Contacts of the helix formed by residues 77 - 105 (chain E) 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 LEU 77 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E PHE* 3.5 38.2 + - + +
75E VAL* 3.3 1.5 - - + +
76E ALA* 1.3 78.7 - - - +
78E ARG* 1.3 59.8 + - - +
79E GLY 3.3 3.1 - - - -
80E LEU* 3.4 4.9 + - + +
81E ALA* 3.0 27.5 + - - +
128E ASP* 3.8 10.3 - - - +
129E ALA* 4.2 13.7 - - + -
197E VAL* 4.2 6.1 - - + -
198E TRP* 4.5 8.5 - - + -
201E ASP* 3.3 29.6 - - + +
190W ARG* 3.7 53.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 78 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E PHE 5.3 0.2 - - - -
76E ALA* 3.6 8.8 + - - +
77E LEU* 1.3 72.5 - - - +
79E GLY* 1.3 57.6 + - - +
81E ALA* 3.4 7.4 + - - +
82E LYS* 2.9 30.7 + - - +
201E ASP* 3.2 4.3 + - - +
202E GLN* 3.3 16.8 + - - +
205E LEU* 3.7 37.0 - - + +
206E HIS* 5.9 0.2 - - - -
183W GLU* 5.0 20.6 - - - +
187W GLN* 3.0 39.7 + - - +
203W MET* 4.0 14.8 - - - +
207W GLU* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 79 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78E ARG* 1.3 76.5 - - - +
80E LEU* 1.3 59.3 + - - +
82E LYS* 3.4 3.0 + - - +
83E PHE* 3.0 28.8 + - - +
201E ASP* 2.9 30.7 + - - -
204E LEU* 3.9 11.2 - - - +
205E LEU* 3.7 20.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70E PHE* 4.0 24.2 - - + -
77E LEU* 3.4 17.7 + - + +
79E GLY* 1.3 69.5 - - - +
81E ALA* 1.3 67.1 + - - +
83E PHE* 3.6 0.6 - - + +
84E PHE* 2.9 47.2 + - + -
129E ALA* 4.3 15.7 - - + +
133E MET* 3.4 38.4 - - + -
188E LEU* 5.6 0.2 - - + -
197E VAL 5.4 0.7 - - - +
200E PHE* 4.7 9.0 - - + -
201E ASP* 2.7 44.8 + - + +
204E LEU* 3.6 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 81 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E PHE* 3.3 23.8 - - + +
70E PHE* 3.9 26.8 - - - +
71E ASP* 4.0 11.2 - - + +
77E LEU 3.0 17.6 + - - +
78E ARG* 3.7 8.5 - - - +
79E GLY 3.3 0.2 - - - -
80E LEU* 1.3 76.9 - - - +
82E LYS* 1.3 56.8 + - - +
84E PHE* 3.4 0.5 + - - -
85E LYS* 2.9 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 82 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E PHE* 5.8 0.2 - - - -
78E ARG 2.9 17.7 + - - +
79E GLY 3.7 4.5 - - - +
80E LEU 3.3 0.2 - - - -
81E ALA* 1.3 76.8 - - - +
83E PHE* 1.3 62.7 + - - +
85E LYS* 3.3 8.1 + - - +
86E GLU* 2.9 63.5 + - + +
204E LEU 5.0 4.3 - - - +
205E LEU* 3.8 38.1 - - + +
207E GLU 6.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E TYR* 5.8 1.8 - + - -
79E GLY 3.0 17.4 + - - +
80E LEU* 3.6 2.7 - - + +
82E LYS* 1.3 78.0 - - - +
84E PHE* 1.3 85.2 + + - +
86E GLU* 3.4 8.5 + - + +
87E SER* 2.8 50.7 + - - -
133E MET* 3.6 26.9 - - + -
136E ALA* 5.3 0.9 - - + -
180E ARG* 3.5 40.6 - - - -
181E ILE* 4.4 18.8 - - + -
