Contacts of the helix formed by residues 34 - 64 (chain D) in PDB entry 4IA4
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 34 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D GLY 4.0 4.9 + - - +
31D GLU* 2.6 35.4 + - + +
32D LEU 3.6 8.1 - - - +
33D LYS* 1.3 74.4 - - - +
35D TRP* 1.3 67.0 + - - +
36D SER* 4.5 6.7 - - - +
37D PHE* 3.6 21.4 + - + +
38D TRP* 4.1 5.7 + - - -
118D ARG* 6.2 2.0 - - - +
191D ASP* 5.2 16.2 - - + +
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Residues in contact with TRP 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B VAL 5.4 3.4 - - - -
33D LYS 3.6 3.4 + - - -
34D LEU* 1.3 72.4 - - - +
36D SER* 1.3 68.2 + - - +
38D TRP* 3.1 29.3 + + + +
39D ARG* 3.6 42.2 + - + +
42D ILE* 5.6 6.3 - - + -
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Residues in contact with SER 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ALA* 6.1 0.5 - - - +
34D LEU* 3.4 7.7 - - - +
35D TRP* 1.3 78.7 - - - +
37D PHE* 1.3 63.2 + - - +
39D ARG* 2.9 23.0 + - - +
40D ALA* 3.0 13.4 + - - +
118D ARG* 5.9 0.4 - - - -
190D ARG* 4.3 25.0 + - - +
191D ASP* 2.7 40.9 + - - +
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Residues in contact with PHE 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D GLU* 3.8 27.8 - - + +
32D LEU* 4.2 16.6 - - + -
34D LEU* 3.6 19.2 + - + +
35D TRP 3.2 1.0 - - - -
36D SER* 1.3 79.2 - - - +
38D TRP* 1.3 101.1 + + - +
40D ALA* 3.6 7.8 + - - +
41D ALA* 3.5 14.7 + - - +
117D LEU* 4.5 6.1 - - + -
118D ARG* 3.6 58.0 - - + +
121D VAL* 3.4 34.3 - - + -
122D TYR* 5.4 2.5 - + - -
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Residues in contact with TRP 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32D LEU* 3.9 44.0 + - + -
34D LEU 4.1 5.1 + - - -
35D TRP* 3.1 23.4 + + + +
37D PHE* 1.3 110.8 - + - +
39D ARG* 1.3 62.8 + - - +
41D ALA* 3.5 9.8 + - + +
42D ILE* 2.8 35.2 + - + +
121D VAL* 4.0 17.3 - - + -
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Residues in contact with ARG 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B TYR 4.9 2.8 + - - -
263B VAL 3.6 12.5 + - - +
264B LEU* 3.0 66.3 + - + +
265B ARG 3.1 5.0 - - - +
266B ALA* 3.3 32.3 - - - +
35D TRP* 3.6 43.4 + - + +
36D SER* 2.9 12.0 + - - +
38D TRP* 1.3 77.8 - - - +
40D ALA* 1.3 58.8 + - - +
42D ILE* 3.0 12.8 + - + +
43D ALA* 2.9 28.8 + - - +
95D ILE* 4.4 3.8 - - + -
190D ARG* 3.3 25.7 - - - +
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Residues in contact with ALA 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D SER 3.0 11.5 + - - +
37D PHE* 3.7 10.1 - - - +
38D TRP 3.3 0.2 - - - -
39D ARG* 1.3 78.0 - - - +
41D ALA* 1.3 59.3 + - - +
43D ALA 3.9 0.2 - - - -
44D GLU* 3.3 15.2 + - - +
95D ILE* 4.2 10.9 - - - +
96D SER* 3.3 32.0 - - - +
118D ARG* 3.9 13.2 - - - +
122D TYR* 3.2 24.4 - - + +
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Residues in contact with ALA 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D PHE* 3.5 9.2 + - + +
38D TRP* 3.5 16.0 + - + +
39D ARG 3.2 0.6 - - - -
40D ALA* 1.3 76.5 - - - +
42D ILE* 1.3 63.0 + - + +
44D GLU* 3.3 3.1 + - - -
45D PHE* 2.9 29.7 + - - +
121D VAL* 4.1 24.7 - - + -
122D TYR* 4.2 9.4 - - + -
125D ALA* 3.6 14.5 - - + +
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Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B TYR* 4.2 20.2 - - + +
