Contacts of the helix formed by residues 64 - 93 (chain N) in PDB entry 2FJC
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 GLU 64 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62N GLY* 4.2 1.2 - - - -
63N ILE* 1.3 100.4 + - + +
65N PHE* 1.3 64.1 + - - +
66N LYS 3.5 1.3 - - - -
67N GLN* 3.2 20.2 + - + +
68N VAL* 3.1 27.6 + - + +
120N ILE* 3.4 26.0 - - + +
64O GLU* 5.1 3.2 - - + +
63P ILE* 3.6 46.2 - - + +
64P GLU* 5.1 3.3 - - + +
67P GLN* 6.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57N HIS 4.2 2.5 - - - -
58N TRP 4.8 2.0 - - - -
60N ILE* 3.4 47.6 - - + -
61N TYR* 4.3 0.4 - - - -
62N GLY 2.9 18.6 + - - +
63N ILE 3.2 1.8 - - - -
64N GLU* 1.3 75.9 - - - +
66N LYS* 1.3 58.7 + - + +
68N VAL* 3.1 0.9 + - - +
69N HIS* 2.6 68.8 + + + +
120N ILE* 3.5 8.8 - - - +
169O TRP* 3.8 21.8 - + - -
170O MET* 3.8 28.7 - - + -
173O ALA* 3.8 18.8 - - + -
174O THR* 3.7 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 66 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N ILE 5.0 0.4 + - - -
64N GLU 3.5 0.4 - - - -
65N PHE* 1.3 88.8 - - + +
67N GLN* 1.3 80.9 + - - +
69N HIS* 3.5 4.4 - - + +
70N GLU* 2.8 57.1 + - - +
67O GLN 5.9 0.9 - - - +
71O LEU* 3.9 39.3 - - + -
74O GLU* 3.7 24.0 + - - -
170O MET* 5.1 17.9 - - + -
174O THR* 4.7 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63N ILE 4.3 4.4 + - - -
64N GLU* 3.2 26.6 + - + +
66N LYS* 1.3 95.6 + - - +
68N VAL* 1.3 60.7 + - + +
70N GLU* 3.4 10.6 + - - +
71N LEU* 2.9 28.0 + - - +
64O GLU* 6.2 2.4 - - - +
67O GLN* 3.5 34.3 - - + +
66P LYS* 5.8 1.4 - - - +
67P GLN* 3.6 40.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 68 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60N ILE* 3.5 17.5 - - + -
64N GLU* 3.1 22.4 + - + +
67N GLN* 1.3 74.5 - - + +
69N HIS* 1.3 61.0 + - - +
71N LEU* 3.5 9.6 - - + +
72N LEU* 2.8 56.2 + - + +
120N ILE* 3.6 28.9 - - + +
124N LEU* 3.9 28.5 - - + -
63P ILE* 5.2 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88M GLU* 3.4 19.6 + - - -
613M FE 3.7 1.6 - - - -
57N HIS* 2.7 85.8 + + - -
58N TRP* 5.0 0.4 - + - -
60N ILE* 3.7 7.5 - - - +
65N PHE* 2.6 44.6 + + + +
66N LYS* 3.5 7.9 - - + +
68N VAL* 1.3 74.3 - - - +
70N GLU* 1.3 69.4 + - + +
72N LEU* 3.5 2.1 + - - +
73N GLU* 3.3 6.4 + - - -
166O LYS* 5.9 1.4 + - - -
169O TRP* 3.7 19.9 - + - -
170O MET* 4.8 10.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 70 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66N LYS* 2.8 56.7 + - - +
67N GLN* 3.7 7.7 - - - +
69N HIS* 1.3 82.3 - - + +
71N LEU* 1.3 65.8 + - - +
73N GLU* 3.1 16.3 + - - +
74N GLU* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67N GLN 2.9 18.0 + - - +
68N VAL* 3.1 10.7 + - + +
70N GLU* 1.3 75.1 - - - +
