Contacts of the helix formed by residues 30 - 55 (chain A) in PDB entry 5V2C
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 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A TRP* 4.0 32.1 - - + -
21A VAL* 3.7 17.4 + - + +
26A ASN* 4.1 12.4 - - + +
28A LEU 3.4 8.7 + - - +
29A TYR* 1.3 88.8 - - - +
31A GLY* 1.3 73.8 + - - +
34A GLY* 3.2 17.5 + - - -
35A VAL* 4.3 12.6 - - + +
38A ILE* 4.2 24.9 - - + -
129A ARG* 3.7 4.9 - - - +
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Residues in contact with GLY 31 (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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21A VAL* 2.8 38.1 + - - +
22A THR* 4.7 0.2 - - - -
29A TYR* 3.4 10.9 - - - -
30A VAL* 1.3 78.3 - - - +
32A TRP* 1.3 60.1 + - - -
33A PHE 3.4 1.6 - - - -
35A VAL* 3.0 21.3 + - - +
132A GLU* 3.1 16.6 - - - -
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Residues in contact with TRP 32 (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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14A TRP* 4.2 12.6 - + - -
17A PHE* 4.1 18.6 - + - -
18A CYS* 3.6 41.7 - - + -
21A VAL* 3.8 26.5 - - + -
22A THR* 3.3 20.9 - - + +
31A GLY* 1.3 67.5 - - - -
33A PHE* 1.3 71.1 + - + +
35A VAL* 3.1 31.4 + - + +
36A ILE* 3.8 8.0 + - - +
132A GLU* 3.0 18.4 + - - +
136A ARG* 4.0 7.4 - - - +
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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
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32A TRP* 1.3 80.0 - - + +
34A GLY* 1.3 57.1 + - - +
36A ILE* 3.1 6.5 + - - +
37A MET* 2.8 22.6 + - - -
124A SER 5.0 2.0 - - - -
125A CYS* 3.4 46.0 - - - +
128A GLY* 3.2 40.6 - - - -
129A ARG* 3.5 7.0 - - - +
131A TRP* 4.1 18.2 - + - -
132A GLU* 3.2 20.7 + - + +
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Residues in contact with GLY 34 (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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30A VAL* 3.2 24.9 + - - -
31A GLY 3.0 4.6 + - - -
33A PHE* 1.3 76.0 - - - +
35A VAL* 1.3 58.9 + - - +
37A MET* 3.6 13.2 - - - -
38A ILE* 2.9 42.2 + - - +
129A ARG* 4.3 9.0 - - - +
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Residues in contact with VAL 35 (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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17A PHE* 5.1 7.2 - - + -
21A VAL* 4.1 14.1 - - + -
30A VAL* 4.3 7.9 - - + -
31A GLY 3.0 16.0 + - - +
32A TRP* 3.1 36.3 + - + +
34A GLY* 1.3 76.9 - - - +
36A ILE* 1.3 66.2 + - + +
38A ILE* 5.4 0.4 - - - -
39A PRO* 3.2 22.3 - - - +
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Residues in contact with ILE 36 (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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32A TRP 4.2 9.4 - - - +
33A PHE* 3.1 7.9 + - - +
35A VAL* 1.3 87.6 - - + +
37A MET* 1.3 64.5 + - - +
38A ILE 3.3 0.4 - - - -
39A PRO* 3.4 3.3 - - - +
40A THR* 2.8 40.8 + - + +
121A LEU* 5.2 9.4 - - + +
125A CYS* 3.6 23.1 - - - -
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Residues in contact with MET 37 (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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33A PHE 2.8 17.6 + - - +
34A GLY* 3.2 4.9 + - - +
36A ILE* 1.3 78.9 - - - +
38A ILE* 1.3 78.4 + - + +
40A THR* 3.2 5.2 + - - -
41A LEU* 2.8 44.2 + - + +
122A GLY* 3.4 16.8 - - - +
125A CYS* 3.8 11.6 - - + +
126A TYR* 3.7 39.9 - - + -
129A ARG* 3.7 37.0 - - - +
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Residues in contact with ILE 38 (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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29A TYR 5.3 1.8 - - - +
