Contacts of the helix formed by residues 37 - 70 (chain A) in PDB entry 3P1Q
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 37 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A GLU 4.1 0.4 + - - -
36A LEU* 1.3 75.3 - - - +
38A ASN* 1.3 65.5 + - - +
39A GLU* 3.6 7.4 + - - +
40A GLU* 2.8 40.4 + - - +
41A ARG* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 38 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 1.3 74.4 - - - +
39A GLU* 1.3 65.8 + - - +
41A ARG* 3.2 33.6 + - - +
42A ASN* 3.1 40.7 + - - +
115A GLU* 5.5 1.4 - - - +
119A PHE* 5.7 1.6 - - - -
168A ILE* 5.1 9.7 - - - +
249A FSC 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 39 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LYS* 3.3 33.8 + - - +
37A SER* 3.3 6.9 + - - +
38A ASN* 1.3 84.3 - - - +
40A GLU* 1.3 60.8 + - + +
42A ASN* 3.2 11.1 + - + +
43A LEU* 3.0 36.5 + - + +
249A FSC 5.6 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 40 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A ARG* 2.7 46.7 + - - -
7A ILE* 3.8 29.4 - - + +
26A MET* 3.4 16.7 - - + +
36A LEU* 3.2 9.7 - - + +
37A SER* 2.8 37.6 + - - +
39A GLU* 1.3 77.0 - - + +
41A ARG* 1.3 58.9 + - - +
43A LEU* 3.1 9.4 + - + -
44A LEU* 2.9 25.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
36A LEU* 3.0 32.2 + - + -
37A SER* 2.9 19.5 + - - +
38A ASN* 3.4 40.9 + - - +
40A GLU* 1.3 76.2 - - - +
42A ASN* 1.3 63.2 + - - +
44A LEU* 3.2 5.4 + - - +
45A SER 2.9 20.1 + - - -
115A GLU* 4.1 25.1 + - - +
116A SER* 3.6 30.2 - - - +
119A PHE* 3.3 31.9 - - + -
120A TYR* 3.2 42.4 + - + +
168A ILE* 5.7 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 42 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 3.1 34.8 + - - +
39A GLU* 3.4 10.6 - - + +
40A GLU 3.2 0.2 - - - -
41A ARG* 1.3 76.8 - - - +
43A LEU* 1.3 56.7 + - - +
45A SER* 3.1 6.3 + - - -
46A VAL* 2.9 36.3 + - - +
119A PHE* 3.3 21.1 - - - -
249A FSC 3.4 60.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ILE* 4.3 11.2 - - + +
10A ALA* 4.6 1.3 - - + -
11A LYS* 3.9 47.1 - - + +
14A GLU* 5.0 2.2 - - + -
22A MET* 3.5 28.1 - - + +
26A MET* 3.8 23.5 - - - +
39A GLU* 3.0 25.5 + - + +
40A GLU* 3.1 13.9 + - + +
42A ASN* 1.3 74.2 - - - +
44A LEU* 1.3 65.3 + - - +
47A ALA* 3.0 25.6 + - - +
249A FSC 3.9 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 44 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A MET* 3.8 30.2 - - + +
30A VAL* 4.1 12.6 - - + -
36A LEU* 4.1 13.0 - - + -
40A GLU 2.9 13.1 + - - +
41A ARG 3.5 8.3 - - - +
43A LEU* 1.3 77.5 - - - +
45A SER* 1.3 63.8 + - - +
47A ALA* 3.4 0.7 + - - +
48A TYR* 3.2 54.6 + - + +
99A VAL* 6.2 1.1 - - + -
102A LEU* 4.3 8.3 - - + -
103A LEU* 5.3 0.7 - - + -
107A LEU* 3.9 28.5 - - + -
120A TYR* 4.5 4.7 - - + -
123A MET* 4.2 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ARG 2.9 6.2 + - - -
42A ASN* 3.1 9.7 + - - -
44A LEU* 1.3 77.2 - - - +
46A VAL* 1.3 59.9 + - - +
48A TYR* 4.0 0.5 - - - +
49A LYS* 2.8 34.3 + - - +
119A PHE* 3.2 34.6 - - - -
123A MET* 4.0 19.3 - - - -
127A TYR* 4.4 1.0 + - - -
249A FSC 3.8 11.2 - - - +
253A CA 2.9 17.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A GLU* 4.7 7.9 - - + +
19A TYR* 4.2 10.3 - - + +
22A MET* 4.1 17.3 - - + -
42A ASN 2.9 22.5 + - - +
43A LEU 4.0 2.7 - - - +
45A SER* 1.3 79.3 + - - +
47A ALA* 1.3 62.8 + - - +
49A LYS* 4.5 1.3 - - - -
50A ASN* 2.9 45.6 + - - +
249A FSC 3.6 52.5 - - + +
