Contacts of the helix formed by residues 37 - 66 (chain g) 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 g).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1487 T 3.9 22.2 - - - +
1497 A 3.9 4.0 - - - +
16f LYS* 4.7 10.1 - - + -
19f ALA* 3.7 17.9 - - + -
20f LYS* 3.6 31.2 - - + -
33g ILE 3.0 21.1 + - - +
34g LEU* 3.5 16.2 - - + +
36g ASN* 1.3 75.5 - - - +
38g SER* 1.3 68.7 + - - +
39g PRO* 3.5 1.8 - - - -
40g VAL* 3.3 8.4 + - + +
41g ALA* 2.9 19.7 + - + +
21h PHE* 4.5 9.4 - - + -
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Residues in contact with SER 38 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34g LEU 2.6 23.0 + - - -
35g SER* 3.3 15.1 - - - -
36g ASN 3.3 0.2 - - - -
37g VAL* 1.3 80.2 - - - +
39g PRO* 1.4 74.7 - - - +
41g ALA* 2.9 10.9 + - - +
42g GLN* 2.9 26.0 + - - +
21h PHE* 3.5 23.1 - - - -
22h ASN* 5.5 2.5 + - - -
25h SER* 4.7 4.9 + - - -
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Residues in contact with PRO 39 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35g SER 4.0 4.5 - - - +
36g ASN 3.6 12.1 - - - +
37g VAL 3.5 1.8 - - - -
38g SER* 1.4 95.7 - - - +
40g VAL* 1.3 68.3 + - + +
42g GLN* 3.5 19.6 + - - +
43g GLN* 3.1 21.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 40 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1487 T 4.8 1.6 - - - +
12f GLN* 5.0 2.2 - - + +
15f ALA* 4.1 30.3 - - + +
16f LYS* 3.9 32.1 - - + +
19f ALA* 4.5 4.5 - - + -
36g ASN 4.3 13.5 - - - +
37g VAL* 3.5 13.2 - - + +
38g SER 3.0 0.4 + - - -
39g PRO* 1.3 79.4 - - + +
41g ALA* 1.3 67.5 + - - +
43g GLN* 3.1 9.3 + - - +
44g ASN* 3.1 32.0 + - - +
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Residues in contact with ALA 41 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477 A 3.9 4.8 - - - +
1487 T 3.5 39.7 - - - +
37g VAL 2.9 18.7 + - - +
38g SER 3.4 4.3 - - - +
40g VAL* 1.3 76.0 - - - +
42g GLN* 1.3 56.6 + - - +
44g ASN* 3.1 2.8 + - - +
45g PHE* 2.8 31.0 + - - +
17h TRP* 4.1 15.2 - - + -
21h PHE* 4.5 8.5 - - + -
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Residues in contact with GLN 42 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38g SER* 2.9 21.7 + - - +
39g PRO* 3.5 30.5 - - - +
41g ALA* 1.3 77.5 - - - +
43g GLN* 1.3 62.8 + - - +
45g PHE* 3.3 1.0 + - - +
46g GLN* 2.9 35.2 + - - +
14h TYR* 3.9 8.6 + - - +
17h TRP* 4.2 12.6 - - + -
18h GLN* 3.2 42.7 - - - +
21h PHE* 5.8 0.9 - - + -
22h ASN* 4.6 2.4 + - - -
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Residues in contact with GLN 43 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12f GLN* 5.3 7.4 - - + +
39g PRO 3.1 11.0 + - - +
40g VAL* 3.1 11.2 + - - +
42g GLN* 1.3 80.2 - - - +
44g ASN* 1.3 60.6 + - - +
46g GLN* 3.7 11.8 + - - +
47g THR* 2.6 60.5 + - - +
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Residues in contact with ASN 44 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1477 A 3.6 23.8 - - - +
1487 T 2.9 20.0 + - - -
8f ARG* 3.7 24.2 - - - +
12f GLN* 2.9 35.1 + - - +
16f LYS* 5.5 4.0 - - - +
40g VAL* 3.1 20.5 + - - +
41g ALA 3.1 7.7 + - - +
43g GLN* 1.3 76.8 - - - +
45g PHE* 1.3 66.2 + - - +
47g THR* 3.4 5.2 + - - -
