Contacts of the strand formed by residues 2 - 42 (chain A) in PDB entry 2AWR
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 ALA 2 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 1.3 78.1 - - - +
3A ARG* 1.3 66.5 + - - +
4A TYR* 4.3 7.3 - - + -
9B ARG* 4.1 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 3 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 5.9 4.9 - - - +
2A ALA* 1.3 77.0 + - - +
4A TYR* 1.3 64.3 + - - +
5A ARG* 3.9 24.5 - - + +
9B ARG* 3.5 13.8 + - - +
10B ARG* 4.4 4.6 - - + -
11B ARG* 3.9 23.4 + - - +
24H A 4.0 12.4 + - - -
25H C 3.0 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 4 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ALA* 5.2 6.1 - - + -
3A ARG* 1.3 79.0 - - - +
5A ARG* 1.3 68.5 + - - +
6A CYS 5.8 0.2 - - - -
11B ARG* 4.9 3.8 - - + -
7C A 4.3 15.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG* 3.9 23.8 + - + +
4A TYR* 1.3 77.7 - - - +
6A CYS* 1.3 62.7 + - - +
7A CYS* 5.3 10.5 - - - -
11B ARG 4.2 12.3 + - - +
12B HIS* 4.3 1.4 - - - -
13B CYS* 3.1 22.9 + - - +
23H T 4.5 4.4 + - - -
24H A 3.1 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A TYR* 5.8 0.4 - - - -
5A ARG* 1.3 74.2 - - - +
7A CYS* 1.3 71.4 + - - +
8A ARG* 6.1 1.1 - - - -
13B CYS* 2.0 51.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 5.3 12.6 - - - -
6A CYS* 1.3 85.3 - - - +
8A ARG* 1.3 61.7 + - - +
13B CYS 3.0 8.9 + - - +
14B SER* 3.4 17.6 + - - +
15B ARG* 3.0 25.3 + - - +
23H T 5.9 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A CYS* 6.4 1.1 - - - -
7A CYS* 1.3 75.8 - - - +
9A SER* 1.3 64.1 + - - +
10A GLN* 5.3 9.3 - - + +
15B ARG* 3.4 13.5 - - + +
8C C 3.7 12.1 + - - -
9C G 3.0 39.0 + - - -
22F G 5.1 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 1.3 75.7 + - - +
10A GLN* 1.3 63.0 + - - +
15B ARG 3.0 11.1 + - - +
16B ARG* 3.4 9.8 - - - +
17B ARG* 3.0 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ARG* 5.3 8.5 - - + +
9A SER* 1.3 79.9 - - - +
11A SER* 1.3 63.9 + - - +
12A ARG* 6.1 0.7 - - - -
17B ARG* 3.4 13.7 - - + +
10C T 5.3 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN* 1.3 76.3 + - - +
12A ARG* 1.3 61.4 + - - +
17B ARG 3.0 9.3 + - - +
18B LEU* 3.4 23.3 - - - +
19B HIS* 3.0 25.3 + - - +
21H C 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLN 6.4 0.4 - - - -
11A SER* 1.3 75.8 - - - +
13A SER* 1.3 63.7 + - - +
14A ARG* 5.4 11.2 - - - +
19B HIS* 3.4 13.5 - - + +
10C T 3.7 12.1 + - - -
11C A 3.0 39.2 + - - -
20F A 5.1 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 1.3 76.3 + - - +
14A ARG* 1.3 61.2 + - - +
15A TYR* 4.1 20.8 + - - -
18B LEU* 6.5 0.2 - - - -
19B HIS 3.0 11.1 + - - +
20B ARG* 3.4 10.2 - - - +
21B ILE* 3.0 26.7 + - - +
20H A 5.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 5.4 9.6 - - - +
13A SER* 1.3 75.4 - - - +
15A TYR* 1.3 74.4 + - - +
16A TYR* 4.7 11.5 - - + -
21B ILE* 3.4 17.7 - - + +
11C A 3.7 9.5 + - - -
12C C 3.0 26.0 + - - -
19F T 3.4 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 4.1 21.3 - - - -
14A ARG* 1.3 85.0 - - - +
16A TYR* 1.3 63.9 + - - +
