Contacts of the helix formed by residues 3 - 34 (chain Z) 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 SER 3 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1Z MET 3.7 1.4 + - - -
2Z LEU* 1.3 75.9 - - - +
4Z GLU* 1.3 59.2 + - - +
5Z ARG* 3.7 3.5 + - - +
6Z MET* 3.2 14.1 + - - +
7Z LEU* 2.9 28.8 + - - +
111Z GLU* 2.7 39.8 + - - -
113Z ASP* 5.4 0.4 + - - -
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Residues in contact with GLU 4 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Z LEU 4.0 0.4 + - - -
3Z SER* 1.3 74.0 - - - +
5Z ARG* 1.3 59.6 + - - +
7Z LEU* 4.1 9.0 - - + +
8Z LYS* 3.4 22.9 + - - +
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Residues in contact with ARG 5 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3Z SER* 3.2 2.7 + - - +
4Z GLU* 1.3 78.6 - - - +
6Z MET* 1.3 59.9 + - - +
8Z LYS* 3.6 7.9 + - + +
9Z ALA* 3.1 26.0 + - - +
107Z LEU* 4.7 20.4 - - + -
111Z GLU* 4.2 13.6 + - - +
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Residues in contact with MET 6 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Z LEU* 4.0 13.5 - - + -
3Z SER* 3.2 26.1 + - - +
5Z ARG* 1.3 74.7 - - - +
7Z LEU* 1.3 59.5 + - - +
9Z ALA* 3.3 4.0 + - - +
10Z LEU* 3.0 35.2 + - + +
104Z LEU* 4.7 13.0 - - - +
107Z LEU* 3.7 20.0 - - + +
108Z ALA* 3.6 35.7 - - + +
111Z GLU* 3.7 17.6 + - - +
113Z ASP* 3.6 20.0 - - - +
116Z THR* 3.8 19.7 - - - +
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Residues in contact with LEU 7 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2Z LEU* 4.0 24.8 - - + +
3Z SER 2.9 16.2 + - - +
4Z GLU* 4.1 9.2 - - + +
6Z MET* 1.3 76.6 - - - +
8Z LYS* 1.3 63.0 + - - +
10Z LEU* 3.4 3.2 + - - +
11Z ASN* 3.1 35.5 + - - +
61Z ILE* 3.8 16.4 - - + -
66Z GLY* 4.2 4.0 - - - -
67Z ARG* 3.6 41.7 - - + +
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Residues in contact with LYS 8 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Z GLU 3.4 16.0 + - - +
5Z ARG* 3.8 8.1 - - + +
6Z MET 3.3 0.2 - - - -
7Z LEU* 1.3 79.1 - - - +
9Z ALA* 1.3 57.6 + - - +
11Z ASN* 3.5 6.6 + - - +
12Z ASP* 3.1 56.3 + - - +
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Residues in contact with ALA 9 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5Z ARG 3.1 18.0 + - - +
6Z MET* 3.3 6.0 + - - +
8Z LYS* 1.3 75.8 - - - +
10Z LEU* 1.3 63.0 + - - +
12Z ASP* 3.4 9.5 + - - +
13Z GLN* 3.3 18.4 + - - +
16Z ARG* 4.5 1.9 + - - -
104Z LEU* 3.7 26.4 - - + +
107Z LEU* 3.8 20.4 - - + -
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Residues in contact with LEU 10 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Z LEU* 3.8 39.3 - - + -
6Z MET* 3.0 23.7 + - + +
7Z LEU* 3.9 4.0 - - - +
9Z ALA* 1.3 72.8 - - - +
11Z ASN* 1.3 63.9 + - - +
13Z GLN 3.5 0.9 + - - -
14Z LEU* 3.1 22.3 + - - +