253A CA 3.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 47 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 4.0 5.3 - - - +
22A MET* 3.6 23.1 - - + +
23A ALA* 3.5 35.9 - - + +
26A MET* 4.8 0.2 - - + -
43A LEU 3.0 17.7 + - - +
44A LEU* 3.7 5.4 - - - +
45A SER 3.2 0.2 - - - -
46A VAL* 1.3 80.0 - - - +
48A TYR* 1.3 64.3 + - + +
50A ASN* 3.3 2.8 + - - +
51A VAL* 3.1 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 48 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A ALA* 3.5 32.3 + - + -
24A ALA* 5.0 0.5 - - - -
27A LYS* 3.4 33.6 - - - +
44A LEU* 3.2 45.8 + - + +
45A SER* 4.4 1.3 - - - +
47A ALA* 1.3 77.0 - - - +
49A LYS* 1.3 64.8 + - - +
51A VAL* 3.2 5.7 + - + +
52A VAL* 2.9 28.1 + - - +
95A VAL* 3.8 21.3 - - + -
98A THR* 3.6 14.8 - - + +
99A VAL* 3.3 32.3 - - + -
102A LEU* 4.1 8.6 - - + +
123A MET* 5.3 1.6 - - + -
127A TYR* 3.2 16.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 49 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A SER* 2.8 19.9 + - - +
46A VAL* 4.0 2.7 - - - +
48A TYR* 1.3 75.7 - - - +
50A ASN* 1.3 59.9 + - - +
52A VAL* 3.7 3.0 - - + +
53A GLY* 2.8 26.7 + - - -
56A ARG* 4.5 2.0 - - - +
122A LYS* 4.8 0.7 - - - +
126A ASP* 4.2 9.9 - - - +
127A TYR* 3.2 14.6 + - + +
130A TYR* 2.9 25.1 + - + +
253A CA 4.0 10.5 - - - -
373P SEP 2.7 38.7 + - - -
374P VAL* 3.5 32.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.4 48.0 + - + -
46A VAL* 2.9 43.2 + - - +
47A ALA 3.7 0.4 - - - +
49A LYS* 1.3 77.4 - - - +
51A VAL* 1.3 65.2 + - - +
53A GLY* 3.8 1.1 - - - -
54A GLY* 3.1 18.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A TYR* 3.5 30.5 - - + +
20A GLU* 3.7 23.8 - - + +
23A ALA* 4.2 8.3 - - + -
47A ALA 3.1 16.8 + - - +
48A TYR* 3.2 8.5 + - + +
50A ASN* 1.3 76.4 - - - +
52A VAL* 1.3 64.4 + - - +
54A GLY* 3.3 1.7 + - - -
55A GLN* 3.2 27.2 + - + +
95A VAL* 4.1 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TYR 2.9 18.6 + - - +
49A LYS* 3.7 6.7 - - + +
51A VAL* 1.3 77.3 - - - +
53A GLY* 1.3 61.3 + - - +
55A GLN* 3.2 18.7 + - - +
56A ARG* 2.7 42.0 + - - +
92A LEU* 4.4 10.1 - - + +
95A VAL* 4.3 8.7 - - + -
96A CYS* 4.0 26.9 - - - -
127A TYR* 3.7 24.0 - - + +
130A TYR* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS 2.8 20.5 + - - -
50A ASN* 3.4 1.8 + - - -
51A VAL 3.2 0.2 - - - -
52A VAL* 1.3 81.6 - - - +
54A GLY* 1.3 55.4 + - - +
56A ARG* 3.4 15.4 + - - +
57A ALA* 2.9 29.6 + - - +
60A ARG* 5.0 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ASN 3.1 13.4 + - - -
51A VAL 3.3 3.5 + - - -
52A VAL 3.2 0.2 - - - -
53A GLY* 1.3 72.7 - - - +
55A GLN* 1.3 59.6 + - - +
57A ALA* 3.5 5.7 + - - +
58A ALA* 2.9 29.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL* 3.2 17.3 + - + +
52A VAL* 3.2 24.4 + - - +
54A GLY* 1.3 77.7 - - - +
56A ARG* 1.4 57.0 + - - +
58A ALA* 3.3 5.7 + - - +
59A TRP* 2.8 29.8 + - - +
88A VAL* 3.7 11.4 - - + +
91A GLU* 3.5 25.4 + - + +
92A LEU* 3.4 30.9 - - + +
95A VAL* 3.5 28.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A LYS* 4.5 2.4 + - - +
52A VAL* 2.7 33.3 + - + +
53A GLY* 3.7 13.7 - - - +
55A GLN* 1.4 70.3 - - - +
57A ALA* 1.3 60.3 + - - +
59A TRP* 3.2 3.3 + - - +
60A ARG* 2.8 48.9 + - - +
92A LEU* 3.9 24.9 - - + -
130A TYR* 3.2 39.2 + - + -
133A GLU* 2.8 40.9 + - - +
370P ARG* 3.9 8.8 - - - +
371P ARG* 3.5 5.1 - - - +
373P SEP 2.8 43.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLY 2.9 17.9 + - - +
54A GLY* 3.8 6.7 - - - +
56A ARG* 1.3 76.0 - - - +
