Contacts of the helix formed by residues 155 - 182 (chain D) in PDB entry 4J4L
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 155 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ALA 4.1 0.6 + - - -
154D GLN* 1.3 79.5 - - - +
156D GLN* 1.3 57.1 + - - +
157D TRP* 3.0 19.8 + - - +
158D LEU* 3.0 36.5 + - - +
159D GLN* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46D LYS* 6.2 1.4 - - - +
104D ARG* 2.8 45.1 + - - +
154D GLN 3.6 1.0 + - - +
155D ASN* 1.3 71.3 + - - +
157D TRP* 1.3 65.7 + - - +
159D GLN* 3.3 10.6 + - - +
160D ASP* 3.1 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D SER* 5.2 4.0 - - - -
49D MET* 3.5 26.5 - - + +
57D LEU* 5.9 1.8 - - + -
155D ASN* 3.0 14.3 + - - +
156D GLN* 1.3 78.1 - - - +
158D LEU* 1.3 99.4 + - + +
159D GLN 3.2 0.3 + - - -
160D ASP* 3.3 10.8 + - - +
161D MET* 3.1 51.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D LEU* 4.2 26.2 - - + -
61D ASN* 5.9 0.4 - - - +
154D GLN* 3.8 36.8 - - + +
155D ASN* 3.0 34.6 + - - +
157D TRP* 1.3 101.6 - - + +
159D GLN* 1.3 54.0 + - - +
161D MET* 3.1 5.9 + - + +
162D THR* 2.9 33.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D TYR* 2.6 48.4 + - - +
104D ARG* 3.5 29.9 + - - +
151D LEU 3.3 16.0 + - - +
152D GLN* 3.1 27.0 - - - +
154D GLN* 3.2 14.4 - - + +
155D ASN 3.0 18.6 + - - +
156D GLN* 3.7 12.5 - - - +
157D TRP 3.2 0.4 - - - -
158D LEU* 1.3 71.1 - - - +
160D ASP* 1.3 61.7 + - - +
162D THR* 3.5 4.0 - - - -
163D THR* 2.9 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D THR* 3.9 12.8 - - + +
46D LYS* 4.1 32.5 + - + +
47D SER* 5.3 1.9 + - - -
49D MET* 3.7 23.8 - - + +
104D ARG* 2.7 31.5 + - - -
156D GLN* 3.1 18.7 + - - +
157D TRP* 3.6 9.5 - - - +
159D GLN* 1.3 77.5 - - - +
161D MET* 1.3 56.2 + - - +
163D THR* 3.5 8.3 - - - -
164D HIS* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 161 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D MET* 3.7 29.6 - - + -
54D LYS* 6.5 0.7 - - + -
55D GLU 3.6 17.5 - - - +
56D ALA* 3.9 3.1 - - - -
57D LEU* 3.4 48.2 - - + +
157D TRP* 3.1 60.9 + - + +
158D LEU* 3.1 8.5 + - + +
160D ASP* 1.3 71.7 - - - +
162D THR* 1.3 67.3 + - - +
164D HIS* 2.9 8.0 + - - +
165D LEU* 2.9 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 162 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D LEU* 3.7 18.1 - - - +
62D LEU* 4.0 16.8 - - + +
100D TYR* 4.2 10.3 - - + +
151D LEU* 4.1 20.0 - - + -
154D GLN* 3.5 15.4 + - - +
158D LEU* 2.9 18.3 + - - +
159D GLN* 3.5 8.5 - - - -
161D MET* 1.3 73.6 - - - +
163D THR* 1.3 63.9 + - - +
165D LEU* 2.9 6.2 + - - +
166D ILE* 2.8 41.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 163 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D THR* 3.8 26.9 - - + +
100D TYR* 3.6 15.1 - - - -
101D LEU* 3.9 11.9 - - + +
104D ARG* 3.7 15.8 + - + +
105D PHE* 4.0 7.2 - - + -
159D GLN 2.9 23.0 + - - -
160D ASP* 3.5 7.9 - - - -
162D THR* 1.3 72.6 - - - +
164D HIS* 1.3 64.6 + - - +
166D ILE* 3.3 10.5 + - - +
167D LEU* 3.0 39.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 164 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A LYS* 5.8 2.7 - - - -
40D ARG* 3.3 47.7 + - + +
43D THR* 5.3 8.3 - - + -
44D CYS* 4.2 1.8 - - - -
49D MET* 5.0 10.8 - - + -
50D CYS* 3.4 26.5 - - + -
56D ALA* 5.5 10.5 - - + +
160D ASP 3.0 13.6 + - - +
161D MET* 2.9 13.5 + - - +
163D THR* 1.3 77.6 - - - +
