Contacts of the helix formed by residues 127 - 157 (chain T) 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 T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122T ASP* 5.0 0.7 - - - -
123T HIS* 2.9 20.7 + - - -
124T ALA 5.0 0.2 - - - -
125T ASP 3.4 2.0 + - - -
126T LYS* 1.3 79.7 - - - +
128T ASP* 1.3 66.5 + - - -
129T ALA 3.4 2.5 - - - -
130T LEU 3.6 1.1 + - - -
131T HIS* 3.1 23.4 + - - +
193T LYS* 4.0 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69T TYR* 4.1 9.2 + - + +
70T PHE* 3.6 15.3 - - + -
75T VAL* 3.5 17.0 - - - +
77T LEU* 3.9 1.5 - - - +
121T PHE 3.5 20.7 - - - +
122T ASP* 3.9 21.8 + - - +
123T HIS 4.3 0.4 - - - +
127T GLY* 1.3 71.7 - - - -
129T ALA* 1.3 72.9 + - - +
131T HIS* 3.4 1.2 + - - +
132T ALA* 2.9 26.9 + - - +
197T VAL* 5.1 0.2 - - - +
190U ARG* 3.3 39.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 129 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70T PHE* 4.2 0.4 - - - -
77T LEU* 4.2 3.8 - - + -
80T LEU* 3.7 27.9 - - + +
127T GLY 3.4 0.4 - - - -
128T ASP* 1.3 83.4 + - - +
130T LEU* 1.3 63.7 + - - +
132T ALA* 3.4 1.9 + - - +
133T MET* 3.0 28.1 + - - +
188T LEU* 3.9 16.2 - - + -
197T VAL* 3.8 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 130 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126T LYS* 3.6 35.2 - - + +
127T GLY 3.6 1.2 + - - -
128T ASP 3.4 0.6 - - - -
129T ALA* 1.3 75.9 - - - +
131T HIS* 1.3 67.2 + - - +
133T MET* 3.3 1.4 + - - -
134T GLU* 2.9 52.6 + - - +
185T VAL* 3.9 28.9 - - + +
188T LEU* 4.0 20.5 - - + +
189T ARG* 3.9 27.8 - - + +
197T VAL* 5.9 2.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 131 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M LEU* 4.3 14.5 - - + +
118T LEU* 5.8 2.8 - - - +
120T ASP 5.4 1.0 + - - -
121T PHE* 3.4 30.2 - - - +
122T ASP 4.1 3.4 + - - -
123T HIS* 3.5 39.2 + + + -
126T LYS* 4.2 14.8 - - + +
127T GLY 3.1 19.5 + - - +
128T ASP 3.7 2.5 - - - +
130T LEU* 1.3 75.1 - - - +
132T ALA* 1.3 57.9 + - - +
134T GLU* 3.3 3.5 + - - +
135T LEU* 2.9 68.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 132 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66T MET* 3.2 34.3 - - + +
70T PHE* 3.4 24.9 - - + -
80T LEU* 4.9 0.4 - - + -
84T PHE* 4.2 5.2 - - + -
121T PHE* 4.6 5.4 - - + -
128T ASP 2.9 16.8 + - - +
129T ALA 3.8 3.1 - - - +
131T HIS* 1.3 79.4 - - - +
133T MET* 1.3 57.6 + - - +
135T LEU* 3.2 6.5 + - - +
136T ALA* 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 133 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80T LEU* 4.2 16.4 - - + -
83T PHE* 3.7 26.0 - - + -
84T PHE* 4.1 12.8 - - + -
129T ALA 3.0 20.1 + - - +
130T LEU 3.8 2.5 - - - +
132T ALA* 1.3 73.8 - - - +
134T GLU* 1.3 61.6 + - - +
136T ALA* 3.4 1.7 + - - -
137T LEU* 2.9 24.3 + - - +
181T ILE* 3.4 18.6 - - + +
184T TYR* 3.5 37.2 - - + -
185T VAL* 3.8 18.1 - - + +
188T LEU* 3.6 19.7 - - + -
200T PHE* 4.7 2.5 - - + -
204T LEU* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25M LEU* 3.8 15.1 - - + +
28M VAL* 4.4 18.7 - - + +
126T LYS* 3.2 36.9 + - - +
