Contacts of the helix formed by residues 37 - 66 (chain Y) in PDB entry 3J9X
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 37 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967 T 3.9 21.8 - - - +
1977 A 3.9 5.2 - - - +
16X LYS* 4.7 10.8 - - + -
19X ALA* 3.7 18.2 - - + -
20X LYS* 3.6 30.3 - - + -
33Y ILE 3.0 20.7 + - - +
34Y LEU* 3.5 15.3 - - + +
36Y ASN* 1.3 75.3 - - - +
38Y SER* 1.3 68.6 + - - +
39Y PRO* 3.5 1.3 - - - -
40Y VAL* 3.9 8.1 - - + -
41Y ALA* 2.9 21.7 + - + +
21Z PHE* 4.5 9.0 - - + -
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Residues in contact with SER 38 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Y LEU 2.6 23.1 + - - -
35Y SER* 3.3 15.9 - - - -
36Y ASN 3.3 0.2 - - - -
37Y VAL* 1.3 80.8 - - - +
39Y PRO* 1.4 72.6 - - - +
41Y ALA* 2.9 11.1 + - - +
42Y GLN* 2.9 26.9 + - - +
21Z PHE* 3.5 21.6 - - - -
22Z ASN* 5.5 1.9 + - - -
25Z SER* 4.7 5.0 + - - -
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Residues in contact with PRO 39 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Y SER 4.0 4.3 - - - +
36Y ASN 3.6 12.6 - - - +
37Y VAL 3.5 2.2 - - - -
38Y SER* 1.4 97.4 - - - +
40Y VAL* 1.3 67.7 + - + +
42Y GLN* 3.5 19.5 + - - +
43Y GLN* 3.1 21.3 + - - +
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Residues in contact with VAL 40 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1967 T 4.8 1.6 - - - +
12X GLN* 5.0 1.6 - - - +
15X ALA* 4.1 30.3 - - + +
16X LYS* 3.9 31.9 - - + +
19X ALA* 4.5 3.8 - - + -
36Y ASN 4.3 13.2 - - - +
37Y VAL* 3.5 12.8 - - + +
38Y SER 3.0 0.8 + - - -
39Y PRO* 1.3 78.9 - - + +
41Y ALA* 1.3 67.4 + - - +
43Y GLN* 3.1 9.6 + - - +
44Y ASN* 3.1 32.8 + - - +
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Residues in contact with ALA 41 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1957 A 3.9 4.6 - - - +
1967 T 3.5 37.9 + - - +
37Y VAL 2.9 18.2 + - - +
38Y SER 3.4 3.6 - - - +
40Y VAL* 1.3 76.3 - - - +
42Y GLN* 1.3 57.0 + - - +
44Y ASN* 3.1 2.8 + - - +
45Y PHE* 2.8 31.7 + - - +
17Z TRP* 4.1 15.2 - - + -
21Z PHE* 4.5 9.6 - - + -
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Residues in contact with GLN 42 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Y SER* 2.9 22.3 + - - +
39Y PRO* 3.5 30.2 - - - +
41Y ALA* 1.3 76.6 - - - +
43Y GLN* 1.3 61.9 + - - +
45Y PHE* 3.3 1.2 + - - +
46Y GLN* 2.9 35.9 + - - +
14Z TYR* 3.9 9.6 + - - +
17Z TRP* 4.2 13.0 - - + -
18Z GLN* 3.2 42.0 - - - +
21Z PHE* 5.6 1.1 - - + -
22Z ASN* 4.6 1.8 + - - -
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Residues in contact with GLN 43 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432 GLN* 3.1 41.3 - - - +
113 SER* 5.1 10.1 - - - -
123 GLN* 6.1 2.6 - - - +
12X GLN* 5.3 8.3 - - + +
39Y PRO 3.1 10.6 + - - +
40Y VAL* 3.3 11.7 - - - +
42Y GLN* 1.3 79.9 - - - +
44Y ASN* 1.3 58.6 + - - +
46Y GLN* 3.4 10.7 + - - +
47Y THR* 2.6 59.8 + - - +
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Residues in contact with ASN 44 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1957 A 3.6 23.3 - - - +
1967 T 2.9 19.8 + - - -
8X ARG* 3.7 24.2 - - - +
12X GLN* 2.9 34.7 + - - +
16X LYS* 5.5 3.4 - - - +
40Y VAL* 3.1 20.5 + - - +
