Contacts of the helix formed by residues 42 - 71 (chain T) in PDB entry 3A68
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 VAL 42 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38T ARG* 3.5 2.7 + - - +
40T LYS* 4.0 3.8 + - - -
41T TYR* 1.3 81.6 - - - +
43T ASP* 1.3 65.9 + - - +
44T GLU* 3.9 6.5 - - + +
45T SER* 3.0 35.0 + - - +
46T GLU 3.1 9.9 + - - -
157T ASN* 3.7 34.5 - - + +
159T ASP* 4.9 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 43 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38T ARG* 3.0 25.3 + - - +
42T VAL* 1.3 74.4 - - - +
44T GLU* 1.3 57.5 + - - +
46T GLU* 3.5 12.6 - - - +
47T SER* 2.8 36.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 44 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42T VAL* 3.2 5.7 - - + +
43T ASP* 1.3 79.6 - - - +
45T SER* 1.3 57.5 + - - +
47T SER* 3.5 5.9 + - - -
48T ALA* 3.0 28.8 + - - +
153T VAL* 3.7 18.8 - - + +
156T LYS* 5.3 6.8 - - - +
157T ASN* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 45 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41T TYR* 4.0 16.6 - - - -
42T VAL* 3.0 22.8 + - - +
44T GLU* 1.3 75.2 - - - +
46T GLU* 1.3 67.6 + - - +
48T ALA* 3.2 2.8 + - - +
49T VAL* 2.9 28.9 + - - +
153T VAL* 4.3 6.7 - - - -
154T ALA* 4.4 4.0 - - - -
157T ASN* 4.2 13.9 + - - +
159T ASP* 4.1 10.5 + - - +
162T LEU* 3.8 23.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 46 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38T ARG* 3.7 25.7 + - - +
41T TYR* 3.8 20.1 - - + -
42T VAL 3.1 11.9 + - - +
43T ASP* 3.5 17.7 - - - +
45T SER* 1.3 77.1 - - - +
47T SER* 1.3 64.1 + - - +
49T VAL 3.4 1.0 + - - -
50T ASN* 3.1 22.2 + - - +
102T GLN* 3.1 28.9 + - - +
107T GLY* 3.5 4.8 - - - -
108T LYS* 2.8 36.2 + - - +
110T LYS* 5.6 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 47 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43T ASP* 2.8 23.8 + - - +
44T GLU* 3.7 7.0 - - - -
46T GLU* 1.3 76.8 + - - +
48T ALA* 1.3 57.4 + - - +
50T ASN* 3.2 10.9 + - - +
51T GLU* 2.9 27.9 + - - +
112T GLN* 5.6 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 48 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44T GLU 3.0 18.6 + - - +
45T SER 3.2 3.3 + - - +
47T SER* 1.3 72.9 - - - +
49T VAL* 1.3 65.0 + - - +
51T GLU* 3.3 9.0 + - - +
52T GLN* 3.0 23.4 + - - +
150T LEU* 3.5 25.0 - - + +
153T VAL* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 49 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41T TYR* 3.3 20.4 - - - +
45T SER 2.9 15.6 + - - +
46T GLU 3.7 4.7 - - - +
48T ALA* 1.3 77.0 - - - +
50T ASN* 1.3 58.1 + - - +
52T GLN* 3.2 5.8 + - - +
53T ILE* 2.9 31.2 + - + +
98T LEU* 3.9 31.1 - - + +
101T TYR* 4.7 3.6 - - + -
102T GLN* 3.6 22.2 - - + +
150T LEU* 4.1 12.1 - - + -
162T LEU* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 50 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46T GLU* 3.1 17.2 + - - +
47T SER* 3.2 11.4 + - - +
49T VAL* 1.3 75.6 - - - +
51T GLU* 1.3 63.3 + - - +
53T ILE* 3.3 14.9 + - - +