165D LEU* 1.3 57.7 + - - +
167D LEU* 3.9 5.0 - - - +
168D ARG* 3.0 38.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D LEU* 4.1 26.9 - - + +
58D ALA 3.8 20.9 - - - +
59D GLU* 4.2 13.5 - - + +
61D ASN* 4.6 0.2 - - + -
62D LEU* 3.6 35.7 - - + +
64D LEU* 4.6 4.3 - - + -
161D MET 2.9 10.9 + - - +
162D THR* 3.3 9.0 - - - +
164D HIS* 1.3 75.2 + - - +
166D ILE* 1.3 60.6 + - - +
168D ARG* 3.8 27.1 - - - +
169D SER* 2.9 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LEU* 4.6 3.4 - - + -
64D LEU* 3.7 13.5 - - + -
94D PHE* 4.2 5.0 - - + -
97D TYR* 3.9 43.7 - - + +
98D LEU* 4.7 8.1 - - + -
100D TYR* 3.7 30.3 - - + -
101D LEU* 4.2 21.3 - - + -
151D LEU* 4.8 0.7 - - + -
162D THR* 2.8 37.2 + - + +
163D THR* 3.6 7.6 - - - +
165D LEU* 1.3 70.7 - - - +
167D LEU* 1.3 62.0 + - + +
169D SER* 3.2 3.5 + - - -
170D PHE* 2.9 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D ILE* 4.2 30.1 - - + +
39D LEU* 3.9 26.0 - - + +
40D ARG* 3.9 36.1 - - + +
43D THR* 4.5 1.1 - - - +
101D LEU* 3.7 28.5 - - + -
105D PHE* 4.3 1.8 - - + -
115D VAL* 6.0 0.2 - - + -
163D THR* 3.0 33.2 + - + +
164D HIS* 3.9 4.7 - - - +
166D ILE* 1.3 78.3 - - + +
168D ARG* 1.3 68.0 + - - +
169D SER 3.2 0.3 + - - -
170D PHE* 3.2 6.6 + - + +
171D LYS* 3.1 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 5.9 0.2 - - - +
102A TYR* 5.3 7.4 + - - -
124A TYR* 4.9 13.6 + - - +
147A LYS* 6.0 3.6 - - - -
40D ARG* 5.4 8.3 - - - +
56D ALA* 5.2 7.9 - - - +
57D LEU 4.7 6.3 + - - -
59D GLU* 3.3 30.3 + - - +
164D HIS* 3.0 35.1 + - + +
165D LEU* 3.8 23.9 - - - +
167D LEU* 1.3 74.6 - - - +
169D SER* 1.3 68.0 + - - +
171D LYS* 3.5 26.4 - - - +
172D GLU* 2.6 71.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D GLU* 4.7 6.9 + - - -
64D LEU* 3.4 32.8 + - - +
65D PRO 4.8 3.8 + - - +
94D PHE* 3.8 4.3 - - - -
165D LEU* 2.9 29.9 + - - +
166D ILE 3.2 4.5 + - - -
168D ARG* 1.3 87.7 + - - +
170D PHE* 1.3 57.7 + - - +
172D GLU* 3.4 6.0 + - - +
173D PHE* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D ILE* 3.9 17.0 - - + -
36D ILE* 3.3 29.4 - - + -
91D LEU* 3.8 24.7 - - + -
94D PHE* 3.5 43.3 - + + -
98D LEU* 4.0 23.3 - - + -
115D VAL* 4.1 5.6 - - + -
119D THR* 3.6 29.4 - - + -
166D ILE* 2.9 19.7 + - + +
167D LEU* 3.8 6.5 - - + +
169D SER* 1.3 72.5 - - - +
171D LYS* 1.3 54.9 + - - +
173D PHE* 3.2 3.6 + - + +
174D LEU* 2.8 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 4.4 17.4 - - - +
123A THR* 5.1 7.4 - - - +
124A TYR* 5.7 0.6 + - - -
147A LYS* 4.9 16.0 - - - +
33D LEU* 4.0 22.4 - - + -
36D ILE* 4.0 16.6 - - + +
40D ARG* 5.6 6.4 - - - +
167D LEU 3.1 12.5 + - - +
168D ARG* 3.5 37.7 - - - +
170D PHE* 1.3 74.1 - - - +
172D GLU* 1.3 69.1 + - - +
174D LEU* 3.1 2.8 + - - +
175D GLN* 2.9 52.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.4 47.8 + - - +
102A TYR* 4.7 5.9 + - - -
59D GLU* 4.3 6.2 - - - +
66D LYS* 4.7 12.5 + - - -
168D ARG* 2.6 62.3 + - - +
169D SER* 3.7 9.0 - - - +
170D PHE 3.3 0.2 - - - -
171D LYS* 1.3 77.0 - - - +
173D PHE* 1.3 61.0 + - - +
175D GLN* 3.6 8.9 + - - +
176D SER* 3.2 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D PRO* 3.8 17.5 - - + +
66D LYS* 4.3 13.7 - - - +
67D MET* 4.0 30.7 - - + +
86D LYS* 3.9 18.4 - - - -
87D ILE* 3.9 12.3 - - - -
90D GLY* 3.6 31.0 - - - -
91D LEU* 3.8 21.5 - - + -
94D PHE* 3.8 22.7 - + + -
169D SER 3.0 14.0 + - - +