130T LEU* 2.9 38.8 + - + +
131T HIS* 3.7 4.2 - - - +
133T MET* 1.3 75.5 - - - +
135T LEU* 1.3 58.7 + - - +
137T LEU* 3.4 6.2 + - - +
138T SER* 3.0 31.7 + - - -
185T VAL* 4.1 14.4 - - + -
189T ARG* 2.7 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M PHE* 4.9 13.2 - - + -
21M VAL* 4.1 21.9 - - + +
25M LEU* 3.4 33.0 - - + -
66T MET* 4.7 5.8 - - + -
118T LEU* 4.9 6.1 - - + -
121T PHE* 3.8 28.9 - - + -
131T HIS* 2.9 44.1 + - + +
132T ALA* 3.5 8.3 - - - +
133T MET 3.2 0.2 - - - -
134T GLU* 1.3 74.5 - - - +
136T ALA* 1.3 59.5 + - - +
138T SER* 3.2 4.2 + - - -
139T LEU* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 136 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63T TYR* 3.7 29.8 + - + +
66T MET* 4.6 3.5 - - + +
83T PHE* 5.4 0.4 - - + -
84T PHE* 4.2 12.6 - - + -
132T ALA 2.9 16.5 + - - +
133T MET* 3.7 8.7 - - - +
135T LEU* 1.3 76.2 - - - +
137T LEU* 1.3 57.8 + - - +
139T LEU* 3.2 6.3 + - - +
140T GLU* 2.9 35.3 + - - +
181T ILE* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 137 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28M VAL* 4.2 24.2 - - + -
36M LEU* 3.8 19.3 - - + +
133T MET 2.9 16.5 + - - +
134T GLU* 3.6 5.6 - - - +
135T LEU 3.2 0.2 - - - -
136T ALA* 1.3 77.4 - - - +
138T SER* 1.3 58.0 + - - +
140T GLU* 3.3 3.3 + - + +
141T LYS* 3.0 40.9 + - + +
178T ILE* 3.8 29.2 - - + +
181T ILE* 3.7 12.2 - - + +
182T SER* 3.4 36.3 - - - +
185T VAL* 4.5 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 138 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21M VAL* 4.4 12.3 - - - -
24M GLU* 3.4 35.4 + - - +
25M LEU* 3.1 28.2 + - - +
28M VAL* 5.1 4.2 - - - +
134T GLU 3.0 14.7 + - - -
135T LEU 3.2 8.3 + - - -
137T LEU* 1.3 76.7 - - - +
139T LEU* 1.3 57.8 + - - +
141T LYS* 3.3 3.0 + - - -
142T LEU* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M PHE* 5.6 1.8 - - + -
17M PRO* 3.9 22.0 - - + -
18M PHE* 6.2 1.6 - - + -
21M VAL* 3.6 24.0 - - + +
58T ASN* 4.8 1.3 - - - +
59T VAL* 3.8 37.2 - - + -
62T VAL* 3.7 32.3 - - + -
63T TYR* 4.5 12.8 - - + +
66T MET* 5.8 0.9 - - - -
135T LEU 2.9 17.0 + - - +
136T ALA* 3.2 6.9 + - - +
138T SER* 1.3 77.8 - - - +
140T GLU* 1.3 56.3 + - - +
142T LEU* 3.4 9.2 + - + +
143T THR* 3.0 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 140 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59T VAL* 4.4 3.8 - - - +
63T TYR* 2.4 35.8 + - - +
91T GLU* 3.7 14.6 - - - +
136T ALA 2.9 20.3 + - - +
137T LEU* 3.8 4.7 - - - +
139T LEU* 1.3 74.0 - - - +
141T LYS* 1.3 61.0 + - - +
143T THR* 3.3 5.1 + - - +
144T ASN* 2.9 24.6 + - - +
174T GLN* 2.6 47.5 + - - +
177T ALA* 4.2 11.4 - - + +
178T ILE* 3.9 13.7 - - + -
181T ILE* 3.5 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 141 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24M GLU* 3.5 24.2 - - + +
27M LEU* 5.8 2.0 + - - +
28M VAL* 5.7 2.6 - - - +
29M PRO* 5.0 9.1 - - - +
35M SER 5.5 0.2 + - - -
36M LEU 2.8 29.0 + - - -
37M ALA 3.7 14.6 - - - -
38M ARG 3.4 17.9 + - - -
39M GLN* 2.9 44.3 + - + +
137T LEU* 3.0 36.3 + - + +
138T SER* 3.7 4.0 - - - +
