Contacts of the helix formed by residues 42 - 71 (chain M) 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 VAL 42 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M ARG* 3.6 2.8 + - - +
40M LYS* 4.0 5.1 - - - +
41M TYR* 1.3 81.5 - - - +
43M ASP* 1.3 66.9 + - - +
44M GLU* 3.8 10.5 - - + +
45M SER* 3.0 25.2 + - - +
46M GLU* 3.1 10.4 + - - +
157M ASN* 3.5 42.2 - - + +
159M ASP* 4.9 0.4 + - - -
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Residues in contact with ASP 43 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M ARG* 3.0 26.0 + - - +
42M VAL* 1.3 72.9 - - - +
44M GLU* 1.3 57.5 + - - +
46M GLU* 3.3 13.3 + - - +
47M SER* 2.8 36.5 + - - +
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Residues in contact with GLU 44 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42M VAL* 3.1 6.0 + - + +
43M ASP* 1.3 79.5 - - - +
45M SER* 1.3 56.7 + - - +
47M SER* 3.5 6.2 + - - -
48M ALA* 3.0 28.1 + - - +
153M VAL* 3.7 21.6 - - + +
156M LYS* 2.9 36.0 + - - +
157M ASN* 2.9 28.2 + - - +
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Residues in contact with SER 45 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41M TYR* 4.0 24.5 - - - -
42M VAL* 3.0 23.2 + - - +
44M GLU* 1.3 76.1 - - - +
46M GLU* 1.3 65.6 + - - +
48M ALA* 3.2 2.8 + - - +
49M VAL* 2.9 28.9 + - - +
153M VAL* 3.9 12.4 + - - +
157M ASN* 3.9 13.5 + - - +
159M ASP* 4.1 9.4 + - - +
162M LEU* 4.0 14.1 - - - +
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Residues in contact with GLU 46 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38M ARG* 3.7 15.5 + - - +
41M TYR* 3.8 20.5 - - + -
42M VAL 3.1 11.6 + - - +
43M ASP* 3.5 26.2 - - - +
45M SER* 1.3 78.4 - - - +
47M SER* 1.3 62.3 + - - +
49M VAL 3.4 0.2 + - - -
50M ASN* 3.1 13.6 + - - +
102M GLN* 3.1 37.4 + - - +
107M GLY* 3.4 6.7 - - - -
108M LYS* 2.7 38.0 + - - +
110M LYS* 5.5 2.4 + - - -
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Residues in contact with SER 47 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43M ASP* 2.8 24.4 + - - +
44M GLU* 3.7 7.4 - - - -
46M GLU* 1.3 76.2 + - - +
48M ALA* 1.3 57.8 + - - +
50M ASN* 3.1 10.2 + - - +
51M GLU* 2.9 30.4 + - - +
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Residues in contact with ALA 48 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44M GLU 3.0 18.5 + - - +
45M SER 3.2 3.1 + - - +
47M SER* 1.3 76.7 - - - +
49M VAL* 1.3 57.5 + - - +
51M GLU* 3.3 10.5 - - - +
52M GLN* 3.0 27.7 + - - +
149M ASN* 5.8 2.0 - - - +
150M LEU* 3.6 25.1 - - + +
153M VAL* 3.9 24.5 - - + -
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Residues in contact with VAL 49 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41M TYR* 3.3 21.3 - - - +
45M SER 2.9 16.9 + - - +
46M GLU 3.7 4.7 - - - +
48M ALA* 1.3 76.1 - - - +
50M ASN* 1.3 56.5 + - - +
52M GLN* 3.2 5.8 + - - +
53M ILE* 2.9 30.2 + - + +
98M LEU* 3.9 30.9 - - + +
101M TYR* 4.6 4.0 - - + -
102M GLN* 3.7 21.5 - - + +
150M LEU* 4.1 18.6 - - + -
162M LEU* 4.1 19.3 - - + -
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Residues in contact with ASN 50 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46M GLU* 3.1 17.8 + - - +
47M SER* 3.6 10.5 - - - +
49M VAL* 1.3 73.2 - - - +
51M GLU* 1.3 65.4 + - - +
53M ILE* 3.4 14.2 + - - +
54M ASN* 3.2 21.8 + - - +
102M GLN* 3.0 18.7 + - - +
108M LYS 3.1 20.6 + - - -