48g ASN* 3.1 24.6 + - - +
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Residues in contact with PHE 45 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467 T 4.5 10.8 - - - -
1477 A 3.5 28.0 - - - -
2048 T 5.3 7.0 - - - -
41g ALA 2.8 16.3 + - - +
42g GLN 3.7 3.8 - - - +
44g ASN* 1.3 76.5 - - - +
46g GLN* 1.3 58.4 + - - +
49g VAL* 2.9 68.7 + - + +
10h TYR* 5.1 1.1 - + - -
13h ARG* 4.4 6.3 - - + -
14h TYR* 3.5 42.8 - + + -
17h TRP* 3.5 57.4 - + + -
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Residues in contact with GLN 46 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42g GLN* 2.9 28.3 + - - +
43g GLN* 3.8 13.5 + - - +
45g PHE* 1.3 79.5 - - - +
47g THR* 1.3 63.7 + - - +
50g PRO* 3.1 25.0 - - - +
10h TYR* 5.2 10.6 + - + +
14h TYR* 3.4 47.2 + - + -
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Residues in contact with THR 47 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12f GLN* 4.9 12.4 + - - +
43g GLN* 2.6 46.0 + - - +
44g ASN* 3.7 7.0 - - - -
45g PHE 3.2 0.2 - - - -
46g GLN* 1.3 80.5 - - - +
48g ASN* 1.3 73.6 + - - +
50g PRO* 4.3 2.1 - - - +
51g LYS* 3.4 23.6 - - - +
----------------------------------------------------------
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Residues in contact with ASN 48 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467 T 3.8 18.8 + - - +
1477 A 3.0 21.2 + - - -
7f SER* 4.5 8.1 + - - -
8f ARG* 3.8 13.1 - - - +
12f GLN* 5.5 3.8 - - - +
44g ASN* 3.1 10.5 + - - +
47g THR* 1.3 86.6 - - - +
49g VAL* 1.3 68.3 + - - +
50g PRO* 3.4 1.8 - - - -
51g LYS* 2.9 49.7 + - + +
52g PHE* 3.4 11.9 - - + -
88g ASN* 4.9 5.4 + - - -
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Residues in contact with VAL 49 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1467 T 3.6 31.9 - - + +
45g PHE* 2.9 59.2 + - + +
48g ASN* 1.3 73.8 - - - +
50g PRO* 1.3 62.4 - - + +
51g LYS 3.0 0.2 - - - -
52g PHE* 2.9 27.2 + - + +
53g THR* 3.0 12.8 + - - +
10h TYR* 4.6 6.3 - - + -
13h ARG* 3.8 29.2 - - + +
----------------------------------------------------------
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Residues in contact with PRO 50 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45g PHE 3.8 0.9 - - - +
46g GLN 3.1 26.0 - - - +
47g THR 4.2 2.2 - - - +
48g ASN 3.4 3.4 - - - +
49g VAL* 1.3 97.0 - - + +
51g LYS* 1.3 61.1 + - + +
53g THR* 3.7 2.2 - - - +
54g SER* 3.2 24.1 + - - -
10h TYR* 3.7 48.2 - - + -
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Residues in contact with LYS 51 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47g THR* 3.4 23.8 + - - +
48g ASN* 2.9 35.9 + - - +
49g VAL 3.0 0.4 - - - -
50g PRO* 1.3 78.6 - - + +
52g PHE* 1.3 63.9 + - + +
54g SER* 2.9 19.2 + - - -
55g VAL* 3.3 12.8 - - - +
84g ALA* 5.5 0.7 - - - +
88g ASN* 3.9 27.0 + - - +
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Residues in contact with PHE 52 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1457 A 3.7 17.3 - - + -
1467 T 3.4 40.6 - - - +
48g ASN* 3.4 19.7 - - + -
49g VAL* 2.9 7.8 + - + +
51g LYS* 1.3 75.6 - - + +
53g THR* 1.3 65.9 + - - +
54g SER 3.2 1.6 - - - -
55g VAL* 3.1 6.8 + - - +
