Contacts of the helix formed by residues 36 - 64 (chain H) in PDB entry 2X17
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 36 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1430 PHE* 5.3 9.4 - - + -
31H PHE* 3.1 22.2 + - + +
32H GLU* 5.0 0.4 - - - -
34H LEU* 4.3 18.4 - - + +
35H GLY* 1.3 74.4 - - - +
37H GLU* 1.3 64.7 + - - +
38H GLY 3.4 0.2 + - - -
39H PHE* 3.4 20.6 + - + +
40H ALA* 3.1 21.1 + - - +
83H PRO* 4.1 26.0 - - + -
151H LEU* 4.2 30.3 - - + +
152H PHE* 5.4 2.2 - - + +
155H ASP* 3.2 29.8 - - + +
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Residues in contact with GLU 37 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1360 LYS* 3.3 44.9 + - + +
32H GLU* 3.4 21.6 - - - +
35H GLY* 3.0 18.3 + - - +
36H LEU* 1.3 69.6 - - - +
38H GLY* 1.3 59.3 - - - +
40H ALA* 3.6 7.5 - - - +
41H ASN* 2.9 42.3 + - - +
155H ASP* 3.5 5.4 + - - +
159H SER* 5.4 0.2 - - - -
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Residues in contact with GLY 38 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37H GLU* 1.3 75.0 - - - +
39H PHE* 1.3 59.4 + - - +
41H ASN* 3.4 1.9 + - - +
42H TRP* 2.9 29.5 + - - +
155H ASP* 2.9 32.8 + - - -
158H LEU* 3.4 11.1 - - - +
159H SER* 3.7 18.7 - - - -
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Residues in contact with PHE 39 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31H PHE* 3.5 32.8 - + + -
36H LEU* 3.7 16.2 - - + +
38H GLY* 1.3 74.2 - - - +
40H ALA* 1.3 62.4 + - - +
42H TRP* 3.3 8.0 + - - +
43H MET* 3.1 27.9 + - - +
83H PRO* 5.2 0.2 - - + -
87H PHE* 3.8 28.2 - + - -
137H ILE* 4.6 2.5 - - + -
141H LEU* 4.1 26.0 - - + -
151H LEU* 3.9 19.3 - - + -
154H LEU* 4.0 15.5 - - + -
155H ASP* 3.1 46.8 + - + -
158H LEU* 3.6 24.9 - - + +
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Residues in contact with ALA 40 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28H ALA* 3.4 29.2 - - - +
31H PHE* 3.8 2.8 - - - +
32H GLU* 3.4 33.9 - - - +
36H LEU 3.1 11.7 + - - +
37H GLU 3.6 8.1 - - - +
39H PHE* 1.3 79.6 - - - +
41H ASN* 1.3 56.9 + - - +
43H MET 3.4 1.4 + - - -
44H LYS* 3.2 33.7 + - - +
58Z TYR* 4.5 0.7 - - - +
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Residues in contact with ASN 41 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32H GLU* 6.0 0.2 - - - -
37H GLU* 2.9 27.5 + - - +
38H GLY* 3.8 6.0 - - - +
40H ALA* 1.3 72.6 - - - +
42H TRP* 1.3 66.3 + - - +
44H LYS* 3.5 19.7 + - - +
45H ALA* 3.1 20.3 + - - +
159H SER* 5.1 9.1 + - - +
161H ARG 3.6 14.7 - - - +
162H ALA* 4.6 5.4 - - - +
163H PRO* 3.4 29.0 - - + +
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Residues in contact with TRP 42 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H TYR* 5.9 1.1 - + - -
38H GLY 2.9 19.2 + - - +
39H PHE* 3.4 7.2 - - - +
41H ASN* 1.3 76.0 - - - +
43H MET* 1.3 92.6 + - + +
45H ALA* 3.4 4.7 + - - +
46H GLN* 3.0 40.7 + - + +
87H PHE* 4.4 10.8 - + - -
133H SER* 3.7 18.4 - - - -
134H VAL* 4.4 18.8 - - + -
137H ILE* 3.6 25.6 - - + +
158H LEU* 3.7 36.5 - - + +
161H ARG* 3.3 53.2 + - + +
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Residues in contact with MET 43 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H TYR* 3.4 50.1 - - + +
27H MET* 3.8 30.7 - - + -
28H ALA* 3.7 13.2 - - + +
31H PHE* 4.1 9.9 - - + -
39H PHE 3.1 20.4 + - - +
