Contacts of the helix formed by residues 127 - 157 (chain M) 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 M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122M ASP* 4.8 0.9 - - - -
123M HIS* 2.8 20.2 + - - -
125M ASP 3.5 1.6 - - - -
126M LYS* 1.3 83.2 - - - +
128M ASP* 1.3 66.5 + - - -
129M ALA 3.4 2.9 + - - -
130M LEU 3.6 0.6 + - - -
131M HIS* 3.1 19.8 + - - +
193M LYS* 4.0 17.3 - - - +
197M VAL* 6.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ARG* 3.2 39.2 + - - -
69M TYR* 3.9 24.0 + - + +
70M PHE* 3.6 9.5 - - + -
75M VAL* 3.6 14.0 - - - +
77M LEU* 3.9 2.1 - - - +
121M PHE 3.4 21.2 - - - +
122M ASP* 3.9 13.5 + - - +
127M GLY* 1.3 71.3 - - - -
129M ALA* 1.3 79.0 + - - +
131M HIS* 3.4 1.4 + - - +
132M ALA* 2.9 27.0 + - - +
197M VAL* 5.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70M PHE* 4.2 9.9 - - - -
77M LEU* 4.2 8.5 - - + -
80M LEU* 4.6 13.9 - - + +
127M GLY 3.4 0.8 - - - -
128M ASP* 1.3 84.4 + - - +
130M LEU* 1.3 63.9 + - - +
132M ALA* 3.9 1.9 - - - +
133M MET* 3.0 24.8 + - - +
188M LEU* 3.7 19.0 - - + +
197M VAL* 3.7 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126M LYS* 3.5 35.9 - - + +
127M GLY 3.6 1.8 + - - -
128M ASP 3.4 0.2 - - - -
129M ALA* 1.3 79.1 - - - +
131M HIS* 1.3 58.6 + - - +
133M MET 3.3 0.7 + - - -
134M GLU* 2.9 53.4 + - - +
185M VAL* 3.8 34.3 - - + +
188M LEU* 3.9 20.5 - - + +
189M ARG* 3.9 24.2 - - + +
197M VAL* 5.8 2.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 131 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L LEU* 4.0 19.7 - - + +
120M ASP 5.5 1.4 + - - -
121M PHE* 3.4 25.2 - - - +
122M ASP 3.8 12.4 + - - -
123M HIS* 3.6 32.0 + + + -
126M LYS* 4.2 14.4 - - + +
127M GLY 3.1 18.9 + - - +
128M ASP 3.7 2.5 - - - +
130M LEU* 1.3 76.9 - - - +
132M ALA* 1.3 56.8 + - - +
134M GLU* 3.3 3.5 + - - +
135M LEU* 2.9 61.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M MET* 4.0 10.7 - - - +
70M PHE* 3.4 40.2 - - + -
84M PHE* 4.2 11.0 - - + -
121M PHE* 4.5 9.9 - - + -
128M ASP 2.9 8.4 + - - +
129M ALA 3.9 2.0 - - - +
131M HIS* 1.3 76.6 - - - +
133M MET* 1.3 58.2 + - - +
135M LEU* 3.3 12.1 + - - +
136M ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 133 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M LEU* 3.3 33.9 - - + -
83M PHE* 4.1 13.9 - - + -
84M PHE* 4.1 12.3 - - - -
129M ALA 3.0 18.3 + - - +
130M LEU* 3.8 3.6 - - - +
132M ALA* 1.3 76.8 - - - +
134M GLU* 1.3 57.9 + - - +
136M ALA* 4.3 1.6 - - - -
137M LEU* 2.9 24.3 + - - +
181M ILE* 3.5 21.9 - - + +
184M TYR* 3.5 48.7 - - + -
185M VAL* 3.8 15.7 - - + +
188M LEU* 3.9 10.3 - - + -
200M PHE* 4.5 6.5 - - + -
204M LEU* 4.3 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25L LEU* 3.8 17.1 - - + +
28L VAL* 4.4 16.3 - - + +
126M LYS* 3.1 38.6 + - - +