56g ASN* 2.9 28.5 + - - +
81g LEU* 3.7 29.6 - - + +
84g ALA* 3.6 26.5 - - + -
85g ARG* 3.6 14.6 - - - -
88g ASN* 3.3 32.1 - - - -
13h ARG* 4.5 5.8 - - - +
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Residues in contact with THR 53 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49g VAL* 3.0 7.3 + - - +
50g PRO 3.8 5.4 - - - -
52g PHE* 1.3 77.9 - - - +
54g SER* 1.3 62.6 + - - +
56g ASN* 3.1 8.8 + - + +
57g GLU* 3.0 24.0 + - + +
8h ARG 4.7 4.3 - - - +
9h SER* 4.2 7.0 - - - -
10h TYR* 3.1 46.1 - - + +
13h ARG* 2.7 29.7 + - - +
----------------------------------------------------------
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Residues in contact with SER 54 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50g PRO 3.2 10.5 + - - -
51g LYS* 2.9 22.5 + - - -
53g THR* 1.3 79.9 - - - +
55g VAL* 1.3 58.5 + - - +
57g GLU* 3.4 6.7 + - - +
58g ASN* 3.0 41.3 + - - -
----------------------------------------------------------
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Residues in contact with VAL 55 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51g LYS 3.3 18.2 - - - +
52g PHE* 3.1 10.7 + - - +
53g THR 3.1 0.4 - - - -
54g SER* 1.3 76.7 + - - +
56g ASN* 1.3 61.7 + - - +
58g ASN* 4.5 2.9 - - - +
59g VAL* 2.8 53.1 + - + +
77g GLN* 5.2 0.4 - - - +
80g GLY* 4.1 13.7 - - - -
81g LEU* 4.3 10.1 - - + +
84g ALA* 4.0 20.4 - - + -
125g ILE* 3.9 26.0 - - + -
----------------------------------------------------------
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Residues in contact with ASN 56 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2058 A 4.8 4.4 + - - +
2068 T 4.1 36.0 + - - +
52g PHE* 2.9 17.6 + - - +
53g THR* 3.1 9.5 + - + +
55g VAL* 1.3 75.6 - - - +
57g GLU* 1.3 57.2 + - - +
60g SER* 2.9 30.5 + - - -
77g GLN* 3.1 21.2 + - - +
81g LEU* 3.3 30.8 - - - +
13h ARG* 4.0 22.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU 57 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53g THR* 3.0 15.0 + - + +
54g SER* 3.5 12.1 - - - +
56g ASN* 1.3 75.4 - - - +
58g ASN* 1.3 72.4 + - - +
60g SER* 3.2 7.5 + - - -
61g ALA* 3.0 23.6 + - + +
----------------------------------------------------------
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Residues in contact with ASN 58 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54g SER* 3.0 23.0 + - - +
55g VAL* 4.1 2.9 - - - +
57g GLU* 1.3 89.8 - - - +
59g VAL* 1.3 63.1 + - - +
61g ALA* 3.2 10.4 + - - +
62g VAL* 3.2 25.0 + - - +
124g ILE* 3.7 26.8 - - + +
----------------------------------------------------------
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Residues in contact with VAL 59 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55g VAL* 2.8 37.7 + - + +
58g ASN* 1.3 74.9 - - + +
60g SER* 1.3 65.6 + - - +
62g VAL* 3.1 9.5 + - - +
63g LEU* 2.9 33.7 + - + +
76g TYR 4.3 1.8 - - - +
77g GLN* 3.3 32.1 - - - +
80g GLY* 4.7 1.8 - - - -
121g VAL* 4.0 38.1 - - + +
124g ILE* 5.5 3.1 - - + -
125g ILE* 4.4 7.2 - - + -
----------------------------------------------------------
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Residues in contact with SER 60 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2068 T 4.9 0.4 - - - -