72N LEU* 1.3 58.4 + - + +
74N GLU* 3.0 19.2 + - - +
75N TYR* 2.9 72.1 + - + +
124N LEU* 4.5 21.3 - - + -
170N MET* 6.6 0.2 - - - -
171N LEU* 4.6 4.7 - - + -
174N THR* 6.2 3.8 - - + -
66P LYS* 3.9 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 72 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N LEU* 4.1 11.1 - - + +
56N TYR* 4.0 12.6 - - + -
57N HIS* 3.9 34.3 - - + +
60N ILE* 3.9 11.0 - - + -
68N VAL* 2.8 41.9 + - + +
69N HIS 3.6 5.2 - - - +
71N LEU* 1.3 77.5 - - + +
73N GLU* 1.3 58.2 + - - +
75N TYR* 3.2 21.6 + - + +
76N TYR* 2.9 31.3 + - - +
123N ALA* 5.5 1.6 - - + -
124N LEU* 4.4 17.5 - - + -
127N VAL* 4.5 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 73 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84M ASP* 5.3 1.6 - - - +
57N HIS* 3.9 17.0 + - + -
69N HIS* 3.3 4.3 + - - +
70N GLU* 3.1 19.7 + - - +
72N LEU* 1.3 76.5 - - - +
74N GLU* 1.3 67.1 + - - +
76N TYR* 3.2 38.0 + - + +
77N VAL* 2.9 36.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70N GLU* 3.0 21.6 + - - +
71N LEU* 3.3 17.1 - - + +
73N GLU* 1.3 77.3 - - + +
75N TYR* 1.3 63.4 + - + +
77N VAL* 3.3 7.2 + - - +
78N SER* 2.9 30.6 + - - -
66P LYS* 3.7 29.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 75 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N LEU* 3.8 15.7 - - + -
71N LEU* 2.9 50.8 + - + +
72N LEU* 3.3 24.9 - - + +
73N GLU 3.1 0.2 - - - -
74N GLU* 1.3 81.6 - - + +
76N TYR* 1.3 57.0 + - - +
78N SER* 3.1 8.8 + - - -
79N VAL* 2.7 31.5 + - - +
124N LEU* 5.2 0.2 - - + -
127N VAL* 4.2 14.6 - - + -
131N PHE* 3.8 31.1 - + + -
167N ALA* 4.0 24.1 + - + +
170N MET* 5.2 4.0 - - - +
171N LEU* 3.6 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 76 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80M THR* 6.5 0.9 - - + -
84M ASP* 3.7 12.3 + - - +
50N TYR* 3.3 33.1 - + + +
53N LEU* 3.6 28.2 - - + +
54N HIS* 3.4 45.8 + + - -
57N HIS* 3.7 27.6 + + - -
72N LEU 2.9 22.8 + - - -
73N GLU* 3.5 42.2 + - + +
75N TYR* 1.3 74.5 - - - +
77N VAL* 1.3 72.0 - - + +
79N VAL* 4.0 2.0 - - - -
80N THR* 2.9 22.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73N GLU* 2.9 29.2 + - + +
74N GLU* 3.5 7.4 - - - +
76N TYR* 1.3 90.8 - - + +
78N SER* 1.3 65.3 + - - +
80N THR* 3.3 12.8 - - + +
81N GLU* 3.1 23.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 78 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74N GLU 2.9 16.9 + - - -
75N TYR* 3.4 9.2 - - - -
77N VAL* 1.3 80.8 - - - +
79N VAL* 1.3 61.8 + - - +
81N GLU* 3.2 17.1 + - - +
82N ALA* 3.1 22.0 + - - +
163N THR* 4.5 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 79 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46N LEU* 3.4 41.6 - - + +
49N LEU* 3.9 17.3 - - + -
50N TYR* 3.9 17.5 - - + +
