Contacts of the helix formed by residues 114 - 144 (chain S) in PDB entry 1BFR
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 TYR 114 (chain S).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102R ARG* 3.7 14.3 - - - +
105R ILE* 3.7 39.9 - - + -
106R GLY* 3.7 13.6 - - - -
109R ASP* 5.9 2.8 - - + +
117R ARG* 5.4 2.9 - - - -
121R ILE* 3.9 24.9 - - + -
124R LEU* 4.1 11.9 - - + -
109S ASP* 4.0 30.4 + - - -
112S HIS* 2.9 58.2 + + + -
113S ASP* 1.3 71.2 - - - +
115S VAL* 1.3 56.6 + - - +
117S ARG* 3.4 20.6 + - - +
118S ASP* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 115 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102R ARG* 5.1 0.8 - - - +
121R ILE* 4.6 5.2 - - + +
124R LEU* 4.0 12.0 - - + +
125R ARG* 3.8 49.7 + - + +
128R GLU* 3.5 34.1 - - + +
61S ARG* 3.7 16.2 - - - +
113S ASP 3.4 0.6 - - - -
114S TYR* 1.3 76.5 - - - +
116S SER* 1.3 60.9 + - - +
118S ASP* 3.4 5.1 + - - +
119S MET* 3.1 23.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 116 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7S VAL* 4.0 12.1 - - - +
11S LEU* 4.3 6.9 - - - +
61S ARG* 3.0 25.9 + - - +
65S LEU* 3.8 7.3 - - - +
108S ALA* 4.6 0.4 - - - -
113S ASP* 2.8 38.6 + - - -
115S VAL* 1.3 73.4 - - - +
117S ARG* 1.3 62.4 + - - +
119S MET* 3.4 8.3 - - - +
120S MET* 3.1 36.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 117 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117R ARG* 3.0 33.8 - - - +
121R ILE* 3.3 14.7 - - - +
105S ILE* 3.6 27.2 - - + +
108S ALA* 4.0 7.5 - - + +
109S ASP* 3.2 39.0 + - - +
113S ASP 3.0 13.9 + - - +
114S TYR* 3.4 16.7 + - - +
116S SER* 1.3 75.9 - - - +
118S ASP* 1.3 85.4 + - - +
120S MET* 3.1 14.0 + - - +
121S ILE* 3.0 25.5 + - + +
109V ASP* 4.8 2.8 + - - -
114V TYR* 5.2 2.6 - - - -
117V ARG* 3.2 27.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 118 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118R ASP* 5.6 3.6 - - - +
121R ILE* 3.3 23.8 - - + +
125R ARG* 3.5 23.3 + - - +
114S TYR 2.9 20.0 + - - +
115S VAL 3.4 2.9 + - - +
117S ARG* 1.3 101.6 + - - +
119S MET* 1.3 63.1 + - - +
121S ILE* 3.1 11.7 + - - +
122S GLU* 3.1 30.6 + - + +
117V ARG* 5.1 0.5 + - - -
118V ASP* 5.7 3.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 119 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11S LEU* 4.3 10.5 - - + -
57S ARG* 3.7 46.9 - - - +
58S TYR* 3.5 37.7 - - + -
61S ARG* 4.0 33.4 - - + -
115S VAL* 3.1 14.7 + - + +
116S SER* 3.4 8.5 - - - +
117S ARG 3.4 0.2 - - - -
118S ASP* 1.3 72.6 - - - +
120S MET* 1.3 73.1 + - + +
122S GLU* 3.4 5.2 + - - +
123S ILE* 3.1 27.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7S VAL* 5.3 2.0 - - + -
10S TYR* 5.7 1.1 - - + -
11S LEU* 3.9 15.7 - - + -
14S LEU* 3.6 27.4 - - - -
58S TYR* 4.4 6.7 - - + -
101S LEU* 3.9 11.0 - - + +
104S ALA* 3.7 23.3 - - + +
105S ILE* 3.6 15.7 - - + +
108S ALA* 3.6 30.5 - - + -
116S SER* 3.1 21.2 + - - +
117S ARG* 3.1 8.5 + - - +
119S MET* 1.3 89.0 - - + +