21B ILE 3.0 11.3 + - - +
22B HIS* 3.4 10.0 - - + +
23B ARG* 3.0 25.3 + - - +
18H G 5.4 0.9 - - - -
19H T 3.5 36.9 + - - -
20H A 5.2 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 4.7 10.1 - - + -
15A TYR* 1.3 82.0 - - - +
17A ARG* 1.3 65.4 + - - +
18A GLN* 4.9 22.1 - - + +
23B ARG* 3.4 13.5 - - + +
13C G 4.3 16.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 1.3 77.9 - - - +
18A GLN* 1.3 65.2 + - - +
19A ARG* 4.5 16.6 - - - +
23B ARG 3.0 11.1 + - - +
24B ARG* 3.4 9.8 - - + +
25B GLN* 3.0 25.3 + - - +
17H C 4.1 13.1 + - - -
18H G 3.0 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A TYR* 4.9 21.5 - - + -
17A ARG* 1.3 82.0 - - - +
19A ARG* 1.3 65.7 + - - +
20A GLN* 5.3 6.3 - - + +
25B GLN* 3.4 13.9 - - + +
14C T 5.3 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ARG* 4.5 15.7 - - - +
18A GLN* 1.3 77.9 - - - +
20A GLN* 1.3 65.2 + - - +
21A ARG* 4.5 16.4 - - - +
25B GLN 3.0 11.1 + - - +
26B HIS* 3.4 10.0 - - + +
27B ARG* 3.0 25.3 + - - +
16H A 4.1 13.1 + - - -
17H C 3.0 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A GLN* 5.3 5.6 - - + +
19A ARG* 1.3 82.0 - - - +
21A ARG* 1.3 65.7 + - - +
27B ARG* 3.4 13.7 - - + +
15C A 5.3 7.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ARG* 4.5 15.7 - - - +
20A GLN* 1.3 77.9 - - - +
22A SER* 1.3 64.0 + - - +
23A ARG* 4.5 16.4 - - - +
27B ARG 3.0 8.9 + - - +
28B SER* 3.4 19.1 + - - +
29B CYS* 3.0 25.1 + - - +
15H T 4.1 13.7 + - - -
16H A 3.0 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 1.3 78.2 + - - +
23A ARG* 1.3 65.0 + - - +
24A ARG* 6.1 0.7 - - - -
29B CYS* 3.4 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A ARG* 4.5 15.7 - - - +
22A SER* 1.3 77.8 - - - +
24A ARG* 1.3 64.1 + - - +
25A ARG* 5.1 11.7 - - - +
29B CYS 3.0 11.1 + - - +
30B ARG* 3.5 10.1 - - + +
31B ARG* 3.1 25.2 + - - +
14H G 4.1 15.5 + - - -
15H T 3.0 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A SER 6.4 0.4 - - - -
23A ARG* 1.3 78.5 - - - +
25A ARG* 1.3 65.8 + - - +
26A ARG* 5.5 11.9 - - - +
31B ARG* 3.7 14.6 - - + +
16C C 3.7 11.9 + - - -
17C G 3.0 39.2 + - - -
14F G 5.1 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ARG* 5.1 10.6 - - - +
24A ARG* 1.3 77.0 - - - +
26A ARG* 1.3 65.8 + - - +
27A ARG* 4.4 20.6 - - - +
31B ARG 3.1 13.2 + - - +
32B ARG* 5.0 7.2 - - + -
33B LYS* 3.3 25.6 + - - +
13H C 3.9 22.0 + - - -
14H G 3.0 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ARG* 5.5 12.2 - - - +
25A ARG* 1.3 80.3 + - - +
27A ARG* 1.3 65.1 + - - +
28A ARG* 4.3 18.0 - - - +
33B LYS* 4.1 10.5 - - + -
17C G 4.0 8.5 + - - -
18C T 2.8 36.8 + - - -
13F C 5.4 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ARG* 4.4 14.3 - - - +
26A ARG* 1.3 77.0 + - - +
28A ARG* 1.3 63.4 + - - +
29A SER* 5.4 8.8 + - - -
33B LYS* 3.5 14.1 + - - +
34B ARG* 5.3 4.9 - - + -
35B ARG* 3.9 23.0 + - - +
12H A 4.0 23.9 + - - -
13H C 3.0 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A ARG* 4.3 17.1 - - - +
27A ARG* 1.3 75.9 - - - +
29A SER* 1.3 65.2 + - - +
35B ARG* 4.9 3.4 - - - -
18C T 3.3 18.2 + - - -