30A VAL* 4.2 30.3 - - + -
34A GLY* 2.9 23.1 + - - +
35A VAL* 5.4 0.9 - - - -
37A MET* 1.3 95.1 - - + +
39A PRO* 1.3 69.2 - - + +
41A LEU* 4.1 1.8 - - - +
42A LEU* 3.1 46.7 + - + +
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Residues in contact with PRO 39 (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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35A VAL* 3.2 25.8 - - - +
36A ILE 3.4 7.6 - - - +
38A ILE* 1.3 99.6 - - + +
40A THR* 1.3 57.9 + - + +
42A LEU* 3.4 7.1 + - + +
43A ALA* 3.0 30.5 + - - +
118A HIS* 5.4 0.2 - - - -
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Residues in contact with THR 40 (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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36A ILE* 2.8 35.9 + - + +
37A MET 3.2 4.3 + - - -
39A PRO* 1.3 79.3 - - + +
41A LEU* 1.3 60.2 + - - +
43A ALA 3.4 0.7 + - - -
44A ALA* 3.0 24.1 + - - +
118A HIS* 3.3 46.5 - - + +
121A LEU* 4.3 16.6 - - + -
122A GLY* 3.3 17.3 - - - -
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Residues in contact with LEU 41 (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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37A MET* 2.8 50.4 + - + +
38A ILE* 4.3 2.2 - - - +
40A THR* 1.3 77.0 + - - +
42A LEU* 1.3 58.9 + - + +
44A ALA* 3.9 3.5 - - + +
45A THR* 2.7 40.4 + - - +
119A PHE* 4.1 28.0 - - + +
122A GLY* 3.7 24.0 - - - +
123A ALA* 4.1 4.0 - - - +
126A TYR* 5.0 8.7 - - + -
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Residues in contact with LEU 42 (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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38A ILE* 3.1 39.9 + - + +
39A PRO* 3.8 6.1 - - + +
41A LEU* 1.3 76.9 - - + +
43A ALA* 1.3 59.9 + - - +
45A THR* 3.4 7.4 + - + -
46A ILE* 2.9 51.7 + - + +
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Residues in contact with ALA 43 (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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39A PRO 3.0 19.6 + - - +
40A THR 3.8 0.2 - - - +
42A LEU* 1.3 74.7 - - - +
44A ALA* 1.4 63.7 + - - +
46A ILE* 3.9 4.7 - - - +
47A CYS* 2.9 28.2 + - - +
114A LEU* 4.3 6.1 - - + +
118A HIS* 3.8 27.1 - - + +
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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 THR 3.0 17.9 + - - +
41A LEU* 3.9 6.5 - - + +
43A ALA* 1.4 76.7 - - - +
45A THR* 1.3 58.0 + - - +
48A PHE* 2.9 31.3 + - - +
114A LEU* 4.9 0.4 - - - -
115A ILE* 3.7 36.9 - - + +
118A HIS* 3.9 5.8 - - + +
119A PHE* 3.8 20.6 - - + +
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Residues in contact with THR 45 (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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41A LEU* 2.7 26.1 + - - +
42A LEU* 3.7 9.9 - - + -
44A ALA* 1.3 75.5 - - - +
46A ILE* 1.3 64.8 + - + +
48A PHE* 3.3 6.4 + - + +
49A VAL* 2.9 41.7 + - + +
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Residues in contact with ILE 46 (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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42A LEU* 2.9 37.5 + - + +
43A ALA* 4.0 4.3 - - - +
45A THR* 1.3 80.1 - - + +
47A CYS* 1.3 64.2 + - - +
49A VAL* 3.9 4.4 - - - +
50A ILE* 3.1 43.7 + - + +
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Residues in contact with CYS 47 (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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43A ALA 2.9 17.9 + - - +
46A ILE* 1.3 79.2 - - - +