41H ASN 3.3 0.2 - - - -
42H TRP* 1.3 92.9 - - + +
44H LYS* 1.3 54.5 + - - +
46H GLN* 3.1 2.9 + - - +
47H ALA* 2.8 34.3 + - - +
87H PHE* 3.7 38.8 - - + -
90H ALA* 4.7 5.4 - - + -
134H VAL* 6.5 0.4 - - + -
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Residues in contact with LYS 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H PHE* 4.7 13.9 - - + +
28H ALA* 3.9 9.2 - - + -
32H GLU* 3.1 21.0 + - - -
40H ALA 3.2 18.6 + - - +
41H ASN* 3.8 24.5 + - - +
43H MET* 1.3 75.1 - - - +
45H ALA* 1.3 62.7 + - - +
47H ALA* 3.4 8.3 + - - +
48H GLU* 3.2 27.2 + - - +
163H PRO* 3.9 20.6 - - + -
55Z LEU* 4.9 12.7 - - + +
58Z TYR* 3.4 38.1 - - - -
59Z ASN* 4.3 7.5 + - - -
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Residues in contact with ALA 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41H ASN 3.1 16.8 + - - +
42H TRP 3.6 5.6 - - - +
44H LYS* 1.3 77.3 - - - +
46H GLN* 1.3 60.1 + - - +
48H GLU* 3.6 8.8 + - - +
49H GLU* 3.5 23.6 + - - +
161H ARG* 3.6 24.0 + - + +
162H ALA 3.6 24.9 - - - +
163H PRO* 4.0 8.7 - - - +
169Z LEU* 5.6 0.2 - - - +
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Residues in contact with GLN 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H TYR* 3.7 23.6 - - + -
42H TRP* 3.0 37.4 + - + +
43H MET* 3.1 9.2 + - - +
45H ALA* 1.3 75.8 - - - +
47H ALA* 1.3 63.5 + - - +
49H GLU* 3.2 16.6 + - - +
50H GLU* 3.1 19.5 + - - +
130H GLU* 2.7 36.6 + - - +
133H SER* 5.2 3.6 + - - -
134H VAL* 6.0 2.4 - - + +
161H ARG* 2.8 32.8 + - - +
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Residues in contact with ALA 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21H ALA* 3.3 42.7 - - + +
24H TYR* 4.2 7.5 - - + +
25H PHE* 4.3 9.9 - - + +
43H MET 2.8 16.3 + - - +
44H LYS* 3.6 9.4 - - - +
46H GLN* 1.3 77.4 - - - +
48H GLU* 1.3 60.8 + - + +
50H GLU* 3.2 3.0 + - - -
51H ILE* 3.1 24.4 + - + +
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Residues in contact with GLU 48 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H LYS 3.2 10.6 + - - +
45H ALA* 3.7 9.7 - - - +
46H GLN 3.3 0.2 - - - -
47H ALA* 1.3 77.0 - - + +
49H GLU* 1.3 57.9 + - - +
51H ILE* 3.5 16.0 + - + +
52H GLY 3.1 20.3 + - - -
163H PRO* 3.3 23.0 - - - +
164H LYS* 2.8 29.8 + - - +
165H LEU* 3.2 35.7 + - + +
166H PRO* 3.7 1.4 - - - +
55Z LEU* 5.6 1.9 - - - +
165Z LEU* 4.0 15.9 - - + +
169Z LEU* 3.8 21.0 - - + +
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Residues in contact with GLU 49 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45H ALA 3.5 6.3 + - - +
46H GLN* 3.2 19.2 + - - +
48H GLU* 1.3 76.1 - - - +
50H GLU* 1.3 58.1 + - - +
52H GLY* 3.2 2.4 + - - -
53H HIS* 2.9 35.6 + - + -
130H GLU* 4.7 0.2 - - - +
161H ARG* 3.5 26.2 + - - +
164H LYS* 4.9 6.8 + - - -
1173H AG 3.3 20.6 - - - -
169Z LEU* 3.4 21.2 - - + +
170Z MET* 3.2 36.2 + - - +
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Residues in contact with GLU 50 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLU* 2.9 48.8 - - - +
20H SER* 3.5 20.0 + - - -
21H ALA 3.6 9.6 - - - +
24H TYR* 3.8 15.6 - - + -
46H GLN* 3.1 32.0 + - - +
47H ALA 3.2 7.7 + - - +
49H GLU* 1.3 74.3 - - - +
51H ILE* 1.3 59.5 + - - +
53H HIS* 3.1 15.4 + - - +
54H ALA* 3.0 24.6 + - - +
94H GLU* 3.9 3.5 - - - +
97H ILE* 5.6 0.9 - - - +
127H GLN* 5.2 3.1 + - - -
130H GLU* 3.1 17.5 - - - +