54T ASN* 3.2 20.4 + - - +
102T GLN* 3.0 18.2 + - - +
108T LYS 3.1 21.0 + - - -
109T VAL* 3.4 4.3 - - - -
110T LYS* 3.0 47.7 + - + +
112T GLN* 4.0 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 51 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ILE* 3.8 12.8 + - - +
15M PHE* 3.6 26.0 - - - +
47T SER 2.9 13.8 + - - +
48T ALA* 3.5 12.3 - - - +
49T VAL 3.2 0.2 - - - -
50T ASN* 1.3 78.3 - - - +
52T GLN* 1.3 59.3 + - - +
54T ASN* 3.1 6.8 + - - +
55T VAL* 3.0 32.7 + - + +
112T GLN* 3.6 22.8 + - - +
146T LYS* 5.4 8.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48T ALA 3.0 13.3 + - - +
49T VAL 3.7 7.2 - - - +
51T GLU* 1.3 73.5 - - - +
53T ILE* 1.3 66.7 + - - +
55T VAL* 3.1 19.2 + - - +
56T GLU* 2.8 55.8 + - - +
98T LEU* 3.5 21.3 - - + -
143T THR* 3.9 4.8 + - - +
146T LYS* 3.4 29.8 - - - +
147T LEU* 3.5 30.1 - - + +
150T LEU* 3.9 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 53 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49T VAL* 2.9 22.4 + - + +
50T ASN* 3.5 29.4 - - - +
52T GLN* 1.3 76.0 - - - +
54T ASN* 1.3 59.2 + - - +
56T GLU* 3.4 4.2 + - - +
57T TYR* 3.0 28.5 + - + +
95T ALA* 3.8 9.9 - - + +
98T LEU* 3.6 28.7 - - + +
99T MET* 3.8 38.1 - - + +
102T GLN* 4.7 0.2 - - + -
109T VAL* 4.3 8.7 - - + -
110T LYS 5.8 1.3 - - - +
111T LEU* 3.7 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 54 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M ILE* 5.0 1.0 - - - +
15M PHE* 3.8 33.1 + - - +
61P TYR* 4.1 6.1 + - - -
50T ASN 3.2 7.4 + - - +
51T GLU* 3.1 10.9 + - - +
53T ILE* 1.3 78.3 - - - +
55T VAL* 1.3 60.4 + - - +
57T TYR* 3.3 4.3 + - - +
58T ASN* 2.8 33.5 + - - +
111T LEU* 6.3 0.4 - - - -
112T GLN* 3.5 44.5 + - + +
113T SER 3.2 24.0 + - - +
114T ILE* 4.3 5.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 55 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M PHE* 4.2 27.1 - - + -
51T GLU* 3.0 33.5 + - + +
52T GLN* 3.1 31.6 + - - +
54T ASN* 1.3 77.5 - - - +
56T GLU* 1.3 63.1 + - - +
58T ASN* 3.3 3.3 + - - +
59T VAL* 3.1 22.9 + - + +
143T THR* 4.2 21.3 - - + +
146T LYS* 4.1 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 56 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52T GLN* 2.8 44.8 + - - +
53T ILE 3.8 3.6 - - - +
55T VAL* 1.3 76.3 - - - +
57T TYR* 1.3 61.8 + - - +
59T VAL* 3.3 5.0 + - - +
60T SER* 3.0 22.2 + - - -
91T GLU* 3.2 17.3 - - - +
94T HIS* 3.6 12.7 - - + +
95T ALA* 3.8 18.4 - - + +
98T LEU* 4.0 15.9 - - + -
143T THR* 3.6 12.4 - - - +
147T LEU* 4.0 9.7 - - - +
170T TYR* 4.2 7.4 - - - -
214T CA 2.5 28.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 57 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P TYR* 5.4 11.9 - + - -
60P SER* 4.9 2.3 + - - -
61P TYR* 3.5 38.7 - + - +
64P HIS* 2.6 42.3 + + - +
88P SER* 4.6 1.4 + - - -
53T ILE* 3.0 16.9 + - + +
54T ASN* 3.7 7.0 - - - +
56T GLU* 1.3 76.3 - - - +
58T ASN* 1.3 63.3 + - - +
60T SER* 3.2 13.5 + - - -
61T TYR* 3.0 21.7 + + + +
92T ARG* 3.7 24.3 + - + -