48A PHE* 1.3 56.2 + - - +
50A ILE* 3.8 5.1 - - - +
51A ALA* 2.9 33.2 + - - +
105A TRP* 4.4 12.1 - - - -
111A PRO* 4.1 20.4 - - - -
114A LEU* 3.8 23.8 - - + -
115A ILE* 3.8 20.0 - - + -
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Residues in contact with PHE 48 (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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44A ALA 2.9 20.1 + - - +
45A THR* 3.6 5.8 - - + +
47A CYS* 1.3 75.6 - - - +
49A VAL* 1.3 71.6 + - + +
51A ALA* 3.8 1.0 - - - +
52A PHE* 2.8 59.0 + + + +
82A VAL* 3.6 24.2 - - + -
115A ILE* 3.6 15.6 - - + +
174A LEU* 3.9 34.5 - - + -
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Residues in contact with VAL 49 (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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45A THR* 2.9 33.1 + - + +
46A ILE* 3.9 4.7 - - - +
48A PHE* 1.3 88.6 - - + +
50A ILE* 1.3 66.2 + - + +
52A PHE* 3.8 3.3 - - - +
53A ILE* 3.1 42.8 + - + +
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Residues in contact with ILE 50 (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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46A ILE* 3.1 35.5 + - + +
47A CYS* 4.0 4.9 - - - +
49A VAL* 1.3 80.5 - - + +
51A ALA* 1.3 53.7 + - - +
53A ILE* 3.7 4.5 - - - +
54A ALA* 2.8 43.7 + - + +
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Residues in contact with ALA 51 (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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47A CYS* 2.9 19.8 + - - +
48A PHE* 4.5 0.2 - - - -
50A ILE* 1.3 78.1 - - - +
52A PHE* 1.3 63.7 + - - +
55A ALA* 3.0 42.0 + - + +
70A SER* 3.4 5.5 + - - -
81A ALA 5.1 1.4 - - - +
82A VAL* 3.8 21.5 - - + -
111A PRO* 4.2 21.8 - - + -
115A ILE* 4.6 0.4 - - + -
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Residues in contact with PHE 52 (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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48A PHE* 2.8 55.1 + + + +
49A VAL* 3.8 4.7 - - - +
51A ALA* 1.3 73.1 - - - +
53A ILE* 1.3 61.0 + - + +
70A SER* 3.2 5.9 - - - +
71A LEU* 2.9 52.2 + - + -
77A ILE* 4.0 31.2 - - + -
80A GLY* 3.6 36.3 - - - -
81A ALA* 3.6 16.2 - - - -
82A VAL* 4.0 4.6 - - + +
174A LEU 4.3 4.0 - - - -
175A GLY* 4.9 2.9 - - - -
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Residues in contact with ILE 53 (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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49A VAL* 3.1 35.9 + - + +
50A ILE* 3.8 4.5 - - - +
52A PHE* 1.3 81.7 - - + +
54A ALA* 1.3 60.1 + - + +
70A SER* 3.5 2.3 - - - -
71A LEU* 3.5 21.7 + - + +
72A LEU* 3.0 50.6 + - + +
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Residues in contact with ALA 54 (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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50A ILE* 2.8 27.1 + - + +
53A ILE* 1.3 79.4 - - + +
55A ALA* 1.3 64.6 + - - +
56A PRO* 3.6 3.1 - - - +
70A SER* 3.8 2.2 - - - -
72A LEU* 4.1 19.5 - - + -
73A TYR* 3.4 14.7 + - - -
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Residues in contact with ALA 55 (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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50A ILE 3.9 0.8 + - - -
51A ALA* 3.0 36.9 + - + +
54A ALA* 1.3 75.1 - - - +
56A PRO* 1.3 78.8 - - + +
58A VAL* 5.7 4.0 - - + -
70A SER* 2.6 30.6 + - - +
73A TYR* 3.4 3.2 - - - +
82A VAL* 6.2 1.3 - - + -
106A LEU* 4.8 11.0 - - + -
111A PRO* 5.3 3.6 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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