Contacts of the helix formed by residues 108 - 137 (chain D) in PDB entry 2AXT
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 108 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D THR* 4.8 3.8 - - - -
79D SER 4.7 8.1 - - - -
81D PRO* 3.8 14.9 - - - +
90D LEU* 3.4 10.7 - - - +
104D TRP 3.4 1.2 + - - -
105D CYS 3.6 6.8 + - - -
106D GLN 3.1 5.6 - - - -
107D LEU* 1.3 80.4 - - - +
109D GLY* 1.3 65.9 + - - +
110D LEU* 3.2 3.8 - - - -
111D TRP* 3.2 20.4 + - - +
112D THR 4.1 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D LEU* 3.5 17.0 - - - +
104D TRP* 2.8 43.6 + - - -
108D GLY* 1.3 72.3 - - - +
110D LEU* 1.3 58.7 + - - +
111D TRP 2.9 12.1 + - - -
112D THR* 3.3 5.5 + - - -
113D PHE* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D GLY* 4.1 19.1 - - - +
50D THR* 5.0 2.9 - - + -
51D GLY* 3.8 19.5 - - - +
55D VAL* 3.4 37.2 - - + -
78D VAL* 3.9 13.5 - - + -
101D PHE* 6.1 0.4 - - + -
104D TRP* 4.3 8.9 + - + -
105D CYS* 4.3 18.4 - - - +
108D GLY* 3.2 1.7 - - - -
109D GLY* 1.3 76.7 - - - +
111D TRP* 1.3 57.5 + - - +
113D PHE* 3.7 11.3 - - + +
114D ILE* 2.9 34.5 + - - +
357D BCR 4.2 28.7 - - + -
47E PHE* 5.9 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78D VAL* 3.4 28.4 - - + +
79D SER 4.4 4.3 - - - +
80D THR* 3.5 21.4 - - + +
81D PRO* 3.8 17.3 - - + -
108D GLY 3.2 12.7 + - - +
109D GLY 2.9 3.4 + - - -
110D LEU* 1.3 75.5 - - - +
112D THR* 1.3 74.7 + - + +
113D PHE 3.0 1.3 - - - -
114D ILE* 3.2 3.4 + - - +
115D ALA* 2.8 46.7 + - + +
157D PHE* 3.5 28.7 - + - -
167D TRP* 3.3 34.5 - + + -
170D ALA* 3.5 24.2 - - + -
171D PRO 3.2 19.3 + - - -
172D SER 4.4 0.2 - - - -
173D PHE* 3.4 24.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D PRO* 5.0 2.5 - - + -
88D SER 3.8 15.5 - - - +
89D LEU* 2.7 30.9 + - - +
90D LEU* 3.3 19.0 - - + +
108D GLY 4.1 0.4 + - - -
109D GLY 3.3 6.4 + - - -
111D TRP* 1.3 98.7 - - + +
113D PHE* 1.3 58.5 + - - +
115D ALA* 4.2 2.7 - - - -
116D LEU* 2.9 45.0 + - + +
167D TRP* 4.0 17.9 - - + +
355D CLA 3.6 2.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43D LEU* 3.0 38.6 - - + -
47D GLY* 4.4 1.8 - - - -
104D TRP* 3.3 22.9 - + + -
109D GLY 3.1 17.7 + - - +
110D LEU* 3.7 11.9 - - + +
111D TRP 3.0 0.2 - - - -
112D THR* 1.3 79.6 + - - +
114D ILE* 1.3 73.7 + - + +
116D LEU* 4.3 0.4 - - - +
117D HIS* 3.0 54.9 + + + +
355D CLA 3.1 48.2 - + - +
357D BCR 3.7 36.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A PHO 3.8 30.9 - - + +
44D ALA* 4.3 16.6 - - + +
47D GLY* 3.8 6.3 - - - -
48D TRP* 3.6 35.7 - - + +
78D VAL* 3.6 25.8 - - + -
110D LEU* 2.9 24.1 + - + +
111D TRP 3.2 3.6 + - - +
113D PHE* 1.3 80.2 - - + +
115D ALA* 1.3 67.6 + - - +
118D GLY* 2.8 23.6 + - - -
173D PHE* 3.9 17.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D TRP* 2.8 51.8 + - + +
112D THR* 3.9 3.4 - - - +
114D ILE* 1.3 73.9 - - - +
116D LEU* 1.3 61.2 + - + +
119D ALA* 2.9 28.3 + - - +