263B VAL* 4.3 19.7 - - + +
264B LEU* 5.2 2.5 - - + -
35D TRP* 5.6 7.0 - - + -
38D TRP* 2.8 30.7 - - + +
39D ARG* 3.0 12.7 + - + +
41D ALA* 1.3 79.2 - - + +
43D ALA* 1.3 59.9 + - - +
45D PHE* 3.6 8.0 + - + +
46D ILE* 3.1 27.8 + - + +
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Residues in contact with ALA 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 5.1 2.0 - - - +
259B TYR* 3.5 14.1 + - - +
264B LEU* 5.2 3.3 - - + +
39D ARG 2.9 14.5 + - - +
40D ALA 3.9 5.4 - - - +
42D ILE* 1.3 74.3 - - - +
44D GLU* 1.3 56.1 + - - +
45D PHE 3.1 0.3 + - - -
46D ILE* 3.1 2.1 + - - +
47D ALA* 2.6 38.9 + - - +
92D THR* 4.1 20.9 - - + +
95D ILE* 4.1 20.6 - - + -
96D SER* 4.3 6.1 - - - -
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Residues in contact with GLU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40D ALA 3.3 16.8 + - - +
41D ALA* 3.6 5.8 - - - +
43D ALA* 1.3 79.9 - - - +
45D PHE* 1.3 60.3 + - - +
47D ALA* 3.9 3.6 - - - -
48D THR* 2.9 29.8 + - - -
92D THR* 4.3 0.3 + - - -
96D SER* 2.7 21.8 + - - +
98D GLY 3.6 0.9 - - - -
99D HIS* 2.7 31.9 + - - +
100D ILE* 2.7 31.4 + - - +
122D TYR* 3.8 17.7 - - + -
125D ALA* 4.2 9.5 - - + +
126D GLN* 3.0 23.2 + - + +
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Residues in contact with PHE 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ALA 2.9 17.0 + - - +
42D ILE* 3.7 9.2 - - + +
43D ALA 3.1 0.2 - - - -
44D GLU* 1.3 79.9 - - - +
46D ILE* 1.3 78.4 + - + +
49D LEU* 2.8 49.6 + - + +
125D ALA* 3.4 28.9 - - + +
128D LEU* 3.2 35.9 - - + -
129D GLY* 3.4 15.3 - - - -
132D CYS* 4.5 11.2 - - + -
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Residues in contact with ILE 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B PHE* 4.1 13.9 - - + -
177B TYR* 4.8 3.4 - - + -
259B TYR* 3.5 37.2 - - + +
42D ILE* 3.1 19.7 + - + +
43D ALA 3.1 1.7 + - - +
45D PHE* 1.3 95.8 - - + +
47D ALA* 1.3 67.1 + - - +
49D LEU* 3.1 13.4 + - + +
50D LEU* 2.7 42.7 + - + +
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Residues in contact with ALA 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B TYR* 6.1 1.5 - - - -
43D ALA 2.6 23.4 + - - +
44D GLU 3.9 3.1 - - - +
46D ILE* 1.3 71.9 - - - +
48D THR* 1.3 52.0 + - - +
50D LEU* 2.7 15.5 + - - +
51D PHE* 2.6 32.3 + - - +
88D LEU* 3.8 13.3 - - + +
92D THR* 4.2 12.8 - - + -
100D ILE* 3.4 34.8 - - + -
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Residues in contact with THR 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D GLU 2.9 17.3 + - - -
45D PHE 3.8 2.7 - - - -
47D ALA* 1.3 77.4 - - - +
49D LEU* 1.3 65.7 + - - +
51D PHE* 3.9 2.2 - - + -
52D LEU* 2.9 33.0 + - + +
100D ILE* 3.5 25.8 - - + +
126D GLN* 3.1 43.7 - - + +
129D GLY* 4.0 1.8 - - - -
130D ALA* 3.3 14.8 - - + +
222D ASN* 5.9 0.4 - - - +
224D ALA* 4.8 3.8 - - + -
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Residues in contact with LEU 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ILE* 5.3 3.1 - - + -
45D PHE* 2.8 36.5 + - + +
46D ILE* 3.4 19.5 - - + +
48D THR* 1.3 75.0 - - - +
50D LEU* 1.3 73.2 + - + +
53D TYR* 3.0 20.0 + - + -
129D GLY* 3.1 15.1 + - - +
132D CYS* 3.9 22.2 - - + +
133D GLY* 3.2 26.9 - - - +
136D LEU* 4.4 20.6 - - + -