184E TYR* 3.7 20.2 - + - -
204E LEU* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 84 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E TYR* 3.5 33.9 - + - +
66E MET* 3.3 39.0 - - + -
67E PHE* 3.7 9.4 - - - +
70E PHE* 3.8 26.9 - + - -
80E LEU* 2.9 43.5 + - + +
83E PHE* 1.3 97.5 - + - +
85E LYS* 1.3 61.4 + - - +
87E SER* 4.1 1.8 - - - -
88E SER* 2.9 30.0 + - - -
132E ALA* 4.1 15.0 - - + -
133E MET* 4.3 10.1 - - - -
136E ALA* 4.1 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 85 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64E HIS* 5.0 1.8 - - - +
67E PHE* 3.6 33.7 - - + +
81E ALA 2.9 18.6 + - - +
82E LYS* 3.6 8.1 - - - +
84E PHE* 1.3 77.8 - - - +
86E GLU* 1.3 63.9 + - + +
88E SER* 3.4 6.6 + - - -
89E GLU* 3.3 20.4 + - - +
92I ARG* 4.5 1.9 + - - -
96I GLU* 3.0 41.4 + - - +
100I GLU* 2.8 27.1 + - - -
216I CA 4.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 86 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E LYS* 2.9 58.5 + - + +
83E PHE* 3.8 7.0 - - + +
85E LYS* 1.3 75.7 - - + +
87E SER* 1.3 61.4 + - - +
89E GLU* 3.3 8.2 + - - +
90E GLU* 3.0 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 87 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E TYR* 3.6 28.9 - - - -
83E PHE* 2.8 47.1 + - - -
84E PHE* 3.7 5.8 - - - -
86E GLU* 1.3 78.3 - - - +
88E SER* 1.3 55.9 - - - +
90E GLU* 3.3 9.5 + - - +
91E GLU* 2.9 34.7 + - - +
180E ARG* 5.6 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 88 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60E SER* 2.7 51.7 + - - +
63E TYR* 3.8 4.9 - - - +
64E HIS* 3.5 22.8 + - - -
84E PHE 2.9 17.9 + - - -
85E LYS 3.6 4.0 - - - -
87E SER* 1.3 77.6 - - - +
89E GLU* 1.3 61.5 + - - +
91E GLU 3.3 0.9 + - - -
92E ARG* 3.1 10.7 + - - +
57I TYR* 4.5 0.2 + - - -
92I ARG* 2.9 19.5 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
85E LYS 3.3 9.6 + - - +
86E GLU* 3.6 10.5 - - - +
87E SER 3.3 0.2 - - - -
88E SER* 1.3 78.5 - - - +
90E GLU* 1.3 63.2 + - - +
92E ARG* 3.3 15.9 + - - +
93E GLU* 3.1 36.3 + - + +
89I GLU* 4.9 14.9 - - - +
92I ARG* 3.0 35.3 + - - +
93I GLU* 4.3 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 90 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86E GLU* 3.0 18.1 + - - +
87E SER* 3.7 9.7 + - - +
89E GLU* 1.3 78.3 - - - +
91E GLU* 1.3 57.2 + - + +
93E GLU* 3.2 11.7 + - + +
94E HIS* 3.0 57.2 + - + +
180E ARG* 5.0 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 91 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E GLU* 3.1 16.7 - - - +
59E VAL* 3.6 25.2 - - + +
60E SER* 3.5 23.8 - - - +
63E TYR* 3.6 19.1 - - + -
87E SER* 2.9 22.1 + - - +
90E GLU* 1.3 73.8 - - - +
92E ARG* 1.3 60.1 + - - +
94E HIS* 3.1 17.3 + - - +
95E ALA* 3.0 25.8 + - - +