121S ILE* 1.3 57.0 + - - +
123S ILE* 3.2 6.9 + - - +
124S LEU* 2.8 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 121 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105S ILE* 3.7 31.6 - - + -
117S ARG* 3.0 27.1 + - - +
118S ASP* 3.1 11.2 + - - +
120S MET* 1.3 69.0 - - - +
122S GLU* 1.3 57.0 + - - +
124S LEU* 3.2 3.4 + - + +
125S ARG* 2.9 35.6 + - - +
114V TYR* 3.8 29.4 - - + +
115V VAL* 4.7 4.3 - - + +
117V ARG* 3.4 28.9 - - - +
118V ASP* 3.5 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125R ARG* 4.7 12.5 + - - -
57S ARG* 3.0 35.2 + - - +
118S ASP* 3.1 16.9 + - - +
119S MET 3.4 7.4 - - - +
121S ILE* 1.3 73.0 - - - +
123S ILE* 1.3 65.2 + - - +
125S ARG* 3.3 28.1 + - - +
126S ASP* 3.2 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S GLU* 4.0 7.4 - - - +
54S HIS* 3.6 47.3 - - + +
57S ARG* 4.1 19.1 - - + +
58S TYR* 3.6 45.1 - - + +
101S LEU* 4.7 4.9 - - + -
119S MET* 3.1 27.1 + - + +
120S MET* 3.2 5.6 + - - +
122S GLU* 1.3 73.7 - - - +
124S LEU* 1.3 62.0 + - - +
126S ASP* 3.1 5.2 + - - +
127S GLU* 3.0 25.0 + - + +
202S MN 4.1 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98S ALA* 4.1 24.7 - - + +
101S LEU* 3.9 26.8 - - + +
102S ARG* 3.8 32.5 - - + +
105S ILE* 3.8 22.7 - - + -
120S MET 2.8 20.4 + - - +
121S ILE* 3.5 5.6 - - - +
123S ILE* 1.3 70.7 - - - +
125S ARG* 1.3 59.0 + - - +
127S GLU* 3.2 3.5 + - + +
128S GLU* 2.9 33.0 + - + +
114V TYR* 4.1 21.5 - - + -
115V VAL* 4.2 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 125 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121S ILE* 2.9 22.2 + - - +
122S GLU* 3.5 32.8 + - - +
123S ILE 3.3 0.2 - - - -
124S LEU* 1.3 75.5 - - - +
126S ASP* 1.3 64.9 + - - +
128S GLU* 3.4 3.4 + - - +
129S GLY* 3.2 17.7 + - - -
115V VAL* 3.7 31.0 - - + +
118V ASP* 3.4 37.4 + - - +
122V GLU* 5.0 8.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 126 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50S ASP* 5.1 7.1 - - - +
54S HIS* 2.8 33.3 + - + -
57S ARG* 5.8 1.4 + - - -
122S GLU 3.2 13.9 + - - +
123S ILE* 3.1 8.0 + - - +
125S ARG* 1.3 78.1 - - - +
127S GLU* 1.3 62.8 + - - +
129S GLY* 3.2 4.4 + - - -
130S HIS* 3.1 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 127 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18S GLU* 4.7 0.4 - - - +
51S GLU* 2.9 7.4 - - - +
54S HIS* 3.1 13.3 - - - -
94S GLU* 2.8 22.6 - - - +
97S GLY* 5.8 2.5 - - - -
98S ALA* 5.2 6.3 - - + +
101S LEU* 4.1 19.7 - - + -
123S ILE* 3.0 14.3 + - + +
124S LEU* 3.2 10.5 + - + +
126S ASP* 1.3 70.8 - - - +
128S GLU* 1.3 66.4 + - - +
130S HIS* 3.0 3.1 + - - -
131S ILE* 2.9 32.6 + - + +
201S MN 2.2 29.1 + - - -
202S MN 2.5 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102S ARG* 2.7 35.5 + - - +
124S LEU* 2.9 26.6 + - + +
125S ARG* 3.8 6.7 - - - +
127S GLU* 1.3 70.8 - - - +
129S GLY* 1.3 55.3 + - - +
131S ILE* 3.3 16.0 + - + +
132S ASP* 2.9 25.3 + - - +
1V MET* 3.7 21.7 - - + +
61V ARG* 2.9 36.8 + - - +
