Contacts of the helix formed by residues 12 - 40 (chain A) in PDB entry 2YW7
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 LYS 12 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 1.3 77.1 - - - +
13A LYS* 1.3 93.1 + - - +
14A ALA 3.3 1.3 - - - -
15A SER* 3.9 14.0 - - - -
16A ASP* 2.9 19.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP 4.4 10.5 - - - +
12A LYS* 1.3 97.6 - - - +
14A ALA* 1.3 60.8 + - + +
15A SER 3.2 0.9 - - - -
16A ASP* 3.3 11.8 + - - +
17A VAL* 3.0 32.5 + - + +
129A ASP 3.1 25.9 + - - -
130A LEU* 3.7 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 3.9 27.4 - - - +
12A LYS 3.3 0.2 - - - -
13A LYS* 1.3 80.9 - - + +
15A SER* 1.3 63.4 + - - +
17A VAL* 3.3 11.7 + - - +
18A ALA* 3.1 22.2 + - - +
75A LEU* 4.2 32.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP 4.6 8.5 + - - -
12A LYS* 3.9 13.1 + - - +
13A LYS 3.2 0.2 - - - -
14A ALA* 1.3 79.8 - - - +
16A ASP* 1.3 59.0 + - - +
18A ALA* 3.1 8.0 + - - +
19A ASP* 2.9 37.0 + - - +
75A LEU 5.1 0.4 + - - -
77A LYS* 3.5 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A LYS* 2.9 24.6 - - - +
13A LYS* 3.3 12.7 + - - +
15A SER* 1.3 74.7 - - - +
17A VAL* 1.3 67.6 + - - +
19A ASP* 3.4 9.6 + - - +
20A LEU* 3.3 21.7 + - - +
130A LEU* 4.5 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A LYS* 3.0 19.8 + - + +
14A ALA* 3.4 10.5 - - - +
15A SER 3.3 0.2 - - - -
16A ASP* 1.3 74.6 - - - +
18A ALA* 1.3 63.6 + - - +
20A LEU* 3.0 17.5 + - - +
21A LEU* 3.0 16.9 + - + +
75A LEU* 3.5 17.5 - - + -
127A LEU* 3.8 13.2 - - + -
130A LEU* 4.2 19.5 - - + +
131A ASP* 3.9 20.0 - - + +
134A SER* 3.3 33.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ALA 3.1 10.2 + - - +
15A SER* 3.3 10.5 - - - +
17A VAL* 1.3 79.5 - - - +
19A ASP* 1.3 53.0 + - - +
21A LEU* 2.9 15.3 + - - +
22A GLN* 2.8 35.8 + - - +
72A ILE* 3.8 12.4 - - + +
75A LEU* 4.5 5.8 - - + +
77A LYS* 3.6 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A SER* 2.9 18.4 + - - +
16A ASP* 3.7 10.0 - - - +
17A VAL 3.2 0.2 - - - -
18A ALA* 1.3 78.0 - - - +
20A LEU* 1.3 60.3 + - - +
22A GLN* 3.7 8.0 + - - +
23A LYS* 3.3 24.6 + - - +
77A LYS* 4.7 13.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A ASP 3.3 12.2 + - - +
17A VAL 3.0 8.1 + - - +
19A ASP* 1.3 78.6 - - - +
21A LEU* 1.3 57.8 - - + +
23A LYS* 3.1 22.4 + - - +
24A GLN* 2.9 26.6 + - - +
123A SER* 3.3 40.5 + - - +
126A LYS* 4.0 31.6 - - + +
127A LEU* 3.8 33.9 - - + -
130A LEU* 4.2 12.6 - - + -
138A LEU* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.0 16.5 + - + +
