Contacts of the helix formed by residues 23 - 52 (chain A) in PDB entry 4IKV
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 LYS 23 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 3.8 16.8 + - + +
16A ARG 3.1 18.5 + - - +
17A GLY* 3.7 24.7 - - - +
18A PHE* 4.3 5.8 - - + -
22A PRO* 1.3 72.1 - - - +
24A GLY* 1.3 57.7 + - - +
26A PHE* 2.9 31.9 + - + +
27A THR 3.4 2.4 + - - -
209A LYS* 3.1 24.6 - - - +
210A ASN* 3.6 34.4 + - + +
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Residues in contact with GLY 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PRO* 3.0 3.4 - - - +
23A LYS* 1.3 75.6 - - - +
25A LEU* 1.3 58.2 + - - +
26A PHE 3.2 0.2 - - - -
27A THR* 3.2 3.8 + - - -
28A LEU* 2.9 34.7 + - - +
146A MET* 3.4 18.2 - - - -
210A ASN* 3.8 20.0 + - - +
211A LEU* 3.7 14.8 - - - -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 3.8 16.8 - - + -
21A HIS* 3.6 30.7 - - + +
22A PRO 2.9 15.3 + - - +
24A GLY* 1.3 73.4 - - - +
26A PHE* 1.3 60.7 + - - +
28A LEU* 4.4 1.3 - - + +
29A PHE* 2.8 35.3 + - + +
143A VAL* 4.5 6.5 - - + -
146A MET* 3.5 21.8 - - + -
147A TYR* 3.6 10.1 - - - +
157A GLY* 3.7 27.1 - - - +
160A ILE* 4.2 13.2 - - + -
161A PHE* 4.1 22.2 - - + +
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Residues in contact with PHE 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A GLY 5.7 0.2 - - - +
18A PHE* 3.5 37.8 - + + -
23A LYS* 2.9 16.8 + - + +
25A LEU* 1.3 78.0 - - - +
27A THR* 1.3 71.6 + - - +
29A PHE* 3.7 0.2 - - - +
30A PHE* 3.0 62.7 + + - +
202A VAL* 3.8 26.9 - - + -
206A THR* 5.2 6.5 - - + -
210A ASN* 4.6 6.5 - - - -
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Residues in contact with THR 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS 3.4 0.4 + - - -
24A GLY* 3.2 12.2 + - - -
26A PHE* 1.3 84.3 - - - +
28A LEU* 1.3 57.8 + - - +
30A PHE* 4.0 1.6 - - - +
31A THR* 2.8 33.1 + - - -
202A VAL* 4.2 5.4 - - - +
203A PHE* 4.1 26.0 - - + +
206A THR* 2.8 28.3 + - - +
207A ARG 4.7 1.6 - - - +
210A ASN* 2.9 24.3 + - - +
211A LEU* 4.0 22.4 - - + -
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLY 2.9 22.6 + - - +
25A LEU* 4.2 3.6 - - - +
27A THR* 1.3 70.9 - - - +
29A PHE* 1.3 67.6 + - - +
31A THR* 3.8 3.5 - - - +
32A GLU* 3.0 26.9 + - - +
139A VAL* 4.4 14.0 - - + +
142A ILE* 3.8 21.3 - - + -
143A VAL* 3.5 39.5 - - + +
146A MET* 4.0 4.7 - - + -
161A PHE* 3.4 20.0 - - + -
203A PHE* 4.3 15.9 - - + -
211A LEU* 3.8 29.8 - - + -
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 4.5 13.0 - + + -
25A LEU* 2.8 25.7 + - + +
26A PHE 3.7 2.9 - - - +
28A LEU* 1.3 74.4 - - - +
30A PHE* 1.3 87.7 + + - +
32A GLU* 3.7 1.9 - - - +
33A PHE* 2.8 41.3 + + + +
160A ILE* 3.3 40.2 - - + -
161A PHE* 4.1 18.2 - - + +
163A MET* 4.4 7.0 - - + -
164A GLY* 3.6 24.5 - - - -
167A LEU* 5.4 7.6 - - + -
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Residues in contact with PHE 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A PHE* 4.7 8.7 - + - -
26A PHE* 3.0 56.9 + + - +
27A THR 4.3 1.3 - - - +
29A PHE* 1.3 99.2 - + + +
31A THR* 1.3 65.2 + - - +
33A PHE* 4.2 14.1 - + - -
34A TRP* 3.0 56.9 + + + -
199A GLY* 5.0 0.9 - - - -
202A VAL* 4.7 16.6 - - + -