153D PHE* 3.7 14.8 - - + -
157D PHE* 5.2 1.3 - - + +
158D LEU* 5.0 10.0 - - + +
173D PHE* 4.2 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B CLA 3.9 28.0 - - + -
89D LEU* 4.4 23.3 - - + +
91D LEU* 5.5 1.1 - - + -
112D THR* 2.9 39.0 + - + +
113D PHE* 4.3 1.6 - - - +
115D ALA* 1.3 75.5 - - + +
117D HIS* 1.3 63.1 + - + +
119D ALA* 3.2 6.2 - - + +
120D PHE* 3.2 29.2 + - + -
158D LEU* 4.9 11.4 - - + -
167D TRP* 6.1 4.3 - - + -
355D CLA 4.1 26.7 - - + +
208H DGD 4.1 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 117 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D CYS* 3.4 24.3 - - + +
43D LEU* 3.5 17.0 - - + +
44D ALA* 4.0 18.8 - - + +
113D PHE* 3.0 62.7 + + - +
116D LEU* 1.3 74.4 - - + +
118D GLY* 1.3 61.8 + - - +
120D PHE* 3.4 1.6 + - - -
121D GLY* 2.9 23.4 + - - -
355D CLA 2.5 71.0 + + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 118 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A PHO 3.7 31.6 - - - -
41D ALA 5.8 0.2 - - - -
44D ALA* 3.8 9.5 - - - +
114D ILE 2.8 17.1 + - - -
117D HIS* 1.3 77.5 - - - +
119D ALA* 1.3 62.9 + - - +
121D GLY* 3.0 3.3 + - - -
122D LEU* 2.9 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ALA 2.9 15.4 + - - +
116D LEU* 3.2 17.0 - - + +
117D HIS 3.1 0.2 - - - -
118D GLY* 1.3 76.4 - - - +
120D PHE* 1.3 59.2 + - + +
122D LEU* 3.0 21.2 + - - +
123D ILE* 3.2 16.6 + - - +
153D PHE* 3.9 19.9 - - + -
154D VAL* 6.2 1.3 - - + -
158D LEU* 4.5 14.1 - - + -
208H DGD 4.9 15.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B CLA 3.8 59.9 - - + -
519B CLA 3.9 29.4 - - + -
36D LEU* 3.9 14.6 - - + +
40D CYS* 3.8 20.4 - - - -
116D LEU* 3.2 20.6 + - + +
117D HIS* 5.1 0.7 - - - -
119D ALA* 1.3 78.8 - - + +
121D GLY* 1.3 58.5 + - - +
123D ILE* 3.4 21.4 - - + +
124D GLY* 2.8 25.6 + - - -
355D CLA 3.7 35.2 - - + -
208H DGD 4.5 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 121 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A PHO 3.9 7.4 - - - +
37D LEU* 3.2 16.4 - - - +
40D CYS* 4.0 12.3 - - - +
41D ALA 4.3 8.1 - - - -
117D HIS 2.9 14.3 + - - -
118D GLY* 3.3 7.0 - - - -
119D ALA 3.0 0.8 - - - -
120D PHE* 1.3 80.5 - - - +
122D LEU* 1.3 57.3 + - - +
125D PHE* 3.0 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562A PHO 3.4 36.3 - - + +
118D GLY 2.9 29.0 + - - +
119D ALA* 3.0 7.4 + - - +
121D GLY* 1.3 76.2 - - - +
123D ILE* 1.3 65.8 + - - +
125D PHE* 3.9 5.6 - - - +
126D MET* 3.2 18.0 + - - +
146D PHE* 3.9 10.8 - - + -
149D PRO 4.6 0.2 - - - +
150D ILE* 3.5 39.7 - - + +
153D PHE* 4.2 28.3 - - + -
154D VAL* 5.9 0.2 - - + -
354D CLA 3.8 28.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B CLA 3.4 62.0 - - + +
519B CLA 4.6 6.7 - - + -
36D LEU* 4.6 4.9 - - + -
119D ALA 3.2 10.1 + - - +
120D PHE* 3.4 42.8 - - + +
121D GLY 3.2 0.2 - - - -
122D LEU* 1.3 76.0 - - + +
124D GLY* 1.3 65.4 + - - +
126D MET* 3.2 3.5 + - - +