2078 A 3.4 10.4 + - - -
56g ASN 2.9 21.9 + - - -
57g GLU* 3.4 9.9 - - - -
58g ASN 3.2 0.2 - - - -
59g VAL* 1.3 76.1 - - - +
61g ALA* 1.3 63.9 + - - +
63g LEU* 3.1 2.8 + - - -
64g THR* 3.0 12.6 + - - -
73g ARG* 2.7 41.2 + - - +
77g GLN* 3.4 13.1 - - - +
89i ARG 4.7 2.8 + - - -
90i ILE 4.7 3.8 + - - -
----------------------------------------------------------
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Residues in contact with ALA 61 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57g GLU* 3.0 16.0 + - + +
58g ASN* 3.4 13.5 - - - +
60g SER* 1.3 77.1 - - - +
62g VAL* 1.3 62.3 + - + +
64g THR* 3.2 7.8 + - - -
65g GLN* 3.1 31.4 + - - +
----------------------------------------------------------
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Residues in contact with VAL 62 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58g ASN 3.2 13.2 + - - +
59g VAL* 3.1 12.0 + - + +
61g ALA* 1.3 77.9 - - + +
63g LEU* 1.3 68.9 + - + +
65g GLN* 2.9 23.4 + - - +
66g TYR* 3.0 39.9 + - + -
117g VAL* 5.3 0.9 - - + +
120g ALA* 4.0 17.5 - - + +
121g VAL* 4.8 7.0 - - + +
124g ILE* 3.6 32.3 - - + -
----------------------------------------------------------
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Residues in contact with LEU 63 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59g VAL* 2.9 33.7 + - + +
60g SER* 3.1 6.7 + - - +
62g VAL* 1.3 78.6 - - + +
64g THR* 1.3 61.7 + - - +
66g TYR* 3.2 2.7 + - - +
67g GLY 3.0 4.7 + - - -
68g ILE* 2.9 43.0 + - + +
73g ARG* 3.5 48.2 - - + +
76g TYR* 3.6 34.3 - - + -
77g GLN* 4.0 10.5 - - + +
117g VAL* 4.1 10.8 - - + -
121g VAL* 5.1 1.3 - - + -
----------------------------------------------------------
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Residues in contact with THR 64 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60g SER 3.0 6.0 + - - -
61g ALA* 3.6 10.7 - - - -
63g LEU* 1.3 76.6 - - - +
65g GLN* 1.3 62.4 + - + +
67g GLY 3.1 9.5 + - - -
73g ARG* 3.0 21.9 + - - +
90i ILE* 2.6 34.4 + - + +
91i GLY 3.8 6.7 - - - +
92i SER 3.3 28.0 - - - +
93i GLY* 4.6 1.6 - - - -
94i PRO* 3.3 4.2 - - + +
95i ALA* 3.3 19.0 + - + +
----------------------------------------------------------
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Residues in contact with GLN 65 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61g ALA* 3.1 19.4 + - - +
62g VAL* 2.9 17.4 + - - +
64g THR* 1.3 78.2 - - + +
66g TYR* 1.3 65.6 + - + +
67g GLY 3.3 0.2 - - - -
94i PRO* 3.4 23.8 - - + +
----------------------------------------------------------
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Residues in contact with TYR 66 (chain g).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62g VAL* 3.0 36.4 + - + +
63g LEU* 3.2 6.5 + - - +
65g GLN* 1.3 84.4 - - + +
67g GLY* 1.3 63.3 + - - +
68g ILE* 3.2 22.1 + - + +
116g GLN* 2.9 43.9 + - - -
117g VAL* 4.1 15.5 - - + -
120g ALA* 3.5 27.1 - - + +
94i PRO* 4.6 0.7 - - - -
----------------------------------------------------------
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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