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Residues in contact with LEU 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B ILE* 3.5 32.3 - - + -
173B PHE* 3.9 20.0 - - + -
174B VAL* 3.5 23.1 - - + -
177B TYR* 4.3 13.0 - - + -
46D ILE* 2.7 34.2 + - + +
47D ALA* 2.7 12.7 + - - +
49D LEU* 1.3 77.5 - - + +
51D PHE* 1.3 62.2 + - - +
53D TYR* 3.1 3.8 + - + +
54D ILE* 3.1 29.0 + - + +
84D MET* 4.2 5.4 - - + -
88D LEU* 4.2 19.1 - - + -
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Residues in contact with PHE 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D ALA 2.6 14.5 + - - +
48D THR* 3.7 3.8 - - + +
50D LEU* 1.3 72.7 - - - +
52D LEU* 1.3 75.1 + - + +
54D ILE* 4.6 0.3 - - - +
55D THR* 2.7 61.5 + - + +
81D PHE* 3.6 32.1 - + + -
84D MET* 4.0 14.8 - - + -
85D ILE* 3.5 27.6 - - + -
88D LEU* 3.2 22.7 - - + +
100D ILE* 3.9 16.6 - - + -
206D VAL* 5.6 1.6 - - + -
210D HIS* 5.8 0.4 - - - -
219D THR* 6.0 0.2 - - + -
222D ASN* 3.7 27.4 - - + -
225D ARG* 4.5 7.6 - - + -
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Residues in contact with LEU 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D THR* 2.9 30.2 + - + +
49D LEU 3.8 2.7 - - - +
51D PHE* 1.3 102.6 - - + +
53D TYR* 1.3 66.3 + - - +
55D THR* 3.5 2.9 - - - +
56D VAL* 3.1 44.5 + - + +
130D ALA* 3.7 26.0 - - + +
133D GLY* 3.9 3.6 - - - +
134D VAL* 3.2 29.4 - - + -
222D ASN* 5.9 0.2 - - - +
225D ARG* 4.1 32.8 - - + +
229D ALA* 5.4 0.2 - - + -
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Residues in contact with TYR 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B ALA* 3.5 22.4 + - - +
170B ILE* 3.2 46.5 - - + +
171B GLY* 5.1 0.9 - - - -
212B ALA* 5.6 1.8 + - + -
213B THR* 4.7 5.5 + - - -
216B ILE* 4.8 4.5 - - - +
49D LEU* 3.0 22.5 + - + +
50D LEU* 3.1 5.4 + - - +
52D LEU* 1.3 76.0 - - - +
54D ILE* 1.3 89.8 + - + +
57D ALA* 2.8 46.3 + - + +
133D GLY* 3.5 14.3 + - - +
136D LEU* 4.0 19.1 - - + -
137D VAL* 3.6 22.9 - - + +
140D PHE* 3.7 21.7 - + - -
141D MET* 5.9 1.1 - - + -
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Residues in contact with ILE 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B GLY* 5.5 2.0 - - - -
174B VAL* 4.5 13.0 - - + -
208B MET* 3.9 17.3 - - + +
209B VAL* 4.1 27.4 - - + +
212B ALA* 3.4 17.5 - - + +
213B THR* 5.3 1.8 - - - +
50D LEU 3.1 14.6 + - - +
53D TYR* 1.3 104.8 - - + +
55D THR* 1.3 66.8 + - - +
58D THR* 3.1 26.5 + - - +
80D ALA* 5.1 4.5 - - + +
84D MET* 3.5 39.5 - - + -
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Residues in contact with THR 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D PHE* 2.7 53.5 + - + +
52D LEU* 3.2 10.7 + - - +
54D ILE* 1.3 75.8 - - - +
56D VAL* 1.3 73.0 + - - +
58D THR* 3.0 15.9 + - - -
59D VAL* 3.0 17.5 + - - +
80D ALA* 3.8 26.3 - - - +
81D PHE* 3.5 31.6 - - + -
84D MET* 4.5 2.0 - - + -
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Residues in contact with VAL 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D LEU* 3.1 41.3 + - + +
53D TYR 4.3 0.4 - - - +
55D THR* 1.3 81.3 + - - +
57D ALA* 1.3 65.9 + - - +
59D VAL* 3.2 10.1 + - + +
60D ILE* 3.2 31.6 + - + +
81D PHE* 5.4 3.8 - - + -
134D VAL* 4.3 16.4 - - + -
137D VAL* 4.3 13.9 - - + -
145D TYR* 4.5 4.9 - - + -
150D GLY 4.4 16.2 - - - +
151D GLY* 4.5 16.8 - - - +
225D ARG* 5.4 3.1 - - - +
229D ALA* 5.7 0.2 - - + -
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ALA* 4.1 20.0 - - + +