57Z PHE* 3.7 36.1 - - + -
60Z TYR* 3.9 15.3 - - + -
61Z ILE* 4.0 17.5 - - + +
104Z LEU* 4.1 11.7 - - + -
116Z THR* 3.9 20.9 - - + -
119Z PHE* 4.3 8.3 - - + -
120Z LEU* 5.2 1.6 - - + -
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Residues in contact with ASN 11 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Z LEU* 3.1 34.3 + - - +
8Z LYS* 3.7 7.9 - - - +
9Z ALA 3.4 0.2 - - - -
10Z LEU* 1.3 75.6 - - - +
12Z ASP* 1.3 65.6 + - - +
14Z LEU* 3.4 8.7 - - - +
15Z ASN* 3.2 21.1 + - - +
61Z ILE* 4.3 6.7 - - - +
67Z ARG 3.2 22.4 + - - -
68Z VAL* 3.4 13.0 - - - +
69Z GLU* 2.9 43.9 + - + +
71Z ASP* 4.9 4.1 - - - +
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Residues in contact with ASP 12 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Z LYS* 3.1 45.7 + - - +
9Z ALA* 3.6 9.2 - - - +
10Z LEU 3.3 0.4 - - - -
11Z ASN* 1.3 76.5 - - - +
13Z GLN* 1.3 59.3 + - - +
15Z ASN* 3.2 9.1 + - - +
16Z ARG* 2.9 51.2 + - - +
71Z ASP* 4.1 12.5 - - - +
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Residues in contact with GLN 13 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Z ALA 3.3 6.8 + - - +
10Z LEU 4.0 4.5 - - - +
11Z ASN 3.4 0.4 - - - -
12Z ASP* 1.3 75.5 - - - +
14Z LEU* 1.3 60.3 + - - +
16Z ARG* 3.1 28.6 + - - +
17Z GLU* 2.8 56.7 + - - +
57Z PHE* 3.5 29.4 - - + -
97Z ILE* 3.8 19.2 - - - +
100Z SER* 2.9 25.4 + - - -
101Z ILE* 3.8 10.8 - - + +
104Z LEU* 3.7 21.0 - - + +
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Residues in contact with LEU 14 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25H PHE* 4.4 6.7 - - + -
10Z LEU 3.1 12.0 + - - +
11Z ASN* 3.4 12.8 - - - +
13Z GLN* 1.3 76.7 - - - +
15Z ASN* 1.3 55.0 + - - +
17Z GLU* 3.5 6.1 + - - +
18Z LEU* 3.1 45.9 + - + +
54Z ALA* 3.5 22.5 - - + +
57Z PHE* 4.0 10.0 - - + -
58Z TYR* 3.6 30.5 - - + +
61Z ILE* 4.0 15.0 - - + -
68Z VAL* 3.9 20.6 - - + -
70Z LEU* 3.9 16.2 - - + -
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Residues in contact with ASN 15 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H TYR* 3.5 10.7 + - - -
11Z ASN 3.2 10.6 + - - +
12Z ASP* 3.4 11.4 - - - +
13Z GLN 3.2 0.4 - - - -
14Z LEU* 1.3 79.1 - - - +
16Z ARG* 1.3 59.2 + - - +
18Z LEU* 3.4 6.7 + - - +
19Z TYR* 3.0 26.9 + - - +
70Z LEU* 5.9 0.8 - - + +
71Z ASP* 3.1 44.2 + - + +
72Z GLU 3.3 18.1 + - - +
73Z ILE* 4.1 5.8 - - - +
74Z PRO* 4.8 6.1 - - - +
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Residues in contact with ARG 16 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Z ALA 4.5 2.8 + - - -
12Z ASP* 2.9 34.4 + - - +
13Z GLN* 3.1 58.4 + - - +
15Z ASN* 1.3 76.3 - - - +
17Z GLU* 1.3 57.6 + - - +
19Z TYR* 3.3 8.8 + - - +
20Z SER* 2.9 31.8 + - - -
93Z HIS* 5.4 0.2 - - - -
96Z PHE* 4.1 26.9 - - + -
97Z ILE* 4.1 7.1 - - + +
100Z SER* 3.8 25.3 + - - -
103Z GLU* 5.2 5.9 + - - -