95T ALA* 3.7 22.2 - - + +
99T MET* 4.5 6.5 - - - -
111T LEU* 4.5 11.2 - - + -
114T ILE* 3.6 22.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 58 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M PHE* 3.0 28.8 + - + +
17M PRO* 2.7 45.4 - - - +
54T ASN* 2.8 20.4 + - - +
55T VAL 3.4 4.9 - - - +
57T TYR* 1.3 77.5 - - - +
59T VAL* 1.3 66.3 + - - +
61T TYR* 2.9 5.9 + - - +
62T VAL* 2.9 24.0 + - - +
114T ILE* 4.3 21.4 - - + +
115T VAL* 4.2 13.5 + - - +
117T PRO* 6.2 0.2 - - - +
139T LEU* 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 59 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15M PHE* 5.5 2.2 - - + -
55T VAL* 3.1 18.2 + - + +
56T GLU* 3.7 2.9 - - - +
58T ASN* 1.3 80.0 - - - +
60T SER* 1.3 62.5 + - - +
62T VAL* 3.3 1.4 + - - +
63T TYR* 2.9 48.5 + - + -
91T GLU* 3.4 24.9 - - - +
139T LEU* 3.8 31.9 - - + -
140T GLU* 4.4 4.5 - - - +
143T THR* 3.4 26.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 60 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P TYR* 5.0 2.5 + - - -
92P ARG* 4.5 4.3 + - - -
56T GLU 3.0 10.2 + - - -
57T TYR* 3.3 15.7 - - - -
59T VAL* 1.3 77.5 - - - +
61T TYR* 1.3 62.2 + - - +
63T TYR 3.4 0.5 + - - -
64T HIS* 3.0 10.9 + - - +
88T SER* 2.8 49.4 + - - +
91T GLU* 3.6 19.2 - - - +
92T ARG* 3.7 18.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 61 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54P ASN* 4.2 5.4 + - - -
57P TYR* 3.6 45.5 - + - +
111P LEU* 3.6 20.8 - - + +
112P GLN 2.7 38.2 + - - -
113P SER* 5.1 0.2 - - - -
114P ILE* 3.6 22.0 - - + +
57T TYR* 3.0 12.2 + + + +
58T ASN* 2.9 9.7 + - - +
60T SER* 1.3 75.9 - - - +
62T VAL* 1.3 64.0 + - + +
64T HIS* 3.2 6.8 + - - +
65T ALA* 3.0 20.8 + - - +
114T ILE* 3.5 29.6 - - + -
115T VAL 4.0 4.5 - - - -
117T PRO* 3.7 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 62 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17M PRO* 3.9 31.0 - - + -
18M PHE* 3.6 34.1 - - + -
58T ASN* 2.9 19.0 + - - +
59T VAL 3.7 6.1 - - - +
61T TYR* 1.3 77.4 - - + +
63T TYR* 1.3 56.8 + - - +
65T ALA* 3.0 5.4 + - - +
66T MET* 3.0 39.9 + - + +
117T PRO* 4.2 12.3 - - + -
121T PHE* 5.2 0.2 - - + -
139T LEU* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 63 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59T VAL* 2.9 33.3 + - + +
60T SER 3.7 4.5 - - - +
62T VAL* 1.3 76.0 - - - +
64T HIS* 1.3 57.7 + - - +
66T MET* 3.2 12.0 + - - +
67T PHE* 2.9 25.3 + - - +
83T PHE* 5.6 1.1 - + - -
84T PHE* 3.6 32.6 - + - +
87T SER* 3.7 20.2 - - - -
88T SER* 3.8 16.2 - - - +
91T GLU* 3.6 20.4 - - + -
136T ALA* 3.7 30.7 + - + +
139T LEU* 4.5 8.6 - - + +
140T GLU* 2.4 42.5 + - - +
181T ILE* 4.0 5.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 64 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57P TYR* 2.6 35.3 + + - +
92P ARG* 3.6 20.9 + - + -
96P GLU* 2.7 40.8 + - + +
99P MET* 3.7 31.2 - - + +
111P LEU* 4.1 8.5 - - + -
60T SER 3.0 8.9 + - - +
61T TYR 3.2 8.7 + - - +
63T TYR* 1.3 76.9 - - - +
65T ALA* 1.3 58.7 + - - +
