Contacts of the helix formed by residues 37 - 69 (chain D) in PDB entry 1IB1
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 SER 37 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLU 3.9 1.6 + - - -
36D LEU* 1.3 77.2 - - - +
38D ASN* 1.3 66.0 + - - +
39D GLU* 3.7 9.4 + - - +
40D GLU* 3.1 38.1 + - - +
41D ARG* 2.8 21.1 + - - +
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Residues in contact with ASN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU 5.5 0.2 - - - +
37D SER* 1.3 73.1 - - - +
39D GLU* 1.3 56.2 + - - +
41D ARG* 3.1 41.3 + - - +
42D ASN* 2.9 29.3 + - - +
113D GLU* 4.5 7.1 + - - +
130H PHE* 6.2 4.0 - - + -
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Residues in contact with GLU 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 4.9 7.8 - - + +
11D LYS* 3.2 37.0 + - - +
37D SER* 3.1 9.1 + - - +
38D ASN* 1.3 78.5 - - - +
40D GLU* 1.3 58.3 + - + +
42D ASN* 3.1 8.5 + - - +
43D LEU* 2.9 42.2 + - + +
133H GLN* 3.8 43.4 + - - +
135H LYS* 5.9 0.2 - - - +
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Residues in contact with GLU 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D LYS* 3.7 26.2 + - - +
4D ASN* 5.8 0.7 + - - -
7D VAL* 4.0 26.2 - - + +
26D MET* 3.3 19.3 - - + +
29D VAL* 3.9 12.0 - - - +
35D GLU 4.6 0.3 - - - +
36D LEU* 3.5 29.8 - - + +
37D SER* 3.1 32.4 + - - +
39D GLU* 1.3 77.2 - - + +
41D ARG* 1.3 57.2 + - - +
43D LEU* 3.4 3.7 + - - -
44D LEU* 3.0 26.3 + - - +
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Residues in contact with ARG 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36D LEU* 4.1 11.6 - - + +
37D SER 2.8 13.0 + - - +
38D ASN* 3.1 39.1 + - - +
40D GLU* 1.3 75.9 - - - +
42D ASN* 1.3 63.6 + - - +
44D LEU* 3.2 4.7 + - - +
45D SER* 3.0 22.3 + - - -
113D GLU* 3.6 25.5 + - - -
114D SER* 3.5 34.6 + - - +
117D PHE* 3.6 40.4 - - + +
118D TYR* 3.3 34.7 - - + +
166D ILE* 4.1 9.9 - - - +
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Residues in contact with ASN 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ASN 2.9 13.2 + - - +
39D GLU* 3.5 9.8 - - - +
41D ARG* 1.3 76.9 - - - +
43D LEU* 1.3 65.7 + - - +
45D SER* 3.2 1.2 + - - -
46D VAL* 2.8 37.9 + - - +
117D PHE* 5.2 0.9 - - - -
35H ASN* 3.0 39.3 + - - +
86H VAL* 3.3 23.0 - - + +
87H GLU* 3.2 27.0 + - - +
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL* 3.6 33.0 - - + +
10D ALA* 4.4 2.7 - - + -
11D LYS* 3.8 25.1 - - + -
14D GLU* 4.6 7.4 - - - +
22D MET* 3.7 26.3 - - + +
26D MET* 3.9 21.9 - - + +
39D GLU* 2.9 26.2 + - + +
40D GLU* 3.5 9.6 - - - +
42D ASN* 1.3 88.3 - - - +
44D LEU* 1.3 57.8 + - - +
46D VAL* 4.6 0.7 - - + -
47D ALA* 2.9 31.4 + - - +
35H ASN* 5.6 1.6 - - - +
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Residues in contact with LEU 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26D MET* 3.5 39.2 - - + +
27D LYS 4.3 0.2 - - - +
30D THR* 3.9 7.0 - - - +
36D LEU* 3.8 21.8 - - + -
40D GLU 3.0 16.8 + - - +
41D ARG 3.2 5.4 + - - +
43D LEU* 1.3 76.9 - - - +
45D SER* 1.3 63.9 + - - +
47D ALA* 3.5 1.0 + - - +
48D TYR* 3.2 56.0 + - + +
100D LEU* 4.5 6.5 - - + -
105D LEU* 3.9 23.3 - - + -
118D TYR* 5.0 5.8 - - + -
121D MET* 4.7 12.8 - - + -
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D ARG 3.0 16.9 + - - -
42D ASN 3.5 4.0 - - - -
44D LEU* 1.3 77.7 - - - +