104Z LEU* 5.2 2.0 - - - +
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Residues in contact with GLU 17 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13Z GLN* 2.8 41.7 + - + +
14Z LEU 3.8 5.2 - - - +
16Z ARG* 1.3 73.9 - - - +
18Z LEU* 1.3 62.8 + - - +
20Z SER* 3.4 4.1 + - - -
21Z ALA* 3.2 17.5 + - - +
50Z GLU* 2.9 52.3 - - - +
53Z HIS* 3.6 26.4 + - + +
54Z ALA* 4.0 10.3 - - + +
57Z PHE* 4.4 7.0 - - + -
97Z ILE* 3.9 14.4 - - - +
101Z ILE* 4.6 1.6 - - - +
123Z PHE* 4.1 15.5 - - - -
127Z GLN* 4.6 1.9 + - - -
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Residues in contact with LEU 18 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22H TYR* 3.6 38.4 - - + +
25H PHE* 4.3 10.8 - - + -
14Z LEU* 3.1 40.5 + - + +
15Z ASN* 3.7 7.4 - - - +
16Z ARG 3.3 0.2 - - - -
17Z GLU* 1.3 75.0 - - - +
19Z TYR* 1.3 62.3 + - - +
21Z ALA* 3.5 7.3 - - + +
22Z TYR* 3.2 19.9 + - - +
50Z GLU 5.3 0.2 - - - -
51Z ILE* 4.9 20.2 - - + -
54Z ALA* 3.8 15.5 - - + -
70Z LEU* 4.0 4.5 - - + -
73Z ILE* 4.2 17.4 - - + +
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Residues in contact with TYR 19 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15Z ASN* 3.0 18.5 + - - +
16Z ARG* 3.3 7.6 + - - +
17Z GLU 3.3 0.2 - - - -
18Z LEU* 1.3 75.6 - - - +
20Z SER* 1.3 54.1 + - - +
22Z TYR* 2.9 4.4 + - + -
23Z LEU* 2.7 47.8 + - + +
73Z ILE* 4.0 15.9 - - + +
74Z PRO* 3.5 48.9 - - + -
75Z LYS 4.5 2.0 + - - -
76Z PRO* 3.9 14.7 - - + +
77Z PRO* 3.7 23.6 - - - +
93Z HIS* 3.7 32.3 - + - -
96Z PHE* 6.2 0.9 - + - -
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Residues in contact with SER 20 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Z ARG 2.9 17.9 + - - -
17Z GLU* 3.4 12.3 + - - -
18Z LEU 3.4 0.2 - - - -
19Z TYR* 1.3 75.4 - - - +
21Z ALA* 1.3 57.1 + - - +
23Z LEU* 3.3 4.3 + - - +
24Z TYR* 3.0 41.3 + - - -
50Z GLU* 3.8 22.2 + - - -
93Z HIS* 3.1 29.9 + - - -
94Z GLU* 5.9 0.7 - - - -
97Z ILE* 3.4 14.3 - - - +
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Residues in contact with ALA 21 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17Z GLU 3.2 5.7 + - - +
18Z LEU* 3.5 12.8 - - + +
20Z SER* 1.3 79.0 - - - +
22Z TYR* 1.3 56.4 + - - +
25Z PHE* 3.0 27.8 + - - +
47Z ALA* 3.3 37.2 - - + +
50Z GLU* 3.7 10.7 - - + +
51Z ILE* 3.7 20.0 - - + -
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Residues in contact with TYR 22 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15H ASN* 4.0 6.1 + - - -
18H LEU* 3.7 30.4 - - + +
70H LEU* 3.4 30.1 - - + +
71H ASP 2.7 31.0 + - - -
73H ILE* 3.7 24.0 - - + +
18Z LEU 3.2 11.1 + - - +
19Z TYR* 2.9 8.6 + - + +
21Z ALA* 1.3 77.0 - - - +
23Z LEU* 1.3 60.8 + - - +
25Z PHE* 3.7 13.2 - + - +
26Z ALA* 3.1 25.5 + - - +
73Z ILE* 3.8 24.0 - - + -
74Z PRO 4.0 4.0 - - - -
76Z PRO* 3.6 31.4 - - + +