58A ALA* 1.3 62.7 + - - +
60A ARG* 3.3 25.5 + - - +
61A VAL* 3.1 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A GLY 2.9 18.4 + - - +
55A GLN* 3.7 5.8 - - - +
57A ALA* 1.3 74.7 - - - +
59A TRP* 1.3 65.9 + - - +
61A VAL* 3.1 9.0 + - - +
62A LEU* 2.9 31.1 + - + +
84A TYR* 6.1 0.7 - - - +
88A VAL* 4.3 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A GLN 2.8 21.4 + - - +
56A ARG* 3.2 4.9 + - - +
58A ALA* 1.3 71.7 - - - +
60A ARG* 1.3 76.7 + - + +
62A LEU* 3.2 4.8 + - - +
63A SER* 2.7 57.0 + - - -
85A ARG* 3.4 23.4 - - + +
88A VAL* 4.0 8.2 - - + +
89A GLU* 2.9 53.2 + - + +
92A LEU* 4.1 9.9 - - + -
133A GLU* 3.7 24.0 - - + -
134A VAL* 3.4 29.1 - - + +
136A THR* 6.2 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLY 5.0 1.0 + - - -
56A ARG* 2.8 47.6 + - - +
57A ALA* 3.6 29.7 - - - +
59A TRP* 1.3 97.8 - - + +
61A VAL* 1.3 61.4 + - + +
63A SER* 3.9 2.5 - - - -
64A SER* 3.0 25.3 + - - -
133A GLU* 4.9 4.0 + - - -
370P ARG* 3.4 55.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 3.1 17.2 + - + +
58A ALA* 3.1 9.6 + - - +
60A ARG* 1.3 76.5 - - + +
62A LEU* 1.3 69.9 + - + +
64A SER* 3.3 6.3 + - - -
65A ILE* 3.1 42.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A ALA* 2.9 23.0 + - + +
59A TRP* 3.8 3.1 - - - +
61A VAL* 1.3 79.8 - - + +
63A SER* 1.3 59.4 + - - +
65A ILE* 3.2 20.5 + - + +
66A GLU* 2.8 28.9 + - - +
81A VAL* 4.1 8.2 - - + +
84A TYR* 3.5 35.9 - - + -
85A ARG* 3.9 27.4 - - + +
88A VAL* 3.5 33.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A TRP* 2.7 56.2 + - - -
60A ARG* 3.9 3.8 - - - -
62A LEU* 1.3 73.9 - - - +
64A SER* 1.3 56.3 + - - +
66A GLU* 3.3 10.8 + - - +
67A GLN* 2.8 40.2 + - - +
85A ARG* 4.0 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG 3.0 14.2 + - - -
61A VAL* 3.4 11.4 - - - -
63A SER* 1.3 72.2 - - - +
65A ILE* 1.3 68.1 + - - +
67A GLN* 3.2 6.1 + - - +
68A LYS* 3.0 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A VAL* 3.1 32.6 + - + +
62A LEU* 3.2 19.0 + - + +
64A SER* 1.3 77.6 - - - +
66A GLU* 1.3 63.8 + - - +
68A LYS* 3.3 8.2 + - - +
69A SER* 2.9 22.2 + - - -
81A VAL* 4.0 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU 2.8 15.2 + - - +
63A SER* 3.5 8.9 + - - +
65A ILE* 1.3 77.7 - - - +
67A GLN* 1.3 63.6 + - + +
69A SER* 2.6 25.2 + - - +
70A ASN* 3.2 22.7 + - - +
81A VAL* 3.5 19.2 - - + +
82A ARG* 3.6 24.5 - - + +
85A ARG* 2.6 51.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A SER* 2.8 29.3 + - - +
64A SER* 3.7 6.7 - - - +
65A ILE 3.2 0.2 - - - -
66A GLU* 1.3 78.4 - - + +
68A LYS* 1.3 62.4 + - + +
70A ASN* 3.1 18.5 + - - +
71A GLU* 3.5 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A SER* 3.0 26.7 + - - +
65A ILE* 3.7 7.6 - - - +
67A GLN* 1.3 76.7 - - + +
69A SER* 1.3 54.1 + - - +
70A ASN 3.1 0.2 - - - -
71A GLU* 3.1 28.7 + - - +
74A SER* 2.6 28.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 2.9 14.0 + - - -
66A GLU* 2.6 26.2 + - - +
68A LYS* 1.3 76.7 - - - +
70A ASN* 1.3 65.9 + - - +
71A GLU 3.4 0.6 - - - +
74A SER* 3.5 21.4 - - - +
75A GLU 4.9 8.8 - - - +
76A GLU* 5.9 0.9 - - - -
77A LYS* 6.1 7.2 - - - -
81A VAL* 5.1 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A GLU* 3.3 25.3 - - - +
67A GLN* 3.1 12.9 + - - +
68A LYS 3.1 1.0 - - - -
69A SER* 1.3 86.1 + - - +
71A GLU* 1.3 62.7 + - - +
72A GLU 4.0 0.5 + - - -
----------------------------------------------------------
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