Contacts of the helix formed by residues 88 - 119 (chain E) in PDB entry 2OZB
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 PRO 88 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 4.2 0.2 - - - -
85E GLU* 3.9 33.2 - - + +
86E ALA 3.4 2.9 - - - -
87E ALA* 1.4 91.3 - - - +
89E GLU* 1.3 64.6 - - - +
90E TYR* 3.8 31.9 - - + +
91E ARG* 3.4 26.2 + - + +
92E VAL* 4.0 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 89 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B PHE* 3.6 29.5 - - + -
117B LYS* 4.7 1.6 - - - +
186B ARG* 3.2 37.1 + - - +
85E GLU* 4.9 1.0 + - - -
88E PRO* 1.3 70.8 - - - +
90E TYR* 1.3 68.0 + - - +
91E ARG 3.0 1.2 + - - -
92E VAL* 3.0 14.9 + - + +
93E ILE* 3.2 16.7 + - + +
207E TYR* 4.6 4.3 + - - +
211E ARG* 2.6 45.8 + - - +
214E PHE* 4.3 1.9 - - - -
215E ILE* 3.6 26.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E PRO* 3.8 29.3 - - + +
89E GLU* 1.3 76.2 - - - +
91E ARG* 1.3 84.9 + - + +
93E ILE* 3.1 5.5 + - - +
94E VAL* 2.8 43.6 + - + +
212E MET* 5.9 2.0 - - - +
215E ILE* 4.0 19.7 - - + +
232E MET* 3.8 36.3 - - + -
233E GLY* 4.4 3.8 - - - -
236E GLY* 3.0 24.2 + - - -
237E GLY* 3.3 29.4 - - - -
238E LEU 5.3 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 5.1 7.0 - - + -
88E PRO* 3.4 24.8 + - + +
89E GLU 3.0 0.8 + - - -
90E TYR* 1.3 102.7 + - + +
92E VAL* 1.3 65.3 + - + +
94E VAL* 3.1 22.9 + - - +
95E ASP* 3.0 56.8 + - - +
233E GLY* 3.5 33.9 + - - -
236E GLY* 5.6 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLU* 3.0 27.2 - - - +
109B ILE* 4.1 21.3 - - + +
110B ILE* 3.7 15.5 - - + -
113B PHE* 3.7 41.3 - - + -
190B ALA* 5.9 0.2 - - + -
87E ALA* 6.0 0.7 - - + -
88E PRO 4.1 4.9 - - - +
89E GLU* 3.0 12.9 + - + +
91E ARG* 1.3 74.9 - - + +
93E ILE* 1.3 58.7 + - + +
95E ASP* 3.4 0.8 + - - -
96E ALA* 2.9 23.0 + - - +
207E TYR* 3.7 24.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E GLU* 3.4 19.5 - - + +
90E TYR* 3.1 6.8 + - - +
92E VAL* 1.3 74.9 - - + +
94E VAL* 1.3 68.5 + - + +
95E ASP 3.2 0.2 - - - -
96E ALA* 3.8 3.3 - - - +
97E ASN* 3.0 23.9 + - - +
207E TYR* 3.6 37.2 - - + +
208E VAL* 3.9 31.0 - - + +
211E ARG* 3.6 18.6 - - + -
212E MET* 3.9 24.5 - - + -
215E ILE* 3.9 18.6 - - + -
229E ALA* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90E TYR* 2.8 31.6 + - + +
91E ARG* 3.5 29.4 - - - +
93E ILE* 1.3 77.3 - - + +
95E ASP* 1.3 61.1 + - - +
97E ASN* 3.6 2.1 - - - +
98E ASN* 2.9 38.2 + - - +
229E ALA* 3.5 33.7 - - - +
230E LYS* 5.5 2.7 - - - -
232E MET* 4.7 1.1 - - + -
233E GLY* 3.7 23.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLU* 3.1 20.7 - - + +
109B ILE* 3.3 26.9 - - + +