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Residues in contact with THR 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR 2.8 21.4 + - - -
28A LEU* 3.8 6.5 - - - -
29A PHE 3.3 0.2 - - - -
30A PHE* 1.3 76.5 - - - +
32A GLU* 1.3 59.4 - - - +
34A TRP* 4.0 1.4 - - - +
35A GLU* 3.0 27.9 + - - +
98A VAL* 4.3 24.2 - - + -
135A LEU* 4.7 10.5 - - + -
139A VAL* 5.2 6.7 - - + -
196A MET* 4.7 3.7 - - + +
199A GLY* 3.7 20.1 + - - +
200A LEU* 5.8 0.7 - - + -
202A VAL* 5.0 0.9 - - - +
203A PHE* 3.5 36.0 + - + +
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A LEU 3.0 17.8 + - - +
29A PHE 3.8 1.8 - - - +
31A THR* 1.3 76.0 - - - +
33A PHE* 1.3 60.9 + - - +
35A GLU* 3.3 13.5 + - - +
36A ARG* 2.9 57.8 + - + +
135A LEU* 4.2 5.0 - - - +
136A LYS* 5.6 5.0 - - - +
139A VAL* 3.6 21.4 - - + +
161A PHE* 3.5 40.7 - - + +
164A GLY 5.2 0.4 - - - -
165A ILE* 3.4 22.8 - - + +
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Residues in contact with PHE 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A PHE* 2.8 36.4 + + + +
30A PHE* 3.9 15.3 - + - +
32A GLU* 1.3 74.9 - - - +
34A TRP* 1.3 99.7 + + - +
36A ARG* 3.7 1.6 - - - +
37A PHE* 2.8 48.8 + + + +
164A GLY* 3.7 26.7 - - - +
167A LEU* 3.5 30.7 - - + -
168A GLY* 3.7 14.6 - - - -
171A LEU* 4.2 12.1 - - + -
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Residues in contact with TRP 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A PHE* 3.0 47.9 + + + +
33A PHE* 1.3 99.1 - + - +
35A GLU* 1.3 66.8 + - - +
37A PHE* 3.6 33.6 - + - +
38A SER* 3.0 27.5 + - - -
195A GLY* 3.2 40.2 - - - +
196A MET* 4.8 1.3 - - - -
198A LEU* 3.7 27.9 - - + +
199A GLY* 3.8 22.7 - - - -
202A VAL* 5.5 3.3 - - + +
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A THR 3.0 18.3 + - - +
32A GLU* 3.6 16.9 - - - +
34A TRP* 1.3 77.6 - - - +
36A ARG* 1.3 99.0 + - - +
38A SER* 3.4 2.0 + - - -
39A TYR* 3.0 31.5 + - - +
105A ILE* 3.9 27.4 - - + +
109A HIS* 5.5 0.2 + - - -
132A THR* 3.9 13.8 + - - +
135A LEU* 4.0 20.5 - - + +
136A LYS* 5.4 3.4 - - - +
196A MET* 3.7 22.1 - - + +
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Residues in contact with ARG 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLU* 2.9 40.9 + - - +
33A PHE 3.8 3.4 - - - +
35A GLU* 1.3 106.8 + - - +
37A PHE* 1.3 58.6 + - - +
39A TYR* 3.2 27.5 + - - -
40A TYR* 2.8 78.2 + - + -
132A THR* 4.0 9.3 - - - +
136A LYS* 3.5 36.5 - - - +
164A GLY 4.5 1.8 - - - +
165A ILE* 4.0 32.0 - - - +
168A GLY* 4.6 1.1 - - - -
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Residues in contact with PHE 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 2.8 40.7 + + + +
34A TRP* 3.6 35.7 - + + +
35A GLU 3.4 0.2 - - - -
36A ARG* 1.3 72.0 - - - +
38A SER* 1.3 66.1 + - - +
41A GLY* 2.8 28.1 + - - -
168A GLY* 3.9 10.0 - - - -
171A LEU* 4.1 9.2 - - + -
172A ALA* 3.0 38.3 - - + +
175A VAL* 3.9 31.9 - - + -
176A VAL* 3.8 21.5 - - + -
191A LEU* 4.4 13.0 - - + -
195A GLY* 4.7 0.7 - - - -
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Residues in contact with SER 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A TRP 3.0 14.9 + - - -
35A GLU 3.8 3.6 - - - -
37A PHE* 1.3 79.2 - - - +
39A TYR* 1.3 57.2 + - - +
42A MET* 3.0 31.7 + - - +
109A HIS* 3.3 21.0 - - - -