215B PRO* 5.8 0.2 - - - +
216B ILE* 5.8 0.4 - - + -
53D TYR* 2.8 36.9 + - + +
54D ILE 3.8 3.1 - - - +
56D VAL* 1.3 74.3 - - - +
58D THR* 1.3 57.4 + - - +
60D ILE* 3.5 3.2 + - - +
61D GLY* 3.0 25.3 + - - -
137D VAL* 3.8 23.7 - - + +
141D MET* 4.3 14.6 - - + +
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Residues in contact with THR 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211B LEU* 3.1 28.2 + - + +
212B ALA* 3.0 24.1 - - - +
215B PRO* 6.3 0.4 - - - -
54D ILE* 3.1 7.1 + - - +
55D THR 3.0 13.0 + - - +
57D ALA* 1.3 75.5 - - - +
59D VAL* 1.3 65.6 + - - +
61D GLY* 3.1 3.5 + - - -
62D HIS* 3.0 21.0 + - - +
72D VAL* 4.5 10.8 - - + +
76D GLY 4.6 0.2 - - - +
77D ILE* 4.0 21.3 - - + +
80D ALA* 3.9 21.1 - - + +
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Residues in contact with VAL 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D THR 3.0 15.0 + - - +
56D VAL* 3.2 13.4 + - + +
58D THR* 1.3 74.8 - - - +
60D ILE* 1.3 68.8 + - + +
62D HIS* 3.1 18.2 - - - +
63D SER* 3.1 18.1 + - - +
77D ILE* 3.7 27.5 - - + +
81D PHE* 4.1 23.8 - - + -
148D PHE 5.6 1.6 - - - +
151D GLY* 4.4 21.5 - - - -
225D ARG* 5.3 3.6 - - - +
----------------------------------------------------------
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Residues in contact with ILE 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56D VAL* 3.2 16.7 + - + +
57D ALA 3.7 7.2 - - - +
59D VAL* 1.3 75.6 - - + +
61D GLY* 1.3 64.9 + - - +
62D HIS 2.8 6.5 + - - -
63D SER* 2.9 13.4 + - - +
64D LYS* 3.0 14.3 + - + +
137D VAL* 4.9 2.9 - - + -
141D MET* 3.6 26.9 - - + -
144D PRO* 4.0 29.4 - - + +
145D TYR* 3.9 28.9 - - + +
148D PHE* 3.4 28.5 - - + +
150D GLY* 4.1 5.6 - - - +
151D GLY 4.2 7.4 - - - +
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Residues in contact with GLY 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B PRO* 4.1 29.5 - - - +
57D ALA 3.0 15.1 + - - -
58D THR* 3.1 4.9 + - - -
60D ILE* 1.3 76.1 - - - +
62D HIS* 1.3 61.6 + - - +
64D LYS* 3.5 22.9 + - - +
65D GLU* 4.0 10.9 + - - +
71D SER* 4.4 3.4 - - - -
141D MET* 5.0 2.9 - - - -
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Residues in contact with HIS 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A CYS 5.4 5.4 - - - -
70A GLY* 5.8 2.4 - - - -
58D THR 3.0 10.3 + - - +
59D VAL 3.1 10.3 - - - +
60D ILE 2.8 1.0 + - - -
61D GLY* 1.3 79.0 - - - +
63D SER* 1.3 64.4 + - - +
65D GLU* 2.8 31.5 + - + +
71D SER* 2.8 33.8 + - - +
72D VAL* 5.1 4.9 - - + -
73D GLY* 4.2 15.0 - - - +
74D LEU* 3.1 33.7 - - + +
77D ILE* 3.8 20.4 - - + -
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Residues in contact with SER 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D VAL* 3.1 18.4 + - - +
60D ILE* 2.9 7.9 + - - -
62D HIS* 1.3 87.2 - - - +
64D LYS* 1.3 60.4 + - - -
65D GLU 3.1 7.0 + - - +
148D PHE* 3.5 48.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B LEU 5.4 3.8 + - - -
159B TYR* 3.5 36.2 + - - +
215B PRO* 5.1 8.4 + - + +
60D ILE* 3.0 18.1 + - + +
61D GLY* 3.5 19.7 - - - +
63D SER* 1.3 74.8 - - - +
65D GLU* 1.3 71.9 + - - +
66D THR* 3.3 11.3 + - - +
141D MET* 5.2 0.2 - - - -
144D PRO* 3.9 35.0 - - + -
148D PHE* 3.7 14.8 - - + -
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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