130M LEU* 2.9 37.4 + - + +
131M HIS* 3.7 3.8 - - - +
133M MET* 1.3 77.7 - - - +
135M LEU* 1.3 61.7 + - - +
137M LEU* 3.4 6.1 + - - +
138M SER* 3.0 25.6 + - - -
185M VAL* 4.0 15.3 - - + -
189M ARG* 2.8 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L PHE* 4.8 12.6 - - + -
21L VAL* 3.7 22.5 - - + +
25L LEU* 3.5 27.8 - - + -
66M MET* 3.9 10.5 - - + -
118M LEU* 6.1 2.2 - - + -
121M PHE* 3.7 30.1 - - + -
131M HIS* 2.9 47.5 + - + +
132M ALA 3.5 4.7 - - - +
133M MET 3.3 0.2 - - - -
134M GLU* 1.3 75.6 - - - +
136M ALA* 1.3 59.5 + - - +
138M SER* 3.2 4.5 + - - -
139M LEU* 2.9 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M TYR* 3.7 31.1 + - + +
66M MET* 4.2 4.1 - - - +
83M PHE* 5.5 0.2 - - + -
84M PHE* 4.1 13.5 - - + -
132M ALA 2.9 16.9 + - - +
133M MET* 3.6 8.1 - - - +
135M LEU* 1.3 73.9 - - - +
137M LEU* 1.3 65.6 + - - +
139M LEU* 3.2 4.7 + - - +
140M GLU* 2.9 29.9 + - - +
181M ILE* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28L VAL* 4.3 20.4 - - + -
36L LEU* 3.9 22.9 - - + +
133M MET 2.9 15.0 + - - +
134M GLU* 3.5 9.9 - - - +
136M ALA* 1.3 76.8 - - - +
138M SER* 1.3 63.4 + - - +
140M GLU* 3.2 3.9 + - + -
141M LYS* 3.0 35.8 + - + +
178M ILE* 3.9 27.1 - - + +
181M ILE* 3.7 12.5 - - + +
182M SER* 3.4 30.5 - - - +
185M VAL* 4.4 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21L VAL* 4.0 22.4 - - - -
24L GLU* 3.0 24.4 + - - +
25L LEU* 3.1 31.3 + - - +
28L VAL* 5.3 3.8 - - - +
134M GLU 3.0 13.4 + - - -
135M LEU* 3.2 8.9 + - - -
137M LEU* 1.3 76.2 - - - +
139M LEU* 1.3 58.4 + - - +
141M LYS* 3.3 2.3 + - - -
142M LEU* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L PHE* 5.4 2.5 - - + -
17L PRO* 3.5 31.9 - - + -
18L PHE* 5.4 4.3 - - + -
21L VAL* 3.6 17.5 - - + -
59M VAL* 4.5 24.9 - - + +
62M VAL* 3.4 37.5 - - + -
63M TYR* 4.6 13.9 - - + +
66M MET* 4.6 4.9 - - + -
135M LEU* 2.9 15.6 + - + +
136M ALA* 3.5 7.9 - - - +
138M SER* 1.3 78.3 - - - +
140M GLU* 1.3 57.1 + - - +
142M LEU* 3.3 6.5 + - + +
143M THR* 2.9 32.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M VAL* 4.3 4.0 - - - +
63M TYR* 2.5 40.1 + - - +
91M GLU* 3.7 15.1 - - - +
136M ALA 2.9 14.7 + - - +
137M LEU* 3.8 4.9 - - - +
139M LEU* 1.3 75.0 - - - +
141M LYS* 1.3 61.5 + - - +
143M THR* 3.4 5.0 + - - +
144M ASN* 2.9 17.5 + - - +
174M GLN* 2.6 53.4 + - - +
177M ALA* 4.2 11.4 - - + +
178M ILE* 3.9 15.5 - - + -
181M ILE* 3.4 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24L GLU* 3.2 32.8 - - + +
27L LEU 6.1 0.6 - - - -
28L VAL* 5.4 3.8 - - - +
29L PRO* 4.9 10.1 - - - +
36L LEU 2.7 29.3 + - - -
37L ALA 3.8 15.0 - - - -
38L ARG 3.5 15.8 + - - -
39L GLN* 2.9 42.6 + - + +
137M LEU* 3.0 37.5 + - + +
138M SER* 5.3 0.4 - - - -
140M GLU* 1.3 75.0 - - - +
142M LEU* 1.3 60.3 + - - +
144M ASN* 3.3 0.7 + - - +