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Residues in contact with LEU 23 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19Z TYR* 2.7 31.2 + - + +
20Z SER* 3.6 5.4 - - - +
22Z TYR* 1.3 73.3 - - - +
24Z TYR* 1.3 65.5 + - + +
25Z PHE 3.2 0.4 - - - -
26Z ALA* 3.1 4.9 + - - +
27Z MET* 2.9 55.7 + - + +
76Z PRO* 4.3 6.9 - - + +
77Z PRO* 3.8 29.8 - - + -
80Z TRP* 4.2 7.4 - - + -
89Z ALA* 5.1 1.3 - - + +
93Z HIS* 3.5 47.1 - - + +
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Residues in contact with TYR 24 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20Z SER* 3.0 31.5 + - - +
21Z ALA 4.2 3.1 - - - +
23Z LEU* 1.3 77.1 - - + +
25Z PHE* 1.3 59.8 + - - +
27Z MET* 3.6 12.3 + - + -
28Z ALA* 3.0 21.8 + - - +
42Z TRP* 5.9 0.4 - + - -
43Z MET* 3.3 51.0 - - + +
46Z GLN* 3.9 16.4 - - + -
47Z ALA* 4.2 3.6 - - + +
50Z GLU* 3.7 33.7 - - + -
90Z ALA* 3.7 29.8 + - + +
93Z HIS* 4.6 10.5 - + - -
94Z GLU* 2.6 34.7 + - - +
134Z VAL* 5.0 5.5 - - + +
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Residues in contact with PHE 25 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H LEU* 4.4 5.6 - - + -
18H LEU* 4.2 20.0 - - + -
54H ALA* 5.2 2.9 - - + -
55H LEU* 3.7 28.3 - - + -
58H TYR* 3.7 37.2 - + + -
70H LEU* 3.7 35.6 - - + +
21Z ALA 3.0 18.9 + - - +
22Z TYR* 3.7 17.0 - + - +
23Z LEU 3.2 0.2 - - - -
24Z TYR* 1.3 77.8 - - - +
26Z ALA* 1.3 57.3 + - - +
28Z ALA* 3.5 8.4 - - + +
29Z ALA* 3.2 23.9 + - - +
43Z MET 5.7 0.2 - - - -
44Z LYS* 4.9 7.6 - - + -
47Z ALA* 4.2 9.8 - - + +
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Residues in contact with ALA 26 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70H LEU* 3.7 11.6 - - + +
22Z TYR 3.1 15.4 + - - +
23Z LEU 3.1 10.0 + - - +
25Z PHE* 1.3 75.6 - - - +
27Z MET* 1.3 59.3 + - - +
29Z ALA* 3.4 7.7 + - - +
30Z TYR* 3.2 23.2 + - - +
76Z PRO* 3.7 18.6 - - + -
77Z PRO 3.6 21.5 - - - +
78Z LYS* 4.5 4.3 - - - +
80Z TRP* 4.0 6.4 - - + -
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Residues in contact with MET 27 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23Z LEU* 2.9 36.3 + - + +
24Z TYR* 3.8 12.3 - - + +
26Z ALA* 1.3 75.1 - - - +
28Z ALA* 1.3 60.4 + - - +
30Z TYR* 3.1 3.0 + - - +
31Z PHE* 2.9 40.9 + - + -
43Z MET* 3.8 30.3 - - + -
80Z TRP* 3.5 38.8 - - + -
86Z ALA* 3.4 29.4 - - + +
89Z ALA* 4.2 5.4 - - + -
90Z ALA* 3.8 23.6 - - + +
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Residues in contact with ALA 28 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58H TYR* 3.0 14.0 + - - +
24Z TYR 3.0 18.7 + - - +
25Z PHE* 3.5 11.4 - - + +
27Z MET* 1.3 76.7 - - - +
29Z ALA* 1.3 56.0 + - - +
31Z PHE 3.4 0.3 + - - -
32Z GLU* 2.9 24.6 + - - +
40Z ALA* 3.4 30.0 - - - +
43Z MET* 3.8 9.6 - - + +
44Z LYS* 3.9 17.3 - - + -
