Contacts of the helix formed by residues 48 - 80 (chain D) in PDB entry 4IRV
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 GLN 48 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41D VAL* 3.6 16.4 - - + -
45D ASP* 3.5 34.3 - - + +
46D PRO 3.1 1.4 - - - -
47D ASP* 1.3 80.3 - - - +
49D LYS* 1.3 66.7 + - - +
50D PRO* 3.2 3.4 - - - -
51D ILE* 3.2 16.3 + - - +
52D VAL* 3.0 23.8 + - - +
159D LYS 5.5 0.9 - - - +
162D ALA* 4.3 11.0 - - + -
163D GLU* 5.7 3.4 - - - -
166D LYS* 2.8 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 49 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39D ASN* 5.2 10.8 - - - +
42D ALA* 3.9 28.5 - - + +
45D ASP 3.9 2.2 + - - -
46D PRO* 3.1 16.2 + - + +
48D GLN* 1.3 78.3 - - - +
50D PRO* 1.4 69.7 - - + +
52D VAL* 3.3 8.3 + - - +
53D ASP* 3.0 53.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 50 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B ASN* 5.5 1.6 + - - -
46D PRO 4.0 2.0 - - - +
47D ASP* 3.6 15.7 - - - +
48D GLN 3.4 4.0 - - - -
49D LYS* 1.4 98.5 - - + +
51D ILE* 1.3 67.8 + - + +
53D ASP* 4.0 5.8 - - + +
54D LYS* 3.3 23.4 + - - +
747F PRO* 6.4 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 51 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLU* 5.2 11.4 - - - +
47D ASP 4.3 8.5 - - - +
48D GLN* 3.8 30.5 - - - +
49D LYS 3.2 0.4 - - - -
50D PRO* 1.3 89.5 - - + +
52D VAL* 1.4 58.6 + - - +
54D LYS* 3.3 4.4 + - - +
55D ASN* 3.0 41.8 + - - +
106D ASP* 5.3 4.0 - - - +
109D SER* 6.0 1.3 - - - +
166D LYS* 4.4 13.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D VAL* 5.0 0.4 - - + -
38D ASP* 3.9 27.6 - - - +
41D VAL* 3.8 28.0 - - + -
42D ALA* 5.7 0.2 - - + -
48D GLN 3.0 15.5 + - - +
49D LYS* 3.4 12.6 - - - +
51D ILE* 1.4 76.5 - - - +
53D ASP* 1.3 69.2 + - - +
55D ASN* 3.3 10.3 + - - +
56D ASP* 2.9 27.2 + - - +
166D LYS* 4.2 17.9 - - + -
169D LYS* 3.9 23.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 53 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ASP* 4.3 13.6 - - - +
39D ASN* 5.5 1.9 + - - -
49D LYS* 3.0 56.6 + - - +
50D PRO* 4.0 6.4 - - + +
52D VAL* 1.3 83.1 - - - +
54D LYS* 1.3 59.9 + - - +
56D ASP* 3.4 8.7 + - - +
57D ARG* 3.1 31.9 + - - +
60D ARG* 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 54 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LYS* 5.2 11.7 - - - +
58B ASP* 5.8 1.2 + - - -
101B LYS 3.8 17.7 - - - +
102B ASP* 2.9 45.2 + - - +
103B ASN* 4.0 18.6 - - - +
50D PRO 3.3 16.9 + - - +
51D ILE* 3.7 4.9 - - - +
53D ASP* 1.3 73.7 - - - +
55D ASN* 1.4 68.9 + - - +
56D ASP 3.0 1.3 + - - -
57D ARG* 3.1 7.4 + - + +
58D ASP* 2.7 53.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 55 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51D ILE* 3.0 30.2 + - - +
52D VAL* 3.3 9.2 + - - +
54D LYS* 1.4 76.2 - - - +
56D ASP* 1.3 58.0 + - - +
58D ASP* 3.2 8.7 + - - +
59D ASN* 2.8 36.9 + - - +
106D ASP* 3.7 28.4 + - - +
166D LYS* 3.7 29.9 + - - +
169D LYS* 4.9 3.6 - - + -
170D GLN* 3.6 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 56 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PHE* 3.3 18.4 - - - -
35D ILE* 4.1 7.4 - - - +
38D ASP* 3.1 25.3 - - - +
52D VAL 2.9 11.2 + - - +
53D ASP* 3.5 7.7 - - - +
54D LYS 3.0 0.4 - - - -
55D ASN* 1.3 78.5 - - - +
57D ARG* 1.3 59.7 + - - +
59D ASN* 3.5 3.9 + - - +
60D ARG* 2.7 57.2 + - - +
169D LYS* 2.6 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 57 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ASP 5.7 0.2 + - - -
101B LYS* 3.5 52.2 + - - +
102B ASP* 3.0 41.8 + - - +
53D ASP* 3.1 15.7 + - - +
54D LYS* 3.1 8.9 + - - +
56D ASP* 1.3 75.8 - - - +
58D ASP* 1.3 58.8 + - - +
