Contacts of the helix formed by residues 17 - 47 (chain L) in PDB entry 5W97
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 ASN 17 (chain L).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L SER* 4.9 1.1 + - - +
15L VAL* 4.5 3.7 - - - -
16L GLU* 1.3 77.5 - - + +
18L LYS* 1.3 59.4 + - - +
19L TRP* 2.7 41.1 + - - +
20L ARG* 2.9 26.9 + - + +
21L LEU* 3.0 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 18 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TRP* 2.9 32.5 + - + +
476A PHE 5.8 0.2 - - - -
477A ALA* 3.3 37.2 - - + +
15L VAL 4.8 2.3 + - - -
16L GLU 4.2 1.4 + - - -
17L ASN* 1.3 72.1 + - - +
19L TRP* 1.3 87.9 + - + +
21L LEU* 3.5 10.0 - - - +
22L LEU* 3.0 10.6 + - - +
8M THR* 3.0 27.6 + - - -
9M PRO 3.2 3.2 + - - -
10M THR* 3.0 24.4 + - - +
14M GLU* 3.1 26.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 19 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TRP* 3.9 14.4 - + - -
17L ASN* 2.7 24.1 + - - +
18L LYS* 1.3 87.8 - - + +
20L ARG* 1.3 63.2 + - - +
21L LEU 3.1 1.3 - - - -
22L LEU* 3.6 32.2 - - + +
23L ALA* 3.2 21.5 + - - +
14M GLU* 3.8 55.3 + - + -
17M ILE* 3.8 26.5 - - + -
18M GLY 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 20 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14L SER* 4.2 17.4 + - - -
17L ASN* 2.9 28.7 + - + +
19L TRP* 1.3 76.2 - - - +
21L LEU* 1.3 61.2 + - - +
23L ALA* 3.3 7.8 + - + +
24L MET* 3.1 41.4 + - + +
101L TGL 3.2 51.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TRP* 4.0 17.9 - - + +
476A PHE* 3.5 37.2 - - + +
477A ALA 4.4 0.9 - - - +
13L PHE* 3.8 31.9 - - + -
14L SER 3.8 11.0 - - - +
15L VAL* 3.8 13.0 - - + -
17L ASN 3.0 17.1 + - - +
18L LYS* 3.5 8.3 - - - +
19L TRP 3.1 0.2 - - - -
20L ARG* 1.3 74.4 - - - +
22L LEU* 1.3 65.3 + - - +
24L MET* 3.3 13.0 + - + +
25L MET* 3.0 38.5 + - + +
101L TGL 5.2 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473A TRP* 3.5 37.8 - - + +
18L LYS 3.0 10.9 + - - +
19L TRP* 3.6 37.5 - - + +
21L LEU* 1.3 76.7 - - - +
23L ALA* 1.3 56.0 + - - +
25L MET* 3.4 3.7 + - + +
26L THR* 3.0 38.0 + - - +
17M ILE* 4.8 0.4 - - + -
18M GLY* 3.9 29.6 - - - +
21M VAL* 4.0 26.7 - - + -
22M THR* 4.0 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 23 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19L TRP 3.2 10.3 + - - +
20L ARG* 3.5 11.7 - - + +
21L LEU 3.1 0.4 - - - -
22L LEU* 1.3 78.1 - - - +
24L MET* 1.3 66.0 + - + +
26L THR* 3.9 7.8 - - - +
27L LEU* 3.2 33.6 + - + +
21M VAL* 6.2 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 24 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13L PHE* 4.4 6.7 - - + -
14L SER 3.5 31.0 - - - +
20L ARG* 3.1 49.1 + - + +
21L LEU* 3.7 13.2 - - + +
23L ALA* 1.3 77.3 - - + +
25L MET* 1.3 59.0 + - - +
27L LEU* 3.4 9.9 + - + +
28L PHE* 3.0 30.0 + - - +