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Residues in contact with ALA 29 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H TYR* 3.4 19.7 + - + -
62H TYR* 2.5 31.2 + - - +
67H ARG* 3.7 10.8 + - - +
68H VAL* 4.3 14.8 - - + +
70H LEU* 5.4 2.5 - - + -
25Z PHE 3.2 11.1 + - - +
26Z ALA* 3.6 11.9 - - - +
27Z MET 3.3 0.2 - - - -
28Z ALA* 1.3 78.3 - - - +
30Z TYR* 1.3 61.4 + - - +
32Z GLU* 4.2 0.2 - - - -
33Z ASP* 3.2 14.6 + - - +
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Residues in contact with TYR 30 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67H ARG* 3.9 19.2 - - - +
26Z ALA 3.2 12.5 + - - +
27Z MET 3.1 10.9 + - - +
29Z ALA* 1.3 77.4 - - - +
31Z PHE* 1.3 74.2 + + - +
33Z ASP* 3.4 13.2 + - + +
34Z LEU* 3.4 41.6 + - + +
78Z LYS 4.2 4.3 - - - +
79Z GLU* 4.3 4.7 - - + -
80Z TRP* 3.1 61.4 + + + -
81Z GLU 3.7 1.7 + - - -
82Z SER* 3.2 24.7 - - - -
83Z PRO* 3.6 1.4 - - - +
86Z ALA* 3.7 24.9 - - + -
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Residues in contact with PHE 31 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Z MET* 2.9 31.4 + - + +
28Z ALA 4.0 1.8 - - - +
30Z TYR* 1.3 81.8 - + - +
32Z GLU* 1.3 62.4 + - - +
33Z ASP 3.3 0.2 - - - -
34Z LEU* 3.5 5.4 + - + +
35Z GLY 3.3 2.6 + - - -
36Z LEU* 2.8 47.6 + - + +
39Z PHE* 3.5 25.6 - + + -
40Z ALA 3.8 18.4 - - - +
43Z MET* 4.1 29.8 - - + -
83Z PRO* 3.6 28.9 - - + -
86Z ALA* 3.8 26.2 - - + -
87Z PHE* 3.9 20.6 - + - -
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Residues in contact with GLU 32 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58H TYR* 3.0 26.1 + - - +
62H TYR* 3.7 34.9 - - + +
28Z ALA 2.9 15.1 + - - +
29Z ALA 3.6 5.8 - - - +
30Z TYR 3.3 0.2 - - - -
31Z PHE* 1.3 75.9 - - - +
33Z ASP* 1.3 63.5 + - - +
35Z GLY* 3.1 13.4 + - - -
36Z LEU 4.8 2.0 - - - +
37Z GLU* 3.6 28.8 - - - +
40Z ALA* 3.4 14.1 - - - +
41Z ASN* 5.2 0.2 - - - +
44Z LYS* 3.2 20.9 + - - -
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Residues in contact with ASP 33 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62H TYR* 3.7 10.6 - - + -
66H GLY 4.4 5.0 - - - +
67H ARG* 3.5 36.4 + - - +
139R ASP* 5.6 1.6 - - - +
29Z ALA 3.2 13.9 + - - +
30Z TYR* 3.5 12.6 - - - +
31Z PHE 3.3 0.2 - - - -
32Z GLU* 1.3 78.5 - - - +
34Z LEU* 1.3 64.9 + - - +
35Z GLY 3.1 0.9 + - - -
79Z GLU* 5.2 3.5 - - - +
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Residues in contact with LEU 34 (chain Z).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139R ASP* 5.9 2.1 - - - +
143R PHE* 5.4 8.1 - - - -
30Z TYR* 3.4 51.6 + - + +
31Z PHE* 3.9 8.7 - - + +
32Z GLU 3.3 0.4 - - - -
33Z ASP* 1.3 81.6 - - - +
35Z GLY* 1.3 60.2 + - - +
36Z LEU* 3.3 28.5 + - + +
83Z PRO* 4.3 10.5 - - + -
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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