67T PHE* 3.3 16.1 + + + +
68T ALA* 3.0 27.9 + - - +
85T LYS* 5.1 1.8 - - + -
88T SER* 3.5 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 65 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111P LEU* 3.7 13.2 - - + +
61T TYR 3.0 11.4 + - - +
62T VAL 3.0 10.6 + - - +
64T HIS* 1.3 77.3 - - - +
66T MET* 1.3 60.9 + - - +
68T ALA* 3.2 7.1 + - - +
69T TYR* 3.1 21.7 + - - +
117T PRO* 3.9 15.5 - - + -
118T LEU 3.4 25.6 - - - +
119T SER* 4.5 4.7 - - - +
121T PHE* 3.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 66 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62T VAL* 3.0 23.9 + - + +
63T TYR* 3.2 31.1 + - - +
65T ALA* 1.3 73.3 - - - +
67T PHE* 1.3 64.3 + - - +
69T TYR* 3.2 1.4 + - - +
70T PHE* 3.1 31.5 + - + -
84T PHE* 3.4 26.5 - - + -
121T PHE* 3.4 35.0 - - + -
132T ALA* 3.2 51.1 - - + +
135T LEU* 4.7 4.0 - - + -
136T ALA* 4.7 5.8 - - - +
139T LEU* 5.8 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 67 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96P GLU* 4.5 6.3 - - + -
99P MET* 4.1 15.5 - - + -
100P GLU* 4.0 23.6 - - + -
103P ASN* 5.4 0.4 - - - -
63T TYR 2.9 13.5 + - - +
64T HIS* 3.5 24.7 - + - +
66T MET* 1.3 75.7 - - - +
68T ALA* 1.3 69.2 + - - +
70T PHE* 3.2 1.9 + - - +
71T ASP* 2.9 52.4 + - + +
81T ALA* 3.2 30.0 - - + +
84T PHE* 3.6 7.5 - - - +
85T LYS* 3.6 53.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 68 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99P MET* 4.0 10.1 - - + -
103P ASN* 3.0 27.9 + - - +
109P VAL* 3.8 37.7 - - + +
64T HIS 3.0 14.2 + - - +
65T ALA* 3.2 11.1 + - - +
67T PHE* 1.3 83.2 - - + +
69T TYR* 1.3 61.6 + - - +
72T ARG* 3.6 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65T ALA 3.1 6.1 + - - +
66T MET 3.6 7.2 - - - +
67T PHE 3.1 0.2 - - - -
68T ALA* 1.3 77.2 - - - +
70T PHE* 1.3 84.8 + + - +
71T ASP 3.1 1.1 - - - -
72T ARG* 3.1 64.0 + - - +
75T VAL* 3.6 34.5 - - + +
119T SER 3.7 8.7 + - - +
120T ASP* 3.9 5.2 - - + -
121T PHE* 3.5 45.3 - + + -
122T ASP* 3.1 32.7 - - + +
128T ASP* 4.1 7.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 70 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66T MET* 3.1 29.4 + - + +
69T TYR* 1.3 92.3 - + - +
71T ASP* 1.3 58.1 + - - +
72T ARG 3.2 2.4 + - - -
75T VAL* 3.7 16.2 - - + -
76T ALA* 3.8 5.4 + - - -
77T LEU* 3.5 47.4 + - + +
78T ARG* 5.2 0.5 - - - -
80T LEU* 3.6 21.3 - - + -
81T ALA* 3.9 24.6 - - - +
84T PHE* 3.9 15.9 - + - -
121T PHE* 4.4 7.4 - + + -
128T ASP* 3.6 25.6 - - + -
132T ALA* 3.4 34.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 71 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100P GLU* 4.2 12.3 - - - +
103P ASN* 2.9 34.6 + - - +
67T PHE* 2.9 46.5 + - + +
69T TYR 3.1 0.2 - - - -
70T PHE* 1.3 75.2 - - - +
72T ARG* 1.3 62.7 + - - +
76T ALA* 5.8 0.2 - - - -
81T ALA* 3.9 6.8 - - + +
179U LYS* 2.9 37.1 + - - -
183U GLU* 4.6 1.8 - - - +
----------------------------------------------------------
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