91E ARG* 3.0 46.7 + - - +
92E VAL* 4.0 1.8 - - - +
94E VAL* 1.3 80.7 - - - +
96E ALA* 1.3 56.3 + - - +
98E ASN* 3.0 14.7 + - + +
99E LEU* 3.0 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B GLU* 3.3 17.9 + - + +
193B MET* 5.7 1.8 - - + -
92E VAL 2.9 17.7 + - - +
93E ILE* 3.8 7.4 - - - +
94E VAL 3.2 0.2 - - - -
95E ASP* 1.3 76.8 - - - +
97E ASN* 1.3 59.1 + - - +
99E LEU* 3.1 25.3 - - + +
100E THR 3.4 1.7 + - - -
204E ILE* 3.4 22.6 - - + +
207E TYR* 4.3 14.1 - - + -
208E VAL* 4.0 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E ILE 3.0 17.3 + - - +
94E VAL 3.6 4.4 - - - +
96E ALA* 1.3 73.6 - - - +
98E ASN* 1.3 64.0 + - - +
100E THR* 2.8 30.1 + - - -
101E VAL* 3.3 8.4 + - - +
205E TYR* 3.6 21.6 - - - -
208E VAL* 3.8 14.6 - - + +
226E SER* 3.3 50.3 + - - +
229E ALA* 4.2 7.0 - - + +
230E LYS* 3.9 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B GLU* 5.7 0.7 - - - +
94E VAL* 2.9 26.6 + - - +
95E ASP* 3.0 21.3 + - - +
97E ASN* 1.3 75.6 + - - +
99E LEU* 1.3 62.7 + - - +
101E VAL* 3.1 21.7 + - - +
102E GLU* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 4.4 10.8 - - + -
102B GLU* 4.1 22.9 - - + +
103B ILE* 3.9 24.5 - - + -
106B GLU* 4.2 24.9 - - + -
197B LEU* 3.6 30.3 - - + -
95E ASP 3.0 8.8 + - - +
96E ALA* 3.1 13.7 - - - +
98E ASN* 1.3 79.5 - - - +
100E THR* 1.3 57.0 + - - +
102E GLU* 3.2 7.9 + - + +
103E ILE* 2.8 38.3 + - + +
204E ILE* 4.2 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E ALA 3.5 5.2 - - - +
97E ASN* 2.8 29.1 + - - +
99E LEU* 1.3 72.1 - - - +
101E VAL* 1.3 63.2 + - - +
103E ILE* 3.2 10.1 + - - +
104E GLU* 2.8 40.9 + - - +
201E LYS* 4.1 21.5 - - - +
204E ILE* 3.5 36.3 - - + -
205E TYR* 4.2 14.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97E ASN* 3.3 11.6 + - - +
98E ASN* 3.1 14.0 + - - +
100E THR* 1.3 83.5 + - - +
102E GLU* 1.3 66.2 + - + +
104E GLU* 3.1 19.8 + - - +
105E ASN* 3.0 41.3 + - - +
226E SER* 5.5 1.3 - - - +
230E LYS* 4.0 30.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.9 17.8 - - + +
102B GLU* 4.5 26.7 - - + +
98E ASN* 3.1 26.3 + - - +
99E LEU* 3.2 9.6 + - - +
101E VAL* 1.3 78.7 - - + +
103E ILE* 1.3 61.6 + - - +
105E ASN* 3.3 19.9 + - - +
106E GLU* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LEU* 3.9 24.0 - - + -
103B ILE* 5.9 4.7 - - + -
99E LEU* 2.8 28.0 + - + +
100E THR* 3.6 9.4 - - - +
102E GLU* 1.3 74.7 - - - +
104E GLU* 1.3 53.3 + - - +
106E GLU* 3.1 3.5 + - - +
107E LEU* 2.7 44.3 + - + +
197E LEU* 3.4 36.1 - - + +
200E SER* 4.7 5.4 - - - +
201E LYS* 3.7 14.8 - - + +
204E ILE* 3.5 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E THR* 2.8 22.9 + - - +