64V PHE* 3.6 16.0 - - + -
113V ASP* 4.9 0.2 - - - +
115V VAL* 3.6 17.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 129 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125S ARG 3.2 12.9 + - - -
126S ASP* 3.2 5.4 + - - -
127S GLU 3.2 0.8 - - - -
128S GLU* 1.3 73.4 - - - +
130S HIS* 1.3 66.1 + - - +
132S ASP* 3.3 8.7 + - - +
133S TRP* 3.2 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 130 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25S TYR* 3.5 14.2 + - - +
47S GLU* 3.5 35.0 - - + +
50S ASP* 2.8 34.7 + - + -
51S GLU* 3.4 13.4 + - - -
54S HIS* 4.9 1.1 - + - -
94S GLU* 3.2 13.0 - - - +
126S ASP* 3.1 17.6 + - - +
127S GLU* 3.0 5.9 + - - -
129S GLY* 1.3 73.6 - - - +
131S ILE* 1.3 63.5 + - - +
133S TRP* 3.2 3.4 + - - +
134S LEU* 3.0 28.4 + - - +
201S MN 2.1 33.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 131 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91S LEU* 3.8 21.1 - - + -
94S GLU* 3.6 23.8 + - + +
95S LEU* 3.7 25.6 - - + -
98S ALA* 4.3 18.8 - - + -
127S GLU 2.9 21.0 + - - +
128S GLU* 3.5 17.3 - - + +
130S HIS* 1.3 75.2 - - - +
132S ASP* 1.3 64.0 + - - +
134S LEU* 3.3 2.9 + - - +
135S GLU* 3.0 44.4 + - - +
1V MET* 4.1 22.7 - - + -
64V PHE* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128S GLU 2.9 10.3 + - - +
129S GLY* 3.6 11.4 - - - +
130S HIS 3.3 0.2 - - - -
131S ILE* 1.3 76.0 - - - +
133S TRP* 1.3 61.8 + - - +
135S GLU* 3.5 6.3 + - - +
136S THR* 3.1 37.5 + - - -
34U ASN* 4.2 12.5 - - - +
64V PHE* 3.5 36.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 133 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S ARG* 4.0 11.0 - - - +
40S LEU* 4.1 21.3 - - + -
43S VAL* 3.5 43.3 - - + +
44S GLU* 3.6 28.5 - - + -
47S GLU* 3.8 18.6 - - - +
87S LEU* 4.8 5.8 - - + -
129S GLY 3.2 9.7 + - - +
130S HIS 3.2 5.8 + - - +
132S ASP* 1.3 77.5 - - - +
134S LEU* 1.3 92.4 + - + +
136S THR* 3.2 5.1 + - - -
137S GLU* 3.0 61.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25S TYR* 3.8 22.0 - - - +
44S GLU* 4.1 5.4 - - - +
47S GLU* 4.6 0.9 - - - +
87S LEU* 3.8 30.7 - - + +
90S ASP* 3.9 14.4 - - + -
91S LEU* 3.8 33.0 - - + +
94S GLU* 4.1 6.7 - - + -
130S HIS 3.0 20.5 + - - +
131S ILE* 3.9 3.1 - - - +
133S TRP* 1.3 101.8 - - + +
135S GLU* 1.3 63.7 + - - +
137S GLU* 3.3 3.8 + - - +
138S LEU* 3.0 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 135 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91S LEU* 4.1 23.9 - - + +
95S LEU* 5.5 2.4 - - - +
131S ILE* 3.0 29.6 + - - +
132S ASP* 3.8 5.0 - - - +
134S LEU* 1.3 77.1 - - - +
136S THR* 1.3 63.7 + - - +
138S LEU* 3.3 4.0 + - - +
139S ASP* 3.0 30.7 + - - +
1V MET* 2.8 44.0 + - - +
64V PHE* 4.1 10.4 - - - -
66V GLU* 4.3 4.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132S ASP* 3.1 25.3 + - - -
133S TRP* 3.7 5.4 - - - -
135S GLU* 1.3 75.6 - - - +
137S GLU* 1.3 66.8 + - - +
139S ASP* 3.2 7.1 + - + +
140S LEU* 2.9 29.1 + - + +
34U ASN* 3.6 13.3 + - - +
35U TRP* 3.7 24.9 - - - +