101L TGL 4.3 60.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 25 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A VAL* 3.5 30.7 - - + +
472A ILE* 3.9 16.4 - - + +
473A TRP* 3.6 39.3 - - + +
476A PHE* 5.4 1.8 - - - -
21L LEU* 3.0 31.1 + - + +
22L LEU* 3.8 6.1 - - + +
23L ALA 3.4 0.2 - - - -
24L MET* 1.3 74.1 - - - +
26L THR* 1.3 56.9 + - - +
28L PHE* 3.1 5.3 + - - -
29L PHE* 2.7 63.1 + - + +
101L TGL 3.6 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 26 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A VAL* 5.7 2.1 - - - +
22L LEU* 3.0 19.6 + - - +
23L ALA* 3.9 9.2 - - - +
25L MET* 1.3 78.4 - - - +
27L LEU* 1.3 61.3 + - + +
29L PHE* 5.3 1.1 - - - -
30L GLY* 3.0 27.4 + - - +
21M VAL* 4.0 21.8 + - + +
22M THR* 4.2 7.3 + - - +
25M SER* 3.4 34.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23L ALA* 3.2 29.8 + - + +
24L MET* 3.8 9.0 - - + +
25L MET 3.3 0.2 - - - -
26L THR* 1.3 78.6 - - + +
28L PHE* 1.3 59.7 + - - +
31L SER* 2.9 35.7 + - - +
101L TGL 4.5 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 28 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU* 3.5 38.4 - - + -
24A ALA* 5.0 0.4 - - + -
25A TRP* 2.8 51.4 + + + -
24L MET 3.0 18.1 + - - +
25L MET* 3.1 5.1 + - - +
27L LEU* 1.3 76.9 - - - +
29L PHE* 1.3 92.3 + + - +
31L SER* 3.0 9.5 + - - -
101L TGL 3.8 85.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A ALA* 3.9 23.3 - - + -
25A TRP* 4.8 0.9 - - - -
28A MET* 3.6 36.2 - - + +
468A MET* 5.7 2.2 - - + -
469A VAL* 3.6 25.6 - - + -
472A ILE* 5.0 6.5 - - + -
25L MET* 2.7 45.4 + - + +
26L THR* 5.3 1.1 - - - -
28L PHE* 1.3 90.9 - + - +
30L GLY* 1.3 65.1 + - - +
32L GLY 3.4 1.7 + - - -
33L PHE* 3.1 23.7 + - - +
101L TGL 3.5 39.3 - - + -
26M PHE* 4.0 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 30 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26L THR* 3.0 21.1 + - - +
29L PHE* 1.3 79.4 - - - +
31L SER* 1.3 61.0 + - - +
33L PHE* 3.4 5.4 + - - +
34L ALA* 3.0 25.2 + - - +
25M SER* 4.1 24.6 + - - +
26M PHE* 5.5 2.2 - - - -
29M PRO* 5.6 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 31 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TRP* 3.3 14.6 + - - -
26L THR 4.2 0.2 + - - -
27L LEU* 2.9 26.5 + - - +
28L PHE 3.0 10.6 + - - -
30L GLY* 1.3 75.2 - - - +
32L GLY* 1.3 55.7 + - - +
34L ALA* 3.5 6.3 + - - +
35L ALA* 3.0 28.8 + - - +
101L TGL 3.9 26.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 32 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TRP* 3.5 27.7 - - - +
28A MET* 4.0 10.5 - - - -
29A VAL* 3.5 17.5 - - - +
29L PHE 3.4 5.6 + - - -
30L GLY 3.3 0.4 - - - -
31L SER* 1.3 79.7 + - - +
33L PHE* 1.3 65.0 + - - +
35L ALA* 3.3 2.2 + - - +
36L PRO* 3.3 19.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 33 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A MET* 3.7 18.8 - - + +
31A THR* 4.2 6.1 - - + -