19C A 2.9 30.4 + - - -
12F A 5.6 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A ARG* 4.2 8.5 + - - -
28A ARG* 1.3 77.2 + - - +
30A CYS* 1.3 61.2 + - - +
31A GLN* 4.8 11.9 + - - +
35B ARG 4.2 11.9 + - - +
36B SER* 4.3 4.6 + - - -
37B CYS* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 1.3 73.3 + - - +
31A GLN* 1.3 77.7 + - - +
32A THR* 5.0 7.0 - - - +
37B CYS* 2.0 51.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A SER* 4.9 10.4 + - - -
30A CYS* 1.3 100.1 + - - +
32A THR* 1.3 64.9 + - - +
37B CYS 3.0 11.5 + - - +
38B ARG* 3.4 11.1 - - + +
39B HIS* 3.0 25.1 + - - +
11H T 4.3 19.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A CYS* 5.0 6.4 - - - +
31A GLN* 1.3 79.6 + - - +
33A ARG* 1.3 68.8 + - - +
34A ARG* 6.0 6.1 - - + -
39B HIS* 3.4 22.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 1.3 80.9 - - - +
34A ARG* 1.3 63.9 + - - +
35A ARG* 5.1 11.3 - - - +
39B HIS 3.0 11.1 + - - +
40B ARG* 3.5 10.1 - - + +
41B ARG* 3.1 25.2 + - - +
9H C 4.1 14.7 + - - -
10H G 3.0 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A THR* 6.0 5.6 - - + -
33A ARG* 1.3 78.2 - - - +
35A ARG* 1.3 65.8 + - - +
41B ARG* 3.7 13.9 - - + +
21C G 3.8 9.9 + - - -
22C T 2.9 39.6 + - - -
9F C 4.9 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A ARG* 5.1 9.8 - - - +
34A ARG* 1.3 77.0 - - - +
36A ALA* 1.3 65.8 + - - +
37A MET* 5.6 9.5 - - - +
41B ARG 3.1 13.2 + - - +
42B ARG* 5.0 7.2 - - + -
43B HIS* 3.3 25.6 + - - +
8H A 3.9 27.8 + - - -
9H C 3.0 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A ARG 4.3 0.4 + - - -
35A ARG* 1.3 80.5 + - - +
37A MET* 1.3 65.2 + - - +
38A ARG* 4.3 0.4 - - - -
43B HIS* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 5.6 9.0 - - - +
36A ALA* 1.3 76.8 - - - +
38A ARG* 1.3 62.5 + - - +
39A CYS* 5.1 13.9 - - - -
43B HIS* 3.5 14.1 + - - +
44B ARG* 5.3 5.2 - - + -
45B ARG* 3.9 23.0 + - - +
7H T 3.7 18.8 - - - +
8H A 3.3 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA 4.3 0.4 - - - -
37A MET* 1.3 74.7 - - - +
39A CYS* 1.3 72.1 + - - +
45B ARG* 4.9 3.4 - - - -
23C A 3.4 17.4 + - - -
24C C 2.9 28.9 + - - -
7F T 3.7 13.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A MET* 4.2 16.7 + - - -
38A ARG* 1.3 87.3 - - - +
40A CYS* 1.3 60.6 + - - +
45B ARG 4.2 12.1 + - - +
46B GLY* 4.3 1.4 - - - -
47B CYS* 3.1 22.9 + - - +
7H T 5.9 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A CYS* 1.3 73.5 - - - +
41A ARG* 1.3 64.8 + - - +
42A PRO* 3.7 15.4 - - + +
47B CYS* 2.0 51.4 - - - -
49B THR* 5.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A CYS* 1.3 77.4 - - - +
42A PRO* 1.3 68.5 - - - +
43A ARG* 4.4 24.1 - - + +
47B CYS 3.0 13.3 + - - +
48B ARG* 3.9 8.2 - - + +
49B THR 3.4 19.3 + - - +
5H C 4.1 12.7 + - - -
6H G 3.0 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A CYS* 3.7 15.2 - - + +
41A ARG* 1.3 90.9 - - - +
43A ARG* 1.3 65.6 + - - +
44A TYR* 5.4 5.2 - - + -
49B THR* 3.7 15.7 - - - +
----------------------------------------------------------
Back to top of page
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