170D PHE* 3.5 9.0 - + - +
172D GLU* 1.3 72.0 - - - +
174D LEU* 1.3 61.5 + - - +
176D SER* 3.5 5.8 + - - -
177D SER* 3.0 42.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ILE* 4.1 20.5 - - + +
32D ILE* 3.7 34.1 - - + -
33D LEU* 3.7 26.2 - - + -
36D ILE* 4.1 9.6 - - + -
91D LEU* 4.0 26.5 - - + -
122D LEU* 4.3 16.4 - - + -
170D PHE* 2.8 29.2 + - + +
171D LYS 3.5 3.4 - - - +
173D PHE* 1.3 70.4 - - - +
175D GLN* 1.3 65.8 + - - +
177D SER* 3.0 8.3 + - - -
178D LEU* 2.9 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 3.5 31.5 + - - +
121A ASN* 5.5 8.4 - - - +
145A ASN* 3.3 42.3 + - - +
33D LEU* 4.5 15.9 - - + +
171D LYS* 2.9 47.7 + - + +
172D GLU* 3.8 8.2 - - - +
174D LEU* 1.3 72.2 - - - +
176D SER* 1.3 61.8 + - - +
178D LEU* 3.4 11.6 + - + +
179D ARG* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A ARG* 6.0 0.2 + - - -
121A ASN* 4.9 11.8 + - - +
67D MET* 3.9 29.4 - - - +
73D CYS* 5.1 1.8 - - - +
74D PHE* 5.3 5.7 - - - -
172D GLU 3.2 14.5 + - - -
173D PHE* 3.7 5.2 - - - -
174D LEU 3.1 0.6 - - - -
175D GLN* 1.3 78.0 - - - +
177D SER* 1.3 65.7 + - - +
179D ARG* 3.7 5.3 + - - +
180D ALA* 3.2 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D ILE* 4.3 11.0 - - - -
67D MET* 3.9 2.7 - - - +
87D ILE* 3.4 42.4 - - - +
91D LEU* 5.5 0.4 - - - +
173D PHE* 3.0 28.8 + - - -
174D LEU* 3.4 14.7 - - - +
176D SER* 1.3 76.4 - - - +
178D LEU* 1.3 52.2 - - - +
180D ALA* 3.3 2.6 + - - +
181D LEU* 2.8 42.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D ASP* 3.3 48.7 - - - +
29D ILE* 4.0 25.6 - - + -
30D ARG* 4.8 10.1 - - - -
33D LEU* 4.8 12.1 - - + -
174D LEU 2.9 14.7 + - - +
175D GLN* 3.6 9.0 - - + +
176D SER 3.2 0.2 - - - -
177D SER* 1.3 74.6 - - - +
179D ARG* 1.3 65.3 + - - +
181D LEU* 2.9 13.0 + - + +
182D ARG* 2.8 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A PRO* 3.6 26.3 + - - +
99A ASN* 3.0 30.1 - - - +
118A GLU 5.4 2.0 + - - -
120A THR* 3.2 27.5 + - - +
121A ASN* 3.5 22.6 + - - +
73D CYS 5.6 3.1 - - - -
74D PHE* 5.2 4.4 - - - +
75D GLN* 5.6 7.2 - - - +
175D GLN 3.2 12.6 + - - +
176D SER* 4.2 5.2 - - - +
178D LEU* 1.3 81.3 - - - +
180D ALA* 1.3 63.7 + - - +
182D ARG* 3.3 18.5 + - - +
183D GLN* 3.6 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D CYS* 3.6 23.6 - - + +
78D PHE* 3.4 13.0 - - + -
83D CYS* 3.7 25.1 - - - -
87D ILE* 4.4 2.5 - - + -
176D SER 3.2 18.3 + - - +
177D SER 3.6 4.3 - - - +
178D LEU 3.1 0.4 - - - -
179D ARG* 1.3 80.4 - - - +
181D LEU* 1.3 61.5 + - - +
183D GLN* 3.2 10.8 + - - +
184D MET* 3.2 18.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D SER* 4.7 10.9 + - - -
25D ILE* 3.8 21.8 - - + -
26D ASP* 6.4 0.7 - - - -
29D ILE* 3.7 27.1 - - + -
84D LEU* 4.0 7.2 - - + -
87D ILE* 4.1 9.9 - - + -
126D LEU* 4.0 27.8 - - + -
129D LYS* 4.5 8.3 + - + +
177D SER* 2.8 24.5 + - - +
178D LEU* 2.9 6.9 + - + +
180D ALA* 1.3 77.0 - - - +
182D ARG* 1.3 61.1 + - + +
183D GLN 3.2 0.4 - - - -
184D MET* 3.3 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ASN* 3.7 21.3 + - - +
26D ASP* 2.9 37.2 + - - +
30D ARG* 4.7 1.6 - - - +
178D LEU* 2.8 43.2 + - + +
179D ARG* 3.9 9.5 - - - +
180D ALA 3.2 0.6 - - - -
181D LEU* 1.3 76.2 - - + +
183D GLN* 1.3 60.9 + - + +
184D MET 3.6 1.2 - - - -
----------------------------------------------------------
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