18A ALA* 2.9 8.3 + - - +
20A LEU* 1.3 77.1 - - + +
22A GLN* 1.3 52.5 + - - +
24A GLN* 3.3 7.6 + - - +
25A LEU 2.7 29.1 + - - -
68A VAL* 3.4 28.1 - - + +
71A ARG* 3.4 30.7 - - + -
72A ILE* 3.5 21.5 - - + +
75A LEU* 3.4 22.7 - - + -
127A LEU* 4.8 8.5 - - + -
134A SER* 3.8 24.9 - - - +
137A LEU* 5.3 1.3 - - + -
138A LEU* 4.8 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A ALA 2.8 19.3 + - - +
19A ASP* 3.8 9.9 - - - +
21A LEU* 1.3 68.9 - - - +
23A LYS* 1.3 65.3 + - - +
25A LEU* 3.1 14.1 + - - +
26A SER* 3.2 19.6 + - - -
72A ILE* 3.7 13.3 - - + +
78A SER 4.3 1.2 - - - +
79A PRO* 3.7 7.4 - - - +
80A LYS* 2.9 56.8 + - + +
85A ALA* 4.9 1.0 - - - +
89A ASP* 3.2 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ASP 3.3 12.9 + - - +
20A LEU* 3.1 28.9 + - - +
22A GLN* 1.3 76.9 - - - +
24A GLN* 1.3 57.4 + - - +
26A SER* 3.7 2.8 + - - -
27A THR* 2.7 33.0 + - - +
89A ASP* 3.9 38.4 - - + +
91A THR* 5.6 9.9 - - + -
92A TRP* 6.4 0.4 - - + -
123A SER* 5.4 2.5 + - - +
126A LYS* 5.1 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU 2.9 11.4 + - - +
21A LEU* 3.4 13.0 - - - +
23A LYS* 1.3 74.9 - - - +
25A LEU* 1.3 67.5 + - - +
27A THR* 3.1 19.8 + - - -
28A TYR* 3.1 43.5 + - + +
68A VAL* 4.5 2.5 - - + -
119A ASP* 4.2 11.9 + - - +
120A THR* 2.9 36.9 + - - +
123A SER* 3.3 26.9 + - - -
138A LEU* 3.6 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU 2.7 17.0 + - - +
22A GLN* 3.1 15.5 + - - +
24A GLN* 1.3 71.1 - - - +
26A SER* 1.3 58.0 + - - +
28A TYR* 2.8 25.6 + - - +
29A ASN* 3.0 39.2 + - - +
65A ALA* 3.6 30.1 - - + +
68A VAL* 3.5 17.7 - - + +
69A ALA* 4.4 1.3 - - + +
72A ILE* 4.4 1.6 - - + -
79A PRO* 4.2 11.2 - - + -
80A LYS 3.3 39.0 - - - +
40E TRP* 4.2 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A GLN* 3.2 17.7 + - - -
23A LYS 4.2 2.9 - - - -
24A GLN 3.4 0.2 - - - -
25A LEU* 1.3 78.8 - - - +
27A THR* 1.3 57.2 + - - +
29A ASN* 3.8 10.4 - - - +
30A ASP* 3.0 32.2 + - - +
80A LYS 4.4 3.1 + - - -
86A ILE* 3.3 30.7 + - - +
89A ASP* 2.7 32.4 + - - -
92A TRP* 4.0 5.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LYS* 2.7 21.9 + - - +
24A GLN* 3.1 20.4 + - - +
25A LEU 3.1 0.6 - - - -
26A SER* 1.3 78.9 - - - +
28A TYR* 1.3 61.0 + - + +
30A ASP* 3.9 2.4 + - - +
31A LEU* 3.1 21.4 + - - +
92A TRP* 3.4 31.6 - - + -
116A VAL* 4.3 38.1 - - + +
119A ASP* 5.0 11.4 + - + +
120A THR* 5.5 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLN* 3.1 41.5 + - + -
25A LEU* 2.8 9.2 + - - +
27A THR* 1.3 79.4 - - + +