109M VAL* 3.4 4.5 - - - -
110M LYS* 3.0 49.2 + - + +
112M GLN* 5.6 3.5 - - + +
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Residues in contact with GLU 51 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L PHE* 5.6 4.9 - - - +
47M SER 2.9 14.5 + - - +
48M ALA* 3.3 14.6 - - - +
50M ASN* 1.3 77.0 - - - +
52M GLN* 1.3 57.7 + - - +
54M ASN* 3.2 8.9 + - - +
55M VAL* 3.0 36.4 + - - +
146M LYS* 3.8 25.7 + - - +
149M ASN* 6.4 0.4 - - - -
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Residues in contact with GLN 52 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48M ALA 3.0 16.1 + - - +
49M VAL 3.2 4.4 + - - +
51M GLU* 1.3 73.5 - - - +
53M ILE* 1.3 67.6 + - - +
55M VAL* 3.1 11.6 + - - +
56M GLU* 2.9 54.9 + - - +
98M LEU* 3.6 21.8 - - + -
143M THR* 3.9 10.9 + - - +
146M LYS* 3.3 29.8 - - - +
147M LEU* 3.4 29.5 - - + +
150M LEU* 3.9 16.6 - - + +
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Residues in contact with ILE 53 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49M VAL* 2.9 23.6 + - + +
50M ASN* 3.6 25.4 - - - +
52M GLN* 1.3 77.3 - - - +
54M ASN* 1.3 58.5 + - - +
56M GLU* 3.3 2.4 + - - +
57M TYR* 3.0 29.5 + - + +
95M ALA* 3.9 11.3 - - + +
98M LEU* 3.5 28.7 - - + +
99M MET* 3.8 38.8 - - + +
102M GLN* 4.7 0.4 - - + -
109M VAL* 4.3 9.0 - - + -
110M LYS 5.9 1.6 - - - +
111M LEU* 3.7 29.4 - - + -
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Residues in contact with ASN 54 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L PHE* 3.7 26.9 - - - +
50M ASN 3.2 10.2 + - - +
51M GLU* 3.5 10.1 - - - +
52M GLN 3.2 0.6 - - - -
53M ILE* 1.3 76.8 - - - +
55M VAL* 1.3 60.5 + - - +
57M TYR* 4.4 3.6 - - - -
58M ASN* 2.9 56.4 + - - +
110M LYS 6.1 0.2 - - - +
112M GLN* 3.8 30.2 - - + +
113M SER 3.1 23.1 + - - +
114M ILE* 4.1 5.2 - - - +
61S TYR* 4.1 3.4 + - - -
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Residues in contact with VAL 55 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L PHE* 4.0 34.4 - - + -
51M GLU* 3.0 30.6 + - - +
52M GLN* 3.1 26.9 + - - +
54M ASN* 1.3 76.5 - - - +
56M GLU* 1.3 62.5 + - - +
58M ASN* 3.3 3.6 + - - +
59M VAL* 3.0 28.2 + - + +
143M THR* 4.1 21.3 - - + +
146M LYS* 4.0 30.1 - - + -
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Residues in contact with GLU 56 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52M GLN* 2.9 43.9 + - - +
53M ILE 3.8 3.6 - - - +
55M VAL* 1.3 75.5 - - - +
57M TYR* 1.3 57.7 + - - +
59M VAL* 3.2 4.5 + - - +
60M SER* 2.9 27.5 + - - -
91M GLU* 3.1 16.8 - - - +
94M HIS* 3.8 11.4 - - + +
95M ALA* 3.8 18.4 - - - +
98M LEU* 3.9 18.6 - - + -
143M THR* 3.5 12.8 - - - +
147M LEU* 4.0 9.2 - - - +
170M TYR* 4.3 6.2 - - - -
214M CA 2.4 29.3 - - - -
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Residues in contact with TYR 57 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53M ILE* 3.0 22.6 + - + +
54M ASN* 3.9 5.2 - - - +
56M GLU* 1.3 76.3 - - - +
58M ASN* 1.3 63.0 + - - +
60M SER* 3.2 13.7 + - - -
61M TYR* 3.0 23.6 + + + +
92M ARG* 3.8 21.2 + - + -
95M ALA* 3.7 23.2 - - + +
99M MET* 4.5 7.2 - - - -
111M LEU* 4.7 2.0 - - + -
114M ILE* 3.7 17.7 - - + +
57S TYR* 5.3 13.7 - + - -
60S SER* 4.9 2.9 + - - -
61S TYR* 3.6 42.5 - + - +
64S HIS* 2.6 41.7 + + - +
88S SER* 4.6 1.9 + - - -
114S ILE* 6.3 1.1 - - + -