192A ALA* 2.2 40.2 + - - +
195A GLY* 3.5 4.2 - - - -
196A MET* 3.0 18.9 + - - -
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Residues in contact with TYR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU* 3.0 20.6 + - - +
36A ARG* 3.7 37.7 - - - +
38A SER* 1.3 78.0 - - - +
40A TYR* 1.3 74.0 + + - +
42A MET* 3.5 22.4 - - + +
43A ARG* 2.9 70.2 + - + +
73A TYR* 4.2 22.0 - + - -
74A GLY* 4.5 6.9 - - - -
77A VAL* 4.5 13.8 - - + +
105A ILE* 6.4 1.6 - - + -
109A HIS* 4.3 7.6 + + - +
128A ILE* 4.3 13.5 - - + -
132A THR* 4.8 5.4 - - + -
136A LYS* 5.9 2.2 - - - -
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Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ARG* 2.8 68.7 + - + +
39A TYR* 1.3 86.8 - + - +
41A GLY* 1.3 59.4 + - - +
43A ARG* 3.8 11.6 - - + +
44A ALA* 3.0 30.0 + - - +
165A ILE* 4.3 13.4 - - + +
169A ALA* 3.5 48.5 - - + +
172A ALA* 4.0 7.0 - - + -
173A PRO* 4.5 3.9 - - + +
339A GLN* 5.7 0.3 - - - +
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Residues in contact with GLY 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE 2.8 21.8 + - - -
38A SER 4.0 0.4 - - - -
40A TYR* 1.3 69.8 - - - +
42A MET* 1.3 67.4 + - - +
44A ALA* 3.3 14.4 + - - +
45A ILE* 3.6 5.2 + - - +
172A ALA* 3.3 17.1 - - - +
176A VAL* 3.3 34.8 - - - +
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Residues in contact with MET 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A SER 3.0 20.3 + - - +
39A TYR* 3.5 28.5 - - + +
41A GLY* 1.3 75.4 - - - +
43A ARG* 1.3 61.3 + - + +
45A ILE* 3.1 7.0 + - - +
46A LEU* 2.9 57.7 + - - +
73A TYR* 3.5 30.3 - - + +
109A HIS* 3.6 19.7 - - + +
112A LEU* 4.1 9.0 - - + -
128A ILE* 4.1 10.8 - - + -
176A VAL* 4.3 1.0 - - - +
189A PHE* 4.0 23.5 - - + -
192A ALA* 4.5 4.4 - - + +
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Residues in contact with ARG 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A TYR* 2.9 62.4 + - + +
40A TYR* 3.8 15.5 - - + +
42A MET* 1.3 87.1 - - + +
44A ALA* 1.3 61.7 + - - +
45A ILE 3.2 0.9 + - - -
46A LEU* 3.4 10.5 + - - -
47A VAL* 4.2 3.6 + - - +
70A MET* 3.5 59.3 + - + +
71A SER* 5.7 0.2 - - - +
73A TYR* 3.7 16.9 - - + +
74A GLY* 4.4 5.5 - - - +
310A GLU* 4.8 8.4 + - - -
313A SER* 2.6 35.9 + - - +
314A THR* 4.3 4.6 - - - +
339A GLN* 5.5 1.2 - - - +
448A GLN* 5.2 3.2 + - - -
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Residues in contact with ALA 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TYR 3.0 18.8 + - - +
41A GLY 3.6 7.0 - - - +
42A MET 3.2 0.4 - - - -
43A ARG* 1.3 76.2 - - - +
45A ILE* 1.3 61.0 + - + +
47A VAL* 4.8 2.4 - - - +
48A TYR* 3.5 13.9 - - - -
173A PRO* 4.0 32.1 - - + -
177A GLY* 5.1 0.7 - - - -
317A ALA* 6.0 0.2 - - - +
336A ALA* 3.4 23.4 - - + +
339A GLN* 4.2 19.6 - - + +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLY 3.7 6.1 - - - +
42A MET 3.5 10.5 - - - +
44A ALA* 1.3 81.5 - - - +
46A LEU* 1.3 60.9 + - - +
47A VAL 3.3 2.7 - - - -
48A TYR* 3.2 10.6 + - - +
49A TYR* 2.9 27.5 + - - +
176A VAL* 4.0 9.9 - - + +
177A GLY* 3.7 28.9 - - - +
180A GLY* 4.1 6.7 - - - -
181A MET* 3.8 26.0 - - + -
185A PHE* 3.8 10.9 - - + +
188A GLY* 4.0 28.0 - - - -
189A PHE* 3.7 26.9 - - + +
336A ALA* 4.2 0.4 - - + -