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Residues in contact with ILE 51 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18H LEU* 4.8 16.4 - - + -
21H ALA* 3.7 15.5 - - + -
47H ALA* 3.1 19.9 + - + +
48H GLU* 3.6 18.8 - - + +
49H GLU 3.4 0.2 - - - -
50H GLU* 1.3 74.3 - - - +
52H GLY* 1.3 57.8 + - - +
54H ALA* 3.3 8.3 + - - +
55H LEU* 3.1 38.0 + - + +
165H LEU* 6.2 1.6 - - + -
51Z ILE* 4.8 26.7 - - + -
165Z LEU* 4.4 18.2 - - + -
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Residues in contact with GLY 52 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48H GLU 3.1 14.3 + - - -
49H GLU 3.2 5.8 + - - -
50H GLU 3.2 0.4 - - - -
51H ILE* 1.3 74.9 - - - +
53H HIS* 1.3 64.8 + - - +
55H LEU* 3.4 11.7 + - - +
56H ARG* 3.3 27.4 + - - +
165Z LEU* 5.2 0.4 - - - +
166Z PRO* 6.3 0.2 - - - -
169Z LEU* 4.2 20.6 - - - -
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Residues in contact with HIS 53 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17H GLU* 3.7 19.2 + - - -
49H GLU* 2.9 24.5 + - + -
50H GLU* 3.1 27.3 + - - +
52H GLY* 1.3 75.5 - - - +
54H ALA* 1.3 63.6 + - - +
56H ARG* 3.2 14.5 + - - +
57H PHE* 3.4 19.3 - - - -
122H TRP* 3.8 23.3 - + - -
123H PHE* 3.6 13.4 - + + -
126H GLU* 3.1 26.6 + - - +
127H GLN* 5.1 0.4 + - - -
130H GLU* 3.4 16.4 - - - -
1173H AG 2.2 31.5 - - - -
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Residues in contact with ALA 54 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 3.5 22.7 - - + +
17H GLU* 3.8 15.2 - - + +
18H LEU* 3.8 33.0 - - + -
50H GLU 3.0 12.4 + - - +
51H ILE* 3.3 9.8 + - + +
53H HIS* 1.3 77.6 - - - +
55H LEU* 1.3 56.4 + - + +
57H PHE* 3.4 3.0 + - - -
58H TYR* 3.1 22.6 + - - +
25Z PHE* 5.5 3.1 - - + -
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Residues in contact with LEU 55 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H ILE* 3.1 34.1 + - + +
52H GLY* 3.7 10.3 - - - +
53H HIS 3.3 0.4 - - - -
54H ALA* 1.3 74.9 - - + +
56H ARG* 1.3 60.6 + - + +
58H TYR* 3.4 12.9 - - + +
59H ASN* 2.9 42.2 + - - +
25Z PHE* 3.7 30.7 - - + -
44Z LYS* 5.0 15.9 - - + +
48Z GLU* 5.7 2.2 - - - +
163Z PRO* 6.4 0.4 - - + -
165Z LEU* 5.5 5.4 - - + -
166Z PRO* 4.4 28.3 - - + -
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Residues in contact with ARG 56 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52H GLY 3.3 15.5 + - - +
53H HIS* 3.2 10.8 + - - +
55H LEU* 1.3 75.2 - - - +
57H PHE* 1.3 59.5 + - - +
59H ASN* 4.0 8.9 - - - +
60H TYR* 3.1 27.9 + - - +
119H PHE* 3.5 9.8 - - + -
122H TRP* 3.3 50.1 - - - +
123H PHE* 3.7 13.9 - - + -
170Z MET 3.5 5.9 + - - -
171Z GLN* 3.4 47.0 - - - +
172Z GLY 3.4 22.4 + - - +
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Residues in contact with PHE 57 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10H LEU* 3.9 34.8 - - + +
13H GLN* 3.4 33.2 - - + -
14H LEU* 3.8 19.5 - - + -
17H GLU* 3.9 14.6 - - + -
53H HIS 3.4 19.6 + - - -
54H ALA* 3.4 8.4 + - - +
55H LEU 3.3 0.2 - - - -
56H ARG* 1.3 76.4 - - - +
58H TYR* 1.3 63.9 + - - +
60H TYR* 3.3 0.9 + + - +
61H ILE* 3.0 31.5 + - + +
101H ILE* 4.1 12.1 - - + -
104H LEU* 4.4 1.1 - - + -
119H PHE* 3.5 24.2 - + - -
120H LEU* 4.1 13.0 - - + -
123H PHE* 3.5 29.2 - + - -
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Residues in contact with TYR 58 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14H LEU* 3.5 11.7 - - + +