53N LEU* 3.7 15.9 - - + -
75N TYR 2.7 21.8 + - - +
76N TYR* 3.8 6.3 - - - +
78N SER* 1.3 75.5 - - - +
80N THR* 1.3 58.8 + - - +
82N ALA* 3.2 7.6 + - - +
83N PHE* 2.8 26.0 + - - +
131N PHE* 4.4 9.2 - - + -
134N LEU* 5.6 0.7 - - + -
164N LEU* 6.4 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 80 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M TYR* 2.7 29.4 + - - +
54M HIS* 4.7 1.7 + - - -
76M TYR* 6.4 0.9 - - + -
50N TYR* 3.6 18.0 - - + -
76N TYR 2.9 16.9 + - - +
77N VAL* 3.3 18.2 - - + +
79N VAL* 1.3 79.7 - - - +
81N GLU* 1.3 62.0 + - - +
83N PHE* 3.2 16.4 - - - +
84N ASP* 3.0 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 81 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77N VAL* 3.1 16.8 + - + +
78N SER* 3.2 18.7 + - - +
79N VAL 3.1 0.2 - - - -
80N THR* 1.3 78.0 - - + +
82N ALA* 1.3 65.7 + - - +
84N ASP* 3.2 6.4 + - - +
85N THR* 3.0 36.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46N LEU* 4.0 16.4 - - + -
78N SER 3.1 8.7 + - - +
79N VAL* 3.6 9.0 - - - +
81N GLU* 1.3 76.9 + - - +
83N PHE* 1.3 66.7 + - - +
85N THR* 4.0 7.4 - - - -
86N ILE* 2.9 30.1 + - - +
160N ILE* 3.7 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 83 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M TYR* 5.3 4.9 - + - -
51M ILE* 5.0 7.2 - - + -
54M HIS* 3.5 41.1 - + + -
58M TRP* 3.5 10.8 - + - -
43N VAL* 3.4 43.2 - - + +
46N LEU* 3.9 15.0 - - + +
47N GLY* 3.7 21.8 - - - -
50N TYR* 6.3 1.3 - - + -
79N VAL* 2.8 15.5 + - + +
80N THR* 3.2 20.9 - - - +
82N ALA* 1.3 76.9 - - - +
84N ASP* 1.3 57.7 + - - +
86N ILE* 4.2 1.0 - - - +
87N ALA* 3.1 29.8 + - - +
104N TYR* 3.3 26.5 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54M HIS* 3.8 8.3 - - + +
57M HIS* 3.7 1.9 - - - -
58M TRP* 3.3 17.0 + - - -
73M GLU* 5.1 2.3 - - - +
76M TYR* 3.5 17.7 + - - +
80N THR 3.0 12.8 + - - +
81N GLU* 3.7 5.8 - - - +
82N ALA 3.2 0.2 - - - -
83N PHE* 1.3 83.6 - - + +
85N THR* 1.3 66.3 + - + +
87N ALA* 3.4 3.9 + - - +
88N GLU* 2.7 39.1 + - - +
614N FE 2.2 30.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 85 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81N GLU* 3.0 25.9 + - + +
82N ALA* 3.5 10.8 + - - -
84N ASP* 1.3 78.7 - - + +
86N ILE* 1.3 60.9 + - - +
88N GLU* 3.4 9.7 + - - +
89N ARG* 3.0 26.7 + - - +
156N ILE* 4.0 23.4 - - - +
160N ILE* 4.3 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 86 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N LEU* 3.8 28.5 - - + +
42N HIS* 4.0 7.2 - - + -
43N VAL* 3.8 18.2 - - + -
46N LEU* 3.9 8.5 - - + -
82N ALA 2.9 17.5 + - - +
83N PHE 4.2 2.0 - - - +
85N THR* 1.3 76.1 + - - +
87N ALA* 1.3 67.9 + - - +
89N ARG* 3.1 8.2 + - - +
90N LEU* 3.0 20.6 + - - +
138N PHE* 3.3 37.5 - - + -