101E VAL* 3.3 25.6 - - - +
103E ILE* 1.3 72.0 - - - +
105E ASN* 1.3 61.5 + - - +
107E LEU* 3.1 10.3 + - + +
108E ASN* 3.0 31.7 + - - +
201E LYS* 3.5 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E VAL* 3.0 26.6 + - - +
102E GLU* 3.7 22.8 - - - +
103E ILE 3.3 0.2 - - - -
104E GLU* 1.3 78.5 - - - +
106E GLU* 1.3 65.4 + - - +
108E ASN* 3.4 13.2 + - - +
109E ILE* 3.0 37.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 2.7 26.4 - - - +
95B ASP* 3.1 26.5 - - + +
96B ALA* 3.4 18.2 + - + +
99B LEU* 3.8 23.6 - - + -
102E GLU 3.0 9.6 + - - +
103E ILE 3.7 5.8 - - - +
105E ASN* 1.3 76.1 - - - +
107E LEU* 1.3 58.3 + - - +
109E ILE* 3.4 8.6 + - - +
110E ILE* 2.9 51.7 + - + +
197E LEU* 3.6 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E ILE* 2.7 28.6 + - + +
104E GLU* 3.2 14.4 - - + +
106E GLU* 1.3 76.1 - - - +
108E ASN* 1.3 59.3 + - + +
110E ILE* 3.3 7.1 + - - +
111E HIS* 2.8 25.8 + - - +
132E ALA* 6.6 0.2 - - + -
133E LEU* 5.3 9.0 - - + -
136E ILE* 5.0 8.1 - - + +
194E ALA* 3.6 31.6 - - + +
197E LEU* 3.4 35.9 - - + -
198E ASN* 3.9 11.7 - - + +
201E LYS* 5.0 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E GLU* 3.0 23.3 + - - +
105E ASN* 3.4 15.2 + - - +
107E LEU* 1.3 73.6 - - + +
109E ILE* 1.3 65.5 + - - +
111E HIS* 3.5 14.7 - - + +
112E LYS* 2.9 60.4 + - - +
132E ALA* 5.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B ARG* 5.0 8.5 - - + +
92B VAL* 3.5 30.9 - - + +
95B ASP* 3.9 23.6 - - + +
105E ASN* 3.0 29.6 + - + +
106E GLU* 3.7 11.9 - - - +
108E ASN* 1.3 78.4 + - - +
110E ILE* 1.3 63.8 + - - +
112E LYS* 3.3 13.5 + - + +
113E PHE* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B VAL* 3.6 16.6 - - + -
207B TYR* 5.1 3.1 - - + +
106E GLU* 2.9 50.3 + - + +
107E LEU* 3.6 5.4 - - - +
109E ILE* 1.3 74.6 - - - +
111E HIS* 1.3 58.4 + - - +
113E PHE* 3.2 8.9 + - + +
114E ILE* 2.8 51.0 + - + +
190E ALA* 3.8 11.7 - - + +
193E MET* 4.3 15.3 - - + -
194E ALA* 3.8 21.3 - - + +
197E LEU* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E LEU 2.8 17.8 + - - +
108E ASN* 3.5 16.6 - - + +
109E ILE 3.3 0.2 - - - -
110E ILE* 1.3 75.8 - - - +
112E LYS* 1.3 66.7 + - + +
114E ILE* 3.1 4.3 + - - +
115E ARG* 3.0 52.0 + - + +
126E GLU* 6.4 0.4 - - + -
129E VAL 5.6 0.4 - - - -
130E PRO 4.4 9.2 + - - -
132E ALA* 3.8 42.1 + - + +
135E TYR* 4.0 28.5 - + + -
136E ILE* 4.3 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA* 4.8 9.4 - - + -
108E ASN* 2.9 40.4 + - - +
109E ILE* 3.6 15.0 - - + +
110E ILE 3.3 0.2 - - - -
111E HIS* 1.3 77.1 - - + +
113E PHE* 1.3 62.6 + - - +
115E ARG* 3.4 36.2 + - - +