140E GLU* 3.7 13.6 - - - +
214E CA 2.5 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 92 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57E TYR* 3.7 29.7 + - + +
60E SER* 3.7 18.1 + - - +
88E SER 3.1 7.4 + - - +
89E GLU* 3.6 16.2 + - - +
91E GLU* 1.3 76.6 - - - +
93E GLU* 1.3 73.6 + - - +
95E ALA* 3.2 7.5 + - - +
96E GLU* 2.9 37.7 + - - +
60I SER* 4.7 2.4 + - - -
64I HIS* 3.7 17.6 + - + -
85I LYS 4.6 1.0 + - - -
88I SER* 2.9 30.7 + - - -
89I GLU* 3.5 36.8 + - - +
92I ARG* 3.3 35.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 93 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E GLU* 3.1 28.3 + - + +
90E GLU* 3.2 12.7 + - + +
92E ARG* 1.3 87.2 + - - +
94E HIS* 1.3 62.5 + - + +
96E GLU* 3.2 9.8 + - - +
97E LYS* 2.9 32.1 + - - +
216E CA 2.8 28.7 - - - -
89I GLU* 5.2 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 94 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56E GLU* 3.4 17.9 - - - +
90E GLU* 3.0 47.5 + - + +
91E GLU* 3.1 19.2 + - - +
93E GLU* 1.3 79.4 - - + +
95E ALA* 1.3 62.8 + - - +
97E LYS* 4.6 11.0 - - - -
98E LEU* 3.4 9.7 + - - +
169E GLU 6.2 0.4 - - - -
170E TYR* 2.7 39.7 + + + -
173E GLU* 6.0 7.0 - - + +
174E GLN* 5.6 2.7 - - - -
214E CA 2.7 23.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 95 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ILE* 3.9 12.2 - - + +
56E GLU* 3.8 21.9 - - + +
57E TYR* 3.7 33.0 - - + +
91E GLU 3.0 9.3 + - - +
92E ARG* 3.5 9.4 - - - +
93E GLU 3.2 0.2 - - - -
94E HIS* 1.3 75.1 - - - +
96E GLU* 1.3 64.6 + - - +
98E LEU* 3.2 7.4 + - - +
99E MET* 3.0 27.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E ARG* 2.9 24.8 + - - +
93E GLU* 3.6 10.2 - - - +
95E ALA* 1.3 76.5 - - - +
97E LYS* 1.3 59.1 + - - +
99E MET* 3.2 10.3 + - - +
100E GLU* 2.9 40.1 + - - +
216E CA 2.6 28.2 - - - -
64I HIS* 2.7 32.8 + - + +
67I PHE* 4.4 7.4 - - + -
85I LYS* 3.1 35.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 97 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E GLU 2.9 16.9 + - - +
94E HIS* 5.3 10.7 - - - +
95E ALA 3.2 0.4 - - - -
96E GLU* 1.3 76.8 - - - +
98E LEU* 1.3 56.5 + - - +
100E GLU* 3.4 15.5 + - - +
101E TYR* 2.9 26.2 + - - +
165E PHE* 4.1 8.5 - - + -
169E GLU* 2.9 53.8 + - + +
170E TYR* 3.3 20.5 - - + +
173E GLU* 5.9 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E VAL* 3.8 22.4 - - + +
52E GLN* 3.6 33.0 - - + +
53E ILE* 3.5 16.6 - - + +
56E GLU* 3.9 14.6 - - + -
94E HIS 3.4 8.4 + - - +
95E ALA 3.2 3.9 + - - +
97E LYS* 1.3 77.8 - - - +
99E MET* 1.3 59.7 + - - +
101E TYR* 3.6 5.2 - - + +
102E GLN* 2.9 29.3 + - - +
147E LEU* 5.4 0.4 - - + -
150E LEU* 4.3 19.7 - - + -
162E LEU* 5.9 0.2 - - + -
165E PHE* 3.8 21.5 - - + -