46D VAL* 1.3 57.9 + - - +
48D TYR* 4.0 0.7 - - - +
49D LYS* 2.8 36.3 + - - +
117D PHE* 3.7 17.9 - - - -
121D MET* 4.1 17.1 - - - +
125D TYR* 4.4 1.6 + - - -
87H GLU* 2.7 33.2 + - - -
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Residues in contact with VAL 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLU* 4.0 21.1 - - - +
19D TYR* 4.7 2.5 - - + -
22D MET* 4.1 11.4 - - + -
42D ASN* 2.8 26.6 + - - +
43D LEU* 4.0 4.0 - - - +
45D SER* 1.3 74.5 - - - +
47D ALA* 1.3 66.3 + - - +
50D ASN* 2.9 43.1 + - - +
34H ALA* 3.9 24.2 - - + +
35H ASN* 3.3 34.3 - - + +
87H GLU* 4.4 3.1 - - + -
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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
----------------------------------------------------------
19D TYR* 4.0 4.1 - - - +
22D MET* 3.6 22.0 - - + +
23D ALA* 3.6 33.7 - - - +
26D MET* 4.8 0.2 - - + -
43D LEU 2.9 19.8 + - - +
44D LEU* 3.8 6.3 - - - +
46D VAL* 1.3 78.7 - - - +
48D TYR* 1.3 58.1 + - + +
50D ASN* 3.3 2.9 + - - +
51D VAL* 2.9 33.3 + - - +
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Residues in contact with TYR 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ALA* 4.1 27.7 + - + +
27D LYS* 3.4 31.2 - - - +
44D LEU* 3.2 47.2 + - + +
45D SER 4.2 0.9 - - - +
47D ALA* 1.3 77.7 - - + +
49D LYS* 1.3 64.8 + - - +
50D ASN 3.0 1.6 - - - -
51D VAL* 3.8 6.0 - - + +
52D VAL* 2.9 29.3 + - - +
93D ILE* 4.0 20.4 - - + -
96D ASP* 3.5 13.9 + - + -
97D VAL* 3.5 29.2 - - + -
100D LEU* 3.9 13.9 - - + +
121D MET* 4.7 4.5 - - + -
125D TYR* 3.3 17.5 - - + +
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Residues in contact with LYS 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45D SER* 2.8 27.2 + - - +
46D VAL 4.0 0.7 - - - +
48D TYR* 1.3 71.8 - - - +
50D ASN* 1.3 58.0 + - - +
52D VAL* 3.6 3.0 - - + +
53D GLY* 3.0 25.5 + - - -
56D ARG* 5.5 1.7 + - - +
120D LYS* 4.6 1.8 - - - +
124D ASP* 3.8 16.3 + - - +
125D TYR* 3.3 12.0 + - + +
128D TYR* 3.1 31.0 + - + +
173D ASN* 4.3 0.2 - - - +
31H TPO 3.6 12.2 + - - +
32H LEU* 3.2 41.2 + - - +
33H PRO* 4.3 4.4 + - + -
34H ALA* 3.6 27.8 - - + +
87H GLU* 4.9 4.4 + - - -
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Residues in contact with ASN 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D TYR* 3.5 54.3 + - + -
46D VAL* 2.9 34.8 + - - +
47D ALA 3.5 0.7 - - - +
48D TYR 3.0 0.4 - - - -
49D LYS* 1.3 78.5 - - - +
51D VAL* 1.3 65.9 + - - +
53D GLY* 3.3 1.1 + - - -
54D ALA* 3.1 24.6 + - - +
34H ALA* 4.0 14.8 + - - +
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D TYR* 3.2 37.9 - - + +
20D ASP* 3.6 24.7 - - - +
23D ALA* 4.0 9.4 - - + -
47D ALA 2.9 16.5 + - - +
48D TYR* 3.8 10.3 - - + +
50D ASN* 1.3 77.5 - - - +
52D VAL* 1.3 60.5 + - - +
54D ALA* 3.7 2.9 - - - +
55D ARG* 3.0 32.3 + - - +
93D ILE* 3.5 31.0 - - + -
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D TYR 2.9 18.8 + - - +
49D LYS* 3.6 8.1 - - + +
51D VAL* 1.3 73.1 - - - +
53D GLY* 1.3 72.8 + - - +
54D ALA 3.1 2.2 - - - -
55D ARG* 3.0 4.0 + - - +
56D ARG* 2.9 34.9 + - - +
90D LEU* 3.4 23.8 - - + -
93D ILE* 4.0 24.9 - - + -
94D CYS* 4.4 10.8 - - - -
125D TYR* 4.1 7.6 - - + +
128D TYR* 4.0 34.3 - - + -
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Residues in contact with GLY 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LYS 3.0 15.2 + - - -