156N ILE* 4.4 9.0 - - + -
157N ILE* 4.8 7.4 - - + -
160N ILE* 3.5 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 87 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M TRP* 3.3 42.8 - - + -
43N VAL* 3.8 16.6 - - + +
83N PHE 3.1 14.9 + - - +
84N ASP 3.7 1.8 - - - +
85N THR 3.4 0.2 - - - -
86N ILE* 1.3 77.0 - - - +
88N GLU* 1.3 57.4 + - - +
90N LEU* 3.1 9.6 - - - +
91N LEU* 3.0 31.0 + - - +
97N ALA* 4.1 9.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 88 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M HIS* 3.5 8.8 + - - -
58M TRP* 3.9 11.5 - - + +
69M HIS* 3.5 16.5 + - - -
84N ASP* 2.7 27.6 + - - +
85N THR* 3.8 8.2 - - - +
86N ILE 3.2 0.2 - - - -
87N ALA* 1.3 73.7 - - - +
89N ARG* 1.3 65.7 + - - +
91N LEU* 3.2 14.3 + - + +
92N GLN* 3.0 35.9 + - - +
614N FE 2.3 29.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 89 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39N LEU* 4.1 13.5 - - + -
85N THR 3.0 14.1 + - - +
86N ILE* 3.1 11.2 + - - +
88N GLU* 1.3 73.4 - - - +
90N LEU* 1.3 66.3 + - - +
92N GLN* 2.8 40.4 + - - +
93N LEU* 2.9 40.0 + - + +
150N ASP* 2.8 28.7 + - - -
152N VAL* 3.4 26.6 - - - +
153N THR* 2.9 24.2 + - + +
156N ILE* 4.0 25.1 - - + -
157N ILE* 6.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 90 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N CYS* 3.5 47.8 - - + +
39N LEU* 3.7 16.1 - - + +
40N ARG* 3.7 35.0 - - + +
43N VAL* 4.5 4.9 - - + -
86N ILE 3.0 11.0 + - - +
87N ALA 3.1 9.6 - - - +
89N ARG* 1.3 78.4 - - - +
91N LEU* 1.3 61.4 + - - +
93N LEU* 3.1 11.3 + - - +
95N ALA* 3.1 35.6 + - + +
96N GLN 4.1 3.8 - - - +
97N ALA* 3.9 10.5 - - + -
98N PRO* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 91 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58M TRP* 3.4 46.7 - - + +
59M HIS* 3.7 31.9 - - + +
69M HIS* 6.2 1.3 - - + -
87N ALA 3.0 17.8 + - - +
88N GLU* 3.4 16.4 - - + +
90N LEU* 1.3 77.2 - - - +
92N GLN* 1.3 62.1 + - + +
94N GLY* 3.0 14.9 + - - -
95N ALA 3.3 18.1 - - - +
96N GLN* 5.7 0.2 - - + -
97N ALA* 3.9 7.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88N GLU* 3.0 26.3 + - + +
89N ARG* 2.8 44.0 + - - +
91N LEU* 1.3 76.6 - - + +
93N LEU* 1.3 59.8 + - - +
94N GLY* 3.0 4.9 + - - -
152N VAL* 4.6 5.5 - - - +
156N ILE* 5.4 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N ILE* 4.3 30.5 - - + +
35N ILE* 4.1 11.0 - - + -
36N CYS* 3.8 22.9 - - - -
39N LEU* 3.8 29.6 - - + -
89N ARG* 2.9 39.9 + - - +
90N LEU 3.1 8.6 + - - +
92N GLN* 1.3 74.9 - - - +
94N GLY* 1.3 58.7 + - - +
95N ALA 3.4 1.6 + - - -
150N ASP* 4.0 7.4 - - - +
153N THR* 4.1 12.3 - - - +
----------------------------------------------------------
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