41Y ALA 3.1 7.7 + - - +
43Y GLN* 1.3 77.3 - - - +
45Y PHE* 1.3 65.7 + - - +
47Y THR* 3.7 4.6 - - - -
48Y ASN* 3.1 24.3 + - - +
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Residues in contact with PHE 45 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1947 T 4.5 10.1 - - - -
1957 A 3.5 28.4 - - - -
1568 T 5.3 6.1 - - - -
41Y ALA 2.8 16.3 + - - +
42Y GLN 3.7 3.1 - - - +
44Y ASN* 1.3 76.1 - - - +
46Y GLN* 1.3 58.3 + - - +
49Y VAL* 2.9 68.8 + - + +
10Z TYR* 5.1 1.1 - + - -
13Z ARG* 4.4 5.4 - - + -
14Z TYR* 3.5 43.5 - + + -
17Z TRP* 3.5 57.9 - + + -
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Residues in contact with GLN 46 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 SER* 2.8 30.8 + - - +
143 TYR* 6.2 1.4 - - - -
42Y GLN* 2.9 27.4 + - - +
43Y GLN* 3.8 12.0 - - - +
45Y PHE* 1.3 80.5 - - - +
47Y THR* 1.3 63.8 - - - +
50Y PRO* 3.1 21.3 - - - +
10Z TYR* 5.2 10.4 + - + +
14Z TYR* 3.4 48.0 + - + -
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Residues in contact with THR 47 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 SER* 5.5 10.9 - - - +
113 SER* 4.1 6.2 - - - -
12X GLN* 4.9 12.4 + - - +
43Y GLN* 2.6 47.6 + - - +
44Y ASN* 3.7 6.9 - - - -
45Y PHE 3.2 0.2 - - - -
46Y GLN* 1.3 80.6 - - - +
48Y ASN* 1.3 72.4 + - - +
50Y PRO* 4.3 2.6 - - - +
51Y LYS* 3.4 23.6 - - - +
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Residues in contact with ASN 48 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1947 T 3.8 18.4 - - - +
1957 A 3.0 20.4 + - - -
7X SER* 4.5 8.3 + - - -
8X ARG* 3.8 13.1 - - - +
12X GLN* 5.5 3.8 - - - +
44Y ASN* 3.1 10.1 + - - +
47Y THR* 1.3 87.6 - - - +
49Y VAL* 1.3 67.3 + - - +
50Y PRO* 3.4 1.3 - - - -
51Y LYS* 2.9 49.3 + - + +
52Y PHE* 3.4 12.5 - - + -
88Y ASN* 4.9 5.2 + - - -
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Residues in contact with VAL 49 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1947 T 3.6 32.5 - - + +
45Y PHE* 2.9 56.6 + - + +
48Y ASN* 1.3 73.1 - - - +
50Y PRO* 1.3 63.6 - - + +
52Y PHE* 2.9 26.5 + - + +
53Y THR* 3.0 13.2 + - - +
10Z TYR* 4.6 7.4 - - + -
13Z ARG* 3.8 29.2 - - - +
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Residues in contact with PRO 50 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103 TYR* 4.9 13.0 - - + -
113 SER* 4.8 2.5 - - - +
504 PRO* 5.8 2.0 - - + -
544 SER* 5.3 1.2 - - - -
45Y PHE 3.8 0.9 - - - +
46Y GLN 3.1 25.1 - - - +
47Y THR 4.2 3.1 - - - +
48Y ASN 3.4 3.1 - - - +
49Y VAL* 1.3 97.5 - - + +
51Y LYS* 1.3 59.8 + - + +
53Y THR* 3.7 1.5 - - - +
54Y SER* 3.2 24.4 + - - -
10Z TYR* 3.7 48.5 - - + -
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Residues in contact with LYS 51 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93 SER* 6.0 5.8 - - - -
574 GLU* 4.2 27.4 - - - +
47Y THR* 3.4 23.4 + - - +
48Y ASN* 2.9 36.8 + - - +
49Y VAL 3.0 0.6 - - - -
50Y PRO* 1.3 77.8 - - + +
52Y PHE* 1.3 63.7 + - + +
54Y SER* 2.9 19.1 + - - -
55Y VAL* 3.3 12.6 - - - +
84Y ALA* 5.5 0.9 - - - +
88Y ASN* 3.9 26.9 + - - +
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Residues in contact with PHE 52 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1937 A 3.7 16.6 - - + -
1947 T 3.4 39.7 - - - +