140T GLU* 1.3 75.0 - - - +
142T LEU* 1.3 63.5 + - - +
144T ASN* 3.2 1.1 + - - +
145T GLU* 3.0 13.0 + - - +
178T ILE* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 142 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M PHE* 3.9 26.7 - - + -
17M PRO* 4.2 2.9 - - + +
20M GLU* 3.6 59.2 - - + +
21M VAL* 4.2 13.0 - - + -
24M GLU* 4.3 12.7 + - + +
138T SER 2.9 17.0 + - - +
139T LEU* 3.6 9.4 - - + +
141T LYS* 1.3 75.1 - - - +
143T THR* 1.3 63.2 + - - +
145T GLU* 3.2 22.8 + - - +
146T LYS* 3.0 31.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 143 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M PHE* 6.0 0.3 - - - -
52T GLN* 3.9 6.7 - - - +
55T VAL* 4.2 7.5 - - + +
56T GLU* 3.6 30.3 - - - +
59T VAL* 3.4 24.3 - - + +
139T LEU* 3.0 15.1 + - - +
140T GLU* 3.6 12.3 + - - -
142T LEU* 1.3 74.6 - - - +
144T ASN* 1.3 59.5 + - - +
146T LYS* 3.1 9.1 + - - +
147T LEU* 2.9 29.6 + - + +
174T GLN* 3.6 18.2 - - - +
214T CA 4.3 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 144 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39M GLN* 3.0 32.1 + - - +
140T GLU 2.9 13.2 + - - +
141T LYS 3.4 9.0 - - - +
143T THR* 1.3 76.3 - - - +
145T GLU* 1.3 62.2 + - - +
147T LEU* 3.2 3.5 + - - +
148T LEU* 2.9 43.4 + - - +
171T LEU* 4.3 15.2 - - - +
174T GLN* 3.4 29.7 - - + +
175T VAL* 5.1 9.1 + - - +
178T ILE* 4.0 8.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 145 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20M GLU* 5.2 2.1 - - - +
23M LYS* 5.1 7.9 + - - -
24M GLU* 4.6 14.7 - - - +
39M GLN* 4.2 5.5 + - - +
40M LYS* 3.1 34.2 + - - +
141T LYS 3.0 12.7 + - - +
142T LEU* 3.2 25.4 + - + +
144T ASN* 1.3 75.2 - - - +
146T LYS* 1.3 64.3 + - + +
148T LEU* 3.3 8.4 + - - +
149T ASN* 3.0 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 146 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M PHE* 3.6 33.6 - - + -
20M GLU* 3.6 21.6 + - - -
51T GLU* 5.4 8.5 + - + +
52T GLN* 3.4 23.0 - - - +
55T VAL* 4.1 21.3 - - + -
142T LEU* 3.0 23.0 + - + +
143T THR 3.1 7.6 + - - +
145T GLU* 1.3 77.5 - - + +
147T LEU* 1.3 55.9 + - - +
149T ASN* 3.1 19.1 + - + +
150T LEU* 2.9 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 147 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52T GLN* 3.5 29.8 - - + +
56T GLU* 4.0 2.5 - - - +
98T LEU* 5.5 0.2 - - + -
143T THR* 2.9 19.9 + - + +
144T ASN* 3.2 5.8 + - - +
146T LYS* 1.3 75.6 - - - +
148T LEU* 1.3 59.2 + - - +
150T LEU* 3.2 9.1 + - + +
151T HIS* 2.9 27.4 + - - +
166T VAL* 3.9 12.7 - - + +
170T TYR* 3.8 43.7 - - + +
171T LEU* 3.8 15.0 - - + -
174T GLN* 3.8 37.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 148 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40M LYS* 3.7 35.7 - - + -
158M GLY 5.1 4.5 - - - +
160M VAL* 3.2 35.4 - - + +
161M GLN* 5.2 3.4 - - + +
144T ASN* 2.9 39.2 + - - +
145T GLU* 3.7 5.2 - - - +
147T LEU* 1.3 76.7 - - - +
149T ASN* 1.3 59.7 + - - +
151T HIS* 3.4 4.9 + - - +
152T SER* 3.0 27.2 + - - -
171T LEU* 4.1 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 149 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145T GLU* 3.0 30.4 + - - +