29A ASN* 1.3 54.4 - - - +
31A LEU* 2.8 13.7 + - + +
32A HIS* 2.8 32.6 + - - -
61A VAL* 3.5 19.9 - - + +
64A TYR* 3.6 14.1 - + + -
65A ALA* 3.7 28.9 - - + -
68A VAL* 4.2 8.7 - - + -
116A VAL* 5.2 2.7 - - + -
120A THR* 4.9 1.4 - - - +
138A LEU* 3.4 15.8 - - - +
141A HIS* 2.6 40.9 + + - +
145A LEU* 4.0 23.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.0 44.5 + - - +
26A SER* 3.4 6.5 + - - +
28A TYR* 1.3 75.4 - - - +
30A ASP* 1.3 67.4 + - - +
31A LEU 3.1 0.2 + - - -
32A HIS* 3.3 22.8 + - - +
33A LEU* 3.1 31.5 + - - +
65A ALA* 3.8 12.0 - - - +
80A LYS 4.6 0.6 + - - -
81A GLY* 4.4 10.5 - - - -
86A ILE* 3.4 26.7 - - + +
33E LEU* 4.0 12.5 - - + +
40E TRP* 4.6 6.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A SER 3.0 17.5 + - - +
27A THR 4.0 0.7 - - - +
29A ASN* 1.3 74.9 - - - +
31A LEU* 1.3 55.7 + - - +
33A LEU* 3.9 10.3 - - - +
34A THR* 2.6 48.2 + - - -
86A ILE* 3.9 7.6 - - + +
90A ARG* 2.8 34.1 + - - -
92A TRP* 3.0 34.5 + - + -
94A ASP* 5.3 0.3 - - - +
95A TYR 5.6 1.9 + - - -
112A VAL* 5.7 4.2 - - - +
83E PRO* 3.4 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR 3.1 16.0 + - - +
28A TYR* 2.8 18.8 + - + +
30A ASP* 1.3 77.4 - - - +
32A HIS* 1.3 54.3 + - - +
34A THR* 3.2 5.0 + - - -
35A LEU* 2.8 41.3 + - + +
61A VAL* 3.7 25.8 - - + -
109A LEU* 5.5 2.0 - - + -
112A VAL* 4.6 16.4 - - + -
113A TYR* 3.6 37.2 - - + +
116A VAL* 4.3 18.6 - - + -
145A LEU* 4.0 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A TYR 2.8 25.2 + - - -
29A ASN* 3.3 33.9 + - - -
31A LEU* 1.3 70.9 - - - +
33A LEU* 1.3 92.5 + - + +
35A LEU* 3.5 8.6 - - - +
36A LYS* 3.0 26.9 + - - +
58A VAL* 4.2 9.1 - - + +
61A VAL* 3.8 18.8 - - + +
62A ARG* 3.8 47.0 + - + +
65A ALA* 4.6 4.3 - - + +
32E HIS* 4.6 11.6 - + - -
33E LEU* 4.4 10.2 - - + +
62E ARG* 5.2 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASN 3.1 24.6 + - - +
30A ASP 3.9 2.2 - - - +
32A HIS* 1.3 88.3 + - + +
34A THR* 1.3 58.6 + - - +
36A LYS* 3.5 5.0 + - - +
37A HIS* 3.0 26.3 + - - +
40A TRP* 5.4 0.7 - - - -
86A ILE* 3.8 15.5 - - + -
29E ASN* 4.4 12.8 - - + +
32E HIS* 4.3 20.2 - - + +
33E LEU* 3.8 25.8 - - + -
81E GLY* 3.4 26.7 - - - +
83E PRO* 3.7 28.3 - - + -
86E ILE* 5.8 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 34 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ASP* 2.6 36.1 + - - +
31A LEU* 3.5 7.0 - - + +
33A LEU* 1.3 73.0 - - - +
35A LEU* 1.3 66.8 + - - +
37A HIS* 3.1 9.3 + - - +
38A VAL* 2.9 24.4 + - + +
95A TYR* 3.5 42.3 + - + +
109A LEU* 4.5 8.1 - - + -
112A VAL* 4.9 9.2 - - + -