145M GLU* 3.0 17.8 + - - +
178M ILE* 4.1 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L PHE* 5.3 11.7 - - + -
17L PRO* 5.4 0.4 - - + +
20L GLU* 3.5 42.8 - - + +
21L VAL* 3.7 20.0 - - + -
24L GLU* 2.8 40.7 + - + +
55M VAL* 5.6 0.4 - - - -
138M SER 2.9 14.3 + - - +
139M LEU* 3.5 13.2 - - + +
141M LYS* 1.3 76.6 - - - +
143M THR* 1.3 62.3 + - - +
145M GLU* 3.3 26.1 + - - +
146M LYS* 3.0 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M GLN* 3.9 5.6 - - - +
55M VAL* 4.1 13.3 - - + +
56M GLU* 3.5 32.8 - - - +
59M VAL* 3.5 22.3 - - - +
91M GLU* 5.2 0.3 + - - -
139M LEU 2.9 18.2 + - - -
140M GLU* 3.6 8.8 + - - -
142M LEU* 1.3 76.1 - - - +
144M ASN* 1.3 55.3 + - - +
146M LYS* 3.1 4.0 + - - +
147M LEU* 2.8 30.5 + - + +
174M GLN* 3.9 20.2 - - - +
214M CA 4.2 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 144 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39L GLN* 3.0 38.2 + - - +
140M GLU 2.9 14.0 + - - +
141M LYS 3.5 2.9 - - - +
142M LEU 3.3 0.2 - - - -
143M THR* 1.3 76.9 - - - +
145M GLU* 1.3 57.1 + - - +
147M LEU* 3.2 3.5 + - - +
148M LEU* 2.9 47.5 + - - +
171M LEU* 4.2 15.9 - - - +
174M GLN* 3.5 28.7 - - + +
175M VAL* 5.1 10.6 - - - +
178M ILE* 3.9 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20L GLU* 5.7 1.6 - - - -
24L GLU* 5.4 3.5 - - - +
39L GLN* 4.2 11.0 + - - +
40L LYS* 4.4 20.6 - - - +
141M LYS 3.0 13.6 + - - +
142M LEU* 3.5 28.6 - - - +
144M ASN* 1.3 76.9 - - - +
146M LYS* 1.3 63.1 + - + +
148M LEU* 3.4 6.3 + - - +
149M ASN* 3.0 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L PHE* 4.1 27.5 - - + +
20L GLU* 4.1 20.1 + - - -
51M GLU* 3.8 23.1 + - - +
52M GLN* 3.3 23.3 - - - +
55M VAL* 4.0 20.6 - - + -
142M LEU* 3.0 17.2 + - - +
143M THR* 3.5 7.0 - - - +
145M GLU* 1.3 83.1 - - + +
147M LEU* 1.3 56.9 + - - +
149M ASN* 3.2 12.5 + - + +
150M LEU* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M GLN* 3.4 31.2 + - + +
56M GLU* 4.0 4.9 - - - +
98M LEU* 5.5 0.2 - - + -
143M THR* 2.8 27.9 + - + +
144M ASN* 3.2 5.1 + - - +
146M LYS* 1.3 72.9 - - - +
148M LEU* 1.3 59.2 + - - +
150M LEU* 3.2 9.8 + - + +
151M HIS* 2.9 27.4 + - - +
166M VAL* 3.9 11.7 - - + +
170M TYR* 3.8 40.6 - - + +
171M LEU* 3.8 15.5 - - + -
174M GLN* 3.9 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L LYS* 3.6 36.1 - - + -
158L GLY 5.4 2.0 - - - +
160L VAL* 4.0 36.9 - - + +
161L GLN* 5.1 4.7 - - + +
144M ASN* 2.9 40.5 + - - +
145M GLU* 3.8 4.0 - - - +
147M LEU* 1.3 76.3 - - - +
149M ASN* 1.3 57.6 + - - +
151M HIS* 3.3 4.5 + - + +
152M SER* 3.0 26.5 + - - -
171M LEU* 4.1 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 149 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M ALA* 5.8 2.2 - - - +
51M GLU* 6.4 0.2 - - - -
145M GLU* 3.0 15.8 + - + +
146M LYS* 3.2 15.0 + - + +