48Y ASN* 3.4 19.5 - - + -
49Y VAL* 2.9 7.4 + - - +
51Y LYS* 1.3 76.8 - - + +
53Y THR* 1.3 66.5 + - - +
54Y SER 3.2 1.1 - - - -
55Y VAL* 3.1 7.2 + - - +
56Y ASN* 2.9 27.5 + - - +
81Y LEU* 3.7 28.5 - - + -
84Y ALA* 3.6 26.5 - - + -
85Y ARG* 3.6 15.5 - - - -
88Y ASN* 3.3 31.4 - - - -
13Z ARG* 4.5 6.7 - - - +
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Residues in contact with THR 53 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49Y VAL* 3.0 7.7 + - - +
50Y PRO 3.4 5.8 + - - -
52Y PHE* 1.3 78.6 - - - +
54Y SER* 1.3 62.6 + - - +
56Y ASN* 3.1 9.4 + - + +
57Y GLU* 3.0 23.2 + - + +
8Z ARG 4.7 5.2 - - - +
9Z SER* 4.2 6.5 - - - -
10Z TYR* 3.1 46.6 - - + +
13Z ARG* 2.7 29.0 + - - +
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Residues in contact with SER 54 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544 SER* 3.3 36.2 - - - -
574 GLU* 5.7 0.7 + - - -
584 ASN* 5.5 4.5 + - - -
50Y PRO 3.2 9.8 + - - -
51Y LYS* 2.9 21.8 + - - -
53Y THR* 1.3 78.4 - - - +
55Y VAL* 1.3 58.1 + - - +
57Y GLU* 3.4 7.0 + - - +
58Y ASN* 3.0 39.4 + - - -
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Residues in contact with VAL 55 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Y LYS 3.3 18.2 - - - +
52Y PHE* 3.1 9.8 + - - +
53Y THR 3.1 0.2 - - - -
54Y SER* 1.3 76.7 + - - +
56Y ASN* 1.3 61.0 + - - +
58Y ASN* 3.3 2.9 + - - +
59Y VAL* 2.8 53.7 + - + +
77Y GLN* 5.2 0.7 - - - +
80Y GLY 4.1 13.9 - - - -
81Y LEU* 4.3 9.6 - - + -
84Y ALA* 4.0 20.0 - - + -
125Y ILE* 3.9 26.5 - - + -
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Residues in contact with ASN 56 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1578 A 4.8 4.2 + - - +
1588 T 4.1 36.0 + - - +
52Y PHE* 2.9 17.2 + - - +
53Y THR* 3.1 9.3 + - + +
55Y VAL* 1.3 75.3 - - - +
57Y GLU* 1.3 57.1 + - - +
60Y SER* 2.9 30.8 + - - -
77Y GLN* 3.1 20.5 + - - +
81Y LEU* 3.3 29.9 - - - +
13Z ARG* 4.0 23.0 - - - +
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Residues in contact with GLU 57 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53Y THR* 3.0 14.2 + - + +
54Y SER* 3.5 11.2 - - - +
55Y VAL 3.1 0.2 - - - -
56Y ASN* 1.3 74.7 - - - +
58Y ASN* 1.3 75.0 + - - +
60Y SER* 3.2 8.4 + - - -
61Y ALA* 3.0 22.6 + - + +
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Residues in contact with ASN 58 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544 SER* 5.3 4.4 + - - -
584 ASN* 4.2 19.8 - - - +
1244 ILE* 4.7 9.2 + - - +
1254 ILE* 4.8 10.0 - - - +
54Y SER* 3.0 24.2 + - - +
55Y VAL* 4.1 3.1 - - - +
57Y GLU* 1.3 89.1 - - - +
59Y VAL* 1.3 62.4 + - + +
61Y ALA* 3.2 9.8 + - - +
62Y VAL* 3.2 25.4 + - - +
124Y ILE* 3.7 24.9 - - + +
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Residues in contact with VAL 59 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55Y VAL* 2.8 37.7 + - + +
58Y ASN* 1.3 74.0 - - + +
60Y SER* 1.3 66.1 + - - +
62Y VAL* 3.1 10.0 + - - +
63Y LEU* 2.9 34.6 + - + +
76Y TYR 4.3 1.3 - - - +
77Y GLN* 3.3 31.6 - - - +
80Y GLY* 4.7 1.6 - - - -
121Y VAL* 4.0 38.1 - - + +
124Y ILE* 5.5 2.9 - - + -
125Y ILE* 4.4 7.4 - - + -
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Residues in contact with SER 60 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1588 T 4.9 0.4 - - - -