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Residues in contact with ASN 58 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L PHE* 3.8 28.7 + - + -
17L PRO* 4.0 6.1 - - + +
54M ASN* 2.9 53.5 + - - +
55M VAL 3.7 3.8 - - - +
56M GLU 3.2 0.2 - - - -
57M TYR* 1.3 77.5 - - - +
59M VAL* 1.3 56.2 + - - +
61M TYR* 3.1 3.5 + - - +
62M VAL* 2.9 33.8 + - - +
113M SER 4.0 5.9 + - - -
114M ILE* 3.2 25.6 - - - +
115M VAL* 3.4 22.3 + - - +
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Residues in contact with VAL 59 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15L PHE* 5.2 4.9 - - + -
55M VAL* 3.0 19.9 + - + +
56M GLU* 3.7 2.7 - - - +
58M ASN* 1.3 72.5 - - - +
60M SER* 1.3 66.6 + - - +
62M VAL* 3.3 6.9 + - - +
63M TYR* 2.9 53.8 + - + +
91M GLU* 3.5 19.7 - - - +
139M LEU* 4.5 26.2 - - + +
140M GLU* 4.3 4.5 - - - +
143M THR* 3.5 24.2 - - + +
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Residues in contact with SER 60 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56M GLU 2.9 10.0 + - - -
57M TYR* 3.2 15.9 + - - -
59M VAL* 1.3 76.3 - - - +
61M TYR* 1.3 58.5 + - - +
63M TYR 3.4 0.2 + - - -
64M HIS* 3.0 14.9 + - - +
88M SER* 2.8 45.1 + - - +
91M GLU* 3.5 24.5 - - - +
92M ARG* 3.7 18.8 + - - +
57S TYR* 4.9 2.6 + - - -
92S ARG* 4.5 4.7 + - - -
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Residues in contact with TYR 61 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57M TYR* 3.0 14.2 + + + +
58M ASN* 3.1 8.5 + - - +
60M SER* 1.3 74.7 - - - +
62M VAL* 1.3 65.7 + - + +
64M HIS* 3.1 6.0 + - - +
65M ALA* 3.0 18.5 + - - +
114M ILE* 3.5 26.9 - - + -
115M VAL 3.8 4.5 - - - -
117M PRO* 3.6 32.8 - - + -
54S ASN* 4.1 5.5 + - - -
57S TYR* 3.5 49.7 - + - +
111S LEU* 3.6 21.8 - - + +
112S GLN 2.6 37.4 + - - -
114S ILE* 3.7 18.6 - - + +
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Residues in contact with VAL 62 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17L PRO* 4.2 18.4 - - + -
18L PHE* 3.6 37.0 - - + -
58M ASN* 2.9 21.2 + - - +
59M VAL 3.7 4.7 - - - +
61M TYR* 1.3 76.6 - - + +
63M TYR* 1.3 57.8 + - - +
65M ALA* 3.1 4.9 + - - +
66M MET* 2.9 40.0 + - + +
117M PRO* 4.2 12.6 - - + -
121M PHE* 5.1 1.6 - - + -
139M LEU* 3.4 29.6 - - + -
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Residues in contact with TYR 63 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59M VAL* 2.9 33.6 + - + +
60M SER 3.8 4.0 - - - +
62M VAL* 1.3 77.0 - - - +
64M HIS* 1.3 58.3 + - - +
66M MET* 3.2 10.4 + - + -
67M PHE* 2.9 24.1 + - - +
83M PHE* 5.9 1.6 - + - -
84M PHE* 3.6 43.3 - + - +
87M SER* 3.7 21.1 - - - -
88M SER 3.8 4.7 - - - +
91M GLU* 3.6 21.1 - - + -
136M ALA* 3.7 33.3 + - + +
139M LEU* 4.6 8.8 - - + +
140M GLU* 2.5 42.7 + - - +
181M ILE* 3.9 4.6 - - + +
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Residues in contact with HIS 64 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60M SER 3.0 8.8 + - - +
61M TYR 3.1 9.4 + - - +
63M TYR* 1.3 76.9 - - - +
65M ALA* 1.3 57.2 + - - +
67M PHE* 3.3 16.3 + + + +
68M ALA* 3.0 28.1 + - - +
85M LYS* 5.2 1.8 - - - -
88M SER* 3.5 17.9 - - - +
57S TYR* 2.6 34.7 + + - +
92S ARG* 3.5 25.7 + - + -
96S GLU* 2.7 39.6 + - + +
99S MET* 3.7 30.5 - - + +
111S LEU* 4.1 8.7 - - + -
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Residues in contact with ALA 65 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61M TYR 3.0 12.3 + - - +