127D LEU* 3.1 28.4 + - + +
150D ILE* 5.6 1.3 - - + -
208H DGD 3.7 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D SER* 4.1 5.2 - - - -
36D LEU* 3.9 16.3 - - - +
37D LEU* 3.9 18.8 - - - -
120D PHE 2.8 16.3 + - - -
121D GLY 3.8 1.3 - - - -
122D LEU 3.3 0.2 - - - -
123D ILE* 1.3 76.2 - - - +
125D PHE* 1.3 62.8 + - - +
127D LEU* 2.9 20.4 + - - +
128D ARG* 3.0 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 125 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A LEU* 3.9 19.7 - - + -
259A ILE* 5.7 2.5 - - + -
562A PHO 3.2 76.3 - + + +
564A PQ9 5.7 1.1 - - + -
485C UNK 5.1 12.6 - - + -
37D LEU* 3.3 19.4 - - + +
121D GLY 3.0 17.8 + - - +
122D LEU* 4.2 4.3 - - - +
124D GLY* 1.3 73.9 - - - +
126D MET* 1.3 61.0 + - - +
128D ARG* 3.3 14.2 - - - +
129D GLN* 3.2 50.1 + - + +
146D PHE* 3.9 13.7 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 126 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ILE* 3.1 32.1 - - + -
518B CLA 3.3 19.3 - - + -
122D LEU 3.2 17.9 + - - +
123D ILE 3.8 0.7 - - - +
124D GLY 3.1 0.8 - - - -
125D PHE* 1.3 73.2 - - - +
127D LEU* 1.3 68.8 + - - +
128D ARG 3.0 1.3 - - - -
129D GLN* 3.1 18.0 + - - +
130D PHE* 3.0 20.9 + - + +
143D ALA* 3.0 33.4 - - + +
146D PHE* 3.2 43.3 - - + +
147D SER* 3.3 9.4 - - - +
150D ILE* 3.6 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B CLA 3.5 81.4 - - + +
481C UNK 4.0 30.2 - - + +
33D SER* 3.8 12.8 - - - -
36D LEU* 4.5 9.0 - - + -
123D ILE* 3.1 18.5 + - + +
124D GLY* 2.9 12.4 + - - +
126D MET* 1.3 75.9 - - - +
128D ARG* 1.3 51.9 + - - +
130D PHE* 3.0 9.8 + - + +
131D GLU* 2.7 34.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 128 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ARG 3.2 17.6 + - - -
258A LEU* 2.6 50.1 + - + -
259A ILE 4.9 0.8 + - - -
485C UNK 3.7 16.3 - - - +
28D VAL* 4.3 2.6 - - - +
29D PHE* 3.5 24.3 + - + +
30D VAL 4.8 2.0 + - - +
33D SER* 3.5 19.7 - - - +
34D GLY* 6.3 0.2 - - - -
37D LEU* 4.4 12.3 - - + +
38D PHE* 2.9 37.5 - - - -
124D GLY 3.0 9.9 + - - +
125D PHE* 3.3 18.7 - - - +
126D MET 3.0 0.2 - - - -
127D LEU* 1.3 73.4 - - - +
129D GLN* 1.3 57.0 - - - +
131D GLU* 2.6 22.6 + - - +
132D ILE* 2.7 32.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 129 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 3.1 22.3 + - - +
258A LEU* 3.7 12.3 - - + -
562A PHO 2.9 18.2 + - - -
125D PHE* 3.3 25.8 - - + +
126D MET* 3.1 29.7 + - - +
128D ARG* 1.3 78.4 - - - +
130D PHE* 1.3 55.6 + - - +
132D ILE* 5.0 0.2 - - - -
133D ALA* 3.0 30.0 + - - +
140D PRO* 5.6 0.3 - - - +
142D ASN* 2.7 37.5 + - - +
143D ALA* 3.8 11.5 - - + +
146D PHE* 3.5 18.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 130 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ILE* 3.8 19.5 - - + -
471B ALA* 3.1 37.7 - - + -
475B PHE* 4.0 16.0 - + + -
518B CLA 3.3 49.1 - + + -
481C UNK 3.9 17.8 - - + +
126D MET* 3.0 10.8 + - + +