32A ALA* 3.1 45.5 - - + +
35A LEU* 3.7 26.0 - - + -
462A LEU* 3.7 22.0 - - + -
29L PHE 3.1 16.5 + - - +
30L GLY* 3.9 4.5 - - - +
32L GLY* 1.3 73.5 - - - +
34L ALA* 1.3 62.1 + - - +
36L PRO* 3.5 1.4 - - - +
37L PHE* 3.3 32.4 - + - -
26M PHE* 3.4 59.0 - + + -
27M LEU* 5.9 0.7 - - + -
29M PRO* 6.6 0.2 - - + -
30M ALA* 4.1 6.3 - - + -
101M DMU 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 34 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30L GLY 3.0 17.9 + - - +
31L SER* 3.7 7.9 - - - +
32L GLY 3.2 0.2 - - - -
33L PHE* 1.3 80.1 - - - +
35L ALA* 1.3 64.9 + - - +
37L PHE* 3.0 20.4 + - - +
38L PHE* 3.2 24.8 + - + -
29M PRO* 4.2 26.0 - - + -
30M ALA 5.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 35 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TRP* 5.2 6.5 - - + -
29A VAL* 4.8 8.1 - - + -
113A LEU* 5.4 7.0 - - + -
31L SER 3.0 17.0 + - - +
32L GLY* 3.6 7.0 - - - +
34L ALA* 1.3 75.3 - - - +
36L PRO* 1.3 72.0 - - + +
38L PHE* 3.2 7.7 + - - +
39L ILE* 3.0 34.1 + - + +
101L TGL 6.2 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 36 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A VAL* 3.4 36.1 - - + +
32A ALA* 4.0 5.4 - - + -
33A LEU* 3.7 28.0 - - + +
36A LEU* 4.1 11.0 - - + -
32L GLY 3.3 15.3 - - - +
33L PHE 3.5 9.4 - - - +
35L ALA* 1.3 91.9 - - + +
37L PHE* 1.3 56.9 + - - +
39L ILE* 3.3 13.2 + - + +
40L VAL* 3.0 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 37 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 3.7 20.0 - - + -
35A LEU* 5.0 0.2 - - + -
36A LEU* 3.7 31.4 - - + -
33L PHE* 3.3 41.3 - + - -
34L ALA* 3.0 10.5 + - - +
36L PRO* 1.3 76.1 - - - +
38L PHE* 1.3 59.0 + - + +
40L VAL* 3.4 4.1 + - - +
41L ARG* 3.1 21.3 + - - +
29M PRO 5.6 0.2 - - - -
30M ALA* 3.6 35.4 - - + -
33M VAL* 3.4 34.6 - - + +
34M LEU* 4.2 25.8 - - + -
101M DMU 4.2 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 38 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34L ALA* 3.2 31.3 + - + +
35L ALA* 3.2 9.5 + - - +
37L PHE* 1.3 77.0 - - + +
39L ILE* 1.3 59.7 + - + +
41L ARG* 3.6 24.0 + - - +
42L HIS* 2.9 29.3 + - - +
29M PRO* 4.5 16.4 - - + -
32M TRP* 4.1 28.7 - + - -
33M VAL* 4.0 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 39 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A LEU* 6.5 0.7 - - + -
56A VAL* 5.7 3.6 - - + -
113A LEU* 3.9 26.0 - - + +
116A SER* 3.4 43.7 - - - +
117A MET* 4.0 20.0 - - + -
35L ALA* 3.0 29.3 + - + +
36L PRO* 3.3 11.6 + - + +
38L PHE* 1.3 77.0 - - + +
40L VAL* 1.3 66.3 + - + +
42L HIS* 3.3 7.9 + - - +
43L GLN* 3.0 24.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 40 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.0 13.7 - - + -
48A LEU* 3.8 26.5 - - + -
53A ILE* 3.8 15.8 - - + +
57A VAL* 3.7 30.5 - - + -
36L PRO 3.0 19.0 + - - +
37L PHE* 3.9 5.2 - - - +
38L PHE 3.3 0.2 - - - -