116E ASP* 2.9 26.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ALA* 3.6 27.3 - - + +
88B PRO 4.5 0.4 - - - -
89B GLU* 3.6 41.7 - - + -
92B VAL* 3.8 21.8 - - + -
207B TYR* 5.2 2.2 - - - -
109E ILE 3.1 10.7 + - - +
110E ILE 3.4 6.7 - - - +
112E LYS* 1.3 78.9 - - - +
114E ILE* 1.3 61.7 + - + +
116E ASP* 3.3 1.7 + - - +
117E LYS* 2.8 54.4 + - + +
186E ARG* 3.4 36.6 - - + -
187E LEU* 5.2 2.2 - - + -
190E ALA* 4.2 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 114 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E ILE* 2.8 40.7 + - + +
111E HIS* 3.1 5.1 + - - +
113E PHE* 1.3 75.0 - - + +
115E ARG* 1.3 57.5 + - - +
118E TYR* 2.9 34.4 + - + +
135E TYR* 4.2 12.1 - - + -
136E ILE* 4.0 17.9 - - + -
139E VAL* 3.8 24.0 - - + -
187E LEU* 3.7 21.1 - - + +
190E ALA* 3.9 15.0 - - + -
191E CYS* 3.7 33.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111E HIS* 3.0 39.3 + - + +
112E LYS* 3.5 37.9 + - - +
114E ILE* 1.3 77.8 - - - +
116E ASP* 1.3 64.3 + - + +
119E SER* 3.1 24.4 + - - -
126E GLU* 3.3 41.2 + - + +
135E TYR* 3.5 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 116 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA* 3.1 38.3 - - - +
87B ALA* 4.3 11.2 - - + -
112E LYS 2.9 18.5 + - - +
113E PHE 3.6 3.1 - - - +
115E ARG* 1.3 78.8 - - + +
117E LYS* 1.3 74.5 + - - +
119E SER* 2.8 27.2 + - - -
120E LYS* 4.4 0.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B GLU 4.5 5.3 + - - -
86B ALA 3.4 5.9 + - - -
87B ALA 2.9 23.6 + - - -
88B PRO* 4.3 5.3 - - - +
89B GLU 4.8 1.8 - - - +
113E PHE* 2.8 47.8 + - + +
116E ASP* 1.3 88.6 + - - +
118E TYR* 1.3 58.1 + - - +
119E SER 3.5 0.4 + - - -
120E LYS* 4.0 15.2 - - - +
179E LEU* 4.4 4.9 - - - +
183E GLU* 6.1 0.6 - - - +
186E ARG* 3.3 36.3 - - - +
187E LEU* 3.8 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E ILE* 2.9 20.8 + - + +
115E ARG 3.9 0.4 - - - -
117E LYS* 1.3 75.5 - - - +
119E SER* 1.3 65.6 + - - +
120E LYS 3.1 2.5 - - - -
121E ARG* 3.1 16.8 + - + +
122E PHE* 3.0 43.6 + + + -
125E LEU* 3.9 17.9 - - + -
135E TYR* 3.8 18.8 - - - +
139E VAL* 4.0 25.8 - - + -
142E LEU* 3.8 10.9 - - - +
143E GLY* 2.9 34.8 + - - -
146E LEU* 3.5 17.8 - - - +
179E LEU* 4.5 2.2 - - + -
187E LEU* 3.5 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 119 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E ARG 3.1 17.1 + - - -
116E ASP* 2.8 18.5 + - - -
118E TYR* 1.3 78.0 - - - +
120E LYS* 1.3 63.2 + - - +
122E PHE 4.4 0.4 - - - -
123E PRO* 3.1 45.3 - - - +
135E TYR* 5.5 0.4 - - - -
----------------------------------------------------------
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