127D LEU* 3.0 13.9 + - + +
128D ARG 2.9 0.4 - - - -
129D GLN* 1.3 76.3 - - - +
131D GLU* 1.3 59.0 + - - +
133D ALA* 4.0 1.6 - - - -
134D ARG* 3.4 22.0 + - - +
140D PRO* 3.3 26.5 - - + -
143D ALA* 3.7 23.8 - - + -
144D ILE* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 131 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481C UNK 4.0 21.4 - - + +
483C UNK 5.4 3.1 - - + -
23D LYS* 4.3 14.3 - - - +
29D PHE* 4.2 8.9 - - + -
31D GLY* 2.8 12.8 - - - -
32D TRP* 2.6 36.6 + - - -
33D SER* 2.7 38.3 + - - +
127D LEU 2.7 8.6 + - - +
128D ARG* 2.6 15.2 + - - +
130D PHE* 1.3 69.9 - - - +
132D ILE* 1.3 63.9 - - + +
133D ALA 3.2 1.1 - - - -
134D ARG* 3.5 3.5 + - - +
135D LEU* 3.1 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 132 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 3.3 35.9 - - + +
257A ARG* 3.0 37.7 - - + +
258A LEU* 3.5 7.4 - - + -
29D PHE* 3.9 28.7 - - + -
128D ARG* 2.7 40.7 + - + +
129D GLN* 5.0 0.2 - - - -
131D GLU* 1.3 73.8 - - - +
133D ALA* 1.3 58.0 + - - +
135D LEU* 3.6 6.2 - - - +
136D VAL* 2.9 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A TYR* 3.5 19.5 - - + -
475B PHE* 3.9 17.9 - - + -
129D GLN 3.0 22.7 + - - +
130D PHE* 4.3 1.3 - - - +
131D GLU 3.2 0.2 - - - -
132D ILE* 1.3 76.4 - - - +
134D ARG* 1.3 64.4 + - - +
137D GLY* 2.9 19.2 + - - -
138D VAL* 3.1 25.5 + - + +
139D ARG 4.6 5.8 - - - +
140D PRO* 4.7 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ARG* 4.1 18.8 - - - +
474B LEU* 3.3 26.5 + - - -
475B PHE* 3.5 17.4 - - + +
477B ASP* 2.7 43.2 + - - -
478B VAL* 3.6 11.5 - - - +
481C UNK 5.1 3.8 - - + -
490C UNK 4.0 25.8 - - + -
130D PHE 3.4 18.3 + - - +
131D GLU* 3.8 5.8 - - - +
132D ILE 3.3 0.2 - - - -
133D ALA* 1.3 79.9 - - - +
135D LEU* 1.3 68.8 + - + +
137D GLY* 3.4 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 135 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D LYS* 3.9 40.2 - - + +
29D PHE* 3.6 37.9 - - + -
131D GLU* 3.1 16.5 + - + +
132D ILE* 3.6 6.7 - - - +
134D ARG* 1.3 80.9 - - + +
136D VAL* 1.3 63.1 + - + +
137D GLY* 2.8 11.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 136 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ALA* 4.3 11.0 - - - +
253A GLY* 4.2 22.4 - - - +
254A TYR* 4.2 9.6 - - + +
257A ARG* 4.1 21.8 - - - +
489B GLU* 4.7 14.8 - - + -
132D ILE* 2.9 33.7 + - + +
133D ALA 4.5 1.1 - - - +
135D LEU* 1.3 74.7 - - + +
137D GLY* 1.3 61.3 + - - +
138D VAL* 3.6 7.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 137 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B VAL* 4.1 17.2 - - - +
482B ILE* 4.2 10.2 - - - +
483B ASP 5.2 1.0 + - - -
133D ALA 2.9 9.1 + - - -
134D ARG* 3.9 16.2 - - - -
135D LEU 2.8 8.9 + - - -
136D VAL* 1.3 79.2 - - - +
138D VAL* 1.3 59.9 + - - +
----------------------------------------------------------
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