62M VAL* 3.1 9.6 + - - +
64M HIS* 1.3 77.4 - - - +
66M MET* 1.3 61.4 + - - +
68M ALA* 3.3 7.0 + - - +
69M TYR* 3.1 21.8 + - - +
117M PRO* 3.9 16.2 - - + -
118M LEU 3.4 25.6 - - - +
119M SER* 4.5 4.4 - - - +
121M PHE* 3.8 6.4 - - + -
111S LEU* 3.7 12.7 - - + +
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Residues in contact with MET 66 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18L PHE* 5.3 1.3 - - + -
62M VAL* 2.9 30.4 + - + +
63M TYR* 3.2 17.7 + - - +
65M ALA* 1.3 74.7 - - - +
67M PHE* 1.3 66.4 + - - +
69M TYR* 3.2 1.7 + - - +
70M PHE* 3.1 31.4 + - + -
84M PHE* 3.6 44.0 - - + -
121M PHE* 3.6 41.7 - - + -
132M ALA* 4.0 9.6 - - + +
135M LEU* 3.9 25.8 - - + -
136M ALA* 4.2 4.9 - - - +
139M LEU* 4.6 4.0 - - + -
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Residues in contact with PHE 67 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M TYR 2.9 13.2 + - - +
64M HIS* 3.3 24.9 + + - +
66M MET* 1.3 77.0 - - - +
68M ALA* 1.3 68.8 + - - +
69M TYR 3.2 0.2 + - - -
70M PHE 3.3 0.7 + - - -
71M ASP* 3.0 47.0 + - + +
81M ALA* 3.4 27.9 - - + +
84M PHE* 3.6 6.8 - - - +
85M LYS* 3.7 45.3 - - + +
96S GLU* 4.5 14.1 - - + -
99S MET* 4.1 17.3 - - + -
100S GLU* 4.0 25.1 - - + -
103S ASN* 5.5 0.2 - - - -
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Residues in contact with ALA 68 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64M HIS 3.0 16.9 + - - +
65M ALA* 3.7 7.4 - - - +
66M MET 3.2 0.4 - - - -
67M PHE* 1.3 82.2 - - + +
69M TYR* 1.3 61.5 + - - +
71M ASP 3.7 0.2 + - - -
72M ARG* 3.6 9.2 + - - +
99S MET* 3.9 9.9 - - + -
103S ASN* 3.0 28.1 + - - +
109S VAL* 3.7 39.2 - - + +
----------------------------------------------------------
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Residues in contact with TYR 69 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65M ALA 3.1 8.3 + - - +
66M MET 3.6 6.5 - - - +
67M PHE 3.2 0.4 - - - -
68M ALA* 1.3 78.1 - - - +
70M PHE* 1.3 80.7 + + - +
71M ASP 3.1 0.4 - - - -
72M ARG* 3.2 61.0 + - - +
75M VAL* 3.6 30.0 - - + +
119M SER 3.7 8.5 + - - +
120M ASP* 4.1 3.6 - - + -
121M PHE* 3.5 42.0 - + + -
122M ASP* 3.4 32.2 + - + +
128M ASP* 3.9 26.1 + - + +
33S GLN* 6.1 0.3 - - - +
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Residues in contact with PHE 70 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66M MET* 3.1 29.8 + - + +
69M TYR* 1.3 96.5 - + - +
71M ASP* 1.3 57.8 + - - +
72M ARG 3.2 2.1 + - - -
75M VAL* 3.6 17.0 - - + -
76M ALA* 3.8 4.9 + - - -
77M LEU* 3.4 62.0 + - + +
78M ARG* 5.2 0.3 - - - -
80M LEU* 3.9 8.3 - - + -
81M ALA* 3.8 15.3 - - - +
84M PHE* 3.7 23.3 - + - -
121M PHE* 4.7 3.1 - - + -
128M ASP* 3.6 20.0 - - + -
129M ALA* 4.1 5.2 - - - -
132M ALA* 3.4 34.3 - - + -
----------------------------------------------------------
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Residues in contact with ASP 71 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C LYS* 3.0 31.5 + - - -
183C GLU* 4.5 2.4 - - - +
67M PHE* 3.0 45.7 + - + +
69M TYR 3.1 0.4 - - - -
70M PHE* 1.3 74.5 - - - +
72M ARG* 1.3 66.1 + - - +
76M ALA* 5.7 0.2 - - - -
81M ALA* 4.2 7.9 - - + +
100S GLU* 4.1 13.0 - - - +
103S ASN* 2.9 33.6 + - - +
----------------------------------------------------------
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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