36U GLY* 3.7 19.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S ARG* 3.1 39.9 + - - -
87S LEU* 4.2 10.3 - - + -
133S TRP* 3.0 45.7 + - + +
134S LEU* 3.7 6.5 - - - +
136S THR* 1.3 76.2 - - - +
138S LEU* 1.3 65.0 + - - +
140S LEU* 3.1 17.2 + - - +
141S ILE* 2.9 28.5 + - - +
149S TYR* 2.6 37.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 138 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84S GLU* 3.9 21.1 - - + +
87S LEU* 3.8 26.9 - - + +
88S ARG* 3.9 49.4 - - + +
91S LEU* 3.7 30.1 - - + -
134S LEU 3.0 19.4 + - - +
135S GLU* 3.8 4.3 - - - +
137S GLU* 1.3 74.9 - - - +
139S ASP* 1.3 63.2 + - - +
141S ILE* 3.6 9.5 + - + +
142S GLN* 2.8 30.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 139 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135S GLU* 3.0 19.9 + - - +
136S THR* 3.6 10.8 - - + +
138S LEU* 1.3 74.6 - - - +
140S LEU* 1.3 61.1 + - + +
142S GLN* 3.1 12.1 + - - +
143S LYS* 2.9 53.0 + - - +
35U TRP* 5.9 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 140 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39S ARG* 6.2 0.2 - - - +
136S THR* 2.9 39.1 + - + +
137S GLU* 3.1 18.4 + - - +
139S ASP* 1.3 72.4 - - + +
141S ILE* 1.3 61.8 + - - +
143S LYS* 3.2 14.9 + - + +
144S MET* 2.9 55.8 + - + +
149S TYR* 4.5 9.0 - - + -
35U TRP 3.3 20.9 - - - +
36U GLY* 4.4 6.7 - - - +
37U LEU* 4.2 15.3 - - + -
150U LEU* 6.0 1.1 - - + -
154U ILE* 4.6 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 141 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83S VAL* 4.6 3.6 - - + -
84S GLU* 4.2 30.5 - - + +
87S LEU* 4.1 18.8 - - + -
137S GLU 2.9 18.6 + - - +
138S LEU* 3.6 20.9 - - + +
139S ASP 3.3 0.2 - - - -
140S LEU* 1.3 73.8 - - - +
142S GLN* 1.3 64.3 + - - +
145S GLY* 3.0 24.1 + - - -
146S LEU* 3.8 29.7 + - + +
149S TYR* 3.7 40.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 142 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84S GLU* 3.2 30.0 + - - +
88S ARG* 3.3 15.3 + - - +
138S LEU* 2.8 25.6 + - - +
139S ASP* 3.1 12.0 + - - +
141S ILE* 1.3 81.4 - - - +
143S LYS* 1.3 64.6 + - + +
145S GLY* 3.7 5.2 + - - -
147U GLN* 4.9 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 143 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139S ASP* 2.9 44.2 + - - +
140S LEU* 3.2 12.9 + - + +
142S GLN* 1.3 76.0 - - + +
144S MET* 1.3 60.1 + - + +
35U TRP* 3.6 45.1 + - - +
37U LEU* 5.9 3.3 - - + +
146U LEU* 6.1 0.7 - - - +
147U GLN* 3.7 15.2 + - - +
150U LEU* 3.9 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 144 (chain S).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140S LEU* 2.9 52.9 + - + +
143S LYS* 1.3 73.1 - - - +
145S GLY* 1.3 67.7 + - - +
148S ASN* 3.3 16.1 + - + +
149S TYR* 3.8 27.6 - - - +
147U GLN* 3.3 40.5 + - - +
150U LEU* 4.3 8.1 - - + -
151U GLN* 4.0 36.6 - - - +
154U ILE* 4.1 19.7 - - + -
----------------------------------------------------------
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