1598 A 3.4 9.6 + - - -
56Y ASN 2.9 21.0 + - - -
57Y GLU* 3.4 10.1 - - - -
59Y VAL* 1.3 76.3 - - - +
61Y ALA* 1.3 62.9 + - - +
63Y LEU* 3.1 2.8 + - - -
64Y THR* 3.0 13.5 + - - -
73Y ARG* 2.7 41.3 + - - +
77Y GLN* 3.4 12.5 - - - +
89a ARG 4.7 3.1 + - - -
90a ILE 4.7 3.3 + - - -
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Residues in contact with ALA 61 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1254 ILE 6.1 0.9 - - - +
1264 THR 5.7 3.4 - - - +
57Y GLU* 3.0 15.8 + - - +
58Y ASN* 3.4 13.2 - - - +
60Y SER* 1.3 78.1 - - - +
62Y VAL* 1.3 62.6 + - + +
64Y THR* 3.2 7.2 + - - -
65Y GLN* 3.1 32.2 + - - +
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Residues in contact with VAL 62 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1264 THR 5.4 5.2 - - - +
1274 GLY* 5.7 0.9 - - - -
58Y ASN 3.2 13.0 + - - +
59Y VAL* 3.1 11.4 + - + +
61Y ALA* 1.3 77.6 - - + +
63Y LEU* 1.3 68.9 + - + +
65Y GLN* 2.9 23.8 + - - +
66Y TYR* 3.0 38.7 + - + -
117Y VAL* 5.3 0.9 - - + +
120Y ALA* 4.0 17.7 - - + +
121Y VAL* 4.8 7.0 - - + +
124Y ILE* 3.6 32.8 - - + -
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Residues in contact with LEU 63 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59Y VAL* 2.9 35.6 + - + +
60Y SER* 3.5 7.2 - - - +
62Y VAL* 1.3 78.9 - - + +
64Y THR* 1.3 60.2 + - - +
66Y TYR* 3.2 2.6 + - - +
67Y GLY 3.0 4.3 + - - -
68Y ILE* 2.9 43.4 + - + -
73Y ARG* 3.5 48.9 - - + +
76Y TYR* 3.6 34.3 - - + -
77Y GLN* 4.0 10.5 - - + +
117Y VAL* 4.1 10.8 - - + -
121Y VAL* 5.1 1.1 - - + -
----------------------------------------------------------
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Residues in contact with THR 64 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60Y SER 3.0 6.3 + - - -
61Y ALA* 3.6 10.5 - - - -
63Y LEU* 1.3 77.2 - - - +
65Y GLN* 1.3 60.9 + - + +
67Y GLY 3.1 9.5 + - - -
73Y ARG* 3.0 21.4 + - - +
90a ILE* 2.6 34.1 + - + +
91a GLY* 3.7 7.0 - - - +
92a SER 3.3 28.5 - - - +
93a GLY* 4.6 1.1 - - - -
94a PRO* 3.3 4.8 - - + +
95a ALA* 3.3 18.8 + - + +
----------------------------------------------------------
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Residues in contact with GLN 65 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924 SER* 5.8 5.7 - - - -
1264 THR* 3.9 21.5 + - - +
1274 GLY* 5.8 1.2 - - - -
1284 SER* 4.9 4.8 + - - -
1344 SER* 3.7 31.7 + - - +
61Y ALA* 3.1 19.1 + - - +
62Y VAL* 2.9 16.0 + - - +
64Y THR* 1.3 78.1 - - + +
66Y TYR* 1.3 64.9 + - + +
67Y GLY 3.3 0.2 - - - -
94a PRO* 3.4 24.1 - - + +
----------------------------------------------------------
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Residues in contact with TYR 66 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62Y VAL* 3.0 36.6 + - + +
63Y LEU* 3.2 7.1 + - - +
65Y GLN* 1.3 84.5 - - + +
67Y GLY* 1.3 62.6 + - - +
68Y ILE* 3.2 22.1 + - + +
116Y GLN* 2.9 42.2 + - - -
117Y VAL* 4.1 16.8 - - + -
120Y ALA* 3.5 28.1 - - + +
94a PRO* 4.6 0.4 - - - -
----------------------------------------------------------
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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