54H ALA 3.1 14.7 + - - +
55H LEU* 3.4 15.7 - - + +
57H PHE* 1.3 77.5 - - - +
59H ASN* 1.3 75.4 + - - +
61H ILE* 3.6 1.4 + - - +
62H TYR* 3.3 43.1 + + + -
68H VAL* 4.1 17.9 - - + -
25Z PHE* 3.7 32.5 - + + -
28Z ALA 3.0 23.9 + - - -
29Z ALA* 3.9 22.9 - - + -
32Z GLU* 3.0 33.0 + - - +
44Z LYS* 3.4 22.6 - - - -
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Residues in contact with ASN 59 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H LEU* 2.9 30.0 + - - +
56H ARG* 4.0 8.1 - - - +
57H PHE 3.3 0.2 - - - -
58H TYR* 1.3 93.4 - - - +
60H TYR* 1.3 60.5 + - - +
62H TYR* 3.6 5.0 + - - +
63H ASP* 3.1 34.7 + - - +
32Z GLU* 5.9 0.3 - - - -
44Z LYS* 4.1 9.5 + - - -
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Residues in contact with TYR 60 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LEU* 4.4 1.1 - - + -
10H LEU* 4.0 23.3 - - + -
56H ARG 3.1 19.6 + - - +
57H PHE 3.9 2.7 - - - +
59H ASN* 1.3 73.5 - - - +
61H ILE* 1.3 67.0 + - + +
63H ASP* 3.0 18.7 + - - +
64H ARG* 3.1 42.0 + - + +
115H SER* 3.1 16.1 - - - -
116H THR* 2.9 42.3 + - + -
119H PHE* 3.6 52.3 - + + -
128R VAL* 4.2 17.3 - - + -
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Residues in contact with ILE 61 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H LEU* 4.3 4.0 - - - +
7H LEU* 3.9 10.8 - - + -
10H LEU* 4.0 37.5 - - + +
11H ASN* 4.1 16.6 - - - +
14H LEU* 3.9 13.9 - - + -
57H PHE* 3.0 22.4 + - - +
58H TYR 3.9 4.3 - - - +
59H ASN 3.4 0.2 - - - -
60H TYR* 1.3 79.4 - - + +
62H TYR* 1.3 60.2 + - + +
64H ARG* 3.2 9.7 + - - +
66H GLY* 2.8 25.1 + - - -
67H ARG 3.5 27.8 - - - +
68H VAL* 3.8 26.5 - - + +
----------------------------------------------------------
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Residues in contact with TYR 62 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H TYR* 3.3 42.8 + + + +
59H ASN* 4.1 4.3 - - - +
60H TYR 3.3 0.4 - - - -
61H ILE* 1.3 72.4 - - - +
63H ASP* 1.3 65.2 - - - +
64H ARG 3.2 1.8 - - - -
65H ASN* 3.4 11.4 + - - -
66H GLY 3.5 22.0 - - - +
67H ARG* 3.4 13.5 + - - -
68H VAL* 3.5 29.7 + - + -
132R ALA* 5.1 1.4 - - - +
29Z ALA* 2.5 34.3 + - - +
32Z GLU* 3.7 28.9 - - + -
33Z ASP* 3.7 25.1 - - + -
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Residues in contact with ASP 63 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59H ASN* 3.1 25.6 + - - +
60H TYR* 3.0 14.3 + - - +
62H TYR* 1.3 79.2 - - - +
64H ARG* 1.3 64.2 + - - +
65H ASN 3.3 1.2 + - - -
128R VAL* 4.1 25.1 - - + +
129R GLU* 5.9 4.1 - - - +
131R GLU* 5.2 1.9 - - - +
132R ALA* 3.4 36.9 + - + +
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Residues in contact with ARG 64 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1H MET* 3.7 36.5 - - - +
2H LEU* 3.8 27.6 + - + +
60H TYR* 3.1 55.8 + - + +
61H ILE 3.2 2.9 + - - +
62H TYR 3.2 0.6 - - - -
63H ASP* 1.3 78.5 + - - +
65H ASN* 1.3 68.7 + - - +
66H GLY* 3.3 2.3 + - - -
113H ASP* 4.3 7.7 + - - -
115H SER* 3.4 27.5 + - - -
102R TYR* 3.4 12.9 + - - -
127R GLN 5.3 0.6 - - - -
128R VAL* 3.8 28.3 - - - +
131R GLU* 4.0 23.9 + - - +
----------------------------------------------------------
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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