82E THR* 3.8 16.6 - - - +
83E PRO* 4.7 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 2.8 26.5 + - + +
32A HIS* 3.5 7.2 - - - +
33A LEU 3.3 0.2 - - - -
34A THR* 1.3 77.7 - - - +
36A LYS* 1.3 56.4 + - - +
38A VAL* 3.0 10.2 - - - +
39A HIS* 2.9 24.4 + - - +
54A ILE* 3.9 18.5 - - + +
57A GLN* 3.8 14.1 - - + -
58A VAL* 3.7 20.2 - - + -
61A VAL* 4.1 12.6 - - + -
109A LEU* 3.7 37.2 - - + -
113A TYR* 3.4 26.7 - - + +
148A PHE* 4.5 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A HIS 3.0 13.8 + - - +
33A LEU* 3.9 4.7 - - - +
35A LEU* 1.3 76.2 - - - +
37A HIS* 1.3 57.5 + - - +
39A HIS* 3.0 22.6 + - + +
40A TRP* 2.9 54.6 + - + +
55A ASP* 5.1 5.4 - - - +
58A VAL* 3.7 34.3 - - + -
59A GLU* 5.9 0.4 - - - -
62A ARG* 3.9 21.4 - - - +
66E ASP* 2.7 48.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 37 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 3.0 15.2 + - - +
34A THR* 3.2 13.9 - - - +
36A LYS* 1.3 76.9 - - - +
38A VAL* 1.3 57.5 + - - +
40A TRP* 3.6 12.1 + - - +
41A ASN* 2.6 38.7 + - - +
95A TYR* 3.6 31.8 + + - -
97A VAL 2.9 24.1 + - - -
98A GLU* 4.8 5.1 + - - -
79E PRO 3.1 25.6 + - - -
80E LYS* 3.4 12.8 + - + -
81E GLY* 2.9 26.0 + - - +
82E THR* 4.3 12.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A THR 2.9 14.1 + - - +
35A LEU* 3.0 19.9 + - - +
37A HIS* 1.3 72.2 - - - +
39A HIS* 1.3 67.9 + - - +
40A TRP 3.1 0.2 - - - -
41A ASN 2.9 0.7 + - - -
42A VAL* 2.8 33.1 + - + +
50A VAL* 5.2 0.4 - - + -
54A ILE* 3.3 24.7 - - + -
95A TYR* 3.5 40.6 - - + +
105A HIS* 3.7 19.1 - - + +
109A LEU* 4.0 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU 2.9 13.0 + - - +
36A LYS* 3.2 28.2 - - + +
38A VAL* 1.3 81.3 - - - +
40A TRP* 1.3 71.3 + + + +
41A ASN 3.3 0.5 + - - -
42A VAL* 4.0 3.3 + - - +
51A HIS* 3.0 71.4 - + - +
54A ILE* 4.1 22.2 - - + -
55A ASP* 3.3 33.0 + - - -
150C TRP* 6.0 0.3 - - - -
66E ASP* 6.0 0.7 - - - -
70E GLU* 5.8 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU 5.4 0.4 - - - -
36A LYS* 2.9 36.3 + - + +
37A HIS* 3.9 14.8 - - - +
38A VAL 3.1 0.2 - - - -
39A HIS* 1.3 87.7 - + + +
41A ASN* 1.3 65.2 + - - +
42A VAL 5.3 0.4 - - - -
150C TRP* 4.6 12.5 - - - -
25E LEU* 4.0 24.5 - - + -
29E ASN* 4.4 7.0 - - - -
65E ALA* 4.3 8.1 - - + -
66E ASP* 2.5 54.4 + - - +
69E ALA* 3.6 23.8 - - + -
70E GLU* 4.6 17.0 - - + +
73E ALA* 4.4 16.8 - - + +
79E PRO* 4.2 19.1 - - + -
81E GLY* 4.2 22.2 - - - -
----------------------------------------------------------
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