148M LEU* 1.3 74.9 - - - +
150M LEU* 1.3 61.4 + - - +
152M SER* 3.2 10.9 + - - -
153M VAL* 2.9 39.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M ALA* 3.6 37.5 - - + +
49M VAL* 3.9 14.4 - - + +
52M GLN* 3.9 31.0 - - + +
98M LEU* 4.3 13.2 - - + -
146M LYS 2.9 13.1 + - - +
147M LEU* 3.2 12.5 + - + +
149M ASN* 1.3 76.4 - - - +
151M HIS* 1.3 57.8 + - - +
153M VAL* 3.2 5.8 + - + +
154M ALA* 2.9 26.9 + - - +
162M LEU* 4.3 10.5 - - + -
166M VAL* 3.7 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 151 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160L VAL* 3.4 38.5 - - + +
147M LEU 2.9 14.0 + - - +
148M LEU* 3.6 12.6 - - - +
149M ASN 3.3 0.2 - - - -
150M LEU* 1.3 77.1 - - - +
152M SER* 1.3 58.8 + - - +
154M ALA* 3.3 6.7 + - - +
155M THR* 3.0 49.4 + - + +
163M ALA* 3.2 25.2 + - + +
166M VAL* 4.1 8.9 - - + +
167M GLU* 2.8 30.4 + - - -
171M LEU* 4.0 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 152 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148M LEU 3.0 14.1 + - - -
149M ASN* 3.2 18.0 + - - -
151M HIS* 1.3 74.5 - - - +
153M VAL* 1.3 67.0 + - - +
155M THR* 3.4 6.9 + - - -
156M LYS* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M GLU* 3.7 52.0 - - + +
45M SER* 3.9 6.5 - - - -
48M ALA* 3.9 20.2 - - + -
149M ASN* 2.9 31.1 + - - +
150M LEU* 3.6 6.7 - - + +
152M SER* 1.3 75.5 - - - +
154M ALA* 1.3 64.2 + - - +
156M LYS* 3.5 8.4 + - + +
157M ASN* 3.0 31.9 + - - +
162M LEU* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45M SER* 4.6 2.2 - - - -
150M LEU 2.9 13.3 + - - +
151M HIS* 3.4 10.1 - - - +
152M SER 3.2 0.2 - - - -
153M VAL* 1.3 76.4 - - - +
155M THR* 1.3 61.7 + - - +
157M ASN 3.1 6.9 + - - -
159M ASP* 2.9 40.2 + - - +
162M LEU* 3.6 34.7 - - + +
163M ALA* 3.7 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 155 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151M HIS* 3.0 38.2 + - + +
152M SER* 3.6 7.8 + - - -
154M ALA* 1.3 71.9 - - - +
156M LYS* 1.3 64.2 + - - +
158M GLY* 3.0 14.8 + - - +
159M ASP 4.5 3.6 - - - +
160M VAL* 5.8 5.2 - - + +
163M ALA* 3.6 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 156 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M GLU* 2.9 40.8 + - - +
152M SER* 2.9 21.9 + - - +
153M VAL* 3.5 8.1 - - + +
155M THR* 1.3 79.1 + - - +
157M ASN* 1.3 62.1 + - - +
158M GLY 3.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 157 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M LYS 5.8 0.3 - - - +
42M VAL* 3.5 39.5 - - + +
44M GLU* 2.9 29.5 + - - +
45M SER* 3.9 5.3 + - - +
153M VAL* 3.0 26.5 + - - +
154M ALA 3.1 5.5 + - - +
156M LYS* 1.3 83.0 - - - +
158M GLY* 1.3 59.5 + - - +
159M ASP* 3.0 8.4 + - + +
----------------------------------------------------------
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