60D ARG* 3.4 33.3 + - - +
61D GLN* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 58 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LYS* 5.7 1.5 + - - -
102B ASP* 4.5 0.7 - - - +
54D LYS* 2.7 55.0 + - - +
55D ASN* 3.6 10.5 - - - +
57D ARG* 1.3 76.7 - - - +
59D ASN* 1.3 66.3 + - - +
61D GLN* 3.3 5.3 + - - +
62D ALA 2.9 18.9 + - - -
102D ASP* 4.4 6.3 - - - +
103D ASN 4.3 6.7 - - - +
104D LEU* 3.6 43.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 59 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PHE* 3.3 37.0 - - + -
55D ASN 2.8 23.6 + - - +
56D ASP 3.7 0.7 - - - +
58D ASP* 1.3 73.7 - - - +
60D ARG* 1.3 58.5 + - - +
62D ALA* 3.2 5.7 + - - +
63D PHE* 2.9 34.9 + - + -
104D LEU 2.9 19.3 - - - +
105D ILE* 4.0 4.4 - - - +
169D LYS* 4.2 3.6 - - - +
170D GLN* 2.9 37.9 + - - -
173D ALA* 3.7 15.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PHE* 4.1 16.8 - - + -
35D ILE* 4.6 10.1 - - + -
53D ASP 5.1 0.2 + - - -
56D ASP* 2.7 53.9 + - - +
57D ARG* 3.9 38.3 - - - +
59D ASN* 1.3 75.8 - - - +
61D GLN* 1.3 61.4 + - - +
63D PHE* 3.3 17.4 + - + +
64D ASP* 3.1 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 61 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57D ARG 2.9 17.7 + - - +
58D ASP* 3.4 9.6 - - - +
60D ARG* 1.3 73.6 - - - +
62D ALA* 1.3 58.3 + - - +
64D ASP* 4.7 10.1 - - - +
65D GLY* 2.8 37.2 + - - +
68D GLN* 4.9 5.5 - - - +
98D LEU* 4.7 5.8 - - + +
104D LEU* 4.2 18.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 62 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D ASP 2.9 13.9 + - - +
59D ASN* 3.2 11.6 + - - +
61D GLN* 1.3 72.8 - - - +
63D PHE* 1.3 68.6 + - - +
66D ILE* 2.9 29.3 + - - +
98D LEU* 4.4 4.7 - - - -
99D ILE* 3.8 25.6 - - + -
104D LEU* 3.9 16.9 - - + +
105D ILE* 4.7 2.2 - - + -
177D ILE* 3.9 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 63 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34D PHE* 3.8 46.0 - + - -
59D ASN 2.9 20.0 + - - -
60D ARG* 3.3 19.9 + - + +
62D ALA* 1.3 76.2 - - - +
64D ASP* 1.4 61.0 + - - +
66D ILE* 4.0 1.8 - - - +
67D SER* 3.1 30.0 + - - -
70D ARG* 5.0 0.2 + - - -
173D ALA* 3.7 20.0 - - + -
176D ILE* 4.1 18.4 - - + -
177D ILE* 3.3 30.5 - - + -
180D GLN* 3.8 32.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 64 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60D ARG* 3.1 17.2 + - - +
61D GLN* 4.0 10.6 + - - +
63D PHE* 1.4 79.8 - - - +
65D GLY* 1.3 61.2 + - - +
67D SER* 3.4 6.9 + - - -
68D GLN* 2.9 40.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 65 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D GLN* 2.8 25.3 + - - +
64D ASP* 1.3 69.3 - - - +
66D ILE* 1.3 66.8 + - - +
68D GLN* 3.2 15.4 + - - +
69D LEU* 3.0 27.6 + - - +
98D LEU* 3.6 20.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D ALA 2.9 22.4 + - - +
63D PHE 4.0 1.8 - - - +
65D GLY* 1.3 75.6 - - - +
67D SER* 1.3 58.9 + - - +
69D LEU* 3.0 5.2 + - - +
70D ARG* 2.9 49.4 + - + +
91D PHE* 4.8 4.3 - - + -
95D SER* 3.9 28.7 - - - +
98D LEU* 3.5 19.0 - - + +
99D ILE* 4.2 15.5 - - + -
177D ILE* 4.2 16.8 - - + -
180D GLN* 5.9 0.2 - - - +
181D ILE* 4.0 23.3 - - + -
212D TRP* 5.9 0.2 - - + -
216D PHE* 4.3 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D PHE 3.1 18.0 + - - -
64D ASP* 3.5 8.1 - - - -
66D ILE* 1.3 76.6 - - - +
68D GLN* 1.3 63.4 + - - +
70D ARG* 3.3 30.3 + - - +
71D GLU* 3.1 32.0 + - - +
180D GLN* 5.8 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 68 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D GLN* 4.9 6.9 - - - +
64D ASP* 2.9 30.6 + - + +
65D GLY* 3.7 15.0 - - - +
66D ILE 3.2 0.2 - - - -
67D SER* 1.3 76.7 - - - +