170E TYR* 3.3 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53E ILE* 3.7 27.1 - - + -
57E TYR* 4.5 3.4 - - - -
95E ALA 3.0 22.0 + - - +
96E GLU* 3.2 10.5 + - - +
98E LEU* 1.3 75.6 - - - +
100E GLU* 1.3 64.1 + - - +
102E GLN* 3.4 5.0 + - - +
103E ASN* 3.2 21.8 + - - -
109E VAL* 3.6 17.9 - - + +
111E LEU* 4.2 20.9 - - + -
64I HIS* 3.6 60.8 - - + +
67I PHE* 4.1 10.8 - - + -
68I ALA* 4.0 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LYS* 5.3 0.5 + - - -
96E GLU* 2.9 26.0 + - - +
97E LYS* 3.6 13.4 - - - +
99E MET* 1.3 75.9 - - - +
101E TYR* 1.3 57.2 + - - +
103E ASN* 3.3 4.5 + - - +
104E LYS* 2.9 43.7 + - + +
67I PHE* 4.0 18.3 - - + -
71I ASP* 4.1 11.7 - - - +
85I LYS* 2.5 37.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 5.2 3.8 - - + -
41E TYR* 4.3 9.0 - + - -
49E VAL* 4.7 6.1 - - + -
97E LYS 2.9 17.4 + - - +
98E LEU* 3.2 5.8 + - - +
100E GLU* 1.3 75.4 - - - +
102E GLN* 1.3 69.7 + - - +
104E LYS* 3.0 20.2 + - + +
105E ARG* 2.9 56.2 + - + +
161E GLN* 2.5 35.2 + - - -
162E LEU* 3.2 32.0 - - + -
165E PHE* 3.6 51.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41E TYR* 2.6 45.7 + - - -
46E GLU* 3.0 33.4 + - - +
49E VAL* 3.8 6.1 - - + +
50E ASN* 3.1 31.7 + - - +
53E ILE* 4.8 0.7 - - + -
98E LEU 2.9 14.6 + - - +
99E MET 3.4 10.5 - - - +
101E TYR* 1.3 77.8 - - - +
103E ASN* 1.3 56.3 + - - +
105E ARG* 3.3 1.9 + - - +
106E GLY 3.1 6.8 + - - -
107E GLY* 2.9 39.8 + - - -
108E LYS 3.8 0.2 + - - -
109E VAL* 3.6 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LYS* 3.7 14.9 - - - +
99E MET 3.2 12.5 + - - -
100E GLU 3.7 4.0 - - - +
101E TYR 3.1 0.6 - - - -
102E GLN* 1.3 77.0 - - - +
104E LYS* 1.3 66.3 + - - +
106E GLY* 3.1 12.0 + - - -
107E GLY 3.6 12.4 - - - +
109E VAL* 4.2 9.3 + - - +
67I PHE* 5.5 0.6 - - - -
68I ALA* 3.0 30.3 + - - +
71I ASP* 2.9 47.1 + - - +
72I ARG* 3.5 20.6 - - - +
73I ASP* 4.3 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 3.8 27.8 - - + +
176B GLU* 2.8 41.0 + - - +
178B ILE* 5.7 0.7 - - - +
179B LYS* 3.9 36.8 - - + +
37E ALA* 4.2 8.0 - - - +
100E GLU* 2.9 31.1 + - - +
101E TYR* 3.0 23.2 + - + +
103E ASN* 1.3 76.4 - - - +
105E ARG* 1.3 59.5 + - - +
106E GLY 3.5 0.2 + - - -
165E PHE* 6.2 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 3.7 24.1 - - - +
37E ALA 4.5 1.5 - - - -
38E ARG* 3.3 25.4 - - - +
39E GLN 3.4 16.3 + - - +
40E LYS* 3.1 27.1 + - - +
41E TYR* 3.5 39.4 - - + +
101E TYR* 2.9 60.9 + - + +
102E GLN 3.9 0.4 - - - +
103E ASN 3.2 0.2 - - - -
104E LYS* 1.3 76.2 - - - +
106E GLY* 1.3 61.7 + - - +
107E GLY 3.6 0.2 + - - -
159E ASP* 2.9 31.1 + - - -
161E GLN* 3.7 14.5 + - - +
162E LEU* 3.7 3.8 - - - +
----------------------------------------------------------
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