39L ILE* 1.3 79.6 - - + +
41L ARG* 1.3 58.2 + - - +
43L GLN* 3.2 5.7 + - - +
44L LEU* 3.0 41.5 + - + +
33M VAL* 5.4 2.9 - - + -
37M LEU* 4.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 41 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L PHE 3.1 16.8 + - - +
38L PHE* 3.6 31.5 + - - +
40L VAL* 1.3 77.9 - - - +
42L HIS* 1.3 64.7 + - - +
44L LEU* 3.2 7.8 + - - +
45L LEU* 2.9 48.7 + - + +
32M TRP* 3.9 18.7 - - - -
33M VAL* 4.2 6.7 - - + +
40M TYR* 2.9 52.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 42 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A SER 4.9 0.2 - - - -
117A MET* 3.1 44.1 + - + +
54J SER* 2.9 41.7 + - - -
55J PHE* 4.0 26.4 - + - -
38L PHE 2.9 18.6 + - - +
39L ILE* 3.4 7.0 - - - +
41L ARG* 1.3 81.4 - - - +
43L GLN* 1.3 67.0 + - + +
45L LEU* 3.5 6.6 + - - +
46L LYS* 3.2 36.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 43 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.9 27.1 - - + +
56A VAL* 6.0 4.9 - - + -
116A SER 2.8 32.4 + - - +
117A MET 3.8 9.3 + - - -
119A GLU 2.9 28.8 + - - +
120A ALA* 3.5 20.7 - - - +
121A GLY 3.8 2.4 - - - +
39L ILE* 3.0 19.9 + - + +
40L VAL* 3.8 5.8 - - - +
41L ARG 3.2 0.2 - - - -
42L HIS* 1.3 75.7 - - + +
44L LEU* 1.3 65.1 + - - +
45L LEU 3.6 0.2 + - - -
46L LYS* 3.6 11.3 + - - +
47L LYS* 3.6 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.4 28.3 - - + +
49A GLY 5.4 0.2 - - - -
50A ASP* 4.4 6.5 - - + +
53A ILE* 3.4 22.0 - - + -
40L VAL* 3.0 28.7 + - + +
41L ARG 3.7 4.5 - - - +
43L GLN* 1.3 77.0 - - - +
45L LEU* 1.3 60.0 + - - +
46L LYS 3.4 0.7 + - - -
47L LYS* 3.5 20.1 + - - +
37M LEU* 3.6 30.7 - - + -
40M TYR* 3.8 30.5 - - + +
41M LYS* 4.4 13.9 - - + -
43M SER* 3.7 10.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 45 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L ARG* 2.9 59.6 + - + +
42L HIS* 4.1 6.3 - - - +
43L GLN 3.3 0.4 - - - -
44L LEU* 1.3 75.0 - - - +
46L LYS* 1.3 61.3 + - - +
40M TYR* 3.9 37.2 - - + +
43M SER* 3.7 13.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 46 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A MET 3.0 12.9 + - - -
119A GLU* 2.8 36.5 + - - +
53J ALA 4.9 0.4 + - - -
54J SER 2.9 22.7 + - - +
55J PHE* 4.7 3.3 - - + -
56J PRO* 4.1 33.4 - - + +
42L HIS* 3.2 38.0 + - + +
43L GLN* 4.0 14.6 - - - +
44L LEU 3.3 0.2 - - - -
45L LEU* 1.3 78.6 - - - +
47L LYS* 1.3 81.4 + - + +
43M SER* 3.2 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 47 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASP* 3.6 21.4 - - - +
119A GLU 6.1 2.0 - - - +
120A ALA* 6.3 3.1 - - + -
56J PRO* 5.1 14.9 - - + +
43L GLN* 3.6 15.6 + - - +
44L LEU* 3.5 15.2 + - - +
46L LYS* 1.3 97.3 - - + +
43M SER* 3.3 26.4 + - - -
----------------------------------------------------------
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