU* 3.2 48.5 + - + -
159B LEU* 3.0 8.9 + - + +
160B SER 3.0 0.4 - - - -
161B LYS* 1.3 98.8 + - + +
163B TYR* 1.3 72.7 + - + +
164B ASN* 3.3 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B TRP* 5.7 1.1 - + - -
14B LEU* 4.8 4.6 - - + +
18B ILE* 3.7 22.0 - - + +
21B ASP* 5.0 1.8 - - - -
28B SER* 2.7 34.4 + - - -
29B LYS* 3.6 40.8 + - + -
32B ILE* 3.5 25.1 - - + +
159B LEU* 3.1 38.0 + - + +
160B SER 3.4 0.6 + - - +
162B TYR* 1.3 89.2 - - + +
164B ASN* 1.3 70.4 + - - +
165B THR* 3.0 19.8 + - + +
167B LEU* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B SER 3.2 10.1 + - - -
161B LYS 4.6 7.8 - - - +
162B TYR 3.3 12.1 + - - -
163B TYR* 1.3 77.6 - - - +
165B THR* 1.3 59.2 + - - +
----------------------------------------------------------
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