69D LEU* 1.3 60.0 + - + +
71D GLU* 3.8 6.0 - - - +
72D GLU* 3.0 30.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D GLY 3.0 18.1 + - - +
66D ILE* 3.0 7.6 + - - +
68D GLN* 1.3 77.6 - - + +
70D ARG* 1.3 63.5 + - - +
72D GLU* 4.0 11.4 - - - +
73D TYR* 3.1 45.2 + - + +
91D PHE* 3.6 15.3 - - + -
94D LYS* 3.8 32.1 - - + +
95D SER* 3.9 29.4 - - - +
98D LEU* 4.2 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D ILE* 2.9 34.8 + - + +
67D SER* 3.7 36.6 + - - +
69D LEU* 1.3 73.6 - - - +
71D GLU* 1.3 61.8 + - - +
74D SER* 2.9 35.5 + - - -
91D PHE* 3.6 15.2 - - + -
180D GLN* 3.5 33.9 + - - +
181D ILE* 3.8 30.9 - - - +
184D ASP* 2.8 34.1 + - - +
187D PHE* 3.8 28.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D SER* 3.1 26.1 + - - +
68D GLN* 3.8 6.3 - - - +
70D ARG* 1.3 79.9 + - + +
72D GLU* 1.3 64.7 + - - +
74D SER* 4.0 2.2 - - - -
75D ASN* 3.0 37.7 + - - +
184D ASP* 4.2 14.2 - - - +
186D LYS* 2.7 36.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 72 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68D GLN 3.0 18.7 + - - +
69D LEU* 3.8 15.3 - - - +
70D ARG 3.4 0.2 - - - -
71D GLU* 1.3 77.8 - - - +
73D TYR* 1.3 88.0 + - + +
75D ASN* 3.8 4.8 - - - +
76D LYS* 3.0 60.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 73 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D LEU* 3.1 39.7 + - + +
70D ARG 4.6 0.2 - - - +
72D GLU* 1.3 109.2 + - + +
74D SER* 1.3 63.4 + - - +
76D LYS* 3.2 17.4 + - + +
77D ALA* 3.0 25.1 + - - +
87D TYR* 3.5 34.2 - + + +
90D ASP* 3.6 27.8 + - + +
91D PHE* 4.0 26.9 - + + -
94D LYS* 3.8 27.5 - - + +
191D PHE* 3.5 11.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 74 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70D ARG 2.9 23.6 + - - -
71D GLU* 3.3 6.5 - - - -
73D TYR* 1.3 72.9 - - - +
75D ASN* 1.3 66.1 + - - +
77D ALA* 3.2 3.3 + - - +
78D ILE* 3.0 27.0 + - - +
184D ASP* 4.9 0.9 + - - -
186D LYS* 3.5 35.8 - - - +
187D PHE* 3.7 16.6 + - - +
190D VAL* 3.8 5.4 - - - +
191D PHE* 3.7 15.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 75 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71D GLU* 3.0 29.4 + - - +
72D GLU* 3.8 5.0 - - - +
74D SER* 1.3 80.9 - - - +
76D LYS* 1.3 64.6 + - + +
78D ILE* 3.2 9.9 + - - +
79D LYS* 2.9 25.0 + - - +
186D LYS* 2.9 32.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 76 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D GLU* 3.0 54.8 + - - +
73D TYR* 3.2 17.8 + - + +
75D ASN* 1.3 77.1 - - + +
77D ALA* 1.3 57.2 + - - +
79D LYS* 3.2 7.5 + - - +
80D ASN* 2.8 25.8 + - - +
87D TYR* 3.4 44.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D TYR 3.0 15.5 + - - +
76D LYS* 1.3 77.0 - - - +
78D ILE* 1.3 61.9 + - - +
80D ASN 4.2 0.9 - - - -
81D PRO* 3.1 29.1 - - - +
84D LYS* 4.4 12.9 - - + +
87D TYR* 3.6 14.5 - - + -
190D VAL* 3.3 27.8 - - + -
191D PHE* 3.8 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D SER 3.0 18.7 + - - +
75D ASN* 3.6 11.7 - - - +
77D ALA* 1.3 75.1 - - - +
79D LYS* 1.3 67.9 + - - +
80D ASN 3.4 0.2 + - - -
81D PRO* 3.7 11.4 - - - +
186D LYS* 3.8 24.5 - - + -
190D VAL* 3.5 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D ASN 2.9 16.9 + - - +
76D LYS* 3.6 7.0 - - - +
78D ILE* 1.3 79.5 - - - +
80D ASN* 1.3 61.0 + - + +
81D PRO* 3.6 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D LYS 2.8 11.2 + - - +
77D ALA 3.4 3.1 - - - +
79D LYS* 1.3 79.4 - - + +
81D PRO* 1.3 65.1 - - - +
82D THR* 3.1 24.2 + - - +
83D LYS* 3.1 38.7 + - - +
84D LYS 3.9 0.9 + - - -
87D TYR* 3.6 23.9 + - - +
----------------------------------------------------------
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