50D ASN* 3.3 1.7 + - - -
52D VAL* 1.3 83.9 - - - +
54D ALA* 1.3 62.8 + - - +
56D ARG* 3.2 17.7 + - - +
57D SER* 2.9 26.4 + - - -
60D ARG* 4.3 3.4 + - - -
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Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50D ASN 3.1 15.7 + - - +
51D VAL* 3.7 8.3 - - - +
52D VAL 3.1 0.6 - - - -
53D GLY* 1.3 76.3 - - - +
55D ARG* 1.3 73.5 + - - +
57D SER* 3.3 5.9 + - - -
58D SER* 3.1 25.4 + - - -
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Residues in contact with ARG 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C ARG* 4.3 10.9 - - - +
20D ASP* 3.2 36.7 + - - -
51D VAL* 3.0 24.4 + - - +
52D VAL* 3.0 3.2 + - - +
54D ALA* 1.3 86.6 - - - +
56D ARG* 1.3 61.4 + - - +
58D SER* 3.3 8.3 + - - -
59D TRP* 2.8 30.1 + - - +
86D ILE* 3.7 9.1 - - + +
89D GLU* 3.0 42.9 + - + +
90D LEU* 3.5 24.5 - - + +
93D ILE* 3.9 19.7 - - + +
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Residues in contact with ARG 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D LYS* 5.5 2.2 - - - +
52D VAL* 2.9 26.0 + - - +
53D GLY* 3.5 17.4 - - - +
55D ARG* 1.3 74.7 - - - +
57D SER* 1.3 58.2 + - - +
59D TRP* 3.1 9.9 + - - +
60D ARG* 2.9 52.3 + - - +
90D LEU* 3.8 18.6 - - + +
128D TYR* 3.6 32.9 - - + +
131D GLU* 2.9 39.8 + - - +
28H ARG* 3.5 19.2 - - - +
29H ARG* 4.2 0.2 - - - +
31H TPO 2.8 40.0 + - - -
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Residues in contact with SER 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLY 2.9 17.7 + - - -
54D ALA* 3.5 6.7 - - - -
56D ARG* 1.3 76.3 - - - +
58D SER* 1.3 63.0 + - - +
59D TRP 3.2 0.2 + - - -
60D ARG* 3.3 25.5 + - - +
61D VAL* 3.2 23.4 + - - +
21H PRO* 5.5 0.3 - - - +
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Residues in contact with SER 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ALA* 2.9 26.0 + - - +
18C ARG* 3.7 26.1 + - - +
54D ALA 3.1 13.6 + - - -
55D ARG* 3.6 10.6 - - - -
57D SER* 1.3 78.3 - - - +
59D TRP* 1.3 57.4 + - - +
61D VAL* 2.9 25.5 - - - +
62D VAL* 3.0 17.9 - - - +
86D ILE* 4.3 6.6 - - - +
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Residues in contact with TRP 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55D ARG 2.8 13.7 + - - +
56D ARG* 3.2 13.7 - - - +
58D SER* 1.3 74.7 - - - +
60D ARG* 1.3 88.2 + - + +
62D VAL* 3.1 7.1 - - - +
63D SER* 2.7 51.5 + - - -
83D ARG* 3.4 22.8 - - + +
86D ILE* 4.3 7.4 - - + +
87D GLU* 3.1 43.7 + - + +
90D LEU* 4.3 7.6 - - + -
131D GLU* 3.4 26.7 - - + -
132D VAL* 3.4 24.7 - - + +
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Residues in contact with ARG 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53D GLY* 4.3 4.4 + - - -
56D ARG* 2.9 45.5 + - + +
57D SER* 3.7 31.2 + - - +
59D TRP* 1.3 93.2 - - + +
61D VAL* 1.3 57.0 + - - +
63D SER* 3.7 3.3 - - - -
64D SER* 3.0 28.9 + - - -
131D GLU* 5.8 0.6 + - - -
19H GLY 4.3 6.3 + - - -
21H PRO* 3.8 25.8 - - + +
28H ARG* 3.3 53.6 - - - +
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Residues in contact with VAL 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C GLN* 4.0 17.3 - - + +
16C ALA* 3.8 18.6 - - + -
57D SER 3.2 12.4 + - - +
58D SER* 2.9 30.7 - - - +
60D ARG* 1.3 79.0 - - - +
62D VAL* 1.3 56.5 + - - +
64D SER* 3.1 4.0 + - - -
65D ILE* 2.9 45.6 + - + +
21H PRO* 4.0 16.3 - - + +