146T LYS* 3.1 21.6 + - + +
148T LEU* 1.3 76.6 - - - +
150T LEU* 1.3 59.3 + - - +
152T SER* 3.2 8.9 + - - -
153T VAL* 3.0 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 150 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48T ALA* 3.5 39.0 - - + +
49T VAL* 3.9 14.8 - - + +
52T GLN* 3.9 30.5 - - + +
98T LEU* 4.6 12.1 - - + -
146T LYS 2.9 12.9 + - - +
147T LEU* 3.5 11.2 - - + +
149T ASN* 1.3 72.0 - - - +
151T HIS* 1.3 67.9 + - - +
153T VAL* 3.2 6.0 + - + +
154T ALA* 3.0 21.0 + - - +
162T LEU* 4.4 10.1 - - + -
166T VAL* 3.6 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 151 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160M VAL* 3.5 36.3 - - + +
147T LEU 2.9 14.7 + - - +
148T LEU* 3.5 11.6 + - - +
150T LEU* 1.3 77.3 - - - +
152T SER* 1.3 60.0 + - - +
154T ALA* 3.4 5.7 + - - +
155T THR* 2.9 54.1 + - + -
163T ALA* 3.3 30.9 - - + +
166T VAL* 4.4 11.4 - - + +
167T GLU* 2.7 36.2 + - + +
171T LEU* 4.6 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 152 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148T LEU 3.0 14.1 + - - -
149T ASN* 3.4 13.7 - - - -
150T LEU 3.1 0.2 - - - -
151T HIS* 1.3 78.0 + - - +
153T VAL* 1.3 60.6 + - - +
155T THR* 3.2 4.6 + - - +
156T LYS* 2.8 57.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 153 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44T GLU* 3.7 45.8 - - + +
45T SER* 4.3 4.5 - - - -
48T ALA* 3.9 17.9 - - + -
149T ASN* 3.0 21.3 + - + +
150T LEU 3.2 6.7 + - - +
152T SER* 1.3 75.5 - - - +
154T ALA* 1.3 64.4 + - - +
156T LYS* 3.5 11.1 + - + +
157T ASN* 3.0 33.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 154 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45T SER* 4.4 3.6 - - - -
150T LEU 3.0 11.4 + - - +
151T HIS* 3.5 9.0 - - - +
153T VAL* 1.3 77.1 - - - +
155T THR* 1.3 60.0 + - - +
157T ASN* 3.2 3.5 + - - -
158T GLY 3.1 3.3 + - - -
159T ASP* 2.8 36.0 + - - +
162T LEU* 3.6 37.4 - - + +
163T ALA* 3.8 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 155 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151T HIS* 2.9 40.2 + - + -
152T SER* 3.2 4.9 + - - -
154T ALA* 1.3 71.6 - - - +
156T LYS* 1.3 67.3 + - - +
157T ASN 3.0 1.6 - - - -
158T GLY* 3.0 14.2 + - - +
159T ASP 4.8 1.8 - - - +
163T ALA* 3.8 10.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 156 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44T GLU* 5.3 5.6 - - - +
152T SER* 2.8 40.7 + - - +
153T VAL* 3.7 10.5 - - + +
155T THR* 1.3 77.1 - - - +
157T ASN* 1.3 66.0 + - - +
158T GLY 3.5 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 157 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42T VAL* 3.7 34.0 - - + +
44T GLU* 2.9 41.3 + - - +
45T SER* 4.2 5.6 + - - +
153T VAL* 3.0 24.9 + - - +
154T ALA 3.2 4.3 + - - +
155T THR 3.0 1.0 - - - -
156T LYS* 1.3 81.9 - - - +
158T GLY* 1.3 63.2 + - - +
159T ASP* 3.2 3.6 + - + +
----------------------------------------------------------
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