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 2.9 25.3 + - - +
43A ARG* 3.4 4.1 + - + +
45A ILE* 1.3 77.0 - - - +
47A VAL* 1.3 64.1 + - - +
49A TYR* 3.3 10.7 + - + +
50A MET* 3.0 41.6 + - + +
70A MET* 4.0 15.9 - - - -
73A TYR* 3.7 35.7 - - + -
112A LEU* 3.8 28.5 - - + -
121A LEU* 4.1 22.2 - - + -
125A MET* 5.1 1.3 - - + -
189A PHE* 4.0 10.8 - - + -
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ARG 4.2 4.9 + - - +
44A ALA 4.8 0.7 - - - +
46A LEU* 1.3 78.7 - - - +
48A TYR* 1.3 89.5 + - + +
50A MET* 3.3 13.7 + - - +
51A TYR* 3.2 37.1 + - + -
66A ALA* 4.8 4.5 - - + +
67A LEU* 4.0 22.9 - - + -
70A MET* 3.5 38.7 - - + -
313A SER 4.6 1.1 - - - +
314A THR 4.9 2.9 - - - +
317A ALA* 4.0 17.7 - - + -
318A ASN 5.5 0.7 - - - +
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Residues in contact with TYR 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA 3.5 26.9 - - - -
45A ILE* 3.2 4.6 + - - +
47A VAL* 1.3 85.5 - - + +
49A TYR* 1.3 61.2 + - - +
51A TYR* 3.3 20.4 - + - -
52A TYR* 2.8 51.2 + - + +
181A MET* 3.6 29.6 - - + -
185A PHE* 3.9 3.6 - - + -
317A ALA* 2.7 38.8 + - + +
318A ASN 4.6 0.2 - - - -
320A ALA* 4.1 0.2 - - - +
321A ASP* 3.3 20.4 - - + -
335A PRO* 3.4 27.5 + - + +
336A ALA* 3.8 16.8 - - - -
339A GLN* 6.1 0.7 - - + +
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Residues in contact with TYR 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE 2.9 17.4 + - - +
46A LEU* 3.3 13.9 + - + +
48A TYR* 1.3 75.7 - - - +
50A MET* 1.3 58.4 + - - +
57A GLY 3.3 27.8 - - - -
58A GLY* 3.2 4.3 - - - -
59A LEU* 2.7 68.6 + - + +
112A LEU* 4.0 18.6 + - + +
116A GLY 3.6 10.9 + - - -
117A GLY 4.7 2.9 + - - -
120A ALA* 6.0 0.7 - - - +
185A PHE* 3.5 32.9 - + + -
186A HIS* 3.3 28.7 + + - -
189A PHE* 3.6 28.3 - + + -
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Residues in contact with MET 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 3.0 29.7 + - + +
47A VAL* 3.6 4.0 - - - +
48A TYR 3.1 0.4 - - - -
49A TYR* 1.3 78.8 - - + +
51A TYR* 1.3 58.2 + - - +
59A LEU* 3.4 13.3 - - + +
60A GLY 3.2 9.0 + - - -
61A LEU* 2.9 30.3 + - + +
66A ALA* 3.3 39.0 - - + +
69A ILE* 3.8 21.1 - - + -
70A MET* 3.5 33.0 - - + +
121A LEU* 3.7 36.1 - - + -
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Residues in contact with TYR 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 3.2 37.3 + - + -
48A TYR* 3.3 14.1 + + - -
50A MET* 1.3 76.8 - - - +
52A TYR* 1.3 80.1 + + - +
53A GLU* 3.6 1.9 + - - +
60A GLY* 4.3 2.6 - - - -
61A LEU 3.4 22.4 - - - +
63A GLU* 3.6 36.1 - - + -
66A ALA* 3.9 13.5 - - + -
67A LEU* 5.4 0.9 - - + -
318A ASN* 3.2 28.5 + - + -
321A ASP* 2.5 40.9 + - - +
322A LYS* 4.0 8.5 - - + +
----------------------------------------------------------
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Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR* 2.8 42.9 + - + +
50A MET 3.6 0.6 - - - -
51A TYR* 1.3 79.9 - + - +
53A GLU* 1.3 67.5 + - - +
56A LYS* 4.2 25.6 - - + -
58A GLY* 3.4 16.7 - - - +
60A GLY 3.0 21.5 + - - -
181A MET* 3.5 25.8 - - + +
185A PHE* 3.8 17.3 - + + -
321A ASP* 2.6 41.7 + - - -
335A PRO* 4.5 2.4 - - - +
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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