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Residues in contact with VAL 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 4.5 7.0 - - + -
16C ALA* 5.1 4.3 - - + -
58D SER 3.0 20.8 + - - +
59D TRP* 3.1 16.8 - - - +
61D VAL* 1.3 78.4 - - + +
63D SER* 1.3 57.2 + - - +
65D ILE* 3.8 9.2 - - - +
66D GLU* 3.0 26.0 + - - +
79D ALA* 3.5 31.4 - - + +
82D TYR* 4.1 17.5 - - + -
83D ARG* 4.0 19.5 - - + +
86D ILE* 3.9 16.8 - - + -
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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 TRP* 2.7 52.7 + - - -
60D ARG* 3.7 6.5 - - - -
62D VAL* 1.3 76.4 - - - +
64D SER* 1.3 55.2 + - - +
66D GLU* 3.1 10.8 + - - +
67D GLN* 2.8 50.9 + - - -
83D ARG* 3.7 9.1 - - - +
----------------------------------------------------------
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Residues in contact with SER 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D ARG 3.0 14.8 + - - -
61D VAL* 3.1 8.0 + - - -
63D SER* 1.3 75.3 - - - +
65D ILE* 1.3 63.0 + - - +
67D GLN* 3.2 7.8 + - - +
68D LYS* 2.8 39.5 + - - +
21H PRO* 3.5 19.8 + - - -
22H GLY* 3.5 24.8 + - - -
----------------------------------------------------------
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Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 3.7 28.3 - - + +
15C GLN* 3.5 46.2 - - + +
61D VAL* 2.9 29.6 + - + +
62D VAL* 3.8 6.7 - - - +
64D SER* 1.3 77.1 - - - +
66D GLU* 1.3 54.2 + - - +
68D LYS* 3.2 6.2 + - - +
69D THR* 2.7 43.2 + - + +
79D ALA* 4.6 4.0 - - + -
----------------------------------------------------------
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Residues in contact with GLU 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D VAL 3.0 18.3 + - - +
63D SER* 3.1 9.3 + - - +
65D ILE* 1.3 73.8 - - - +
67D GLN* 1.3 72.8 + - - +
69D THR* 2.8 20.7 + - - -
76D GLN* 3.3 44.3 + - + +
79D ALA* 3.7 10.3 - - + -
80D ARG* 3.4 26.7 + - - -
83D ARG* 3.0 43.3 + - - +
----------------------------------------------------------
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Residues in contact with GLN 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D SER* 2.8 35.4 + - - +
64D SER* 3.3 11.7 - - - +
66D GLU* 1.3 84.2 + - - +
68D LYS* 1.3 75.3 + - + +
69D THR 4.0 0.2 - - - -
70D GLU* 3.2 23.0 - - - +
76D GLN* 4.7 2.8 + - - +
----------------------------------------------------------
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Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64D SER* 2.8 40.6 + - - +
65D ILE* 3.5 6.1 - - - +
67D GLN* 1.3 82.5 - - + +
69D THR* 1.3 56.6 + - - +
70D GLU* 2.8 16.8 + - - +
141G TRP* 3.9 42.0 - - + +
170G ARG* 4.8 9.6 + - - +
22H GLY* 4.0 18.1 + - - -
----------------------------------------------------------
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Residues in contact with THR 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D ILE* 2.7 24.9 + - + +
66D GLU* 2.8 18.8 + - - -
67D GLN 4.0 0.7 - - - -
68D LYS* 1.3 73.2 - - - +
70D GLU* 1.3 60.3 + - - +
71D GLY 3.8 1.6 + - - -
72D ALA* 4.2 7.5 + - + -
75D LYS* 3.7 45.3 - - + +
76D GLN* 3.5 41.3 + - - +
79D ALA* 4.6 0.9 - - + +
----------------------------------------------------------
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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